diff --git a/pygmx/__init__.py b/pygmx/__init__.py new file mode 100644 index 0000000..1240731 --- /dev/null +++ b/pygmx/__init__.py @@ -0,0 +1,9 @@ +""" +Python wrapper for gromacs tools. +""" + +from . import tpxio +from . import xtcio +from . import tngio + +from .tpxio import TPXReader diff --git a/pygmx/fileio.pxd b/pygmx/fileio.pxd new file mode 100644 index 0000000..7188a15 --- /dev/null +++ b/pygmx/fileio.pxd @@ -0,0 +1,12 @@ + +from utility cimport * + +cdef extern from "gromacs/fileio/gmxfio.h": + ctypedef struct t_fileio: + pass + + int gmx_fio_seek(t_fileio *fio, gmx_off_t fpos) + + gmx_off_t gmx_fio_ftell(t_fileio *fio) + + int xtc_seek_time(t_fileio *fio, real time, int natoms, gmx_bool bSeekForwardOnly) diff --git a/pygmx/math.pxd b/pygmx/math.pxd new file mode 100644 index 0000000..cd91510 --- /dev/null +++ b/pygmx/math.pxd @@ -0,0 +1,7 @@ + +from utility cimport real + +cdef extern from "gromacs/math/vectypes.h": + ctypedef real rvec[3] + ctypedef real matrix[3][3] + ctypedef real tensor[3][3] diff --git a/pygmx/mdtypes.pxd b/pygmx/mdtypes.pxd new file mode 100644 index 0000000..a5caaf8 --- /dev/null +++ b/pygmx/mdtypes.pxd @@ -0,0 +1,175 @@ + +from utility cimport * +from math cimport * + +cdef extern from "gromacs/mdtypes/inputrec.h": + ctypedef struct t_simtemp: + pass + ctypedef struct t_lambda: + pass + ctypedef struct t_expanded: + pass + ctypedef struct t_rot: + pass + ctypedef struct t_IMD: + pass + ctypedef struct t_grpopts: + int ngtc + real *ref_t # Coupling temperature per group */ + + ctypedef struct t_cosines: + pass + ctypedef struct t_swapcoords: + pass + + ctypedef struct t_inputrec: + int eI # Integration method */ + int nsteps # number of steps to be taken */ + int simulation_part # Used in checkpointing to separate chunks */ + int init_step # start at a stepcount >0 (used w. convert-tpr) */ + int nstcalcenergy # frequency of energy calc. and T/P coupl. upd. */ + int cutoff_scheme # group or verlet cutoffs */ + int ns_type # which ns method should we use? */ + int nstlist # number of steps before pairlist is generated */ + int ndelta # number of cells per rlong */ + int nstcomm # number of steps after which center of mass */ + # motion is removed */ + int comm_mode # Center of mass motion removal algorithm */ + int nstlog # number of steps after which print to logfile */ + int nstxout # number of steps after which X is output */ + int nstvout # id. for V */ + int nstfout # id. for F */ + int nstenergy # number of steps after which energies printed */ + int nstxout_compressed # id. for compressed trj (.xtc,.tng) */ + double init_t # initial time (ps) */ + double delta_t # time step (ps) */ + double x_compression_precision # precision of x in compressed trajectory file */ + double fourier_spacing # requested fourier_spacing, when nk? not set */ + int nkx, nky, nkz # number of k vectors in each spatial dimension*/ + # for fourier methods for long range electrost.*/ + int pme_order # interpolation order for PME */ + double ewald_rtol # double space tolerance for Ewald, determines */ + # the double/reciprocal space relative weight */ + double ewald_rtol_lj # double space tolerance for LJ-Ewald */ + int ewald_geometry # normal/3d ewald, or pseudo-2d LR corrections */ + double epsilon_surface # Epsilon for PME dipole correction */ + int ljpme_combination_rule # Type of combination rule in LJ-PME */ + int ePBC # Type of periodic boundary conditions */ + int bPeriodicMols # Periodic molecules */ + bint bContinuation # Continuation run: starting state is correct */ + int etc # temperature coupling */ + int nsttcouple # interval in steps for temperature coupling */ + bint bPrintNHChains # whether to print nose-hoover chains */ + int epc # pressure coupling */ + int epct # pressure coupling type */ + int nstpcouple # interval in steps for pressure coupling */ + double tau_p # pressure coupling time (ps) */ + tensor ref_p # reference pressure (kJ/(mol nm^3)) */ + tensor compress # compressability ((mol nm^3)/kJ) */ + int refcoord_scaling # How to scale absolute reference coordinates */ + rvec posres_com # The COM of the posres atoms */ + rvec posres_comB # The B-state COM of the posres atoms */ + int andersen_seed # Random seed for Andersen thermostat (obsolete) */ + double verletbuf_tol # Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer */ + double rlist # short range pairlist cut-off (nm) */ + double rtpi # Radius for test particle insertion */ + int coulombtype # Type of electrostatics treatment */ + int coulomb_modifier # Modify the Coulomb interaction */ + double rcoulomb_switch # Coulomb switch range start (nm) */ + double rcoulomb # Coulomb cutoff (nm) */ + double epsilon_r # relative dielectric constant */ + double epsilon_rf # relative dielectric constant of the RF */ + int implicit_solvent # No (=explicit water), or GBSA solvent models */ + int gb_algorithm # Algorithm to use for calculation Born radii */ + int nstgbradii # Frequency of updating Generalized Born radii */ + double rgbradii # Cutoff for GB radii calculation */ + double gb_saltconc # Salt concentration (M) for GBSA models */ + double gb_epsilon_solvent # dielectric coeff. of implicit solvent */ + double gb_obc_alpha # 1st scaling factor for Bashford-Case GB */ + double gb_obc_beta # 2nd scaling factor for Bashford-Case GB */ + double gb_obc_gamma # 3rd scaling factor for Bashford-Case GB */ + double gb_dielectric_offset # Dielectric offset for Still/HCT/OBC */ + int sa_algorithm # Algorithm for SA part of GBSA */ + double sa_surface_tension # Energy factor for SA part of GBSA */ + int vdwtype # Type of Van der Waals treatment */ + int vdw_modifier # Modify the VdW interaction */ + double rvdw_switch # Van der Waals switch range start (nm) */ + double rvdw # Van der Waals cutoff (nm) */ + int eDispCorr # Perform Long range dispersion corrections */ + double tabext # Extension of the table beyond the cut-off, * + # * as well as the table length for 1-4 interac. */ + double shake_tol # tolerance for shake */ + int efep # free energy calculations */ + t_lambda *fepvals # Data for the FEP state */ + bint bSimTemp # Whether to do simulated tempering */ + t_simtemp *simtempvals # Variables for simulated tempering */ + bint bExpanded # Whether expanded ensembles are used */ + t_expanded *expandedvals # Expanded ensemble parameters */ + int eDisre # Type of distance restraining */ + double dr_fc # force constant for ta_disre */ + int eDisreWeighting # type of weighting of pairs in one restraints */ + bint bDisreMixed # Use comb of time averaged and instan. viol's */ + int nstdisreout # frequency of writing pair distances to enx */ + double dr_tau # time constant for memory function in disres */ + double orires_fc # force constant for orientational restraints */ + double orires_tau # time constant for memory function in orires */ + int nstorireout # frequency of writing tr(SD) to enx */ + double em_stepsize # The stepsize for updating */ + double em_tol # The tolerance */ + int niter # Number of iterations for convergence of */ + # steepest descent in relax_shells */ + double fc_stepsize # Stepsize for directional minimization */ + # in relax_shells */ + int nstcgsteep # number of steps after which a steepest */ + # descents step is done while doing cg */ + int nbfgscorr # Number of corrections to the hessian to keep */ + int eConstrAlg # Type of constraint algorithm */ + int nProjOrder # Order of the LINCS Projection Algorithm */ + double LincsWarnAngle # If bond rotates more than %g degrees, warn */ + int nLincsIter # Number of iterations in the final Lincs step */ + bint bShakeSOR # Use successive overrelaxation for shake */ + double bd_fric # Friction coefficient for BD (amu/ps) */ + int ld_seed # Random seed for SD and BD */ + int nwall # The number of walls */ + int wall_type # The type of walls */ + double wall_r_linpot # The potentail is linear for r<=wall_r_linpot */ + int wall_atomtype[2] # The atom type for walls */ + double wall_density[2] # Number density for walls */ + double wall_ewald_zfac # Scaling factor for the box for Ewald */ + + # COM pulling data */ + bint bPull # Do we do COM pulling? */ + #struct pull_params_t *pull # The data for center of mass pulling */ + #struct pull_t *pull_work # The COM pull force calculation data structure TODO this pointer should live somewhere else */ + + # Enforced rotation data */ + bint bRot # Calculate enforced rotation potential(s)? */ + t_rot *rot # The data for enforced rotation potentials */ + + int eSwapCoords # Do ion/water position exchanges (CompEL)? */ + t_swapcoords *swap + + bint bIMD # Allow interactive MD sessions for this .tpr? */ + t_IMD *imd # Interactive molecular dynamics */ + + double cos_accel # Acceleration for viscosity calculation */ + tensor deform # Triclinic deformation velocities (nm/ps) */ + int userint1 # User determined parameters */ + int userint2 + int userint3 + int userint4 + double userdouble1 + double userdouble2 + double userdouble3 + double userdouble4 + t_grpopts opts # Group options */ + t_cosines ex[0] # Electric field stuff (spatial part) */ + t_cosines et[0] # Electric field stuff (time part) */ + bint bQMMM # QM/MM calculation */ + int QMconstraints # constraints on QM bonds */ + int QMMMscheme # Scheme: ONIOM or normal */ + double scalefactor # factor for scaling the MM charges in QM calc.*/ + + # Fields for removed features go here (better caching) */ + bint bAdress # Whether AdResS is enabled - always false if a valid .tpr was read + bint useTwinRange # Whether twin-range scheme is active - always false if a valid .tpr was read diff --git a/pygmx/reader.py b/pygmx/reader.py new file mode 100644 index 0000000..d07e87e --- /dev/null +++ b/pygmx/reader.py @@ -0,0 +1,495 @@ +import xdrlib +import io +import os +# from .coordinates import decompress +from ..utils import hash_anything, merge_hashes +from functools import partial +import numpy as np + +TRR_MAGIC = 1993 +XTC_MAGIC = 1995 +INDEX_MAGIC = 2015 + +def index_filename_for_xtc(xtcfile): + """ + Get the filename for the index file of a xtc file. + + In general, the index file is located in the same directory as the xtc file. + If the xtc file is located in a read-only directory (for the current user) + and does not exist, the index file will be instead located in a subdirectory + of ~/.xtcindex, of the current user. + + The directory for user index files can be changed by setting the environment + variable 'XTCINDEXDIR'. + + Example: + xtcfile = '/data/niels/test.xtc' + + # case 1: index file exists, or current user is niels + index_filename_for_xtc(xtcfile) == '/data/niels/.test.xtc.xtcindex' + + # case 2: index file doesn't exist, and nor write permission in /data/niels + index_filename_for_xtc(xtcfile) == '~/.xtcindex/data/niels/.test.xtc.xtcindex' + + Warning: + At this point, the index file is not checked for validity. If an invalid + index file is present in the xtc files directory, this will be used and an + error will be risen by XTCReader. + + Warning: + On most systems, the home directory is on the local drive so that the indexing + has probably to do be done on every system if it can not be saved in the directory + of the xtc file. + """ + base = os.path.basename(xtcfile) + filename = "." + base + ".xtcindex" + + dir = os.path.abspath(os.path.dirname(xtcfile)) + + if not os.path.exists(os.path.join(dir, filename)) and not os.access(dir, os.W_OK): + if 'XTCINDEXDIR' in os.environ: + index_dir = os.environ['XTCINDEXDIR'] + else: + index_dir = os.path.join(os.environ['HOME'], '.xtcindex') + dir = os.path.join(index_dir, dir.lstrip('/')) + os.makedirs(dir, exist_ok=True) + + return os.path.join(dir, filename) + + +class NumpyUnpacker(xdrlib.Unpacker): + + def unpack_float_array(self, n_items): + i = self.get_position() + j = i + 4 * n_items + self.set_position(j) + data = self.get_buffer()[i:j] + + if len(data) < 4: + raise EOFError + + ret = np.frombuffer(data, '>f') + if len(ret) != n_items: + raise EOFError + return ret + + def unpack_double_array(self, n_items): + i = self.get_position() + j = i + 8 * n_items + self.set_position(j) + data = self.get_buffer()[i:j] + + if len(data) < 8: + raise EOFError + + ret = np.frombuffer(data, '>d') + if len(ret) != n_items: + raise EOFError + return ret + + +class InvalidMagicException(Exception): + pass + + +class InvalidIndexException(Exception): + pass + + +class UnknownLenError(Exception): + pass + + +class SubscriptableReader: + + def __init__(self, fd): + self.fd = fd + self.len = os.stat(self.fd.fileno()).st_size + + def __getitem__(self, r): + if isinstance(r, slice): + if r.start is not None: + if r.start < 0: + self.fd.seek(r.start, io.SEEK_END) + else: + self.fd.seek(r.start, io.SEEK_SET) + + if r.step is not None: + raise NotImplementedError + + return self.fd.read(r.stop - r.start) + else: + self.fd.seek(r, io.SEEK_SET) + return self.fd.read(1) + + def __len__(self): + return self.len + + +class XTCFrame: + __slots__ = ['_coordinates', 'index', 'time', 'box', '_compressed_coordinates'] + + def __init__(self): + self._coordinates = None + + @property + def coordinates(self): + if self._coordinates is None: + self._coordinates = self._compressed_coordinates() + return self._coordinates + + +class BaseReader: + + def __init__(self, file): + self.fd = open(file, 'rb') + self.filename = file + + self.reader = SubscriptableReader(self.fd) + self.xdr_reader = NumpyUnpacker(self.reader) + + def __exit__(self, *_): + self.fd.close() + + def __enter__(self, *_): + return self + + def get_position(self): + return self.fd.tell() + + def set_position(self, pos): + return self.fd.seek(pos) + + def skip_frames(self, num): + for i in range(num): + self.skip_frame() + + def skip_frame(self): + self._read_header() + self._read_frame() + + def dump_frame(self): + raise NotImplemented + + def _read_header(self): + raise NotImplemented + + def _read_frame(self): + raise NotImplemented + +XTC_HEADER_SIZE = 4 * 4 +XTC_FRAME_HEADER_SIZE = 9 * 4 + 10 * 4 + + +class XTCReader(BaseReader): + + len_available = False + + def __init__(self, xtcfile, load_cache_file=True): + super().__init__(xtcfile) + self._cache = [0] + self._times = None + self.current_frame = 0 + + index_file_name = index_filename_for_xtc(xtcfile) + if load_cache_file: + self.load_index(index_file_name) + + def load_index(self, filename): + xtc_stat = os.stat(self.filename) + c_time = int(xtc_stat.st_ctime) + m_time = int(xtc_stat.st_mtime) + size = xtc_stat.st_size + + with open(filename, 'rb') as index_file_fd: + # TODO: Is NumpyUnpacker even necessary at this point? + # Seems like xdrlib.Unpacker would be sufficient here ... + reader = NumpyUnpacker(SubscriptableReader(index_file_fd)) + + if reader.unpack_hyper() != INDEX_MAGIC: + raise InvalidMagicException + if reader.unpack_hyper() != c_time: + raise InvalidIndexException + if reader.unpack_hyper() != m_time: + raise InvalidIndexException + if reader.unpack_hyper() != size: + raise InvalidIndexException + + self._cache = [] + self._times = [] + try: + while True: + self._cache.append(reader.unpack_hyper()) + self._times.append(reader.unpack_float()) + except EOFError: + pass + self.len_available = True + + def _raw_header(self): + if len(self._cache) == self.current_frame: + self._cache.append(self.get_position()) + return self.fd.read(XTC_HEADER_SIZE) + + def _raw_frame(self): + frame_header = self.fd.read(XTC_FRAME_HEADER_SIZE) + blob_size = xdrlib.Unpacker(frame_header[-4:]).unpack_int() + blob_size = (blob_size + 3) // 4 * 4 # Padding to 4 bytes + frame_blob = self.fd.read(blob_size) + + self.current_frame += 1 + return frame_header + frame_blob + + def _unpack_header(self, raw_header): + unpacker = xdrlib.Unpacker(raw_header) + + magic = unpacker.unpack_int() + + if magic != XTC_MAGIC: + raise InvalidMagicException + + n_atoms = unpacker.unpack_int() + step = unpacker.unpack_int() + time = unpacker.unpack_float() + + return n_atoms, step, time + + def _read_header(self): + raw_header = self._raw_header() + return self._unpack_header(raw_header) + + def _unpack_frame(self, raw_frame): + unpacker = xdrlib.Unpacker(raw_frame) + + raw_box = unpacker.unpack_farray(9, unpacker.unpack_float) + box = np.array(raw_box).reshape(3, 3) + num_coords = unpacker.unpack_int() + precision = unpacker.unpack_float() + maxint = unpacker.unpack_farray(3, unpacker.unpack_int) + minint = unpacker.unpack_farray(3, unpacker.unpack_int) + smallindex = unpacker.unpack_int() + + blob_len = unpacker.unpack_int() + blob = unpacker.unpack_fopaque(blob_len) + + return box, precision, num_coords, minint, maxint, smallindex, blob + + def _read_frame(self): + raw_frame = self._raw_frame() + return self._unpack_frame(raw_frame) + + def decode_frame(self, header=None, body=None): + n_atoms, step, time = header or self._read_header() + box, precision, num_coords, minint, maxint, smallindex, blob = body or self._read_frame() + coordinates = partial(decompress, num_coords, precision, minint, maxint, smallindex, blob) + + frame = XTCFrame() + frame._compressed_coordinates = coordinates + frame.index = step + frame.time = time + frame.box = box + return frame + + def dump_frame(self): + """ + :return: Tuple: The binary data of the frame, the frame itself + """ + + raw_header = self._raw_header() + header = self._unpack_header(raw_header) + + raw_body = self._raw_frame() + body = self._unpack_frame(raw_body) + + return (raw_header + raw_body, self.decode_frame(header, body)) + + def cached_position(self, item): + try: + return self._cache[item] + except IndexError: + return None + + def __getitem__(self, item): + position = self.cached_position(item) + + if position is not None: + self.set_position(position) + self.current_frame = item + return self.decode_frame() + # TODO: Use elif and one single return at the end + # Also: skip_frames is in fact not implemented at all! + # TODO: Catch EOFError and raise IndexError + if self.current_frame <= item: + self.skip_frames(item - self.current_frame) + return self.decode_frame() + else: + self.set_position(0) + self.current_frame = 0 + self.skip_frames(item) + return self.decode_frame() + + def __len__(self): + if self.len_available: + return len(self._cache) + raise UnknownLenError + + def times_of_indices(self, indices): + return [self[i].time for i in indices] + + def __hash__(self): + return merge_hashes(hash(self.filename), hash_anything(self._cache)) + + +class TRRHeader: + __slots__ = ['ir_size', 'e_size', 'box_size', 'vir_size', 'pres_size', 'top_size', 'sym_size', 'x_size', 'v_size', + 'f_size', 'n_atoms', 'step', 'nre', 't', 'λ', 'is_double'] + + @property + def frame_size(self): + return self.ir_size + \ + self.e_size + \ + self.box_size + \ + self.vir_size + \ + self.top_size + \ + self.sym_size + \ + self.x_size + \ + self.v_size + \ + self.f_size + + +class TRRFrame: + __slots__ = ['header', 'box', 'x', 'v', 'f'] + + +class TRRReader(BaseReader): + + def __iter__(self): + return TRRIterator(self.filename) + + def _unpack_float(self, is_double): + if is_double: + return self.xdr_reader.unpack_double() + else: + return self.xdr_reader.unpack_float() + + def _unpack_np_float(self, is_double, *dim): + total = np.product(dim) + + if is_double: + box = self.xdr_reader.unpack_double_array(total) + else: + box = self.xdr_reader.unpack_float_array(total) + + box = box.reshape(*dim) + return box + + def _read_header(self): + + data = self.fd.read(8) # 4 Magic + 4 VersionStringLen + unpacker = NumpyUnpacker(data) + + magic = unpacker.unpack_int() + + if magic != TRR_MAGIC: + raise InvalidMagicException + + version_string_len = unpacker.unpack_int() + data = self.fd.read(version_string_len + 55) # 4 Magic + 4 VersionStringLen + unpacker.reset(data) + + version = unpacker.unpack_string() + assert version == b'GMX_trn_file' + + header = TRRHeader() + + header.ir_size = unpacker.unpack_int() + header.e_size = unpacker.unpack_int() + header.box_size = unpacker.unpack_int() + header.vir_size = unpacker.unpack_int() + header.pres_size = unpacker.unpack_int() + header.top_size = unpacker.unpack_int() + header.sym_size = unpacker.unpack_int() + header.x_size = unpacker.unpack_int() + header.v_size = unpacker.unpack_int() + header.f_size = unpacker.unpack_int() + header.n_atoms = unpacker.unpack_int() + header.step = unpacker.unpack_int() + header.nre = unpacker.unpack_int() + + if header.x_size is not None: + header.is_double = (header.x_size // header.n_atoms) == 8 + elif header.v_size is not None: + header.is_double = (header.v_size // header.n_atoms) == 8 + elif header.f_size is not None: + header.is_double = (header.f_size // header.n_atoms) == 8 + + if header.is_double: + data = self.fd.read(16) + else: + data = self.fd.read(8) + unpacker.reset(data) + self.xdr_reader = unpacker + + header.t = self._unpack_float(header.is_double) + header.λ = self._unpack_float(header.is_double) + + return header + + def _read_frame(self, header): + frame = TRRFrame() + frame.header = header + + data = self.fd.read(header.frame_size) + self.xdr_reader = NumpyUnpacker(data) + + frame.box = None + if header.box_size: + frame.box = self._unpack_np_float(header.is_double, 3, 3) + + if header.vir_size: + for i in range(9): + self._unpack_float(header.is_double) + + if header.pres_size: + for i in range(9): + self._unpack_float(header.is_double) + + frame.x = None + if header.x_size: + frame.x = self._unpack_np_float(header.is_double, header.n_atoms, 3) + + frame.v = None + if header.v_size: + frame.v = self._unpack_np_float(header.is_double, header.n_atoms, 3) + + frame.f = None + if header.f_size: + frame.f = self._unpack_np_float(header.is_double, header.n_atoms, 3) + + return frame + + def decode_frame(self): + h = self._read_header() + return self._read_frame(h) + + def get_position(self): + return self.fd.tell() + + def set_position(self, pos): + self.fd.seek(pos) + + +class TRRIterator(): + + def __init__(self, file): + self.__reader = TRRReader(file) + self.__reader.__enter__() + + def __next__(self): + try: + return self.__reader.decode_frame() + except EOFError as err: + self.__reader.__exit__() + raise StopIteration + + def __iter__(self): + return self diff --git a/pygmx/tngio.c b/pygmx/tngio.c new file mode 100644 index 0000000..a4a2d83 --- /dev/null +++ b/pygmx/tngio.c @@ -0,0 +1,8838 @@ +/* Generated by Cython 0.23.4 */ + +/* BEGIN: Cython Metadata +{ + "distutils": { + "depends": [ + "/home/niels/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h", + "/home/niels/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/ufuncobject.h", + "gromacs/src/external/tng_io/include/tng/tng_io.h", + "gromacs/src/external/tng_io/include/tng/tng_io_fwd.h" + ], + "include_dirs": [ + "/home/niels/anaconda3/lib/python3.5/site-packages/numpy/core/include", + "gromacs/src", + "gromacs/src/external/tng_io/include" + ], + "libraries": [ + "gromacs" + ], + "library_dirs": [ + "/home/niels/Uni/pygmx/gromacs/build/lib", + "/home/niels/Uni/pygmx/gromacs/src/external/tng_io/build/lib" + ], + "runtime_library_dirs": [ + "/home/niels/Uni/pygmx/gromacs/build/lib", + "/home/niels/Uni/pygmx/gromacs/src/external/tng_io/build/lib" + ] + } +} +END: Cython Metadata */ + +#define PY_SSIZE_T_CLEAN +#include "Python.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) + #error Cython requires Python 2.6+ or Python 3.2+. +#else +#define CYTHON_ABI "0_23_4" +#include +#ifndef offsetof +#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION +#define CYTHON_COMPILING_IN_PYPY 1 +#define CYTHON_COMPILING_IN_CPYTHON 0 +#else +#define CYTHON_COMPILING_IN_PYPY 0 +#define CYTHON_COMPILING_IN_CPYTHON 1 +#endif +#if !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000 +#define CYTHON_USE_PYLONG_INTERNALS 1 +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) +#define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#ifndef Py_TPFLAGS_CHECKTYPES + #define Py_TPFLAGS_CHECKTYPES 0 +#endif +#ifndef Py_TPFLAGS_HAVE_INDEX + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#ifndef Py_TPFLAGS_HAVE_NEWBUFFER + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#ifndef Py_TPFLAGS_HAVE_FINALIZE + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) +#else + #define CYTHON_PEP393_ENABLED 0 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) +#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) +#else + #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyStringObject PyUnicodeObject + #define PyString_Type PyUnicode_Type + #define PyString_Check PyUnicode_Check + #define PyString_CheckExact PyUnicode_CheckExact +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) + #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) +#else + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) +#endif +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) +#endif +#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#if PY_MAJOR_VERSION >= 3 + #define PyIntObject PyLongObject + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define PyNumber_Int PyNumber_Long +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBoolObject PyLongObject +#endif +#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY + #ifndef PyUnicode_InternFromString + #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) + #endif +#endif +#if PY_VERSION_HEX < 0x030200A4 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t PyInt_AsLong +#else + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) +#else + #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) +#endif +#if PY_VERSION_HEX >= 0x030500B1 +#define __Pyx_PyAsyncMethodsStruct PyAsyncMethods +#define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) +#elif CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 +typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; +} __Pyx_PyAsyncMethodsStruct; +#define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) +#else +#define __Pyx_PyType_AsAsync(obj) NULL +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) + +#ifndef CYTHON_INLINE + #if defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif + + +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#define __PYX_HAVE__pygmx__tngio +#define __PYX_HAVE_API__pygmx__tngio +#include "string.h" +#include "stdio.h" +#include "stdlib.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#include "tng/tng_io_fwd.h" +#include "tng/tng_io.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#ifdef PYREX_WITHOUT_ASSERTIONS +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# endif +#endif +typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ + (sizeof(type) < sizeof(Py_ssize_t)) ||\ + (sizeof(type) > sizeof(Py_ssize_t) &&\ + likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX) &&\ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ + v == (type)PY_SSIZE_T_MIN))) ||\ + (sizeof(type) == sizeof(Py_ssize_t) &&\ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) && defined (_M_X64) + #define __Pyx_sst_abs(value) _abs64(value) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) +#if PY_MAJOR_VERSION < 3 +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) +{ + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#else +#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen +#endif +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_COMPILING_IN_CPYTHON +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ + +static PyObject *__pyx_m; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "pygmx/tngio.pyx", + "__init__.pxd", + "type.pxd", +}; +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":725 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":726 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":727 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":728 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":734 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":735 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":739 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":740 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":749 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":750 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":751 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":753 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":754 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":755 + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_intp intp_t + */ +typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":757 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":761 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif + + +/*--- Type declarations ---*/ +struct __pyx_obj_5pygmx_5tngio_TNGTrajectory; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":764 + * ctypedef npy_longdouble longdouble_t + * + * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t + */ +typedef npy_cfloat __pyx_t_5numpy_cfloat_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":765 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":766 + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cdouble complex_t + */ +typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":768 + * ctypedef npy_clongdouble clongdouble_t + * + * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew1(a): + */ +typedef npy_cdouble __pyx_t_5numpy_complex_t; +struct __pyx_opt_args_5pygmx_5tngio_check_status; + +/* "pygmx/tngio.pyx":79 + * + * + * cdef check_status(status, message=''): # <<<<<<<<<<<<<< + * if status != TNG_SUCCESS: + * print(message) + */ +struct __pyx_opt_args_5pygmx_5tngio_check_status { + int __pyx_n; + PyObject *message; +}; + +/* "pygmx/tngio.pyx":87 + * # return arr + * + * cdef class TNGTrajectory: # <<<<<<<<<<<<<< + * cdef: + * tng_trajectory_t trajectory + */ +struct __pyx_obj_5pygmx_5tngio_TNGTrajectory { + PyObject_HEAD + tng_trajectory_t trajectory; + int nframes; + int natoms; + int stride; +}; + + +/* --- Runtime support code (head) --- */ +#ifndef CYTHON_REFNANNY + #define CYTHON_REFNANNY 0 +#endif +#if CYTHON_REFNANNY + typedef struct { + void (*INCREF)(void*, PyObject*, int); + void (*DECREF)(void*, PyObject*, int); + void (*GOTREF)(void*, PyObject*, int); + void (*GIVEREF)(void*, PyObject*, int); + void* (*SetupContext)(const char*, int, const char*); + void (*FinishContext)(void**); + } __Pyx_RefNannyAPIStruct; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); + #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; +#ifdef WITH_THREAD + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + if (acquire_gil) {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + PyGILState_Release(__pyx_gilstate_save);\ + } else {\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + } +#else + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) +#endif + #define __Pyx_RefNannyFinishContext()\ + __Pyx_RefNanny->FinishContext(&__pyx_refnanny) + #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_XINCREF(r) do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0) + #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0) + #define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0) + #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0) +#else + #define __Pyx_RefNannyDeclarations + #define __Pyx_RefNannySetupContext(name, acquire_gil) + #define __Pyx_RefNannyFinishContext() + #define __Pyx_INCREF(r) Py_INCREF(r) + #define __Pyx_DECREF(r) Py_DECREF(r) + #define __Pyx_GOTREF(r) + #define __Pyx_GIVEREF(r) + #define __Pyx_XINCREF(r) Py_XINCREF(r) + #define __Pyx_XDECREF(r) Py_XDECREF(r) + #define __Pyx_XGOTREF(r) + #define __Pyx_XGIVEREF(r) +#endif +#define __Pyx_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_XDECREF(tmp);\ + } while (0) +#define __Pyx_DECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_DECREF(tmp);\ + } while (0) +#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) +#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); +#else +#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) +#endif + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, + __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); +#else +#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) +#endif + +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ + const char* function_name); + +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL) +static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_setattro)) + return tp->tp_setattro(obj, attr_name, value); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_setattr)) + return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value); +#endif + return PyObject_SetAttr(obj, attr_name, value); +} +#else +#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n) +#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v) +#endif + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); + +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { + PyObject *value; + value = PyDict_GetItemWithError(d, key); + if (unlikely(!value)) { + if (!PyErr_Occurred()) { + PyObject* args = PyTuple_Pack(1, key); + if (likely(args)) + PyErr_SetObject(PyExc_KeyError, args); + Py_XDECREF(args); + } + return NULL; + } + Py_INCREF(value); + return value; +} +#else + #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) +#endif + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); + +static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); + +#define __Pyx_CyFunction_USED 1 +#include +#define __Pyx_CYFUNCTION_STATICMETHOD 0x01 +#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 +#define __Pyx_CYFUNCTION_CCLASS 0x04 +#define __Pyx_CyFunction_GetClosure(f)\ + (((__pyx_CyFunctionObject *) (f))->func_closure) +#define __Pyx_CyFunction_GetClassObj(f)\ + (((__pyx_CyFunctionObject *) (f))->func_classobj) +#define __Pyx_CyFunction_Defaults(type, f)\ + ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) +#define __Pyx_CyFunction_SetDefaultsGetter(f, g)\ + ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) +typedef struct { + PyCFunctionObject func; +#if PY_VERSION_HEX < 0x030500A0 + PyObject *func_weakreflist; +#endif + PyObject *func_dict; + PyObject *func_name; + PyObject *func_qualname; + PyObject *func_doc; + PyObject *func_globals; + PyObject *func_code; + PyObject *func_closure; + PyObject *func_classobj; + void *defaults; + int defaults_pyobjects; + int flags; + PyObject *defaults_tuple; + PyObject *defaults_kwdict; + PyObject *(*defaults_getter)(PyObject *); + PyObject *func_annotations; +} __pyx_CyFunctionObject; +static PyTypeObject *__pyx_CyFunctionType = 0; +#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code)\ + __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, globals, code) +static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, + int flags, PyObject* qualname, + PyObject *self, + PyObject *module, PyObject *globals, + PyObject* code); +static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, + size_t size, + int pyobjects); +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, + PyObject *tuple); +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m, + PyObject *dict); +static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m, + PyObject *dict); +static int __pyx_CyFunction_init(void); + +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases); + +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname, + PyObject *mkw, PyObject *modname, PyObject *doc); +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict, + PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass); + +typedef struct { + int code_line; + PyCodeObject* code_object; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; +static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_tng_function_status(tng_function_status value); + +static int __Pyx_Print(PyObject*, PyObject *, int); +#if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3 +static PyObject* __pyx_print = 0; +static PyObject* __pyx_print_kwargs = 0; +#endif + +static int __Pyx_PrintOne(PyObject* stream, PyObject *o); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *); + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eqf(a, b) ((a)==(b)) + #define __Pyx_c_sumf(a, b) ((a)+(b)) + #define __Pyx_c_difff(a, b) ((a)-(b)) + #define __Pyx_c_prodf(a, b) ((a)*(b)) + #define __Pyx_c_quotf(a, b) ((a)/(b)) + #define __Pyx_c_negf(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zerof(z) ((z)==(float)0) + #define __Pyx_c_conjf(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_absf(z) (::std::abs(z)) + #define __Pyx_c_powf(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zerof(z) ((z)==0) + #define __Pyx_c_conjf(z) (conjf(z)) + #if 1 + #define __Pyx_c_absf(z) (cabsf(z)) + #define __Pyx_c_powf(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq(a, b) ((a)==(b)) + #define __Pyx_c_sum(a, b) ((a)+(b)) + #define __Pyx_c_diff(a, b) ((a)-(b)) + #define __Pyx_c_prod(a, b) ((a)*(b)) + #define __Pyx_c_quot(a, b) ((a)/(b)) + #define __Pyx_c_neg(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero(z) ((z)==(double)0) + #define __Pyx_c_conj(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs(z) (::std::abs(z)) + #define __Pyx_c_pow(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero(z) ((z)==0) + #define __Pyx_c_conj(z) (conj(z)) + #if 1 + #define __Pyx_c_abs(z) (cabs(z)) + #define __Pyx_c_pow(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +static int __Pyx_check_binary_version(void); + +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +static PyObject *__Pyx_ImportModule(const char *name); + +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'libc.stdlib' */ + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'pygmx.tngio' */ +static PyTypeObject *__pyx_ptype_5pygmx_5tngio_TNGTrajectory = 0; +static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; +#define __Pyx_MODULE_NAME "pygmx.tngio" +int __pyx_module_is_main_pygmx__tngio = 0; + +/* Implementation of 'pygmx.tngio' */ +static PyObject *__pyx_builtin_IndexError; +static PyObject *__pyx_builtin_OSError; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_RuntimeError; +static char __pyx_k_[] = ""; +static char __pyx_k_B[] = "B"; +static char __pyx_k_H[] = "H"; +static char __pyx_k_I[] = "I"; +static char __pyx_k_L[] = "L"; +static char __pyx_k_O[] = "O"; +static char __pyx_k_Q[] = "Q"; +static char __pyx_k_b[] = "b"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; +static char __pyx_k_i[] = "i"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; +static char __pyx_k_np[] = "np"; +static char __pyx_k_doc[] = "__doc__"; +static char __pyx_k_end[] = "end"; +static char __pyx_k_len[] = "__len__"; +static char __pyx_k_ceil[] = "ceil"; +static char __pyx_k_file[] = "file"; +static char __pyx_k_init[] = "__init__"; +static char __pyx_k_item[] = "item"; +static char __pyx_k_main[] = "__main__"; +static char __pyx_k_math[] = "math"; +static char __pyx_k_self[] = "self"; +static char __pyx_k_test[] = "__test__"; +static char __pyx_k_dtype[] = "dtype"; +static char __pyx_k_empty[] = "empty"; +static char __pyx_k_numpy[] = "numpy"; +static char __pyx_k_print[] = "print"; +static char __pyx_k_range[] = "range"; +static char __pyx_k_encode[] = "encode"; +static char __pyx_k_format[] = "format"; +static char __pyx_k_import[] = "__import__"; +static char __pyx_k_module[] = "__module__"; +static char __pyx_k_OSError[] = "OSError"; +static char __pyx_k_float32[] = "float32"; +static char __pyx_k_getitem[] = "__getitem__"; +static char __pyx_k_nstxout[] = "nstxout"; +static char __pyx_k_prepare[] = "__prepare__"; +static char __pyx_k_filename[] = "filename"; +static char __pyx_k_qualname[] = "__qualname__"; +static char __pyx_k_TNGReader[] = "TNGReader"; +static char __pyx_k_metaclass[] = "__metaclass__"; +static char __pyx_k_IndexError[] = "IndexError"; +static char __pyx_k_ValueError[] = "ValueError"; +static char __pyx_k_trajectory[] = "trajectory"; +static char __pyx_k_pygmx_tngio[] = "pygmx.tngio"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; +static char __pyx_k_TNGReader___len[] = "TNGReader.__len__"; +static char __pyx_k_TNGReader___init[] = "TNGReader.__init__"; +static char __pyx_k_TNGReader___getitem[] = "TNGReader.__getitem__"; +static char __pyx_k_get_position_interval[] = "get_position_interval"; +static char __pyx_k_Filename_must_not_be_null[] = "Filename must not be null."; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static char __pyx_k_Trajectory_frame_out_of_range[] = "Trajectory frame {} out of range."; +static char __pyx_k_Trajectory_could_not_be_opened[] = "Trajectory could not be opened."; +static char __pyx_k_home_niels_Uni_pygmx_pygmx_tngi[] = "/home/niels/Uni/pygmx/pygmx/tngio.pyx"; +static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_kp_s_; +static PyObject *__pyx_kp_s_Filename_must_not_be_null; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_n_s_IndexError; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_s_OSError; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_TNGReader; +static PyObject *__pyx_n_s_TNGReader___getitem; +static PyObject *__pyx_n_s_TNGReader___init; +static PyObject *__pyx_n_s_TNGReader___len; +static PyObject *__pyx_kp_s_Trajectory_could_not_be_opened; +static PyObject *__pyx_kp_s_Trajectory_frame_out_of_range; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_n_s_ceil; +static PyObject *__pyx_n_s_doc; +static PyObject *__pyx_n_s_dtype; +static PyObject *__pyx_n_s_empty; +static PyObject *__pyx_n_s_encode; +static PyObject *__pyx_n_s_end; +static PyObject *__pyx_n_s_file; +static PyObject *__pyx_n_s_filename; +static PyObject *__pyx_n_s_float32; +static PyObject *__pyx_n_s_format; +static PyObject *__pyx_n_s_get_position_interval; +static PyObject *__pyx_n_s_getitem; +static PyObject *__pyx_kp_s_home_niels_Uni_pygmx_pygmx_tngi; +static PyObject *__pyx_n_s_import; +static PyObject *__pyx_n_s_init; +static PyObject *__pyx_n_s_item; +static PyObject *__pyx_n_s_len; +static PyObject *__pyx_n_s_main; +static PyObject *__pyx_n_s_math; +static PyObject *__pyx_n_s_metaclass; +static PyObject *__pyx_n_s_module; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_np; +static PyObject *__pyx_n_s_nstxout; +static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_n_s_prepare; +static PyObject *__pyx_n_s_print; +static PyObject *__pyx_n_s_pygmx_tngio; +static PyObject *__pyx_n_s_qualname; +static PyObject *__pyx_n_s_range; +static PyObject *__pyx_n_s_self; +static PyObject *__pyx_n_s_test; +static PyObject *__pyx_n_s_trajectory; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; +static PyObject *__pyx_pf_5pygmx_5tngio_13TNGTrajectory_get_position_interval(struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_pf_5pygmx_5tngio_13TNGTrajectory_2__len__(struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tngio_13TNGTrajectory_4__getitem__(struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *__pyx_v_self, PyObject *__pyx_v_frame); /* proto */ +static int __pyx_pf_5pygmx_5tngio_13TNGTrajectory_6__init__(struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tngio_9TNGReader___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tngio_9TNGReader_2__len__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tngio_9TNGReader_4__getitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static PyObject *__pyx_tp_new_5pygmx_5tngio_TNGTrajectory(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_int_3; +static PyObject *__pyx_tuple__2; +static PyObject *__pyx_tuple__3; +static PyObject *__pyx_tuple__4; +static PyObject *__pyx_tuple__5; +static PyObject *__pyx_tuple__6; +static PyObject *__pyx_tuple__7; +static PyObject *__pyx_tuple__8; +static PyObject *__pyx_tuple__9; +static PyObject *__pyx_tuple__11; +static PyObject *__pyx_tuple__13; +static PyObject *__pyx_codeobj__10; +static PyObject *__pyx_codeobj__12; +static PyObject *__pyx_codeobj__14; + +/* "pygmx/tngio.pyx":79 + * + * + * cdef check_status(status, message=''): # <<<<<<<<<<<<<< + * if status != TNG_SUCCESS: + * print(message) + */ + +static PyObject *__pyx_f_5pygmx_5tngio_check_status(PyObject *__pyx_v_status, struct __pyx_opt_args_5pygmx_5tngio_check_status *__pyx_optional_args) { + PyObject *__pyx_v_message = ((PyObject *)__pyx_kp_s_); + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("check_status", 0); + if (__pyx_optional_args) { + if (__pyx_optional_args->__pyx_n > 0) { + __pyx_v_message = __pyx_optional_args->message; + } + } + + /* "pygmx/tngio.pyx":80 + * + * cdef check_status(status, message=''): + * if status != TNG_SUCCESS: # <<<<<<<<<<<<<< + * print(message) + * + */ + __pyx_t_1 = __Pyx_PyInt_From_tng_function_status(TNG_SUCCESS); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_status, __pyx_t_1, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (__pyx_t_3) { + + /* "pygmx/tngio.pyx":81 + * cdef check_status(status, message=''): + * if status != TNG_SUCCESS: + * print(message) # <<<<<<<<<<<<<< + * + * #cdef ptr_to_array(float *ptr, np.npy_intp *shape, int np): + */ + if (__Pyx_PrintOne(0, __pyx_v_message) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tngio.pyx":80 + * + * cdef check_status(status, message=''): + * if status != TNG_SUCCESS: # <<<<<<<<<<<<<< + * print(message) + * + */ + } + + /* "pygmx/tngio.pyx":79 + * + * + * cdef check_status(status, message=''): # <<<<<<<<<<<<<< + * if status != TNG_SUCCESS: + * print(message) + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pygmx.tngio.check_status", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tngio.pyx":92 + * int nframes, natoms, stride + * + * def get_position_interval(self): # <<<<<<<<<<<<<< + * cdef: + * double time + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tngio_13TNGTrajectory_1get_position_interval(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static PyObject *__pyx_pw_5pygmx_5tngio_13TNGTrajectory_1get_position_interval(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("get_position_interval (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tngio_13TNGTrajectory_get_position_interval(((struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tngio_13TNGTrajectory_get_position_interval(struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *__pyx_v_self) { + double __pyx_v_time; + char __pyx_v_data_type; + int __pyx_v_frame1; + int __pyx_v_frame2; + PyArrayObject *__pyx_v_positions = 0; + void *__pyx_v_data; + __Pyx_LocalBuf_ND __pyx_pybuffernd_positions; + __Pyx_Buffer __pyx_pybuffer_positions; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyArrayObject *__pyx_t_6 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("get_position_interval", 0); + __pyx_pybuffer_positions.pybuffer.buf = NULL; + __pyx_pybuffer_positions.refcount = 0; + __pyx_pybuffernd_positions.data = NULL; + __pyx_pybuffernd_positions.rcbuffer = &__pyx_pybuffer_positions; + + /* "pygmx/tngio.pyx":98 + * int frame1, frame2 + * + * cdef np.ndarray[float, ndim=2] positions = np.empty((self.natoms, 3), dtype=np.float32) # <<<<<<<<<<<<<< + * cdef void *data = positions.data + * + */ + __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->natoms); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1); + __Pyx_INCREF(__pyx_int_3); + __Pyx_GIVEREF(__pyx_int_3); + PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_int_3); + __pyx_t_1 = 0; + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3); + __pyx_t_3 = 0; + __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_float32); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = ((PyArrayObject *)__pyx_t_5); + { + __Pyx_BufFmt_StackElem __pyx_stack[1]; + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_positions.rcbuffer->pybuffer, (PyObject*)__pyx_t_6, &__Pyx_TypeInfo_float, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + __pyx_v_positions = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_positions.rcbuffer->pybuffer.buf = NULL; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } else {__pyx_pybuffernd_positions.diminfo[0].strides = __pyx_pybuffernd_positions.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_positions.diminfo[0].shape = __pyx_pybuffernd_positions.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_positions.diminfo[1].strides = __pyx_pybuffernd_positions.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_positions.diminfo[1].shape = __pyx_pybuffernd_positions.rcbuffer->pybuffer.shape[1]; + } + } + __pyx_t_6 = 0; + __pyx_v_positions = ((PyArrayObject *)__pyx_t_5); + __pyx_t_5 = 0; + + /* "pygmx/tngio.pyx":99 + * + * cdef np.ndarray[float, ndim=2] positions = np.empty((self.natoms, 3), dtype=np.float32) + * cdef void *data = positions.data # <<<<<<<<<<<<<< + * + * tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame1, &time) + */ + __pyx_v_data = ((void *)__pyx_v_positions->data); + + /* "pygmx/tngio.pyx":101 + * cdef void *data = positions.data + * + * tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame1, &time) # <<<<<<<<<<<<<< + * tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame2, &time) + * del positions + */ + tng_util_particle_data_next_frame_read(__pyx_v_self->trajectory, TNG_TRAJ_POSITIONS, (&__pyx_v_data), (&__pyx_v_data_type), (&__pyx_v_frame1), (&__pyx_v_time)); + + /* "pygmx/tngio.pyx":102 + * + * tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame1, &time) + * tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame2, &time) # <<<<<<<<<<<<<< + * del positions + * return frame2 - frame1 + */ + tng_util_particle_data_next_frame_read(__pyx_v_self->trajectory, TNG_TRAJ_POSITIONS, (&__pyx_v_data), (&__pyx_v_data_type), (&__pyx_v_frame2), (&__pyx_v_time)); + + /* "pygmx/tngio.pyx":103 + * tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame1, &time) + * tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame2, &time) + * del positions # <<<<<<<<<<<<<< + * return frame2 - frame1 + * + */ + __Pyx_DECREF(((PyObject *)__pyx_v_positions)); + __pyx_v_positions = NULL; + + /* "pygmx/tngio.pyx":104 + * tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame2, &time) + * del positions + * return frame2 - frame1 # <<<<<<<<<<<<<< + * + * def __len__(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_5 = __Pyx_PyInt_From_int((__pyx_v_frame2 - __pyx_v_frame1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __pyx_r = __pyx_t_5; + __pyx_t_5 = 0; + goto __pyx_L0; + + /* "pygmx/tngio.pyx":92 + * int nframes, natoms, stride + * + * def get_position_interval(self): # <<<<<<<<<<<<<< + * cdef: + * double time + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + { PyObject *__pyx_type, *__pyx_value, *__pyx_tb; + __Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_positions.rcbuffer->pybuffer); + __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} + __Pyx_AddTraceback("pygmx.tngio.TNGTrajectory.get_position_interval", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + goto __pyx_L2; + __pyx_L0:; + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_positions.rcbuffer->pybuffer); + __pyx_L2:; + __Pyx_XDECREF((PyObject *)__pyx_v_positions); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tngio.pyx":106 + * return frame2 - frame1 + * + * def __len__(self): # <<<<<<<<<<<<<< + * return self.nframes + * + */ + +/* Python wrapper */ +static Py_ssize_t __pyx_pw_5pygmx_5tngio_13TNGTrajectory_3__len__(PyObject *__pyx_v_self); /*proto*/ +static Py_ssize_t __pyx_pw_5pygmx_5tngio_13TNGTrajectory_3__len__(PyObject *__pyx_v_self) { + Py_ssize_t __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__len__ (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tngio_13TNGTrajectory_2__len__(((struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static Py_ssize_t __pyx_pf_5pygmx_5tngio_13TNGTrajectory_2__len__(struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *__pyx_v_self) { + Py_ssize_t __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__len__", 0); + + /* "pygmx/tngio.pyx":107 + * + * def __len__(self): + * return self.nframes # <<<<<<<<<<<<<< + * + * def __getitem__(self, frame): + */ + __pyx_r = __pyx_v_self->nframes; + goto __pyx_L0; + + /* "pygmx/tngio.pyx":106 + * return frame2 - frame1 + * + * def __len__(self): # <<<<<<<<<<<<<< + * return self.nframes + * + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tngio.pyx":109 + * return self.nframes + * + * def __getitem__(self, frame): # <<<<<<<<<<<<<< + * cdef np.ndarray[float, ndim=2] positions = np.empty((self.natoms, 3), dtype=np.float32) + * cdef float *pos = positions.data + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tngio_13TNGTrajectory_5__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_frame); /*proto*/ +static PyObject *__pyx_pw_5pygmx_5tngio_13TNGTrajectory_5__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_frame) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tngio_13TNGTrajectory_4__getitem__(((struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *)__pyx_v_self), ((PyObject *)__pyx_v_frame)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tngio_13TNGTrajectory_4__getitem__(struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *__pyx_v_self, PyObject *__pyx_v_frame) { + PyArrayObject *__pyx_v_positions = 0; + float *__pyx_v_pos; + __Pyx_LocalBuf_ND __pyx_pybuffernd_positions; + __Pyx_Buffer __pyx_pybuffer_positions; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyArrayObject *__pyx_t_6 = NULL; + int64_t __pyx_t_7; + int64_t __pyx_t_8; + int __pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__getitem__", 0); + __pyx_pybuffer_positions.pybuffer.buf = NULL; + __pyx_pybuffer_positions.refcount = 0; + __pyx_pybuffernd_positions.data = NULL; + __pyx_pybuffernd_positions.rcbuffer = &__pyx_pybuffer_positions; + + /* "pygmx/tngio.pyx":110 + * + * def __getitem__(self, frame): + * cdef np.ndarray[float, ndim=2] positions = np.empty((self.natoms, 3), dtype=np.float32) # <<<<<<<<<<<<<< + * cdef float *pos = positions.data + * + */ + __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->natoms); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1); + __Pyx_INCREF(__pyx_int_3); + __Pyx_GIVEREF(__pyx_int_3); + PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_int_3); + __pyx_t_1 = 0; + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3); + __pyx_t_3 = 0; + __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_float32); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = ((PyArrayObject *)__pyx_t_5); + { + __Pyx_BufFmt_StackElem __pyx_stack[1]; + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_positions.rcbuffer->pybuffer, (PyObject*)__pyx_t_6, &__Pyx_TypeInfo_float, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + __pyx_v_positions = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_positions.rcbuffer->pybuffer.buf = NULL; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } else {__pyx_pybuffernd_positions.diminfo[0].strides = __pyx_pybuffernd_positions.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_positions.diminfo[0].shape = __pyx_pybuffernd_positions.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_positions.diminfo[1].strides = __pyx_pybuffernd_positions.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_positions.diminfo[1].shape = __pyx_pybuffernd_positions.rcbuffer->pybuffer.shape[1]; + } + } + __pyx_t_6 = 0; + __pyx_v_positions = ((PyArrayObject *)__pyx_t_5); + __pyx_t_5 = 0; + + /* "pygmx/tngio.pyx":111 + * def __getitem__(self, frame): + * cdef np.ndarray[float, ndim=2] positions = np.empty((self.natoms, 3), dtype=np.float32) + * cdef float *pos = positions.data # <<<<<<<<<<<<<< + * + * #check_status( + */ + __pyx_v_pos = ((float *)__pyx_v_positions->data); + + /* "pygmx/tngio.pyx":115 + * #check_status( + * if (TNG_SUCCESS != + * tng_util_pos_read_range(self.trajectory, frame, frame, &pos, &self.stride)#, # <<<<<<<<<<<<<< + * #'Reading of frame not successful.' + * ): + */ + __pyx_t_7 = __Pyx_PyInt_As_int64_t(__pyx_v_frame); if (unlikely((__pyx_t_7 == (int64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyInt_As_int64_t(__pyx_v_frame); if (unlikely((__pyx_t_8 == (int64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tngio.pyx":114 + * + * #check_status( + * if (TNG_SUCCESS != # <<<<<<<<<<<<<< + * tng_util_pos_read_range(self.trajectory, frame, frame, &pos, &self.stride)#, + * #'Reading of frame not successful.' + */ + __pyx_t_9 = ((TNG_SUCCESS != tng_util_pos_read_range(__pyx_v_self->trajectory, __pyx_t_7, __pyx_t_8, (&__pyx_v_pos), (&__pyx_v_self->stride))) != 0); + if (__pyx_t_9) { + + /* "pygmx/tngio.pyx":118 + * #'Reading of frame not successful.' + * ): + * raise IndexError() # <<<<<<<<<<<<<< + * + * return positions + */ + __pyx_t_5 = __Pyx_PyObject_CallNoArg(__pyx_builtin_IndexError); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_Raise(__pyx_t_5, 0, 0, 0); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tngio.pyx":114 + * + * #check_status( + * if (TNG_SUCCESS != # <<<<<<<<<<<<<< + * tng_util_pos_read_range(self.trajectory, frame, frame, &pos, &self.stride)#, + * #'Reading of frame not successful.' + */ + } + + /* "pygmx/tngio.pyx":120 + * raise IndexError() + * + * return positions # <<<<<<<<<<<<<< + * + * def __init__(self, filename): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(((PyObject *)__pyx_v_positions)); + __pyx_r = ((PyObject *)__pyx_v_positions); + goto __pyx_L0; + + /* "pygmx/tngio.pyx":109 + * return self.nframes + * + * def __getitem__(self, frame): # <<<<<<<<<<<<<< + * cdef np.ndarray[float, ndim=2] positions = np.empty((self.natoms, 3), dtype=np.float32) + * cdef float *pos = positions.data + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + { PyObject *__pyx_type, *__pyx_value, *__pyx_tb; + __Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_positions.rcbuffer->pybuffer); + __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} + __Pyx_AddTraceback("pygmx.tngio.TNGTrajectory.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + goto __pyx_L2; + __pyx_L0:; + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_positions.rcbuffer->pybuffer); + __pyx_L2:; + __Pyx_XDECREF((PyObject *)__pyx_v_positions); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tngio.pyx":122 + * return positions + * + * def __init__(self, filename): # <<<<<<<<<<<<<< + * assert filename, 'Filename must not be null.' + * if isinstance(filename, str): + */ + +/* Python wrapper */ +static int __pyx_pw_5pygmx_5tngio_13TNGTrajectory_7__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pygmx_5tngio_13TNGTrajectory_7__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_filename = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,0}; + PyObject* values[1] = {0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_filename)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 1) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + } + __pyx_v_filename = values[0]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_L3_error:; + __Pyx_AddTraceback("pygmx.tngio.TNGTrajectory.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return -1; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pygmx_5tngio_13TNGTrajectory_6__init__(((struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *)__pyx_v_self), __pyx_v_filename); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_5pygmx_5tngio_13TNGTrajectory_6__init__(struct __pyx_obj_5pygmx_5tngio_TNGTrajectory *__pyx_v_self, PyObject *__pyx_v_filename) { + int __pyx_r; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + char const *__pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__init__", 0); + __Pyx_INCREF(__pyx_v_filename); + + /* "pygmx/tngio.pyx":123 + * + * def __init__(self, filename): + * assert filename, 'Filename must not be null.' # <<<<<<<<<<<<<< + * if isinstance(filename, str): + * filename = filename.encode() + */ + #ifndef CYTHON_WITHOUT_ASSERTIONS + if (unlikely(!Py_OptimizeFlag)) { + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_filename); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_1)) { + PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_Filename_must_not_be_null); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + } + #endif + + /* "pygmx/tngio.pyx":124 + * def __init__(self, filename): + * assert filename, 'Filename must not be null.' + * if isinstance(filename, str): # <<<<<<<<<<<<<< + * filename = filename.encode() + * + */ + __pyx_t_1 = PyString_Check(__pyx_v_filename); + __pyx_t_2 = (__pyx_t_1 != 0); + if (__pyx_t_2) { + + /* "pygmx/tngio.pyx":125 + * assert filename, 'Filename must not be null.' + * if isinstance(filename, str): + * filename = filename.encode() # <<<<<<<<<<<<<< + * + * if (tng_util_trajectory_open(filename, b'r', &self.trajectory) != TNG_SUCCESS): + */ + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_filename, __pyx_n_s_encode); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_5)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + } + } + if (__pyx_t_5) { + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + } else { + __pyx_t_3 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF_SET(__pyx_v_filename, __pyx_t_3); + __pyx_t_3 = 0; + + /* "pygmx/tngio.pyx":124 + * def __init__(self, filename): + * assert filename, 'Filename must not be null.' + * if isinstance(filename, str): # <<<<<<<<<<<<<< + * filename = filename.encode() + * + */ + } + + /* "pygmx/tngio.pyx":127 + * filename = filename.encode() + * + * if (tng_util_trajectory_open(filename, b'r', &self.trajectory) != TNG_SUCCESS): # <<<<<<<<<<<<<< + * raise OSError('Trajectory could not be opened.') + * + */ + __pyx_t_6 = __Pyx_PyObject_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = ((tng_util_trajectory_open(__pyx_t_6, 'r', (&__pyx_v_self->trajectory)) != TNG_SUCCESS) != 0); + if (__pyx_t_2) { + + /* "pygmx/tngio.pyx":128 + * + * if (tng_util_trajectory_open(filename, b'r', &self.trajectory) != TNG_SUCCESS): + * raise OSError('Trajectory could not be opened.') # <<<<<<<<<<<<<< + * + * tng_num_frames_get(self.trajectory, &self.nframes) + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_OSError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tngio.pyx":127 + * filename = filename.encode() + * + * if (tng_util_trajectory_open(filename, b'r', &self.trajectory) != TNG_SUCCESS): # <<<<<<<<<<<<<< + * raise OSError('Trajectory could not be opened.') + * + */ + } + + /* "pygmx/tngio.pyx":130 + * raise OSError('Trajectory could not be opened.') + * + * tng_num_frames_get(self.trajectory, &self.nframes) # <<<<<<<<<<<<<< + * tng_num_particles_get(self.trajectory, &self.natoms) + * + */ + tng_num_frames_get(__pyx_v_self->trajectory, (&__pyx_v_self->nframes)); + + /* "pygmx/tngio.pyx":131 + * + * tng_num_frames_get(self.trajectory, &self.nframes) + * tng_num_particles_get(self.trajectory, &self.natoms) # <<<<<<<<<<<<<< + * + * + */ + tng_num_particles_get(__pyx_v_self->trajectory, (&__pyx_v_self->natoms)); + + /* "pygmx/tngio.pyx":122 + * return positions + * + * def __init__(self, filename): # <<<<<<<<<<<<<< + * assert filename, 'Filename must not be null.' + * if isinstance(filename, str): + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("pygmx.tngio.TNGTrajectory.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_filename); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tngio.pyx":137 + * + * class TNGReader: + * def __init__(self, filename): # <<<<<<<<<<<<<< + * self.trajectory = TNGTrajectory(filename) + * self.nstxout = self.trajectory.get_position_interval() + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tngio_9TNGReader_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pygmx_5tngio_9TNGReader_1__init__ = {"__init__", (PyCFunction)__pyx_pw_5pygmx_5tngio_9TNGReader_1__init__, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_5pygmx_5tngio_9TNGReader_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_self = 0; + PyObject *__pyx_v_filename = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_filename,0}; + PyObject* values[2] = {0,0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_self)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + case 1: + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_filename)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + } + __pyx_v_self = values[0]; + __pyx_v_filename = values[1]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_L3_error:; + __Pyx_AddTraceback("pygmx.tngio.TNGReader.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pygmx_5tngio_9TNGReader___init__(__pyx_self, __pyx_v_self, __pyx_v_filename); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tngio_9TNGReader___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__init__", 0); + + /* "pygmx/tngio.pyx":138 + * class TNGReader: + * def __init__(self, filename): + * self.trajectory = TNGTrajectory(filename) # <<<<<<<<<<<<<< + * self.nstxout = self.trajectory.get_position_interval() + * + */ + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_INCREF(__pyx_v_filename); + __Pyx_GIVEREF(__pyx_v_filename); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename); + __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5pygmx_5tngio_TNGTrajectory), __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_trajectory, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pygmx/tngio.pyx":139 + * def __init__(self, filename): + * self.trajectory = TNGTrajectory(filename) + * self.nstxout = self.trajectory.get_position_interval() # <<<<<<<<<<<<<< + * + * def __len__(self): + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_trajectory); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_get_position_interval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_1)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_1); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_3, function); + } + } + if (__pyx_t_1) { + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + } else { + __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_nstxout, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pygmx/tngio.pyx":137 + * + * class TNGReader: + * def __init__(self, filename): # <<<<<<<<<<<<<< + * self.trajectory = TNGTrajectory(filename) + * self.nstxout = self.trajectory.get_position_interval() + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pygmx.tngio.TNGReader.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tngio.pyx":141 + * self.nstxout = self.trajectory.get_position_interval() + * + * def __len__(self): # <<<<<<<<<<<<<< + * return ceil(len(self.trajectory) / self.nstxout) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tngio_9TNGReader_3__len__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static PyMethodDef __pyx_mdef_5pygmx_5tngio_9TNGReader_3__len__ = {"__len__", (PyCFunction)__pyx_pw_5pygmx_5tngio_9TNGReader_3__len__, METH_O, 0}; +static PyObject *__pyx_pw_5pygmx_5tngio_9TNGReader_3__len__(PyObject *__pyx_self, PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__len__ (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tngio_9TNGReader_2__len__(__pyx_self, ((PyObject *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tngio_9TNGReader_2__len__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + Py_ssize_t __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__len__", 0); + + /* "pygmx/tngio.pyx":142 + * + * def __len__(self): + * return ceil(len(self.trajectory) / self.nstxout) # <<<<<<<<<<<<<< + * + * def __getitem__(self, item): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_ceil); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_trajectory); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_Length(__pyx_t_3); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_nstxout); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = __Pyx_PyNumber_Divide(__pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_5)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + if (!__pyx_t_5) { + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_GOTREF(__pyx_t_1); + } else { + __pyx_t_3 = PyTuple_New(1+1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5); __pyx_t_5 = NULL; + __Pyx_GIVEREF(__pyx_t_6); + PyTuple_SET_ITEM(__pyx_t_3, 0+1, __pyx_t_6); + __pyx_t_6 = 0; + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + } + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pygmx/tngio.pyx":141 + * self.nstxout = self.trajectory.get_position_interval() + * + * def __len__(self): # <<<<<<<<<<<<<< + * return ceil(len(self.trajectory) / self.nstxout) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_AddTraceback("pygmx.tngio.TNGReader.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tngio.pyx":144 + * return ceil(len(self.trajectory) / self.nstxout) + * + * def __getitem__(self, item): # <<<<<<<<<<<<<< + * try: + * return self.trajectory[item * self.nstxout] + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tngio_9TNGReader_5__getitem__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pygmx_5tngio_9TNGReader_5__getitem__ = {"__getitem__", (PyCFunction)__pyx_pw_5pygmx_5tngio_9TNGReader_5__getitem__, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_5pygmx_5tngio_9TNGReader_5__getitem__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_self = 0; + PyObject *__pyx_v_item = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_item,0}; + PyObject* values[2] = {0,0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_self)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + case 1: + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_item)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("__getitem__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__getitem__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + } + __pyx_v_self = values[0]; + __pyx_v_item = values[1]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__getitem__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_L3_error:; + __Pyx_AddTraceback("pygmx.tngio.TNGReader.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pygmx_5tngio_9TNGReader_4__getitem__(__pyx_self, __pyx_v_self, __pyx_v_item); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tngio_9TNGReader_4__getitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_item) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + int __pyx_t_7; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__getitem__", 0); + + /* "pygmx/tngio.pyx":145 + * + * def __getitem__(self, item): + * try: # <<<<<<<<<<<<<< + * return self.trajectory[item * self.nstxout] + * except IndexError: + */ + { + __Pyx_ExceptionSave(&__pyx_t_1, &__pyx_t_2, &__pyx_t_3); + __Pyx_XGOTREF(__pyx_t_1); + __Pyx_XGOTREF(__pyx_t_2); + __Pyx_XGOTREF(__pyx_t_3); + /*try:*/ { + + /* "pygmx/tngio.pyx":146 + * def __getitem__(self, item): + * try: + * return self.trajectory[item * self.nstxout] # <<<<<<<<<<<<<< + * except IndexError: + * raise IndexError('Trajectory frame {} out of range.'.format(item)) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_trajectory); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 146; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_nstxout); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 146; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = PyNumber_Multiply(__pyx_v_item, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 146; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = PyObject_GetItem(__pyx_t_4, __pyx_t_6); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 146; __pyx_clineno = __LINE__; goto __pyx_L3_error;}; + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __pyx_r = __pyx_t_5; + __pyx_t_5 = 0; + goto __pyx_L7_try_return; + + /* "pygmx/tngio.pyx":145 + * + * def __getitem__(self, item): + * try: # <<<<<<<<<<<<<< + * return self.trajectory[item * self.nstxout] + * except IndexError: + */ + } + __pyx_L3_error:; + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + + /* "pygmx/tngio.pyx":147 + * try: + * return self.trajectory[item * self.nstxout] + * except IndexError: # <<<<<<<<<<<<<< + * raise IndexError('Trajectory frame {} out of range.'.format(item)) + */ + __pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_IndexError); + if (__pyx_t_7) { + __Pyx_AddTraceback("pygmx.tngio.TNGReader.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_GOTREF(__pyx_t_6); + __Pyx_GOTREF(__pyx_t_4); + + /* "pygmx/tngio.pyx":148 + * return self.trajectory[item * self.nstxout] + * except IndexError: + * raise IndexError('Trajectory frame {} out of range.'.format(item)) # <<<<<<<<<<<<<< + */ + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Trajectory_frame_out_of_range, __pyx_n_s_format); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_9))) { + __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_9); + if (likely(__pyx_t_10)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9); + __Pyx_INCREF(__pyx_t_10); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_9, function); + } + } + if (!__pyx_t_10) { + __pyx_t_8 = __Pyx_PyObject_CallOneArg(__pyx_t_9, __pyx_v_item); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_8); + } else { + __pyx_t_11 = PyTuple_New(1+1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_11); + __Pyx_GIVEREF(__pyx_t_10); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_10); __pyx_t_10 = NULL; + __Pyx_INCREF(__pyx_v_item); + __Pyx_GIVEREF(__pyx_v_item); + PyTuple_SET_ITEM(__pyx_t_11, 0+1, __pyx_v_item); + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_11, NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + } + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_GIVEREF(__pyx_t_8); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8); + __pyx_t_8 = 0; + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_IndexError, __pyx_t_9, NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_Raise(__pyx_t_8, 0, 0, 0); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + } + goto __pyx_L5_except_error; + __pyx_L5_except_error:; + + /* "pygmx/tngio.pyx":145 + * + * def __getitem__(self, item): + * try: # <<<<<<<<<<<<<< + * return self.trajectory[item * self.nstxout] + * except IndexError: + */ + __Pyx_XGIVEREF(__pyx_t_1); + __Pyx_XGIVEREF(__pyx_t_2); + __Pyx_XGIVEREF(__pyx_t_3); + __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3); + goto __pyx_L1_error; + __pyx_L7_try_return:; + __Pyx_XGIVEREF(__pyx_t_1); + __Pyx_XGIVEREF(__pyx_t_2); + __Pyx_XGIVEREF(__pyx_t_3); + __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3); + goto __pyx_L0; + } + + /* "pygmx/tngio.pyx":144 + * return ceil(len(self.trajectory) / self.nstxout) + * + * def __getitem__(self, item): # <<<<<<<<<<<<<< + * try: + * return self.trajectory[item * self.nstxout] + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_XDECREF(__pyx_t_10); + __Pyx_XDECREF(__pyx_t_11); + __Pyx_AddTraceback("pygmx.tngio.TNGReader.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":197 + * # experimental exception made for __getbuffer__ and __releasebuffer__ + * # -- the details of this may change. + * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< + * # This implementation of getbuffer is geared towards Cython + * # requirements, and does not yet fullfill the PEP. + */ + +/* Python wrapper */ +static CYTHON_UNUSED int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static CYTHON_UNUSED int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__getbuffer__ (wrapper)", 0); + __pyx_r = __pyx_pf_5numpy_7ndarray___getbuffer__(((PyArrayObject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info), ((int)__pyx_v_flags)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { + int __pyx_v_copy_shape; + int __pyx_v_i; + int __pyx_v_ndim; + int __pyx_v_endian_detector; + int __pyx_v_little_endian; + int __pyx_v_t; + char *__pyx_v_f; + PyArray_Descr *__pyx_v_descr = 0; + int __pyx_v_offset; + int __pyx_v_hasfields; + int __pyx_r; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_t_4; + int __pyx_t_5; + PyObject *__pyx_t_6 = NULL; + char *__pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__getbuffer__", 0); + if (__pyx_v_info != NULL) { + __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); + __Pyx_GIVEREF(__pyx_v_info->obj); + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":203 + * # of flags + * + * if info == NULL: return # <<<<<<<<<<<<<< + * + * cdef int copy_shape, i, ndim + */ + __pyx_t_1 = ((__pyx_v_info == NULL) != 0); + if (__pyx_t_1) { + __pyx_r = 0; + goto __pyx_L0; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":206 + * + * cdef int copy_shape, i, ndim + * cdef int endian_detector = 1 # <<<<<<<<<<<<<< + * cdef bint little_endian = ((&endian_detector)[0] != 0) + * + */ + __pyx_v_endian_detector = 1; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":207 + * cdef int copy_shape, i, ndim + * cdef int endian_detector = 1 + * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< + * + * ndim = PyArray_NDIM(self) + */ + __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":209 + * cdef bint little_endian = ((&endian_detector)[0] != 0) + * + * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< + * + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + */ + __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":211 + * ndim = PyArray_NDIM(self) + * + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * copy_shape = 1 + * else: + */ + __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":212 + * + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + * copy_shape = 1 # <<<<<<<<<<<<<< + * else: + * copy_shape = 0 + */ + __pyx_v_copy_shape = 1; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":211 + * ndim = PyArray_NDIM(self) + * + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * copy_shape = 1 + * else: + */ + goto __pyx_L4; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":214 + * copy_shape = 1 + * else: + * copy_shape = 0 # <<<<<<<<<<<<<< + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) + */ + /*else*/ { + __pyx_v_copy_shape = 0; + } + __pyx_L4:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":216 + * copy_shape = 0 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") + */ + __pyx_t_2 = (((__pyx_v_flags & PyBUF_C_CONTIGUOUS) == PyBUF_C_CONTIGUOUS) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L6_bool_binop_done; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":217 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< + * raise ValueError(u"ndarray is not C contiguous") + * + */ + __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L6_bool_binop_done:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":216 + * copy_shape = 0 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") + */ + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":218 + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":216 + * copy_shape = 0 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":220 + * raise ValueError(u"ndarray is not C contiguous") + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") + */ + __pyx_t_2 = (((__pyx_v_flags & PyBUF_F_CONTIGUOUS) == PyBUF_F_CONTIGUOUS) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L9_bool_binop_done; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":221 + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< + * raise ValueError(u"ndarray is not Fortran contiguous") + * + */ + __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L9_bool_binop_done:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":220 + * raise ValueError(u"ndarray is not C contiguous") + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") + */ + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":222 + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< + * + * info.buf = PyArray_DATA(self) + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":220 + * raise ValueError(u"ndarray is not C contiguous") + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":224 + * raise ValueError(u"ndarray is not Fortran contiguous") + * + * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< + * info.ndim = ndim + * if copy_shape: + */ + __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":225 + * + * info.buf = PyArray_DATA(self) + * info.ndim = ndim # <<<<<<<<<<<<<< + * if copy_shape: + * # Allocate new buffer for strides and shape info. + */ + __pyx_v_info->ndim = __pyx_v_ndim; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":226 + * info.buf = PyArray_DATA(self) + * info.ndim = ndim + * if copy_shape: # <<<<<<<<<<<<<< + * # Allocate new buffer for strides and shape info. + * # This is allocated as one block, strides first. + */ + __pyx_t_1 = (__pyx_v_copy_shape != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":229 + * # Allocate new buffer for strides and shape info. + * # This is allocated as one block, strides first. + * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) # <<<<<<<<<<<<<< + * info.shape = info.strides + ndim + * for i in range(ndim): + */ + __pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2))); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":230 + * # This is allocated as one block, strides first. + * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) + * info.shape = info.strides + ndim # <<<<<<<<<<<<<< + * for i in range(ndim): + * info.strides[i] = PyArray_STRIDES(self)[i] + */ + __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":231 + * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) + * info.shape = info.strides + ndim + * for i in range(ndim): # <<<<<<<<<<<<<< + * info.strides[i] = PyArray_STRIDES(self)[i] + * info.shape[i] = PyArray_DIMS(self)[i] + */ + __pyx_t_4 = __pyx_v_ndim; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":232 + * info.shape = info.strides + ndim + * for i in range(ndim): + * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< + * info.shape[i] = PyArray_DIMS(self)[i] + * else: + */ + (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":233 + * for i in range(ndim): + * info.strides[i] = PyArray_STRIDES(self)[i] + * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< + * else: + * info.strides = PyArray_STRIDES(self) + */ + (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":226 + * info.buf = PyArray_DATA(self) + * info.ndim = ndim + * if copy_shape: # <<<<<<<<<<<<<< + * # Allocate new buffer for strides and shape info. + * # This is allocated as one block, strides first. + */ + goto __pyx_L11; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":235 + * info.shape[i] = PyArray_DIMS(self)[i] + * else: + * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< + * info.shape = PyArray_DIMS(self) + * info.suboffsets = NULL + */ + /*else*/ { + __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":236 + * else: + * info.strides = PyArray_STRIDES(self) + * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< + * info.suboffsets = NULL + * info.itemsize = PyArray_ITEMSIZE(self) + */ + __pyx_v_info->shape = ((Py_ssize_t *)PyArray_DIMS(__pyx_v_self)); + } + __pyx_L11:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":237 + * info.strides = PyArray_STRIDES(self) + * info.shape = PyArray_DIMS(self) + * info.suboffsets = NULL # <<<<<<<<<<<<<< + * info.itemsize = PyArray_ITEMSIZE(self) + * info.readonly = not PyArray_ISWRITEABLE(self) + */ + __pyx_v_info->suboffsets = NULL; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":238 + * info.shape = PyArray_DIMS(self) + * info.suboffsets = NULL + * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< + * info.readonly = not PyArray_ISWRITEABLE(self) + * + */ + __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":239 + * info.suboffsets = NULL + * info.itemsize = PyArray_ITEMSIZE(self) + * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< + * + * cdef int t + */ + __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":242 + * + * cdef int t + * cdef char* f = NULL # <<<<<<<<<<<<<< + * cdef dtype descr = self.descr + * cdef int offset + */ + __pyx_v_f = NULL; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":243 + * cdef int t + * cdef char* f = NULL + * cdef dtype descr = self.descr # <<<<<<<<<<<<<< + * cdef int offset + * + */ + __pyx_t_3 = ((PyObject *)__pyx_v_self->descr); + __Pyx_INCREF(__pyx_t_3); + __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); + __pyx_t_3 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":246 + * cdef int offset + * + * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< + * + * if not hasfields and not copy_shape: + */ + __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":248 + * cdef bint hasfields = PyDataType_HASFIELDS(descr) + * + * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< + * # do not call releasebuffer + * info.obj = None + */ + __pyx_t_2 = ((!(__pyx_v_hasfields != 0)) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L15_bool_binop_done; + } + __pyx_t_2 = ((!(__pyx_v_copy_shape != 0)) != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L15_bool_binop_done:; + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":250 + * if not hasfields and not copy_shape: + * # do not call releasebuffer + * info.obj = None # <<<<<<<<<<<<<< + * else: + * # need to call releasebuffer + */ + __Pyx_INCREF(Py_None); + __Pyx_GIVEREF(Py_None); + __Pyx_GOTREF(__pyx_v_info->obj); + __Pyx_DECREF(__pyx_v_info->obj); + __pyx_v_info->obj = Py_None; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":248 + * cdef bint hasfields = PyDataType_HASFIELDS(descr) + * + * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< + * # do not call releasebuffer + * info.obj = None + */ + goto __pyx_L14; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":253 + * else: + * # need to call releasebuffer + * info.obj = self # <<<<<<<<<<<<<< + * + * if not hasfields: + */ + /*else*/ { + __Pyx_INCREF(((PyObject *)__pyx_v_self)); + __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); + __Pyx_GOTREF(__pyx_v_info->obj); + __Pyx_DECREF(__pyx_v_info->obj); + __pyx_v_info->obj = ((PyObject *)__pyx_v_self); + } + __pyx_L14:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":255 + * info.obj = self + * + * if not hasfields: # <<<<<<<<<<<<<< + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or + */ + __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":256 + * + * if not hasfields: + * t = descr.type_num # <<<<<<<<<<<<<< + * if ((descr.byteorder == c'>' and little_endian) or + * (descr.byteorder == c'<' and not little_endian)): + */ + __pyx_t_4 = __pyx_v_descr->type_num; + __pyx_v_t = __pyx_t_4; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":257 + * if not hasfields: + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + __pyx_t_2 = ((__pyx_v_descr->byteorder == '>') != 0); + if (!__pyx_t_2) { + goto __pyx_L20_next_or; + } else { + } + __pyx_t_2 = (__pyx_v_little_endian != 0); + if (!__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L19_bool_binop_done; + } + __pyx_L20_next_or:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":258 + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or + * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< + * raise ValueError(u"Non-native byte order not supported") + * if t == NPY_BYTE: f = "b" + */ + __pyx_t_2 = ((__pyx_v_descr->byteorder == '<') != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L19_bool_binop_done; + } + __pyx_t_2 = ((!(__pyx_v_little_endian != 0)) != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L19_bool_binop_done:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":257 + * if not hasfields: + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":259 + * if ((descr.byteorder == c'>' and little_endian) or + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< + * if t == NPY_BYTE: f = "b" + * elif t == NPY_UBYTE: f = "B" + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":257 + * if not hasfields: + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":260 + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< + * elif t == NPY_UBYTE: f = "B" + * elif t == NPY_SHORT: f = "h" + */ + switch (__pyx_v_t) { + case NPY_BYTE: + __pyx_v_f = __pyx_k_b; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":261 + * raise ValueError(u"Non-native byte order not supported") + * if t == NPY_BYTE: f = "b" + * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< + * elif t == NPY_SHORT: f = "h" + * elif t == NPY_USHORT: f = "H" + */ + case NPY_UBYTE: + __pyx_v_f = __pyx_k_B; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":262 + * if t == NPY_BYTE: f = "b" + * elif t == NPY_UBYTE: f = "B" + * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< + * elif t == NPY_USHORT: f = "H" + * elif t == NPY_INT: f = "i" + */ + case NPY_SHORT: + __pyx_v_f = __pyx_k_h; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":263 + * elif t == NPY_UBYTE: f = "B" + * elif t == NPY_SHORT: f = "h" + * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< + * elif t == NPY_INT: f = "i" + * elif t == NPY_UINT: f = "I" + */ + case NPY_USHORT: + __pyx_v_f = __pyx_k_H; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":264 + * elif t == NPY_SHORT: f = "h" + * elif t == NPY_USHORT: f = "H" + * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< + * elif t == NPY_UINT: f = "I" + * elif t == NPY_LONG: f = "l" + */ + case NPY_INT: + __pyx_v_f = __pyx_k_i; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":265 + * elif t == NPY_USHORT: f = "H" + * elif t == NPY_INT: f = "i" + * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< + * elif t == NPY_LONG: f = "l" + * elif t == NPY_ULONG: f = "L" + */ + case NPY_UINT: + __pyx_v_f = __pyx_k_I; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":266 + * elif t == NPY_INT: f = "i" + * elif t == NPY_UINT: f = "I" + * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< + * elif t == NPY_ULONG: f = "L" + * elif t == NPY_LONGLONG: f = "q" + */ + case NPY_LONG: + __pyx_v_f = __pyx_k_l; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":267 + * elif t == NPY_UINT: f = "I" + * elif t == NPY_LONG: f = "l" + * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< + * elif t == NPY_LONGLONG: f = "q" + * elif t == NPY_ULONGLONG: f = "Q" + */ + case NPY_ULONG: + __pyx_v_f = __pyx_k_L; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":268 + * elif t == NPY_LONG: f = "l" + * elif t == NPY_ULONG: f = "L" + * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< + * elif t == NPY_ULONGLONG: f = "Q" + * elif t == NPY_FLOAT: f = "f" + */ + case NPY_LONGLONG: + __pyx_v_f = __pyx_k_q; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":269 + * elif t == NPY_ULONG: f = "L" + * elif t == NPY_LONGLONG: f = "q" + * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< + * elif t == NPY_FLOAT: f = "f" + * elif t == NPY_DOUBLE: f = "d" + */ + case NPY_ULONGLONG: + __pyx_v_f = __pyx_k_Q; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":270 + * elif t == NPY_LONGLONG: f = "q" + * elif t == NPY_ULONGLONG: f = "Q" + * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< + * elif t == NPY_DOUBLE: f = "d" + * elif t == NPY_LONGDOUBLE: f = "g" + */ + case NPY_FLOAT: + __pyx_v_f = __pyx_k_f; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":271 + * elif t == NPY_ULONGLONG: f = "Q" + * elif t == NPY_FLOAT: f = "f" + * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< + * elif t == NPY_LONGDOUBLE: f = "g" + * elif t == NPY_CFLOAT: f = "Zf" + */ + case NPY_DOUBLE: + __pyx_v_f = __pyx_k_d; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":272 + * elif t == NPY_FLOAT: f = "f" + * elif t == NPY_DOUBLE: f = "d" + * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< + * elif t == NPY_CFLOAT: f = "Zf" + * elif t == NPY_CDOUBLE: f = "Zd" + */ + case NPY_LONGDOUBLE: + __pyx_v_f = __pyx_k_g; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":273 + * elif t == NPY_DOUBLE: f = "d" + * elif t == NPY_LONGDOUBLE: f = "g" + * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< + * elif t == NPY_CDOUBLE: f = "Zd" + * elif t == NPY_CLONGDOUBLE: f = "Zg" + */ + case NPY_CFLOAT: + __pyx_v_f = __pyx_k_Zf; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":274 + * elif t == NPY_LONGDOUBLE: f = "g" + * elif t == NPY_CFLOAT: f = "Zf" + * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< + * elif t == NPY_CLONGDOUBLE: f = "Zg" + * elif t == NPY_OBJECT: f = "O" + */ + case NPY_CDOUBLE: + __pyx_v_f = __pyx_k_Zd; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":275 + * elif t == NPY_CFLOAT: f = "Zf" + * elif t == NPY_CDOUBLE: f = "Zd" + * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< + * elif t == NPY_OBJECT: f = "O" + * else: + */ + case NPY_CLONGDOUBLE: + __pyx_v_f = __pyx_k_Zg; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":276 + * elif t == NPY_CDOUBLE: f = "Zd" + * elif t == NPY_CLONGDOUBLE: f = "Zg" + * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + */ + case NPY_OBJECT: + __pyx_v_f = __pyx_k_O; + break; + default: + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":278 + * elif t == NPY_OBJECT: f = "O" + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< + * info.format = f + * return + */ + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_6 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_GIVEREF(__pyx_t_6); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_6); + __pyx_t_6 = 0; + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_6, 0, 0, 0); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + break; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":279 + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + * info.format = f # <<<<<<<<<<<<<< + * return + * else: + */ + __pyx_v_info->format = __pyx_v_f; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":280 + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + * info.format = f + * return # <<<<<<<<<<<<<< + * else: + * info.format = stdlib.malloc(_buffer_format_string_len) + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":255 + * info.obj = self + * + * if not hasfields: # <<<<<<<<<<<<<< + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":282 + * return + * else: + * info.format = stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< + * info.format[0] = c'^' # Native data types, manual alignment + * offset = 0 + */ + /*else*/ { + __pyx_v_info->format = ((char *)malloc(0xFF)); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":283 + * else: + * info.format = stdlib.malloc(_buffer_format_string_len) + * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< + * offset = 0 + * f = _util_dtypestring(descr, info.format + 1, + */ + (__pyx_v_info->format[0]) = '^'; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":284 + * info.format = stdlib.malloc(_buffer_format_string_len) + * info.format[0] = c'^' # Native data types, manual alignment + * offset = 0 # <<<<<<<<<<<<<< + * f = _util_dtypestring(descr, info.format + 1, + * info.format + _buffer_format_string_len, + */ + __pyx_v_offset = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":285 + * info.format[0] = c'^' # Native data types, manual alignment + * offset = 0 + * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< + * info.format + _buffer_format_string_len, + * &offset) + */ + __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_f = __pyx_t_7; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":288 + * info.format + _buffer_format_string_len, + * &offset) + * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< + * + * def __releasebuffer__(ndarray self, Py_buffer* info): + */ + (__pyx_v_f[0]) = '\x00'; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":197 + * # experimental exception made for __getbuffer__ and __releasebuffer__ + * # -- the details of this may change. + * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< + * # This implementation of getbuffer is geared towards Cython + * # requirements, and does not yet fullfill the PEP. + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_AddTraceback("numpy.ndarray.__getbuffer__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + if (__pyx_v_info != NULL && __pyx_v_info->obj != NULL) { + __Pyx_GOTREF(__pyx_v_info->obj); + __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = NULL; + } + goto __pyx_L2; + __pyx_L0:; + if (__pyx_v_info != NULL && __pyx_v_info->obj == Py_None) { + __Pyx_GOTREF(Py_None); + __Pyx_DECREF(Py_None); __pyx_v_info->obj = NULL; + } + __pyx_L2:; + __Pyx_XDECREF((PyObject *)__pyx_v_descr); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":290 + * f[0] = c'\0' # Terminate format string + * + * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) + */ + +/* Python wrapper */ +static CYTHON_UNUSED void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/ +static CYTHON_UNUSED void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__releasebuffer__ (wrapper)", 0); + __pyx_pf_5numpy_7ndarray_2__releasebuffer__(((PyArrayObject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info) { + __Pyx_RefNannyDeclarations + int __pyx_t_1; + __Pyx_RefNannySetupContext("__releasebuffer__", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":291 + * + * def __releasebuffer__(ndarray self, Py_buffer* info): + * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + */ + __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":292 + * def __releasebuffer__(ndarray self, Py_buffer* info): + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) # <<<<<<<<<<<<<< + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + * stdlib.free(info.strides) + */ + free(__pyx_v_info->format); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":291 + * + * def __releasebuffer__(ndarray self, Py_buffer* info): + * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":293 + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * stdlib.free(info.strides) + * # info.shape was stored after info.strides in the same block + */ + __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":294 + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + * stdlib.free(info.strides) # <<<<<<<<<<<<<< + * # info.shape was stored after info.strides in the same block + * + */ + free(__pyx_v_info->strides); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":293 + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * stdlib.free(info.strides) + * # info.shape was stored after info.strides in the same block + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":290 + * f[0] = c'\0' # Terminate format string + * + * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) + */ + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":770 + * ctypedef npy_cdouble complex_t + * + * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(1, a) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":771 + * + * cdef inline object PyArray_MultiIterNew1(a): + * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew2(a, b): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":770 + * ctypedef npy_cdouble complex_t + * + * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(1, a) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew1", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":773 + * return PyArray_MultiIterNew(1, a) + * + * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(2, a, b) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":774 + * + * cdef inline object PyArray_MultiIterNew2(a, b): + * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew3(a, b, c): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(2, ((void *)__pyx_v_a), ((void *)__pyx_v_b)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":773 + * return PyArray_MultiIterNew(1, a) + * + * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(2, a, b) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew2", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":776 + * return PyArray_MultiIterNew(2, a, b) + * + * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(3, a, b, c) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":777 + * + * cdef inline object PyArray_MultiIterNew3(a, b, c): + * return PyArray_MultiIterNew(3, a, b, c) # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew4(a, b, c, d): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(3, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":776 + * return PyArray_MultiIterNew(2, a, b) + * + * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(3, a, b, c) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew3", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":779 + * return PyArray_MultiIterNew(3, a, b, c) + * + * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(4, a, b, c, d) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":780 + * + * cdef inline object PyArray_MultiIterNew4(a, b, c, d): + * return PyArray_MultiIterNew(4, a, b, c, d) # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(4, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":779 + * return PyArray_MultiIterNew(3, a, b, c) + * + * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(4, a, b, c, d) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew4", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":782 + * return PyArray_MultiIterNew(4, a, b, c, d) + * + * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(5, a, b, c, d, e) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":783 + * + * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): + * return PyArray_MultiIterNew(5, a, b, c, d, e) # <<<<<<<<<<<<<< + * + * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(5, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d), ((void *)__pyx_v_e)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":782 + * return PyArray_MultiIterNew(4, a, b, c, d) + * + * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(5, a, b, c, d, e) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew5", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":785 + * return PyArray_MultiIterNew(5, a, b, c, d, e) + * + * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< + * # Recursive utility function used in __getbuffer__ to get format + * # string. The new location in the format string is returned. + */ + +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx_v_descr, char *__pyx_v_f, char *__pyx_v_end, int *__pyx_v_offset) { + PyArray_Descr *__pyx_v_child = 0; + int __pyx_v_endian_detector; + int __pyx_v_little_endian; + PyObject *__pyx_v_fields = 0; + PyObject *__pyx_v_childname = NULL; + PyObject *__pyx_v_new_offset = NULL; + PyObject *__pyx_v_t = NULL; + char *__pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + Py_ssize_t __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_t_5; + int __pyx_t_6; + int __pyx_t_7; + long __pyx_t_8; + char *__pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("_util_dtypestring", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":790 + * + * cdef dtype child + * cdef int endian_detector = 1 # <<<<<<<<<<<<<< + * cdef bint little_endian = ((&endian_detector)[0] != 0) + * cdef tuple fields + */ + __pyx_v_endian_detector = 1; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":791 + * cdef dtype child + * cdef int endian_detector = 1 + * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< + * cdef tuple fields + * + */ + __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":794 + * cdef tuple fields + * + * for childname in descr.names: # <<<<<<<<<<<<<< + * fields = descr.fields[childname] + * child, new_offset = fields + */ + if (unlikely(__pyx_v_descr->names == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; + for (;;) { + if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + #endif + __Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3); + __pyx_t_3 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":795 + * + * for childname in descr.names: + * fields = descr.fields[childname] # <<<<<<<<<<<<<< + * child, new_offset = fields + * + */ + if (unlikely(__pyx_v_descr->fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __Pyx_GOTREF(__pyx_t_3); + if (!(likely(PyTuple_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "tuple", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); + __pyx_t_3 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":796 + * for childname in descr.names: + * fields = descr.fields[childname] + * child, new_offset = fields # <<<<<<<<<<<<<< + * + * if (end - f) - (new_offset - offset[0]) < 15: + */ + if (likely(__pyx_v_fields != Py_None)) { + PyObject* sequence = __pyx_v_fields; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_4 = PyTuple_GET_ITEM(sequence, 1); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(__pyx_t_4); + #else + __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + #endif + } else { + __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_dtype))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_XDECREF_SET(__pyx_v_child, ((PyArray_Descr *)__pyx_t_3)); + __pyx_t_3 = 0; + __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); + __pyx_t_4 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":798 + * child, new_offset = fields + * + * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + */ + __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyNumber_Subtract(__pyx_v_new_offset, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); + if (__pyx_t_6) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":799 + * + * if (end - f) - (new_offset - offset[0]) < 15: + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< + * + * if ((child.byteorder == c'>' and little_endian) or + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":798 + * child, new_offset = fields + * + * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":801 + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + __pyx_t_7 = ((__pyx_v_child->byteorder == '>') != 0); + if (!__pyx_t_7) { + goto __pyx_L8_next_or; + } else { + } + __pyx_t_7 = (__pyx_v_little_endian != 0); + if (!__pyx_t_7) { + } else { + __pyx_t_6 = __pyx_t_7; + goto __pyx_L7_bool_binop_done; + } + __pyx_L8_next_or:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":802 + * + * if ((child.byteorder == c'>' and little_endian) or + * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< + * raise ValueError(u"Non-native byte order not supported") + * # One could encode it in the format string and have Cython + */ + __pyx_t_7 = ((__pyx_v_child->byteorder == '<') != 0); + if (__pyx_t_7) { + } else { + __pyx_t_6 = __pyx_t_7; + goto __pyx_L7_bool_binop_done; + } + __pyx_t_7 = ((!(__pyx_v_little_endian != 0)) != 0); + __pyx_t_6 = __pyx_t_7; + __pyx_L7_bool_binop_done:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":801 + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + if (__pyx_t_6) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":803 + * if ((child.byteorder == c'>' and little_endian) or + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< + * # One could encode it in the format string and have Cython + * # complain instead, BUT: < and > in format strings also imply + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":801 + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":813 + * + * # Output padding bytes + * while offset[0] < new_offset: # <<<<<<<<<<<<<< + * f[0] = 120 # "x"; pad byte + * f += 1 + */ + while (1) { + __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_v_new_offset, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (!__pyx_t_6) break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":814 + * # Output padding bytes + * while offset[0] < new_offset: + * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< + * f += 1 + * offset[0] += 1 + */ + (__pyx_v_f[0]) = 0x78; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":815 + * while offset[0] < new_offset: + * f[0] = 120 # "x"; pad byte + * f += 1 # <<<<<<<<<<<<<< + * offset[0] += 1 + * + */ + __pyx_v_f = (__pyx_v_f + 1); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":816 + * f[0] = 120 # "x"; pad byte + * f += 1 + * offset[0] += 1 # <<<<<<<<<<<<<< + * + * offset[0] += child.itemsize + */ + __pyx_t_8 = 0; + (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":818 + * offset[0] += 1 + * + * offset[0] += child.itemsize # <<<<<<<<<<<<<< + * + * if not PyDataType_HASFIELDS(child): + */ + __pyx_t_8 = 0; + (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":820 + * offset[0] += child.itemsize + * + * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< + * t = child.type_num + * if end - f < 5: + */ + __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); + if (__pyx_t_6) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":821 + * + * if not PyDataType_HASFIELDS(child): + * t = child.type_num # <<<<<<<<<<<<<< + * if end - f < 5: + * raise RuntimeError(u"Format string allocated too short.") + */ + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_child->type_num); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); + __pyx_t_4 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":822 + * if not PyDataType_HASFIELDS(child): + * t = child.type_num + * if end - f < 5: # <<<<<<<<<<<<<< + * raise RuntimeError(u"Format string allocated too short.") + * + */ + __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); + if (__pyx_t_6) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":823 + * t = child.type_num + * if end - f < 5: + * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< + * + * # Until ticket #99 is fixed, use integers to avoid warnings + */ + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_Raise(__pyx_t_4, 0, 0, 0); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":822 + * if not PyDataType_HASFIELDS(child): + * t = child.type_num + * if end - f < 5: # <<<<<<<<<<<<<< + * raise RuntimeError(u"Format string allocated too short.") + * + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":826 + * + * # Until ticket #99 is fixed, use integers to avoid warnings + * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< + * elif t == NPY_UBYTE: f[0] = 66 #"B" + * elif t == NPY_SHORT: f[0] = 104 #"h" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_BYTE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 98; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":827 + * # Until ticket #99 is fixed, use integers to avoid warnings + * if t == NPY_BYTE: f[0] = 98 #"b" + * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< + * elif t == NPY_SHORT: f[0] = 104 #"h" + * elif t == NPY_USHORT: f[0] = 72 #"H" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UBYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 66; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":828 + * if t == NPY_BYTE: f[0] = 98 #"b" + * elif t == NPY_UBYTE: f[0] = 66 #"B" + * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< + * elif t == NPY_USHORT: f[0] = 72 #"H" + * elif t == NPY_INT: f[0] = 105 #"i" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_SHORT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x68; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":829 + * elif t == NPY_UBYTE: f[0] = 66 #"B" + * elif t == NPY_SHORT: f[0] = 104 #"h" + * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< + * elif t == NPY_INT: f[0] = 105 #"i" + * elif t == NPY_UINT: f[0] = 73 #"I" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_USHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 72; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":830 + * elif t == NPY_SHORT: f[0] = 104 #"h" + * elif t == NPY_USHORT: f[0] = 72 #"H" + * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< + * elif t == NPY_UINT: f[0] = 73 #"I" + * elif t == NPY_LONG: f[0] = 108 #"l" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_INT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x69; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":831 + * elif t == NPY_USHORT: f[0] = 72 #"H" + * elif t == NPY_INT: f[0] = 105 #"i" + * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< + * elif t == NPY_LONG: f[0] = 108 #"l" + * elif t == NPY_ULONG: f[0] = 76 #"L" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UINT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 73; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":832 + * elif t == NPY_INT: f[0] = 105 #"i" + * elif t == NPY_UINT: f[0] = 73 #"I" + * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< + * elif t == NPY_ULONG: f[0] = 76 #"L" + * elif t == NPY_LONGLONG: f[0] = 113 #"q" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x6C; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":833 + * elif t == NPY_UINT: f[0] = 73 #"I" + * elif t == NPY_LONG: f[0] = 108 #"l" + * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< + * elif t == NPY_LONGLONG: f[0] = 113 #"q" + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_ULONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 76; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":834 + * elif t == NPY_LONG: f[0] = 108 #"l" + * elif t == NPY_ULONG: f[0] = 76 #"L" + * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" + * elif t == NPY_FLOAT: f[0] = 102 #"f" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONGLONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x71; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":835 + * elif t == NPY_ULONG: f[0] = 76 #"L" + * elif t == NPY_LONGLONG: f[0] = 113 #"q" + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< + * elif t == NPY_FLOAT: f[0] = 102 #"f" + * elif t == NPY_DOUBLE: f[0] = 100 #"d" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_ULONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 81; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":836 + * elif t == NPY_LONGLONG: f[0] = 113 #"q" + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" + * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< + * elif t == NPY_DOUBLE: f[0] = 100 #"d" + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_FLOAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x66; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":837 + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" + * elif t == NPY_FLOAT: f[0] = 102 #"f" + * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_DOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x64; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":838 + * elif t == NPY_FLOAT: f[0] = 102 #"f" + * elif t == NPY_DOUBLE: f[0] = 100 #"d" + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x67; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":839 + * elif t == NPY_DOUBLE: f[0] = 100 #"d" + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd + * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CFLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 90; + (__pyx_v_f[1]) = 0x66; + __pyx_v_f = (__pyx_v_f + 1); + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":840 + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< + * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg + * elif t == NPY_OBJECT: f[0] = 79 #"O" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CDOUBLE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 90; + (__pyx_v_f[1]) = 0x64; + __pyx_v_f = (__pyx_v_f + 1); + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":841 + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd + * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< + * elif t == NPY_OBJECT: f[0] = 79 #"O" + * else: + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 90; + (__pyx_v_f[1]) = 0x67; + __pyx_v_f = (__pyx_v_f + 1); + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":842 + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd + * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg + * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_OBJECT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 79; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":844 + * elif t == NPY_OBJECT: f[0] = 79 #"O" + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< + * f += 1 + * else: + */ + /*else*/ { + __pyx_t_3 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); + __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_L15:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":845 + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + * f += 1 # <<<<<<<<<<<<<< + * else: + * # Cython ignores struct boundary information ("T{...}"), + */ + __pyx_v_f = (__pyx_v_f + 1); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":820 + * offset[0] += child.itemsize + * + * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< + * t = child.type_num + * if end - f < 5: + */ + goto __pyx_L13; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":849 + * # Cython ignores struct boundary information ("T{...}"), + * # so don't output it + * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< + * return f + * + */ + /*else*/ { + __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_f = __pyx_t_9; + } + __pyx_L13:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":794 + * cdef tuple fields + * + * for childname in descr.names: # <<<<<<<<<<<<<< + * fields = descr.fields[childname] + * child, new_offset = fields + */ + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":850 + * # so don't output it + * f = _util_dtypestring(child, f, end, offset) + * return f # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = __pyx_v_f; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":785 + * return PyArray_MultiIterNew(5, a, b, c, d, e) + * + * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< + * # Recursive utility function used in __getbuffer__ to get format + * # string. The new location in the format string is returned. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("numpy._util_dtypestring", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_child); + __Pyx_XDECREF(__pyx_v_fields); + __Pyx_XDECREF(__pyx_v_childname); + __Pyx_XDECREF(__pyx_v_new_offset); + __Pyx_XDECREF(__pyx_v_t); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":966 + * + * + * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< + * cdef PyObject* baseptr + * if base is None: + */ + +static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObject *__pyx_v_base) { + PyObject *__pyx_v_baseptr; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + __Pyx_RefNannySetupContext("set_array_base", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":968 + * cdef inline void set_array_base(ndarray arr, object base): + * cdef PyObject* baseptr + * if base is None: # <<<<<<<<<<<<<< + * baseptr = NULL + * else: + */ + __pyx_t_1 = (__pyx_v_base == Py_None); + __pyx_t_2 = (__pyx_t_1 != 0); + if (__pyx_t_2) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":969 + * cdef PyObject* baseptr + * if base is None: + * baseptr = NULL # <<<<<<<<<<<<<< + * else: + * Py_INCREF(base) # important to do this before decref below! + */ + __pyx_v_baseptr = NULL; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":968 + * cdef inline void set_array_base(ndarray arr, object base): + * cdef PyObject* baseptr + * if base is None: # <<<<<<<<<<<<<< + * baseptr = NULL + * else: + */ + goto __pyx_L3; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":971 + * baseptr = NULL + * else: + * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< + * baseptr = base + * Py_XDECREF(arr.base) + */ + /*else*/ { + Py_INCREF(__pyx_v_base); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":972 + * else: + * Py_INCREF(base) # important to do this before decref below! + * baseptr = base # <<<<<<<<<<<<<< + * Py_XDECREF(arr.base) + * arr.base = baseptr + */ + __pyx_v_baseptr = ((PyObject *)__pyx_v_base); + } + __pyx_L3:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":973 + * Py_INCREF(base) # important to do this before decref below! + * baseptr = base + * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< + * arr.base = baseptr + * + */ + Py_XDECREF(__pyx_v_arr->base); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":974 + * baseptr = base + * Py_XDECREF(arr.base) + * arr.base = baseptr # <<<<<<<<<<<<<< + * + * cdef inline object get_array_base(ndarray arr): + */ + __pyx_v_arr->base = __pyx_v_baseptr; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":966 + * + * + * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< + * cdef PyObject* baseptr + * if base is None: + */ + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr + * + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + __Pyx_RefNannySetupContext("get_array_base", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":977 + * + * cdef inline object get_array_base(ndarray arr): + * if arr.base is NULL: # <<<<<<<<<<<<<< + * return None + * else: + */ + __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":978 + * cdef inline object get_array_base(ndarray arr): + * if arr.base is NULL: + * return None # <<<<<<<<<<<<<< + * else: + * return arr.base + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_None); + __pyx_r = Py_None; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":977 + * + * cdef inline object get_array_base(ndarray arr): + * if arr.base is NULL: # <<<<<<<<<<<<<< + * return None + * else: + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":980 + * return None + * else: + * return arr.base # <<<<<<<<<<<<<< + */ + /*else*/ { + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(((PyObject *)__pyx_v_arr->base)); + __pyx_r = ((PyObject *)__pyx_v_arr->base); + goto __pyx_L0; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr + * + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_tp_new_5pygmx_5tngio_TNGTrajectory(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + return o; +} + +static void __pyx_tp_dealloc_5pygmx_5tngio_TNGTrajectory(PyObject *o) { + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + (*Py_TYPE(o)->tp_free)(o); +} +static PyObject *__pyx_sq_item_5pygmx_5tngio_TNGTrajectory(PyObject *o, Py_ssize_t i) { + PyObject *r; + PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; + r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); + Py_DECREF(x); + return r; +} + +static PyMethodDef __pyx_methods_5pygmx_5tngio_TNGTrajectory[] = { + {"get_position_interval", (PyCFunction)__pyx_pw_5pygmx_5tngio_13TNGTrajectory_1get_position_interval, METH_NOARGS, 0}, + {0, 0, 0, 0} +}; + +static PySequenceMethods __pyx_tp_as_sequence_TNGTrajectory = { + __pyx_pw_5pygmx_5tngio_13TNGTrajectory_3__len__, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + __pyx_sq_item_5pygmx_5tngio_TNGTrajectory, /*sq_item*/ + 0, /*sq_slice*/ + 0, /*sq_ass_item*/ + 0, /*sq_ass_slice*/ + 0, /*sq_contains*/ + 0, /*sq_inplace_concat*/ + 0, /*sq_inplace_repeat*/ +}; + +static PyMappingMethods __pyx_tp_as_mapping_TNGTrajectory = { + __pyx_pw_5pygmx_5tngio_13TNGTrajectory_3__len__, /*mp_length*/ + __pyx_pw_5pygmx_5tngio_13TNGTrajectory_5__getitem__, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyTypeObject __pyx_type_5pygmx_5tngio_TNGTrajectory = { + PyVarObject_HEAD_INIT(0, 0) + "pygmx.tngio.TNGTrajectory", /*tp_name*/ + sizeof(struct __pyx_obj_5pygmx_5tngio_TNGTrajectory), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_5pygmx_5tngio_TNGTrajectory, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + &__pyx_tp_as_sequence_TNGTrajectory, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_TNGTrajectory, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ + 0, /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_5pygmx_5tngio_TNGTrajectory, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_5pygmx_5tngio_13TNGTrajectory_7__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_5pygmx_5tngio_TNGTrajectory, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; + +static PyMethodDef __pyx_methods[] = { + {0, 0, 0, 0} +}; + +#if PY_MAJOR_VERSION >= 3 +static struct PyModuleDef __pyx_moduledef = { + #if PY_VERSION_HEX < 0x03020000 + { PyObject_HEAD_INIT(NULL) NULL, 0, NULL }, + #else + PyModuleDef_HEAD_INIT, + #endif + "tngio", + 0, /* m_doc */ + -1, /* m_size */ + __pyx_methods /* m_methods */, + NULL, /* m_reload */ + NULL, /* m_traverse */ + NULL, /* m_clear */ + NULL /* m_free */ +}; +#endif + +static __Pyx_StringTabEntry __pyx_string_tab[] = { + {&__pyx_kp_s_, __pyx_k_, sizeof(__pyx_k_), 0, 0, 1, 0}, + {&__pyx_kp_s_Filename_must_not_be_null, __pyx_k_Filename_must_not_be_null, sizeof(__pyx_k_Filename_must_not_be_null), 0, 0, 1, 0}, + {&__pyx_kp_u_Format_string_allocated_too_shor, __pyx_k_Format_string_allocated_too_shor, sizeof(__pyx_k_Format_string_allocated_too_shor), 0, 1, 0, 0}, + {&__pyx_kp_u_Format_string_allocated_too_shor_2, __pyx_k_Format_string_allocated_too_shor_2, sizeof(__pyx_k_Format_string_allocated_too_shor_2), 0, 1, 0, 0}, + {&__pyx_n_s_IndexError, __pyx_k_IndexError, sizeof(__pyx_k_IndexError), 0, 0, 1, 1}, + {&__pyx_kp_u_Non_native_byte_order_not_suppor, __pyx_k_Non_native_byte_order_not_suppor, sizeof(__pyx_k_Non_native_byte_order_not_suppor), 0, 1, 0, 0}, + {&__pyx_n_s_OSError, __pyx_k_OSError, sizeof(__pyx_k_OSError), 0, 0, 1, 1}, + {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1}, + {&__pyx_n_s_TNGReader, __pyx_k_TNGReader, sizeof(__pyx_k_TNGReader), 0, 0, 1, 1}, + {&__pyx_n_s_TNGReader___getitem, __pyx_k_TNGReader___getitem, sizeof(__pyx_k_TNGReader___getitem), 0, 0, 1, 1}, + {&__pyx_n_s_TNGReader___init, __pyx_k_TNGReader___init, sizeof(__pyx_k_TNGReader___init), 0, 0, 1, 1}, + {&__pyx_n_s_TNGReader___len, __pyx_k_TNGReader___len, sizeof(__pyx_k_TNGReader___len), 0, 0, 1, 1}, + {&__pyx_kp_s_Trajectory_could_not_be_opened, __pyx_k_Trajectory_could_not_be_opened, sizeof(__pyx_k_Trajectory_could_not_be_opened), 0, 0, 1, 0}, + {&__pyx_kp_s_Trajectory_frame_out_of_range, __pyx_k_Trajectory_frame_out_of_range, sizeof(__pyx_k_Trajectory_frame_out_of_range), 0, 0, 1, 0}, + {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, + {&__pyx_n_s_ceil, __pyx_k_ceil, sizeof(__pyx_k_ceil), 0, 0, 1, 1}, + {&__pyx_n_s_doc, __pyx_k_doc, sizeof(__pyx_k_doc), 0, 0, 1, 1}, + {&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1}, + {&__pyx_n_s_empty, __pyx_k_empty, sizeof(__pyx_k_empty), 0, 0, 1, 1}, + {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1}, + {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1}, + {&__pyx_n_s_file, __pyx_k_file, sizeof(__pyx_k_file), 0, 0, 1, 1}, + {&__pyx_n_s_filename, __pyx_k_filename, sizeof(__pyx_k_filename), 0, 0, 1, 1}, + {&__pyx_n_s_float32, __pyx_k_float32, sizeof(__pyx_k_float32), 0, 0, 1, 1}, + {&__pyx_n_s_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 0, 1, 1}, + {&__pyx_n_s_get_position_interval, __pyx_k_get_position_interval, sizeof(__pyx_k_get_position_interval), 0, 0, 1, 1}, + {&__pyx_n_s_getitem, __pyx_k_getitem, sizeof(__pyx_k_getitem), 0, 0, 1, 1}, + {&__pyx_kp_s_home_niels_Uni_pygmx_pygmx_tngi, __pyx_k_home_niels_Uni_pygmx_pygmx_tngi, sizeof(__pyx_k_home_niels_Uni_pygmx_pygmx_tngi), 0, 0, 1, 0}, + {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, + {&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1}, + {&__pyx_n_s_item, __pyx_k_item, sizeof(__pyx_k_item), 0, 0, 1, 1}, + {&__pyx_n_s_len, __pyx_k_len, sizeof(__pyx_k_len), 0, 0, 1, 1}, + {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, + {&__pyx_n_s_math, __pyx_k_math, sizeof(__pyx_k_math), 0, 0, 1, 1}, + {&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1}, + {&__pyx_n_s_module, __pyx_k_module, sizeof(__pyx_k_module), 0, 0, 1, 1}, + {&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0}, + {&__pyx_kp_u_ndarray_is_not_Fortran_contiguou, __pyx_k_ndarray_is_not_Fortran_contiguou, sizeof(__pyx_k_ndarray_is_not_Fortran_contiguou), 0, 1, 0, 0}, + {&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1}, + {&__pyx_n_s_nstxout, __pyx_k_nstxout, sizeof(__pyx_k_nstxout), 0, 0, 1, 1}, + {&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1}, + {&__pyx_n_s_prepare, __pyx_k_prepare, sizeof(__pyx_k_prepare), 0, 0, 1, 1}, + {&__pyx_n_s_print, __pyx_k_print, sizeof(__pyx_k_print), 0, 0, 1, 1}, + {&__pyx_n_s_pygmx_tngio, __pyx_k_pygmx_tngio, sizeof(__pyx_k_pygmx_tngio), 0, 0, 1, 1}, + {&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 0, 0, 1, 1}, + {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1}, + {&__pyx_n_s_self, __pyx_k_self, sizeof(__pyx_k_self), 0, 0, 1, 1}, + {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, + {&__pyx_n_s_trajectory, __pyx_k_trajectory, sizeof(__pyx_k_trajectory), 0, 0, 1, 1}, + {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0}, + {0, 0, 0, 0, 0, 0, 0} +}; +static int __Pyx_InitCachedBuiltins(void) { + __pyx_builtin_IndexError = __Pyx_GetBuiltinName(__pyx_n_s_IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_OSError = __Pyx_GetBuiltinName(__pyx_n_s_OSError); if (!__pyx_builtin_OSError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + return 0; + __pyx_L1_error:; + return -1; +} + +static int __Pyx_InitCachedConstants(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); + + /* "pygmx/tngio.pyx":128 + * + * if (tng_util_trajectory_open(filename, b'r', &self.trajectory) != TNG_SUCCESS): + * raise OSError('Trajectory could not be opened.') # <<<<<<<<<<<<<< + * + * tng_num_frames_get(self.trajectory, &self.nframes) + */ + __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_Trajectory_could_not_be_opened); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__2); + __Pyx_GIVEREF(__pyx_tuple__2); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":218 + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + */ + __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__3); + __Pyx_GIVEREF(__pyx_tuple__3); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":222 + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< + * + * info.buf = PyArray_DATA(self) + */ + __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__4); + __Pyx_GIVEREF(__pyx_tuple__4); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":259 + * if ((descr.byteorder == c'>' and little_endian) or + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< + * if t == NPY_BYTE: f = "b" + * elif t == NPY_UBYTE: f = "B" + */ + __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__5); + __Pyx_GIVEREF(__pyx_tuple__5); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":799 + * + * if (end - f) - (new_offset - offset[0]) < 15: + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< + * + * if ((child.byteorder == c'>' and little_endian) or + */ + __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__6); + __Pyx_GIVEREF(__pyx_tuple__6); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":803 + * if ((child.byteorder == c'>' and little_endian) or + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< + * # One could encode it in the format string and have Cython + * # complain instead, BUT: < and > in format strings also imply + */ + __pyx_tuple__7 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__7); + __Pyx_GIVEREF(__pyx_tuple__7); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":823 + * t = child.type_num + * if end - f < 5: + * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< + * + * # Until ticket #99 is fixed, use integers to avoid warnings + */ + __pyx_tuple__8 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__8); + __Pyx_GIVEREF(__pyx_tuple__8); + + /* "pygmx/tngio.pyx":137 + * + * class TNGReader: + * def __init__(self, filename): # <<<<<<<<<<<<<< + * self.trajectory = TNGTrajectory(filename) + * self.nstxout = self.trajectory.get_position_interval() + */ + __pyx_tuple__9 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_filename); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__9); + __Pyx_GIVEREF(__pyx_tuple__9); + __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_niels_Uni_pygmx_pygmx_tngi, __pyx_n_s_init, 137, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tngio.pyx":141 + * self.nstxout = self.trajectory.get_position_interval() + * + * def __len__(self): # <<<<<<<<<<<<<< + * return ceil(len(self.trajectory) / self.nstxout) + * + */ + __pyx_tuple__11 = PyTuple_Pack(1, __pyx_n_s_self); if (unlikely(!__pyx_tuple__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__11); + __Pyx_GIVEREF(__pyx_tuple__11); + __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_niels_Uni_pygmx_pygmx_tngi, __pyx_n_s_len, 141, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tngio.pyx":144 + * return ceil(len(self.trajectory) / self.nstxout) + * + * def __getitem__(self, item): # <<<<<<<<<<<<<< + * try: + * return self.trajectory[item * self.nstxout] + */ + __pyx_tuple__13 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_item); if (unlikely(!__pyx_tuple__13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__13); + __Pyx_GIVEREF(__pyx_tuple__13); + __pyx_codeobj__14 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__13, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_niels_Uni_pygmx_pygmx_tngi, __pyx_n_s_getitem, 144, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_RefNannyFinishContext(); + return 0; + __pyx_L1_error:; + __Pyx_RefNannyFinishContext(); + return -1; +} + +static int __Pyx_InitGlobals(void) { + if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + return 0; + __pyx_L1_error:; + return -1; +} + +#if PY_MAJOR_VERSION < 3 +PyMODINIT_FUNC inittngio(void); /*proto*/ +PyMODINIT_FUNC inittngio(void) +#else +PyMODINIT_FUNC PyInit_tngio(void); /*proto*/ +PyMODINIT_FUNC PyInit_tngio(void) +#endif +{ + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannyDeclarations + #if CYTHON_REFNANNY + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny"); + if (!__Pyx_RefNanny) { + PyErr_Clear(); + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny"); + if (!__Pyx_RefNanny) + Py_FatalError("failed to import 'refnanny' module"); + } + #endif + __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_tngio(void)", 0); + if (__Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #ifdef __Pyx_CyFunction_USED + if (__pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_FusedFunction_USED + if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_Coroutine_USED + if (__pyx_Coroutine_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_Generator_USED + if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_StopAsyncIteration_USED + if (__pyx_StopAsyncIteration_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + /*--- Library function declarations ---*/ + /*--- Threads initialization code ---*/ + #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS + #ifdef WITH_THREAD /* Python build with threading support? */ + PyEval_InitThreads(); + #endif + #endif + /*--- Module creation code ---*/ + #if PY_MAJOR_VERSION < 3 + __pyx_m = Py_InitModule4("tngio", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); + #else + __pyx_m = PyModule_Create(&__pyx_moduledef); + #endif + if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + Py_INCREF(__pyx_d); + __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if CYTHON_COMPILING_IN_PYPY + Py_INCREF(__pyx_b); + #endif + if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + /*--- Initialize various global constants etc. ---*/ + if (__Pyx_InitGlobals() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) + if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + if (__pyx_module_is_main_pygmx__tngio) { + if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if PY_MAJOR_VERSION >= 3 + { + PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!PyDict_GetItemString(modules, "pygmx.tngio")) { + if (unlikely(PyDict_SetItemString(modules, "pygmx.tngio", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + } + #endif + /*--- Builtin init code ---*/ + if (__Pyx_InitCachedBuiltins() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Constants init code ---*/ + if (__Pyx_InitCachedConstants() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Global init code ---*/ + /*--- Variable export code ---*/ + /*--- Function export code ---*/ + /*--- Type init code ---*/ + if (PyType_Ready(&__pyx_type_5pygmx_5tngio_TNGTrajectory) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_5pygmx_5tngio_TNGTrajectory.tp_print = 0; + if (PyObject_SetAttrString(__pyx_m, "TNGTrajectory", (PyObject *)&__pyx_type_5pygmx_5tngio_TNGTrajectory) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pygmx_5tngio_TNGTrajectory = &__pyx_type_5pygmx_5tngio_TNGTrajectory; + /*--- Type import code ---*/ + __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", + #if CYTHON_COMPILING_IN_PYPY + sizeof(PyTypeObject), + #else + sizeof(PyHeapTypeObject), + #endif + 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Variable import code ---*/ + /*--- Function import code ---*/ + /*--- Execution code ---*/ + #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) + if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + + /* "pygmx/tngio.pyx":2 + * + * import numpy as np # <<<<<<<<<<<<<< + * + * cimport numpy as np + */ + __pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pygmx/tngio.pyx":134 + * + * + * from math import ceil # <<<<<<<<<<<<<< + * + * class TNGReader: + */ + __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_INCREF(__pyx_n_s_ceil); + __Pyx_GIVEREF(__pyx_n_s_ceil); + PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_ceil); + __pyx_t_2 = __Pyx_Import(__pyx_n_s_math, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_2, __pyx_n_s_ceil); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_ceil, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pygmx/tngio.pyx":136 + * from math import ceil + * + * class TNGReader: # <<<<<<<<<<<<<< + * def __init__(self, filename): + * self.trajectory = TNGTrajectory(filename) + */ + __pyx_t_2 = __Pyx_Py3MetaclassPrepare((PyObject *) NULL, __pyx_empty_tuple, __pyx_n_s_TNGReader, __pyx_n_s_TNGReader, (PyObject *) NULL, __pyx_n_s_pygmx_tngio, (PyObject *) NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + + /* "pygmx/tngio.pyx":137 + * + * class TNGReader: + * def __init__(self, filename): # <<<<<<<<<<<<<< + * self.trajectory = TNGTrajectory(filename) + * self.nstxout = self.trajectory.get_position_interval() + */ + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pygmx_5tngio_9TNGReader_1__init__, 0, __pyx_n_s_TNGReader___init, NULL, __pyx_n_s_pygmx_tngio, __pyx_d, ((PyObject *)__pyx_codeobj__10)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyObject_SetItem(__pyx_t_2, __pyx_n_s_init, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pygmx/tngio.pyx":141 + * self.nstxout = self.trajectory.get_position_interval() + * + * def __len__(self): # <<<<<<<<<<<<<< + * return ceil(len(self.trajectory) / self.nstxout) + * + */ + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pygmx_5tngio_9TNGReader_3__len__, 0, __pyx_n_s_TNGReader___len, NULL, __pyx_n_s_pygmx_tngio, __pyx_d, ((PyObject *)__pyx_codeobj__12)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyObject_SetItem(__pyx_t_2, __pyx_n_s_len, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pygmx/tngio.pyx":144 + * return ceil(len(self.trajectory) / self.nstxout) + * + * def __getitem__(self, item): # <<<<<<<<<<<<<< + * try: + * return self.trajectory[item * self.nstxout] + */ + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pygmx_5tngio_9TNGReader_5__getitem__, 0, __pyx_n_s_TNGReader___getitem, NULL, __pyx_n_s_pygmx_tngio, __pyx_d, ((PyObject *)__pyx_codeobj__14)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyObject_SetItem(__pyx_t_2, __pyx_n_s_getitem, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pygmx/tngio.pyx":136 + * from math import ceil + * + * class TNGReader: # <<<<<<<<<<<<<< + * def __init__(self, filename): + * self.trajectory = TNGTrajectory(filename) + */ + __pyx_t_1 = __Pyx_Py3ClassCreate(((PyObject*)&__Pyx_DefaultClassType), __pyx_n_s_TNGReader, __pyx_empty_tuple, __pyx_t_2, NULL, 0, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_TNGReader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pygmx/tngio.pyx":2 + * + * import numpy as np # <<<<<<<<<<<<<< + * + * cimport numpy as np + */ + __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr + * + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None + */ + + /*--- Wrapped vars code ---*/ + + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + if (__pyx_m) { + if (__pyx_d) { + __Pyx_AddTraceback("init pygmx.tngio", __pyx_clineno, __pyx_lineno, __pyx_filename); + } + Py_DECREF(__pyx_m); __pyx_m = 0; + } else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_ImportError, "init pygmx.tngio"); + } + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + #if PY_MAJOR_VERSION < 3 + return; + #else + return __pyx_m; + #endif +} + +/* --- Runtime support code --- */ +#if CYTHON_REFNANNY +static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { + PyObject *m = NULL, *p = NULL; + void *r = NULL; + m = PyImport_ImportModule((char *)modname); + if (!m) goto end; + p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); + if (!p) goto end; + r = PyLong_AsVoidPtr(p); +end: + Py_XDECREF(p); + Py_XDECREF(m); + return (__Pyx_RefNannyAPIStruct *)r; +} +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); + if (unlikely(!result)) { + PyErr_Format(PyExc_NameError, +#if PY_MAJOR_VERSION >= 3 + "name '%U' is not defined", name); +#else + "name '%.200s' is not defined", PyString_AS_STRING(name)); +#endif + } + return result; +} + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + PyObject *result; +#if CYTHON_COMPILING_IN_CPYTHON + result = PyDict_GetItem(__pyx_d, name); + if (likely(result)) { + Py_INCREF(result); + } else { +#else + result = PyObject_GetItem(__pyx_d, name); + if (!result) { + PyErr_Clear(); +#endif + result = __Pyx_GetBuiltinName(name); + } + return result; +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { + unsigned int n = 1; + return *(unsigned char*)(&n) != 0; +} +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static CYTHON_INLINE PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} +static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { + buf->buf = NULL; + buf->obj = NULL; + buf->strides = __Pyx_zeros; + buf->shape = __Pyx_zeros; + buf->suboffsets = __Pyx_minusones; +} +static CYTHON_INLINE int __Pyx_GetBufferAndValidate( + Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, + int nd, int cast, __Pyx_BufFmt_StackElem* stack) +{ + if (obj == Py_None || obj == NULL) { + __Pyx_ZeroBuffer(buf); + return 0; + } + buf->buf = NULL; + if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; + if (buf->ndim != nd) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + nd, buf->ndim); + goto fail; + } + if (!cast) { + __Pyx_BufFmt_Context ctx; + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned)buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", + buf->itemsize, (buf->itemsize > 1) ? "s" : "", + dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); + goto fail; + } + if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; + return 0; +fail:; + __Pyx_ZeroBuffer(buf); + return -1; +} +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { + if (info->buf == NULL) return; + if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; + __Pyx_ReleaseBuffer(info); +} + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { + return __Pyx_PyObject_CallMethO(func, NULL); + } + } + return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); +} +#endif + +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + int is_subclass = PyObject_IsSubclass(instance_class, type); + if (!is_subclass) { + instance_class = NULL; + } else if (unlikely(is_subclass == -1)) { + goto bad; + } else { + type = instance_class; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } +#if PY_VERSION_HEX >= 0x03030000 + if (cause) { +#else + if (cause && cause != Py_None) { +#endif + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { +#if CYTHON_COMPILING_IN_PYPY + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#else + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } +#endif + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +#endif + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +#else + PyErr_GetExcInfo(type, value, tb); +#endif +} +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(type, value, tb); +#endif +} + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *local_type, *local_value, *local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { + PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); + if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Format(PyExc_ImportError, + #if PY_MAJOR_VERSION < 3 + "cannot import name %.230s", PyString_AS_STRING(name)); + #else + "cannot import name %S", name); + #endif + } + return value; +} + +static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { + PyObject* fake_module; + PyTypeObject* cached_type = NULL; + fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI); + if (!fake_module) return NULL; + Py_INCREF(fake_module); + cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name); + if (cached_type) { + if (!PyType_Check((PyObject*)cached_type)) { + PyErr_Format(PyExc_TypeError, + "Shared Cython type %.200s is not a type object", + type->tp_name); + goto bad; + } + if (cached_type->tp_basicsize != type->tp_basicsize) { + PyErr_Format(PyExc_TypeError, + "Shared Cython type %.200s has the wrong size, try recompiling", + type->tp_name); + goto bad; + } + } else { + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; + PyErr_Clear(); + if (PyType_Ready(type) < 0) goto bad; + if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0) + goto bad; + Py_INCREF(type); + cached_type = type; + } +done: + Py_DECREF(fake_module); + return cached_type; +bad: + Py_XDECREF(cached_type); + cached_type = NULL; + goto done; +} + +static PyObject * +__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) +{ + if (unlikely(op->func_doc == NULL)) { + if (op->func.m_ml->ml_doc) { +#if PY_MAJOR_VERSION >= 3 + op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); +#else + op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); +#endif + if (unlikely(op->func_doc == NULL)) + return NULL; + } else { + Py_INCREF(Py_None); + return Py_None; + } + } + Py_INCREF(op->func_doc); + return op->func_doc; +} +static int +__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp = op->func_doc; + if (value == NULL) { + value = Py_None; + } + Py_INCREF(value); + op->func_doc = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op) +{ + if (unlikely(op->func_name == NULL)) { +#if PY_MAJOR_VERSION >= 3 + op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); +#else + op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); +#endif + if (unlikely(op->func_name == NULL)) + return NULL; + } + Py_INCREF(op->func_name); + return op->func_name; +} +static int +__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp; +#if PY_MAJOR_VERSION >= 3 + if (unlikely(value == NULL || !PyUnicode_Check(value))) { +#else + if (unlikely(value == NULL || !PyString_Check(value))) { +#endif + PyErr_SetString(PyExc_TypeError, + "__name__ must be set to a string object"); + return -1; + } + tmp = op->func_name; + Py_INCREF(value); + op->func_name = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op) +{ + Py_INCREF(op->func_qualname); + return op->func_qualname; +} +static int +__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp; +#if PY_MAJOR_VERSION >= 3 + if (unlikely(value == NULL || !PyUnicode_Check(value))) { +#else + if (unlikely(value == NULL || !PyString_Check(value))) { +#endif + PyErr_SetString(PyExc_TypeError, + "__qualname__ must be set to a string object"); + return -1; + } + tmp = op->func_qualname; + Py_INCREF(value); + op->func_qualname = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) +{ + PyObject *self; + self = m->func_closure; + if (self == NULL) + self = Py_None; + Py_INCREF(self); + return self; +} +static PyObject * +__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op) +{ + if (unlikely(op->func_dict == NULL)) { + op->func_dict = PyDict_New(); + if (unlikely(op->func_dict == NULL)) + return NULL; + } + Py_INCREF(op->func_dict); + return op->func_dict; +} +static int +__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp; + if (unlikely(value == NULL)) { + PyErr_SetString(PyExc_TypeError, + "function's dictionary may not be deleted"); + return -1; + } + if (unlikely(!PyDict_Check(value))) { + PyErr_SetString(PyExc_TypeError, + "setting function's dictionary to a non-dict"); + return -1; + } + tmp = op->func_dict; + Py_INCREF(value); + op->func_dict = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op) +{ + Py_INCREF(op->func_globals); + return op->func_globals; +} +static PyObject * +__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op) +{ + Py_INCREF(Py_None); + return Py_None; +} +static PyObject * +__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) +{ + PyObject* result = (op->func_code) ? op->func_code : Py_None; + Py_INCREF(result); + return result; +} +static int +__Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) { + int result = 0; + PyObject *res = op->defaults_getter((PyObject *) op); + if (unlikely(!res)) + return -1; + #if CYTHON_COMPILING_IN_CPYTHON + op->defaults_tuple = PyTuple_GET_ITEM(res, 0); + Py_INCREF(op->defaults_tuple); + op->defaults_kwdict = PyTuple_GET_ITEM(res, 1); + Py_INCREF(op->defaults_kwdict); + #else + op->defaults_tuple = PySequence_ITEM(res, 0); + if (unlikely(!op->defaults_tuple)) result = -1; + else { + op->defaults_kwdict = PySequence_ITEM(res, 1); + if (unlikely(!op->defaults_kwdict)) result = -1; + } + #endif + Py_DECREF(res); + return result; +} +static int +__Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value) { + PyObject* tmp; + if (!value) { + value = Py_None; + } else if (value != Py_None && !PyTuple_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "__defaults__ must be set to a tuple object"); + return -1; + } + Py_INCREF(value); + tmp = op->defaults_tuple; + op->defaults_tuple = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) { + PyObject* result = op->defaults_tuple; + if (unlikely(!result)) { + if (op->defaults_getter) { + if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL; + result = op->defaults_tuple; + } else { + result = Py_None; + } + } + Py_INCREF(result); + return result; +} +static int +__Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value) { + PyObject* tmp; + if (!value) { + value = Py_None; + } else if (value != Py_None && !PyDict_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "__kwdefaults__ must be set to a dict object"); + return -1; + } + Py_INCREF(value); + tmp = op->defaults_kwdict; + op->defaults_kwdict = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op) { + PyObject* result = op->defaults_kwdict; + if (unlikely(!result)) { + if (op->defaults_getter) { + if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL; + result = op->defaults_kwdict; + } else { + result = Py_None; + } + } + Py_INCREF(result); + return result; +} +static int +__Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value) { + PyObject* tmp; + if (!value || value == Py_None) { + value = NULL; + } else if (!PyDict_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "__annotations__ must be set to a dict object"); + return -1; + } + Py_XINCREF(value); + tmp = op->func_annotations; + op->func_annotations = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op) { + PyObject* result = op->func_annotations; + if (unlikely(!result)) { + result = PyDict_New(); + if (unlikely(!result)) return NULL; + op->func_annotations = result; + } + Py_INCREF(result); + return result; +} +static PyGetSetDef __pyx_CyFunction_getsets[] = { + {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, + {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, + {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, + {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, + {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0}, + {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0}, + {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, + {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, + {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, + {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, + {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, + {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, + {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, + {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, + {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0}, + {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0}, + {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0}, + {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0}, + {0, 0, 0, 0, 0} +}; +static PyMemberDef __pyx_CyFunction_members[] = { + {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, + {0, 0, 0, 0, 0} +}; +static PyObject * +__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) +{ +#if PY_MAJOR_VERSION >= 3 + return PyUnicode_FromString(m->func.m_ml->ml_name); +#else + return PyString_FromString(m->func.m_ml->ml_name); +#endif +} +static PyMethodDef __pyx_CyFunction_methods[] = { + {"__reduce__", (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, + {0, 0, 0, 0} +}; +#if PY_VERSION_HEX < 0x030500A0 +#define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func_weakreflist) +#else +#define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func.m_weakreflist) +#endif +static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname, + PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { + __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); + if (op == NULL) + return NULL; + op->flags = flags; + __Pyx_CyFunction_weakreflist(op) = NULL; + op->func.m_ml = ml; + op->func.m_self = (PyObject *) op; + Py_XINCREF(closure); + op->func_closure = closure; + Py_XINCREF(module); + op->func.m_module = module; + op->func_dict = NULL; + op->func_name = NULL; + Py_INCREF(qualname); + op->func_qualname = qualname; + op->func_doc = NULL; + op->func_classobj = NULL; + op->func_globals = globals; + Py_INCREF(op->func_globals); + Py_XINCREF(code); + op->func_code = code; + op->defaults_pyobjects = 0; + op->defaults = NULL; + op->defaults_tuple = NULL; + op->defaults_kwdict = NULL; + op->defaults_getter = NULL; + op->func_annotations = NULL; + PyObject_GC_Track(op); + return (PyObject *) op; +} +static int +__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) +{ + Py_CLEAR(m->func_closure); + Py_CLEAR(m->func.m_module); + Py_CLEAR(m->func_dict); + Py_CLEAR(m->func_name); + Py_CLEAR(m->func_qualname); + Py_CLEAR(m->func_doc); + Py_CLEAR(m->func_globals); + Py_CLEAR(m->func_code); + Py_CLEAR(m->func_classobj); + Py_CLEAR(m->defaults_tuple); + Py_CLEAR(m->defaults_kwdict); + Py_CLEAR(m->func_annotations); + if (m->defaults) { + PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); + int i; + for (i = 0; i < m->defaults_pyobjects; i++) + Py_XDECREF(pydefaults[i]); + PyMem_Free(m->defaults); + m->defaults = NULL; + } + return 0; +} +static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) +{ + PyObject_GC_UnTrack(m); + if (__Pyx_CyFunction_weakreflist(m) != NULL) + PyObject_ClearWeakRefs((PyObject *) m); + __Pyx_CyFunction_clear(m); + PyObject_GC_Del(m); +} +static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) +{ + Py_VISIT(m->func_closure); + Py_VISIT(m->func.m_module); + Py_VISIT(m->func_dict); + Py_VISIT(m->func_name); + Py_VISIT(m->func_qualname); + Py_VISIT(m->func_doc); + Py_VISIT(m->func_globals); + Py_VISIT(m->func_code); + Py_VISIT(m->func_classobj); + Py_VISIT(m->defaults_tuple); + Py_VISIT(m->defaults_kwdict); + if (m->defaults) { + PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); + int i; + for (i = 0; i < m->defaults_pyobjects; i++) + Py_VISIT(pydefaults[i]); + } + return 0; +} +static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type) +{ + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) { + Py_INCREF(func); + return func; + } + if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) { + if (type == NULL) + type = (PyObject *)(Py_TYPE(obj)); + return __Pyx_PyMethod_New(func, type, (PyObject *)(Py_TYPE(type))); + } + if (obj == Py_None) + obj = NULL; + return __Pyx_PyMethod_New(func, obj, type); +} +static PyObject* +__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) +{ +#if PY_MAJOR_VERSION >= 3 + return PyUnicode_FromFormat("", + op->func_qualname, (void *)op); +#else + return PyString_FromFormat("", + PyString_AsString(op->func_qualname), (void *)op); +#endif +} +#if CYTHON_COMPILING_IN_PYPY +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyCFunctionObject* f = (PyCFunctionObject*)func; + PyCFunction meth = f->m_ml->ml_meth; + PyObject *self = f->m_self; + Py_ssize_t size; + switch (f->m_ml->ml_flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) { + case METH_VARARGS: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) + return (*meth)(self, arg); + break; + case METH_VARARGS | METH_KEYWORDS: + return (*(PyCFunctionWithKeywords)meth)(self, arg, kw); + case METH_NOARGS: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) { + size = PyTuple_GET_SIZE(arg); + if (likely(size == 0)) + return (*meth)(self, NULL); + PyErr_Format(PyExc_TypeError, + "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + case METH_O: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) { + size = PyTuple_GET_SIZE(arg); + if (likely(size == 1)) { + PyObject *result, *arg0 = PySequence_ITEM(arg, 0); + if (unlikely(!arg0)) return NULL; + result = (*meth)(self, arg0); + Py_DECREF(arg0); + return result; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + default: + PyErr_SetString(PyExc_SystemError, "Bad call flags in " + "__Pyx_CyFunction_Call. METH_OLDARGS is no " + "longer supported!"); + return NULL; + } + PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", + f->m_ml->ml_name); + return NULL; +} +#else +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + return PyCFunction_Call(func, arg, kw); +} +#endif +static PyTypeObject __pyx_CyFunctionType_type = { + PyVarObject_HEAD_INIT(0, 0) + "cython_function_or_method", + sizeof(__pyx_CyFunctionObject), + 0, + (destructor) __Pyx_CyFunction_dealloc, + 0, + 0, + 0, +#if PY_MAJOR_VERSION < 3 + 0, +#else + 0, +#endif + (reprfunc) __Pyx_CyFunction_repr, + 0, + 0, + 0, + 0, + __Pyx_CyFunction_Call, + 0, + 0, + 0, + 0, + Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, + 0, + (traverseproc) __Pyx_CyFunction_traverse, + (inquiry) __Pyx_CyFunction_clear, + 0, +#if PY_VERSION_HEX < 0x030500A0 + offsetof(__pyx_CyFunctionObject, func_weakreflist), +#else + offsetof(PyCFunctionObject, m_weakreflist), +#endif + 0, + 0, + __pyx_CyFunction_methods, + __pyx_CyFunction_members, + __pyx_CyFunction_getsets, + 0, + 0, + __Pyx_CyFunction_descr_get, + 0, + offsetof(__pyx_CyFunctionObject, func_dict), + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, +#if PY_VERSION_HEX >= 0x030400a1 + 0, +#endif +}; +static int __pyx_CyFunction_init(void) { +#if !CYTHON_COMPILING_IN_PYPY + __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; +#endif + __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type); + if (__pyx_CyFunctionType == NULL) { + return -1; + } + return 0; +} +static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults = PyMem_Malloc(size); + if (!m->defaults) + return PyErr_NoMemory(); + memset(m->defaults, 0, size); + m->defaults_pyobjects = pyobjects; + return m->defaults; +} +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults_tuple = tuple; + Py_INCREF(tuple); +} +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults_kwdict = dict; + Py_INCREF(dict); +} +static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->func_annotations = dict; + Py_INCREF(dict); +} + +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) { + Py_ssize_t i, nbases = PyTuple_GET_SIZE(bases); + for (i=0; i < nbases; i++) { + PyTypeObject *tmptype; + PyObject *tmp = PyTuple_GET_ITEM(bases, i); + tmptype = Py_TYPE(tmp); +#if PY_MAJOR_VERSION < 3 + if (tmptype == &PyClass_Type) + continue; +#endif + if (!metaclass) { + metaclass = tmptype; + continue; + } + if (PyType_IsSubtype(metaclass, tmptype)) + continue; + if (PyType_IsSubtype(tmptype, metaclass)) { + metaclass = tmptype; + continue; + } + PyErr_SetString(PyExc_TypeError, + "metaclass conflict: " + "the metaclass of a derived class " + "must be a (non-strict) subclass " + "of the metaclasses of all its bases"); + return NULL; + } + if (!metaclass) { +#if PY_MAJOR_VERSION < 3 + metaclass = &PyClass_Type; +#else + metaclass = &PyType_Type; +#endif + } + Py_INCREF((PyObject*) metaclass); + return (PyObject*) metaclass; +} + +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, + PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) { + PyObject *ns; + if (metaclass) { + PyObject *prep = __Pyx_PyObject_GetAttrStr(metaclass, __pyx_n_s_prepare); + if (prep) { + PyObject *pargs = PyTuple_Pack(2, name, bases); + if (unlikely(!pargs)) { + Py_DECREF(prep); + return NULL; + } + ns = PyObject_Call(prep, pargs, mkw); + Py_DECREF(prep); + Py_DECREF(pargs); + } else { + if (unlikely(!PyErr_ExceptionMatches(PyExc_AttributeError))) + return NULL; + PyErr_Clear(); + ns = PyDict_New(); + } + } else { + ns = PyDict_New(); + } + if (unlikely(!ns)) + return NULL; + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad; + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad; + if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad; + return ns; +bad: + Py_DECREF(ns); + return NULL; +} +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, + PyObject *dict, PyObject *mkw, + int calculate_metaclass, int allow_py2_metaclass) { + PyObject *result, *margs; + PyObject *owned_metaclass = NULL; + if (allow_py2_metaclass) { + owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass); + if (owned_metaclass) { + metaclass = owned_metaclass; + } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) { + PyErr_Clear(); + } else { + return NULL; + } + } + if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) { + metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases); + Py_XDECREF(owned_metaclass); + if (unlikely(!metaclass)) + return NULL; + owned_metaclass = metaclass; + } + margs = PyTuple_Pack(3, name, bases, dict); + if (unlikely(!margs)) { + result = NULL; + } else { + result = PyObject_Call(metaclass, margs, mkw); + Py_DECREF(margs); + } + Py_XDECREF(owned_metaclass); + return result; +} + +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = start + (end - start) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_tng_function_status(tng_function_status value) { + const tng_function_status neg_one = (tng_function_status) -1, const_zero = (tng_function_status) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(tng_function_status) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(tng_function_status) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(tng_function_status) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(tng_function_status) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(tng_function_status) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(tng_function_status), + little, !is_unsigned); + } +} + +#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 +static PyObject *__Pyx_GetStdout(void) { + PyObject *f = PySys_GetObject((char *)"stdout"); + if (!f) { + PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout"); + } + return f; +} +static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { + int i; + if (!f) { + if (!(f = __Pyx_GetStdout())) + return -1; + } + Py_INCREF(f); + for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { + PyObject* v; + if (PyFile_SoftSpace(f, 1)) { + if (PyFile_WriteString(" ", f) < 0) + goto error; + } + v = PyTuple_GET_ITEM(arg_tuple, i); + if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) + goto error; + if (PyString_Check(v)) { + char *s = PyString_AsString(v); + Py_ssize_t len = PyString_Size(v); + if (len > 0) { + switch (s[len-1]) { + case ' ': break; + case '\f': case '\r': case '\n': case '\t': case '\v': + PyFile_SoftSpace(f, 0); + break; + default: break; + } + } + } + } + if (newline) { + if (PyFile_WriteString("\n", f) < 0) + goto error; + PyFile_SoftSpace(f, 0); + } + Py_DECREF(f); + return 0; +error: + Py_DECREF(f); + return -1; +} +#else +static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { + PyObject* kwargs = 0; + PyObject* result = 0; + PyObject* end_string; + if (unlikely(!__pyx_print)) { + __pyx_print = PyObject_GetAttr(__pyx_b, __pyx_n_s_print); + if (!__pyx_print) + return -1; + } + if (stream) { + kwargs = PyDict_New(); + if (unlikely(!kwargs)) + return -1; + if (unlikely(PyDict_SetItem(kwargs, __pyx_n_s_file, stream) < 0)) + goto bad; + if (!newline) { + end_string = PyUnicode_FromStringAndSize(" ", 1); + if (unlikely(!end_string)) + goto bad; + if (PyDict_SetItem(kwargs, __pyx_n_s_end, end_string) < 0) { + Py_DECREF(end_string); + goto bad; + } + Py_DECREF(end_string); + } + } else if (!newline) { + if (unlikely(!__pyx_print_kwargs)) { + __pyx_print_kwargs = PyDict_New(); + if (unlikely(!__pyx_print_kwargs)) + return -1; + end_string = PyUnicode_FromStringAndSize(" ", 1); + if (unlikely(!end_string)) + return -1; + if (PyDict_SetItem(__pyx_print_kwargs, __pyx_n_s_end, end_string) < 0) { + Py_DECREF(end_string); + return -1; + } + Py_DECREF(end_string); + } + kwargs = __pyx_print_kwargs; + } + result = PyObject_Call(__pyx_print, arg_tuple, kwargs); + if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs)) + Py_DECREF(kwargs); + if (!result) + return -1; + Py_DECREF(result); + return 0; +bad: + if (kwargs != __pyx_print_kwargs) + Py_XDECREF(kwargs); + return -1; +} +#endif + +#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 +static int __Pyx_PrintOne(PyObject* f, PyObject *o) { + if (!f) { + if (!(f = __Pyx_GetStdout())) + return -1; + } + Py_INCREF(f); + if (PyFile_SoftSpace(f, 0)) { + if (PyFile_WriteString(" ", f) < 0) + goto error; + } + if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0) + goto error; + if (PyFile_WriteString("\n", f) < 0) + goto error; + Py_DECREF(f); + return 0; +error: + Py_DECREF(f); + return -1; + /* the line below is just to avoid C compiler + * warnings about unused functions */ + return __Pyx_Print(f, NULL, 0); +} +#else +static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { + int res; + PyObject* arg_tuple = PyTuple_Pack(1, o); + if (unlikely(!arg_tuple)) + return -1; + res = __Pyx_Print(stream, arg_tuple, 1); + Py_DECREF(arg_tuple); + return res; +} +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ + } + +#if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" +#endif + +static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) { + const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int64_t) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int64_t, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int64_t) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int64_t) 0; + case 1: __PYX_VERIFY_RETURN_INT(int64_t, digit, digits[0]) + case 2: + if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int64_t) >= 2 * PyLong_SHIFT) { + return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int64_t) >= 3 * PyLong_SHIFT) { + return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int64_t) >= 4 * PyLong_SHIFT) { + return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int64_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(int64_t) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int64_t) 0; + case -1: __PYX_VERIFY_RETURN_INT(int64_t, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(int64_t, digit, +digits[0]) + case -2: + if (8 * sizeof(int64_t) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { + return (int64_t) (((int64_t)-1)*(((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { + return (int64_t) ((((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { + return (int64_t) (((int64_t)-1)*(((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { + return (int64_t) ((((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { + return (int64_t) (((int64_t)-1)*(((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { + return (int64_t) ((((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); + } + } + break; + } +#endif + if (sizeof(int64_t) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int64_t, long, PyLong_AsLong(x)) + } else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int64_t, PY_LONG_LONG, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int64_t val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int64_t) -1; + } + } else { + int64_t val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int64_t) -1; + val = __Pyx_PyInt_As_int64_t(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int64_t"); + return (int64_t) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int64_t"); + return (int64_t) -1; +} + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + } +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + } +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +#ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility", + module_name, class_name); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling", + module_name, class_name); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { +#if PY_VERSION_HEX < 0x03030000 + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +#else + if (__Pyx_PyUnicode_READY(o) == -1) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (PyUnicode_IS_ASCII(o)) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +#endif + } else +#endif +#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { + PyNumberMethods *m; + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (PyInt_Check(x) || PyLong_Check(x)) +#else + if (PyLong_Check(x)) +#endif + return __Pyx_NewRef(x); + m = Py_TYPE(x)->tp_as_number; +#if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = PyNumber_Long(x); + } +#else + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Long(x); + } +#endif + if (res) { +#if PY_MAJOR_VERSION < 3 + if (!PyInt_Check(res) && !PyLong_Check(res)) { +#else + if (!PyLong_Check(res)) { +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + name, name, Py_TYPE(res)->tp_name); + Py_DECREF(res); + return NULL; + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(x); + } +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + } + } + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/pygmx/tngio.pyx b/pygmx/tngio.pyx new file mode 100644 index 0000000..91633df --- /dev/null +++ b/pygmx/tngio.pyx @@ -0,0 +1,148 @@ + +import numpy as np + +cimport numpy as np +#from libc.stdlib cimport free + +cdef extern from "tng/tng_io_fwd.h": + cdef struct tng_trajectory: + pass + + ctypedef tng_trajectory *tng_trajectory_t + + +cdef extern from "tng/tng_io.h": + ctypedef int int64_t + cdef int64_t TNG_TRAJ_POSITIONS "TNG_TRAJ_POSITIONS" + cdef int64_t TNG_TRAJ_VELOCITIES "TNG_TRAJ_VELOCITIES" + cdef int64_t TNG_TRAJ_FORCES "TNG_TRAJ_FORCES" + + ctypedef enum tng_function_status: + TNG_SUCCESS, TNG_FAILURE, TNG_CRITICAL + + tng_function_status tng_util_trajectory_open(const char *filename, const char mode, tng_trajectory_t *tng_data_p) + + tng_function_status tng_util_trajectory_close(tng_trajectory_t *tng_data_p) + + tng_function_status tng_util_time_of_frame_get(const tng_trajectory_t tng_data, const int64_t frame_nr, double *time) + + tng_function_status tng_util_pos_read_range(const tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float **positions, + int64_t *stride_length) + + tng_function_status tng_util_vel_read_range(const tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float **velocities, + int64_t *stride_length) + + tng_function_status tng_util_force_read_range(const tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float **forces, + int64_t *stride_length) + + tng_function_status tng_util_box_shape_read_range(const tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float **box_shape, + int64_t *stride_length) + + tng_function_status tng_num_frames_get(const tng_trajectory_t tng_data, int64_t *n) + + tng_function_status tng_num_particles_get(const tng_trajectory_t tng_data, int64_t *n); + + tng_function_status tng_medium_stride_length_get(const tng_trajectory_t tng_data, int64_t *len); + + tng_function_status tng_long_stride_length_get(const tng_trajectory_t tng_data, int64_t *len); + + tng_function_status tng_util_trajectory_next_frame_present_data_blocks_find( + const tng_trajectory_t tng_data, + int64_t current_frame, + const int64_t n_requested_data_block_ids, + const int64_t *requested_data_block_ids, + int64_t *next_frame, + int64_t *n_data_blocks_in_next_frame, + int64_t **data_block_ids_in_next_frame) + + tng_function_status tng_util_particle_data_next_frame_read( + const tng_trajectory_t tng_data, + const int64_t block_id, + void **values, + char *data_type, + int64_t *retrieved_frame_number, + double *retrieved_time) + + +cdef check_status(status, message=''): + if status != TNG_SUCCESS: + print(message) + +#cdef ptr_to_array(float *ptr, np.npy_intp *shape, int np): +# arr = np.PyArray_SimpleNewFromData(np, shape, np.NPY_FLOAT, ptr) +# return arr + +cdef class TNGTrajectory: + cdef: + tng_trajectory_t trajectory + int nframes, natoms, stride + + def get_position_interval(self): + cdef: + double time + char data_type + int frame1, frame2 + + cdef np.ndarray[float, ndim=2] positions = np.empty((self.natoms, 3), dtype=np.float32) + cdef void *data = positions.data + + tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame1, &time) + tng_util_particle_data_next_frame_read(self.trajectory, TNG_TRAJ_POSITIONS, &data, &data_type, &frame2, &time) + del positions + return frame2 - frame1 + + def __len__(self): + return self.nframes + + def __getitem__(self, frame): + cdef np.ndarray[float, ndim=2] positions = np.empty((self.natoms, 3), dtype=np.float32) + cdef float *pos = positions.data + + #check_status( + if (TNG_SUCCESS != + tng_util_pos_read_range(self.trajectory, frame, frame, &pos, &self.stride)#, + #'Reading of frame not successful.' + ): + raise IndexError() + + return positions + + def __init__(self, filename): + assert filename, 'Filename must not be null.' + if isinstance(filename, str): + filename = filename.encode() + + if (tng_util_trajectory_open(filename, b'r', &self.trajectory) != TNG_SUCCESS): + raise OSError('Trajectory could not be opened.') + + tng_num_frames_get(self.trajectory, &self.nframes) + tng_num_particles_get(self.trajectory, &self.natoms) + + +from math import ceil + +class TNGReader: + def __init__(self, filename): + self.trajectory = TNGTrajectory(filename) + self.nstxout = self.trajectory.get_position_interval() + + def __len__(self): + return ceil(len(self.trajectory) / self.nstxout) + + def __getitem__(self, item): + try: + return self.trajectory[item * self.nstxout] + except IndexError: + raise IndexError('Trajectory frame {} out of range.'.format(item)) diff --git a/pygmx/topology.pxd b/pygmx/topology.pxd new file mode 100644 index 0000000..4d30edf --- /dev/null +++ b/pygmx/topology.pxd @@ -0,0 +1,107 @@ + +from utility cimport * +from math cimport * +from mdtypes cimport * + +cdef extern from "gromacs/topology/atoms.h": + ctypedef struct t_atom: + real m, q; # Mass and charge */ + real mB, qB; # Mass and charge for Free Energy calc */ + unsigned short type; # Atom type */ + unsigned short typeB; # Atom type for Free Energy calc */ + int ptype; # Particle type */ + int resind; # Index into resinfo (in t_atoms) */ + int atomnumber; # Atomic Number or 0 */ + char elem[4]; # Element name */ + + ctypedef struct t_resinfo: + char **name; # Pointer to the residue name */ + int nr; # Residue number */ + unsigned char ic; # Code for insertion of residues */ + int chainnum; # Iincremented at TER or new chain id */ + char chainid; # Chain identifier written/read to pdb */ + char **rtp; # rtp building block name (optional) */ + + ctypedef struct t_pdbinfo: + pass + + ctypedef struct t_atoms: + int nr # Nr of atoms */ + t_atom *atom # Array of atoms (dim: nr) */ + # The following entries will not */ + # always be used (nres==0) */ + char ***atomname # Array of pointers to atom name */ + # use: (*(atomname[i])) */ + char ***atomtype # Array of pointers to atom types */ + # use: (*(atomtype[i])) */ + char ***atomtypeB # Array of pointers to B atom types */ + # use: (*(atomtypeB[i])) */ + int nres # The number of resinfo entries */ + t_resinfo *resinfo # Array of residue names and numbers */ + t_pdbinfo *pdbinfo # PDB Information, such as aniso. Bfac */ + + ctypedef struct t_atomtypes: + pass + +#ctypedef t_atoms *t_atoms_ptr + +cdef extern from "gromacs/topology/symtab.h": + ctypedef struct t_symtab: + pass + +cdef extern from "gromacs/topology/block.h": + ctypedef struct t_block: + pass + ctypedef struct t_blocka: + pass + +cdef extern from "gromacs/topology/idef.h": + ctypedef struct t_ilist: + pass + + ctypedef struct gmx_ffparams_t: + pass + +cdef extern from "gromacs/topology/topology.h": + ctypedef struct gmx_moltype_t: + char **name; # Name of the molecule type */ + t_atoms atoms; # The atoms in this molecule */ + t_ilist ilist[0]; # Interaction list with local indices */ + t_block cgs; # The charge groups */ + t_blocka excls; # The exclusions */ + + ctypedef struct gmx_molblock_t: + int type; # The molcule type index in mtop.moltype */ + int nmol; # The number of molecules in this block */ + int natoms_mol; # The number of atoms in one molecule */ + int nposres_xA; # The number of posres coords for top A */ + rvec *posres_xA; # The posres coords for top A */ + int nposres_xB; # The number of posres coords for top B */ + rvec *posres_xB; # The posres coords for top B */ + + ctypedef struct gmx_groups_t: + pass + + ctypedef struct gmx_mtop_t: + char **name # Name of the topology */ + gmx_ffparams_t ffparams + int nmoltype + gmx_moltype_t *moltype + int nmolblock + gmx_molblock_t *molblock + bint bIntermolecularInteractions # Are there intermolecular + # interactions? */ + t_ilist *intermolecular_ilist # List of intermolecular interactions + # using system wide atom indices, + # either NULL or size F_NRE */ + int natoms + int maxres_renum # Parameter for residue numbering */ + int maxresnr # The maximum residue number in moltype */ + t_atomtypes atomtypes # Atomtype properties */ + t_block mols # The molecules */ + gmx_groups_t groups + t_symtab symtab # The symbol table */ + +# cdef extern from "gromacs/topology/topology.h": + # generate a t_atoms struct for the system from gmx_mtop_t + # t_atoms* mtop2atoms(gmx_mtop_t *mtop) diff --git a/pygmx/tpxio.c b/pygmx/tpxio.c new file mode 100644 index 0000000..7ea73bb --- /dev/null +++ b/pygmx/tpxio.c @@ -0,0 +1,8530 @@ +/* Generated by Cython 0.23.4 */ + +/* BEGIN: Cython Metadata +{ + "distutils": { + "depends": [ + "/home/niels/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h", + "/home/niels/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/ufuncobject.h", + "gromacs/src/gromacs/fileio/tpxio.h", + "gromacs/src/gromacs/math/vectypes.h", + "gromacs/src/gromacs/mdtypes/inputrec.h", + "gromacs/src/gromacs/topology/atoms.h", + "gromacs/src/gromacs/topology/block.h", + "gromacs/src/gromacs/topology/idef.h", + "gromacs/src/gromacs/topology/symtab.h", + "gromacs/src/gromacs/topology/topology.h", + "gromacs/src/gromacs/utility/basedefinitions.h", + "gromacs/src/gromacs/utility/futil.h", + "gromacs/src/gromacs/utility/real.h" + ], + "include_dirs": [ + "/home/niels/anaconda3/lib/python3.5/site-packages/numpy/core/include", + "gromacs/src", + "gromacs/src/external/tng_io/include" + ], + "language": "c", + "libraries": [ + "gromacs" + ], + "library_dirs": [ + "/home/niels/Uni/pygmx/gromacs/build/lib", + "/home/niels/Uni/pygmx/gromacs/src/external/tng_io/build/lib" + ], + "runtime_library_dirs": [ + "/home/niels/Uni/pygmx/gromacs/build/lib", + "/home/niels/Uni/pygmx/gromacs/src/external/tng_io/build/lib" + ] + } +} +END: Cython Metadata */ + +#define PY_SSIZE_T_CLEAN +#include "Python.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) + #error Cython requires Python 2.6+ or Python 3.2+. +#else +#define CYTHON_ABI "0_23_4" +#include +#ifndef offsetof +#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION +#define CYTHON_COMPILING_IN_PYPY 1 +#define CYTHON_COMPILING_IN_CPYTHON 0 +#else +#define CYTHON_COMPILING_IN_PYPY 0 +#define CYTHON_COMPILING_IN_CPYTHON 1 +#endif +#if !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000 +#define CYTHON_USE_PYLONG_INTERNALS 1 +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) +#define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#ifndef Py_TPFLAGS_CHECKTYPES + #define Py_TPFLAGS_CHECKTYPES 0 +#endif +#ifndef Py_TPFLAGS_HAVE_INDEX + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#ifndef Py_TPFLAGS_HAVE_NEWBUFFER + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#ifndef Py_TPFLAGS_HAVE_FINALIZE + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) +#else + #define CYTHON_PEP393_ENABLED 0 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) +#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) +#else + #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyStringObject PyUnicodeObject + #define PyString_Type PyUnicode_Type + #define PyString_Check PyUnicode_Check + #define PyString_CheckExact PyUnicode_CheckExact +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) + #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) +#else + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) +#endif +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) +#endif +#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#if PY_MAJOR_VERSION >= 3 + #define PyIntObject PyLongObject + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define PyNumber_Int PyNumber_Long +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBoolObject PyLongObject +#endif +#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY + #ifndef PyUnicode_InternFromString + #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) + #endif +#endif +#if PY_VERSION_HEX < 0x030200A4 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t PyInt_AsLong +#else + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) +#else + #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) +#endif +#if PY_VERSION_HEX >= 0x030500B1 +#define __Pyx_PyAsyncMethodsStruct PyAsyncMethods +#define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) +#elif CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 +typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; +} __Pyx_PyAsyncMethodsStruct; +#define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) +#else +#define __Pyx_PyType_AsAsync(obj) NULL +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) + +#ifndef CYTHON_INLINE + #if defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif + + +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#define __PYX_HAVE__pygmx__tpxio +#define __PYX_HAVE_API__pygmx__tpxio +#include "string.h" +#include "stdio.h" +#include "stdlib.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#include "gromacs/utility/basedefinitions.h" +#include "gromacs/utility/real.h" +#include "gromacs/utility/futil.h" +#include "gromacs/math/vectypes.h" +#include "gromacs/mdtypes/inputrec.h" +#include "gromacs/topology/atoms.h" +#include "gromacs/topology/symtab.h" +#include "gromacs/topology/block.h" +#include "gromacs/topology/idef.h" +#include "gromacs/topology/topology.h" +#include "gromacs/fileio/tpxio.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#ifdef PYREX_WITHOUT_ASSERTIONS +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# endif +#endif +typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "utf8" +#define __Pyx_PyObject_FromString __Pyx_PyUnicode_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ + (sizeof(type) < sizeof(Py_ssize_t)) ||\ + (sizeof(type) > sizeof(Py_ssize_t) &&\ + likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX) &&\ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ + v == (type)PY_SSIZE_T_MIN))) ||\ + (sizeof(type) == sizeof(Py_ssize_t) &&\ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) && defined (_M_X64) + #define __Pyx_sst_abs(value) _abs64(value) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) +#if PY_MAJOR_VERSION < 3 +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) +{ + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#else +#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen +#endif +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_COMPILING_IN_CPYTHON +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ + +static PyObject *__pyx_m; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "pygmx/tpxio.pyx", + "__init__.pxd", + "type.pxd", +}; +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":725 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":726 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":727 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":728 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":734 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":735 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":739 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":740 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":749 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":750 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":751 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":753 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":754 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":755 + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_intp intp_t + */ +typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":757 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":761 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; + +/* "utility.pxd":4 + * + * #cdef extern from "inttypes.h": + * ctypedef int __int64 # <<<<<<<<<<<<<< + * + * cdef extern from "gromacs/utility/basedefinitions.h": + */ +typedef int __pyx_t_5pygmx_7utility___int64; +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif + + +/*--- Type declarations ---*/ +struct __pyx_obj_5pygmx_5tpxio_TPXWrapper; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":764 + * ctypedef npy_longdouble longdouble_t + * + * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t + */ +typedef npy_cfloat __pyx_t_5numpy_cfloat_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":765 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":766 + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cdouble complex_t + */ +typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":768 + * ctypedef npy_clongdouble clongdouble_t + * + * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew1(a): + */ +typedef npy_cdouble __pyx_t_5numpy_complex_t; + +/* "pygmx/tpxio.pyx":56 + * + * + * cdef class TPXWrapper: # <<<<<<<<<<<<<< + * cdef: + * t_tpxheader header + */ +struct __pyx_obj_5pygmx_5tpxio_TPXWrapper { + PyObject_HEAD + struct t_tpxheader header; + t_inputrec input_record; + gmx_mtop_t topology; + real box[3][3]; + int n_atoms; + int n_tcouple_groups; + int n_mol; +}; + + +/* --- Runtime support code (head) --- */ +#ifndef CYTHON_REFNANNY + #define CYTHON_REFNANNY 0 +#endif +#if CYTHON_REFNANNY + typedef struct { + void (*INCREF)(void*, PyObject*, int); + void (*DECREF)(void*, PyObject*, int); + void (*GOTREF)(void*, PyObject*, int); + void (*GIVEREF)(void*, PyObject*, int); + void* (*SetupContext)(const char*, int, const char*); + void (*FinishContext)(void**); + } __Pyx_RefNannyAPIStruct; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); + #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; +#ifdef WITH_THREAD + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + if (acquire_gil) {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + PyGILState_Release(__pyx_gilstate_save);\ + } else {\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + } +#else + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) +#endif + #define __Pyx_RefNannyFinishContext()\ + __Pyx_RefNanny->FinishContext(&__pyx_refnanny) + #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_XINCREF(r) do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0) + #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0) + #define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0) + #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0) +#else + #define __Pyx_RefNannyDeclarations + #define __Pyx_RefNannySetupContext(name, acquire_gil) + #define __Pyx_RefNannyFinishContext() + #define __Pyx_INCREF(r) Py_INCREF(r) + #define __Pyx_DECREF(r) Py_DECREF(r) + #define __Pyx_GOTREF(r) + #define __Pyx_GIVEREF(r) + #define __Pyx_XINCREF(r) Py_XINCREF(r) + #define __Pyx_XDECREF(r) Py_XDECREF(r) + #define __Pyx_XGOTREF(r) + #define __Pyx_XGIVEREF(r) +#endif +#define __Pyx_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_XDECREF(tmp);\ + } while (0) +#define __Pyx_DECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_DECREF(tmp);\ + } while (0) +#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) +#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); +#else +#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); +#else +#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) +#endif + +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ + const char* function_name); + +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, + __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); + +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL) +static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_setattro)) + return tp->tp_setattro(obj, attr_name, value); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_setattr)) + return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value); +#endif + return PyObject_SetAttr(obj, attr_name, value); +} +#else +#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n) +#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v) +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len)) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) +#endif + +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { + PyObject *value; + value = PyDict_GetItemWithError(d, key); + if (unlikely(!value)) { + if (!PyErr_Occurred()) { + PyObject* args = PyTuple_Pack(1, key); + if (likely(args)) + PyErr_SetObject(PyExc_KeyError, args); + Py_XDECREF(args); + } + return NULL; + } + Py_INCREF(value); + return value; +} +#else + #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) +#endif + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); + +#define __Pyx_CyFunction_USED 1 +#include +#define __Pyx_CYFUNCTION_STATICMETHOD 0x01 +#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 +#define __Pyx_CYFUNCTION_CCLASS 0x04 +#define __Pyx_CyFunction_GetClosure(f)\ + (((__pyx_CyFunctionObject *) (f))->func_closure) +#define __Pyx_CyFunction_GetClassObj(f)\ + (((__pyx_CyFunctionObject *) (f))->func_classobj) +#define __Pyx_CyFunction_Defaults(type, f)\ + ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) +#define __Pyx_CyFunction_SetDefaultsGetter(f, g)\ + ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) +typedef struct { + PyCFunctionObject func; +#if PY_VERSION_HEX < 0x030500A0 + PyObject *func_weakreflist; +#endif + PyObject *func_dict; + PyObject *func_name; + PyObject *func_qualname; + PyObject *func_doc; + PyObject *func_globals; + PyObject *func_code; + PyObject *func_closure; + PyObject *func_classobj; + void *defaults; + int defaults_pyobjects; + int flags; + PyObject *defaults_tuple; + PyObject *defaults_kwdict; + PyObject *(*defaults_getter)(PyObject *); + PyObject *func_annotations; +} __pyx_CyFunctionObject; +static PyTypeObject *__pyx_CyFunctionType = 0; +#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code)\ + __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, globals, code) +static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, + int flags, PyObject* qualname, + PyObject *self, + PyObject *module, PyObject *globals, + PyObject* code); +static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, + size_t size, + int pyobjects); +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, + PyObject *tuple); +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m, + PyObject *dict); +static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m, + PyObject *dict); +static int __pyx_CyFunction_init(void); + +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases); + +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname, + PyObject *mkw, PyObject *modname, PyObject *doc); +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict, + PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass); + +typedef struct { + int code_line; + PyCodeObject* code_object; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; +static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_char(char value); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +static int __Pyx_Print(PyObject*, PyObject *, int); +#if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3 +static PyObject* __pyx_print = 0; +static PyObject* __pyx_print_kwargs = 0; +#endif + +static int __Pyx_PrintOne(PyObject* stream, PyObject *o); + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eqf(a, b) ((a)==(b)) + #define __Pyx_c_sumf(a, b) ((a)+(b)) + #define __Pyx_c_difff(a, b) ((a)-(b)) + #define __Pyx_c_prodf(a, b) ((a)*(b)) + #define __Pyx_c_quotf(a, b) ((a)/(b)) + #define __Pyx_c_negf(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zerof(z) ((z)==(float)0) + #define __Pyx_c_conjf(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_absf(z) (::std::abs(z)) + #define __Pyx_c_powf(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zerof(z) ((z)==0) + #define __Pyx_c_conjf(z) (conjf(z)) + #if 1 + #define __Pyx_c_absf(z) (cabsf(z)) + #define __Pyx_c_powf(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq(a, b) ((a)==(b)) + #define __Pyx_c_sum(a, b) ((a)+(b)) + #define __Pyx_c_diff(a, b) ((a)-(b)) + #define __Pyx_c_prod(a, b) ((a)*(b)) + #define __Pyx_c_quot(a, b) ((a)/(b)) + #define __Pyx_c_neg(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero(z) ((z)==(double)0) + #define __Pyx_c_conj(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs(z) (::std::abs(z)) + #define __Pyx_c_pow(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero(z) ((z)==0) + #define __Pyx_c_conj(z) (conj(z)) + #if 1 + #define __Pyx_c_abs(z) (cabs(z)) + #define __Pyx_c_pow(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + +static int __Pyx_check_binary_version(void); + +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +static PyObject *__Pyx_ImportModule(const char *name); + +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'libc.stdlib' */ + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'pygmx.utility' */ + +/* Module declarations from 'pygmx.math' */ + +/* Module declarations from 'pygmx.mdtypes' */ + +/* Module declarations from 'pygmx.topology' */ + +/* Module declarations from 'pygmx.tpxio' */ +static PyTypeObject *__pyx_ptype_5pygmx_5tpxio_TPXWrapper = 0; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn_real = { "real", NULL, sizeof(real), { 0 }, 0, 'R', 0, 0 }; +#define __Pyx_MODULE_NAME "pygmx.tpxio" +int __pyx_module_is_main_pygmx__tpxio = 0; + +/* Implementation of 'pygmx.tpxio' */ +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_RuntimeError; +static char __pyx_k_B[] = "B"; +static char __pyx_k_H[] = "H"; +static char __pyx_k_I[] = "I"; +static char __pyx_k_L[] = "L"; +static char __pyx_k_O[] = "O"; +static char __pyx_k_Q[] = "Q"; +static char __pyx_k_b[] = "b"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; +static char __pyx_k_i[] = "i"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; +static char __pyx_k_np[] = "np"; +static char __pyx_k_box[] = "box"; +static char __pyx_k_doc[] = "__doc__"; +static char __pyx_k_end[] = "end"; +static char __pyx_k_tpr[] = "tpr"; +static char __pyx_k_tpx[] = "tpx"; +static char __pyx_k_cstr[] = "cstr"; +static char __pyx_k_file[] = "file"; +static char __pyx_k_init[] = "__init__"; +static char __pyx_k_main[] = "__main__"; +static char __pyx_k_self[] = "self"; +static char __pyx_k_test[] = "__test__"; +static char __pyx_k_dtype[] = "dtype"; +static char __pyx_k_empty[] = "empty"; +static char __pyx_k_fname[] = "fname"; +static char __pyx_k_instr[] = "instr"; +static char __pyx_k_numpy[] = "numpy"; +static char __pyx_k_print[] = "print"; +static char __pyx_k_range[] = "range"; +static char __pyx_k_encode[] = "encode"; +static char __pyx_k_import[] = "__import__"; +static char __pyx_k_module[] = "__module__"; +static char __pyx_k_natoms[] = "natoms"; +static char __pyx_k_record[] = "record"; +static char __pyx_k_float32[] = "float32"; +static char __pyx_k_prepare[] = "__prepare__"; +static char __pyx_k_filename[] = "filename"; +static char __pyx_k_load_tpx[] = "load_tpx"; +static char __pyx_k_qualname[] = "__qualname__"; +static char __pyx_k_topology[] = "topology"; +static char __pyx_k_TPRReader[] = "TPRReader"; +static char __pyx_k_metaclass[] = "__metaclass__"; +static char __pyx_k_velocites[] = "velocites"; +static char __pyx_k_ValueError[] = "ValueError"; +static char __pyx_k_coordinates[] = "coordinates"; +static char __pyx_k_pygmx_tpxio[] = "pygmx.tpxio"; +static char __pyx_k_return_code[] = "return_code"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; +static char __pyx_k_TPRReader___init[] = "TPRReader.__init__"; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static char __pyx_k_home_niels_Uni_pygmx_pygmx_tpxi[] = "/home/niels/Uni/pygmx/pygmx/tpxio.pyx"; +static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_TPRReader; +static PyObject *__pyx_n_s_TPRReader___init; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_n_s_box; +static PyObject *__pyx_n_s_coordinates; +static PyObject *__pyx_n_s_cstr; +static PyObject *__pyx_n_s_doc; +static PyObject *__pyx_n_s_dtype; +static PyObject *__pyx_n_s_empty; +static PyObject *__pyx_n_s_encode; +static PyObject *__pyx_n_s_end; +static PyObject *__pyx_n_s_file; +static PyObject *__pyx_n_s_filename; +static PyObject *__pyx_n_s_float32; +static PyObject *__pyx_n_s_fname; +static PyObject *__pyx_kp_s_home_niels_Uni_pygmx_pygmx_tpxi; +static PyObject *__pyx_n_s_i; +static PyObject *__pyx_n_s_import; +static PyObject *__pyx_n_s_init; +static PyObject *__pyx_n_s_instr; +static PyObject *__pyx_n_s_load_tpx; +static PyObject *__pyx_n_s_main; +static PyObject *__pyx_n_s_metaclass; +static PyObject *__pyx_n_s_module; +static PyObject *__pyx_n_s_natoms; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_np; +static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_n_s_prepare; +static PyObject *__pyx_n_s_print; +static PyObject *__pyx_n_s_pygmx_tpxio; +static PyObject *__pyx_n_s_qualname; +static PyObject *__pyx_n_s_range; +static PyObject *__pyx_n_s_record; +static PyObject *__pyx_n_s_return_code; +static PyObject *__pyx_n_s_self; +static PyObject *__pyx_n_s_test; +static PyObject *__pyx_n_s_topology; +static PyObject *__pyx_n_s_tpr; +static PyObject *__pyx_n_s_tpx; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; +static PyObject *__pyx_n_s_velocites; +static PyObject *__pyx_pf_5pygmx_5tpxio_cstr(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_instr); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tpxio_10TPXWrapper_5atoms___get__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self); /* proto */ +static int __pyx_pf_5pygmx_5tpxio_10TPXWrapper___cinit__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tpxio_10TPXWrapper_7n_atoms___get__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tpxio_10TPXWrapper_16n_tcouple_groups___get__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tpxio_10TPXWrapper_5n_mol___get__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tpxio_9TPRReader___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static PyObject *__pyx_pf_5pygmx_5tpxio_2load_tpx(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static PyObject *__pyx_tp_new_5pygmx_5tpxio_TPXWrapper(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_int_3; +static PyObject *__pyx_tuple_; +static PyObject *__pyx_tuple__2; +static PyObject *__pyx_tuple__3; +static PyObject *__pyx_tuple__4; +static PyObject *__pyx_tuple__5; +static PyObject *__pyx_tuple__6; +static PyObject *__pyx_tuple__7; +static PyObject *__pyx_tuple__9; +static PyObject *__pyx_tuple__11; +static PyObject *__pyx_codeobj__8; +static PyObject *__pyx_codeobj__10; +static PyObject *__pyx_codeobj__12; + +/* "pygmx/tpxio.pyx":50 + * + * + * def cstr(instr): # <<<<<<<<<<<<<< + * if isinstance(instr, str): + * instr = instr.encode() + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tpxio_1cstr(PyObject *__pyx_self, PyObject *__pyx_v_instr); /*proto*/ +static PyMethodDef __pyx_mdef_5pygmx_5tpxio_1cstr = {"cstr", (PyCFunction)__pyx_pw_5pygmx_5tpxio_1cstr, METH_O, 0}; +static PyObject *__pyx_pw_5pygmx_5tpxio_1cstr(PyObject *__pyx_self, PyObject *__pyx_v_instr) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("cstr (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tpxio_cstr(__pyx_self, ((PyObject *)__pyx_v_instr)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tpxio_cstr(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_instr) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("cstr", 0); + __Pyx_INCREF(__pyx_v_instr); + + /* "pygmx/tpxio.pyx":51 + * + * def cstr(instr): + * if isinstance(instr, str): # <<<<<<<<<<<<<< + * instr = instr.encode() + * return instr + */ + __pyx_t_1 = PyString_Check(__pyx_v_instr); + __pyx_t_2 = (__pyx_t_1 != 0); + if (__pyx_t_2) { + + /* "pygmx/tpxio.pyx":52 + * def cstr(instr): + * if isinstance(instr, str): + * instr = instr.encode() # <<<<<<<<<<<<<< + * return instr + * + */ + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_instr, __pyx_n_s_encode); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_5)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + } + } + if (__pyx_t_5) { + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + } else { + __pyx_t_3 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF_SET(__pyx_v_instr, __pyx_t_3); + __pyx_t_3 = 0; + + /* "pygmx/tpxio.pyx":51 + * + * def cstr(instr): + * if isinstance(instr, str): # <<<<<<<<<<<<<< + * instr = instr.encode() + * return instr + */ + } + + /* "pygmx/tpxio.pyx":53 + * if isinstance(instr, str): + * instr = instr.encode() + * return instr # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_instr); + __pyx_r = __pyx_v_instr; + goto __pyx_L0; + + /* "pygmx/tpxio.pyx":50 + * + * + * def cstr(instr): # <<<<<<<<<<<<<< + * if isinstance(instr, str): + * instr = instr.encode() + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("pygmx.tpxio.cstr", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_instr); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tpxio.pyx":65 + * + * property atoms: + * def __get__(self): # <<<<<<<<<<<<<< + * cdef: + * t_atoms *c_atoms + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tpxio_10TPXWrapper_5atoms_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pygmx_5tpxio_10TPXWrapper_5atoms_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tpxio_10TPXWrapper_5atoms___get__(((struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tpxio_10TPXWrapper_5atoms___get__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self) { + t_atoms *__pyx_v_c_atoms; + PyObject *__pyx_v_atoms = NULL; + int __pyx_v_i; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + char *__pyx_t_4; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + int __pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pygmx/tpxio.pyx":68 + * cdef: + * t_atoms *c_atoms + * c_atoms = mtop2atoms(&self.topology) # <<<<<<<<<<<<<< + * + * atoms = [] + */ + __pyx_v_c_atoms = mtop2atoms((&__pyx_v_self->topology)); + + /* "pygmx/tpxio.pyx":70 + * c_atoms = mtop2atoms(&self.topology) + * + * atoms = [] # <<<<<<<<<<<<<< + * for i in range(c_atoms.nr): + * atoms.append(( + */ + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_atoms = ((PyObject*)__pyx_t_1); + __pyx_t_1 = 0; + + /* "pygmx/tpxio.pyx":71 + * + * atoms = [] + * for i in range(c_atoms.nr): # <<<<<<<<<<<<<< + * atoms.append(( + * *c_atoms.atomname[0][i], + */ + __pyx_t_2 = __pyx_v_c_atoms->nr; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "pygmx/tpxio.pyx":73 + * for i in range(c_atoms.nr): + * atoms.append(( + * *c_atoms.atomname[0][i], # <<<<<<<<<<<<<< + * c_atoms.atomtype[0][i], + * c_atoms.resinfo.nr, + */ + __pyx_t_1 = __Pyx_PyUnicode_FromString(__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + + /* "pygmx/tpxio.pyx":74 + * atoms.append(( + * *c_atoms.atomname[0][i], + * c_atoms.atomtype[0][i], # <<<<<<<<<<<<<< + * c_atoms.resinfo.nr, + * c_atoms.resinfo.name[0][i] + */ + __pyx_t_5 = __Pyx_PyUnicode_FromString(((__pyx_v_c_atoms->atomtype[0])[__pyx_v_i])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + + /* "pygmx/tpxio.pyx":75 + * *c_atoms.atomname[0][i], + * c_atoms.atomtype[0][i], + * c_atoms.resinfo.nr, # <<<<<<<<<<<<<< + * c_atoms.resinfo.name[0][i] + * )) + */ + __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_c_atoms->resinfo->nr); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); + + /* "pygmx/tpxio.pyx":76 + * c_atoms.atomtype[0][i], + * c_atoms.resinfo.nr, + * c_atoms.resinfo.name[0][i] # <<<<<<<<<<<<<< + * )) + * + */ + __pyx_t_7 = __Pyx_PyInt_From_char(((__pyx_v_c_atoms->resinfo->name[0])[__pyx_v_i])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + + /* "pygmx/tpxio.pyx":73 + * for i in range(c_atoms.nr): + * atoms.append(( + * *c_atoms.atomname[0][i], # <<<<<<<<<<<<<< + * c_atoms.atomtype[0][i], + * c_atoms.resinfo.nr, + */ + __pyx_t_8 = PyTuple_New(4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1); + __Pyx_GIVEREF(__pyx_t_5); + PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_5); + __Pyx_GIVEREF(__pyx_t_6); + PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_6); + __Pyx_GIVEREF(__pyx_t_7); + PyTuple_SET_ITEM(__pyx_t_8, 3, __pyx_t_7); + __pyx_t_1 = 0; + __pyx_t_5 = 0; + __pyx_t_6 = 0; + __pyx_t_7 = 0; + + /* "pygmx/tpxio.pyx":72 + * atoms = [] + * for i in range(c_atoms.nr): + * atoms.append(( # <<<<<<<<<<<<<< + * *c_atoms.atomname[0][i], + * c_atoms.atomtype[0][i], + */ + __pyx_t_9 = __Pyx_PyList_Append(__pyx_v_atoms, __pyx_t_8); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + } + + /* "pygmx/tpxio.pyx":79 + * )) + * + * return atoms # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_atoms); + __pyx_r = __pyx_v_atoms; + goto __pyx_L0; + + /* "pygmx/tpxio.pyx":65 + * + * property atoms: + * def __get__(self): # <<<<<<<<<<<<<< + * cdef: + * t_atoms *c_atoms + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_AddTraceback("pygmx.tpxio.TPXWrapper.atoms.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_atoms); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tpxio.pyx":82 + * + * + * def __cinit__(self, filename): # <<<<<<<<<<<<<< + * filename = cstr(filename) + * read_tpxheader(filename, &self.header, True) + */ + +/* Python wrapper */ +static int __pyx_pw_5pygmx_5tpxio_10TPXWrapper_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pygmx_5tpxio_10TPXWrapper_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_filename = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,0}; + PyObject* values[1] = {0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_filename)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 1) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + } + __pyx_v_filename = values[0]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_L3_error:; + __Pyx_AddTraceback("pygmx.tpxio.TPXWrapper.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return -1; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pygmx_5tpxio_10TPXWrapper___cinit__(((struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *)__pyx_v_self), __pyx_v_filename); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_5pygmx_5tpxio_10TPXWrapper___cinit__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self, PyObject *__pyx_v_filename) { + PyArrayObject *__pyx_v_coordinates = 0; + PyArrayObject *__pyx_v_velocites = 0; + CYTHON_UNUSED int __pyx_v_return_code; + __Pyx_LocalBuf_ND __pyx_pybuffernd_coordinates; + __Pyx_Buffer __pyx_pybuffer_coordinates; + __Pyx_LocalBuf_ND __pyx_pybuffernd_velocites; + __Pyx_Buffer __pyx_pybuffer_velocites; + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + char *__pyx_t_5; + int __pyx_t_6; + PyObject *__pyx_t_7 = NULL; + PyArrayObject *__pyx_t_8 = NULL; + PyArrayObject *__pyx_t_9 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__cinit__", 0); + __Pyx_INCREF(__pyx_v_filename); + __pyx_pybuffer_coordinates.pybuffer.buf = NULL; + __pyx_pybuffer_coordinates.refcount = 0; + __pyx_pybuffernd_coordinates.data = NULL; + __pyx_pybuffernd_coordinates.rcbuffer = &__pyx_pybuffer_coordinates; + __pyx_pybuffer_velocites.pybuffer.buf = NULL; + __pyx_pybuffer_velocites.refcount = 0; + __pyx_pybuffernd_velocites.data = NULL; + __pyx_pybuffernd_velocites.rcbuffer = &__pyx_pybuffer_velocites; + + /* "pygmx/tpxio.pyx":83 + * + * def __cinit__(self, filename): + * filename = cstr(filename) # <<<<<<<<<<<<<< + * read_tpxheader(filename, &self.header, True) + * self.n_atoms = self.header.natoms + */ + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_cstr); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + if (!__pyx_t_3) { + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_filename); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + } else { + __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); __pyx_t_3 = NULL; + __Pyx_INCREF(__pyx_v_filename); + __Pyx_GIVEREF(__pyx_v_filename); + PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_filename); + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + } + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF_SET(__pyx_v_filename, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pygmx/tpxio.pyx":84 + * def __cinit__(self, filename): + * filename = cstr(filename) + * read_tpxheader(filename, &self.header, True) # <<<<<<<<<<<<<< + * self.n_atoms = self.header.natoms + * self.n_tcouple_groups = self.header.ngtc + */ + __pyx_t_5 = __Pyx_PyObject_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + read_tpxheader(((char *)__pyx_t_5), (&__pyx_v_self->header), 1); + + /* "pygmx/tpxio.pyx":85 + * filename = cstr(filename) + * read_tpxheader(filename, &self.header, True) + * self.n_atoms = self.header.natoms # <<<<<<<<<<<<<< + * self.n_tcouple_groups = self.header.ngtc + * + */ + __pyx_t_6 = __pyx_v_self->header.natoms; + __pyx_v_self->n_atoms = __pyx_t_6; + + /* "pygmx/tpxio.pyx":86 + * read_tpxheader(filename, &self.header, True) + * self.n_atoms = self.header.natoms + * self.n_tcouple_groups = self.header.ngtc # <<<<<<<<<<<<<< + * + * cdef np.ndarray[real, ndim=2] coordinates = np.empty((self.natoms, 3), dtype=np.float32) + */ + __pyx_t_6 = __pyx_v_self->header.ngtc; + __pyx_v_self->n_tcouple_groups = __pyx_t_6; + + /* "pygmx/tpxio.pyx":88 + * self.n_tcouple_groups = self.header.ngtc + * + * cdef np.ndarray[real, ndim=2] coordinates = np.empty((self.natoms, 3), dtype=np.float32) # <<<<<<<<<<<<<< + * cdef np.ndarray[real, ndim=2] velocites = np.empty((self.natoms, 3), dtype=np.float32) + * + */ + __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_natoms); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); + __Pyx_INCREF(__pyx_int_3); + __Pyx_GIVEREF(__pyx_int_3); + PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_int_3); + __pyx_t_1 = 0; + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_4); + __pyx_t_4 = 0; + __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_float32); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (!(likely(((__pyx_t_7) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_7, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = ((PyArrayObject *)__pyx_t_7); + { + __Pyx_BufFmt_StackElem __pyx_stack[1]; + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coordinates.rcbuffer->pybuffer, (PyObject*)__pyx_t_8, &__Pyx_TypeInfo_nn_real, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + __pyx_v_coordinates = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.buf = NULL; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } else {__pyx_pybuffernd_coordinates.diminfo[0].strides = __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_coordinates.diminfo[0].shape = __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_coordinates.diminfo[1].strides = __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_coordinates.diminfo[1].shape = __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.shape[1]; + } + } + __pyx_t_8 = 0; + __pyx_v_coordinates = ((PyArrayObject *)__pyx_t_7); + __pyx_t_7 = 0; + + /* "pygmx/tpxio.pyx":89 + * + * cdef np.ndarray[real, ndim=2] coordinates = np.empty((self.natoms, 3), dtype=np.float32) + * cdef np.ndarray[real, ndim=2] velocites = np.empty((self.natoms, 3), dtype=np.float32) # <<<<<<<<<<<<<< + * + * return_code = read_tpx( + */ + __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_empty); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_natoms); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_GIVEREF(__pyx_t_7); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7); + __Pyx_INCREF(__pyx_int_3); + __Pyx_GIVEREF(__pyx_int_3); + PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_3); + __pyx_t_7 = 0; + __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_1); + __pyx_t_1 = 0; + __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_float32); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = ((PyArrayObject *)__pyx_t_3); + { + __Pyx_BufFmt_StackElem __pyx_stack[1]; + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_velocites.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__Pyx_TypeInfo_nn_real, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + __pyx_v_velocites = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_velocites.rcbuffer->pybuffer.buf = NULL; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } else {__pyx_pybuffernd_velocites.diminfo[0].strides = __pyx_pybuffernd_velocites.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_velocites.diminfo[0].shape = __pyx_pybuffernd_velocites.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_velocites.diminfo[1].strides = __pyx_pybuffernd_velocites.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_velocites.diminfo[1].shape = __pyx_pybuffernd_velocites.rcbuffer->pybuffer.shape[1]; + } + } + __pyx_t_9 = 0; + __pyx_v_velocites = ((PyArrayObject *)__pyx_t_3); + __pyx_t_3 = 0; + + /* "pygmx/tpxio.pyx":92 + * + * return_code = read_tpx( + * filename, # <<<<<<<<<<<<<< + * &self.input_record, + * self.box, + */ + __pyx_t_5 = __Pyx_PyObject_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tpxio.pyx":91 + * cdef np.ndarray[real, ndim=2] velocites = np.empty((self.natoms, 3), dtype=np.float32) + * + * return_code = read_tpx( # <<<<<<<<<<<<<< + * filename, + * &self.input_record, + */ + __pyx_v_return_code = read_tpx(((char *)__pyx_t_5), (&__pyx_v_self->input_record), __pyx_v_self->box, (&__pyx_v_self->n_atoms), ((rvec *)__pyx_v_coordinates->data), ((rvec *)__pyx_v_velocites->data), (&__pyx_v_self->topology)); + + /* "pygmx/tpxio.pyx":82 + * + * + * def __cinit__(self, filename): # <<<<<<<<<<<<<< + * filename = cstr(filename) + * read_tpxheader(filename, &self.header, True) + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_7); + { PyObject *__pyx_type, *__pyx_value, *__pyx_tb; + __Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_coordinates.rcbuffer->pybuffer); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_velocites.rcbuffer->pybuffer); + __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} + __Pyx_AddTraceback("pygmx.tpxio.TPXWrapper.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + goto __pyx_L2; + __pyx_L0:; + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_coordinates.rcbuffer->pybuffer); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_velocites.rcbuffer->pybuffer); + __pyx_L2:; + __Pyx_XDECREF((PyObject *)__pyx_v_coordinates); + __Pyx_XDECREF((PyObject *)__pyx_v_velocites); + __Pyx_XDECREF(__pyx_v_filename); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tpxio.pyx":62 + * gmx_mtop_t topology + * real box[3][3] + * readonly int n_atoms, n_tcouple_groups, n_mol # <<<<<<<<<<<<<< + * + * property atoms: + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tpxio_10TPXWrapper_7n_atoms_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pygmx_5tpxio_10TPXWrapper_7n_atoms_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tpxio_10TPXWrapper_7n_atoms___get__(((struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tpxio_10TPXWrapper_7n_atoms___get__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->n_atoms); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pygmx.tpxio.TPXWrapper.n_atoms.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tpxio_10TPXWrapper_16n_tcouple_groups_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pygmx_5tpxio_10TPXWrapper_16n_tcouple_groups_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tpxio_10TPXWrapper_16n_tcouple_groups___get__(((struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tpxio_10TPXWrapper_16n_tcouple_groups___get__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->n_tcouple_groups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pygmx.tpxio.TPXWrapper.n_tcouple_groups.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tpxio_10TPXWrapper_5n_mol_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pygmx_5tpxio_10TPXWrapper_5n_mol_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tpxio_10TPXWrapper_5n_mol___get__(((struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tpxio_10TPXWrapper_5n_mol___get__(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->n_mol); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pygmx.tpxio.TPXWrapper.n_mol.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tpxio.pyx":105 + * class TPRReader: + * + * def __init__(self, filename): # <<<<<<<<<<<<<< + * self.tpr = TPXWrapper(filename) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tpxio_9TPRReader_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pygmx_5tpxio_9TPRReader_1__init__ = {"__init__", (PyCFunction)__pyx_pw_5pygmx_5tpxio_9TPRReader_1__init__, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_5pygmx_5tpxio_9TPRReader_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_self = 0; + PyObject *__pyx_v_filename = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_filename,0}; + PyObject* values[2] = {0,0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_self)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + case 1: + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_filename)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + } + __pyx_v_self = values[0]; + __pyx_v_filename = values[1]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_L3_error:; + __Pyx_AddTraceback("pygmx.tpxio.TPRReader.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pygmx_5tpxio_9TPRReader___init__(__pyx_self, __pyx_v_self, __pyx_v_filename); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tpxio_9TPRReader___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__init__", 0); + + /* "pygmx/tpxio.pyx":106 + * + * def __init__(self, filename): + * self.tpr = TPXWrapper(filename) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_INCREF(__pyx_v_filename); + __Pyx_GIVEREF(__pyx_v_filename); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename); + __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5pygmx_5tpxio_TPXWrapper), __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_tpr, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pygmx/tpxio.pyx":105 + * class TPRReader: + * + * def __init__(self, filename): # <<<<<<<<<<<<<< + * self.tpr = TPXWrapper(filename) + * + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pygmx.tpxio.TPRReader.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pygmx/tpxio.pyx":109 + * + * + * def load_tpx(fname): # <<<<<<<<<<<<<< + * fname = cstr(fname) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pygmx_5tpxio_3load_tpx(PyObject *__pyx_self, PyObject *__pyx_v_fname); /*proto*/ +static PyMethodDef __pyx_mdef_5pygmx_5tpxio_3load_tpx = {"load_tpx", (PyCFunction)__pyx_pw_5pygmx_5tpxio_3load_tpx, METH_O, 0}; +static PyObject *__pyx_pw_5pygmx_5tpxio_3load_tpx(PyObject *__pyx_self, PyObject *__pyx_v_fname) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("load_tpx (wrapper)", 0); + __pyx_r = __pyx_pf_5pygmx_5tpxio_2load_tpx(__pyx_self, ((PyObject *)__pyx_v_fname)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pygmx_5tpxio_2load_tpx(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname) { + struct t_tpxheader __pyx_v_tpx; + int __pyx_v_natoms; + t_inputrec __pyx_v_record; + gmx_mtop_t __pyx_v_topology; + real __pyx_v_box[3][3]; + PyArrayObject *__pyx_v_coordinates = 0; + PyArrayObject *__pyx_v_velocites = 0; + CYTHON_UNUSED int __pyx_v_return_code; + long __pyx_v_i; + __Pyx_LocalBuf_ND __pyx_pybuffernd_coordinates; + __Pyx_Buffer __pyx_pybuffer_coordinates; + __Pyx_LocalBuf_ND __pyx_pybuffernd_velocites; + __Pyx_Buffer __pyx_pybuffer_velocites; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + char *__pyx_t_5; + int __pyx_t_6; + PyObject *__pyx_t_7 = NULL; + PyArrayObject *__pyx_t_8 = NULL; + PyArrayObject *__pyx_t_9 = NULL; + long __pyx_t_10; + long __pyx_t_11; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("load_tpx", 0); + __Pyx_INCREF(__pyx_v_fname); + __pyx_pybuffer_coordinates.pybuffer.buf = NULL; + __pyx_pybuffer_coordinates.refcount = 0; + __pyx_pybuffernd_coordinates.data = NULL; + __pyx_pybuffernd_coordinates.rcbuffer = &__pyx_pybuffer_coordinates; + __pyx_pybuffer_velocites.pybuffer.buf = NULL; + __pyx_pybuffer_velocites.refcount = 0; + __pyx_pybuffernd_velocites.data = NULL; + __pyx_pybuffernd_velocites.rcbuffer = &__pyx_pybuffer_velocites; + + /* "pygmx/tpxio.pyx":110 + * + * def load_tpx(fname): + * fname = cstr(fname) # <<<<<<<<<<<<<< + * + * cdef t_tpxheader tpx + */ + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_cstr); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + if (!__pyx_t_3) { + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_fname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + } else { + __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); __pyx_t_3 = NULL; + __Pyx_INCREF(__pyx_v_fname); + __Pyx_GIVEREF(__pyx_v_fname); + PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_fname); + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + } + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF_SET(__pyx_v_fname, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pygmx/tpxio.pyx":113 + * + * cdef t_tpxheader tpx + * read_tpxheader(fname, &tpx, True) # <<<<<<<<<<<<<< + * + * cdef: + */ + __pyx_t_5 = __Pyx_PyObject_AsString(__pyx_v_fname); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + read_tpxheader(((char *)__pyx_t_5), (&__pyx_v_tpx), 1); + + /* "pygmx/tpxio.pyx":116 + * + * cdef: + * int natoms = tpx.natoms # <<<<<<<<<<<<<< + * t_inputrec record + * gmx_mtop_t topology + */ + __pyx_t_6 = __pyx_v_tpx.natoms; + __pyx_v_natoms = __pyx_t_6; + + /* "pygmx/tpxio.pyx":121 + * real box[3][3] + * + * cdef np.ndarray[real, ndim=2] coordinates = np.empty((natoms,3), dtype=np.float32) # <<<<<<<<<<<<<< + * cdef np.ndarray[real, ndim=2] velocites = np.empty((natoms,3), dtype=np.float32) + * + */ + __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_natoms); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); + __Pyx_INCREF(__pyx_int_3); + __Pyx_GIVEREF(__pyx_int_3); + PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_int_3); + __pyx_t_1 = 0; + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_4); + __pyx_t_4 = 0; + __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_float32); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (!(likely(((__pyx_t_7) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_7, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = ((PyArrayObject *)__pyx_t_7); + { + __Pyx_BufFmt_StackElem __pyx_stack[1]; + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coordinates.rcbuffer->pybuffer, (PyObject*)__pyx_t_8, &__Pyx_TypeInfo_nn_real, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + __pyx_v_coordinates = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.buf = NULL; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } else {__pyx_pybuffernd_coordinates.diminfo[0].strides = __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_coordinates.diminfo[0].shape = __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_coordinates.diminfo[1].strides = __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_coordinates.diminfo[1].shape = __pyx_pybuffernd_coordinates.rcbuffer->pybuffer.shape[1]; + } + } + __pyx_t_8 = 0; + __pyx_v_coordinates = ((PyArrayObject *)__pyx_t_7); + __pyx_t_7 = 0; + + /* "pygmx/tpxio.pyx":122 + * + * cdef np.ndarray[real, ndim=2] coordinates = np.empty((natoms,3), dtype=np.float32) + * cdef np.ndarray[real, ndim=2] velocites = np.empty((natoms,3), dtype=np.float32) # <<<<<<<<<<<<<< + * + * return_code = read_tpx( + */ + __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_empty); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_natoms); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_GIVEREF(__pyx_t_7); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7); + __Pyx_INCREF(__pyx_int_3); + __Pyx_GIVEREF(__pyx_int_3); + PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_3); + __pyx_t_7 = 0; + __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_1); + __pyx_t_1 = 0; + __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_float32); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_7, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = ((PyArrayObject *)__pyx_t_3); + { + __Pyx_BufFmt_StackElem __pyx_stack[1]; + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_velocites.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__Pyx_TypeInfo_nn_real, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + __pyx_v_velocites = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_velocites.rcbuffer->pybuffer.buf = NULL; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } else {__pyx_pybuffernd_velocites.diminfo[0].strides = __pyx_pybuffernd_velocites.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_velocites.diminfo[0].shape = __pyx_pybuffernd_velocites.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_velocites.diminfo[1].strides = __pyx_pybuffernd_velocites.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_velocites.diminfo[1].shape = __pyx_pybuffernd_velocites.rcbuffer->pybuffer.shape[1]; + } + } + __pyx_t_9 = 0; + __pyx_v_velocites = ((PyArrayObject *)__pyx_t_3); + __pyx_t_3 = 0; + + /* "pygmx/tpxio.pyx":125 + * + * return_code = read_tpx( + * fname, # <<<<<<<<<<<<<< + * &record, + * box, + */ + __pyx_t_5 = __Pyx_PyObject_AsString(__pyx_v_fname); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tpxio.pyx":124 + * cdef np.ndarray[real, ndim=2] velocites = np.empty((natoms,3), dtype=np.float32) + * + * return_code = read_tpx( # <<<<<<<<<<<<<< + * fname, + * &record, + */ + __pyx_v_return_code = read_tpx(((char *)__pyx_t_5), (&__pyx_v_record), __pyx_v_box, (&__pyx_v_natoms), ((rvec *)__pyx_v_coordinates->data), ((rvec *)__pyx_v_velocites->data), (&__pyx_v_topology)); + + /* "pygmx/tpxio.pyx":133 + * &topology + * ) + * for i in range(tpx.ngtc+2): # <<<<<<<<<<<<<< + * print(i) + * print(topology.name[i]) + */ + __pyx_t_10 = (__pyx_v_tpx.ngtc + 2); + for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) { + __pyx_v_i = __pyx_t_11; + + /* "pygmx/tpxio.pyx":134 + * ) + * for i in range(tpx.ngtc+2): + * print(i) # <<<<<<<<<<<<<< + * print(topology.name[i]) + * + */ + __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_i); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_PrintOne(0, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pygmx/tpxio.pyx":135 + * for i in range(tpx.ngtc+2): + * print(i) + * print(topology.name[i]) # <<<<<<<<<<<<<< + * + * print([record.opts.ref_t[i] for i in range(record.opts.ngtc)]) + */ + __pyx_t_3 = __Pyx_PyUnicode_FromString((__pyx_v_topology.name[__pyx_v_i])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_PrintOne(0, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + } + + /* "pygmx/tpxio.pyx":137 + * print(topology.name[i]) + * + * print([record.opts.ref_t[i] for i in range(record.opts.ngtc)]) # <<<<<<<<<<<<<< + */ + __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_6 = __pyx_v_record.opts.ngtc; + for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_6; __pyx_t_10+=1) { + __pyx_v_i = __pyx_t_10; + __pyx_t_1 = PyFloat_FromDouble((__pyx_v_record.opts.ref_t[__pyx_v_i])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (unlikely(__Pyx_ListComp_Append(__pyx_t_3, (PyObject*)__pyx_t_1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + } + if (__Pyx_PrintOne(0, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pygmx/tpxio.pyx":109 + * + * + * def load_tpx(fname): # <<<<<<<<<<<<<< + * fname = cstr(fname) + * + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_7); + { PyObject *__pyx_type, *__pyx_value, *__pyx_tb; + __Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_coordinates.rcbuffer->pybuffer); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_velocites.rcbuffer->pybuffer); + __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} + __Pyx_AddTraceback("pygmx.tpxio.load_tpx", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + goto __pyx_L2; + __pyx_L0:; + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_coordinates.rcbuffer->pybuffer); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_velocites.rcbuffer->pybuffer); + __pyx_L2:; + __Pyx_XDECREF((PyObject *)__pyx_v_coordinates); + __Pyx_XDECREF((PyObject *)__pyx_v_velocites); + __Pyx_XDECREF(__pyx_v_fname); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":197 + * # experimental exception made for __getbuffer__ and __releasebuffer__ + * # -- the details of this may change. + * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< + * # This implementation of getbuffer is geared towards Cython + * # requirements, and does not yet fullfill the PEP. + */ + +/* Python wrapper */ +static CYTHON_UNUSED int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static CYTHON_UNUSED int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__getbuffer__ (wrapper)", 0); + __pyx_r = __pyx_pf_5numpy_7ndarray___getbuffer__(((PyArrayObject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info), ((int)__pyx_v_flags)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { + int __pyx_v_copy_shape; + int __pyx_v_i; + int __pyx_v_ndim; + int __pyx_v_endian_detector; + int __pyx_v_little_endian; + int __pyx_v_t; + char *__pyx_v_f; + PyArray_Descr *__pyx_v_descr = 0; + int __pyx_v_offset; + int __pyx_v_hasfields; + int __pyx_r; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_t_4; + int __pyx_t_5; + PyObject *__pyx_t_6 = NULL; + char *__pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__getbuffer__", 0); + if (__pyx_v_info != NULL) { + __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); + __Pyx_GIVEREF(__pyx_v_info->obj); + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":203 + * # of flags + * + * if info == NULL: return # <<<<<<<<<<<<<< + * + * cdef int copy_shape, i, ndim + */ + __pyx_t_1 = ((__pyx_v_info == NULL) != 0); + if (__pyx_t_1) { + __pyx_r = 0; + goto __pyx_L0; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":206 + * + * cdef int copy_shape, i, ndim + * cdef int endian_detector = 1 # <<<<<<<<<<<<<< + * cdef bint little_endian = ((&endian_detector)[0] != 0) + * + */ + __pyx_v_endian_detector = 1; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":207 + * cdef int copy_shape, i, ndim + * cdef int endian_detector = 1 + * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< + * + * ndim = PyArray_NDIM(self) + */ + __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":209 + * cdef bint little_endian = ((&endian_detector)[0] != 0) + * + * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< + * + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + */ + __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":211 + * ndim = PyArray_NDIM(self) + * + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * copy_shape = 1 + * else: + */ + __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":212 + * + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + * copy_shape = 1 # <<<<<<<<<<<<<< + * else: + * copy_shape = 0 + */ + __pyx_v_copy_shape = 1; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":211 + * ndim = PyArray_NDIM(self) + * + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * copy_shape = 1 + * else: + */ + goto __pyx_L4; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":214 + * copy_shape = 1 + * else: + * copy_shape = 0 # <<<<<<<<<<<<<< + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) + */ + /*else*/ { + __pyx_v_copy_shape = 0; + } + __pyx_L4:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":216 + * copy_shape = 0 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") + */ + __pyx_t_2 = (((__pyx_v_flags & PyBUF_C_CONTIGUOUS) == PyBUF_C_CONTIGUOUS) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L6_bool_binop_done; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":217 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< + * raise ValueError(u"ndarray is not C contiguous") + * + */ + __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L6_bool_binop_done:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":216 + * copy_shape = 0 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") + */ + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":218 + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":216 + * copy_shape = 0 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":220 + * raise ValueError(u"ndarray is not C contiguous") + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") + */ + __pyx_t_2 = (((__pyx_v_flags & PyBUF_F_CONTIGUOUS) == PyBUF_F_CONTIGUOUS) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L9_bool_binop_done; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":221 + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< + * raise ValueError(u"ndarray is not Fortran contiguous") + * + */ + __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L9_bool_binop_done:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":220 + * raise ValueError(u"ndarray is not C contiguous") + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") + */ + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":222 + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< + * + * info.buf = PyArray_DATA(self) + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":220 + * raise ValueError(u"ndarray is not C contiguous") + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":224 + * raise ValueError(u"ndarray is not Fortran contiguous") + * + * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< + * info.ndim = ndim + * if copy_shape: + */ + __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":225 + * + * info.buf = PyArray_DATA(self) + * info.ndim = ndim # <<<<<<<<<<<<<< + * if copy_shape: + * # Allocate new buffer for strides and shape info. + */ + __pyx_v_info->ndim = __pyx_v_ndim; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":226 + * info.buf = PyArray_DATA(self) + * info.ndim = ndim + * if copy_shape: # <<<<<<<<<<<<<< + * # Allocate new buffer for strides and shape info. + * # This is allocated as one block, strides first. + */ + __pyx_t_1 = (__pyx_v_copy_shape != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":229 + * # Allocate new buffer for strides and shape info. + * # This is allocated as one block, strides first. + * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) # <<<<<<<<<<<<<< + * info.shape = info.strides + ndim + * for i in range(ndim): + */ + __pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2))); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":230 + * # This is allocated as one block, strides first. + * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) + * info.shape = info.strides + ndim # <<<<<<<<<<<<<< + * for i in range(ndim): + * info.strides[i] = PyArray_STRIDES(self)[i] + */ + __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":231 + * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) + * info.shape = info.strides + ndim + * for i in range(ndim): # <<<<<<<<<<<<<< + * info.strides[i] = PyArray_STRIDES(self)[i] + * info.shape[i] = PyArray_DIMS(self)[i] + */ + __pyx_t_4 = __pyx_v_ndim; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":232 + * info.shape = info.strides + ndim + * for i in range(ndim): + * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< + * info.shape[i] = PyArray_DIMS(self)[i] + * else: + */ + (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":233 + * for i in range(ndim): + * info.strides[i] = PyArray_STRIDES(self)[i] + * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< + * else: + * info.strides = PyArray_STRIDES(self) + */ + (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":226 + * info.buf = PyArray_DATA(self) + * info.ndim = ndim + * if copy_shape: # <<<<<<<<<<<<<< + * # Allocate new buffer for strides and shape info. + * # This is allocated as one block, strides first. + */ + goto __pyx_L11; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":235 + * info.shape[i] = PyArray_DIMS(self)[i] + * else: + * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< + * info.shape = PyArray_DIMS(self) + * info.suboffsets = NULL + */ + /*else*/ { + __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":236 + * else: + * info.strides = PyArray_STRIDES(self) + * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< + * info.suboffsets = NULL + * info.itemsize = PyArray_ITEMSIZE(self) + */ + __pyx_v_info->shape = ((Py_ssize_t *)PyArray_DIMS(__pyx_v_self)); + } + __pyx_L11:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":237 + * info.strides = PyArray_STRIDES(self) + * info.shape = PyArray_DIMS(self) + * info.suboffsets = NULL # <<<<<<<<<<<<<< + * info.itemsize = PyArray_ITEMSIZE(self) + * info.readonly = not PyArray_ISWRITEABLE(self) + */ + __pyx_v_info->suboffsets = NULL; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":238 + * info.shape = PyArray_DIMS(self) + * info.suboffsets = NULL + * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< + * info.readonly = not PyArray_ISWRITEABLE(self) + * + */ + __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":239 + * info.suboffsets = NULL + * info.itemsize = PyArray_ITEMSIZE(self) + * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< + * + * cdef int t + */ + __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":242 + * + * cdef int t + * cdef char* f = NULL # <<<<<<<<<<<<<< + * cdef dtype descr = self.descr + * cdef int offset + */ + __pyx_v_f = NULL; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":243 + * cdef int t + * cdef char* f = NULL + * cdef dtype descr = self.descr # <<<<<<<<<<<<<< + * cdef int offset + * + */ + __pyx_t_3 = ((PyObject *)__pyx_v_self->descr); + __Pyx_INCREF(__pyx_t_3); + __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); + __pyx_t_3 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":246 + * cdef int offset + * + * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< + * + * if not hasfields and not copy_shape: + */ + __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":248 + * cdef bint hasfields = PyDataType_HASFIELDS(descr) + * + * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< + * # do not call releasebuffer + * info.obj = None + */ + __pyx_t_2 = ((!(__pyx_v_hasfields != 0)) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L15_bool_binop_done; + } + __pyx_t_2 = ((!(__pyx_v_copy_shape != 0)) != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L15_bool_binop_done:; + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":250 + * if not hasfields and not copy_shape: + * # do not call releasebuffer + * info.obj = None # <<<<<<<<<<<<<< + * else: + * # need to call releasebuffer + */ + __Pyx_INCREF(Py_None); + __Pyx_GIVEREF(Py_None); + __Pyx_GOTREF(__pyx_v_info->obj); + __Pyx_DECREF(__pyx_v_info->obj); + __pyx_v_info->obj = Py_None; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":248 + * cdef bint hasfields = PyDataType_HASFIELDS(descr) + * + * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< + * # do not call releasebuffer + * info.obj = None + */ + goto __pyx_L14; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":253 + * else: + * # need to call releasebuffer + * info.obj = self # <<<<<<<<<<<<<< + * + * if not hasfields: + */ + /*else*/ { + __Pyx_INCREF(((PyObject *)__pyx_v_self)); + __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); + __Pyx_GOTREF(__pyx_v_info->obj); + __Pyx_DECREF(__pyx_v_info->obj); + __pyx_v_info->obj = ((PyObject *)__pyx_v_self); + } + __pyx_L14:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":255 + * info.obj = self + * + * if not hasfields: # <<<<<<<<<<<<<< + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or + */ + __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":256 + * + * if not hasfields: + * t = descr.type_num # <<<<<<<<<<<<<< + * if ((descr.byteorder == c'>' and little_endian) or + * (descr.byteorder == c'<' and not little_endian)): + */ + __pyx_t_4 = __pyx_v_descr->type_num; + __pyx_v_t = __pyx_t_4; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":257 + * if not hasfields: + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + __pyx_t_2 = ((__pyx_v_descr->byteorder == '>') != 0); + if (!__pyx_t_2) { + goto __pyx_L20_next_or; + } else { + } + __pyx_t_2 = (__pyx_v_little_endian != 0); + if (!__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L19_bool_binop_done; + } + __pyx_L20_next_or:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":258 + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or + * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< + * raise ValueError(u"Non-native byte order not supported") + * if t == NPY_BYTE: f = "b" + */ + __pyx_t_2 = ((__pyx_v_descr->byteorder == '<') != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L19_bool_binop_done; + } + __pyx_t_2 = ((!(__pyx_v_little_endian != 0)) != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L19_bool_binop_done:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":257 + * if not hasfields: + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":259 + * if ((descr.byteorder == c'>' and little_endian) or + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< + * if t == NPY_BYTE: f = "b" + * elif t == NPY_UBYTE: f = "B" + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":257 + * if not hasfields: + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":260 + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< + * elif t == NPY_UBYTE: f = "B" + * elif t == NPY_SHORT: f = "h" + */ + switch (__pyx_v_t) { + case NPY_BYTE: + __pyx_v_f = __pyx_k_b; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":261 + * raise ValueError(u"Non-native byte order not supported") + * if t == NPY_BYTE: f = "b" + * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< + * elif t == NPY_SHORT: f = "h" + * elif t == NPY_USHORT: f = "H" + */ + case NPY_UBYTE: + __pyx_v_f = __pyx_k_B; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":262 + * if t == NPY_BYTE: f = "b" + * elif t == NPY_UBYTE: f = "B" + * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< + * elif t == NPY_USHORT: f = "H" + * elif t == NPY_INT: f = "i" + */ + case NPY_SHORT: + __pyx_v_f = __pyx_k_h; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":263 + * elif t == NPY_UBYTE: f = "B" + * elif t == NPY_SHORT: f = "h" + * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< + * elif t == NPY_INT: f = "i" + * elif t == NPY_UINT: f = "I" + */ + case NPY_USHORT: + __pyx_v_f = __pyx_k_H; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":264 + * elif t == NPY_SHORT: f = "h" + * elif t == NPY_USHORT: f = "H" + * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< + * elif t == NPY_UINT: f = "I" + * elif t == NPY_LONG: f = "l" + */ + case NPY_INT: + __pyx_v_f = __pyx_k_i; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":265 + * elif t == NPY_USHORT: f = "H" + * elif t == NPY_INT: f = "i" + * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< + * elif t == NPY_LONG: f = "l" + * elif t == NPY_ULONG: f = "L" + */ + case NPY_UINT: + __pyx_v_f = __pyx_k_I; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":266 + * elif t == NPY_INT: f = "i" + * elif t == NPY_UINT: f = "I" + * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< + * elif t == NPY_ULONG: f = "L" + * elif t == NPY_LONGLONG: f = "q" + */ + case NPY_LONG: + __pyx_v_f = __pyx_k_l; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":267 + * elif t == NPY_UINT: f = "I" + * elif t == NPY_LONG: f = "l" + * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< + * elif t == NPY_LONGLONG: f = "q" + * elif t == NPY_ULONGLONG: f = "Q" + */ + case NPY_ULONG: + __pyx_v_f = __pyx_k_L; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":268 + * elif t == NPY_LONG: f = "l" + * elif t == NPY_ULONG: f = "L" + * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< + * elif t == NPY_ULONGLONG: f = "Q" + * elif t == NPY_FLOAT: f = "f" + */ + case NPY_LONGLONG: + __pyx_v_f = __pyx_k_q; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":269 + * elif t == NPY_ULONG: f = "L" + * elif t == NPY_LONGLONG: f = "q" + * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< + * elif t == NPY_FLOAT: f = "f" + * elif t == NPY_DOUBLE: f = "d" + */ + case NPY_ULONGLONG: + __pyx_v_f = __pyx_k_Q; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":270 + * elif t == NPY_LONGLONG: f = "q" + * elif t == NPY_ULONGLONG: f = "Q" + * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< + * elif t == NPY_DOUBLE: f = "d" + * elif t == NPY_LONGDOUBLE: f = "g" + */ + case NPY_FLOAT: + __pyx_v_f = __pyx_k_f; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":271 + * elif t == NPY_ULONGLONG: f = "Q" + * elif t == NPY_FLOAT: f = "f" + * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< + * elif t == NPY_LONGDOUBLE: f = "g" + * elif t == NPY_CFLOAT: f = "Zf" + */ + case NPY_DOUBLE: + __pyx_v_f = __pyx_k_d; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":272 + * elif t == NPY_FLOAT: f = "f" + * elif t == NPY_DOUBLE: f = "d" + * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< + * elif t == NPY_CFLOAT: f = "Zf" + * elif t == NPY_CDOUBLE: f = "Zd" + */ + case NPY_LONGDOUBLE: + __pyx_v_f = __pyx_k_g; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":273 + * elif t == NPY_DOUBLE: f = "d" + * elif t == NPY_LONGDOUBLE: f = "g" + * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< + * elif t == NPY_CDOUBLE: f = "Zd" + * elif t == NPY_CLONGDOUBLE: f = "Zg" + */ + case NPY_CFLOAT: + __pyx_v_f = __pyx_k_Zf; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":274 + * elif t == NPY_LONGDOUBLE: f = "g" + * elif t == NPY_CFLOAT: f = "Zf" + * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< + * elif t == NPY_CLONGDOUBLE: f = "Zg" + * elif t == NPY_OBJECT: f = "O" + */ + case NPY_CDOUBLE: + __pyx_v_f = __pyx_k_Zd; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":275 + * elif t == NPY_CFLOAT: f = "Zf" + * elif t == NPY_CDOUBLE: f = "Zd" + * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< + * elif t == NPY_OBJECT: f = "O" + * else: + */ + case NPY_CLONGDOUBLE: + __pyx_v_f = __pyx_k_Zg; + break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":276 + * elif t == NPY_CDOUBLE: f = "Zd" + * elif t == NPY_CLONGDOUBLE: f = "Zg" + * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + */ + case NPY_OBJECT: + __pyx_v_f = __pyx_k_O; + break; + default: + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":278 + * elif t == NPY_OBJECT: f = "O" + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< + * info.format = f + * return + */ + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_6 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_GIVEREF(__pyx_t_6); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_6); + __pyx_t_6 = 0; + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_6, 0, 0, 0); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + break; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":279 + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + * info.format = f # <<<<<<<<<<<<<< + * return + * else: + */ + __pyx_v_info->format = __pyx_v_f; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":280 + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + * info.format = f + * return # <<<<<<<<<<<<<< + * else: + * info.format = stdlib.malloc(_buffer_format_string_len) + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":255 + * info.obj = self + * + * if not hasfields: # <<<<<<<<<<<<<< + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":282 + * return + * else: + * info.format = stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< + * info.format[0] = c'^' # Native data types, manual alignment + * offset = 0 + */ + /*else*/ { + __pyx_v_info->format = ((char *)malloc(0xFF)); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":283 + * else: + * info.format = stdlib.malloc(_buffer_format_string_len) + * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< + * offset = 0 + * f = _util_dtypestring(descr, info.format + 1, + */ + (__pyx_v_info->format[0]) = '^'; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":284 + * info.format = stdlib.malloc(_buffer_format_string_len) + * info.format[0] = c'^' # Native data types, manual alignment + * offset = 0 # <<<<<<<<<<<<<< + * f = _util_dtypestring(descr, info.format + 1, + * info.format + _buffer_format_string_len, + */ + __pyx_v_offset = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":285 + * info.format[0] = c'^' # Native data types, manual alignment + * offset = 0 + * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< + * info.format + _buffer_format_string_len, + * &offset) + */ + __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_f = __pyx_t_7; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":288 + * info.format + _buffer_format_string_len, + * &offset) + * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< + * + * def __releasebuffer__(ndarray self, Py_buffer* info): + */ + (__pyx_v_f[0]) = '\x00'; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":197 + * # experimental exception made for __getbuffer__ and __releasebuffer__ + * # -- the details of this may change. + * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< + * # This implementation of getbuffer is geared towards Cython + * # requirements, and does not yet fullfill the PEP. + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_AddTraceback("numpy.ndarray.__getbuffer__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + if (__pyx_v_info != NULL && __pyx_v_info->obj != NULL) { + __Pyx_GOTREF(__pyx_v_info->obj); + __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = NULL; + } + goto __pyx_L2; + __pyx_L0:; + if (__pyx_v_info != NULL && __pyx_v_info->obj == Py_None) { + __Pyx_GOTREF(Py_None); + __Pyx_DECREF(Py_None); __pyx_v_info->obj = NULL; + } + __pyx_L2:; + __Pyx_XDECREF((PyObject *)__pyx_v_descr); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":290 + * f[0] = c'\0' # Terminate format string + * + * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) + */ + +/* Python wrapper */ +static CYTHON_UNUSED void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/ +static CYTHON_UNUSED void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__releasebuffer__ (wrapper)", 0); + __pyx_pf_5numpy_7ndarray_2__releasebuffer__(((PyArrayObject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info) { + __Pyx_RefNannyDeclarations + int __pyx_t_1; + __Pyx_RefNannySetupContext("__releasebuffer__", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":291 + * + * def __releasebuffer__(ndarray self, Py_buffer* info): + * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + */ + __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":292 + * def __releasebuffer__(ndarray self, Py_buffer* info): + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) # <<<<<<<<<<<<<< + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + * stdlib.free(info.strides) + */ + free(__pyx_v_info->format); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":291 + * + * def __releasebuffer__(ndarray self, Py_buffer* info): + * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":293 + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * stdlib.free(info.strides) + * # info.shape was stored after info.strides in the same block + */ + __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":294 + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + * stdlib.free(info.strides) # <<<<<<<<<<<<<< + * # info.shape was stored after info.strides in the same block + * + */ + free(__pyx_v_info->strides); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":293 + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * stdlib.free(info.strides) + * # info.shape was stored after info.strides in the same block + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":290 + * f[0] = c'\0' # Terminate format string + * + * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) + */ + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":770 + * ctypedef npy_cdouble complex_t + * + * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(1, a) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":771 + * + * cdef inline object PyArray_MultiIterNew1(a): + * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew2(a, b): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":770 + * ctypedef npy_cdouble complex_t + * + * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(1, a) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew1", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":773 + * return PyArray_MultiIterNew(1, a) + * + * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(2, a, b) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":774 + * + * cdef inline object PyArray_MultiIterNew2(a, b): + * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew3(a, b, c): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(2, ((void *)__pyx_v_a), ((void *)__pyx_v_b)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":773 + * return PyArray_MultiIterNew(1, a) + * + * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(2, a, b) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew2", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":776 + * return PyArray_MultiIterNew(2, a, b) + * + * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(3, a, b, c) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":777 + * + * cdef inline object PyArray_MultiIterNew3(a, b, c): + * return PyArray_MultiIterNew(3, a, b, c) # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew4(a, b, c, d): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(3, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":776 + * return PyArray_MultiIterNew(2, a, b) + * + * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(3, a, b, c) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew3", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":779 + * return PyArray_MultiIterNew(3, a, b, c) + * + * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(4, a, b, c, d) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":780 + * + * cdef inline object PyArray_MultiIterNew4(a, b, c, d): + * return PyArray_MultiIterNew(4, a, b, c, d) # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(4, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":779 + * return PyArray_MultiIterNew(3, a, b, c) + * + * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(4, a, b, c, d) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew4", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":782 + * return PyArray_MultiIterNew(4, a, b, c, d) + * + * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(5, a, b, c, d, e) + * + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":783 + * + * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): + * return PyArray_MultiIterNew(5, a, b, c, d, e) # <<<<<<<<<<<<<< + * + * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyArray_MultiIterNew(5, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d), ((void *)__pyx_v_e)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":782 + * return PyArray_MultiIterNew(4, a, b, c, d) + * + * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< + * return PyArray_MultiIterNew(5, a, b, c, d, e) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("numpy.PyArray_MultiIterNew5", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":785 + * return PyArray_MultiIterNew(5, a, b, c, d, e) + * + * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< + * # Recursive utility function used in __getbuffer__ to get format + * # string. The new location in the format string is returned. + */ + +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx_v_descr, char *__pyx_v_f, char *__pyx_v_end, int *__pyx_v_offset) { + PyArray_Descr *__pyx_v_child = 0; + int __pyx_v_endian_detector; + int __pyx_v_little_endian; + PyObject *__pyx_v_fields = 0; + PyObject *__pyx_v_childname = NULL; + PyObject *__pyx_v_new_offset = NULL; + PyObject *__pyx_v_t = NULL; + char *__pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + Py_ssize_t __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_t_5; + int __pyx_t_6; + int __pyx_t_7; + long __pyx_t_8; + char *__pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("_util_dtypestring", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":790 + * + * cdef dtype child + * cdef int endian_detector = 1 # <<<<<<<<<<<<<< + * cdef bint little_endian = ((&endian_detector)[0] != 0) + * cdef tuple fields + */ + __pyx_v_endian_detector = 1; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":791 + * cdef dtype child + * cdef int endian_detector = 1 + * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< + * cdef tuple fields + * + */ + __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":794 + * cdef tuple fields + * + * for childname in descr.names: # <<<<<<<<<<<<<< + * fields = descr.fields[childname] + * child, new_offset = fields + */ + if (unlikely(__pyx_v_descr->names == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; + for (;;) { + if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + #endif + __Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3); + __pyx_t_3 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":795 + * + * for childname in descr.names: + * fields = descr.fields[childname] # <<<<<<<<<<<<<< + * child, new_offset = fields + * + */ + if (unlikely(__pyx_v_descr->fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __Pyx_GOTREF(__pyx_t_3); + if (!(likely(PyTuple_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "tuple", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); + __pyx_t_3 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":796 + * for childname in descr.names: + * fields = descr.fields[childname] + * child, new_offset = fields # <<<<<<<<<<<<<< + * + * if (end - f) - (new_offset - offset[0]) < 15: + */ + if (likely(__pyx_v_fields != Py_None)) { + PyObject* sequence = __pyx_v_fields; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_4 = PyTuple_GET_ITEM(sequence, 1); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(__pyx_t_4); + #else + __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + #endif + } else { + __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_dtype))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_XDECREF_SET(__pyx_v_child, ((PyArray_Descr *)__pyx_t_3)); + __pyx_t_3 = 0; + __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); + __pyx_t_4 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":798 + * child, new_offset = fields + * + * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + */ + __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyNumber_Subtract(__pyx_v_new_offset, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); + if (__pyx_t_6) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":799 + * + * if (end - f) - (new_offset - offset[0]) < 15: + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< + * + * if ((child.byteorder == c'>' and little_endian) or + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":798 + * child, new_offset = fields + * + * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":801 + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + __pyx_t_7 = ((__pyx_v_child->byteorder == '>') != 0); + if (!__pyx_t_7) { + goto __pyx_L8_next_or; + } else { + } + __pyx_t_7 = (__pyx_v_little_endian != 0); + if (!__pyx_t_7) { + } else { + __pyx_t_6 = __pyx_t_7; + goto __pyx_L7_bool_binop_done; + } + __pyx_L8_next_or:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":802 + * + * if ((child.byteorder == c'>' and little_endian) or + * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< + * raise ValueError(u"Non-native byte order not supported") + * # One could encode it in the format string and have Cython + */ + __pyx_t_7 = ((__pyx_v_child->byteorder == '<') != 0); + if (__pyx_t_7) { + } else { + __pyx_t_6 = __pyx_t_7; + goto __pyx_L7_bool_binop_done; + } + __pyx_t_7 = ((!(__pyx_v_little_endian != 0)) != 0); + __pyx_t_6 = __pyx_t_7; + __pyx_L7_bool_binop_done:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":801 + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + if (__pyx_t_6) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":803 + * if ((child.byteorder == c'>' and little_endian) or + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< + * # One could encode it in the format string and have Cython + * # complain instead, BUT: < and > in format strings also imply + */ + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":801 + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":813 + * + * # Output padding bytes + * while offset[0] < new_offset: # <<<<<<<<<<<<<< + * f[0] = 120 # "x"; pad byte + * f += 1 + */ + while (1) { + __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_v_new_offset, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (!__pyx_t_6) break; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":814 + * # Output padding bytes + * while offset[0] < new_offset: + * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< + * f += 1 + * offset[0] += 1 + */ + (__pyx_v_f[0]) = 0x78; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":815 + * while offset[0] < new_offset: + * f[0] = 120 # "x"; pad byte + * f += 1 # <<<<<<<<<<<<<< + * offset[0] += 1 + * + */ + __pyx_v_f = (__pyx_v_f + 1); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":816 + * f[0] = 120 # "x"; pad byte + * f += 1 + * offset[0] += 1 # <<<<<<<<<<<<<< + * + * offset[0] += child.itemsize + */ + __pyx_t_8 = 0; + (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":818 + * offset[0] += 1 + * + * offset[0] += child.itemsize # <<<<<<<<<<<<<< + * + * if not PyDataType_HASFIELDS(child): + */ + __pyx_t_8 = 0; + (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":820 + * offset[0] += child.itemsize + * + * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< + * t = child.type_num + * if end - f < 5: + */ + __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); + if (__pyx_t_6) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":821 + * + * if not PyDataType_HASFIELDS(child): + * t = child.type_num # <<<<<<<<<<<<<< + * if end - f < 5: + * raise RuntimeError(u"Format string allocated too short.") + */ + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_child->type_num); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); + __pyx_t_4 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":822 + * if not PyDataType_HASFIELDS(child): + * t = child.type_num + * if end - f < 5: # <<<<<<<<<<<<<< + * raise RuntimeError(u"Format string allocated too short.") + * + */ + __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); + if (__pyx_t_6) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":823 + * t = child.type_num + * if end - f < 5: + * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< + * + * # Until ticket #99 is fixed, use integers to avoid warnings + */ + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_Raise(__pyx_t_4, 0, 0, 0); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":822 + * if not PyDataType_HASFIELDS(child): + * t = child.type_num + * if end - f < 5: # <<<<<<<<<<<<<< + * raise RuntimeError(u"Format string allocated too short.") + * + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":826 + * + * # Until ticket #99 is fixed, use integers to avoid warnings + * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< + * elif t == NPY_UBYTE: f[0] = 66 #"B" + * elif t == NPY_SHORT: f[0] = 104 #"h" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_BYTE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 98; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":827 + * # Until ticket #99 is fixed, use integers to avoid warnings + * if t == NPY_BYTE: f[0] = 98 #"b" + * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< + * elif t == NPY_SHORT: f[0] = 104 #"h" + * elif t == NPY_USHORT: f[0] = 72 #"H" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UBYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 66; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":828 + * if t == NPY_BYTE: f[0] = 98 #"b" + * elif t == NPY_UBYTE: f[0] = 66 #"B" + * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< + * elif t == NPY_USHORT: f[0] = 72 #"H" + * elif t == NPY_INT: f[0] = 105 #"i" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_SHORT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x68; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":829 + * elif t == NPY_UBYTE: f[0] = 66 #"B" + * elif t == NPY_SHORT: f[0] = 104 #"h" + * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< + * elif t == NPY_INT: f[0] = 105 #"i" + * elif t == NPY_UINT: f[0] = 73 #"I" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_USHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 72; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":830 + * elif t == NPY_SHORT: f[0] = 104 #"h" + * elif t == NPY_USHORT: f[0] = 72 #"H" + * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< + * elif t == NPY_UINT: f[0] = 73 #"I" + * elif t == NPY_LONG: f[0] = 108 #"l" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_INT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x69; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":831 + * elif t == NPY_USHORT: f[0] = 72 #"H" + * elif t == NPY_INT: f[0] = 105 #"i" + * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< + * elif t == NPY_LONG: f[0] = 108 #"l" + * elif t == NPY_ULONG: f[0] = 76 #"L" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UINT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 73; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":832 + * elif t == NPY_INT: f[0] = 105 #"i" + * elif t == NPY_UINT: f[0] = 73 #"I" + * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< + * elif t == NPY_ULONG: f[0] = 76 #"L" + * elif t == NPY_LONGLONG: f[0] = 113 #"q" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x6C; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":833 + * elif t == NPY_UINT: f[0] = 73 #"I" + * elif t == NPY_LONG: f[0] = 108 #"l" + * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< + * elif t == NPY_LONGLONG: f[0] = 113 #"q" + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_ULONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 76; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":834 + * elif t == NPY_LONG: f[0] = 108 #"l" + * elif t == NPY_ULONG: f[0] = 76 #"L" + * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" + * elif t == NPY_FLOAT: f[0] = 102 #"f" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONGLONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x71; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":835 + * elif t == NPY_ULONG: f[0] = 76 #"L" + * elif t == NPY_LONGLONG: f[0] = 113 #"q" + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< + * elif t == NPY_FLOAT: f[0] = 102 #"f" + * elif t == NPY_DOUBLE: f[0] = 100 #"d" + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_ULONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 81; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":836 + * elif t == NPY_LONGLONG: f[0] = 113 #"q" + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" + * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< + * elif t == NPY_DOUBLE: f[0] = 100 #"d" + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_FLOAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x66; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":837 + * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" + * elif t == NPY_FLOAT: f[0] = 102 #"f" + * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_DOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x64; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":838 + * elif t == NPY_FLOAT: f[0] = 102 #"f" + * elif t == NPY_DOUBLE: f[0] = 100 #"d" + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 0x67; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":839 + * elif t == NPY_DOUBLE: f[0] = 100 #"d" + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd + * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CFLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 90; + (__pyx_v_f[1]) = 0x66; + __pyx_v_f = (__pyx_v_f + 1); + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":840 + * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< + * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg + * elif t == NPY_OBJECT: f[0] = 79 #"O" + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CDOUBLE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 90; + (__pyx_v_f[1]) = 0x64; + __pyx_v_f = (__pyx_v_f + 1); + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":841 + * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd + * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< + * elif t == NPY_OBJECT: f[0] = 79 #"O" + * else: + */ + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 90; + (__pyx_v_f[1]) = 0x67; + __pyx_v_f = (__pyx_v_f + 1); + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":842 + * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd + * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg + * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + */ + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_OBJECT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_6) { + (__pyx_v_f[0]) = 79; + goto __pyx_L15; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":844 + * elif t == NPY_OBJECT: f[0] = 79 #"O" + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< + * f += 1 + * else: + */ + /*else*/ { + __pyx_t_3 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); + __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_L15:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":845 + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + * f += 1 # <<<<<<<<<<<<<< + * else: + * # Cython ignores struct boundary information ("T{...}"), + */ + __pyx_v_f = (__pyx_v_f + 1); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":820 + * offset[0] += child.itemsize + * + * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< + * t = child.type_num + * if end - f < 5: + */ + goto __pyx_L13; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":849 + * # Cython ignores struct boundary information ("T{...}"), + * # so don't output it + * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< + * return f + * + */ + /*else*/ { + __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_f = __pyx_t_9; + } + __pyx_L13:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":794 + * cdef tuple fields + * + * for childname in descr.names: # <<<<<<<<<<<<<< + * fields = descr.fields[childname] + * child, new_offset = fields + */ + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":850 + * # so don't output it + * f = _util_dtypestring(child, f, end, offset) + * return f # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = __pyx_v_f; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":785 + * return PyArray_MultiIterNew(5, a, b, c, d, e) + * + * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< + * # Recursive utility function used in __getbuffer__ to get format + * # string. The new location in the format string is returned. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("numpy._util_dtypestring", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_child); + __Pyx_XDECREF(__pyx_v_fields); + __Pyx_XDECREF(__pyx_v_childname); + __Pyx_XDECREF(__pyx_v_new_offset); + __Pyx_XDECREF(__pyx_v_t); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":966 + * + * + * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< + * cdef PyObject* baseptr + * if base is None: + */ + +static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObject *__pyx_v_base) { + PyObject *__pyx_v_baseptr; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + __Pyx_RefNannySetupContext("set_array_base", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":968 + * cdef inline void set_array_base(ndarray arr, object base): + * cdef PyObject* baseptr + * if base is None: # <<<<<<<<<<<<<< + * baseptr = NULL + * else: + */ + __pyx_t_1 = (__pyx_v_base == Py_None); + __pyx_t_2 = (__pyx_t_1 != 0); + if (__pyx_t_2) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":969 + * cdef PyObject* baseptr + * if base is None: + * baseptr = NULL # <<<<<<<<<<<<<< + * else: + * Py_INCREF(base) # important to do this before decref below! + */ + __pyx_v_baseptr = NULL; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":968 + * cdef inline void set_array_base(ndarray arr, object base): + * cdef PyObject* baseptr + * if base is None: # <<<<<<<<<<<<<< + * baseptr = NULL + * else: + */ + goto __pyx_L3; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":971 + * baseptr = NULL + * else: + * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< + * baseptr = base + * Py_XDECREF(arr.base) + */ + /*else*/ { + Py_INCREF(__pyx_v_base); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":972 + * else: + * Py_INCREF(base) # important to do this before decref below! + * baseptr = base # <<<<<<<<<<<<<< + * Py_XDECREF(arr.base) + * arr.base = baseptr + */ + __pyx_v_baseptr = ((PyObject *)__pyx_v_base); + } + __pyx_L3:; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":973 + * Py_INCREF(base) # important to do this before decref below! + * baseptr = base + * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< + * arr.base = baseptr + * + */ + Py_XDECREF(__pyx_v_arr->base); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":974 + * baseptr = base + * Py_XDECREF(arr.base) + * arr.base = baseptr # <<<<<<<<<<<<<< + * + * cdef inline object get_array_base(ndarray arr): + */ + __pyx_v_arr->base = __pyx_v_baseptr; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":966 + * + * + * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< + * cdef PyObject* baseptr + * if base is None: + */ + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +/* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr + * + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None + */ + +static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + __Pyx_RefNannySetupContext("get_array_base", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":977 + * + * cdef inline object get_array_base(ndarray arr): + * if arr.base is NULL: # <<<<<<<<<<<<<< + * return None + * else: + */ + __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); + if (__pyx_t_1) { + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":978 + * cdef inline object get_array_base(ndarray arr): + * if arr.base is NULL: + * return None # <<<<<<<<<<<<<< + * else: + * return arr.base + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_None); + __pyx_r = Py_None; + goto __pyx_L0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":977 + * + * cdef inline object get_array_base(ndarray arr): + * if arr.base is NULL: # <<<<<<<<<<<<<< + * return None + * else: + */ + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":980 + * return None + * else: + * return arr.base # <<<<<<<<<<<<<< + */ + /*else*/ { + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(((PyObject *)__pyx_v_arr->base)); + __pyx_r = ((PyObject *)__pyx_v_arr->base); + goto __pyx_L0; + } + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr + * + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_tp_new_5pygmx_5tpxio_TPXWrapper(PyTypeObject *t, PyObject *a, PyObject *k) { + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + if (unlikely(__pyx_pw_5pygmx_5tpxio_10TPXWrapper_1__cinit__(o, a, k) < 0)) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_5pygmx_5tpxio_TPXWrapper(PyObject *o) { + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + (*Py_TYPE(o)->tp_free)(o); +} + +static PyObject *__pyx_getprop_5pygmx_5tpxio_10TPXWrapper_atoms(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pygmx_5tpxio_10TPXWrapper_5atoms_1__get__(o); +} + +static PyObject *__pyx_getprop_5pygmx_5tpxio_10TPXWrapper_n_atoms(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pygmx_5tpxio_10TPXWrapper_7n_atoms_1__get__(o); +} + +static PyObject *__pyx_getprop_5pygmx_5tpxio_10TPXWrapper_n_tcouple_groups(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pygmx_5tpxio_10TPXWrapper_16n_tcouple_groups_1__get__(o); +} + +static PyObject *__pyx_getprop_5pygmx_5tpxio_10TPXWrapper_n_mol(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pygmx_5tpxio_10TPXWrapper_5n_mol_1__get__(o); +} + +static PyMethodDef __pyx_methods_5pygmx_5tpxio_TPXWrapper[] = { + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_5pygmx_5tpxio_TPXWrapper[] = { + {(char *)"atoms", __pyx_getprop_5pygmx_5tpxio_10TPXWrapper_atoms, 0, 0, 0}, + {(char *)"n_atoms", __pyx_getprop_5pygmx_5tpxio_10TPXWrapper_n_atoms, 0, 0, 0}, + {(char *)"n_tcouple_groups", __pyx_getprop_5pygmx_5tpxio_10TPXWrapper_n_tcouple_groups, 0, 0, 0}, + {(char *)"n_mol", __pyx_getprop_5pygmx_5tpxio_10TPXWrapper_n_mol, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_5pygmx_5tpxio_TPXWrapper = { + PyVarObject_HEAD_INIT(0, 0) + "pygmx.tpxio.TPXWrapper", /*tp_name*/ + sizeof(struct __pyx_obj_5pygmx_5tpxio_TPXWrapper), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_5pygmx_5tpxio_TPXWrapper, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ + 0, /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_5pygmx_5tpxio_TPXWrapper, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_5pygmx_5tpxio_TPXWrapper, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_5pygmx_5tpxio_TPXWrapper, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; + +static PyMethodDef __pyx_methods[] = { + {0, 0, 0, 0} +}; + +#if PY_MAJOR_VERSION >= 3 +static struct PyModuleDef __pyx_moduledef = { + #if PY_VERSION_HEX < 0x03020000 + { PyObject_HEAD_INIT(NULL) NULL, 0, NULL }, + #else + PyModuleDef_HEAD_INIT, + #endif + "tpxio", + 0, /* m_doc */ + -1, /* m_size */ + __pyx_methods /* m_methods */, + NULL, /* m_reload */ + NULL, /* m_traverse */ + NULL, /* m_clear */ + NULL /* m_free */ +}; +#endif + +static __Pyx_StringTabEntry __pyx_string_tab[] = { + {&__pyx_kp_u_Format_string_allocated_too_shor, __pyx_k_Format_string_allocated_too_shor, sizeof(__pyx_k_Format_string_allocated_too_shor), 0, 1, 0, 0}, + {&__pyx_kp_u_Format_string_allocated_too_shor_2, __pyx_k_Format_string_allocated_too_shor_2, sizeof(__pyx_k_Format_string_allocated_too_shor_2), 0, 1, 0, 0}, + {&__pyx_kp_u_Non_native_byte_order_not_suppor, __pyx_k_Non_native_byte_order_not_suppor, sizeof(__pyx_k_Non_native_byte_order_not_suppor), 0, 1, 0, 0}, + {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1}, + {&__pyx_n_s_TPRReader, __pyx_k_TPRReader, sizeof(__pyx_k_TPRReader), 0, 0, 1, 1}, + {&__pyx_n_s_TPRReader___init, __pyx_k_TPRReader___init, sizeof(__pyx_k_TPRReader___init), 0, 0, 1, 1}, + {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, + {&__pyx_n_s_box, __pyx_k_box, sizeof(__pyx_k_box), 0, 0, 1, 1}, + {&__pyx_n_s_coordinates, __pyx_k_coordinates, sizeof(__pyx_k_coordinates), 0, 0, 1, 1}, + {&__pyx_n_s_cstr, __pyx_k_cstr, sizeof(__pyx_k_cstr), 0, 0, 1, 1}, + {&__pyx_n_s_doc, __pyx_k_doc, sizeof(__pyx_k_doc), 0, 0, 1, 1}, + {&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1}, + {&__pyx_n_s_empty, __pyx_k_empty, sizeof(__pyx_k_empty), 0, 0, 1, 1}, + {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1}, + {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1}, + {&__pyx_n_s_file, __pyx_k_file, sizeof(__pyx_k_file), 0, 0, 1, 1}, + {&__pyx_n_s_filename, __pyx_k_filename, sizeof(__pyx_k_filename), 0, 0, 1, 1}, + {&__pyx_n_s_float32, __pyx_k_float32, sizeof(__pyx_k_float32), 0, 0, 1, 1}, + {&__pyx_n_s_fname, __pyx_k_fname, sizeof(__pyx_k_fname), 0, 0, 1, 1}, + {&__pyx_kp_s_home_niels_Uni_pygmx_pygmx_tpxi, __pyx_k_home_niels_Uni_pygmx_pygmx_tpxi, sizeof(__pyx_k_home_niels_Uni_pygmx_pygmx_tpxi), 0, 0, 1, 0}, + {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1}, + {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, + {&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1}, + {&__pyx_n_s_instr, __pyx_k_instr, sizeof(__pyx_k_instr), 0, 0, 1, 1}, + {&__pyx_n_s_load_tpx, __pyx_k_load_tpx, sizeof(__pyx_k_load_tpx), 0, 0, 1, 1}, + {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, + {&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1}, + {&__pyx_n_s_module, __pyx_k_module, sizeof(__pyx_k_module), 0, 0, 1, 1}, + {&__pyx_n_s_natoms, __pyx_k_natoms, sizeof(__pyx_k_natoms), 0, 0, 1, 1}, + {&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0}, + {&__pyx_kp_u_ndarray_is_not_Fortran_contiguou, __pyx_k_ndarray_is_not_Fortran_contiguou, sizeof(__pyx_k_ndarray_is_not_Fortran_contiguou), 0, 1, 0, 0}, + {&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1}, + {&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1}, + {&__pyx_n_s_prepare, __pyx_k_prepare, sizeof(__pyx_k_prepare), 0, 0, 1, 1}, + {&__pyx_n_s_print, __pyx_k_print, sizeof(__pyx_k_print), 0, 0, 1, 1}, + {&__pyx_n_s_pygmx_tpxio, __pyx_k_pygmx_tpxio, sizeof(__pyx_k_pygmx_tpxio), 0, 0, 1, 1}, + {&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 0, 0, 1, 1}, + {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1}, + {&__pyx_n_s_record, __pyx_k_record, sizeof(__pyx_k_record), 0, 0, 1, 1}, + {&__pyx_n_s_return_code, __pyx_k_return_code, sizeof(__pyx_k_return_code), 0, 0, 1, 1}, + {&__pyx_n_s_self, __pyx_k_self, sizeof(__pyx_k_self), 0, 0, 1, 1}, + {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, + {&__pyx_n_s_topology, __pyx_k_topology, sizeof(__pyx_k_topology), 0, 0, 1, 1}, + {&__pyx_n_s_tpr, __pyx_k_tpr, sizeof(__pyx_k_tpr), 0, 0, 1, 1}, + {&__pyx_n_s_tpx, __pyx_k_tpx, sizeof(__pyx_k_tpx), 0, 0, 1, 1}, + {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0}, + {&__pyx_n_s_velocites, __pyx_k_velocites, sizeof(__pyx_k_velocites), 0, 0, 1, 1}, + {0, 0, 0, 0, 0, 0, 0} +}; +static int __Pyx_InitCachedBuiltins(void) { + __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + return 0; + __pyx_L1_error:; + return -1; +} + +static int __Pyx_InitCachedConstants(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":218 + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + */ + __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple_); + __Pyx_GIVEREF(__pyx_tuple_); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":222 + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< + * + * info.buf = PyArray_DATA(self) + */ + __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__2); + __Pyx_GIVEREF(__pyx_tuple__2); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":259 + * if ((descr.byteorder == c'>' and little_endian) or + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< + * if t == NPY_BYTE: f = "b" + * elif t == NPY_UBYTE: f = "B" + */ + __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__3); + __Pyx_GIVEREF(__pyx_tuple__3); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":799 + * + * if (end - f) - (new_offset - offset[0]) < 15: + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< + * + * if ((child.byteorder == c'>' and little_endian) or + */ + __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__4); + __Pyx_GIVEREF(__pyx_tuple__4); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":803 + * if ((child.byteorder == c'>' and little_endian) or + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< + * # One could encode it in the format string and have Cython + * # complain instead, BUT: < and > in format strings also imply + */ + __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__5); + __Pyx_GIVEREF(__pyx_tuple__5); + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":823 + * t = child.type_num + * if end - f < 5: + * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< + * + * # Until ticket #99 is fixed, use integers to avoid warnings + */ + __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__6); + __Pyx_GIVEREF(__pyx_tuple__6); + + /* "pygmx/tpxio.pyx":50 + * + * + * def cstr(instr): # <<<<<<<<<<<<<< + * if isinstance(instr, str): + * instr = instr.encode() + */ + __pyx_tuple__7 = PyTuple_Pack(1, __pyx_n_s_instr); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__7); + __Pyx_GIVEREF(__pyx_tuple__7); + __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_niels_Uni_pygmx_pygmx_tpxi, __pyx_n_s_cstr, 50, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tpxio.pyx":105 + * class TPRReader: + * + * def __init__(self, filename): # <<<<<<<<<<<<<< + * self.tpr = TPXWrapper(filename) + * + */ + __pyx_tuple__9 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_filename); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__9); + __Pyx_GIVEREF(__pyx_tuple__9); + __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_niels_Uni_pygmx_pygmx_tpxi, __pyx_n_s_init, 105, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "pygmx/tpxio.pyx":109 + * + * + * def load_tpx(fname): # <<<<<<<<<<<<<< + * fname = cstr(fname) + * + */ + __pyx_tuple__11 = PyTuple_Pack(10, __pyx_n_s_fname, __pyx_n_s_tpx, __pyx_n_s_natoms, __pyx_n_s_record, __pyx_n_s_topology, __pyx_n_s_box, __pyx_n_s_coordinates, __pyx_n_s_velocites, __pyx_n_s_return_code, __pyx_n_s_i); if (unlikely(!__pyx_tuple__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__11); + __Pyx_GIVEREF(__pyx_tuple__11); + __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(1, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_niels_Uni_pygmx_pygmx_tpxi, __pyx_n_s_load_tpx, 109, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_RefNannyFinishContext(); + return 0; + __pyx_L1_error:; + __Pyx_RefNannyFinishContext(); + return -1; +} + +static int __Pyx_InitGlobals(void) { + if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + return 0; + __pyx_L1_error:; + return -1; +} + +#if PY_MAJOR_VERSION < 3 +PyMODINIT_FUNC inittpxio(void); /*proto*/ +PyMODINIT_FUNC inittpxio(void) +#else +PyMODINIT_FUNC PyInit_tpxio(void); /*proto*/ +PyMODINIT_FUNC PyInit_tpxio(void) +#endif +{ + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannyDeclarations + #if CYTHON_REFNANNY + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny"); + if (!__Pyx_RefNanny) { + PyErr_Clear(); + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny"); + if (!__Pyx_RefNanny) + Py_FatalError("failed to import 'refnanny' module"); + } + #endif + __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_tpxio(void)", 0); + if (__Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #ifdef __Pyx_CyFunction_USED + if (__pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_FusedFunction_USED + if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_Coroutine_USED + if (__pyx_Coroutine_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_Generator_USED + if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_StopAsyncIteration_USED + if (__pyx_StopAsyncIteration_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + /*--- Library function declarations ---*/ + /*--- Threads initialization code ---*/ + #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS + #ifdef WITH_THREAD /* Python build with threading support? */ + PyEval_InitThreads(); + #endif + #endif + /*--- Module creation code ---*/ + #if PY_MAJOR_VERSION < 3 + __pyx_m = Py_InitModule4("tpxio", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); + #else + __pyx_m = PyModule_Create(&__pyx_moduledef); + #endif + if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + Py_INCREF(__pyx_d); + __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if CYTHON_COMPILING_IN_PYPY + Py_INCREF(__pyx_b); + #endif + if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + /*--- Initialize various global constants etc. ---*/ + if (__Pyx_InitGlobals() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) + if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + if (__pyx_module_is_main_pygmx__tpxio) { + if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if PY_MAJOR_VERSION >= 3 + { + PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!PyDict_GetItemString(modules, "pygmx.tpxio")) { + if (unlikely(PyDict_SetItemString(modules, "pygmx.tpxio", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + } + #endif + /*--- Builtin init code ---*/ + if (__Pyx_InitCachedBuiltins() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Constants init code ---*/ + if (__Pyx_InitCachedConstants() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Global init code ---*/ + /*--- Variable export code ---*/ + /*--- Function export code ---*/ + /*--- Type init code ---*/ + if (PyType_Ready(&__pyx_type_5pygmx_5tpxio_TPXWrapper) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_5pygmx_5tpxio_TPXWrapper.tp_print = 0; + if (PyObject_SetAttrString(__pyx_m, "TPXWrapper", (PyObject *)&__pyx_type_5pygmx_5tpxio_TPXWrapper) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pygmx_5tpxio_TPXWrapper = &__pyx_type_5pygmx_5tpxio_TPXWrapper; + /*--- Type import code ---*/ + __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", + #if CYTHON_COMPILING_IN_PYPY + sizeof(PyTypeObject), + #else + sizeof(PyHeapTypeObject), + #endif + 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Variable import code ---*/ + /*--- Function import code ---*/ + /*--- Execution code ---*/ + #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) + if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + + /* "pygmx/tpxio.pyx":6 + * # from cython cimport view + * # from array import array + * import numpy as np # <<<<<<<<<<<<<< + * cimport numpy as np + * + */ + __pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pygmx/tpxio.pyx":50 + * + * + * def cstr(instr): # <<<<<<<<<<<<<< + * if isinstance(instr, str): + * instr = instr.encode() + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pygmx_5tpxio_1cstr, NULL, __pyx_n_s_pygmx_tpxio); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_cstr, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pygmx/tpxio.pyx":103 + * + * + * class TPRReader: # <<<<<<<<<<<<<< + * + * def __init__(self, filename): + */ + __pyx_t_1 = __Pyx_Py3MetaclassPrepare((PyObject *) NULL, __pyx_empty_tuple, __pyx_n_s_TPRReader, __pyx_n_s_TPRReader, (PyObject *) NULL, __pyx_n_s_pygmx_tpxio, (PyObject *) NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + + /* "pygmx/tpxio.pyx":105 + * class TPRReader: + * + * def __init__(self, filename): # <<<<<<<<<<<<<< + * self.tpr = TPXWrapper(filename) + * + */ + __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pygmx_5tpxio_9TPRReader_1__init__, 0, __pyx_n_s_TPRReader___init, NULL, __pyx_n_s_pygmx_tpxio, __pyx_d, ((PyObject *)__pyx_codeobj__10)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + if (PyObject_SetItem(__pyx_t_1, __pyx_n_s_init, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pygmx/tpxio.pyx":103 + * + * + * class TPRReader: # <<<<<<<<<<<<<< + * + * def __init__(self, filename): + */ + __pyx_t_2 = __Pyx_Py3ClassCreate(((PyObject*)&__Pyx_DefaultClassType), __pyx_n_s_TPRReader, __pyx_empty_tuple, __pyx_t_1, NULL, 0, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_TPRReader, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pygmx/tpxio.pyx":109 + * + * + * def load_tpx(fname): # <<<<<<<<<<<<<< + * fname = cstr(fname) + * + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pygmx_5tpxio_3load_tpx, NULL, __pyx_n_s_pygmx_tpxio); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_load_tpx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pygmx/tpxio.pyx":1 + * # cython: c_string_type=unicode, c_string_encoding=utf8 # <<<<<<<<<<<<<< + * # Cython wrapper around tpxio.cpp + * + */ + __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "../../anaconda3/lib/python3.5/site-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr + * + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None + */ + + /*--- Wrapped vars code ---*/ + + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + if (__pyx_m) { + if (__pyx_d) { + __Pyx_AddTraceback("init pygmx.tpxio", __pyx_clineno, __pyx_lineno, __pyx_filename); + } + Py_DECREF(__pyx_m); __pyx_m = 0; + } else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_ImportError, "init pygmx.tpxio"); + } + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + #if PY_MAJOR_VERSION < 3 + return; + #else + return __pyx_m; + #endif +} + +/* --- Runtime support code --- */ +#if CYTHON_REFNANNY +static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { + PyObject *m = NULL, *p = NULL; + void *r = NULL; + m = PyImport_ImportModule((char *)modname); + if (!m) goto end; + p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); + if (!p) goto end; + r = PyLong_AsVoidPtr(p); +end: + Py_XDECREF(p); + Py_XDECREF(m); + return (__Pyx_RefNannyAPIStruct *)r; +} +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); + if (unlikely(!result)) { + PyErr_Format(PyExc_NameError, +#if PY_MAJOR_VERSION >= 3 + "name '%U' is not defined", name); +#else + "name '%.200s' is not defined", PyString_AS_STRING(name)); +#endif + } + return result; +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { + return __Pyx_PyObject_CallMethO(func, NULL); + } + } + return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); +} +#endif + +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + PyObject *result; +#if CYTHON_COMPILING_IN_CPYTHON + result = PyDict_GetItem(__pyx_d, name); + if (likely(result)) { + Py_INCREF(result); + } else { +#else + result = PyObject_GetItem(__pyx_d, name); + if (!result) { + PyErr_Clear(); +#endif + result = __Pyx_GetBuiltinName(name); + } + return result; +} + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { + unsigned int n = 1; + return *(unsigned char*)(&n) != 0; +} +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static CYTHON_INLINE PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} +static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { + buf->buf = NULL; + buf->obj = NULL; + buf->strides = __Pyx_zeros; + buf->shape = __Pyx_zeros; + buf->suboffsets = __Pyx_minusones; +} +static CYTHON_INLINE int __Pyx_GetBufferAndValidate( + Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, + int nd, int cast, __Pyx_BufFmt_StackElem* stack) +{ + if (obj == Py_None || obj == NULL) { + __Pyx_ZeroBuffer(buf); + return 0; + } + buf->buf = NULL; + if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; + if (buf->ndim != nd) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + nd, buf->ndim); + goto fail; + } + if (!cast) { + __Pyx_BufFmt_Context ctx; + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned)buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", + buf->itemsize, (buf->itemsize > 1) ? "s" : "", + dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); + goto fail; + } + if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; + return 0; +fail:; + __Pyx_ZeroBuffer(buf); + return -1; +} +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { + if (info->buf == NULL) return; + if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; + __Pyx_ReleaseBuffer(info); +} + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + int is_subclass = PyObject_IsSubclass(instance_class, type); + if (!is_subclass) { + instance_class = NULL; + } else if (unlikely(is_subclass == -1)) { + goto bad; + } else { + type = instance_class; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } +#if PY_VERSION_HEX >= 0x03030000 + if (cause) { +#else + if (cause && cause != Py_None) { +#endif + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { +#if CYTHON_COMPILING_IN_PYPY + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#else + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } +#endif + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { + PyObject* fake_module; + PyTypeObject* cached_type = NULL; + fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI); + if (!fake_module) return NULL; + Py_INCREF(fake_module); + cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name); + if (cached_type) { + if (!PyType_Check((PyObject*)cached_type)) { + PyErr_Format(PyExc_TypeError, + "Shared Cython type %.200s is not a type object", + type->tp_name); + goto bad; + } + if (cached_type->tp_basicsize != type->tp_basicsize) { + PyErr_Format(PyExc_TypeError, + "Shared Cython type %.200s has the wrong size, try recompiling", + type->tp_name); + goto bad; + } + } else { + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; + PyErr_Clear(); + if (PyType_Ready(type) < 0) goto bad; + if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0) + goto bad; + Py_INCREF(type); + cached_type = type; + } +done: + Py_DECREF(fake_module); + return cached_type; +bad: + Py_XDECREF(cached_type); + cached_type = NULL; + goto done; +} + +static PyObject * +__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) +{ + if (unlikely(op->func_doc == NULL)) { + if (op->func.m_ml->ml_doc) { +#if PY_MAJOR_VERSION >= 3 + op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); +#else + op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); +#endif + if (unlikely(op->func_doc == NULL)) + return NULL; + } else { + Py_INCREF(Py_None); + return Py_None; + } + } + Py_INCREF(op->func_doc); + return op->func_doc; +} +static int +__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp = op->func_doc; + if (value == NULL) { + value = Py_None; + } + Py_INCREF(value); + op->func_doc = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op) +{ + if (unlikely(op->func_name == NULL)) { +#if PY_MAJOR_VERSION >= 3 + op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); +#else + op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); +#endif + if (unlikely(op->func_name == NULL)) + return NULL; + } + Py_INCREF(op->func_name); + return op->func_name; +} +static int +__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp; +#if PY_MAJOR_VERSION >= 3 + if (unlikely(value == NULL || !PyUnicode_Check(value))) { +#else + if (unlikely(value == NULL || !PyString_Check(value))) { +#endif + PyErr_SetString(PyExc_TypeError, + "__name__ must be set to a string object"); + return -1; + } + tmp = op->func_name; + Py_INCREF(value); + op->func_name = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op) +{ + Py_INCREF(op->func_qualname); + return op->func_qualname; +} +static int +__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp; +#if PY_MAJOR_VERSION >= 3 + if (unlikely(value == NULL || !PyUnicode_Check(value))) { +#else + if (unlikely(value == NULL || !PyString_Check(value))) { +#endif + PyErr_SetString(PyExc_TypeError, + "__qualname__ must be set to a string object"); + return -1; + } + tmp = op->func_qualname; + Py_INCREF(value); + op->func_qualname = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) +{ + PyObject *self; + self = m->func_closure; + if (self == NULL) + self = Py_None; + Py_INCREF(self); + return self; +} +static PyObject * +__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op) +{ + if (unlikely(op->func_dict == NULL)) { + op->func_dict = PyDict_New(); + if (unlikely(op->func_dict == NULL)) + return NULL; + } + Py_INCREF(op->func_dict); + return op->func_dict; +} +static int +__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp; + if (unlikely(value == NULL)) { + PyErr_SetString(PyExc_TypeError, + "function's dictionary may not be deleted"); + return -1; + } + if (unlikely(!PyDict_Check(value))) { + PyErr_SetString(PyExc_TypeError, + "setting function's dictionary to a non-dict"); + return -1; + } + tmp = op->func_dict; + Py_INCREF(value); + op->func_dict = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op) +{ + Py_INCREF(op->func_globals); + return op->func_globals; +} +static PyObject * +__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op) +{ + Py_INCREF(Py_None); + return Py_None; +} +static PyObject * +__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) +{ + PyObject* result = (op->func_code) ? op->func_code : Py_None; + Py_INCREF(result); + return result; +} +static int +__Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) { + int result = 0; + PyObject *res = op->defaults_getter((PyObject *) op); + if (unlikely(!res)) + return -1; + #if CYTHON_COMPILING_IN_CPYTHON + op->defaults_tuple = PyTuple_GET_ITEM(res, 0); + Py_INCREF(op->defaults_tuple); + op->defaults_kwdict = PyTuple_GET_ITEM(res, 1); + Py_INCREF(op->defaults_kwdict); + #else + op->defaults_tuple = PySequence_ITEM(res, 0); + if (unlikely(!op->defaults_tuple)) result = -1; + else { + op->defaults_kwdict = PySequence_ITEM(res, 1); + if (unlikely(!op->defaults_kwdict)) result = -1; + } + #endif + Py_DECREF(res); + return result; +} +static int +__Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value) { + PyObject* tmp; + if (!value) { + value = Py_None; + } else if (value != Py_None && !PyTuple_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "__defaults__ must be set to a tuple object"); + return -1; + } + Py_INCREF(value); + tmp = op->defaults_tuple; + op->defaults_tuple = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) { + PyObject* result = op->defaults_tuple; + if (unlikely(!result)) { + if (op->defaults_getter) { + if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL; + result = op->defaults_tuple; + } else { + result = Py_None; + } + } + Py_INCREF(result); + return result; +} +static int +__Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value) { + PyObject* tmp; + if (!value) { + value = Py_None; + } else if (value != Py_None && !PyDict_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "__kwdefaults__ must be set to a dict object"); + return -1; + } + Py_INCREF(value); + tmp = op->defaults_kwdict; + op->defaults_kwdict = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op) { + PyObject* result = op->defaults_kwdict; + if (unlikely(!result)) { + if (op->defaults_getter) { + if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL; + result = op->defaults_kwdict; + } else { + result = Py_None; + } + } + Py_INCREF(result); + return result; +} +static int +__Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value) { + PyObject* tmp; + if (!value || value == Py_None) { + value = NULL; + } else if (!PyDict_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "__annotations__ must be set to a dict object"); + return -1; + } + Py_XINCREF(value); + tmp = op->func_annotations; + op->func_annotations = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op) { + PyObject* result = op->func_annotations; + if (unlikely(!result)) { + result = PyDict_New(); + if (unlikely(!result)) return NULL; + op->func_annotations = result; + } + Py_INCREF(result); + return result; +} +static PyGetSetDef __pyx_CyFunction_getsets[] = { + {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, + {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, + {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, + {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, + {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0}, + {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0}, + {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, + {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, + {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, + {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, + {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, + {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, + {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, + {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, + {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0}, + {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0}, + {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0}, + {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0}, + {0, 0, 0, 0, 0} +}; +static PyMemberDef __pyx_CyFunction_members[] = { + {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, + {0, 0, 0, 0, 0} +}; +static PyObject * +__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) +{ +#if PY_MAJOR_VERSION >= 3 + return PyUnicode_FromString(m->func.m_ml->ml_name); +#else + return PyString_FromString(m->func.m_ml->ml_name); +#endif +} +static PyMethodDef __pyx_CyFunction_methods[] = { + {"__reduce__", (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, + {0, 0, 0, 0} +}; +#if PY_VERSION_HEX < 0x030500A0 +#define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func_weakreflist) +#else +#define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func.m_weakreflist) +#endif +static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname, + PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { + __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); + if (op == NULL) + return NULL; + op->flags = flags; + __Pyx_CyFunction_weakreflist(op) = NULL; + op->func.m_ml = ml; + op->func.m_self = (PyObject *) op; + Py_XINCREF(closure); + op->func_closure = closure; + Py_XINCREF(module); + op->func.m_module = module; + op->func_dict = NULL; + op->func_name = NULL; + Py_INCREF(qualname); + op->func_qualname = qualname; + op->func_doc = NULL; + op->func_classobj = NULL; + op->func_globals = globals; + Py_INCREF(op->func_globals); + Py_XINCREF(code); + op->func_code = code; + op->defaults_pyobjects = 0; + op->defaults = NULL; + op->defaults_tuple = NULL; + op->defaults_kwdict = NULL; + op->defaults_getter = NULL; + op->func_annotations = NULL; + PyObject_GC_Track(op); + return (PyObject *) op; +} +static int +__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) +{ + Py_CLEAR(m->func_closure); + Py_CLEAR(m->func.m_module); + Py_CLEAR(m->func_dict); + Py_CLEAR(m->func_name); + Py_CLEAR(m->func_qualname); + Py_CLEAR(m->func_doc); + Py_CLEAR(m->func_globals); + Py_CLEAR(m->func_code); + Py_CLEAR(m->func_classobj); + Py_CLEAR(m->defaults_tuple); + Py_CLEAR(m->defaults_kwdict); + Py_CLEAR(m->func_annotations); + if (m->defaults) { + PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); + int i; + for (i = 0; i < m->defaults_pyobjects; i++) + Py_XDECREF(pydefaults[i]); + PyMem_Free(m->defaults); + m->defaults = NULL; + } + return 0; +} +static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) +{ + PyObject_GC_UnTrack(m); + if (__Pyx_CyFunction_weakreflist(m) != NULL) + PyObject_ClearWeakRefs((PyObject *) m); + __Pyx_CyFunction_clear(m); + PyObject_GC_Del(m); +} +static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) +{ + Py_VISIT(m->func_closure); + Py_VISIT(m->func.m_module); + Py_VISIT(m->func_dict); + Py_VISIT(m->func_name); + Py_VISIT(m->func_qualname); + Py_VISIT(m->func_doc); + Py_VISIT(m->func_globals); + Py_VISIT(m->func_code); + Py_VISIT(m->func_classobj); + Py_VISIT(m->defaults_tuple); + Py_VISIT(m->defaults_kwdict); + if (m->defaults) { + PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); + int i; + for (i = 0; i < m->defaults_pyobjects; i++) + Py_VISIT(pydefaults[i]); + } + return 0; +} +static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type) +{ + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) { + Py_INCREF(func); + return func; + } + if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) { + if (type == NULL) + type = (PyObject *)(Py_TYPE(obj)); + return __Pyx_PyMethod_New(func, type, (PyObject *)(Py_TYPE(type))); + } + if (obj == Py_None) + obj = NULL; + return __Pyx_PyMethod_New(func, obj, type); +} +static PyObject* +__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) +{ +#if PY_MAJOR_VERSION >= 3 + return PyUnicode_FromFormat("", + op->func_qualname, (void *)op); +#else + return PyString_FromFormat("", + PyString_AsString(op->func_qualname), (void *)op); +#endif +} +#if CYTHON_COMPILING_IN_PYPY +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyCFunctionObject* f = (PyCFunctionObject*)func; + PyCFunction meth = f->m_ml->ml_meth; + PyObject *self = f->m_self; + Py_ssize_t size; + switch (f->m_ml->ml_flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) { + case METH_VARARGS: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) + return (*meth)(self, arg); + break; + case METH_VARARGS | METH_KEYWORDS: + return (*(PyCFunctionWithKeywords)meth)(self, arg, kw); + case METH_NOARGS: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) { + size = PyTuple_GET_SIZE(arg); + if (likely(size == 0)) + return (*meth)(self, NULL); + PyErr_Format(PyExc_TypeError, + "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + case METH_O: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) { + size = PyTuple_GET_SIZE(arg); + if (likely(size == 1)) { + PyObject *result, *arg0 = PySequence_ITEM(arg, 0); + if (unlikely(!arg0)) return NULL; + result = (*meth)(self, arg0); + Py_DECREF(arg0); + return result; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + default: + PyErr_SetString(PyExc_SystemError, "Bad call flags in " + "__Pyx_CyFunction_Call. METH_OLDARGS is no " + "longer supported!"); + return NULL; + } + PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", + f->m_ml->ml_name); + return NULL; +} +#else +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + return PyCFunction_Call(func, arg, kw); +} +#endif +static PyTypeObject __pyx_CyFunctionType_type = { + PyVarObject_HEAD_INIT(0, 0) + "cython_function_or_method", + sizeof(__pyx_CyFunctionObject), + 0, + (destructor) __Pyx_CyFunction_dealloc, + 0, + 0, + 0, +#if PY_MAJOR_VERSION < 3 + 0, +#else + 0, +#endif + (reprfunc) __Pyx_CyFunction_repr, + 0, + 0, + 0, + 0, + __Pyx_CyFunction_Call, + 0, + 0, + 0, + 0, + Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, + 0, + (traverseproc) __Pyx_CyFunction_traverse, + (inquiry) __Pyx_CyFunction_clear, + 0, +#if PY_VERSION_HEX < 0x030500A0 + offsetof(__pyx_CyFunctionObject, func_weakreflist), +#else + offsetof(PyCFunctionObject, m_weakreflist), +#endif + 0, + 0, + __pyx_CyFunction_methods, + __pyx_CyFunction_members, + __pyx_CyFunction_getsets, + 0, + 0, + __Pyx_CyFunction_descr_get, + 0, + offsetof(__pyx_CyFunctionObject, func_dict), + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, +#if PY_VERSION_HEX >= 0x030400a1 + 0, +#endif +}; +static int __pyx_CyFunction_init(void) { +#if !CYTHON_COMPILING_IN_PYPY + __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; +#endif + __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type); + if (__pyx_CyFunctionType == NULL) { + return -1; + } + return 0; +} +static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults = PyMem_Malloc(size); + if (!m->defaults) + return PyErr_NoMemory(); + memset(m->defaults, 0, size); + m->defaults_pyobjects = pyobjects; + return m->defaults; +} +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults_tuple = tuple; + Py_INCREF(tuple); +} +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults_kwdict = dict; + Py_INCREF(dict); +} +static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->func_annotations = dict; + Py_INCREF(dict); +} + +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) { + Py_ssize_t i, nbases = PyTuple_GET_SIZE(bases); + for (i=0; i < nbases; i++) { + PyTypeObject *tmptype; + PyObject *tmp = PyTuple_GET_ITEM(bases, i); + tmptype = Py_TYPE(tmp); +#if PY_MAJOR_VERSION < 3 + if (tmptype == &PyClass_Type) + continue; +#endif + if (!metaclass) { + metaclass = tmptype; + continue; + } + if (PyType_IsSubtype(metaclass, tmptype)) + continue; + if (PyType_IsSubtype(tmptype, metaclass)) { + metaclass = tmptype; + continue; + } + PyErr_SetString(PyExc_TypeError, + "metaclass conflict: " + "the metaclass of a derived class " + "must be a (non-strict) subclass " + "of the metaclasses of all its bases"); + return NULL; + } + if (!metaclass) { +#if PY_MAJOR_VERSION < 3 + metaclass = &PyClass_Type; +#else + metaclass = &PyType_Type; +#endif + } + Py_INCREF((PyObject*) metaclass); + return (PyObject*) metaclass; +} + +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, + PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) { + PyObject *ns; + if (metaclass) { + PyObject *prep = __Pyx_PyObject_GetAttrStr(metaclass, __pyx_n_s_prepare); + if (prep) { + PyObject *pargs = PyTuple_Pack(2, name, bases); + if (unlikely(!pargs)) { + Py_DECREF(prep); + return NULL; + } + ns = PyObject_Call(prep, pargs, mkw); + Py_DECREF(prep); + Py_DECREF(pargs); + } else { + if (unlikely(!PyErr_ExceptionMatches(PyExc_AttributeError))) + return NULL; + PyErr_Clear(); + ns = PyDict_New(); + } + } else { + ns = PyDict_New(); + } + if (unlikely(!ns)) + return NULL; + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad; + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad; + if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad; + return ns; +bad: + Py_DECREF(ns); + return NULL; +} +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, + PyObject *dict, PyObject *mkw, + int calculate_metaclass, int allow_py2_metaclass) { + PyObject *result, *margs; + PyObject *owned_metaclass = NULL; + if (allow_py2_metaclass) { + owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass); + if (owned_metaclass) { + metaclass = owned_metaclass; + } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) { + PyErr_Clear(); + } else { + return NULL; + } + } + if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) { + metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases); + Py_XDECREF(owned_metaclass); + if (unlikely(!metaclass)) + return NULL; + owned_metaclass = metaclass; + } + margs = PyTuple_Pack(3, name, bases, dict); + if (unlikely(!margs)) { + result = NULL; + } else { + result = PyObject_Call(metaclass, margs, mkw); + Py_DECREF(margs); + } + Py_XDECREF(owned_metaclass); + return result; +} + +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = start + (end - start) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ + } + +#if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + } +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_char(char value) { + const char neg_one = (char) -1, const_zero = (char) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(char) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(char) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(char) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(char), + little, !is_unsigned); + } +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = (long) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + } +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 +static PyObject *__Pyx_GetStdout(void) { + PyObject *f = PySys_GetObject((char *)"stdout"); + if (!f) { + PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout"); + } + return f; +} +static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { + int i; + if (!f) { + if (!(f = __Pyx_GetStdout())) + return -1; + } + Py_INCREF(f); + for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { + PyObject* v; + if (PyFile_SoftSpace(f, 1)) { + if (PyFile_WriteString(" ", f) < 0) + goto error; + } + v = PyTuple_GET_ITEM(arg_tuple, i); + if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) + goto error; + if (PyString_Check(v)) { + char *s = PyString_AsString(v); + Py_ssize_t len = PyString_Size(v); + if (len > 0) { + switch (s[len-1]) { + case ' ': break; + case '\f': case '\r': case '\n': case '\t': case '\v': + PyFile_SoftSpace(f, 0); + break; + default: break; + } + } + } + } + if (newline) { + if (PyFile_WriteString("\n", f) < 0) + goto error; + PyFile_SoftSpace(f, 0); + } + Py_DECREF(f); + return 0; +error: + Py_DECREF(f); + return -1; +} +#else +static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { + PyObject* kwargs = 0; + PyObject* result = 0; + PyObject* end_string; + if (unlikely(!__pyx_print)) { + __pyx_print = PyObject_GetAttr(__pyx_b, __pyx_n_s_print); + if (!__pyx_print) + return -1; + } + if (stream) { + kwargs = PyDict_New(); + if (unlikely(!kwargs)) + return -1; + if (unlikely(PyDict_SetItem(kwargs, __pyx_n_s_file, stream) < 0)) + goto bad; + if (!newline) { + end_string = PyUnicode_FromStringAndSize(" ", 1); + if (unlikely(!end_string)) + goto bad; + if (PyDict_SetItem(kwargs, __pyx_n_s_end, end_string) < 0) { + Py_DECREF(end_string); + goto bad; + } + Py_DECREF(end_string); + } + } else if (!newline) { + if (unlikely(!__pyx_print_kwargs)) { + __pyx_print_kwargs = PyDict_New(); + if (unlikely(!__pyx_print_kwargs)) + return -1; + end_string = PyUnicode_FromStringAndSize(" ", 1); + if (unlikely(!end_string)) + return -1; + if (PyDict_SetItem(__pyx_print_kwargs, __pyx_n_s_end, end_string) < 0) { + Py_DECREF(end_string); + return -1; + } + Py_DECREF(end_string); + } + kwargs = __pyx_print_kwargs; + } + result = PyObject_Call(__pyx_print, arg_tuple, kwargs); + if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs)) + Py_DECREF(kwargs); + if (!result) + return -1; + Py_DECREF(result); + return 0; +bad: + if (kwargs != __pyx_print_kwargs) + Py_XDECREF(kwargs); + return -1; +} +#endif + +#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 +static int __Pyx_PrintOne(PyObject* f, PyObject *o) { + if (!f) { + if (!(f = __Pyx_GetStdout())) + return -1; + } + Py_INCREF(f); + if (PyFile_SoftSpace(f, 0)) { + if (PyFile_WriteString(" ", f) < 0) + goto error; + } + if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0) + goto error; + if (PyFile_WriteString("\n", f) < 0) + goto error; + Py_DECREF(f); + return 0; +error: + Py_DECREF(f); + return -1; + /* the line below is just to avoid C compiler + * warnings about unused functions */ + return __Pyx_Print(f, NULL, 0); +} +#else +static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { + int res; + PyObject* arg_tuple = PyTuple_Pack(1, o); + if (unlikely(!arg_tuple)) + return -1; + res = __Pyx_Print(stream, arg_tuple, 1); + Py_DECREF(arg_tuple); + return res; +} +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } +} + +static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +#ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility", + module_name, class_name); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling", + module_name, class_name); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { +#if PY_VERSION_HEX < 0x03030000 + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +#else + if (__Pyx_PyUnicode_READY(o) == -1) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (PyUnicode_IS_ASCII(o)) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +#endif + } else +#endif +#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { + PyNumberMethods *m; + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (PyInt_Check(x) || PyLong_Check(x)) +#else + if (PyLong_Check(x)) +#endif + return __Pyx_NewRef(x); + m = Py_TYPE(x)->tp_as_number; +#if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = PyNumber_Long(x); + } +#else + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Long(x); + } +#endif + if (res) { +#if PY_MAJOR_VERSION < 3 + if (!PyInt_Check(res) && !PyLong_Check(res)) { +#else + if (!PyLong_Check(res)) { +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + name, name, Py_TYPE(res)->tp_name); + Py_DECREF(res); + return NULL; + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(x); + } +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + } + } + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/pygmx/tpxio.pyx b/pygmx/tpxio.pyx new file mode 100644 index 0000000..b82a1db --- /dev/null +++ b/pygmx/tpxio.pyx @@ -0,0 +1,191 @@ +# cython: c_string_type=unicode, c_string_encoding=utf8 +# Cython wrapper around tpxio.cpp + +# from cython cimport view +# from array import array +import numpy as np +cimport numpy as np + +from utility cimport * +from math cimport * +from mdtypes cimport * +from topology cimport * + + +cdef extern from "gromacs/fileio/tpxio.h": + void read_tpxheader(const char *fn, t_tpxheader *tpx, bint TopOnlyOK) + + cdef struct t_tpxheader: + bint bIr # Non zero if input_rec is present */ + bint bBox # Non zero if a box is present */ + bint bTop # Non zero if a topology is present */ + bint bX # Non zero if coordinates are present */ + bint bV # Non zero if velocities are present */ + bint bF # Non zero if forces are present (no longer + # supported, but retained so old .tpr can be read) */ + int natoms # The total number of atoms */ + int ngtc # The number of temperature coupling groups */ + real _lambda # Current value of lambda */ + int fep_state # Current value of the alchemical state -- + + + int read_tpx(const char *fname, + t_inputrec *ir, + double box[3][3], + int *natoms, + rvec *x, + rvec *v, + gmx_mtop_t *mtop) + + +def cstr(instr): + if isinstance(instr, str): + instr = instr.encode() + return instr + +cdef atoms_from_topology(gmx_mtop_t *topology): + cdef: + t_atoms c_atoms + int moltype, resind + + atoms = [] + masses = [] + charges = [] + residues = [] + for i_molblock in range(topology.nmolblock): + moltype = topology.molblock[i_molblock].type + + c_atoms = topology.moltype[moltype].atoms + mol_atoms = [] + mol_q = [] + mol_m = [] + for i_atom in range(c_atoms.nr): + resind = c_atoms.atom[i_atom].resind + resname = c_atoms.resinfo[resind].name[0] + if resname not in residues: + residues.append(resname) + resid = residues.index(resname) + 1 + mol_atoms.append(( + resid, + resname, + c_atoms.atomname[0][i_atom], + )) + mol_q.append(c_atoms.atom[i_atom].q) + mol_m.append(c_atoms.atom[i_atom].m) + n_mol = topology.molblock[i_molblock].nmol + atoms += mol_atoms * n_mol + charges += mol_q * n_mol + masses += mol_m * n_mol + + return np.array(atoms) + +ctypedef object (*atom_func)(t_atom) + +cdef atom_charge(t_atom atom): + return atom.q + + +cdef atom_mass(t_atom atom): + return atom.m + +cdef class TPXReader: + cdef: + t_tpxheader header + t_inputrec input_record + gmx_mtop_t topology + real box[3][3] + readonly int n_atoms, n_tcouple_groups, n_mol + readonly char *topology_name + + cdef _map_atoms(self, object (*func)(t_atom)): + cdef t_atoms atoms + map = [] + for i_molblock in range(self.topology.nmolblock): + moltype = self.topology.molblock[i_molblock].type + nmol = self.topology.molblock[i_molblock].nmol + atoms = self.topology.moltype[moltype].atoms + mol_map = [] + for i_atom in range(atoms.nr): + mol_map.append(func(atoms.atom[i_atom])) + map += mol_map * nmol + return map + + property atoms: + """ + Get a list of tuples describing all atoms in the system: + + Returns: + List of tuples: (atom_name, residue_id, resiude_name) + """ + def __get__(self): + return atoms_from_topology(&self.topology) + + property mass2: + def __get__(self): + return np.array(self._map_atoms(atom_mass)) + + property mass: + "Get the masses of all atoms in the system." + def __get__(self): + cdef t_atoms atoms + masses = [] + for i_molblock in range(self.topology.nmolblock): + moltype = self.topology.molblock[i_molblock].type + nmol = self.topology.molblock[i_molblock].nmol + atoms = self.topology.moltype[moltype].atoms + mol_masses = [] + for i_atom in range(atoms.nr): + mol_masses.append(atoms.atom[i_atom].m) + masses += mol_masses * nmol + return np.array(masses) + + property charge: + "Get the partial charge of all atoms in the system." + def __get__(self): + cdef t_atoms atoms + charges = [] + for i_molblock in range(self.topology.nmolblock): + moltype = self.topology.molblock[i_molblock].type + nmol = self.topology.molblock[i_molblock].nmol + atoms = self.topology.moltype[moltype].atoms + mol_charges = [] + for i_atom in range(atoms.nr): + mol_charges.append(atoms.atom[i_atom].q) + charges += mol_charges * nmol + return np.array(charges) + + property type: + "Get the type of all atoms in the system." + def __get__(self): + cdef t_atoms atoms + types = [] + for i_molblock in range(self.topology.nmolblock): + moltype = self.topology.molblock[i_molblock].type + nmol = self.topology.molblock[i_molblock].nmol + atoms = self.topology.moltype[moltype].atoms + mol_type = [] + for i_atom in range(atoms.nr): + mol_type.append(atoms.atom[i_atom].type) + types += mol_type * nmol + return np.array(types) + + + def __cinit__(self, filename): + filename = cstr(filename) + read_tpxheader(filename, &self.header, True) + self.n_atoms = self.header.natoms + self.n_tcouple_groups = self.header.ngtc + + cdef np.ndarray[real, ndim=2] coordinates = np.empty((self.n_atoms, 3), dtype=np.float32) + cdef np.ndarray[real, ndim=2] velocites = np.empty((self.n_atoms, 3), dtype=np.float32) + + return_code = read_tpx( + filename, + &self.input_record, + self.box, + &self.n_atoms, + coordinates.data, + velocites.data, + &self.topology + ) + self.topology_name = self.topology.name[0] diff --git a/pygmx/utility.pxd b/pygmx/utility.pxd new file mode 100644 index 0000000..243ff0b --- /dev/null +++ b/pygmx/utility.pxd @@ -0,0 +1,14 @@ +# C-API in gromacs/utility + +#cdef extern from "inttypes.h": +ctypedef int __int64 + +cdef extern from "gromacs/utility/basedefinitions.h": + ctypedef int gmx_bool + ctypedef __int64 gmx_int64_t + +cdef extern from "gromacs/utility/real.h": + ctypedef double real + +cdef extern from "gromacs/utility/futil.h": + ctypedef gmx_int64_t gmx_off_t diff --git a/pygmx/xtcio.pyx b/pygmx/xtcio.pyx new file mode 100644 index 0000000..ce681d9 --- /dev/null +++ b/pygmx/xtcio.pyx @@ -0,0 +1,95 @@ +# Wrapper for xtcio.h: I/O for xtc files. + +import numpy as np +cimport numpy as np + +from utility cimport * +from math cimport * +from fileio cimport * + +cdef extern from "gromacs/fileio/xtcio.h": + t_fileio *open_xtc(const char *filename, const char *mode) + + void close_xtc(t_fileio *fio) + + int read_first_xtc(t_fileio *fio, + int *natoms, int *step, real *time, + matrix box, rvec **x, real *prec, gmx_bool *_bOK) + + int read_next_xtc(t_fileio *fio, + int natoms, int *step, real *time, + matrix box, rvec *x, real *prec, gmx_bool *_bOK) + + +if sizeof(real) == 4: + np_real = np.float32 +else: + np_real = np.float + + +cdef class XTCReader: + cdef: + t_fileio *fio + int natoms, cur_step + real start_time, timestep, prec, cur_time + dict _cache + #rvec *coords + + def nearest_cache(self, index): + nearest = 0 + cur_dist = 99999999 + for ind in self._cache: + dist = abs(ind - index) + if dist < cur_dist: + nearest = ind + cur_dist = dist + return nearest + + + def seek(self, index): + if index in self._cache: + gmx_fio_seek(self.fio, self._cache[index]) + else: + nearest = self.nearest_cache(index) + gmx_fio_seek(self.fio, self._cache[nearest]) + self.cur_step = index + self.cur_time = index * self.timestep + self.start_time + xtc_seek_time(self.fio, self.cur_time, self.natoms, index > nearest) + self._cache[index] = gmx_fio_ftell(self.fio) + + + def __init__(self, filename): + if isinstance(filename, str): + filename = filename.encode() + + cdef: + matrix box + gmx_bool _bOK + real time + cdef rvec *coords # = np.empty((1,3), dtype=np.float32) + + self._cache = {} + self.fio = open_xtc(filename, b'r') + read_first_xtc(self.fio, &self.natoms, &self.cur_step, &self.start_time, box, + &coords, &self.prec, &_bOK) + self._cache[self.cur_step] = gmx_fio_ftell(self.fio) + + read_next_xtc(self.fio, self.natoms, &self.cur_step, &time, box, + coords, &self.prec, &_bOK) + + self._cache[self.cur_step] = gmx_fio_ftell(self.fio) + self.timestep = time - self.start_time + + + def __getitem__(self, item): + cdef matrix box + cdef gmx_bool _bOK + cdef real time + cdef np.ndarray[real, ndim=2] coords = np.empty((self.natoms, 3), dtype=np_real) + + self.seek(item) + + read_next_xtc(self.fio, self.natoms, &self.cur_step, &time, box, + coords.data, &self.prec, &_bOK) + + return coords