From eed1d10f631c1adcd01cf9689c847b072d4317a0 Mon Sep 17 00:00:00 2001 From: Markus Rosenstihl Date: Wed, 10 Jun 2015 07:03:32 +0000 Subject: [PATCH] added Oleg Petrov's *write_to_tecmag* result function --- src/data/Accumulation.py | 149 +++++++++++++++++++++++++++++++++++++-- 1 file changed, 144 insertions(+), 5 deletions(-) diff --git a/src/data/Accumulation.py b/src/data/Accumulation.py index 15fa1f0..7874321 100644 --- a/src/data/Accumulation.py +++ b/src/data/Accumulation.py @@ -13,18 +13,24 @@ from Errorable import Errorable from Drawable import Drawable from DamarisFFT import DamarisFFT from Signalpath import Signalpath + +#from DataPool import DataPool + import sys import threading import types import tables import numpy -import datetime +import datetime # added by Oleg Petrov +import ctypes # added by Oleg Petrov +import struct # added by Oleg Petrov +import os # added by Oleg Petrov class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): def __init__(self, x = None, y = None, y_2 = None, n = None, index = None, sampl_freq = None, error = False): Errorable.__init__(self) Drawable.__init__(self) - + # Title of this accumulation (plotted in GUI -> look Drawable) self.__title_pattern = "Accumulation: n = %d" @@ -35,6 +41,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): self.common_descriptions=None self.time_period=[] + self.job_id = None # added by Oleg Petrov self.use_error = error @@ -192,7 +199,8 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): return max(tmp_max) def get_job_id(self): - return None + # return None + return self.job_id # modified by Oleg Petrov def write_to_csv(self, destination=sys.stdout, delimiter=" "): """ @@ -236,7 +244,8 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): finally: self.lock.release() - def write_to_simpson(self, destination=sys.stdout, delimiter=" "): +# ------------- added by Oleg Petrov, 14 Feb 2012 ---------------------- + def write_to_simpson(self, destination=sys.stdout, delimiter=" ", frequency=100e6): """ writes the data to a text file or sys.stdout in Simpson format, for further processing with the NMRnotebook software; @@ -246,13 +255,14 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): the_destination=destination if type(destination) in types.StringTypes: the_destination=file(destination, "w") - + self.lock.acquire() try: xdata=self.get_xdata() the_destination.write("SIMP\n") the_destination.write("%s%i%s"%("NP=", len(xdata), "\n")) the_destination.write("%s%i%s"%("SW=", self.get_sampling_rate(), "\n")) + the_destination.write("%s%i%s"%("REF=", frequency, "\n")) the_destination.write("TYPE=FID\n") the_destination.write("DATA\n") ch_no=self.get_number_of_channels() @@ -267,6 +277,127 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): finally: self.lock.release() +# ------------- added by Oleg Petrov, 10 Sep 2013 ----------------------- + def write_to_tecmag(self, destination=sys.stdout, nrecords=1,\ + frequency=100e6,\ + last_delay = 1.,\ + receiver_phase=0.,\ + nucleus='1H'): + """ + writes the data to a binary file in TecMag format; + destination can be a file object or a filename; + nrecords determines the 2nd dimension of data; + """ + + if self.job_id == None or self.n == 0: + raise ValueError("write_to_tecmag: cannot get a record number") + else: + record = self.job_id/self.n + 1 + + the_destination=destination + if type(destination) in types.StringTypes: + if record == 1 and os.path.exists(destination): + os.rename(destination, os.path.dirname(destination)+'/~'+os.path.basename(destination)) + the_destination=file(destination, "ab") + + self.lock.acquire() + try: + npts = [len(self), nrecords, 1, 1] + dwell = 1./self.get_sampling_rate() + sw = 0.5/dwell + + base_freq = [frequency, 100., 0., 0.] + offset_freq = [0., 0., 0., 0.] + ob_freq = [sum(x) for x in zip(base_freq, offset_freq)] + date = self.time_period[0].strftime("%Y/%m/%d %H:%M:%S") + + if record == 1: + buff = ctypes.create_string_buffer(1056) + + struct.pack_into('8s', buff, 0, 'TNT1.005') # 'TNT1.000' version ID + struct.pack_into('4s', buff, 8, 'TMAG') # 'TMAG' tag + struct.pack_into('?', buff, 12, True) # BOOLean value + struct.pack_into('i', buff, 16, 1024) # length of Tecmag struct + + #Initialize TECMAG structure: + struct.pack_into('4i', buff, 20, *npts) # npts[4] + struct.pack_into('4i', buff, 36, *npts) # actual_npts[4] + struct.pack_into('i', buff, 52, npts[0]) # acq_points + struct.pack_into('4i', buff, 56, 1, 1, 1, 1) # npts_start[4] + struct.pack_into('i', buff, 72, self.n) # scans + struct.pack_into('i', buff, 76, self.n) # actual_scans + struct.pack_into('i', buff, 88, 1) # sadimension + + struct.pack_into('4d', buff, 104, *ob_freq) # ob_freq[4] + struct.pack_into('4d', buff, 136, *base_freq) # base_freq[4] + struct.pack_into('4d', buff, 168, *offset_freq) # offset_freq[4] + struct.pack_into('d', buff, 200, 0.0) # ref_freq + struct.pack_into('h', buff, 216, 1) # obs_channel + struct.pack_into('42s', buff, 218, 42*'2') # space2[42] + + struct.pack_into('4d', buff, 260, sw, 0., 0., 0.) # sw[4], sw = 0.5/dwell + struct.pack_into('4d', buff, 292, dwell, 0., 0., 0.) # dwell[4] + struct.pack_into('d', buff, 324, sw) # filter, = 0.5/dwell + struct.pack_into('d', buff, 340, (npts[0]*dwell)) # acq_time + struct.pack_into('d', buff, 348, 1.) # last_delay (5*T1 minus sequence length) + struct.pack_into('h', buff, 356, 1) # spectrum_direction + struct.pack_into('16s', buff, 372, 16*'2') # space3[16] + + struct.pack_into('d', buff, 396, receiver_phase) # receiver_phase + struct.pack_into('4s', buff, 404, 4*'2') # space4[4] + struct.pack_into('16s', buff, 444, 16*'2') # space5[16] + struct.pack_into('264s', buff, 608, 264*'2') # space6[264] + + struct.pack_into('32s', buff, 884, date) # date[32] + struct.pack_into('16s', buff, 916, nucleus) # nucleus[16] + # TECMAG Structure total => 1024 + + struct.pack_into('4s', buff, 1044, 'DATA') # 'DATA' tag + struct.pack_into('?', buff, 1048, True) # BOOLean + struct.pack_into('i', buff, 1052, 2*4*npts[0]*npts[1]) # length of data (2 = [Re, Im]; 4 = len(c_float)) + + the_destination.write(buff) + + # append data to the file as they appear in an experiment (RIRIRIRI blocks in linear order): + ch_no=self.get_number_of_channels() + + ydata = map(self.get_ydata, xrange(ch_no)) + if ch_no == 1: + ydata = [ydata, numpy.zeros(len(ydata))] + + data = numpy.append([ydata[0]], [ydata[1]], axis=0) + data = data.T + data = data.flatten() + + buff = ctypes.create_string_buffer(4*len(data)) + struct.pack_into('%sf' % len(data), buff, 0, *data) + the_destination.write(buff) + + if record == nrecords: + buff = ctypes.create_string_buffer(2068) + + struct.pack_into('4s', buff, 0, 'TMG2') # 'TMG2' tag + struct.pack_into('?', buff, 4, True) # BOOLean + struct.pack_into('i', buff, 8, 2048) # length of Tecmag2 struct + + # Leave TECMAG2 structure empty: + struct.pack_into('52s', buff, 372, 52*'2') # space[52] + struct.pack_into('866s', buff, 1194, 866*'2') # space[610]+names+strings + # TECMAG2 Structure total => 2048 + + struct.pack_into('4s', buff, 2060, 'PSEQ') # 'PSEQ' tag 658476 + struct.pack_into('?', buff, 2064, False) # BOOLean 658480 + + the_destination.write(buff) + + the_destination = None + ydata=None + + finally: + self.lock.release() + +# ----------------------------------------------------------------------- + def write_to_hdf(self, hdffile, where, name, title, complib=None, complevel=None): accu_group=hdffile.createGroup(where=where,name=name,title=title) accu_group._v_attrs.damaris_type="Accumulation" @@ -458,6 +589,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): else: r = Accumulation(x = numpy.array(other.x, dtype="Float64"), y = tmp_y, index = other.index, sampl_freq = other.sampling_rate, n = 1, error = False) r.time_period=[other.job_date,other.job_date] + r.job_id = other.job_id # added by Oleg Petrov r.common_descriptions=other.description.copy() self.lock.release() return r @@ -485,6 +617,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, n = self.n + 1, index = self.index, sampl_freq = self.sampling_rate, error = False) r.time_period=[min(self.time_period[0],other.job_date), max(self.time_period[1],other.job_date)] + r.job_id = other.job_id # added by Oleg Petrov if self.common_descriptions is not None: r.common_descriptions={} for key in self.common_descriptions.keys(): @@ -516,6 +649,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): tmp_y.append(other.y[i]) tmp_ysquare.append(other.y_square[i]) r.time_period=other.time_period[:] + r.job_id = other.job_id # added by Oleg Petrov if other.common_descriptions is not None: r.common_descriptions=othter.common_descriptions.copy() else: @@ -549,6 +683,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): r.time_period=[min(self.time_period[0],other.time_period[0]), max(self.time_period[1],other.time_period[1])] + r.job_id = other.job_id # added by Oleg Petrov r.common_descriptions={} if self.common_descriptions is not None and other.common_descriptions is not None: for key in self.common_descriptions.keys(): @@ -614,6 +749,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): self.lock.release() self.time_period=[other.job_date,other.job_date] + self.job_id = other.job_id # added by Oleg Petrov self.common_descriptions=other.description.copy() return self @@ -636,6 +772,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): self.n += 1 self.time_period=[min(self.time_period[0],other.job_date), max(self.time_period[1],other.job_date)] + self.job_id = other.job_id # added by Oleg Petrov if self.common_descriptions is not None: for key in self.common_descriptions.keys(): if not (key in other.description and self.common_descriptions[key]==other.description[key]): @@ -670,6 +807,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): self.set_title(self.__title_pattern % self.n) self.common_descriptions=other.common_desriptions.copy() self.time_period=other.time_period[:] + self.job_id = other.job_id # added by Oleg Petrov self.lock.release() return self @@ -691,6 +829,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath): self.n += other.n self.time_period=[min(self.time_period[0],other.time_period[0]), max(self.time_period[1],other.time_period[1])] + self.job_id = other.job_id # added by Oleg Petrov if self.common_descriptions is not None and other.common_descriptions is not None: for key in self.common_descriptions.keys(): if not (key in other.description and