added full_output option to non gaussian parameter so that correct statistics can be done afterwards

Reviewed-on: #2

src/mdevaluate/__init__.py

@@ -16,7 +16,7 @@ from . import reader
 from . import system
 from . import utils
 from . import extra
-from .logging import logger
+from .logging_util import logger
 
 
 def open(

src/mdevaluate/autosave.py

@@ -5,7 +5,7 @@ from typing import Optional, Callable, Iterable
 
 import numpy as np
 from .checksum import checksum
-from .logging import logger
+from .logging_util import logger
 
 autosave_directory: Optional[str] = None
 load_autosave_data = False

src/mdevaluate/checksum.py

@@ -1,9 +1,14 @@
 import functools
 import hashlib
-from .logging import logger
+from .logging_util import logger
 from types import ModuleType, FunctionType
 import inspect
 from typing import Iterable
+import ast
+import io
+import tokenize
+import re
+import textwrap
 
 import numpy as np
 
@@ -28,19 +33,46 @@ def version(version_nr: int, calls: Iterable = ()):
     return decorator
 
 
-def strip_comments(s: str):
-    """Strips comment lines and docstring from Python source string."""
-    o = ""
-    in_docstring = False
-    for l in s.split("\n"):
-        if l.strip().startswith(("#", '"', "'")) or in_docstring:
-            in_docstring = l.strip().startswith(('"""', "'''")) + in_docstring == 1
+def strip_comments(source: str) -> str:
+    """Removes docstrings, comments, and irrelevant whitespace from Python source code."""
+
+    # Step 1: Remove docstrings using AST
+    def remove_docstrings(node):
+        if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef, ast.ClassDef, ast.Module)):
+            if (doc := ast.get_docstring(node, clean=False)):
+                first_stmt = node.body[0]
+                if isinstance(first_stmt, ast.Expr) and isinstance(first_stmt.value, ast.Constant):
+                    node.body.pop(0)  # Remove the docstring entirely
+        for child in ast.iter_child_nodes(node):
+            remove_docstrings(child)
+
+    tree = ast.parse(textwrap.dedent(source))
+    remove_docstrings(tree)
+    code_without_docstrings = ast.unparse(tree)
+
+    # Step 2: Remove comments using tokenize
+    tokens = tokenize.generate_tokens(io.StringIO(code_without_docstrings).readline)
+    result = []
+    last_lineno = -1
+    last_col = 0
+
+    for toknum, tokval, (srow, scol), (erow, ecol), line in tokens:
+        if toknum == tokenize.COMMENT:
             continue
-        o += l + "\n"
-    return o
+        if srow > last_lineno:
+            last_col = 0
+        if scol > last_col:
+            result.append(" " * (scol - last_col))
+        result.append(tokval)
+        last_lineno, last_col = erow, ecol
+
+    code_no_comments = ''.join(result)
+
+    # Step 3: Remove empty lines (whitespace-only or truly blank)
+    return "\n".join([line for line in code_no_comments.splitlines() if line.strip() != ""])
 
 
-def checksum(*args, csum=None):
+def checksum(*args, csum=None, _seen=None):
     """
     Calculate a checksum of any object, by sha1 hash.
 
@@ -60,7 +92,15 @@ def checksum(*args, csum=None):
         csum = hashlib.sha1()
         csum.update(str(SALT).encode())
 
+    if _seen is None:
+        _seen = set()
+
     for arg in args:
+        obj_id = id(arg)
+        if obj_id in _seen:
+            continue
+        _seen.add(obj_id)
+
         if hasattr(arg, "__checksum__"):
             logger.debug("Checksum via __checksum__: %s", str(arg))
             csum.update(str(arg.__checksum__()).encode())
@@ -73,17 +113,19 @@ def checksum(*args, csum=None):
         elif isinstance(arg, FunctionType):
             csum.update(strip_comments(inspect.getsource(arg)).encode())
             c = inspect.getclosurevars(arg)
-            for v in {**c.nonlocals, **c.globals}.values():
+            merged = {**c.nonlocals, **c.globals}
+            for key in sorted(merged):  # deterministic ordering
+                v = merged[key]
                 if v is not arg:
-                    checksum(v, csum=csum)
+                    checksum(v, csum=csum, _seen=_seen)
         elif isinstance(arg, functools.partial):
             logger.debug("Checksum via partial for %s", str(arg))
-            checksum(arg.func, csum=csum)
+            checksum(arg.func, csum=csum, _seen=_seen)
             for x in arg.args:
-                checksum(x, csum=csum)
+                checksum(x, csum=csum, _seen=_seen)
             for k in sorted(arg.keywords.keys()):
                 csum.update(k.encode())
-                checksum(arg.keywords[k], csum=csum)
+                checksum(arg.keywords[k], csum=csum, _seen=_seen)
         elif isinstance(arg, np.ndarray):
             csum.update(arg.tobytes())
         else:

src/mdevaluate/coordinates.py

@@ -1,6 +1,6 @@
 from functools import partial, wraps
 from copy import copy
-from .logging import logger
+from .logging_util import logger
 from typing import Optional, Callable, List, Tuple
 
 import numpy as np

src/mdevaluate/correlation.py

@@ -18,7 +18,7 @@ def log_indices(first: int, last: int, num: int = 100) -> np.ndarray:
     return np.unique(np.int_(ls) - 1 + first)
 
 
-@autosave_data(2)
+@autosave_data(nargs=2, kwargs_keys=('selector', 'segments', 'skip', 'window', 'average', 'points',), version=1.0)
 def shifted_correlation(
     function: Callable,
     frames: Coordinates,
@@ -199,7 +199,7 @@ def msd(
         raise ValueError('Parameter axis has to be ether "all", "x", "y", or "z"!')
 
 
-def isf(
+def isf_raw(
     start_frame: CoordinateFrame,
     end_frame: CoordinateFrame,
     q: float = 22.7,
@@ -216,29 +216,59 @@ def isf(
         displacements = displacements_without_drift(start_frame, end_frame, trajectory)
     if axis == "all":
         distance = (displacements**2).sum(axis=1) ** 0.5
-        return np.sinc(distance * q / np.pi).mean()
+        return np.sinc(distance * q / np.pi)
     elif axis == "xy" or axis == "yx":
         distance = (displacements[:, [0, 1]]**2).sum(axis=1) ** 0.5
-        return np.real(jn(0, distance * q)).mean()
+        return np.real(jn(0, distance * q))
     elif axis == "xz" or axis == "zx":
         distance = (displacements[:, [0, 2]]**2).sum(axis=1) ** 0.5
-        return np.real(jn(0, distance * q)).mean()
+        return np.real(jn(0, distance * q))
     elif axis == "yz" or axis == "zy":
         distance = (displacements[:, [1, 2]]**2).sum(axis=1) ** 0.5
-        return np.real(jn(0, distance * q)).mean()
+        return np.real(jn(0, distance * q))
     elif axis == "x":
         distance = np.abs(displacements[:, 0])
-        return np.mean(np.cos(np.abs(q * distance)))
+        return np.cos(np.abs(q * distance))
     elif axis == "y":
         distance = np.abs(displacements[:, 1])
-        return np.mean(np.cos(np.abs(q * distance)))
+        return np.cos(np.abs(q * distance))
     elif axis == "z":
         distance = np.abs(displacements[:, 2])
-        return np.mean(np.cos(np.abs(q * distance)))
+        return np.cos(np.abs(q * distance))
     else:
         raise ValueError('Parameter axis has to be ether "all", "x", "y", or "z"!')
 
 
+def isf(
+    start_frame: CoordinateFrame,
+    end_frame: CoordinateFrame,
+    q: float = 22.7,
+    trajectory: Coordinates = None,
+    axis: str = "all",
+) -> float:
+    """
+    Incoherent intermediate scattering function averaged over all particles.
+    See isf_raw for details.
+    """
+    return isf_raw(start_frame, end_frame, q=q, trajectory=trajectory, axis=axis).mean()
+
+
+def isf_mean_var(
+    start_frame: CoordinateFrame,
+    end_frame: CoordinateFrame,
+    q: float = 22.7,
+    trajectory: Coordinates = None,
+    axis: str = "all",
+) -> float:
+    """
+    Incoherent intermediate scattering function averaged over all particles and the
+    variance.
+    See isf_raw for details.
+    """
+    values = isf_raw(start_frame, end_frame, q=q, trajectory=trajectory, axis=axis)
+    return values.mean(), values.var()
+
+
 def rotational_autocorrelation(
     start_frame: CoordinateFrame, end_frame: CoordinateFrame, order: int = 2
 ) -> float:
@@ -430,10 +460,11 @@ def non_gaussian_parameter(
     end_frame: CoordinateFrame,
     trajectory: Coordinates = None,
     axis: str = "all",
+    full_output = False,
 ) -> float:
-    """
+    r"""
     Calculate the non-Gaussian parameter.
-    ..math:
+    .. math:
       \alpha_2 (t) =
         \frac{3}{5}\frac{\langle r_i^4(t)\rangle}{\langle r_i^2(t)\rangle^2} - 1
     """
@@ -442,27 +473,41 @@ def non_gaussian_parameter(
     else:
         vectors = displacements_without_drift(start_frame, end_frame, trajectory)
     if axis == "all":
-        r = (vectors**2).sum(axis=1)
+        r2 = (vectors**2).sum(axis=1)
         dimensions = 3
     elif axis == "xy" or axis == "yx":
-        r = (vectors[:, [0, 1]]**2).sum(axis=1)
+        r2 = (vectors[:, [0, 1]]**2).sum(axis=1)
         dimensions = 2
     elif axis == "xz" or axis == "zx":
-        r = (vectors[:, [0, 2]]**2).sum(axis=1)
+        r2 = (vectors[:, [0, 2]]**2).sum(axis=1)
         dimensions = 2
     elif axis == "yz" or axis == "zy":
-        r = (vectors[:, [1, 2]]**2).sum(axis=1)
+        r2 = (vectors[:, [1, 2]]**2).sum(axis=1)
         dimensions = 2
     elif axis == "x":
-        r = vectors[:, 0] ** 2
+        r2 = vectors[:, 0] ** 2
         dimensions = 1
     elif axis == "y":
-        r = vectors[:, 1] ** 2
+        r2 = vectors[:, 1] ** 2
         dimensions = 1
     elif axis == "z":
-        r = vectors[:, 2] ** 2
+        r2 = vectors[:, 2] ** 2
         dimensions = 1
     else:
         raise ValueError('Parameter axis has to be ether "all", "x", "y", or "z"!')
+    
+    m2 = np.mean(r2)
+    m4 = np.mean(r2**2)
+    if m2 == 0.0:
+        if full_output:
+            return 0.0, 0.0, 0.0
+        else:
+            return 0.0
+
+    alpha_2 = (m4 / ((1 + 2 / dimensions) * m2**2)) - 1
+    if full_output:
+        return alpha_2, m2, m4
+    else:
+        return alpha_2
+
 
-    return (np.mean(r**2) / ((1 + 2 / dimensions) * (np.mean(r) ** 2))) - 1

src/mdevaluate/distribution.py

@@ -182,10 +182,10 @@ def tetrahedral_order(
     )
 
     # Connection vectors
-    neighbors_1 -= atoms
-    neighbors_2 -= atoms
-    neighbors_3 -= atoms
-    neighbors_4 -= atoms
+    neighbors_1 = pbc_diff(neighbors_1, atoms, box=atoms.box)
+    neighbors_2 = pbc_diff(neighbors_2, atoms, box=atoms.box)
+    neighbors_3 = pbc_diff(neighbors_3, atoms, box=atoms.box)
+    neighbors_4 = pbc_diff(neighbors_4, atoms, box=atoms.box)
 
     # Normed Connection vectors
     neighbors_1 /= np.linalg.norm(neighbors_1, axis=-1).reshape(-1, 1)

src/mdevaluate/pbc.py

@@ -7,7 +7,7 @@ from numpy.typing import ArrayLike, NDArray
 
 from itertools import product
 
-from .logging import logger
+from .logging_util import logger
 
 if TYPE_CHECKING:
     from mdevaluate.coordinates import CoordinateFrame

src/mdevaluate/reader.py

@@ -19,13 +19,13 @@ import MDAnalysis
 from scipy import sparse
 
 from .checksum import checksum
-from .logging import logger
+from .logging_util import logger
 from . import atoms
 from .coordinates import Coordinates
 
 CSR_ATTRS = ("data", "indices", "indptr")
 NOJUMP_MAGIC = 2016
-Group_RE = re.compile("\[ ([-+\w]+) \]")
+Group_RE = re.compile(r"\[ ([-+\w]+) \]")
 
 
 class NojumpError(Exception):

src/mdevaluate/utils.py

@@ -14,7 +14,7 @@ from scipy.ndimage import uniform_filter1d
 from scipy.interpolate import interp1d
 from scipy.optimize import curve_fit
 
-from .logging import logger
+from .logging_util import logger
 from .functions import kww, kww_1e
 
 
@@ -357,6 +357,37 @@ def quick1etau(t: ArrayLike, C: ArrayLike, n: int = 7) -> float:
     return tau_est
 
 
+def quicknongaussfit(t, C, width=2):
+    """
+    Estimates the time and height of the peak in the non-Gaussian function.
+    C is C(t) the correlation function
+    """
+    def ffunc(t,y0,A_main,log_tau_main,sig_main):
+        main_peak = A_main*np.exp(-(t - log_tau_main)**2 / (2 * sig_main**2))
+        return y0 + main_peak
+    
+    # first rough estimate, the closest time. This is returned if the interpolation fails!
+    tau_est = t[np.argmax(C)]
+    nG_max = np.amax(C)
+    try:
+        with np.errstate(invalid='ignore'):
+            corr = C[t > 0]
+            time = np.log10(t[t > 0])
+            tau = time[np.argmax(corr)]
+            mask = (time>tau-width/2) & (time<tau+width/2)
+            time = time[mask] ; corr = corr[mask]
+            nG_min = C[t > 0].min()
+            guess = [nG_min, nG_max-nG_min, tau, 0.6]
+            popt = curve_fit(ffunc, time, corr, p0=guess, maxfev=10000)[0]
+            tau_est = 10**popt[-2]
+            nG_max = popt[0] + popt[1]
+    except:
+        pass
+    if np.isnan(tau_est):
+        tau_est = np.inf
+    return tau_est, nG_max
+
+
 def susceptibility(
     time: NDArray, correlation: NDArray, **kwargs
 ) -> tuple[NDArray, NDArray]: