parseq 2024.5.0__zip → 2024.11.1__zip

{parseq-2024.5.0 → parseq-2024.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: parseq
-Version: 2024.5.0
+Version: 2024.11.1
 Summary: ParSeq is a python software library for Parallel execution of Sequential data analysis.
 Home-page: http://parseq.readthedocs.io
 Author: Konstantin Klementiev
@@ -50,12 +50,6 @@ implement particular analysis pipelines as lightweight Python packages.
 
 ParSeq is intended for synchrotron based techniques, first of all spectroscopy.
 
-A screenshot of ParSeq-XAS (an EXAFS analysis pipeline) as an application
-example:
-
-.. image:: _images/XAS-foils.gif
-   :scale: 50 %
-
 Main features
 -------------
 
@@ -73,13 +67,13 @@ Main features
 -  Entering into the analysis pipeline at any node, not only at the head of the
    pipeline.
 
--  Creation of cross-data combinations (e.g. averaging, RMS or PCA) and their
+-  Creation of cross-data combinations (e.g. averaging, PCA) and their
    propagation downstream the pipeline together with the parental data. The
    possibility of termination of the parental data at any selected downstream
    node.
 
 -  General data correction routines for 1D data: range deletion, scaling,
-   replacement by a spline and jump correction.
+   replacement by a spline, deletion of spikes and jump correction.
 
 -  Parallel execution of data transformations with multiprocessing or
    multithreading (can be opted by the pipeline application).
@@ -87,15 +81,15 @@ Main features
 -  Optional curve fitting solvers, also executed in parallel for multiple data
    items.
 
--  Informative error handling that provides alerts and stack traceback -- the
+-  Informative error handling that provides alerts and stack traceback with the
    type and location of the occurred error.
 
 -  Optional time profiling of the pipeline, as controlled by a command-line
    argument.
 
 -  Export of the workflow into a project file. Export of data into various data
-   formats with accompanied Python scripts that visualize the exported data for
-   the user to tune their publication plots.
+   formats with accompanied Python scripts that visualize the exported data in
+   publication-quality plots.
 
 -  ParSeq understands container files (presently only hdf5) and adds them to
    the system file tree as subfolders. The file tree, including hdf5
@@ -116,11 +110,14 @@ and curve fits are exemplified by separately installed analysis packages:
 - `ParSeq-XAS <https://github.com/kklmn/ParSeq-XAS>`_
 - `ParSeq-XES-scan <https://github.com/kklmn/ParSeq-XES-scan>`_
 
-Dependencies
+Installation
 ------------
 
-- `silx <https://github.com/silx-kit/silx>`_ -- plotting, hdf5 handling, Qt
-- `sphinx <https://github.com/sphinx-doc/sphinx>`_ -- building documentation
+Install it by pip or conda or get ParSeq from
+`GitHub <https://github.com/kklmn/ParSeq>`_ and use it with or without
+installation.
+The documentation is available online on
+`Read the Docs <http://parseq.readthedocs.io>`_.
 
 Launch an example
 -----------------

{parseq-2024.5.0 → parseq-2024.11.1}/parseq/core/commons.py

@@ -46,7 +46,7 @@ def expandDotAttr(attr):
 
 def expandTransformParam(prop):
     "add `transformParams` from the left of the prop name"
-    if isinstance(prop, type("")):
+    if isinstance(prop, str):
         if '.' not in prop:
             # then a single attribute
             return '.'.join(('transformParams', prop))
@@ -59,7 +59,7 @@ def shrinkTransformParam(prop):
     if isinstance(prop, (list, tuple)):
         if 'transformParams' in prop:
             prop = [pr for pr in prop if pr != 'transformParams']
-    elif isinstance(prop, type("")):
+    elif isinstance(prop, str):
         if 'transformParams.' in prop:
             prop = prop.replace('transformParams.', '')
     return prop

{parseq-2024.5.0 → parseq-2024.11.1}/parseq/core/config.py

@@ -10,29 +10,33 @@ try:
 except ImportError:
     from ConfigParser import ConfigParser  # python 2
 
+from . import singletons as csi
+
 iniDir = os.path.expanduser(os.path.join('~', '.parseq'))
 if not os.path.exists(iniDir):
     os.makedirs(iniDir)
 
 encoding = 'utf-8'
 
-iniFileLoad = (os.path.join(iniDir, 'load.ini'))
+iniFileLoad = os.path.join(iniDir, '{0}_load.ini'.format(csi.pipelineName))
 configLoad = ConfigParser()
 configLoad.read(iniFileLoad, encoding=encoding)
 
-iniFileGUI = (os.path.join(iniDir, 'gui.ini'))
+iniFileGUI = os.path.join(iniDir, '{0}_gui.ini'.format(csi.pipelineName))
 configGUI = ConfigParser()
 configGUI.read(iniFileGUI, encoding=encoding)
 
-iniFileTransforms = (os.path.join(iniDir, 'transforms.ini'))
+iniFileTransforms = os.path.join(
+    iniDir, '{0}_transforms.ini'.format(csi.pipelineName))
 configTransforms = ConfigParser()
 configTransforms.read(iniFileTransforms, encoding=encoding)
 
-iniFileFits = (os.path.join(iniDir, 'fits.ini'))
+iniFileFits = os.path.join(iniDir, '{0}_fits.ini'.format(csi.pipelineName))
 configFits = ConfigParser()
 configFits.read(iniFileFits, encoding=encoding)
 
-iniFileFormats = (os.path.join(iniDir, 'formats.ini'))
+iniFileFormats = os.path.join(
+    iniDir, '{0}_formats.ini'.format(csi.pipelineName))
 configFormats = ConfigParser()
 configFormats.read(iniFileFormats, encoding=encoding)
 configFormats.optionxform = str  # makes it case sensitive
@@ -41,7 +45,7 @@ configFormats.optionxform = str  # makes it case sensitive
 def get(conf, section, entry, default=None):
     if conf.has_option(section, entry):
         res = conf.get(section, entry)
-        if isinstance(default, (type(''), type(u''))):
+        if isinstance(default, str):
             return res
         else:
             try:

parseq-2024.11.1/parseq/core/correction.py

@@ -0,0 +1,162 @@
+# -*- coding: utf-8 -*-
+r"""
+Data corrections
+----------------
+
+General (not pipeline-specific) data corrections were designed in ParSeq for
+the amendment of data distortions. One example of data correction is the
+removal of diffraction peaks arriving at a fluorescence detector during x-ray
+absorption measurements. In this case, diffraction peaks may appear as sharp
+artefacts seen by different detector channels at different x-ray energies. The
+correction can be a simple deletion of a few data points or a replacement by a
+spline segment, where the comparison with undistorted spectra can guide the
+decisions.
+
+The ParSeq corrections operate in a transformation node and are applied to all
+data arrays defined in that node. The corrections are calculated following the
+incoming transformations that lead to the node.
+
+.. note::
+   When setting up a correction that depends on y-coordinates (e,g. spline
+   correction) in the ParSeq GUI, make sure that the plot widget does not
+   apply a normalization or any other modification affecting the y-axis.
+
+In the present version, only 1D nodes can receive corrections. Each correction
+defines a dictionary of parameters. The following corrections are defined.
+
++------------------+------------------+
+|    correction    |    description   |
++==================+==================+
+|  delete region   | |text_del|       |
++------------------+------------------+
+|  scale region    | |text_scl|       |
++------------------+------------------+
+| replace region   |                  |
+| by spline        | |text_spl|       |
++------------------+------------------+
+| delete spikes    | |text_spk|       |
++------------------+------------------+
+| remove data step | |text_stp|       |
++------------------+------------------+
+
+.. |text_del| replace::
+   (*lim*: 2-sequence)
+   All points within the (lim[0], lim[1]) interval are deleted from the node
+   arrays.
+
+.. |text_scl| replace::
+   (*lim*: 2-sequence, *scale*: float)
+   All points within the (lim[0], lim[1]) interval are vertically scaled toward
+   the straight line connecting the end data points that fall within the
+   interval. The scaling factor depends on the vertical distance from the
+   `scale` parameter to the straight line.
+
+.. |text_spl| replace::
+   (*lim*: 2-sequence, *knots*: list of 2-lists ((x, y) points))
+   A spline drawn through the given knots replaces the points within the
+   (lim[0], lim[1]) interval.
+
+.. |text_spk| replace::
+   (*lim*: 2-sequence, *cutoff*: float)
+   The first y-array defined in the node is used to calculate its second
+   difference. The second difference is normalized to its maximum and compared
+   with `cutoff`. The exciding points are deleted from the node arrays.
+   The automatic cutoff is set as 0.7.
+
+.. |text_stp| replace::
+   (*left*: float (x-coordinate), *right*: 2-sequence ((x, y) point))
+   All data points to the right of the `right` point are shifted vertically by
+   the height difference at the `right` point. The points within the interval
+   from left to right are linearly shifted from zero at the left to the found
+   constant shift at the right.
+
+"""
+
+__author__ = "Konstantin Klementiev"
+__date__ = "22 Nov 2024"
+# !!! SEE CODERULES.TXT !!!
+
+import numpy as np
+from scipy.interpolate import InterpolatedUnivariateSpline
+
+AUTO_CUTOFF = 0.7  # for 'spikes', fraction of max(d²y)
+
+
+def calc_correction(x, y, correction, datainds=None):
+    if 'lim' not in correction and 'range' in correction:  # compatibility
+        correction['lim'] = correction.pop('range')
+    if correction['kind'] == 'delete':
+        lim = correction['lim']
+        args = np.argwhere((lim[0] < x) & (x < lim[1]))
+        return np.delete(x, args), np.delete(y, args)
+    elif correction['kind'] == 'scale':
+        lim = correction['lim']
+        where = (lim[0] < x) & (x < lim[1])
+        wx = x[where]
+        if len(wx) == 0:
+            return
+        wy = y[where]
+        if len(wy) == 0:
+            return
+        dy = wy.max() - wy.min()
+        if dy == 0:
+            return
+        scale = correction['scale']
+        factor = (scale - wy.min()) / dy
+        yn = np.array(y)
+        line = (wy[-1] - wy[0])/(wx[-1] - wx[0])*(wx - wx[0]) + wy[0]
+        yn[where] = (wy - line)*factor + line
+        return x, yn
+    elif correction['kind'] == 'spline':
+        lim = correction['lim']
+        where = (lim[0] < x) & (x < lim[1])
+        wx = x[where]
+        if len(wx) == 0:
+            return
+        yn = np.array(y)
+        kns = correction['knots']
+        if len(kns) == 1:
+            yn[where] = kns[0][1]
+        else:  # len(knots) >= 2:
+            k = min(len(kns)-1, 3)
+            try:
+                spl = InterpolatedUnivariateSpline(kns[:, 0], kns[:, 1], k=k)
+                yn[where] = spl(wx)
+            except ValueError:
+                return
+        return x, yn
+    elif correction['kind'] == 'spikes':
+        lim, cutoff = correction['lim'], correction['cutoff']
+        if cutoff is None:
+            return x, y
+        elif isinstance(cutoff, str):
+            cutoff = AUTO_CUTOFF
+        if not (0 < cutoff < 1):
+            return x, y
+        if datainds is None:
+            where = np.argwhere((lim[0] < x) & (x < lim[1])).flatten()
+            y2der = np.gradient(np.gradient(y))
+            y2derw = y2der[where]
+            if len(y2derw) == 0:
+                return x, y
+            y2derC = abs(y2derw).max() * cutoff
+            args = np.argwhere((y2der < -y2derC) | (y2der > y2derC)).flatten()
+            argsd = np.intersect1d(where, args)
+        else:
+            argsd = datainds
+        return np.delete(x, argsd), np.delete(y, argsd), argsd
+    elif correction['kind'] == 'step':
+        left = correction['left']
+        right = correction['right']
+        inStep = (left < x) & (x < right[0])
+        afterStep = x >= right[0]
+        eAfterStep = x[afterStep]
+        if len(eAfterStep) == 0:
+            return
+        dyAfter = y[afterStep][0] - right[1]
+        yn = np.array(y)
+        yn[afterStep] -= dyAfter
+        xInStep = x[inStep]
+        if len(xInStep) > 0:
+            yn[inStep] -= dyAfter / (right[0] - left) * (xInStep - left)
+        return x, yn

{parseq-2024.5.0 → parseq-2024.11.1}/parseq/core/plotExport.py

@@ -298,7 +298,7 @@ def plotSavedData(plots, lib='mpl'):
         ndim = nodeData[2]
         plotFuncName = 'plot{0}D{1}'.format(ndim, lib)  # e.g. plot1Dmpl
         plotFunc = globals()[plotFuncName]
-        widgets.append(plotFunc(nodeData))  # to keep references to silx polots
+        widgets.append(plotFunc(nodeData))  # to keep references to silx plots
     if lib == 'mpl':
         plt.show()  # end plotSavedData
 

{parseq-2024.5.0 → parseq-2024.11.1}/parseq/core/spectra.py

@@ -111,7 +111,7 @@ class TreeItem(object):
         else:
             res = ""
             if hasattr(self, 'name'):  # instance of TreeItem
-                if isinstance(self.name, type("")):
+                if isinstance(self.name, str):
                     res = self.name
             elif hasattr(self, 'madeOf'):  # instance of Spectrum
                 if self.error is not None:
@@ -119,13 +119,13 @@ class TreeItem(object):
                 elif self.beingTransformed:
                     res = '{0} is {1:.0f}% done'.format(self.beingTransformed,
                                                         self.progress*100)
-                elif isinstance(self.madeOf, (type(""), dict, tuple, list)):
-                    if isinstance(self.madeOf, type("")):
+                elif isinstance(self.madeOf, (str, dict, tuple, list)):
+                    if isinstance(self.madeOf, str):
                         res = str(self.madeOf)
                     elif isinstance(self.madeOf, (tuple, list)) and\
                             'combine' in self.dataFormat:
                         what = self.dataFormat['combine']
-                        if type(self.madeOf[0]) is str:
+                        if isinstance(self.madeOf[0], str):
                             names = self.madeOf
                         else:
                             names = [it.alias for it in self.madeOf]
@@ -139,7 +139,7 @@ class TreeItem(object):
                         res += ': {0}'.format(self.aliasExtra)
                     dataSource = self.dataFormat.get('dataSource', [])
                     for ds in dataSource:
-                        if isinstance(ds, type("")):
+                        if isinstance(ds, str):
                             if ds.startswith('silx'):
                                 if res:
                                     res += '\n'
@@ -1271,6 +1271,7 @@ class Spectrum(TreeItem):
 
         keys = re.findall(r'\[(.*?)\]', colStr)
         if len(keys) == 0:
+            colStr = colStr.replace('col', 'Col')
             if "Col" in colStr:
                 regex = re.compile('Col([0-9]*)')
                 # remove possible duplicates by list(dict.fromkeys())
@@ -1707,12 +1708,16 @@ class Spectrum(TreeItem):
         if csi.model is not None:
             csi.model.endResetModel()
 
+    @logger(minLevel=50, attrs=[(0, 'alias'), (1, 'name')])
     def make_corrections(self, node):
-        wasCorrected = False
         corr_param_name = 'correction_' + node.name
         if corr_param_name not in self.transformParams:
-            return wasCorrected
+            return False
         corrections = self.transformParams[corr_param_name]
+        if corrections is None:
+            return False
+
+        wasCorrected = False
         for correction in corrections:
             # if correction['kind'] in ('delete',):
             #     prop = 'raw'
@@ -1735,6 +1740,7 @@ class Spectrum(TreeItem):
                 shapeBefore = x.shape
 
                 corrKeys = []
+                datainds = None
                 for k, arr in node.arrays.items():
                     key = node.get_prop(k, prop)
                     if key == xkey:
@@ -1748,15 +1754,16 @@ class Spectrum(TreeItem):
                         #     x, y = \
                         #         node.widget.transformWidget.extraPlotTransform(
                         #             self, xkey, x, k, y)
-                        res = calc_correction(x, y, correction)
+                        res = calc_correction(x, y, correction, datainds)
                         if res is None:
                             continue
                         wasCorrected = True
-                        xn, yn = res
+                        xn, yn = res[:2]
+                        datainds = res[2] if len(res) > 2 else None
                         setattr(self, key, yn)
                         corrKeys.append(key)
 
-                if correction['kind'] == 'delete':
+                if correction['kind'] in ('delete', 'spikes'):
                     for nodeOther in csi.nodes.values():
                         if nodeOther is node:
                             continue
@@ -1776,7 +1783,8 @@ class Spectrum(TreeItem):
                             if key in corrKeys:
                                 continue
                             if attr is not None and attr.shape == shapeBefore:
-                                _, aC = calc_correction(x, attr, correction)
+                                aC = calc_correction(
+                                    x, attr, correction, datainds)[1]
                                 setattr(self, key, aC)
                     setattr(self, xkey, xn)
 

{parseq-2024.5.0 → parseq-2024.11.1}/parseq/core/transforms.py

@@ -310,10 +310,10 @@ class Transform(object):
         self.run_pre(params, items, updateUndo)
 
         nC = multiprocessing.cpu_count()
-        if isinstance(self.nThreads, type('')):
+        if isinstance(self.nThreads, str):
             self.nThreads = max(nC//2, 1) if self.nThreads.startswith('h')\
                 else nC
-        if isinstance(self.nProcesses, type('')):
+        if isinstance(self.nProcesses, str):
             self.nProcesses = max(nC//2, 1) if self.nProcesses.startswith('h')\
                 else nC
 
@@ -407,6 +407,7 @@ class Transform(object):
             if self.toNode.widget is not None:
                 self.toNode.widget.onTransform = True
         if self.sendSignals:
+            csi.mainWindow.afterTransformSignal.emit(self.fromNode.widget)
             csi.mainWindow.beforeTransformSignal.emit(self.toNode.widget)
 
     # @staticmethod
@@ -734,6 +735,7 @@ def run_transforms(items, parentItem):
                 tr.run(dataItems=its)
                 if hasattr(tr, 'widget'):  # when with GUI
                     tr.widget.replotAllDownstream(tr.name)
+
             if tr.fromNode is tr.toNode:
                 break
 

{parseq-2024.5.0 → parseq-2024.11.1}/parseq/description.py

@@ -18,7 +18,7 @@ A screenshot of ParSeq-XAS (an EXAFS analysis pipeline) as an application
 example:
 
 .. image:: _images/XAS-foils.gif
-   :scale: 50 %
+   :scale: 60 %
 
 Main features
 -------------
@@ -37,13 +37,13 @@ Main features
 -  Entering into the analysis pipeline at any node, not only at the head of the
    pipeline.
 
--  Creation of cross-data combinations (e.g. averaging, RMS or PCA) and their
+-  Creation of cross-data combinations (e.g. averaging, PCA) and their
    propagation downstream the pipeline together with the parental data. The
    possibility of termination of the parental data at any selected downstream
    node.
 
 -  General data correction routines for 1D data: range deletion, scaling,
-   replacement by a spline and jump correction.
+   replacement by a spline, deletion of spikes and jump correction.
 
 -  Parallel execution of data transformations with multiprocessing or
    multithreading (can be opted by the pipeline application).
@@ -51,15 +51,15 @@ Main features
 -  Optional curve fitting solvers, also executed in parallel for multiple data
    items.
 
--  Informative error handling that provides alerts and stack traceback -- the
+-  Informative error handling that provides alerts and stack traceback with the
    type and location of the occurred error.
 
 -  Optional time profiling of the pipeline, as controlled by a command-line
    argument.
 
 -  Export of the workflow into a project file. Export of data into various data
-   formats with accompanied Python scripts that visualize the exported data for
-   the user to tune their publication plots.
+   formats with accompanied Python scripts that visualize the exported data in
+   publication-quality plots.
 
 -  ParSeq understands container files (presently only hdf5) and adds them to
    the system file tree as subfolders. The file tree, including hdf5
@@ -80,11 +80,19 @@ and curve fits are exemplified by separately installed analysis packages:
 - `ParSeq-XAS <https://github.com/kklmn/ParSeq-XAS>`_
 - `ParSeq-XES-scan <https://github.com/kklmn/ParSeq-XES-scan>`_
 
-Dependencies
+Installation
 ------------
 
-- `silx <https://github.com/silx-kit/silx>`_ -- plotting, hdf5 handling, Qt
-- `sphinx <https://github.com/sphinx-doc/sphinx>`_ -- building documentation
+Install it by pip or conda or get ParSeq from
+`GitHub <https://github.com/kklmn/ParSeq>`_ and use it with or without
+installation.
+See :ref:`detailed installation instructions <instructions>`.
+
+Documentation
+-------------
+
+The documentation is available online on
+`Read the Docs <http://parseq.readthedocs.io>`_.
 
 Launch an example
 -----------------

{parseq-2024.5.0 → parseq-2024.11.1}/parseq/fits/basefit.py

@@ -253,10 +253,10 @@ class Fit:
         self.run_pre(params, items, updateUndo)
 
         nC = multiprocessing.cpu_count()
-        if isinstance(self.nThreads, type('')):
+        if isinstance(self.nThreads, str):
             self.nThreads = max(nC//2, 1) if self.nThreads.startswith('h')\
                 else nC
-        if isinstance(self.nProcesses, type('')):
+        if isinstance(self.nProcesses, str):
             self.nProcesses = max(nC//2, 1) if self.nProcesses.startswith('h')\
                 else nC
 

{parseq-2024.5.0 → parseq-2024.11.1}/parseq/fits/exafsfit.py

@@ -4,6 +4,8 @@ __date__ = "5 Nov 2023"
 # !!! SEE CODERULES.TXT !!!
 
 import numpy as np
+if not hasattr(np, 'trapezoid'):
+    np.trapezoid = np.trapz
 from scipy.optimize import curve_fit
 from scipy.interpolate import interp1d
 from scipy.linalg import eigh
@@ -147,7 +149,8 @@ class EXAFSFit(Fit):
         fitw = fit * data.ftfitwindow
         if 'forceFT0' in dtparams:
             if dtparams['forceFT0']:
-                fitw -= np.trapz(fitw, x) / np.trapz(np.ones_like(fitw), x)
+                fitw -= np.trapezoid(fitw, x=x) / np.trapezoid(
+                    np.ones_like(fitw), x=x)
         fitft = np.fft.rfft(fitw, n=cls.nfft) * dk/2
         r = np.fft.rfftfreq(cls.nfft, dk/np.pi)
         wherer = r <= dtparams['rmax'] if 'rmax' in dtparams else None
@@ -202,14 +205,20 @@ class EXAFSFit(Fit):
                     v['value'] = vMin
 
             if kRangeUse:
-                wherek = (kRange[0] <= x) & (x <= kRange[1]) \
-                    if isinstance(kRange, (list, tuple)) else None
+                try:
+                    wherek = (kRange[0] <= x) & (x <= kRange[1])
+                except Exception:
+                    if 'kmin' in dtparams and 'kmax' in dtparams:
+                        kRange = [dtparams['kmin'], dtparams['kmax']]
+                    else:
+                        kRange = [0, x.max()]
+                    wherek = (kRange[0] <= x) & (x <= kRange[1])
                 xw, yw = x[wherek], y[wherek]
-                Deltak = kRange[1] - kRange[0]
+                Deltak = kRange[1] - kRange[0] \
+                    if isinstance(kRange, (list, tuple)) else x.max() - x.min()
             else:
                 wherek = None
-                if not rRangeUse:
-                    xw, yw = x, y
+                xw, yw = x, y
                 Deltak = x.max() - x.min()
             sigmax = xw**kw
 
@@ -217,8 +226,14 @@ class EXAFSFit(Fit):
                 dk = x[1] - x[0]
                 ft = np.fft.rfft(y, n=cls.nfft) * dk/2
                 r = np.fft.rfftfreq(cls.nfft, dk/np.pi)
-                wherer = (rRange[0] <= r) & (r <= rRange[1]) \
-                    if isinstance(rRange, (list, tuple)) else None
+                try:
+                    wherer = (rRange[0] <= r) & (r <= rRange[1])
+                except Exception:
+                    if 'rmax' in dtparams:
+                        rRange = [0, dtparams['rmax']]
+                    else:
+                        rRange = [0, r.max()]
+                    wherer = (rRange[0] <= r) & (r <= rRange[1])
                 Deltar = rRange[1] - rRange[0]
                 rw, ftwr, ftwi = r[wherer], ft.real[wherer], ft.imag[wherer]
                 # ftwm = np.abs(ft)[wherer]
@@ -316,7 +331,9 @@ class EXAFSFit(Fit):
         if nu > 0:
             H = cls.get_Hessian_chi2(xw, chi2opt, fitStruct, err, popt, bounds)
             H *= nu / chi2opt
-            Hii = np.where(np.diag(H) > 0, np.diag(H)**0.5, 1e-28)
+            diagH = np.array(np.diag(H))
+            diagH[diagH < 0] = 1e-28
+            Hii = diagH**0.5
             fitProps['corr'] = H / np.dot(Hii.reshape(P, 1), Hii.reshape(1, P))
 
             errA = np.sqrt(2) / Hii

{parseq-2024.5.0 → parseq-2024.11.1}/parseq/gui/aboutDialog.py

@@ -155,7 +155,7 @@ class AboutDialog(qt.QDialog):
         strSphinx = 'Sphinx {0}'.format(sphinx.__version__)
         strSilx = r'silx {0}'.format(versilx)
         strParSeq = '{0}'.format(PARSEQPATH).replace('\\', '/')
-        if type(self.parseq_pypi_version) is tuple:
+        if isinstance(self.parseq_pypi_version, tuple):
             pypiver, curver = self.parseq_pypi_version
             pstr = "`PyPI <https://pypi.python.org/pypi/parseq>`_"
             if curver < pypiver:
@@ -204,9 +204,9 @@ class AboutDialog(qt.QDialog):
         return txt
 
     def makeThreadProcessStr(self, nThreads, nProcesses):
-        if isinstance(nThreads, type('')):
+        if isinstance(nThreads, str):
             nThreads = max(nC//2, 1) if nThreads.startswith('h') else nC
-        if isinstance(nProcesses, type('')):
+        if isinstance(nProcesses, str):
             nProcesses = max(nC//2, 1) if nProcesses.startswith('h') else nC
 
         res = ''