PyMca5 5.9.5__tar.gz → 5.9.5rc4__tar.gz

{pymca5-5.9.5/src/PyMca5.egg-info → pymca5-5.9.5rc4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyMca5
-Version: 5.9.5
+Version: 5.9.5rc4
 Summary: Mapping and X-Ray Fluorescence Analysis
 Author: V. Armando Sole
 Author-email: sole@esrf.fr

{pymca5-5.9.5 → pymca5-5.9.5rc4}/changelog.txt

@@ -1,14 +1,6 @@
 VERSION 5.9.5
 -------------
 
-- Add the possibility to white NaN values in RGB Correlator.
-
-- IO. Improved sorting of scans in HDF5 files.
-
-- XRF. Add support for standard batch fitting of BCF files.
-
-- XRF. Support three incoming beam filters.
-
 - XRF. Support secondary excitation calculations fitting M subshells.
 
 VERSION 5.9.4

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaGui/io/hdf5/HDF5Widget.py

@@ -991,7 +991,7 @@ def _getFilenameDialog(parent=None):
     """Open a dialog to select a file in a filesystem tree view.
     Return the selected filename."""
     from PyMca5.PyMcaGui.io import PyMcaFileDialogs
-    fileTypeList = ['HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)',
+    fileTypeList = ['HDF5 Files (*.h5 *.nxs *.hdf)',
                     'HDF5 Files (*)']
     message = "Open HDF5 file"
     filenamelist, ffilter = PyMcaFileDialogs.getFileList(parent=parent,

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaGui/math/fitting/SimpleFitBatchGui.py

@@ -100,11 +100,10 @@ class SimpleFitBatchParameters(qt.QWidget):
             self._inputDir = PyMcaDirs.inputDir
         elif os.path.exists(self._inputDir):
             PyMcaDirs.inputDir = self._inputDir
-        filetypes = []
-        if HDF5SUPPORT:
-            filetypes.append("HDF5 Files(*.nxs *.h5 *.hdf *.hdf5)")
-        filetypes  += ["Mca Files (*.mca)",
+        filetypes  = ["Mca Files (*.mca)",
                       "Edf Files (*.edf)"]
+        if HDF5SUPPORT:
+            filetypes.append("HDF5 Files(*.nxs *.h5 *.hdf)")
         filetypes.append("SPEC Files (*.spec)")
         filetypes.append("SPEC Files (*.dat)")
         filetypes.append("All files (*)")

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaGui/physics/xrf/AttenuatorsTable.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2025 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -94,11 +94,11 @@ class AttenuatorsTab(qt.QWidget):
                 if rheight > 40:
                     self.table.setMinimumHeight(10*rheight)
                 else:
-                    self.table.setMinimumHeight(14*rheight)
+                    self.table.setMinimumHeight(13*rheight)
             else:
                 self.editor = MaterialEditor.MaterialEditor(graph=graph)
-                self.table.setMinimumHeight(14*rheight)
-            self.table.setMaximumHeight(14*rheight)
+                self.table.setMinimumHeight(13*rheight)
+            self.table.setMaximumHeight(13*rheight)
         self.userAttenuators = TransmissionTableGui.TransmissionTableGui()
         self.mainTab.addTab(self.editor, "Material Editor")
         self.mainTab.addTab(self.userAttenuators, "User Attenuators")
@@ -322,12 +322,9 @@ class AttenuatorsTableWidget(QTable):
     def __init__(self, parent=None, name="Attenuators Table",
                  attenuators=None, matrixmode=None, compoundmode=None,
                  layerindex=0, funnyfilters=False):
-
-        beamFilters0 = ["BeamFilter1", "BeamFilter2", "BeamFilter3"] # this needs to be synchronized with FitParam.py
         attenuators0 = ["Atmosphere", "Air", "Window", "Contact", "DeadLayer",
-                       "Filter5", "Filter6", "Filter7"] + beamFilters0 +  ["Detector", "Matrix"]
-        self.__attenuators0 = attenuators0
-        self.__beamFilters0 = beamFilters0
+                       "Filter5", "Filter6", "Filter7", "BeamFilter1",
+                       "BeamFilter2", "Detector", "Matrix"]
 
         QTable.__init__(self, parent)
         self.setWindowTitle(name)
@@ -388,12 +385,12 @@ class AttenuatorsTableWidget(QTable):
 
         self.sigValueChanged[int,int].connect(self.mySlot)
 
-    def __build(self, nfilters=13):
+    def __build(self, nfilters=12):
         n = 0
         if (not self.matrixMode) and (not self.compoundMode):
-            n = len(self.__beamFilters0) + 2
+            n = 4
             #self.setNumRows(nfilters+n)
-            self.setRowCount(len(self.__attenuators0))
+            self.setRowCount(12)
         else:
             self.setRowCount(nfilters)
         rheight = self.horizontalHeader().sizeHint().height()
@@ -460,11 +457,10 @@ class AttenuatorsTableWidget(QTable):
             #self.setItem(idx,2,combo)
             combo.sigMaterialComboBoxSignal.connect(self._comboSlot)
 
-        nBeamFilters = len(self.__beamFilters0)
-        for i in range(nBeamFilters):
+        for i in range(2):
             #BeamFilter(i)
             item = qt.QCheckBox(self)
-            idx = self.rowCount() - (n - i)
+            idx = self.rowCount() - (4 - i)
             self.setCellWidget(idx, 0, item)
             text = "BeamFilter%d" % i
             item.setText(text)

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaGui/physics/xrf/FitParam.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2025 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -69,7 +69,7 @@ FitParamHeaders= ["FIT", "DETECTOR","BEAM","PEAKS", "PEAK SHAPE", "ATTENUATORS",
 
 class FitParamWidget(FitParamForm):
     attenuators= ["Filter 0", "Filter 1", "Filter 2", "Filter 3", "Filter 4", "Filter 5",
-                   "Filter 6","Filter 7","BeamFilter0", "BeamFilter1", "BeamFilter2","Detector", "Matrix"]
+                   "Filter 6","Filter 7","BeamFilter0", "BeamFilter1","Detector", "Matrix"]
     def __init__(self, parent=None):
         FitParamForm.__init__(self, parent)
         self._channels = None
@@ -616,9 +616,12 @@ class FitParamWidget(FitParamForm):
                 else:
                     current['AlphaScatteringFlag'] = 0
                 self.matrixGeometry.setParameters(current)
-            elif att.upper().startswith("BEAMFILTER"):
+            elif att.upper() == "BEAMFILTER0":
                 attpar= self.__get("attenuators", att, [0, "-", 0., 0.], None)
-                row = self.attTable.rowCount() - 2 - (3 - int(att[-1])) # maximum 3 BeamFilter
+                row = self.attTable.rowCount() - 4
+            elif att.upper() == "BEAMFILTER1":
+                attpar= self.__get("attenuators", att, [0, "-", 0., 0.], None)
+                row = self.attTable.rowCount() - 3
             elif att.upper() == "DETECTOR":
                 attpar= self.__get("attenuators", att, [0, "-", 0., 0.], None)
                 row = self.attTable.rowCount() - 2
@@ -642,7 +645,7 @@ class FitParamWidget(FitParamForm):
                 attpar.append(1.0)
             self.attTable.setText(row, 3, str(attpar[2]))
             self.attTable.setText(row, 4, str(attpar[3]))
-            if not (att.upper() in ["MATRIX", "DETECTOR"] or att.upper().startswith("BEAMFILTER")):
+            if att.upper() not in ["MATRIX", "DETECTOR", "BEAMFILTER1", "BEAMFILTER2"]:
                 self.attTable.setText(row, 5, str(attpar[4]))
             else:
                 self.attTable.setText(row, 5, "1.0")

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaGui/pymca/ExternalImagesStackPluginBase.py

@@ -57,15 +57,15 @@ class ExternalImagesStackPluginBase(StackPluginBase.StackPluginBase):
         StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw)
 
     def _loadImageFiles(self):
-        fileTypeList = ['HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)',
-                        "PNG Files (*png)",
+        fileTypeList = ["PNG Files (*png)",
                         "JPEG Files (*jpg *jpeg)",
                         "IMAGE Files (*)",
                         "DAT Files (*dat)",
                         "CSV Files (*csv)",
                         "EDF Files (*edf)",
                         "EDF Files (*ccd)",
-                        "EDF Files (*)"]
+                        "EDF Files (*)",
+                        'HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)']
         filenamelist, filefilter = PyMcaFileDialogs.getFileList(parent=None,
                                     filetypelist=fileTypeList,
                                     message="Open image file",

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaGui/pymca/LegacyPyMcaBatch.py

@@ -626,10 +626,9 @@ class McaBatchGUI(qt.QWidget):
             self.inputDir =  os.getcwd()
         wdir = self.inputDir
         wfilter = self.inputFilter
-        filetypes = ""
+        filetypes  = "McaFiles (*.mca)\nEdfFiles (*.edf)\n"
         if HDF5SUPPORT:
             filetypes += "HDF5 (*.nxs *.h5 *.hdf *.hdf5)\n"
-        filetypes += "McaFiles (*.mca)\nEdfFiles (*.edf)\n"
         filetypes += "SpecFiles (*.spec)\nSpecFiles (*.dat)\nAll files (*)"
         filetypelist = filetypes.split("\n")
         filelist, filefilter = PyMcaFileDialogs.getFileList(self,

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaGui/pymca/PyMcaBatch.py

@@ -1143,10 +1143,9 @@ class McaBatchGUI(qt.QWidget):
             self.inputDir =  os.getcwd()
         wdir = self.inputDir
         wfilter = self.inputFilter
-        filetypes = ""
+        filetypes = "McaFiles (*.mca)\nEdfFiles (*.edf)\nCSV (*.csv *.CSV)\n"
         if HDF5SUPPORT:
             filetypes += "HDF5 (*.nxs *.h5 *.hdf *.hdf5)\n"
-        filetypes += "McaFiles (*.mca)\nEdfFiles (*.edf)\nCSV (*.csv *.CSV)\n"
         filetypes += "SpecFiles (*.spec)\nSpecFiles (*.dat)\nAll files (*)"
         filetypelist = filetypes.split("\n")
         filelist, filefilter = PyMcaFileDialogs.getFileList(self,

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaGui/pymca/QDispatcher.py

@@ -51,12 +51,7 @@ class QDispatcher(qt.QWidget):
         self.mainLayout.setContentsMargins(0, 0, 0, 0)
         self.mainLayout.setSpacing(0)
         self.sourceList = []
-        fileTypeList = []
-        if QDataSource.NEXUS:
-            fileTypeList.append("HDF5 Files (*.nxs *.hdf *.h5 *.hdf5)")
-            if "silx" in sys.modules:
-                fileTypeList.append("HDF5-like Files (*)")
-        fileTypeList += ["Spec Files (*mca)",
+        fileTypeList = ["Spec Files (*mca)",
                         "Spec Files (*dat)",
                         "Spec Files (*spec)",
                         "SPE Files (*SPE *spe)",
@@ -65,6 +60,10 @@ class QDispatcher(qt.QWidget):
                         "TIFF Files (*.tif *.tiff *.TIF *.TIFF)",
                         "CSV Files (*csv)",
                         "JCAMP-DX Files (*.jdx *.JDX *.dx *.DX)"]
+        if QDataSource.NEXUS:
+            fileTypeList.append("HDF5 Files (*.nxs *.hdf *.h5 *.hdf5)")
+            if "silx" in sys.modules:
+                fileTypeList.append("HDF5-like Files (*)")
         fileTypeList.append("All Files (*)")
 
         self.sourceSelector = QSourceSelector.QSourceSelector(self,

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaGui/pymca/XMCDWindow.py

@@ -1,5 +1,5 @@
 # /*##########################################################################
-# Copyright (C) 2004-2025 European Synchrotron Radiation Facility
+# Copyright (C) 2004-2023 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -1058,7 +1058,7 @@ class XMCDScanWindow(ScanWindow.ScanWindow):
                         idx * motorsPerLine, min((idx + 1) * motorsPerLine, len(motors))
                     ):
                         motorNamesText += "  " + motorNames[i]
-                        motorValuesText += "  " + "%s" % motorValues[i]
+                        motorValuesText += "  " + motorValues[i]
                         n += 1
                     motorNamesText += NEWLINE
                     motorValuesText += NEWLINE

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaMath/fitting/SimpleFitModule.py

@@ -447,7 +447,7 @@ class SimpleFit(object):
         niter = self._fitConfiguration['fit']['stripiterations']
         if niter > 0:
             _logger.debug("CALCULATING STRIP")
-            _logger.debug("iterations = %s", niter)
+            _logger.debug("iterations = ", niter)
             _logger.debug("constant   = %s",
                           self._fitConfiguration['fit']['stripconstant'])
             _logger.debug("width      = %s",

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaMath/mva/PCATools.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2025 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2021 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF by the Software group.
@@ -692,7 +692,6 @@ def numpyPCA(stack, index=-1, ncomponents=10, binning=None,
                     tmpData = (tmpData[:, ::binning] - avgSpectrum) / standardDeviation
                 else:
                     tmpData = tmpData[:, ::binning]
-                tmpData = tmpData.reshape(nChannels)
                 for j in range(ncomponents):
                     images[j, i] = numpy.dot(tmpData, eigenvectors[j])
             # reshape the images
@@ -707,7 +706,6 @@ def numpyPCA(stack, index=-1, ncomponents=10, binning=None,
                         tmpData = (tmpData[:, ::binning] - avgSpectrum) / standardDeviation
                     else:
                         tmpData = tmpData[:, ::binning]
-                    tmpData = tmpData.reshape(nChannels)
                     for j in range(ncomponents):
                         images[j, i] = numpy.dot(tmpData, eigenvectors[j])
                     i += 1

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaPhysics/xrf/McaAdvancedFitBatch.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2025 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -44,8 +44,6 @@ from PyMca5.PyMcaIO import AifiraMap
 from PyMca5.PyMcaIO import EDFStack
 from PyMca5.PyMcaIO import LispixMap
 from PyMca5.PyMcaIO import NumpyStack
-from PyMca5.PyMcaIO import BrukerBCF
-
 try:
     import h5py
     from PyMca5.PyMcaIO import HDF5Stack1D
@@ -340,10 +338,6 @@ class McaAdvancedFitBatch(object):
                                                    scanlist=scanlist)
 
             ffile = self.__tryEdf(inputfile)
-            if ffile is None:
-                if BrukerBCF.HAS_BCF_SUPPORT:
-                    if BrukerBCF.isBrukerBCFFile(inputfile):
-                        ffile = BrukerBCF.BrukerBCF(inputfile)
             if ffile is None:
                 ffile = self.__tryLucia(inputfile)
             if ffile is None:

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/PyMcaPlugins/StackNormalizationPlugin.py

@@ -159,10 +159,9 @@ class StackNormalizationPlugin(StackPluginBase.StackPluginBase):
 
     def _loadExternalData(self):
         getfilter = True
-        fileTypeList = []
+        fileTypeList = ["EDF Files (*edf *ccd *tif)"]
         if HDF5:
             fileTypeList.append('HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)')
-        fileTypeList.append("EDF Files (*edf *ccd *tif)")
         fileTypeList.append('ASCII Files (*)') 
         fileTypeList.append("EDF Files (*)")
         message = "Open data file"

{pymca5-5.9.5 → pymca5-5.9.5rc4}/src/PyMca5/__init__.py

@@ -27,7 +27,7 @@ __author__ = "V.A. Sole"
 __contact__ = "sole@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__version__ = "5.9.5"
+__version__ = "5.9.5rc4"
 
 import os
 import sys

{pymca5-5.9.5 → pymca5-5.9.5rc4/src/PyMca5.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyMca5
-Version: 5.9.5
+Version: 5.9.5rc4
 Summary: Mapping and X-Ray Fluorescence Analysis
 Author: V. Armando Sole
 Author-email: sole@esrf.fr