PyMca5 5.9.5rc2__tar.gz → 5.9.6__tar.gz

{pymca5-5.9.5rc2/src/PyMca5.egg-info → pymca5-5.9.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyMca5
-Version: 5.9.5rc2
+Version: 5.9.6
 Summary: Mapping and X-Ray Fluorescence Analysis
 Author: V. Armando Sole
 Author-email: sole@esrf.fr

{pymca5-5.9.5rc2 → pymca5-5.9.6}/changelog.txt

@@ -1,6 +1,19 @@
+Unreleased
+----------
+
+- XRF. Bug fix in batch processing when using fit files.
+
 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

pymca5-5.9.6/package/pyinstaller/codesign.sh

@@ -0,0 +1,65 @@
+#!/usr/bin/env bash
+
+# The script codesigns the application bundle.
+
+# Exit immediately if a command exits with a non-zero status.
+set -e
+# Print commands and their arguments as they are executed (debug mode).
+set -x
+
+log() {
+  echo "$(date "+%Y-%m-%d %H:%M:%S") INFO [codesign] $1"
+}
+
+# Check if required environment variables are set,
+if [[ -z "${APPLE_TEAM_ID}" || -z "${KEYCHAIN_PASSWORD}" || -z "${CERTIFICATE_BASE64}" || -z "${CERTIFICATE_PASSWORD}" ]]; then
+  log "Skipping code signing; the required environment variables (APPLE_TEAM_ID, KEYCHAIN_PASSWORD, CERTIFICATE_BASE64, CERTIFICATE_PASSWORD) are not set."
+  exit 0
+fi
+
+log "Setting the required environment variables."
+APP_NAME="PyMca"
+ROOT="${PWD}"
+APP_PATH="${ROOT}/dist/${APP_NAME}.app"
+KEYCHAIN_PATH="${ROOT}/notarize.keychain-db"
+CERTIFICATE_PATH="${ROOT}/certificate.p12"
+APPLE_SIGNING_ID="Developer ID Application: MARIUS SEPTIMIU RETEGAN (${APPLE_TEAM_ID})"
+
+log "Creating a temporary keychain."
+security create-keychain -p "${KEYCHAIN_PASSWORD}" "${KEYCHAIN_PATH}"
+security set-keychain-settings -lut 21600 "${KEYCHAIN_PATH}"
+security unlock-keychain -p "${KEYCHAIN_PASSWORD}" "${KEYCHAIN_PATH}"
+
+log "Importing the certificate from the base64 string."
+echo "${CERTIFICATE_BASE64}" | base64 --decode -o "${CERTIFICATE_PATH}"
+
+log "Importing the certificate to the keychain."
+security import "${CERTIFICATE_PATH}" \
+  -P "${CERTIFICATE_PASSWORD}" \
+  -A -t cert -f pkcs12 \
+  -k "${KEYCHAIN_PATH}"
+
+log "Configuring keychain access control for codesigning without UI prompts."
+security set-key-partition-list \
+  -S "apple-tool:,apple:,codesign:" \
+  -s -k "${KEYCHAIN_PASSWORD}" \
+  -D "${APPLE_SIGNING_ID}" \
+  -t private \
+  "${KEYCHAIN_PATH}"
+  
+log "Setting the keychain as the default so codesign can find the certificate."
+security list-keychains -s "${KEYCHAIN_PATH}"
+
+log "Codesigning the application bundle."
+codesign -vvv --force --deep --strict --sign "${APPLE_SIGNING_ID}" \
+  --timestamp \
+  --options runtime \
+  --entitlements "./entitlements.plist" \
+  --keychain "${KEYCHAIN_PATH}" \
+  "${APP_PATH}"
+
+log "Cleanup the keychain and certificate file."
+rm -f "${CERTIFICATE_PATH}"
+security delete-keychain "${KEYCHAIN_PATH}"
+
+log "Codesigning completed successfully."

pymca5-5.9.6/package/pyinstaller/create-dmg.sh

@@ -0,0 +1,125 @@
+#!/usr/bin/env bash
+
+# The script creates a DMG file for the application bundle.
+
+# Exit immediately if a command exits with a non-zero status
+set -e
+# Print commands and their arguments as they are executed (debug mode)
+set -x
+
+log() {
+  echo "$(date '+%Y-%m-%d %H:%M:%S') INFO [create-dmg] $1"
+}
+
+log "Setting environment variables."
+APP_NAME="PyMca"
+ROOT="${PWD}"
+APP="${ROOT}/dist/${APP_NAME}.app"
+RESOURCES="${ROOT}" # The path to resources (volume icon, background, ...)."
+
+log "Setting derived environment variables."
+ARTIFACTS="${ROOT}/artifacts"
+TEMPLATE="${ARTIFACTS}/template"
+TEMPLATE_DMG="${ARTIFACTS}/template.dmg"
+APP_DMG="${ARTIFACTS}/${APP_NAME}.dmg"
+
+SLEEP_INTERVAL=5
+
+log "Checking if artifacts folder exists."
+[ -d "${ARTIFACTS}" ] && rm -rf "${ARTIFACTS}"
+
+log "Creating the artifacts folder."
+mkdir -p "${ARTIFACTS}"
+
+log "Removing any previous images."
+if [[ -e "${TEMPLATE}" ]]; then rm -rf "${TEMPLATE}"; fi
+if [[ -e "${APP_DMG}" ]]; then rm -rf "${APP_DMG}"; fi
+
+log "Copying required files."
+mkdir -p "${TEMPLATE}/.background"
+cp -a "${RESOURCES}/background.pdf" "${TEMPLATE}/.background/background.pdf"
+cp -a "${RESOURCES}/../../icons/PyMca.icns" "${TEMPLATE}/.VolumeIcon.icns"
+cp -a "${RESOURCES}/DS_Store" "${TEMPLATE}/.DS_Store"
+cp -a "${APP}" "${TEMPLATE}/${APP_NAME}.app"
+ln -s "/Applications/" "${TEMPLATE}/Applications"
+
+log "Creating a regular .fseventsd/no_log file."
+mkdir "${TEMPLATE}/.fseventsd"
+touch "${TEMPLATE}/.fseventsd/no_log"
+
+log "Sleeping for a few seconds."
+sleep "${SLEEP_INTERVAL}"
+
+log "Creating the temporary disk image."
+hdiutil create -verbose -format UDRW -volname "${APP_NAME}" -fs APFS \
+       -srcfolder "${TEMPLATE}" \
+       "${TEMPLATE_DMG}"
+
+log "Sleeping for a few seconds."
+sleep "${SLEEP_INTERVAL}"
+
+log "Detaching the temporary disk image if still attached."
+hdiutil detach -verbose "/Volumes/${APP_NAME}" -force || true
+
+log "Attaching the temporary disk image in read/write mode."
+MOUNT_OUTPUT=$(hdiutil attach -readwrite -noverify -noautoopen "${TEMPLATE_DMG}" | grep '^/dev/')
+DEV_NAME=$(echo -n "${MOUNT_OUTPUT}" | head -n 1 | awk '{print $1}')
+MOUNT_POINT=$(echo -n "${MOUNT_OUTPUT}" | tail -n 1 | awk '{print $3}')
+
+log "Fixing permissions."
+chmod -Rf go-w "${TEMPLATE}" || true
+
+log "Hiding the background directory even more."
+SetFile -a V "${MOUNT_POINT}/.background"
+
+log "Seting the custom icon volume flag so that volume has nice icon."
+SetFile -a C "${MOUNT_POINT}"
+
+log "Moving the icons to the appropriate position relative to the background."
+WINDOW_SIZE="{0, 0, 500, 300}"
+APP_ICON_POSITION="{114, 124}"
+APPLICATIONS_ICON_POSITION="{386, 124}"
+
+osascript <<EOF
+tell application "Finder"
+    tell disk "${APP_NAME}"
+        open
+        set current view of container window to icon view
+        set toolbar visible of container window to false
+        set statusbar visible of container window to false
+        set bounds of container window to ${WINDOW_SIZE}
+
+        set viewOptions to the icon view options of container window
+        set arrangement of viewOptions to not arranged
+        set icon size of viewOptions to 96
+        set background picture of viewOptions to file ".background:background.pdf"
+
+        set position of item "${APP_NAME}" to ${APP_ICON_POSITION}
+        set position of item "Applications" to ${APPLICATIONS_ICON_POSITION}
+
+        close
+        open
+        delay 1
+        update without registering applications
+    end tell
+end tell
+EOF
+
+log "Sleeping for a few seconds."
+sleep "${SLEEP_INTERVAL}"
+
+log "Detaching the temporary disk image"
+hdiutil detach "${DEV_NAME}" -force || true
+
+log "Sleeping for a few seconds."
+sleep "${SLEEP_INTERVAL}"
+
+log "Converting the temporary image to a compressed image."
+hdiutil convert "${TEMPLATE_DMG}" \
+       -format UDZO \
+       -imagekey zlib-level=9 \
+       -o "${APP_DMG}"
+
+log "Cleaning up."
+rm -rf "${TEMPLATE}"
+rm -rf "${TEMPLATE_DMG}"

pymca5-5.9.6/package/pyinstaller/entitlements.plist

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+        <!-- These are required for binaries built by PyInstaller -->
+        <key>com.apple.security.cs.allow-jit</key>
+        <true/>
+        <key>com.apple.security.cs.allow-unsigned-executable-memory</key>
+        <true/>
+        <key>com.apple.security.cs.disable-library-validation</key>
+        <true/>
+</dict>
+</plist>

pymca5-5.9.6/package/pyinstaller/notarize.sh

@@ -0,0 +1,35 @@
+#!/usr/bin/env bash
+
+# The script submits the application for notarization to Apple.
+
+# Exit immediately if a command exits with a non-zero status
+set -e
+# Print commands and their arguments as they are executed (debug mode)
+set -x
+
+log() {
+  echo "$(date '+%Y-%m-%d %H:%M:%S') INFO [notarize] $1"
+}
+
+# Check if the required environment variables are set.
+if [[ -z "${APPLE_ID}" || -z "${APPLE_TEAM_ID}" || -z "${APPLICATION_SPECIFIC_PASSWORD}" ]]; then
+  log "Skipping notarization; the required environment variables (APPLE_ID, APPLE_TEAM_ID, APPLICATION_SPECIFIC_PASSWORD) are not set."
+  exit 0
+fi
+
+log "Setting the required environment variables."
+APP_NAME="PyMca"
+ROOT="${PWD}"
+APP_DMG="${ROOT}/artifacts/${APP_NAME}.dmg"
+
+log "Submiting the application for notarization."
+xcrun notarytool submit \
+  --apple-id "${APPLE_ID}" \
+  --team-id "${APPLE_TEAM_ID}" \
+  --password "${APPLICATION_SPECIFIC_PASSWORD}" \
+  --wait "${APP_DMG}"
+
+log "Stapling the notarization ticket to the application bundle."
+xcrun stapler staple "${APP_DMG}"
+
+log "Notarization completed successfully."

{pymca5-5.9.5rc2 → pymca5-5.9.6}/package/pyinstaller/pyinstaller_github.spec

@@ -49,6 +49,8 @@ hiddenimports += collect_submodules('hdf5plugin')
 hiddenimports += collect_submodules('fisx')
 hiddenimports += collect_submodules('PyMca5.PyMcaGui.PyMcaQt')
 hiddenimports += collect_submodules('PyMca5.PyMcaGui.pymca')
+hiddenimports += collect_submodules('multiprocessing')
+hiddenimports += collect_submodules('multiprocessing.spawn')
 
 my_binaries = []
 

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaCore/PyMcaMatplotlibSave.py

@@ -658,7 +658,7 @@ if __name__ == "__main__":
     import sys
     if len(sys.argv) < 2:
         a=numpy.arange(1200.)
-        a.shape = 20, 60
+        a = a.reshape(20, 60)
         PyMcaMatplotlibSaveImage(a, "filename.png", colormap="rainbow")
         print("Image filename.png saved")
     else:

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaCore/SpecFileDataSource.py

@@ -543,7 +543,7 @@ class SpecFileDataSource(object):
                     output.data[i,:] = mcaData
                 #I have all the MCA data ready for image plot
                 if selectiontype == 'STACK':
-                    output.data.shape = 1, npoints, -1
+                    output.data = output.data.reshape(1, npoints, -1)
                     shape = output.data.shape
                     for i in range(len(shape)):
                         key = 'Dim_%d' % (i+1,)

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaCore/StackBase.py

@@ -302,7 +302,7 @@ class StackBase(object):
                     numpy.add(self._stackImageData[i:i+step,:],
                               numpy.sum(tmpData, 2),
                               self._stackImageData[i:i+step,:])
-                    tmpData.shape = step*shape[1], shape[2]
+                    tmpData = tmpData.reshape(step*shape[1], shape[2])
                     tmpMax = numpy.nanmax(tmpData, axis=0)
                     numpy.add(mcaData0, numpy.sum(tmpData, 0), mcaData0)
                     mcaMax =numpy.max([mcaMax, tmpMax], axis=0)
@@ -317,7 +317,7 @@ class StackBase(object):
                 step = 1
                 for i in range(shape[0]):
                     tmpData = self._stack.data[i:i+step,:,:]
-                    tmpData.shape = tmpData.shape[1:]
+                    tmpData = tmpData.reshape(tmpData.shape[1:])
                     numpy.add(self._stackImageData,
                               tmpData,
                               self._stackImageData)
@@ -748,7 +748,7 @@ class StackBase(object):
                             row_dict[r].append(c)
                         for r in row_list:
                             tmpMcaData = self._stack.data[r:r + 1, row_dict[r], :]
-                            tmpMcaData.shape = -1, mcaData.shape[0]
+                            tmpMcaData = tmpMcaData.reshape(-1, mcaData.shape[0])
                             mcaData += numpy.sum(tmpMcaData, axis=0, dtype=numpy.float64)
                             if mcamax:
                                 mcaMax = numpy.max([mcaMax, numpy.max(tmpMcaData, axis=0)], axis=0)
@@ -793,7 +793,7 @@ class StackBase(object):
                             row_dict[r].append(c)
                         for r in row_list:
                             tmpMcaData = self._stack.data[r:r + 1, row_dict[r], :]
-                            tmpMcaData.shape = -1, mcaData.shape[0]
+                            tmpMcaData = tmpMcaData.reshape(-1, mcaData.shape[0])
                             mcaData += tmpMcaData.sum(axis=0, dtype=numpy.float64)
                             if mcamax:
                                 mcaMax = numpy.max([mcaMax, numpy.max(tmpMcaData, axis=0)], axis=0)
@@ -832,7 +832,7 @@ class StackBase(object):
         if "McaLiveTime" in self._stack.info:
             selectedPixels = actualSelectionMask > 0
             liveTime = self._stack.info["McaLiveTime"][:]
-            liveTime.shape = actualSelectionMask.shape
+            liveTime = liveTime.reshape(actualSelectionMask.shape)
             liveTime = liveTime[selectedPixels].sum()
             if normalize:
                 liveTime = liveTime / float(npixels)
@@ -940,7 +940,7 @@ class StackBase(object):
                         minImage = numpy.zeros(leftImage.shape, numpy.int32)
                         for i in range(i1, i2):
                             tmpData = self._stack.data[i]
-                            tmpData.shape = leftImage.shape
+                            tmpData = tmpData.reshape(leftImage.shape)
                             if i == i1:
                                 minImageData = tmpData * 1.0
                                 maxImageData = tmpData * 1.0
@@ -974,7 +974,7 @@ class StackBase(object):
                     istep = 1
                     for i in range(i1, i2):
                         tmpData = self._stack.data[i:i + istep]
-                        tmpData.shape = roiImage.shape
+                        tmpData = tmpData.reshape(roiImage.shape)
                         if i == i1:
                             minImageData = tmpData * 1.0
                             maxImageData = tmpData * 1.0

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGraph/Colormap.py

@@ -130,7 +130,7 @@ def applyColormap(data, colormap='gray', norm='linear', bounds=None):
 
 if __name__ == "__main__":
     data = np.arange(1024 * 1024.)
-    data.shape = 1024, -1
+    data = data.reshape(1024, -1)
 
     for colormap in COLORMAPS:
         pixmap, _ = applyColormap(data, colormap)

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGraph/backends/GLSupport/GLPlotCurve.py

@@ -1163,7 +1163,7 @@ class GLPlotCurve2D(object):
 
             if self.fill is not None:
                 xData = self.xData[:]
-                xData.shape = xData.size, 1
+                xData = xData.reshape(xData.size, 1)
                 zero = np.array((1e-32,), dtype=self.yData.dtype)
 
                 # Add one point before data: (x0, 0.)

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGraph/backends/GLSupport/PlotEvents.py

@@ -50,7 +50,7 @@ def prepareDrawingSignal(event, type_, points, parameters=None):
     eventDict['event'] = event
     eventDict['type'] = type_
     points = np.array(points, dtype=np.float32)
-    points.shape = -1, 2
+    points = points.reshape(-1, 2)
     eventDict['points'] = points
     eventDict['xdata'] = points[:, 0]
     eventDict['ydata'] = points[:, 1]

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGraph/backends/GLUTOpenGLBackend.py

@@ -113,7 +113,7 @@ if __name__ == "__main__":
     w = Plot(None, backend=GLUTOpenGLBackend)
     size = 4096
     data = np.arange(float(size)*size, dtype=np.dtype(np.float32))
-    data.shape = size, size
+    data = data.reshape(size, size)
 
     colormap = {'name': 'gray', 'normalization': 'linear',
                 'autoscale': True, 'vmin': 0.0, 'vmax': 1.0,

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGraph/backends/MatplotlibBackend.py

@@ -1217,7 +1217,7 @@ class MatplotlibGraph(FigureCanvas):
         #print(dir(self._drawingPatch))
         a = self._drawingPatch.get_xy()
         ddict['points'] = numpy.array(a)
-        ddict['points'].shape = -1, 2
+        ddict['points'] = ddict['points'].reshape(-1, 2)
         ddict['xdata'] = ddict['points'][:, 0]
         ddict['ydata'] = ddict['points'][:, 1]
         #print(numpyvstack(a))
@@ -1751,8 +1751,8 @@ class MatplotlibBackend(PlotBackend.PlotBackend):
             if fill:
                 item.set_hatch('.')
         elif shape in ['polygon']:
-            xView.shape = 1, -1
-            yView.shape = 1, -1
+            xView = xView.reshape(1, -1)
+            yView = yView.reshape(1, -1)
             item = Polygon(numpyvstack((xView, yView)).T,
                             closed=True,
                             fill=False,
@@ -2858,7 +2858,7 @@ if __name__ == "__main__":
     w.replot()
     #w.invertYAxis(True)
     data = numpy.arange(1000.*1000)
-    data.shape = 10000,100
+    data = data.reshape(10000, 100)
     #plot.replot()
     #w.invertYAxis(True)
     #w.replot()

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGraph/backends/OSMesaGLBackend.py

@@ -251,7 +251,7 @@ if __name__ == "__main__":
 
     size = 1024
     data = np.arange(float(size)*size, dtype=np.uint16)
-    data.shape = size, size
+    data = data.reshape(size, size)
 
     colormap = {'name': 'gray', 'normalization': 'linear',
                 'autoscale': True, 'vmin': 0.0, 'vmax': 1.0,

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGraph/backends/OpenGLBackend.py

@@ -152,7 +152,7 @@ if __name__ == "__main__":
 
     size = 4096
     data = np.arange(float(size)*size, dtype=np.dtype(np.float32))
-    data.shape = size, size
+    data = data.reshape(size, size)
 
     colormap = {'name': 'gray', 'normalization': 'linear',
                 'autoscale': True, 'vmin': 0.0, 'vmax': 1.0,

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGraph/ctools/_ctools/cython/Colormap.pyx

@@ -135,7 +135,7 @@ def dataToRGBAColormap(data,
                            c_nanColorPtr,
                            &c_pixmap[0, 0])
 
-    pixmap.shape = data.shape + (4,)
+    pixmap = pixmap.reshape(data.shape + (4,))
     return pixmap, (c_start, c_end)
 
 def fastLog10(double value):

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGraph/ctools/_ctools/test/testColormap.py

@@ -128,7 +128,7 @@ class _TestColormap(unittest.TestCase):
                                  dtype=np.uint32)
 
         pixmap = np.take(colormap, indices, axis=0)
-        pixmap.shape = data.shape + (4,)
+        pixmap = pixmap.reshape(data.shape + (4,))
         return np.ascontiguousarray(pixmap)
 
     @staticmethod
@@ -158,7 +158,7 @@ class _TestColormap(unittest.TestCase):
                                                 (start, end),
                                                 (0, 255),
                                                 1)
-        pixmap.shape = data.shape[0], data.shape[1], 4
+        pixmap = pixmap.reshape(data.shape[0], data.shape[1], 4)
 
         return pixmap
 
@@ -188,8 +188,8 @@ class _TestColormap(unittest.TestCase):
                 # Only works with red colormap and even size
                 # as it needs 2D data
                 if len(data.shape) == 1:
-                    data.shape = data.size // 2, -1
-                    pixmap.shape = data.shape + (4,)
+                    data = data.reshape(data.size // 2, -1)
+                    pixmap = pixmap.reshape(data.shape + (4,))
                 control = self.buildSPSLUTRedPixmap(data, start, end, isLog10)
                 controlType = 'SPS LUT'
 
@@ -243,7 +243,7 @@ class TestColormap(_TestColormap):
             for isLog10 in (False, True):
                 data = np.array((), dtype=dtype)
                 result = np.array((), dtype=np.uint8)
-                result.shape = 0, 4
+                result = result.reshape(0, 4)
                 duration = self._testColormap(data, self.COLORMAPS['red 256'],
                                               None, None, result, isLog10)
                 self._log('No data', 'red 256', dtype, len(data), (None, None),
@@ -359,7 +359,7 @@ class TestLinearColormap(_TestColormap):
                         # Increasing values
                         data = np.arange(size * size, dtype=dtype)
                         data = np.nan_to_num(data)
-                        data.shape = size, size
+                        data = data.reshape(size, size)
                         duration = self._testColormap(data, colormap,
                                                       start, end)
 
@@ -493,7 +493,7 @@ class TestLog10Colormap(_TestColormap):
                         # Increasing values
                         data = np.arange(size * size, dtype=dtype) + 1
                         data = np.nan_to_num(data)
-                        data.shape = size, size
+                        data = data.reshape(size, size)
                         duration = self._testColormap(data, colormap,
                                                       start, end,
                                                       isLog10=True)

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGui/io/QEdfFileWidget.py

@@ -987,7 +987,7 @@ class QEdfFileWidget(qt.QWidget):
                                 (colormap[2],colormap[3]),
                                 (0,255), 1)
 
-        pixmap.shape = [data.shape[0], data.shape[1], 4]
+        pixmap = pixmap.reshape(data.shape[0], data.shape[1], 4)
         if not goodData:
             pixmap[finiteData < 1] = 255
         return pixmap

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGui/io/hdf5/HDF5Widget.py

@@ -1,5 +1,5 @@
 #/*##########################################################################
-# Copyright (C) 2004-2025 V.A. Sole, ESRF - D. Dale CHESS
+# Copyright (C) 2004-2026 V.A. Sole, ESRF - D. Dale CHESS
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -195,9 +195,20 @@ class H5NodeProxy(object):
                             finalListIsTrue = True
                         if hasattr(dataset, "shape"):
                             if not len(dataset.shape):
-                                # it can still be a string
+                                # it can still be a string or a scalar
                                 if hasattr(dataset, "dtype"):
-                                    if safe_str(dataset.dtype).startswith("|S"):
+                                    dataset_dtype_print = safe_str(dataset.dtype)
+                                    if dataset_dtype_print.startswith("|S"):
+                                        pass
+                                    elif dataset_dtype_print.startswith("float"):
+                                        pass
+                                    elif dataset_dtype_print.startswith("int"):
+                                        pass
+                                    elif dataset_dtype_print.startswith("uint"):
+                                        pass
+                                    elif dataset_dtype_print.startswith("bool"):
+                                        pass
+                                    elif dataset_dtype_print.startswith("complex"):
                                         pass
                                     elif safe_str(dataset.dtype) == "object":
                                         # issue 1059
@@ -991,7 +1002,7 @@ 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)',
+    fileTypeList = ['HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)',
                     'HDF5 Files (*)']
     message = "Open HDF5 file"
     filenamelist, ffilter = PyMcaFileDialogs.getFileList(parent=parent,

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGui/math/FFTAlignmentWindow.py

@@ -295,7 +295,7 @@ class FFTAlignmentDialog(qt.QDialog):
 
     def setDummyStack(self):
         dummyStack = numpy.arange(2 * 128 *256)
-        dummyStack.shape = 2, 128, 256
+        dummyStack = dummyStack.reshape(2, 128, 256)
         self.setStack(dummyStack, index=0)
 
     def getParameters(self):

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGui/math/NNMADialog.py

@@ -123,14 +123,14 @@ class NNMADialog(qt.QDialog):
                     images, eigenvalues, eigenvectors = threadResult
                 except Exception:
                     if isinstance(data, numpy.ndarray):
-                        self._data.shape = old_shape
+                        self._data = self._data.reshape(*old_shape)
                     msg = qt.QMessageBox(self)
                     msg.setIcon(qt.QMessageBox.Critical)
                     msg.setText("%s" % sys.exc_info()[1])
                     msg.exec()
                     return
             if isinstance(self._data, numpy.ndarray):
-                self._data.shape = old_shape
+                self._data = self._data.reshape(*old_shape)
             _logger.debug("NNMA Elapsed = %s", time.time() - t0)
             self.nnmaWindow.setPCAData(images,
                                        eigenvalues,

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGui/math/NNMAWindow.py

@@ -272,15 +272,15 @@ class NNMAParametersDialog(qt.QDialog):
         binning = int(self.binningCombo.currentText())
         x = self._x * 1.0
         y = self._y * 1.0
-        x.shape = 1, -1
-        y.shape = 1, -1
+        x = x.reshape(1, -1)
+        y = y.reshape(1, -1)
         r, c = x.shape
-        x.shape = r, int(c / binning), binning
-        y.shape = r, int(c / binning), binning
+        x = x.reshape(r, int(c / binning), binning)
+        y = y.reshape(r, int(c / binning), binning)
         x = x.sum(axis=-1, dtype=numpy.float32) / binning
         y = y.sum(axis=-1, dtype=numpy.float32)
-        x.shape = -1
-        y.shape = -1
+        x = numpy.ravel(x)
+        y = numpy.ravel(y)
         self._binnedX = x
         self._binnedY = y
         if self.graph:
@@ -411,7 +411,7 @@ def test():
     app.lastWindowClosed.connect(app.quit)
     container = NNMAWindow()
     data = numpy.arange(20000)
-    data.shape = 2, 100, 100
+    data = data.reshape(2, 100, 100)
     data[1, 0:100, 0:50] = 100
     container.setPCAData(
         data,

{pymca5-5.9.5rc2 → pymca5-5.9.6}/src/PyMca5/PyMcaGui/math/PCADialog.py

@@ -145,14 +145,14 @@ class PCADialog(qt.QDialog):
                     images, eigenvalues, eigenvectors = threadResult
                 except Exception:
                     if isinstance(data, numpy.ndarray):
-                        self._data.shape = old_shape
+                        self._data = self._data.reshape(*old_shape)
                     msg = qt.QMessageBox(self)
                     msg.setIcon(qt.QMessageBox.Critical)
                     msg.setText("%s" % sys.exc_info()[1])
                     msg.exec()
                     return
             if isinstance(self._data, numpy.ndarray):
-                self._data.shape = old_shape
+                self._data = self._data.reshape(old_shape)
             _logger.debug("PCA Elapsed = %s", time.time() - t0)
             methodlabel = pcaParameters.get('methodlabel', "")
             imagenames = None