Multivolume 3d render

.github/workflows/build-macos_pyqt5.yml

@@ -32,6 +32,7 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         python -m pip install -e .
         python -m pip install -r requirements_gui_pyqt5.txt
+        python -m pip install -r requirements_test.txt
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -40,4 +41,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        pytest -vv -s

.github/workflows/build-macos_pyqt6.yml

@@ -32,6 +32,7 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         python -m pip install -e .
         python -m pip install -r requirements_gui_pyqt6.txt
+        python -m pip install -r requirements_test.txt
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -40,4 +41,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        pytest -vv -s

.github/workflows/build-ubuntu_pyqt5.yml

@@ -38,6 +38,7 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         python -m pip install -e .
         python -m pip install -r requirements_gui_pyqt5.txt
+        python -m pip install -r requirements_test.txt
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -46,4 +47,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        pytest -vv -s

.github/workflows/build-windows_pyqt5.yml

@@ -31,6 +31,7 @@ jobs:
         python -m pip install flake8 pytest
         python -m pip install -e .
         python -m pip install -r requirements_gui_pyqt5.txt
+        python -m pip install -r requirements_test.txt
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -39,4 +40,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        pytest -vv -s

.github/workflows/build-windows_pyqt6.yml

@@ -31,6 +31,7 @@ jobs:
         python -m pip install flake8 pytest
         python -m pip install -e .
         python -m pip install -r requirements_gui_pyqt6.txt
+        python -m pip install -r requirements_test.txt
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -39,4 +40,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        pytest -vv -s

cellacdc/__init__.py

@@ -89,7 +89,7 @@ def _warn_ask_install_package(
     print(text)
 
     message_on_exit = (
-        '[WARNING]: Execution aborted. Run the following commands before '
+        '[WARNING]: Execution cancelled. Run the following commands before '
         f'running spotMAX again:\n\n{commands_txt}\n'
     )
     msg_on_invalid = (

cellacdc/_main.py

@@ -1029,7 +1029,7 @@ def getSelectedPosPath(self, utilityName):
             buttonsTexts=('Cancel', 'Ok')
         )
         if msg.cancel:
-            print(f'{utilityName} aborted by the user.')
+            print(f'{utilityName} cancelled by the user.')
             return
 
         mostRecentPath = myutils.getMostRecentPath()
@@ -1038,7 +1038,7 @@ def getSelectedPosPath(self, utilityName):
             mostRecentPath
         )
         if not exp_path:
-            print(f'{utilityName} aborted by the user.')
+            print(f'{utilityName} cancelled by the user.')
             return
 
         myutils.addToRecentPaths(exp_path)
@@ -1072,7 +1072,7 @@ def getSelectedPosPath(self, utilityName):
                     buttonsTexts=('Cancel', 'Try again')
                 )
                 if msg.cancel:
-                    print(f'{utilityName} aborted by the user.')
+                    print(f'{utilityName} cancelled by the user.')
                     return
 
         if len(posFolders) > 1:
@@ -1111,7 +1111,7 @@ def getSelectedExpPaths(
                 buttonsTexts=('Cancel', 'Ok')
             )
             if msg.cancel:
-                self.logger.info(f'{utilityName} aborted by the user.')
+                self.logger.info(f'{utilityName} cancelled by the user.')
                 return
 
         expPaths = {}
@@ -1150,7 +1150,7 @@ def getSelectedExpPaths(
                 if not selected_exp_paths:
                     cancel = self.warnNoValidExpPaths(exp_path)
                     if cancel:
-                        self.logger.info(f'{utilityName} aborted by the user.')
+                        self.logger.info(f'{utilityName} cancelled by the user.')
                         return
                     continue
 
@@ -1162,7 +1162,7 @@ def getSelectedExpPaths(
                             selected_path, exp_path
                         )
                         if not proceed:
-                            self.logger.info(f'{utilityName} aborted by the user.')
+                            self.logger.info(f'{utilityName} cancelled by the user.')
                             return
                         warn_exp_already_selected = False
                     expPaths[exp_path].extend(pos_folders)
@@ -1185,7 +1185,7 @@ def getSelectedExpPaths(
                 break
 
         if not expPaths:
-            self.logger.info(f'{utilityName} aborted by the user.')
+            self.logger.info(f'{utilityName} cancelled by the user.')
             return
 
         if len(expPaths) > 1 or is_multi_pos:
@@ -1197,7 +1197,7 @@ def getSelectedExpPaths(
             )
             selectPosWin.exec_()
             if selectPosWin.cancel:
-                self.logger.info(f'{utilityName} aborted by the user.')
+                self.logger.info(f'{utilityName} cancelled by the user.')
                 return
             selectedExpPaths = selectPosWin.selectedPaths
         else:
@@ -1839,7 +1839,7 @@ def _showDataStructWin(self):
             buttonsTexts=('Cancel', *buttons)
         )
         if msg.cancel:
-            self.logger.info('Creating data structure process aborted by the user.')
+            self.logger.info('Creating data structure process cancelled by the user.')
             self.restoreDefaultButtons()
             return
 

cellacdc/_run.py

@@ -434,11 +434,21 @@ def download_model_params():
             )
             print(e)
             pass
-                
+
 def _setup_app(splashscreen=False, icon_path=None, logo_path=None, scheme=None):
     from qtpy import QtCore
     if QtCore.QCoreApplication.instance() is not None:
-        return QtCore.QCoreApplication.instance(), None
+        class DummySplashScreen:
+            def __init__(self):
+                pass
+
+            def show(self):
+                pass
+
+            def close(self):
+                pass
+
+        return QtCore.QCoreApplication.instance(), DummySplashScreen()
 
     from qtpy import QtWidgets
     # Handle high resolution displays:

cellacdc/cca_functions.py

@@ -78,7 +78,7 @@ def configuration_dialog():
             win.exec_()
             if win.cancel:
                 print('******************************')
-                print('Execution aborted by the user')
+                print('Execution cancelled by the user')
                 print('******************************')
                 raise InterruptedError
             pos = win.selectedItemsText
@@ -131,7 +131,7 @@ def get_segm_endname(images_path, basename):
     )
     selectSegmWin.exec_()
     if selectSegmWin.cancel:
-        raise FileNotFoundError(f'Segmentation file selection aborted by the user.')
+        raise FileNotFoundError(f'Segmentation file selection cancelled by the user.')
 
     return selectSegmWin.selectedItemsText[0]
 

cellacdc/cli.py

@@ -103,7 +103,7 @@ def quit(self, error=None):
             print('-'*60)
             self.logger.info(f'[ERROR]: {error}{error_up_str}')
             err_msg = (
-                'Cell-ACDC aborted due to **error**. '
+                'Cell-ACDC cancelled due to **error**. '
                 'More details above or in the following log file:\n\n'
                 f'{self.log_path}\n\n'
                 'If you cannot solve it, you can report this error by opening '

cellacdc/colors.py

@@ -20,9 +20,14 @@
 try:
     import networkx as nx
     NETWORKX_INSTALLED = True
-except:
+except Exception as err:
     NETWORKX_INSTALLED = False
 
+try:
+    from vispy.color import Colormap as VisPyColormap
+except Exception as err:
+    pass
+
 __all__ = ['ColorMap']
 
 FLUO_CHANNELS_COLORS = {
@@ -366,4 +371,29 @@ def grayscale_apply_lut(image, lut):
 
 def get_complementary_color(rgba_str: str) -> str:
     r, g, b, a = rgba_str_to_values(rgba_str)
-    return f'rgba({255 - r}, {255 - g}, {255 - b}, {a})'
+    return f'rgba({255 - r}, {255 - g}, {255 - b}, {a})'
+
+def pg_to_vispy_cmap(pg_cmap, n=256):
+    """Convert PyQtGraph colormap to vispy
+
+    Parameters
+    ----------
+    pg_cmap : pyqtgraph.colormap.ColorMap
+        PyQtGraph Colormap. For example, it can be obtained with 
+        `pyqtgraph.HistogramLUTItem.gradient.colorMap()`
+    n : int, optional
+        Number of colors, by default 256
+
+    Returns
+    -------
+    vispy.color.Colormap
+        VisPy colormap
+    """
+
+    # Sample the colormap
+    colors = pg_cmap.getLookupTable(0.0, 1.0, n)
+
+    # Normalize to 0–1 (VisPy expects floats)
+    colors = np.array(colors) / 255.0
+
+    return VisPyColormap(colors)

cellacdc/dataPrep.py

@@ -2347,7 +2347,7 @@ def prepData(self, event):
                 )
                 if msg.cancel:
                     self.setEnabledCropActions(True)
-                    self.titleLabel.setText('Process aborted', color='w')
+                    self.titleLabel.setText('Process cancelled', color='w')
                     return
                 if yes == msg.clickedButton:
                     doZip = True

cellacdc/dataStruct.py

@@ -1303,7 +1303,7 @@ def checkInstallPythonBioformats(self, parent):
             cancel = myutils.install_javabridge_help(parent=self)
             if cancel:
                 raise ModuleNotFoundError(
-                    'User aborted javabridge installation'
+                    'User cancelled javabridge installation'
                 )
 
             isGitInstalled = myutils.check_git_installed(parent=self)
@@ -1357,7 +1357,7 @@ def checkInstallPythonBioformats(self, parent):
                 cancel = myutils.install_java()
                 if cancel:
                     raise ModuleNotFoundError(
-                        'User aborted Java installation'
+                        'User cancelled Java installation'
                     )
                     return
 
@@ -1371,7 +1371,7 @@ def checkInstallPythonBioformats(self, parent):
             cancel = myutils.install_java()
             if cancel:
                 raise ModuleNotFoundError(
-                    'User aborted Java installation'
+                    'User cancelled Java installation'
                 )
                 return
             myutils.install_javabridge(