unit testing mmMap in core

Author: cudmore

src/pymapmanager/annotations/baseAnnotationsCore.py

@@ -28,7 +28,8 @@ def getUserTypeMarkers_mpl():
 class AnnotationsCore:
     def __init__(self,
                  timeSeriesCore : TimeSeriesCore,  # multi timepoint
-                 timepoint : int = 0,
+                #  timepoint : int = 0,
+                 timepoint,
                  ):
         """
         Parameters

src/pymapmanager/interface2/core/scatter_plot_widget.py

@@ -1250,7 +1250,8 @@ def selectHighlighterPoints(self, rowIndexes : List[int]):
             rowIndexes: indexes of rows that need to be selected within highlighter plot
         """
         if rowIndexes is None or rowIndexes == []:
-            self.myHighlighter._setData([], [])
+            if self.myHighlighter is not None:
+                self.myHighlighter._setData([], [])
         else: 
             columnNameX = self.xPlotWidget.getCurrentStat()
             columnNameY = self.yPlotWidget.getCurrentStat()

src/pymapmanager/interface2/mainMenus.py

@@ -120,7 +120,7 @@ def _buildMenus(self, mainMenu, mainWindow):
     def _refreshPluginsMenu(self):
         """Build a plugin menu with all available stack and map plugins.
         """
-        logger.info('re-create plugin menu with available stack and map plugins')
+        # logger.info('re-create plugin menu with available stack and map plugins')
 
         # start with an empy menu
         self.pluginsMenu.clear()
@@ -141,7 +141,7 @@ def _refreshPluginsMenu(self):
         _activateStackPlugins = windowType in ['stack', 'stackWithMap']
         """If our front window is a stack widget."""
         for pluginName in stackPluginDict.keys():
-            logger.info(f'pluginName:{pluginName}')
+            # logger.info(f'pluginName:{pluginName}')
             action = QtWidgets.QAction(pluginName, self.getApp(), checkable=True)
             action.setEnabled(_activateStackPlugins)
             action.triggered.connect(partial(self._onPluginMenuAction, pluginName, 'stack'))

src/pymapmanager/interface2/mapWidgets/mapTableWidget.py

@@ -121,8 +121,9 @@ def _getToolbar(self) -> QtWidgets.QVBoxLayout:
         # aLabel = QtWidgets.QLabel('Link')
         # hLayout.addWidget(aLabel)
 
-        linkCheckbox = QtWidgets.QCheckBox('Link')
-        hLayout.addWidget(linkCheckbox)
+        # abb turn off for single timepoint
+        # linkCheckbox = QtWidgets.QCheckBox('Link')
+        # hLayout.addWidget(linkCheckbox)
 
         closeAllButton = QtWidgets.QPushButton('Close All')
         hLayout.addWidget(closeAllButton)

src/pymapmanager/interface2/mapWidgets/mapWidget.py

@@ -393,16 +393,18 @@ def _buildUI(self):
         # logger.warning('abb add dendrogram widget back in')
         # dendrogramWidget = pmm.interface2.mapWidgets.dendrogramWidget(self)
 
-        # to hide form circular imports
-        from pymapmanager.interface2.mapWidgets.mapDendrogramWidget import MapDendrogramWidget
-        dendrogramWidget = MapDendrogramWidget(self)
-        dendrogramWidget.signalOpenRun.connect(self.openStackRun)
-        
-        # as a dock
-        # dendrogramWidgetName = dendrogramWidget._widgetName
-        # dendrogramDock = self._addDockWidget(dendrogramWidget, 'right', '')
-        # self._widgetDict[dendrogramWidgetName] = dendrogramDock  # the dock, not the widget ???
-        hBoxLayout_main.addWidget(dendrogramWidget)
+        # to hide from circular imports
+        # logger.info('turned off dendrogram widget to focus on single timepoints')
+        if 0:
+            from pymapmanager.interface2.mapWidgets.mapDendrogramWidget import MapDendrogramWidget
+            dendrogramWidget = MapDendrogramWidget(self)
+            dendrogramWidget.signalOpenRun.connect(self.openStackRun)
+            
+            # as a dock
+            # dendrogramWidgetName = dendrogramWidget._widgetName
+            # dendrogramDock = self._addDockWidget(dendrogramWidget, 'right', '')
+            # self._widgetDict[dendrogramWidgetName] = dendrogramDock  # the dock, not the widget ???
+            hBoxLayout_main.addWidget(dendrogramWidget)
 
     def contextMenu(self):
         logger.info('')

src/pymapmanager/interface2/pyMapManagerApp2.py

@@ -262,7 +262,7 @@ def openWidgetFromPath(self, path : str) -> Union[stackWidget2, mapWidget]:
 
             numTimepoints = _timeSeriesCore.numSessions
 
-            logger.info(f'numtimepoints:{numTimepoints}')
+            logger.info(f'_timeSeriesCore.numSessions is:{numTimepoints}')
 
             if numTimepoints == 1:
                 # single timepoint map

src/pymapmanager/interface2/runInterfaceBob.py

@@ -1,6 +1,7 @@
 """Open a stack widget.
 """
 
+import os
 import sys
 
 import mapmanagercore.data
@@ -43,6 +44,22 @@ def run():
     # path = getTiffChannel_1()
 
     path = '/Users/cudmore/Desktop/single_timepoint_20250108.mmap'
+
+    path = '/Users/cudmore/Desktop/zarrLoader_3.mmap'
+
+    path = '/Users/cudmore/Desktop/single_timepoint_20250322.mmap'
+    
+    path = '/Users/cudmore/Desktop/sample_mmaps/zarLoader2.mmap'
+    path = '/Users/cudmore/Desktop/sample_mmaps/zarLoader_1.mmap'
+    # path = '/Users/cudmore/Desktop/sample_mmaps/zarLoader_3.mmap'
+    
+    if not os.path.isdir(path):
+        logger.error('did not find folder path')
+        logger.error(path)
+        return
+    
+    # corrupt ???
+    # path = '/Users/cudmore/Desktop/single_timepoint_20250322.mmap.zip'
 
     app = PyMapManagerApp(sys.argv)
     # mw will be map widget if path has multiple timepoints, otherwise mw is a stackwidget2

src/pymapmanager/interface2/stackWidgets/analysisParamWidget2.py

@@ -60,6 +60,9 @@ def __init__(self, stackWidget: stackWidget2, pmmApp : pyMapManagerApp2 = None):
         # self.changedDict = {}
         self._buildGUI()
 
+    def on_bool_combo_box(self, paramName, value):
+        logger.warning(f'TODO: paramName:{paramName} value:{value}')
+        
     def on_spin_box(self, paramName, value):
         """
         When QDoubldeSpinBox accepts None, value is -1e9

src/pymapmanager/interface2/stackWidgets/base/annotationPlotWidget2.py

@@ -922,9 +922,14 @@ def undoEvent(self, event : UndoEvent):
         logger.info(f'event:{event}')
 
         _undoEvent = event.getUndoEvent()
-
+        if _undoEvent is None:
+            return
+        
         # logger.info(f'abj _undoEvent: {_undoEvent}')
 
+        if _undoEvent is None:
+            return False
+        
         if _undoEvent.category != "Spine":
             return
 
@@ -955,6 +960,9 @@ def redoEvent(self, event : RedoEvent):
         # TODO: on undo move, redraw label
         _redoEvent = event.getRedoEvent()
 
+        if _redoEvent is None:
+            return False
+        
         if _redoEvent.category != "Spine":
             return
 
@@ -1586,6 +1594,9 @@ def undoEvent(self, event : UndoEvent):
         """
 
         # abj: avoiding unnecessary updates, but can remove
+        if event.getUndoEvent() is None:
+            return
+        
         if event.getUndoEvent().category != "Segment": 
             return
 
@@ -1598,7 +1609,9 @@ def undoEvent(self, event : UndoEvent):
     def redoEvent(self, event : RedoEvent):
         """
         """
-
+        if event.getRedoEvent() is None:
+            return False
+        
         if event.getRedoEvent().category != "Segment": # abj
             return
 

src/pymapmanager/interface2/stackWidgets/base/mmWidget2.py

@@ -259,10 +259,12 @@ def getFirstPointRoiType(self):
     #
     def setSegmentSelection(self, items : List[int]):
         if items is None:
-            pass
+            items = []
         elif not isinstance(items, list):
             items = [items]
 
+        logger.error(f'yyy items:{items}')
+
         for _idx, item in enumerate(items):
             items[_idx] = int(item)