Merge branch 'johnson-dev' into cudmore-dev

Author: cudmore

src/pymapmanager/interface/stackWidgets/base/editDataclass.py

@@ -184,7 +184,15 @@ def _buildLayout(self) -> QtWidgets.QVBoxLayout:
         return vLayout
 
     def on_bool_combo_box(self, paramName, value):
-        logger.warning(f'TODO: paramName:{paramName} value:{value}')
+        # logger.warning(f'TODO: paramName:{paramName} value:{value}')
+        if value == "False":
+            newVal = False
+        elif value == "True":
+            newVal = True
+        else:
+            logger.error(f"Value: {value} is not a boolean")
+        self._dict[paramName]["currentValue"] = newVal
+        self._enableButtons()
 
     def on_text_edit(self, paramName):
         # get str from widget

src/pymapmanager/interface/stackWidgets/histogramWidget2.py

@@ -48,7 +48,10 @@ def _refreshSlice(self):
     def _setSlice(self, sliceNumber):        
         self._sliceNumber = sliceNumber
 
-        for histWidget in self.histWidgetList:
+        # for histWidget in self.histWidgetList:
+        #     histWidget._setSlice(sliceNumber)
+
+        for histWidget in self.histWidgetDict.values():
             histWidget._setSlice(sliceNumber)
 
     def setSliceEvent(self, event: pmmEvent):
@@ -69,9 +72,9 @@ def slot_setChannel(self, channelIdx : int):
         # need to set max of spinbox and slider(s)
         # self.minSpinBox.setMaximum(globalMax)
 
-        _channelKeys = self.getStackWidget().getChannelKeys()
+        _channelKeys = self._myStack.getChannelKeys()
         if channelIdx in _channelKeys:
-            for histWidget in self.histWidgetList:
+            for histWidget in self.histWidgetDict.values():
                 histWidget.isRgb = False
                 if histWidget._channelIdx == channelIdx:
                     histWidget.show()
@@ -81,7 +84,8 @@ def slot_setChannel(self, channelIdx : int):
                     histWidget.hide()
         elif channelIdx == 'rgb':
             # show all
-            for histWidget in self.histWidgetList:
+            # for histWidget in self.histWidgetList:
+            for histWidget in self.histWidgetDict.values():
                 histWidget.isRgb = True
                 histWidget.show()
                 histWidget._refreshContrast()
@@ -126,7 +130,8 @@ def _checkbox_callback(self, isChecked):
             self.repaint()
 
         elif title == 'Log':
-            for histWidget in self.histWidgetList:
+            # for histWidget in self.histWidgetList:
+            for histWidget in self.histWidgetDict.values():
                 histWidget.setLog(isChecked)
 
     def _buildUI(self):
@@ -170,25 +175,45 @@ def _buildUI(self):
         hBoxLayout2 = QtWidgets.QHBoxLayout() # main layout
 
         # a _histogram for each channel
-        self.histWidgetList = []
+        # self.histWidgetList = []
+        self.histWidgetDict = {}
         for channelIdx in self._myStack.getChannelKeys():
+            #TODO: add check for to integer?
+            # logger.info(f"channelIdx when initializing {channelIdx}")
             oneHistWidget = _histogram(self, self._myStack, channelIdx, sliceNumber=self._sliceNumber)
             oneHistWidget.signalContrastChange.connect(self.slot_contrastChanged)
-            self.histWidgetList.append(oneHistWidget)
+            # self.histWidgetList.append(oneHistWidget)
+            self.histWidgetDict[channelIdx] = oneHistWidget
             hBoxLayout2.addWidget(oneHistWidget)
         vBoxLayout.addLayout(hBoxLayout2)
 
     def _onAutoContrast(self):
         """Reset to min/max from metadata.
         """
         logger.error('BROKEN')
-    
-        self._myStack.getChannelMetadata(self._channelIdx).resetAutoContrast()
+        logger.info(f"self._channelIdx {self._channelIdx}")
+        logger.info(f"self._channel {self._channel}")
+
+        #  TODO: fix this abj - need to figure out decisively when its  rgb
+        # For some reason channel idx 2 is being used instead of 1 for resetting slider in rgb
+
+        if self._channel == "rgb":
+            # TODO: loop through all channel indexes and reset rgb contrast
+            for channelIdx in self._myStack.getChannelKeys():
+                logger.info(f"channelIdx being reset {channelIdx} type {type(channelIdx)}")
+                self._myStack.getChannelMetadata(channelIdx).resetAutoRgbContrast()
+                self.getStackWidget().slot_contrastChanged()
+                # TODO: switch from list to dictionary?
+                # self.histWidgetList[channelIdx]._refreshContrast()
+                self.histWidgetDict[channelIdx]._refreshContrast()
 
-        self.getStackWidget().slot_contrastChanged()
+        else:
+            self._myStack.getChannelMetadata(self._channelIdx).resetAutoContrast()
+            self.getStackWidget().slot_contrastChanged()
 
-        # cludge, need to properly connect signal/slot
-        self.histWidgetList[self._channelIdx]._refreshContrast()
+            # cludge, need to properly connect signal/slot
+            # self.histWidgetList[self._channelIdx]._refreshContrast()
+            self.histWidgetDict[self._channelIdx]._refreshContrast()
 
 #class _histogram(QtWidgets.QToolBar):
 class _histogram(QtWidgets.QWidget):
@@ -232,6 +257,8 @@ def _sliderValueChanged(self):
         theMin = self.minContrastSlider.value()
         theMax = self.maxContrastSlider.value()
 
+        # logger.info(f"theMin {theMin} theMax {theMax}")
+
         # set spinbox(s) to current slider values
         self.minSpinBox.setValue(theMin)
         self.maxSpinBox.setValue(theMax)
@@ -260,19 +287,23 @@ def _spinBoxValueChanged(self):
     def _updateContrast(self, theMin, theMax):
         # set contrast in metadata
         if self.isRgb:
-            self._myStack.getChannelMetadata(self._channelIdx).setValue('minAutoContrast_rgb', theMin)
-            self._myStack.getChannelMetadata(self._channelIdx).setValue('maxAutoContrast_rgb', theMax)
+            # self._myStack.getChannelMetadata(self._channelIdx).setValue('minAutoContrast_rgb', theMin)
+            # self._myStack.getChannelMetadata(self._channelIdx).setValue('maxAutoContrast_rgb', theMax)
+            # logger.info(f"upadting min and max rgb to {theMin} and {theMax}")
+            # logger.info(f"self._channelIdx being updated in rgb{ self._channelIdx}")
+            self._myStack.getChannelMetadata(self._channelIdx).setValue('minContrast_rgb', theMin)
+            self._myStack.getChannelMetadata(self._channelIdx).setValue('maxContrast_rgb', theMax)
         else:
             self._myStack.getChannelMetadata(self._channelIdx).setUserContrast(theMin, theMax)
 
     def _refreshSlice(self):
         self._setSlice(self._sliceNumber)
 
     def _setSlice(self, sliceNumber, doInit=False):
-        logger.info(f'_histogram _channelIdx:{self._channelIdx} sliceNumber:{sliceNumber}')
+        # logger.info(f'_histogram _channelIdx:{self._channelIdx} sliceNumber:{sliceNumber}')
 
-        if not self.isVisible():
-            return
+        # if not self.isVisible(): # abj: not needed prevents initial loading
+        #     return
 
         self._sliceNumber = sliceNumber
 
@@ -297,7 +328,6 @@ def _setSlice(self, sliceNumber, doInit=False):
         if self._plotLogHist:
             y = np.log10(y, where=y>0)
 
-            
         self.pgHist.setData(x=x, y=y)
 
         # color the hist based on channel number
@@ -320,26 +350,30 @@ def setLog(self, value):
 
     def _refreshContrast(self):
         _channelMetadata = self._myStack.getChannelMetadata(self._channelIdx)
-        
+
         globalMin = 0
         if self.isRgb:
-            minContrast = _channelMetadata.getValue('minAutoContrast_rgb')
-            maxContrast = _channelMetadata.getValue('maxAutoContrast_rgb')
+            # minContrast = _channelMetadata.getValue('minAutoContrast_rgb')
+            # maxContrast = _channelMetadata.getValue('maxAutoContrast_rgb')
+            minContrast = _channelMetadata.getValue('minContrast_rgb')
+            maxContrast = _channelMetadata.getValue('maxContrast_rgb')
             globalMax = 256
         else:
             minContrast, maxContrast = _channelMetadata.getUserContrast()
             globalMax = _channelMetadata.getValue('maxInt')
 
-        # logger.info(f'isRgb:{self.isRgb} _channelIdx:{self._channelIdx} minContrast:{minContrast} maxContrast:{maxContrast}')
+        logger.info(f'isRgb:{self.isRgb} _channelIdx:{self._channelIdx} minContrast:{minContrast} maxContrast:{maxContrast}')
 
         # set the x-range of histogram plot
         self.pgPlotWidget.setXRange(globalMin, globalMax, padding=0)
 
         self.maxSpinBox.setMaximum(globalMax)  # order matters, must be first
+        self.minSpinBox.setMaximum(globalMax) # abj: ensure minimum doesnt go above max
         self.minSpinBox.setValue(minContrast)
         self.maxSpinBox.setValue(maxContrast)
 
         self.maxContrastSlider.setMaximum(globalMax)  # order matters, must be first
+        self.minContrastSlider.setMaximum(globalMax) # abj: ensure minimum doesnt go above max
         self.minContrastSlider.setValue(minContrast)
         self.maxContrastSlider.setValue(maxContrast)
 

src/pymapmanager/interface/stackWidgets/imagePlotWidget2.py

@@ -669,26 +669,44 @@ def hex_to_rgb(hex_color):
 
     def _setContrast(self):
         if self._channelIsRGB():
-            logger.warning(f'TODO: hard coding min/max for rgb -->> fix')
+            # logger.warning(f'TODO: hard coding min/max for rgb -->> fix')
             tmpLevelList = []  # list of [min,max]
             for channelIdx in self._myStack.getChannelKeys():
-                # oneMinContrast = self._myStack.contrast.getValue(channelIdx, 'minAutoContrast_rgb')
-                # oneMaxContrast = self._myStack.contrast.getValue(channelIdx, 'maxAutoContrast_rgb')
-                oneMinContrast = 0
-                oneMaxContrast = 200
-
-                # convert to [0..255]
-                maxInt = 2**8  # rgb has bit depth of 8 per color channel
-                oneMinContrast = int(oneMinContrast / maxInt * 255)
-                oneMaxContrast = int(oneMaxContrast / maxInt * 255)
-
-                oneLevel = [oneMinContrast, oneMaxContrast]
-                tmpLevelList.append(oneLevel)
-            
-            levelList = [None] * 3
-            levelList[0] = tmpLevelList[1]
-            levelList[1] = tmpLevelList[0]  # green
-            levelList[2] = tmpLevelList[1]
+                min_c = self._myStack.getChannelMetadata(channelIdx).getValue('minContrast_rgb')
+                max_c = self._myStack.getChannelMetadata(channelIdx).getValue('maxContrast_rgb')
+
+                # logger.info(f"Channel {channelIdx}: min={min_c}, max={max_c}")
+
+                # Handle missing metadata
+                if min_c is None or max_c is None:
+                    logger.warning(f"Missing contrast metadata for channel {channelIdx}, using defaults.")
+                    min_c, max_c = 0, 255
+
+                # Handle reversed values
+                # if min_c > max_c:
+                #     logger.warning(f"Min > Max for channel {channelIdx}, swapping values.")
+                #     min_c, max_c = max_c, min_c
+
+                # # convert to [0..255] 
+                maxInt = 2**8 # rgb has bit depth of 8 per color channel 
+                oneMinContrast = int(min_c / maxInt * 255)
+                oneMaxContrast = int(max_c / maxInt * 255)
+
+                tmpLevelList.append([oneMinContrast, oneMaxContrast])
+                # tmpLevelList.append([min_c, max_c])
+
+                if channelIdx == 3:
+                    break
+
+            # Expecting exactly 2 channels
+            if len(tmpLevelList) == 2:
+                levelList = [None] * 3
+                levelList[0] = tmpLevelList[1]  # R from channel 1
+                levelList[1] = tmpLevelList[0]  # G from channel 0
+                levelList[2] = tmpLevelList[1]  # B from channel 1 again
+            else:
+                logger.error(f"Expected 2 channels, got {len(tmpLevelList)} — falling back to defaults.")
+                levelList = [[0, 255]] * 3
 
             #
             # logger.info(f'{self._displayThisChannelIdx} levelList:{levelList}')