updated rgb slice

Author: cudmore

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

@@ -354,7 +354,7 @@ def plotMenuChange(self, action):
     def setCurrentChannel(self, channelIdx):
         """ set current channel selected
         """
-        logger.info(f"setCurrentChannel {channelIdx}")
+        logger.info(f"setCurrentChannel {channelIdx} {type(channelIdx)}")
         self._currentChannel = channelIdx
 
     def getCurrentChannel(self):

src/pymapmanager/interface/stackWidgets/histogramWidget2.py

@@ -259,8 +259,8 @@ 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)
         else:
             self._myStack.getChannelMetadata(self._channelIdx).setUserContrast(theMin, theMax)
 
@@ -322,8 +322,8 @@ def _refreshContrast(self):
 
         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')
             globalMax = 256
         else:
             minContrast, maxContrast = _channelMetadata.getUserContrast()

src/pymapmanager/interface/stackWidgets/imagePlotWidget2.py

@@ -64,7 +64,7 @@ def __init__(self, stackWidget):
         """
         super().__init__(stackWidget)
 
-        self._myStack = stackWidget.getStack()
+        self._myStack: pymapmanager.stack = stackWidget.getStack()
         self._displayOptionsDict = stackWidget._displayOptionsDict
 
         self._currentSlice = 0
@@ -634,10 +634,11 @@ def _setColorLut(self, update=False):
 
     def _setContrast(self):
         if self._channelIsRGB():
+            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 = self._myStack.contrast.getValue(channelIdx, 'minAutoContrast_rgb')
+                # oneMaxContrast = self._myStack.contrast.getValue(channelIdx, 'maxAutoContrast_rgb')
                 oneMinContrast = 0
                 oneMaxContrast = 200
 
@@ -659,8 +660,8 @@ def _setContrast(self):
             self._myImage.setLevels(levelList, update=True)
 
         else:
-            logger.warning('abb turned off contrast, using auto contrast')
-            return
+            # logger.warning('abb turned off contrast, using auto contrast')
+            # return
 
             # one channel
             minUserContrast, maxUserContrast = \
@@ -694,7 +695,7 @@ def _setSlice(self, sliceNumber : int, doEmit = True):
         TODO: get rid of doEmit, use _blockSlots
         """
 
-        logger.warning(f'xxx EXPENSIVE ONLY CALL ONCE sliceNumber:{sliceNumber} doEmit:{doEmit}')
+        # logger.warning(f'xxx EXPENSIVE ONLY CALL ONCE sliceNumber:{sliceNumber} doEmit:{doEmit}')
 
         if isinstance(sliceNumber, float):
             sliceNumber = int(sliceNumber)
@@ -707,58 +708,69 @@ def _setSlice(self, sliceNumber : int, doEmit = True):
         upDownSlices = self._displayOptionsDict['windowState']['zPlusMinus']
 
         if self._channelIsRGB():
-            logger.warning('TODO: remove hard coded two channel assumption for rgb')
-            logger.warning('    use core loader channel metadata to get actual channel keys.')
+            logger.info(f'-->> setSlice rgb sliceNumber:{sliceNumber}')
+            # logger.warning('TODO: remove hard coded two channel assumption for rgb')
+            # logger.warning('    use core loader channel metadata to get actual channel keys.')
 
-            # ch1_image = self._myStack.getImageSlice(imageSlice=sliceNumber, channelIdx=0)
-            # ch2_image = self._myStack.getImageSlice(imageSlice=sliceNumber, channelIdx=1)
-            ch0_image = self._myStack.getMaxProjectSlice(sliceNumber,
-                                    channelIdx=1,
-                                    upSlices=upDownSlices, downSlices=upDownSlices,
-                                    func=np.max)
-            ch1_image = self._myStack.getMaxProjectSlice(sliceNumber,
-                                    channelIdx=2,
-                                    upSlices=upDownSlices, downSlices=upDownSlices,
-                                    func=np.max)
+            channelKeys = self._myStack.getChannelKeys()
 
-            # logger.info(f"check ch0_image min {ch1_image.min()} max {ch1_image.max()}")
+            if len(channelKeys) < 2:
+                logger.error(f'Expected at least 2 channels for RGB, found {len(channelKeys)}')
+                return
 
-            # rgb requires 8-bit images
-            ch0_image = ch0_image/ch0_image.max() * 2**8
-            ch1_image = ch1_image/ch1_image.max() * 2**8
-
-            ch0_image = ch0_image.astype(np.uint8)
-            ch1_image = ch1_image.astype(np.uint8)
+            _shape = self._myStack.getMetadata().shape  # (z, y, x)
+            _xShape = _shape[2]
+            _yShape = _shape[1]
 
-            # print('2) ch1_image:', ch1_image.shape, ch1_image.dtype)
+            # make the 3d slice we will return
+            sliceImage = np.zeros((_xShape,_yShape,3), dtype=np.uint8)
+
+            _redIdx = 0
+            _greenIdx = 1
+            _blueIdx = 2
+
+            maxImageDict = {}
+            channelColorDict = {}
+            for sliceChannel, channelKey in enumerate(channelKeys):
+                ch_image = self._myStack.getMaxProjectSlice(sliceNumber,
+                                    channelIdx=channelKey,
+                                    upSlices=upDownSlices, downSlices=upDownSlices,
+                                    func=np.max)
+                # rgb requires 8-bit images
+                ch_image = ch_image/ch_image.max() * 2**8
+                ch_image = ch_image.astype(np.uint8)
+                
+                # here is where we need a user option for channel color
+                sliceImage[:,:,sliceChannel] = ch_image
 
-            _xShape = ch0_image.shape[0]
-            _yShape = ch0_image.shape[1]
-            sliceImage = np.ndarray((_xShape,_yShape,3))
+                maxImageDict[channelKey] = ch_image
+            
+                # redundant, all channels have same shape
+                # _xShape = ch_image.shape[0]
+                # _yShape = ch_image.shape[1]
+            
+                _color = self._myStack.getChannelColor(channelKey)
+                _color = self.colorToHex(_color)
+                _color = to_rgb(_color)  # for ch0_image
+                channelColorDict[channelKey] = _color
 
             # # magenta is blue + red
             # sliceImage[:,:,0] = ch1_image  # red
             # sliceImage[:,:,1] = ch0_image  # green
             # sliceImage[:,:,2] = ch1_image  # blue
 
-            # Get first two channel colors
-            color0 = self._myStack.getChannelColor(1)
-            color1 = self._myStack.getChannelColor(2)
-
-            color0 = self.colorToHex(color0)
-            color1 = self.colorToHex(color1)
-            logger.info(f"color0 {color0} color1 {color1}")
-
-            # Convert hex color to RGB arrays
-            rgb0 = to_rgb(color0)  # for ch0_image
-            rgb1 = to_rgb(color1)  # for ch1_image
-
             brightness_factor = 2
             for i in range(3):  # R, G, B
+                # channelKeys is a list (we don't care if it is [int] or [str])
+                if i == 2:
+                    _channelKey = channelKeys[1]
+                else:
+                    _channelKey = channelKeys[i]
+
                 sliceImage[:,:,i] = (
                     brightness_factor *
-                    (ch0_image * (rgb0[i])) + 
-                    (ch1_image * (rgb1[i])) * i 
+                    (maxImageDict[_channelKey] * (channelColorDict[_channelKey][0])) + 
+                    (maxImageDict[_channelKey] * (channelColorDict[_channelKey][1])) * i 
                 ).clip(0, 255).astype(np.uint8)
 
         else:

src/pymapmanager/interface/stackWidgets/stackWidget.py

@@ -1346,10 +1346,12 @@ def loadInNewChannel(self, path:Optional[str] = None):
         # refresh stackToolBar
         self._topToolbar._setStack(theStack=self._stack)
 
-        _pmmEvent = pmmEvent(pmmEventType.setColorChannel, self)
-        _pmmEvent.setColorChannel(newChannelNum)
-        self.setColorChannelEvent(_pmmEvent) # chooses it in toptool bar
-        self.slot_setChannel(newChannelNum) # actually changes image in imageplotwidget
+        # abb 20250808
+        if newChannelNum is not None:
+            _pmmEvent = pmmEvent(pmmEventType.setColorChannel, self)
+            _pmmEvent.setColorChannel(newChannelNum)
+            self.setColorChannelEvent(_pmmEvent) # chooses it in toptool bar
+            self.slot_setChannel(newChannelNum) # actually changes image in imageplotwidget
 
     def deleteChannel(self, channelIdx):
         """ Delete channel in backend
@@ -1366,7 +1368,8 @@ def deleteChannel(self, channelIdx):
             _imagePlotWidget = self._widgetDict[self._imagePlotName]
             _imagePlotWidget.hide()
 
-        currentChannel = self._topToolbar.getCurrentChannel() # top tool bar is 1 based, incoming channelIdx is 0
+        # top tool bar is 1 based, incoming channelIdx is 0
+        currentChannel = self._topToolbar.getCurrentChannel()
         logger.info(f"currentChannel {currentChannel}")
         logger.info(f"channelIdx {channelIdx}")
 

src/pymapmanager/stack.py

@@ -43,7 +43,7 @@ def __init__(self,
         self.getImageSlice(0, defaultChannelIdx)
 
     def importChannels(self, importPath: str):
-        """Import channels from a .mmap file.
+        """Import channels from a file.
         
         Parameters
         ----------
@@ -54,7 +54,7 @@ def importChannels(self, importPath: str):
 
         # import channels from another .mmap file
         # this will add channels to the current timepoint
-        self._fullMap.importChannels(importPath, self)
+        self._fullMap.importChannels(importPath, self.timepoint)
 
         # important (this refreshes timepoint for new aggregate columns)
         self.getPointAnnotations().updateChannel()
@@ -105,7 +105,7 @@ def updateChannelName(self, channelIdx: int, newChannelName: str):
     def getTimeSeriesCore(self) -> pymapmanager.TimeSeriesCore:
         return self._fullMap
 
-    def getMetadata(self) -> TimepointMetadata:  #Metadata:
+    def getMetadata(self) -> TimepointMetadata:
         """Get metadata from the core map.
         """
         return self._fullMap.getTimepointMetadata(self.timepoint)
@@ -191,7 +191,7 @@ def getImageSlice(self,
 
     def getMaxProjectSlice(self, 
                             imageSlice : int, 
-                            channelIdx : int = 1, 
+                            channelIdx : int, 
                             upSlices : int = 1, 
                             downSlices : int = 1,
                             func = np.max
@@ -205,7 +205,12 @@ def getMaxProjectSlice(self,
             downSlices:
             func: Reference to np funtion to use like np.max
         """
-
+        # make sure we have channelId in metadata
+        if channelIdx not in self.getChannelKeys():
+            logger.error(f'channelIdx {channelIdx} not in channel keys {self.getChannelKeys()}')
+            return None
+        
+        # make sure imageSlice is an integer
         if not isinstance(imageSlice, int):
             #logger.warning('not an integer, converting')
             imageSlice = int(imageSlice)
@@ -294,7 +299,7 @@ def saveAs(self, path):
     def getLastSaveTime(self):
         return self._fullMap.getLastSaveTime()
 
-    def getChannelKeys(self) -> List[int]:
+    def getChannelKeys(self) -> list[int]:
         """Get list of channel keys.
         """
         return self.getMetadata().channelKeys

src/pymapmanager/timeseriesCore.py

@@ -347,7 +347,7 @@ def importChannels(self, importPath:str, time:int):
         # elif isinstance(self._fullMap._images, MultiImageLoader):
         #     self._fullMap.loader.appendChannels(importPath, time)
 
-        logger.warning('abb imageImport')
+        logger.warning(f'abb imageImport importPath {importPath} time:{time}')
         channelNum = self._fullMap.loader.importChannel(importPath, time)
         if channelNum is not None:
             return channelNum