???

src/pymapmanager/interface2/runInterfaceBob.py

@@ -33,9 +33,13 @@ def run():
     path = '/Users/cudmore/Sites/MapManagerCore-Data/data/Animal_145_Slice_1_Right.mmap.zip'
     path = '/Users/cudmore/Desktop/Animal_145_Slice_1_Right.mmap.zip'
 
-    from mapmanagercore.data import getNd2Channel_1, getSingleTimepointMap_nd2
+    from mapmanagercore.data import getNd2Channel_1, getSingleTimepointMap_nd2, getTiffChannel_1
     path = getNd2Channel_1()
-    path = getSingleTimepointMap_nd2()
+    # path = getSingleTimepointMap_nd2()
+
+    path = '/Users/cudmore/Desktop/Animal_145_Slice_1_Right.mmap.zip'
+
+    # path = getTiffChannel_1()
 
     app = PyMapManagerApp(sys.argv)
     # mw will be map widget if path has multiple timepoints, otherwise mw is a stackwidget2

src/pymapmanager/interface2/stackWidgets/stackWidget2.py

@@ -1302,57 +1302,66 @@ def getOpenPluginDict(self):
         """
         return self._openPluginDict 
 
-    def loadInNewChannel(self, path = None, channel = None):
-        """ self, path: Union[str, np.ndarray], time: int = 0, channel: int = 0):
+    def loadInNewChannel(self, path:Optional[str] = None, channel = None):
+        """Given a file path append channels from file (can be more than one channel).
+        
+        self, path: Union[str, np.ndarray], time: int = 0, channel: int = 0):
         """
         if path is None:
-            newTifPath = QtWidgets.QFileDialog.getOpenFileName(None, 'New Tif File')[0]
+            importPath = QtWidgets.QFileDialog.getOpenFileName(None, 'New Tif File')[0]
         else:
-            newTifPath = path
-
-        # check to ensure it is a tif file, Note: might need to expand to list of supported files
-        _path, _ext = os.path.splitext(newTifPath)
-        if _ext not in IMPORT_FILE_EXTENSIONS:
-            logger.error(f'import must have extension "{IMPORT_FILE_EXTENSIONS}", got "{_ext}" -->> did not load.')
-            QtWidgets.QMessageBox.critical(self, "Error: Incorrect Extension", "Please use .tif as the file extension to save")
-            return
+            importPath = path
 
-        #Check to ensure it is a valid image channel (same size)
-        from PIL import Image
-
-        # with Image.open(newTifPath) as img:
-        #     newImgWidth, newImgHeight = img.size
-        #     # print("Width:", newImgWidth)
-        #     # print("Height:", newImgHeight)
-        #     newImgSlices = img.n_frames  # z dimension
-
-        # # Get old tif path
-        stackHeader = self.getStack().header
-        x = stackHeader["xPixels"]
-        y = stackHeader["yPixels"]
-        z = stackHeader["numSlices"]
-        # if newImgHeight != y or newImgWidth != x or newImgSlices != z:
-        #     logger.error(f'Incorrect shape when loading in new image.')
-        #     QtWidgets.QMessageBox.critical(self, "Error: Incorrect Image Size", 
-        #                                    f"Please upload an image with size x: {x}, y: {y}, z: {z} ")
-        #     return
+        time = self.getStack().timepoint
 
-        time = self._stack.timepoint
+        useImageImporter = True
+        if useImageImporter:
+            self.getTimeSeriesCore().importChannels(importPath, time=time)
 
-        isImgValid = self.getTimeSeriesCore().validateNewChannel(newTifPath, time)
+        else:
+            # check to ensure it is a tif file, Note: might need to expand to list of supported files
+            _path, _ext = os.path.splitext(importPath)
+            if _ext not in IMPORT_FILE_EXTENSIONS:
+                logger.error(f'import must have extension "{IMPORT_FILE_EXTENSIONS}", got "{_ext}" -->> did not load.')
+                QtWidgets.QMessageBox.critical(self, "Error: Incorrect Extension", "Please use .tif as the file extension to save")
+                return
 
-        if not isImgValid:
-            logger.error(f'Incorrect shape when loading in new image.')
-            QtWidgets.QMessageBox.critical(self, "Error: Incorrect Image Size", 
-                                           f"Please upload an image with size x: {x}, y: {y}, z: {z} ")
-            return
+            #Check to ensure it is a valid image channel (same size)
+            # from PIL import Image
+
+            # with Image.open(newTifPath) as img:
+            #     newImgWidth, newImgHeight = img.size
+            #     # print("Width:", newImgWidth)
+            #     # print("Height:", newImgHeight)
+            #     newImgSlices = img.n_frames  # z dimension
+
+            # # Get old tif path
+            stackHeader = self.getStack().header
+            x = stackHeader["xPixels"]
+            y = stackHeader["yPixels"]
+            z = stackHeader["numSlices"]
+            # if newImgHeight != y or newImgWidth != x or newImgSlices != z:
+            #     logger.error(f'Incorrect shape when loading in new image.')
+            #     QtWidgets.QMessageBox.critical(self, "Error: Incorrect Image Size", 
+            #                                    f"Please upload an image with size x: {x}, y: {y}, z: {z} ")
+            #     return
+
+            isImgValid = self.getTimeSeriesCore().validateNewChannel(importPath, time)
+
+            if not isImgValid:
+                logger.error(f'Incorrect shape when loading in new image.')
+                QtWidgets.QMessageBox.critical(self, "Error: Incorrect Image Size", 
+                                            f"Please upload an image with size x: {x}, y: {y}, z: {z} ")
+                return
 
-        if channel is None:
-            channel = self._stack.getTimeSeriesTotalChannels() # len of total channels = new channel, since it is 0 based
-
-        logger.info(f"channel num {channel}")
-        self.getTimeSeriesCore().loadInNewChannel(newTifPath, time=time, channel=channel)
+            if channel is None:
+                channel = self._stack.getTimeSeriesTotalChannels() # len of total channels = new channel, since it is 0 based
+        
+            logger.info(f"channel num {channel}")
+            self.getTimeSeriesCore().loadInNewChannel(importPath, time=time, channel=channel)
 
+        # abb TODO make a signalChannelUpdate for add/remove/edit (channel name)
+
         # reset stackToolBar
         self._topToolbar._setStack(theStack=self._stack)
 

src/pymapmanager/timeseriesCore.py

@@ -336,13 +336,6 @@ def _import_tiff(self):
                             points=pd.DataFrame())
 
         self._fullMap : MapAnnotations = map
-
-    def _import_ome_zarr(self):
-        from mapmanagercore.image_importers.image_importer_ome_zarr import ImageImporter_Ome_Zarr
-        path = self.path
-        flz = ImageImporter_Ome_Zarr(path)
-        map = flz.getMapAnnotations()
-        self._fullMap : MapAnnotations = map
 
     def save(self):
         """ Stack saves changes to its .mmap Zarr file that is stored
@@ -390,6 +383,17 @@ def redo(self):
         # self.getPointAnnotations()._buildTimepoint()  # rebuild single timepoint
         # self.getPointAnnotations()._buildDataFrame()
 
+    # abb imageImport can we just always have a zarr loader or a MultiImageLoader (not both)
+    def importChannels(self, importPath:str, time:int):
+        # if isinstance(self._fullMap._images, ZarrLoader):
+        #     logger.error('abb NOT IMPLEMENTED for ZarrLoader')
+        #     # self._fullMap._images.read(path, time=time, channel=channel)
+        # elif isinstance(self._fullMap._images, MultiImageLoader):
+        #     self._fullMap.loader.appendChannels(importPath, time)
+
+        logger.warning('abb imageImport')
+        self._fullMap.loader.appendChannels(importPath, time)
+
     def loadInNewChannel(self, path: Union[str, np.ndarray], time: int = 0, channel: int = 0):
         """ Call loadInNewChannel in backend MapManagerCore
 
@@ -454,7 +458,8 @@ def swapChannels(self, tp, srcChannel, destChannel):
                                   destTimePoint = tp, destChannel = destChannel)
 
     def updateChannel(self, tp, channelIdx, newChannelName: str):
-        """"""
+        """
+        """
 
         # dict uses one based indexing
         updateDict = {"name" : newChannelName,