Merge branch 'master' of https://github.com/openUC2/imSwitch

Author: beniroquai

dockerfile

@@ -183,14 +183,6 @@ RUN cd /opt/Vimba_6_0/VimbaPython/Source && \
 # Set environment variable for GenTL detection
 ENV GENICAM_GENTL64_PATH="${GENICAM_GENTL64_PATH}:/opt/Vimba_6_0/VimbaUSBTL/CTI/arm_64bit"
 
-# install IOHub - as it will be installed via ImSwitch again
-#         "iohub @ https://github.com/czbiohub-sf/iohub/archive/refs/heads/main.zip"
-RUN /bin/bash -c "source /opt/conda/bin/activate imswitch && pip install --no-cache-dir Cython"
-RUN git clone https://github.com/czbiohub-sf/iohub /tmp/iohub && \
-    cd /tmp/iohub && \
-    /bin/bash -c "source /opt/conda/bin/activate imswitch && \
-                  pip install --no-build-isolation /tmp/iohub" && \
-    rm -rf /tmp/iohub
 
 # Always pull the latest version of ImSwitch and UC2-REST repositories
 # Adding a dynamic build argument to prevent caching

imswitch/imcontrol/controller/controllers/HistoScanController.py

@@ -38,12 +38,6 @@
 import numpy as np
 from io import BytesIO
 from PIL import Image
-try:
-    from iohub.ngff import open_ome_zarr
-    IS_IOHUB = True
-except ImportError:
-    IS_IOHUB = False
-    isZARR=False
 isZARR=False
 
 try:
@@ -1585,55 +1579,23 @@ def add_image(self, img, coords, metadata):
             self.queue.append((img, coords, metadata))
 
     def _process_queue(self):
-        if isZARR:
-           
-            tmp_dir = TemporaryDirectory()  
-            store_path = os.path.join(tmp_dir.name, "tiled.zarr")
-            print("Zarr store path", store_path)
-            
-            # define grid 
-            with open_ome_zarr(store_path, layout="tiled", mode="a", channel_names=["Mono"]) as dataset:
-                tiles = dataset.make_tiles(
-                    "tiled_raw", grid_shape=self.grid_shape, tile_shape=self.tile_shape, dtype=self.dtype
-                )
-                while self.isRunning:
-                    if not self.queue:
-                        time.sleep(.02) # unload CPU
-                        continue
-                    img, coords, metadata = self.queue.popleft()
-                    
-                    # flip image if needed
-                    if self.flipX:
-                        img = np.fliplr(img)
-                    if self.flipY:
-                        img = np.flipud(img)
-                    self._place_on_canvas(img, coords)
-
-                    # write image to disk
-                    # tif.write(data=img, metadata=metadata)                
-                    row = metadata['Plane']['IndexX']
-                    column = metadata['Plane']['IndexY']
-                    tiles.write_tile(img, row, column)
-
-        
-        else:
-            with tifffile.TiffWriter(self.file_path, bigtiff=True, append=True) as tif:
-                while self.isRunning:
-                    if not self.queue:
-                        time.sleep(.02) # unload CPU
-                        continue
-                    img, coords, metadata = self.queue.popleft()
-                    
-                    # flip image if needed
-                    if self.flipX:
-                        img = np.fliplr(img)
-                    if self.flipY:
-                        img = np.flipud(img)
-                    
-                    self._place_on_canvas(img, coords)
-                    # write image to disk
-                    #metadata e.g. {"Pixels": {"PhysicalSizeX": 0.2, "PhysicalSizeXUnit": "\\u00b5m", "PhysicalSizeY": 0.2, "PhysicalSizeYUnit": "\\u00b5m"}, "Plane": {"PositionX": -100, "PositionY": -100, "IndexX": 0, "IndexY": 0}}
-                    tif.write(data=img, metadata=metadata)
+        with tifffile.TiffWriter(self.file_path, bigtiff=True, append=True) as tif:
+            while self.isRunning:
+                if not self.queue:
+                    time.sleep(.02) # unload CPU
+                    continue
+                img, coords, metadata = self.queue.popleft()
+                
+                # flip image if needed
+                if self.flipX:
+                    img = np.fliplr(img)
+                if self.flipY:
+                    img = np.flipud(img)
+                
+                self._place_on_canvas(img, coords)
+                # write image to disk
+                #metadata e.g. {"Pixels": {"PhysicalSizeX": 0.2, "PhysicalSizeXUnit": "\\u00b5m", "PhysicalSizeY": 0.2, "PhysicalSizeYUnit": "\\u00b5m"}, "Plane": {"PositionX": -100, "PositionY": -100, "IndexX": 0, "IndexY": 0}}
+                tif.write(data=img, metadata=metadata)
 
     def _place_on_canvas(self, img, coords):
         if self.isStitchAshlar and IS_ASHLAR_AVAILABLE:

imswitch/imcontrol/controller/controllers/WorkflowController.py

@@ -47,11 +47,6 @@
 from typing import List, Dict, Any, Optional
 import uuid
 
-try:
-    from iohub.ngff import open_ome_zarr
-    IS_IOHUB = True
-except ImportError:
-    IS_IOHUB = False
 
 
 isZARR=True
@@ -564,6 +559,8 @@ def start_xyz_histo_workflow(self,
         self._logger.debug("Zarr store path: "+store_path)
 
         # Let's assume single channel "Mono" for simplicity, but can adapt for more.
+        def open_ome_zarr(store_path, layout="tiled", mode="a", channel_names=None):
+            return None # TODO: Implement this function to open or create a Zarr dataset with the specified layout and channel names.
         dataset = open_ome_zarr(store_path, layout="tiled", mode="a", channel_names=[channel])
         # Calculate grid shape based on the number of xy positions
         grid_shape = (len(ys), len(xs))

imswitch/imcontrol/controller/server/_serialize.py

@@ -57,8 +57,7 @@ def get_version():
         "Send2Trash >= 1.8",
         "tifffile >= 2020.11.26",
         "ome_zarr >= 0.9.0",
-        "Pyro5 >= 5.14",
-        "dask[complete] >= 2024.11.2",
+        "dask[complete] >= 2024.8.0",
         "fastAPI >= 0.86.0",
         "uvicorn[standard] >= 0.19.0",
         "matplotlib == 3.9.2",
@@ -96,9 +95,7 @@ def get_version():
             "qtpy >= 1.9"
         ],
         'Ashlar': [
-            "ashlarUC2",
-            "iohub==0.2.0a1", 
-
+            "ashlarUC2"
         ],
         'arkitekt':
             [