change(imageviewer): fixed RemoteImageViewer

image_id found from OMERO; added skip_channels

src/wela/imageviewer.py

@@ -6,10 +6,10 @@ import h5py
 import napari
 import numpy as np
 from agora.io.cells import Cells
-from agora.io.metadata import parse_metadata
 from aliby.io.image import dispatch_image
-from aliby.tile.tiler import Tiler
+from aliby.io.omero import Dataset
 from aliby.io.omero import UnsafeImage as OImage
+from aliby.tile.tiler import Tiler
 
 
 def colormap(channel):
@@ -32,10 +32,23 @@ class BaseImageViewer(ABC):
         print(f"Viewing {str(h5file_path)}")
         self.full = {}
 
-    def get_tiles(self, trap_id, tps, cell_only=True):
+    def print_trap_info(self, cells):
+        """List available traps - those with identified cells."""
+        traps_with_labels = [
+            i for i, labels in enumerate(cells.labels) if labels
+        ]
+        print(f"Traps with labelled cells {traps_with_labels}.")
+        print(f"Maximum number of time points {cells.ntimepoints}.")
+
+    def get_tiles(self, trap_id, tps, channels_to_skip=None, cell_only=True):
         """Get dict of tiles with channel indices as keys."""
         tiles_dict = {}
-        channels = self.tiler.channels
+        if channels_to_skip is None:
+            channels = self.tiler.channels
+        else:
+            channels = [
+                ch for ch in self.tiler.channels if ch not in channels_to_skip
+            ]
         channel_indices = [channels.index(ch) for ch in channels]
         for ch_index, ch in zip(channel_indices, channels):
             tile_dict_for_ch = self.get_all_tiles(tps, ch_index)
@@ -99,23 +112,24 @@ class BaseImageViewer(ABC):
         """
         Get dict with time points as keys and all available tiles as values.
 
-        We assume there is only a single channel.
+        We assume only a single channel.
         """
         z = z or self.tiler.ref_z
         ch_tps = [(channel_index, tp) for tp in tps]
         for ch, tp in ch_tps:
             if (ch, tp) not in self.full:
+                print(f"Getting {self.tiler.channels[ch]} at time point {tp}.")
                 self.full[(ch, tp)] = self.tiler.get_tiles_timepoint(
                     tp, channels=[ch], z=[z]
                 )[:, 0, 0, z, ...]
         tile_dict = {tp: self.full[(ch, tp)] for ch, tp in ch_tps}
         return tile_dict
 
-    def get_data_for_viewing(self, trap_id, tps):
+    def get_data_for_viewing(self, trap_id, tps, channels_to_skip):
         """Get images and outlines as multidimensional arrays for Napari."""
         # get outlines and tiles
         outlines = self.get_outlines(trap_id, tps)
-        tiles_dict = self.get_tiles(trap_id, tps)
+        tiles_dict = self.get_tiles(trap_id, tps, channels_to_skip)
         channels = list(tiles_dict.keys())
         # put time series into one array with dimensions TCZYX
         ydim, xdim = tiles_dict[list(tiles_dict.keys())[0]][0].shape
@@ -134,7 +148,7 @@ class BaseImageViewer(ABC):
             ts_labels[tp_index, 0, ...] = outlines[tp_index]
         return ts_images, ts_labels, channels
 
-    def view(self, trap_id, tps=10):
+    def view(self, trap_id, tps=10, channels_to_skip=None):
         """
         Use Napari to view all channels and outlines for a particular trap.
 
@@ -155,7 +169,7 @@ class BaseImageViewer(ABC):
         elif type(tps) is int:
             tps = np.arange(tps)
         ts_images, ts_labels, channels = self.get_data_for_viewing(
-            trap_id, tps
+            trap_id, tps, channels_to_skip
         )
         # launch napari
         viewer = napari.Viewer()
@@ -192,11 +206,7 @@ class LocalImageViewer(BaseImageViewer):
             with dispatch_image(image_file_path)(image_file_path) as image:
                 self.tiler = Tiler.from_h5(image, h5file_path)
             self.cells = Cells.from_source(h5file_path)
-            traps_with_labels = [
-                i for i, labels in enumerate(self.cells.labels) if labels
-            ]
-            print(f"Traps with labels {traps_with_labels}.")
-            print(f"Maximum number of time points {self.cells.ntimepoints}.")
+            self.print_trap_info(self.cells)
         else:
             if not h5file_path.exists():
                 print(f" Trouble loading {h5file}.")
@@ -214,13 +224,22 @@ class RemoteImageViewer(BaseImageViewer):
         h5file_path = Path(h5file)
         super().__init__(h5file_path)
         with h5py.File(h5file_path, "r") as f:
-            breakpoint()
-            self.image_id = f.attrs.get("image_id")
-
-        image = OImage(omero_id, **server_info)
-        breakpoint()
-        self.tiler = Tiler.from_h5(image, h5file_path)
-        self.cells = Cells.from_source(h5file_path)
+            # get image_id from the h5 file
+            image_id = f.attrs.get("image_id")
+        if image_id is None:
+            # get image_id from OMERO
+            with Dataset(omero_id, **server_info) as dataset_om:
+                positions = dataset_om.get_position_ids()
+                image_id = positions.get(h5file_path.name.split(".")[0])
+        if image_id is None:
+            print("Can't find an image.")
+        else:
+            self.image_id = image_id
+            image = OImage(image_id, **server_info)
+            print("Connected to OMERO.")
+            self.tiler = Tiler.from_h5(image, h5file_path)
+            self.cells = Cells.from_source(h5file_path)
+            self.print_trap_info(self.cells)
 
 
 def get_files(