Added accessor method to get multiple channels

model_server/base/accessors.py

@@ -331,11 +331,17 @@ class PatchStack(InMemoryDataAccessor):
             tifffile.imwrite(fpath, tzcyx, imagej=True)
 
     def get_one_channel_data(self, channel: int, mip: bool = False):
-        c = int(channel)
+        return self.get_channels([channel], mip=mip)
+
+    def get_channels(self, channels: list, mip: bool = False):
+        carr = [int(c) for c in channels]
         if mip:
-            return PatchStack(self.pyxcz[:, :, :, c:(c + 1), :].max(axis=-1, keepdims=True))
+            return PatchStack(self.pyxcz[:, :, :, carr, :].max(axis=-1, keepdims=True))
         else:
-            return PatchStack(self.pyxcz[:, :, :, c:(c + 1), :])
+            return PatchStack(self.pyxcz[:, :, :, carr, :])
+
+    def gch(self, args):
+        return self.get_channels(args)
 
     @property
     def shape_dict(self):

model_server/base/roiset.py

@@ -308,11 +308,24 @@ class RoiSet(object):
         return zi_st
 
 
-    def classify_by(self, name: str, channel: int, object_classification_model: InstanceSegmentationModel, ):
+    def classify_by(self, name: str, channels: int, object_classification_model: InstanceSegmentationModel, derived_channel_functions: dict[callable()] = None):
+
+        raw_acc = self.get_patches_acc(expanded=False, pad_to=None)  # all channels
+        if derived_channel_functions:
+            mono_data = [raw_acc.get_one_channel_data(c).data for c in range(0, raw_acc.chroma)]
+            for k, fcn in derived_channel_functions.keys():
+                der = fcn(raw_acc).data
+                assert der.shape == mono_data[0].shape
+                mono_data.append(der)
+            # combine channels
+            input_acc = PatchStack(np.concatenate([mono_data], axis=3))
+
+        else:
+            input_acc = raw_acc
 
         # do this on a patch basis, i.e. only one object per frame
         obmap_patches = object_classification_model.label_patch_stack(
-            self.get_patches_acc(channel=channel, expaned=False, pad_to=None),
+            input_acc,
             self.get_patch_masks_acc(expanded=False, pad_to=None)
         )