Merge pull request #30 from will-moore/handle_masks

Support opening of masks

Author: joshmoore

ome_zarr.py

@@ -102,6 +102,20 @@ def is_zarr(self):
     def is_ome_zarr(self):
         return self.zgroup and "multiscales" in self.root_attrs
 
+    def has_ome_masks(self):
+        "Does the zarr Image also include /masks sub-dir"
+        return self.get_json('masks/.zgroup')
+
+    def is_ome_mask(self):
+        return self.zarr_path.endswith('masks/') and self.get_json('.zgroup')
+
+    def get_mask_names(self):
+        """
+        Called if is_ome_mask is true
+        """
+        # If this is a mask, the names are in root .zattrs
+        return self.root_attrs.get('masks', [])
+
     def get_json(self, subpath):
         raise NotImplementedError("unknown")
 
@@ -110,6 +124,10 @@ def get_reader_function(self):
             raise Exception(f"not a zarr: {self}")
         return self.reader_function
 
+    def to_rgba(self, v):
+        """Get rgba (0-1) e.g. (1, 0.5, 0, 1) from integer"""
+        return [x/255 for x in v.to_bytes(4, signed=True, byteorder='big')]
+
     def reader_function(self, path: PathLike) -> List[LayerData]:
         """Take a path or list of paths and return a list of LayerData tuples."""
 
@@ -118,12 +136,22 @@ def reader_function(self, path: PathLike) -> List[LayerData]:
             # TODO: safe to ignore this path?
 
         if self.is_ome_zarr():
-            return [self.load_ome_zarr()]
+            layers = [self.load_ome_zarr()]
+            # If the Image contains masks...
+            if self.has_ome_masks():
+                mask_path = os.path.join(self.zarr_path, 'masks')
+                # Create a new OME Zarr Reader to load masks
+                masks = self.__class__(mask_path).reader_function(None)
+                layers.extend(masks)
+            return layers
 
         elif self.zarray:
             data = da.from_zarr(f"{self.zarr_path}")
             return [(data,)]
 
+        elif self.is_ome_mask():
+            return self.load_ome_masks()
+
     def load_omero_metadata(self, assert_channel_count=None):
         """Load OMERO metadata as json and convert for napari"""
         metadata = {}
@@ -191,7 +219,6 @@ def load_omero_metadata(self, assert_channel_count=None):
 
         return metadata
 
-
     def load_ome_zarr(self):
 
         resolutions = ["0"]  # TODO: could be first alphanumeric dataset on err
@@ -219,6 +246,25 @@ def load_ome_zarr(self):
         return (pyramid, {'channel_axis': 1, **metadata})
 
 
+    def load_ome_masks(self):
+        # look for masks in this dir...
+        mask_names = self.get_mask_names()
+        masks = []
+        for name in mask_names:
+            mask_path = os.path.join(self.zarr_path, name)
+            mask_attrs = self.get_json(f'{name}/.zattrs')
+            colors = {}
+            if 'color' in mask_attrs:
+                color_dict = mask_attrs.get('color')
+                colors = {int(k):self.to_rgba(v) for (k, v) in color_dict.items()}
+            data = da.from_zarr(mask_path)
+            # Split masks into separate channels, 1 per layer
+            for n in range(data.shape[1]):
+                masks.append((data[:,n,:,:,:],
+                              {'name': name, 'color': colors},
+                              'labels'))
+        return masks
+
 
 class LocalZarr(BaseZarr):
 
@@ -231,7 +277,6 @@ def get_json(self, subpath):
         with open(filename) as f:
             return json.loads(f.read())
 
-
 class RemoteZarr(BaseZarr):
 
     def get_json(self, subpath):
@@ -249,7 +294,6 @@ def get_json(self, subpath):
             LOGGER.error(f"({rsp.status_code}): {rsp.text}")
             return {}
 
-
 def info(path):
     """
     print information about the ome-zarr fileset