Merge pull request #61 from DragaDoncila/add-label-properties

Add support for label properties in zattrs and plugin

.github/workflows/posix.yml

@@ -19,7 +19,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Setup miniconda
-        uses: conda-incubator/setup-miniconda@v1
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           channels: conda-forge,ome

.github/workflows/windows.yml

@@ -20,7 +20,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Setup miniconda
-        uses: conda-incubator/setup-miniconda@v1
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           channels: conda-forge,ome

ome_zarr/data.py

@@ -155,11 +155,14 @@ def create_zarr(
         write_multiscale(labels, label_grp)
 
         colors = []
+        properties = []
         for x in range(1, 9):
             rgba = [randrange(0, 256) for i in range(4)]
             colors.append({"label-value": x, "rgba": rgba})
+            properties.append({"label-value": x, "class": f"class {x}"})
         label_grp.attrs["image-label"] = {
             "version": "0.1",
             "colors": colors,
+            "properties": properties,
             "source": {"image": "../../"},
         }

ome_zarr/napari.py

@@ -6,7 +6,7 @@
 
 import logging
 import warnings
-from typing import Any, Callable, Dict, Iterator, List, Optional
+from typing import Any, Callable, Dict, Iterator, List, Optional, Set
 
 from .data import CHANNEL_DIMENSION
 from .io import parse_url
@@ -62,6 +62,25 @@ def f(*args: Any, **kwargs: Any) -> List[LayerData]:
                     layer_type = "labels"
                     if "colormap" in metadata:
                         del metadata["colormap"]
+                    if "properties" in metadata:
+                        props = metadata["properties"]
+                        reader_props = {}
+                        label_indices = list(props.keys())
+                        reader_props["index"] = label_indices
+
+                        # properties may be ragged, so we need all possible properties
+                        all_keys: Set[str]
+                        all_keys = set()
+                        for index in label_indices:
+                            all_keys = all_keys.union(set(props[index].keys()))
+
+                        # napari expects lists of equal length so we must fill with None
+                        for prop_key in all_keys:
+                            reader_props[prop_key] = [
+                                props[i][prop_key] if prop_key in props[i] else None
+                                for i in label_indices
+                            ]
+                        metadata["properties"] = reader_props
 
                 elif shape[CHANNEL_DIMENSION] > 1:
                     metadata["channel_axis"] = CHANNEL_DIMENSION

ome_zarr/reader.py

@@ -223,6 +223,14 @@ def __init__(self, node: Node) -> None:
                 except Exception as e:
                     LOGGER.error(f"invalid color - {color}: {e}")
 
+        properties: Dict[int, Dict[str, str]] = {}
+        props_list = image_label.get("properties", [])
+        if props_list:
+            for props in props_list:
+                label_val = props["label-value"]
+                properties[label_val] = dict(props)
+                del properties[label_val]["label-value"]
+
         # TODO: a metadata transform should be provided by specific impls.
         name = self.zarr.basename()
         node.metadata.update(
@@ -233,6 +241,8 @@ def __init__(self, node: Node) -> None:
                 "metadata": {"image": self.lookup("image", {}), "path": name},
             }
         )
+        if properties:
+            node.metadata.update({"properties": properties})
 
 
 class Multiscales(Spec):

tests/test_napari.py

@@ -13,7 +13,7 @@ def initdir(self, tmpdir):
         self.path = tmpdir.mkdir("data")
         create_zarr(str(self.path), astronaut, "astronaut")
 
-    def assert_layers(self, layers, visible_1, visible_2):
+    def assert_layers(self, layers, visible_1, visible_2, label_props=None):
         # TODO: check name
 
         assert len(layers) == 2
@@ -27,6 +27,8 @@ def assert_layers(self, layers, visible_1, visible_2):
 
         data, metadata, layer_type = self.assert_layer(label)
         assert visible_2 == metadata["visible"]
+        if label_props:
+            assert label_props == metadata["properties"]
 
     def assert_layer(self, layer_data):
         data, metadata, layer_type = layer_data
@@ -47,7 +49,11 @@ def test_labels(self):
     def test_label(self):
         filename = str(self.path.join("labels", "astronaut"))
         layers = napari_get_reader(filename)()
-        self.assert_layers(layers, False, True)
+        properties = {
+            "index": [i for i in range(1, 9)],
+            "class": [f"class {i}" for i in range(1, 9)],
+        }
+        self.assert_layers(layers, False, True, properties)
 
     @pytest.mark.skipif(
         not sys.platform.startswith("darwin") or sys.version_info < (3, 7),