Merge branch 'main' of github.com:vitessce/vitessce-python into kelle…

…r-mark/image-wrappers
vitessce · Jan 24, 2024 · 2ed3f5e · 2ed3f5e
2 parents 7c671c3 + 611819e
commit 2ed3f5e
Show file tree

Hide file tree

Showing 4 changed files with 78 additions and 63 deletions.
diff --git a/.github/workflows/test_demos.yml b/.github/workflows/test_demos.yml
@@ -11,6 +11,7 @@ jobs:
         with:
           python-version: '3.9'
       - run: |
+          pip install "pulp==2.7.0"
           pip install snakemake
           pip install pyyaml
       - name: Install vitessce

diff --git a/pyproject.toml b/pyproject.toml
@@ -34,7 +34,7 @@ dependencies = [
   'numpy>=1.21.2',
   'anndata>=0.7.8,<0.9',
   'scanpy>=1.9.3',
-  'ome-zarr==0.2.1',
+  'ome-zarr==0.8.3',
   'tifffile>=2020.10.1',
   'jsonschema>=3.2'
 ]
@@ -50,6 +50,16 @@ dev = [
 docs = [
   'sphinx==4.2.0',
   'sphinx-rtd-theme==1.0.0',
+
+  # Pin sub-dependencies of sphinx
+  # Reference: https://github.com/sphinx-doc/sphinx/issues/11130
+  'sphinxcontrib-applehelp==1.0.4',
+  'sphinxcontrib-devhelp==1.0.2',
+  'sphinxcontrib-htmlhelp==2.0.1',
+  'sphinxcontrib-jsmath==1.0.1',
+  'sphinxcontrib-qthelp==1.0.3',
+  'sphinxcontrib-serializinghtml==1.1.5',
+
   'nbsphinx==0.8.8',
   'nbclean==0.3.2',
   # Pin sqlalchemy to before 1.4 to fix issue importing nbclean.NotebookCleaner

diff --git a/tests/test_ome_utils.py b/tests/test_ome_utils.py
@@ -50,41 +50,44 @@ def setUp(self):
     def test_rgb_img_to_ome_zarr(self):
         img_arr = self.img_arr
         out_path = data_path / "rgb_out.ome.zarr"
-        rgb_img_to_ome_zarr(img_arr, out_path, img_name="Test", axes="cyx", chunks=(1, 3, 3))
+        rgb_img_to_ome_zarr(img_arr, out_path, img_name="Test", axes="cyx", chunks=(1, 3, 3), scaler=None)
 
         z_root = zarr.open(out_path, mode="r")
 
         assert dict(z_root.attrs) == {
             'multiscales': [
                 {
-                    'axes': ['c', 'y', 'x'],
+                    'axes': [
+                        {'name': 'c', 'type': 'channel'},
+                        {'name': 'y', 'type': 'space'},
+                        {'name': 'x', 'type': 'space'}
+                    ],
                     'datasets': [
-                        {'path': '0'},
-                        {'path': '1'},
-                        {'path': '2'},
-                        {'path': '3'},
-                        {'path': '4'}
+                        {
+                            'coordinateTransformations': [
+                                {'scale': [1.0, 1.0, 1.0], 'type': 'scale'}
+                            ],
+                            'path': '0'
+                        }
                     ],
-                    'version': '0.3'
+                    'name': '/',
+                    'version': '0.4'
                 }
             ],
             'omero': {
                 'channels': [
-                    {
-                        'color': 'FF0000',
-                        'label': 'R',
-                        'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
-                    },
-                    {
-                        'color': '00FF00',
-                        'label': 'G',
-                        'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
-                    },
-                    {
-                        'color': '0000FF',
-                        'label': 'B',
-                        'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
-                    }
+                    {'color': 'FF0000',
+                     'label': 'R',
+                     'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
+                     },
+                    {'color': '00FF00',
+                     'label': 'G',
+                     'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
+                     },
+                    {'color': '0000FF',
+                     'label': 'B',
+                     'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
+                     }
                 ],
                 'name': 'Test',
                 'rdefs': {},

diff --git a/vitessce/data_utils/ome.py b/vitessce/data_utils/ome.py
@@ -49,7 +49,7 @@ def multiplex_img_to_ome_tiff(img_arr, channel_names, output_path, axes="CYX"):
     tiff_writer.close()
 
 
-def rgb_img_to_ome_zarr(img_arr, output_path, img_name="Image", chunks=(1, 256, 256), axes="cyx"):
+def rgb_img_to_ome_zarr(img_arr, output_path, img_name="Image", chunks=(1, 256, 256), axes="cyx", **kwargs):
     """
     Convert an RGB image to OME-Zarr v0.3.
 
@@ -75,30 +75,31 @@ def rgb_img_to_ome_zarr(img_arr, output_path, img_name="Image", chunks=(1, 256,
         image=img_arr,
         group=z_root,
         axes=axes,
-        omero={
-            "name": img_name,
-            "version": "0.3",
-            "rdefs": {},
-            "channels": [
-                {
-                    "label": "R",
-                    "color": "FF0000",
-                    "window": default_window
-                },
-                {
-                    "label": "G",
-                    "color": "00FF00",
-                    "window": default_window
-                },
-                {
-                    "label": "B",
-                    "color": "0000FF",
-                    "window": default_window
-                }
-            ]
-        },
-        chunks=chunks
+        storage_options=dict(chunks=chunks),
+        **kwargs,
     )
+    z_root.attrs["omero"] = {
+        "name": img_name,
+        "version": "0.3",
+        "rdefs": {},
+        "channels": [
+            {
+                "label": "R",
+                "color": "FF0000",
+                "window": default_window
+            },
+            {
+                "label": "G",
+                "color": "00FF00",
+                "window": default_window
+            },
+            {
+                "label": "B",
+                "color": "0000FF",
+                "window": default_window
+            }
+        ]
+    }
 
 
 def multiplex_img_to_ome_zarr(img_arr, channel_names, output_path, img_name="Image", chunks=(1, 256, 256), axes="cyx", channel_colors=None):
@@ -132,19 +133,19 @@ def multiplex_img_to_ome_zarr(img_arr, channel_names, output_path, img_name="Ima
         image=img_arr,
         group=z_root,
         axes=axes,
-        omero={
-            "name": img_name,
-            "version": "0.3",
-            "rdefs": {},
-            "channels": [
-                {
-                    "label": channel_name,
-                    "color": channel_colors[channel_name] if channel_colors is not None else "FFFFFF",
-                    "window": default_window
-                }
-                for channel_name
-                in channel_names
-            ]
-        },
-        chunks=chunks
+        storage_options=dict(chunks=chunks)
     )
+    z_root.attrs["omero"] = {
+        "name": img_name,
+        "version": "0.3",
+        "rdefs": {},
+        "channels": [
+            {
+                "label": channel_name,
+                "color": channel_colors[channel_name] if channel_colors is not None else "FFFFFF",
+                "window": default_window
+            }
+            for channel_name
+            in channel_names
+        ]
+    }