Support additional parameters for imaging wrapper classes to support … (

#313) * Support additional parameters for imaging wrapper classes to support spatialBeta view. * Lint * Fix tests
vitessce · Jan 24, 2024 · 4fb4fab · 4fb4fab
1 parent 4f251b4
commit 4fb4fab
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diff --git a/tests/test_wrappers.py b/tests/test_wrappers.py
@@ -16,6 +16,10 @@
     AnnDataWrapper,
     CsvWrapper,
     MultivecZarrWrapper,
+    ImageOmeTiffWrapper,
+    ObsSegmentationsOmeTiffWrapper,
+    ImageOmeZarrWrapper,
+    ObsSegmentationsOmeZarrWrapper,
 )
 
 from vitessce.wrappers import file_path_to_url_path
@@ -139,6 +143,70 @@ def test_ome_zarr_with_base_dir(self):
             'url': 'http://localhost:8000/test.ome.zarr'
         })
 
+    def test_image_ome_tiff(self):
+        w = ImageOmeTiffWrapper(img_path=data_path / 'test.ome.tif')
+        w.local_img_uid = 'test.ome.tif'
+        w.local_offsets_uid = 'test.offsets.json'
+
+        file_def_creator = w.make_raster_file_def_creator(
+            "A",
+            "0"
+        )
+        file_def = file_def_creator('http://localhost:8000')
+        self.assertEqual(file_def, {
+            'fileType': 'image.ome-tiff',
+            'url': 'http://localhost:8000/A/0/test.ome.tif',
+            'options': {
+                'offsetsUrl': 'http://localhost:8000/A/0/test.offsets.json'
+            }
+        })
+
+    def test_image_ome_zarr(self):
+        w = ImageOmeZarrWrapper(img_path=data_path / 'test.ome.zarr')
+        w.local_dir_uid = 'test.ome.zarr'
+
+        file_def_creator = w.make_image_file_def_creator(
+            "A",
+            "0"
+        )
+        file_def = file_def_creator('http://localhost:8000')
+        self.assertEqual(file_def, {
+            'fileType': 'image.ome-zarr',
+            'url': 'http://localhost:8000/A/0/test.ome.zarr'
+        })
+
+    def test_obs_segmentations_ome_tiff(self):
+        w = ObsSegmentationsOmeTiffWrapper(img_path=data_path / 'test.ome.tif')
+        w.local_img_uid = 'test.ome.tif'
+        w.local_offsets_uid = 'test.offsets.json'
+
+        file_def_creator = w.make_raster_file_def_creator(
+            "A",
+            "0"
+        )
+        file_def = file_def_creator('http://localhost:8000')
+        self.assertEqual(file_def, {
+            'fileType': 'obsSegmentations.ome-tiff',
+            'url': 'http://localhost:8000/A/0/test.ome.tif',
+            'options': {
+                'offsetsUrl': 'http://localhost:8000/A/0/test.offsets.json'
+            }
+        })
+
+    def test_obs_segmentations_ome_zarr(self):
+        w = ObsSegmentationsOmeZarrWrapper(img_path=data_path / 'test.ome.zarr')
+        w.local_dir_uid = 'test.ome.zarr'
+
+        file_def_creator = w.make_image_file_def_creator(
+            "A",
+            "0"
+        )
+        file_def = file_def_creator('http://localhost:8000')
+        self.assertEqual(file_def, {
+            'fileType': 'obsSegmentations.ome-zarr',
+            'url': 'http://localhost:8000/A/0/test.ome.zarr'
+        })
+
     def test_anndata(self):
         adata_path = data_path / 'test.h5ad.zarr'
         w = AnnDataWrapper(adata_path,

diff --git a/vitessce/__init__.py b/vitessce/__init__.py
@@ -44,6 +44,10 @@
         CsvWrapper,
         AnnDataWrapper,
         MultivecZarrWrapper,
+        ImageOmeTiffWrapper,
+        ObsSegmentationsOmeTiffWrapper,
+        ImageOmeZarrWrapper,
+        ObsSegmentationsOmeZarrWrapper,
     )
 except ModuleNotFoundError as e:  # pragma: no cover
     warn(f'Extra installs are necessary to use wrappers: {e}')