Support additional parameters for imaging wrapper classes to support … (#313)

* Support additional parameters for imaging wrapper classes to support spatialBeta view.

* Lint

* Fix tests

Author: keller-mark

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,

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}')