Update description (#126)

Update description fields

mobie/image_data.py

@@ -219,7 +219,8 @@ def add_image(input_path, input_key,
                                           source_type="image", source_name=image_name,
                                           menu_name=menu_name, view=view,
                                           is_default_dataset=is_default_dataset,
-                                          contrast_limits=contrast_limits)
+                                          contrast_limits=contrast_limits,
+                                          description=description)
 
     dataset_folder = os.path.join(root, dataset_name)
 
@@ -244,7 +245,7 @@ def add_image(input_path, input_key,
                           channel=channel)
 
     metadata.add_source_to_dataset(dataset_folder, "image", image_name, image_metadata_path,
-                                   view=view, description=description, channel=channel)
+                                   view=view, channel=channel)
 
     if transformation is not None:
         utils.update_transformation_parameter(image_metadata_path, transformation, file_format)

mobie/metadata/source_metadata.py

@@ -160,7 +160,7 @@ def _get_file_format(path):
     return file_format
 
 
-def _get_image_metadata(dataset_folder, path, type_, file_format, channel, description):
+def _get_image_metadata(dataset_folder, path, type_, file_format, channel):
     file_format = _get_file_format(path) if file_format is None else file_format
 
     if file_format.startswith("bdv"):
@@ -181,23 +181,20 @@ def _get_image_metadata(dataset_folder, path, type_, file_format, channel, descr
         format_["channel"] = channel
 
     source_metadata = {"imageData": {file_format: format_}}
-    if description is not None:
-        assert isinstance(description, str)
-        source_metadata["description"] = description
     return {type_: source_metadata}
 
 
 def get_image_metadata(dataset_folder, metadata_path,
-                       file_format=None, channel=None, description=None):
+                       file_format=None, channel=None):
     return _get_image_metadata(dataset_folder, metadata_path, "image",
-                               file_format=file_format, channel=channel, description=description)
+                               file_format=file_format, channel=channel)
 
 
 def get_segmentation_metadata(dataset_folder, metadata_path,
                               table_location=None, file_format=None,
-                              channel=None, description=None):
+                              channel=None):
     source_metadata = _get_image_metadata(dataset_folder, metadata_path, "segmentation",
-                                          file_format=file_format, channel=channel, description=description)
+                                          file_format=file_format, channel=channel)
     if table_location is not None:
         relative_table_location = os.path.relpath(table_location, dataset_folder)
         source_metadata["segmentation"]["tableData"] = get_table_metadata(relative_table_location)
@@ -207,8 +204,7 @@ def get_segmentation_metadata(dataset_folder, metadata_path,
 def get_spot_metadata(dataset_folder, table_folder,
                       bounding_box_min,
                       bounding_box_max,
-                      unit,
-                      description=None):
+                      unit):
     relative_table_location = os.path.relpath(table_folder, dataset_folder)
     table_data = get_table_metadata(relative_table_location)
 
@@ -220,8 +216,6 @@ def get_spot_metadata(dataset_folder, table_folder,
             "unit": unit,
         }
     }
-    if description is not None:
-        source_metadata["spots"]["description"] = description
     return source_metadata
 
 
@@ -234,7 +228,6 @@ def add_source_to_dataset(
     view=None,
     table_folder=None,
     overwrite=True,
-    description=None,
     channel=None,
     suppress_warnings=False,
     **kwargs,
@@ -253,7 +246,6 @@ def add_source_to_dataset(
             If empty dict, will not add a view (default: None)
         table_folder [str] - table folder for segmentations and spots. (default: None)
         overwrite [bool] - whether to overwrite existing entries (default: True)
-        description [str] - description for this source (default: None)
         channel [int] - the channel to load from the data.
             Currently only supported for the ome.zarr format (default: None)
         suppress_warnings [bool] - a flag to suppress warnings raised by the metadata validation (default: False)
@@ -273,19 +265,16 @@ def add_source_to_dataset(
     if source_type == "image":
         source_metadata = get_image_metadata(dataset_folder, image_metadata_path,
                                              file_format=file_format,
-                                             channel=channel,
-                                             description=description)
+                                             channel=channel)
     elif source_type == "segmentation":
         source_metadata = get_segmentation_metadata(dataset_folder,
                                                     image_metadata_path,
                                                     table_folder,
                                                     file_format=file_format,
-                                                    channel=channel,
-                                                    description=description)
+                                                    channel=channel)
     elif source_type == "spots":
         source_metadata = get_spot_metadata(dataset_folder,
                                             table_folder,
-                                            description=description,
                                             **kwargs)
     else:
         raise ValueError(f"Invalid source type: {source_type}, expect one of 'image', 'segmentation' or 'spots'")

mobie/metadata/view_metadata.py

@@ -300,7 +300,7 @@ def get_viewer_transform(affine=None, normalized_affine=None, position=None, nor
 
 
 def get_view(names, source_types, sources, display_settings,
-             is_exclusive, menu_name,
+             is_exclusive, menu_name, description=None,
              source_transforms=None, viewer_transform=None, region_displays=None):
     """ Create view for a multiple sources and optional transformations.
 
@@ -311,6 +311,7 @@ def get_view(names, source_types, sources, display_settings,
         display_settings [list[dict]] - list of display settings in this view.
         is_exclusive [bool] - is this an exclusive view.
         menu_name [str] - menu name for this view
+        description [str] - description for this view (default: None)
         source_transforms [list[dict]] - (default: None)
         viewer_transform [dict] - (default: None)
         region_displays dict[str, dict] - dictionary from region display name
@@ -321,6 +322,8 @@ def get_view(names, source_types, sources, display_settings,
         lens = f"{len(names)} {len(source_types)}, {len(sources)}, {len(display_settings)}"
         raise ValueError(f"Different length of names, types, sources and settings: {lens}")
     view = {"isExclusive": is_exclusive, "uiSelectionGroup": menu_name}
+    if description is not None:
+        view["description"] = description
 
     source_displays = []
     for name, source_type, source_list, display_setting in zip(names, source_types, sources, display_settings):
@@ -404,7 +407,8 @@ def get_view(names, source_types, sources, display_settings,
 
 
 def get_default_view(source_type, source_name, menu_name=None,
-                     source_transform=None, viewer_transform=None, **kwargs):
+                     source_transform=None, viewer_transform=None,
+                     description=None, **kwargs):
     """ Create default view metadata for a single source.
 
     Arguments:
@@ -414,6 +418,7 @@ def get_default_view(source_type, source_name, menu_name=None,
         source_transform [dict] - dict with affine source transform.
             If given, must contain "parameters" and may contain "timepoints" (default: None).
         viewer_transform [dict] - dict with viewer transform (default: None)
+        description [str] - description for this view (default: None).
         **kwargs - additional settings for this view
     """
     if menu_name is None:
@@ -428,7 +433,7 @@ def get_default_view(source_type, source_name, menu_name=None,
         ]
 
     view = get_view([source_name], [source_type], [[source_name]], [kwargs],
-                    is_exclusive=False, menu_name=menu_name,
+                    is_exclusive=False, menu_name=menu_name, description=description,
                     source_transforms=source_transforms, viewer_transform=viewer_transform)
     return view
 

mobie/segmentation.py

@@ -61,7 +61,8 @@ def add_segmentation(input_path, input_key,
                                                 source_type="segmentation",
                                                 source_name=segmentation_name,
                                                 menu_name=menu_name, view=view,
-                                                is_default_dataset=is_default_dataset)
+                                                is_default_dataset=is_default_dataset,
+                                                description=description)
 
     dataset_folder = os.path.join(root, dataset_name)
     tmp_folder = f"tmp_{dataset_name}_{segmentation_name}" if tmp_folder is None else tmp_folder
@@ -118,8 +119,7 @@ def add_segmentation(input_path, input_key,
     # add the segmentation to the dataset metadata
     mobie.metadata.add_source_to_dataset(dataset_folder, "segmentation",
                                          segmentation_name, image_metadata_path,
-                                         table_folder=table_folder, view=view,
-                                         description=description)
+                                         table_folder=table_folder, view=view)
 
 
 def main():

mobie/spots.py

@@ -79,7 +79,8 @@ def add_spots(input_table, root, dataset_name, spot_name,
                                                 source_type="spots",
                                                 source_name=spot_name,
                                                 menu_name=menu_name, view=view,
-                                                is_default_dataset=False)
+                                                is_default_dataset=False,
+                                                description=description)
     dataset_folder = os.path.join(root, dataset_name)
 
     metadata = mobie.metadata.read_dataset_metadata(dataset_folder)
@@ -98,8 +99,7 @@ def add_spots(input_table, root, dataset_name, spot_name,
     # add the spot source to the dataset metadata
     mobie.metadata.add_source_to_dataset(dataset_folder, "spots", spot_name,
                                          image_metadata_path=None,
-                                         table_folder=table_folder, view=view,
-                                         description=description, unit=unit,
+                                         table_folder=table_folder, view=view, unit=unit,
                                          bounding_box_min=bounding_box_min,
                                          bounding_box_max=bounding_box_max)
 

mobie/traces.py

@@ -48,7 +48,8 @@ def add_traces(input_folder, root, dataset_name, traces_name,
                                           source_type="segmentation",
                                           source_name=traces_name,
                                           menu_name=menu_name, view=view,
-                                          is_default_dataset=False)
+                                          is_default_dataset=False,
+                                          description=description)
 
     # get the path to the reference data
     dataset_folder = os.path.join(root, dataset_name)
@@ -85,8 +86,7 @@ def add_traces(input_folder, root, dataset_name, traces_name,
 
     metadata.add_source_to_dataset(dataset_folder, 'segmentation',
                                    traces_name, image_metadata_path,
-                                   view=view, table_folder=table_folder,
-                                   description=description)
+                                   view=view, table_folder=table_folder)
 
 
 def main():

mobie/utils.py

@@ -73,13 +73,14 @@ def require_dataset(root, dataset_name):
 
 def require_dataset_and_view(root, dataset_name, file_format,
                              source_type, source_name, menu_name,
-                             view, is_default_dataset, contrast_limits=None):
+                             view, is_default_dataset,
+                             contrast_limits=None, description=None):
     ds_exists = require_dataset(root, dataset_name)
 
     dataset_folder = os.path.join(root, dataset_name)
     if view is None:
         kwargs = {"contrastLimits": contrast_limits} if source_type == "image" else {}
-        view = metadata.get_default_view(source_type, source_name, menu_name=menu_name, **kwargs)
+        view = metadata.get_default_view(source_type, source_name, menu_name=menu_name, description=description, **kwargs)
     elif view == {}:
         pass
     else:

test/metadata/test_source_metadata.py

@@ -13,8 +13,7 @@ def test_image_source(self):
         source = get_image_metadata(ds_folder, xml_path, file_format="bdv.n5")
         validate_with_schema(source, "source")
 
-        source = get_image_metadata(ds_folder, xml_path, file_format="bdv.n5",
-                                    description="My shiny image")
+        source = get_image_metadata(ds_folder, xml_path, file_format="bdv.n5")
         validate_with_schema(source, "source")
 
         source = get_image_metadata(ds_folder, xml_path, file_format="bdv.n5")
@@ -68,8 +67,7 @@ def test_segmentation_source(self):
         source = get_segmentation_metadata(ds_folder, xml_path, file_format="bdv.n5")
         validate_with_schema(source, "source")
 
-        source = get_segmentation_metadata(ds_folder, xml_path, file_format="bdv.n5",
-                                           description="My shiny segmentation")
+        source = get_segmentation_metadata(ds_folder, xml_path, file_format="bdv.n5")
         validate_with_schema(source, "source")
 
         source = get_segmentation_metadata(ds_folder, xml_path,

test/metadata/test_view_metadata.py

@@ -25,6 +25,7 @@ def test_image_view(self):
 
         # test custom image settings
         custom_kwargs = [
+            {"description": "Lorem ipsum"},
             {"contrastLimits": [0., 255.], "color": "white"},
             {"contrastLimits": [0., 2000.], "color": "red"},
             {"contrastLimits": [-10., 20000000.]},

test/test_image_data.py

@@ -243,7 +243,8 @@ def test_numpy(self):
         mobie.add_image(self.data, None, self.root, self.dataset_name, im_name,
                         resolution=(1, 1, 1), scale_factors=scales,
                         chunks=(64, 64, 64), tmp_folder=self.tmp_folder,
-                        target="local", max_jobs=self.max_jobs)
+                        target="local", max_jobs=self.max_jobs,
+                        description="Lorem ipsum.")
         self.check_data(os.path.join(self.root, self.dataset_name), im_name)
 
     def test_with_view(self):
@@ -329,6 +330,12 @@ def check_data(self, dataset_folder, name):
             data = f[key][:]
         self.assertTrue(np.array_equal(data, exp_data))
 
+        # check the vew
+        views = metadata["views"]
+        self.assertIn(name, views)
+        view = views[name]
+        mobie.validation.validate_view_metadata(view, sources=sources, dataset_folder=dataset_folder)
+
 
 if __name__ == "__main__":
     unittest.main()