Add brain hierarchy root parameter.

BlueBrain · Feb 6, 2024 · b156c96 · b156c96
1 parent 3c429d7
commit b156c96
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Showing 3 changed files with 15 additions and 9 deletions.
diff --git a/atlas_densities/app/cell_densities.py b/atlas_densities/app/cell_densities.py
@@ -742,7 +742,7 @@ def measurements_to_average_densities(
     "--region-name",
     type=str,
     default="root",
-    help="Name of the region in the hierarchy",
+    help="Name of the root region in the hierarchy",
 )
 @click.option(
     "--neuron-density-path",
@@ -912,8 +912,8 @@ def fit_average_densities(
     L.info("Loading average densities dataframe ...")
     average_densities_df = pd.read_csv(average_densities_path)
     homogenous_regions_df = pd.read_csv(homogenous_regions_path)
-    remove_unknown_regions(average_densities_df, region_map, annotation.raw)
-    remove_unknown_regions(homogenous_regions_df, region_map, annotation.raw)
+    remove_unknown_regions(average_densities_df, region_map, annotation.raw, root=region_name)
+    remove_unknown_regions(homogenous_regions_df, region_map, annotation.raw, root=region_name)
 
     L.info("Fitting of average densities: started")
     fitted_densities_df, fitting_maps = linear_fitting(
@@ -945,7 +945,7 @@ def fit_average_densities(
     "--region-name",
     type=str,
     default="root",
-    help="Name of the region in the hierarchy",
+    help="Name of the root region in the hierarchy",
 )
 @click.option(
     "--neuron-density-path",

diff --git a/atlas_densities/densities/measurement_to_density.py b/atlas_densities/densities/measurement_to_density.py
@@ -258,7 +258,10 @@ def cell_count_per_slice_to_density(
 
 
 def remove_unknown_regions(
-    measurements: "pd.DataFrame", region_map: RegionMap, annotation: AnnotationT
+    measurements: "pd.DataFrame",
+    region_map: RegionMap,
+    annotation: AnnotationT,
+    root: str = "root",
 ):
     """
     Drop lines from the measurements dataframe which brain regions are not in the AIBS brain region
@@ -271,8 +274,9 @@ def remove_unknown_regions(
         region_map: RegionMap object to navigate the brain regions hierarchy.
         annotation: int array of shape (W, H, D) holding the annotation of the whole AIBS
             mouse brain. (The integers W, H and D are the dimensions of the array).
+        root: name of the root region to consider in the hierarchy.
     """
-    hierarchy_info = get_hierarchy_info(region_map)
+    hierarchy_info = get_hierarchy_info(region_map, root)
     pd.set_option("display.max_colwidth", None)
     indices_ids = measurements.index[
         ~measurements["brain_region"].isin(hierarchy_info["brain_region"])
@@ -284,7 +288,7 @@ def remove_unknown_regions(
             f"{measurements.loc[indices_ids, 'brain_region'].to_string()}",
             AtlasDensitiesWarning,
         )
-    measurements.drop(indices_ids, inplace=True)
+        measurements.drop(indices_ids, inplace=True)
 
     u_regions = np.unique(annotation)
     u_regions = np.delete(u_regions, 0)  # don't take 0, i.e: outside of the brain
@@ -302,7 +306,7 @@ def remove_unknown_regions(
             f"annotation volume: \n{measurements.loc[indices_ann, 'brain_region'].to_string()}",
             AtlasDensitiesWarning,
         )
-    measurements.drop(indices_ann, inplace=True)
+        measurements.drop(indices_ann, inplace=True)
 
 
 def measurement_to_average_density(

diff --git a/tests/densities/test_measurement_to_density.py b/tests/densities/test_measurement_to_density.py
@@ -75,7 +75,9 @@ def test_remove_unknown_regions(region_map, annotations):
             "source_title": ["Article 1", "Article 2", "Article 1"],
         }
     )
-    tested.remove_unknown_regions(measurements, region_map, annotations)
+    tested.remove_unknown_regions(
+        measurements, region_map, annotations, root="Basic cell groups and regions"
+    )
     expected = pd.DataFrame(
         {
             "brain_region": [