Updates to IHC evaluation

Author: constantinpape

scripts/measurements/evaluate_sgn_therapy.py

@@ -15,8 +15,7 @@ def check_project(save=False):
     project_info = json.loads(content.read())
 
     cochleae = [
-        "M_LR_000144_L", "M_LR_000145_L",
-        "M_LR_000151_R", "M_LR_000155_L",
+        "M_LR_000144_L", "M_LR_000145_L", "M_LR_000151_R", "M_LR_000155_L",
     ]
 
     sgn_name = "SGN_resized_v2"
@@ -32,8 +31,8 @@ def check_project(save=False):
             continue
 
         # Get the ihc table folder.
-        ihc = sources[sgn_name]["segmentation"]
-        table_folder = os.path.join(BUCKET_NAME, cochlea, ihc["tableData"]["tsv"]["relativePath"])
+        sgn = sources[sgn_name]["segmentation"]
+        table_folder = os.path.join(BUCKET_NAME, cochlea, sgn["tableData"]["tsv"]["relativePath"])
 
         # For debugging.
         x = s3.ls(table_folder)
@@ -42,11 +41,14 @@ def check_project(save=False):
 
         default_table = s3.open(os.path.join(table_folder, "default.tsv"), mode="rb")
         default_table = pd.read_csv(default_table, sep="\t")
+        main_ids = default_table[default_table.component_labels == 1].label_id
 
         measurement_table = s3.open(
             os.path.join(table_folder, "GFP-resized_SGN-resized-v2_object-measures.tsv"), mode="rb"
         )
         measurement_table = pd.read_csv(measurement_table, sep="\t")
+        measurement_table = measurement_table[measurement_table.label_id.isin(main_ids)]
+        assert len(measurement_table) == len(main_ids)
 
         if save:
             os.makedirs(OUTPUT_FOLDER, exist_ok=True)

scripts/validation/IHCs/run_evaluation.py

@@ -12,7 +12,7 @@
 ANNOTATION_FOLDERS = ["consensus_annotation"]
 
 
-def run_evaluation(root, annotation_folders, result_file, cache_folder):
+def run_evaluation(root, annotation_folders, result_file, cache_folder, segmentation_name):
     results = {
         "annotator": [],
         "cochlea": [],
@@ -32,12 +32,12 @@ def run_evaluation(root, annotation_folders, result_file, cache_folder):
             print(annotation_path)
             cochlea, slice_id = _parse_annotation_path(annotation_path)
 
-            # For the cochlea M_LR_000226_R the actual component is 2, not 1
-            component = 2 if "226_R" in cochlea else 1
+            # For the cochlea M_LR_000226_R the actual component is 2, not 1. (Only for IHC_v2).
+            component = 2 if ("226_R" in cochlea and segmentation_name == "IHC_v2") else 1
             print("Run evaluation for", annotator, cochlea, "z=", slice_id)
             segmentation, annotations = fetch_data_for_evaluation(
                 annotation_path, components_for_postprocessing=[component],
-                seg_name="IHC_v2",
+                seg_name=segmentation_name,
                 cache_path=None if cache_folder is None else os.path.join(cache_folder, f"{cochlea}_{slice_id}.tif")
             )
             scores = compute_scores_for_annotated_slice(segmentation, annotations, matching_tolerance=5)
@@ -59,9 +59,10 @@ def main():
     parser.add_argument("-i", "--input", default=ROOT)
     parser.add_argument("--folders", default=ANNOTATION_FOLDERS)
     parser.add_argument("--result_file", default="results.csv")
+    parser.add_argument("--segmentation_name", default="IHC_v2")
     parser.add_argument("--cache_folder")
     args = parser.parse_args()
-    run_evaluation(args.input, args.folders, args.result_file, args.cache_folder)
+    run_evaluation(args.input, args.folders, args.result_file, args.cache_folder, args.segmentation_name)
 
 
 if __name__ == "__main__":