added several file extension support with elf.open_file

Author: lufre1

scripts/cooper/training/evaluate_mitochondria.py

@@ -9,6 +9,8 @@
 
 from elf.evaluation import matching, symmetric_best_dice_score
 
+from elf.io.files import open_file
+
 
 def evaluate(labels, vesicles):
     assert labels.shape == vesicles.shape
@@ -35,6 +37,8 @@ def evaluate_file(labels_path, seg_path, model_name, segment_key, anno_key, mask
     labels, seg = None, None
     if ".tif" in labels_path:
         labels = imread(labels_path)
+    elif anno_key is not None:
+        labels = open_file(labels_path, "r")[anno_key][:]
     if ".tif" in seg_path:
         seg = imread(seg_path)
     if labels is None or seg is None:
@@ -69,11 +73,14 @@ def evaluate_file(labels_path, seg_path, model_name, segment_key, anno_key, mask
     summarize_eval(results)
 
 
-def evaluate_folder(labels_path, segmentation_path, model_name, segment_key, anno_key, mask_key, output_folder):
+def evaluate_folder(labels_path, segmentation_path, model_name, segment_key, anno_key,
+                    anno_ext, mask_key, output_folder):
     print(f"Evaluating folder {segmentation_path}")
     print(f"Using labels stored in {labels_path}")
-
-    label_paths = get_file_paths(labels_path, ext=".tif")
+    if labels_path is not None:
+        label_paths = get_file_paths(labels_path, ext=anno_ext)
+    else:
+        label_paths = _get_default_label_paths()
     seg_paths = get_file_paths(segmentation_path, ext=".tif")
     if label_paths is None or seg_paths is None:
         print("Could not find label file or segmentation file")
@@ -108,29 +115,42 @@ def find_label_file(given_path: str, label_paths: list) -> str:
         str: The path to the matching label file, or None if no match is found.
     """
     raw_base = os.path.splitext(os.path.basename(given_path))[0]  # Remove extension
-
+    raw_base = raw_base.replace("prediction", "").replace("pred", "")
+    raw_base = raw_base.replace("segmentation", "").replace("seg", "")
+    raw_base = raw_base.rstrip("_")
     for label_path in label_paths:
         label_base = os.path.splitext(os.path.basename(label_path))[0]  # Remove extension
-        if raw_base in label_base:  # Ensure raw name is contained in label name
+        if raw_base.strip().lower() in label_base.strip().lower():  # Ensure raw name is contained in label name
             return label_path
 
     return None  # No match found
 
 
+def _get_default_label_paths():
+    return ['/scratch-grete/projects/nim00007/data/mitochondria/wichmann/refined_mitos/M2_eb10_model.h5',
+            '/scratch-grete/projects/nim00007/data/mitochondria/wichmann/refined_mitos/WT21_eb3_model2.h5',
+            '/scratch-grete/projects/nim00007/data/mitochondria/wichmann/refined_mitos/M10_eb9_model.h5',
+            '/scratch-grete/projects/nim00007/data/mitochondria/wichmann/refined_mitos/KO9_eb4_model.h5',
+            '/scratch-grete/projects/nim00007/data/mitochondria/wichmann/refined_mitos/M7_eb11_model.h5',
+            '/scratch-grete/projects/nim00007/data/mitochondria/cooper/fidi_down_s2/36859_J1_66K_TS_CA3_PS_25_rec_2Kb1dawbp_crop_downscaled.h5'
+            ]
+
+
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument("-sp", "--segmentation_path", required=True)
-    parser.add_argument("-gp", "--groundtruth_path", required=True)
+    parser.add_argument("-gp", "--groundtruth_path", default=None)
     parser.add_argument("-n", "--model_name", required=True)
     parser.add_argument("-sk", "--segmentation_key", default=None)
     parser.add_argument("-gk", "--groundtruth_key", default=None)
+    parser.add_argument("-ae", "--annotation_extension", default=None)
     parser.add_argument("-m", "--mask_key", default=None)
     parser.add_argument("-o", "--output_folder", required=True)
     args = parser.parse_args()
 
     if os.path.isdir(args.segmentation_path):
         evaluate_folder(args.groundtruth_path, args.segmentation_path, args.model_name, args.segmentation_key,
-                        args.groundtruth_key,
+                        args.groundtruth_key, args.annotation_extension,
                         args.mask_key, args.output_folder)
     else:
         evaluate_file(args.groundtruth_path, args.segmentation_path, args.model_name, args.segmentation_key,