Update annotation comparison

Author: constantinpape

scripts/validation/IHCs/compare_annotations.py

@@ -0,0 +1,81 @@
+import os
+from glob import glob
+
+import napari
+import pandas as pd
+import tifffile
+
+ROOT = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/AnnotatedImageCrops/F1ValidationIHCs"
+# ANNOTATION_FOLDERS = ["AnnotationsEK", "AnnotationsAMD", "AnnotationsLR"]
+ANNOTATION_FOLDERS = ["Annotations_AMD", "Annotations_LR"]
+COLOR = ["green", "yellow", "orange"]
+
+
+def _match_annotations(image_path):
+    prefix = os.path.basename(image_path).split("_")[:3]
+    prefix = "_".join(prefix)
+
+    annotations = {}
+    for annotation_folder in ANNOTATION_FOLDERS:
+        all_annotations = glob(os.path.join(ROOT, annotation_folder, "*.csv"))
+        matches = [ann for ann in all_annotations if os.path.basename(ann).startswith(prefix)]
+        if len(matches) == 0:
+            continue
+        assert len(matches) == 1
+        annotation_path = matches[0]
+
+        annotation = pd.read_csv(annotation_path)[["axis-0", "axis-1", "axis-2"]].values
+        annotations[annotation_folder] = annotation
+
+    return annotations
+
+
+def compare_annotations(image_path):
+    annotations = _match_annotations(image_path)
+
+    image = tifffile.memmap(image_path)
+    v = napari.Viewer()
+    v.add_image(image)
+    for i, (name, annotation) in enumerate(annotations.items()):
+        v.add_points(annotation, name=name, face_color=COLOR[i])
+    v.title = os.path.basename(image_path)
+    napari.run()
+
+
+def visualize(image_paths):
+    for image_path in image_paths:
+        compare_annotations(image_path)
+
+
+def check_annotations(image_paths):
+    annotation_status = {"file": []}
+    annotation_status.update({ann: [] for ann in ANNOTATION_FOLDERS})
+    for image_path in image_paths:
+        annotations = _match_annotations(image_path)
+        annotation_status["file"].append(os.path.basename(image_path))
+        for ann in ANNOTATION_FOLDERS:
+            annotation_status[ann].append("Yes" if ann in annotations else "No")
+    annotation_status = pd.DataFrame(annotation_status)
+    print(annotation_status)
+
+
+def main():
+    import argparse
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--images", nargs="+")
+    parser.add_argument("--check", action="store_true")
+    args = parser.parse_args()
+
+    if args.images is None:
+        image_paths = sorted(glob(os.path.join(ROOT, "*.tif")))
+    else:
+        image_paths = args.images
+
+    if args.check:
+        check_annotations(image_paths)
+    else:
+        visualize(image_paths)
+
+
+if __name__ == "__main__":
+    main()

scripts/validation/IHCs/run_evaluation.py

@@ -7,7 +7,8 @@
 )
 
 ROOT = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/AnnotatedImageCrops/F1ValidationIHCs"
-ANNOTATION_FOLDERS = ["Annotations_LR"]
+# ANNOTATION_FOLDERS = ["AnnotationsEK", "AnnotationsAMD", "AnnotationsLR"]
+ANNOTATION_FOLDERS = ["Annotations_AMD", "Annotations_LR"]
 
 
 def run_evaluation(root, annotation_folders, result_file, cache_folder):

scripts/validation/SGNs/compare_annotations.py

@@ -6,7 +6,7 @@
 import tifffile
 
 ROOT = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/AnnotatedImageCrops/F1ValidationSGNs"
-ANNOTATION_FOLDERS = ["AnnotationsEK", "AnnotationsAMD", "AnnotationLR"]
+ANNOTATION_FOLDERS = ["AnnotationsEK", "AnnotationsAMD", "AnnotationsLR"]
 COLOR = ["green", "yellow", "orange"]
 
 
@@ -18,8 +18,9 @@ def _match_annotations(image_path):
     for annotation_folder in ANNOTATION_FOLDERS:
         all_annotations = glob(os.path.join(ROOT, annotation_folder, "*.csv"))
         matches = [ann for ann in all_annotations if os.path.basename(ann).startswith(prefix)]
-        if len(matches) != 1:
+        if len(matches) == 0:
             continue
+        assert len(matches) == 1
         annotation_path = matches[0]
 
         annotation = pd.read_csv(annotation_path)[["axis-0", "axis-1", "axis-2"]].values
@@ -40,19 +41,39 @@ def compare_annotations(image_path):
     napari.run()
 
 
+def visualize(image_paths):
+    for image_path in image_paths:
+        compare_annotations(image_path)
+
+
+def check_annotations(image_paths):
+    annotation_status = {"file": []}
+    annotation_status.update({ann: [] for ann in ANNOTATION_FOLDERS})
+    for image_path in image_paths:
+        annotations = _match_annotations(image_path)
+        annotation_status["file"].append(os.path.basename(image_path))
+        for ann in ANNOTATION_FOLDERS:
+            annotation_status[ann].append("Yes" if ann in annotations else "No")
+    annotation_status = pd.DataFrame(annotation_status)
+    print(annotation_status)
+
+
 def main():
     import argparse
     parser = argparse.ArgumentParser()
     parser.add_argument("--images", nargs="+")
+    parser.add_argument("--check", action="store_true")
     args = parser.parse_args()
 
     if args.images is None:
         image_paths = sorted(glob(os.path.join(ROOT, "*.tif")))
     else:
         image_paths = args.images
 
-    for image_path in image_paths:
-        compare_annotations(image_path)
+    if args.check:
+        check_annotations(image_paths)
+    else:
+        visualize(image_paths)
 
 
 if __name__ == "__main__":