Update validation visualization

Author: constantinpape

flamingo_tools/validation.py

@@ -245,13 +245,17 @@ def for_visualization(segmentation, annotations, matches):
 
     point_vis = annotations.copy()
     tps = matches["tp_annotations"]
+    match_properties = ["tp" if aid in tps else "fn" for aid in range(len(annotations))]
+    # The color cycle assigns the first color to the first property etc.
+    # So we need to set the first color to red if the first id is a false negative and vice versa.
+    color_cycle = green_red[::-1] if match_properties[0] == "fn" else green_red
     point_props = dict(
         properties={
             "id": list(range(len(annotations))),
-            "match": ["tp" if aid in tps else "fn" for aid in range(len(annotations))]
+            "match": match_properties,
         },
         face_color="match",
-        face_color_cycle=green_red[::-1],
+        face_color_cycle=color_cycle,
         border_width=0.25,
         size=10,
     )

scripts/validation/visualize_validation.py

@@ -1,28 +1,34 @@
+import argparse
 import os
 
 import imageio.v3 as imageio
 import napari
 
-from flamingo_tools.validation import fetch_data_for_evaluation, compute_matches_for_annotated_slice, for_visualization
+from flamingo_tools.validation import (
+    fetch_data_for_evaluation, compute_matches_for_annotated_slice, for_visualization, parse_annotation_path
+)
 
 # ROOT = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/AnnotatedImageCrops/F1Validation"
 ROOT = "annotation_data"
-TEST_ANNOTATION = os.path.join(ROOT, "AnnotationsEK/MAMD58L_PV_z771_base_full_annotationsEK.csv")
 
 
 def main():
-    image = imageio.imread(os.path.join(ROOT, "MAMD58L_PV_z771_base_full.tif"))
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--image", required=True)
+    parser.add_argument("--annotation", required=True)
+    parser.add_argument("--cache_folder")
+    args = parser.parse_args()
+    cache_folder = args.cache_folder
+
+    cochlea, slice_id = parse_annotation_path(args.annotation)
+    cache_path = None if cache_folder is None else os.path.join(cache_folder, f"{cochlea}_{slice_id}.tif")
+
+    image = imageio.imread(args.image)
     segmentation, annotations = fetch_data_for_evaluation(
-        TEST_ANNOTATION, cache_path="./seg.tif", components_for_postprocessing=[1],
+        args.annotation, cache_path=cache_path, components_for_postprocessing=[1],
     )
 
-    # v = napari.Viewer()
-    # v.add_image(image)
-    # v.add_labels(segmentation)
-    # v.add_points(annotations)
-    # napari.run()
-
-    matches = compute_matches_for_annotated_slice(segmentation, annotations)
+    matches = compute_matches_for_annotated_slice(segmentation, annotations, matching_tolerance=5)
     tps, fns = matches["tp_annotations"], matches["fn"]
     vis_segmentation, vis_points, seg_props, point_props = for_visualization(segmentation, annotations, matches)