Add annotation script

Author: constantinpape

scripts/cooper/ground_truth/compartments/run_annotation_04.py

@@ -0,0 +1,55 @@
+import os
+from glob import glob
+
+import h5py
+import napari
+from magicgui import magicgui
+
+
+def run_annotation(input_path, output_path):
+    with h5py.File(input_path, "r") as f:
+        raw = f["raw"][:]
+        seg = f["labels/compartments"][:]
+
+    v = napari.Viewer()
+    v.add_image(raw)
+    v.add_labels(seg)
+
+    @magicgui(call_button="Save Annotations")
+    def save_annotations():
+        seg = v.layers["seg"].data
+
+        if os.path.exists(output_path):
+            with h5py.File(output_path, "a") as f:
+                f["labels/compartments"][:] = seg
+        else:
+            with h5py.File(output_path, "a") as f:
+                f.create_dataset("raw", data=raw, compression="gzip")
+                f.create_dataset("labels/compartments", data=seg, compression="gzip")
+
+    v.window.add_dock_widget(save_annotations)
+
+    napari.run()
+
+
+def main():
+    inputs = sorted(glob("./predictions/**/*.h5", recursive=True))
+
+    output_folder = "./annotations"
+
+    for input_path in inputs:
+        ds_name, fname = os.path.split(input_path)
+        ds_name = os.path.split(ds_name)[1]
+        ds_folder = os.path.join(output_folder, ds_name)
+        output_path = os.path.join(ds_folder, fname)
+
+        if os.path.exists(output_path):
+            print("Skipping annotations for", output_path)
+            continue
+
+        os.makedirs(ds_folder, exist_ok=True)
+        run_annotation(input_path, output_path)
+
+
+if __name__ == "__main__":
+    main()