Merge branch 'syn-marker-training' of https://github.com/computational-cell-analytics/flamingo-tools into syn-marker-training

Author: constantinpape

scripts/synapse_marker_detection/check_synapse_prediction.py

@@ -1,5 +1,7 @@
 import h5py
+import napari
 import zarr
+
 from torch_em.util import load_model
 from torch_em.util.prediction import predict_with_halo
 from train_synapse_detection import get_paths
@@ -16,9 +18,18 @@ def run_prediction(val_image):
 def main():
     val_paths, _ = get_paths("val")
     val_image = zarr.open(val_paths[0])["raw"][:]
-    pred = run_prediction(val_image)
-    with h5py.File("pred.h5", "a") as f:
-        f.create_dataset("pred", data=pred, compression="gzip")
+
+    # pred = run_prediction(val_image)
+    # with h5py.File("pred.h5", "a") as f:
+    #     f.create_dataset("pred", data=pred, compression="gzip")
+
+    with h5py.File("pred.h5", "r") as f:
+        pred = f["pred"][:]
+
+    v = napari.Viewer()
+    v.add_image(val_image)
+    v.add_image(pred)
+    napari.run()
 
 
 if __name__ == "__main__":

scripts/synapse_marker_detection/train_synapse_detection.py

@@ -3,8 +3,8 @@
 
 from detection_dataset import DetectionDataset
 
-# sys.path.append("/home/pape/Work/my_projects/czii-protein-challenge")
-sys.path.append("/user/pape41/u12086/Work/my_projects/czii-protein-challenge")
+sys.path.append("/home/pape/Work/my_projects/czii-protein-challenge")
+# sys.path.append("/user/pape41/u12086/Work/my_projects/czii-protein-challenge")
 
 from utils.training.training import supervised_training  # noqa