Add script to check synapse prediction

Author: constantinpape

scripts/synapse_marker_detection/check_synapse_prediction.py

@@ -0,0 +1,25 @@
+import h5py
+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
+
+
+def run_prediction(val_image):
+    model = load_model("./checkpoints/synapse_detection_v1")
+    block_shape = (32, 384, 384)
+    halo = (8, 64, 64)
+    pred = predict_with_halo(val_image, model, [0], block_shape, halo)
+    return pred.squeeze()
+
+
+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")
+
+
+if __name__ == "__main__":
+    main()