Update data export scripts

Author: constantinpape

scripts/export_lower_resolution.py

@@ -7,7 +7,7 @@
 import zarr
 
 from flamingo_tools.s3_utils import get_s3_path, BUCKET_NAME, SERVICE_ENDPOINT
-# from skimage.segmentation import relabel_sequential
+from skimage.segmentation import relabel_sequential
 
 
 def filter_component(fs, segmentation, cochlea, seg_name, components):
@@ -22,7 +22,8 @@ def filter_component(fs, segmentation, cochlea, seg_name, components):
     filter_mask = ~np.isin(segmentation, keep_label_ids)
     segmentation[filter_mask] = 0
 
-    # segmentation, _, _ = relabel_sequential(segmentation)
+    segmentation, _, _ = relabel_sequential(segmentation)
+    segmentation = segmentation.astype("uint16")
     return segmentation
 
 
@@ -41,7 +42,7 @@ def export_lower_resolution(args):
         s3_store, fs = get_s3_path(internal_path, bucket_name=BUCKET_NAME, service_endpoint=SERVICE_ENDPOINT)
         with zarr.open(s3_store, mode="r") as f:
             data = f[input_key][:]
-        print(data.shape)
+
         if args.filter_by_components is not None:
             data = filter_component(fs, data, args.cochlea, channel, args.filter_by_components)
         if args.binarize:

scripts/export_synapse_detections.py

@@ -12,6 +12,7 @@
 from tqdm import tqdm
 
 
+# TODO
 def export_synapse_detections(cochlea, scale, output_folder, synapse_name, reference_ihcs, max_dist, radius):
     s3 = create_s3_target()
 
@@ -53,14 +54,18 @@ def export_synapse_detections(cochlea, scale, output_folder, synapse_name, refer
     coordinates /= (2 ** scale)
     coordinates = np.round(coordinates, 0).astype("int")
 
+    ihc_ids = syn_table["matched_ihc"].values
+
     # Create the output.
     output = np.zeros(shape, dtype="uint16")
     mask = ball(radius).astype(bool)
 
-    for coord in tqdm(coordinates, desc="Writing synapses to volume"):
+    for coord, matched_ihc in tqdm(
+        zip(coordinates, ihc_ids), total=len(coordinates), desc="Writing synapses to volume"
+    ):
         bb = tuple(slice(c - radius, c + radius + 1) for c in coord)
         try:
-            output[bb][mask] = 1
+            output[bb][mask] = matched_ihc
         except IndexError:
             print("Index error for", coord)
             continue