Updated documentation

Author: schilling40

scripts/measurements/measure_synapses.py

@@ -12,11 +12,18 @@
 def check_project(plot=False, save_ihc_table=False, max_dist=None):
     s3 = create_s3_target()
     cochleae = ['M_LR_000226_L', 'M_LR_000226_R', 'M_LR_000227_L', 'M_LR_000227_R', 'M_AMD_OTOF1_L']
-    synapse_table_name = "synapse_v3_ihc_v4c"
-    ihc_table_name = "IHC_v4c"
 
     results = {}
     for cochlea in cochleae:
+        synapse_table_name = "synapse_v3_ihc_v4c"
+        ihc_table_name = "IHC_v4c"
+        component_id = [1]
+
+        if cochlea == 'M_AMD_OTOF1_L':
+            synapse_table_name = "synapse_v3_ihc_v4b"
+            ihc_table_name = "IHC_v4b"
+            component_id = [3, 11]
+
         content = s3.open(f"{BUCKET_NAME}/{cochlea}/dataset.json", mode="r", encoding="utf-8")
         info = json.loads(content.read())
         sources = info["sources"]
@@ -38,8 +45,7 @@ def check_project(plot=False, save_ihc_table=False, max_dist=None):
         ihc_table = pd.read_csv(table_content, sep="\t")
 
         # Keep only the synapses that were matched to a valid IHC.
-        component_id = 1
-        valid_ihcs = ihc_table.label_id[ihc_table.component_labels == component_id].values.astype("int")
+        valid_ihcs = ihc_table.label_id[ihc_table.component_labels.isin(component_id)].values.astype("int")
 
         valid_syn_table = syn_table[syn_table.matched_ihc.isin(valid_ihcs)]
         n_synapses = len(valid_syn_table)

scripts/prediction/postprocess_ihc_synapse.py

@@ -14,9 +14,9 @@ def main():
     parser = argparse.ArgumentParser(
         description="Script to postprocess IHC segmentation based on the number of synapses per IHC.")
 
-    parser.add_argument('--base_path', type=str, required=True, help="Base segmentation.")
+    parser.add_argument('--base_path', type=str, required=True, help="Base segmentation. WARNING: Will be edited.")
     parser.add_argument('--ref_path', type=str, required=True, help="Reference segmentation.")
-    parser.add_argument('--out_path', type=str, required=True, help="Output segmentation.")
+    parser.add_argument('--out_path_tif', type=str, default=None, help="Output segmentation for tif output.")
 
     parser.add_argument('--base_table', type=str, required=True, help="Synapse per IHC table of base segmentation.")
 
@@ -42,6 +42,10 @@ def main():
 
     args = parser.parse_args()
 
+    if args.tif:
+        if args.out_path_tif is None:
+            raise ValueError("Specify out_path_tif for saving TIF file.")
+
     if args.base_key is None:
         data_base = read_image_data(args.base_path, args.base_key)
     else:
@@ -54,12 +58,12 @@ def main():
     if args.crop:
         output_ = ihc_synapse_postprocessing.postprocess_ihc_synapse_crop(
             data_base, data_ref, table_base=table_base, synapse_limit=25, min_overlap=0.5,
-            )
+        )
     else:
         output_ = ihc_synapse_postprocessing.postprocess_ihc_synapse(
             data_base, data_ref, table_base=table_base, synapse_limit=25, min_overlap=0.5,
             resolution=0.38, roi_pad=40,
-            )
+        )
 
     if args.tif:
         imageio.imwrite(args.out_path, output_, compression="zlib")