Fix: Variable name matches function

Author: schilling40

flamingo_tools/segmentation/postprocessing.py

@@ -324,7 +324,7 @@ def graph_connected_components(coords: dict, min_edge_distance: float, min_compo
 
     Args:
         coords: Dictionary containing label IDs as keys and their position as value.
-        min_edge_distance: Minimal edge distance between graph nodes to create an edge between nodes.
+        min_edge_distance: Maximal edge distance between graph nodes to create an edge between nodes.
         min_component_length: Minimal length of nodes of connected component. Filtered out if lower.
 
     Returns:
@@ -372,7 +372,7 @@ def components_sgn(
         keyword: Keyword of the dataframe column for erosion.
         threshold_erode: Threshold of column value after erosion step with spatial statistics.
         min_component_length: Minimal length for filtering out connected components.
-        min_edge_distance: Minimal distance in micrometer between points to create edges for connected components.
+        min_edge_distance: Maximal distance in micrometer between points to create edges for connected components.
         iterations_erode: Number of iterations for erosion, normally determined automatically.
         postprocess_threshold: Post-process graph connected components by searching for points closer than threshold.
         postprocess_components: Post-process specific graph connected components ([0] for largest component only).
@@ -460,7 +460,7 @@ def label_components_sgn(
         min_size: Minimal number of pixels for filtering small instances.
         threshold_erode: Threshold of column value after erosion step with spatial statistics.
         min_component_length: Minimal length for filtering out connected components.
-        min_edge_distance: Minimal distance in micrometer between points to create edges for connected components.
+        min_edge_distance: Maximal distance in micrometer between points to create edges for connected components.
         iterations_erode: Number of iterations for erosion, normally determined automatically.
         postprocess_threshold: Post-process graph connected components by searching for points closer than threshold.
         postprocess_components: Post-process specific graph connected components ([0] for largest component only).
@@ -506,7 +506,7 @@ def postprocess_sgn_seg(
         min_size: Minimal number of pixels for filtering small instances.
         threshold_erode: Threshold of column value after erosion step with spatial statistics.
         min_component_length: Minimal length for filtering out connected components.
-        min_edge_distance: Minimal distance in micrometer between points to create edges for connected components.
+        min_edge_distance: Maximal distance in micrometer between points to create edges for connected components.
         iterations_erode: Number of iterations for erosion, normally determined automatically.
 
     Returns:
@@ -532,7 +532,7 @@ def components_ihc(
     Args:
         table: Dataframe of segmentation table.
         min_component_length: Minimal length for filtering out connected components.
-        min_edge_distance: Minimal distance in micrometer between points to create edges for connected components.
+        min_edge_distance: Maximal distance in micrometer between points to create edges for connected components.
 
     Returns:
         Subgraph components as lists of label_ids of dataframe.
@@ -559,7 +559,7 @@ def label_components_ihc(
         table: Dataframe of segmentation table.
         min_size: Minimal number of pixels for filtering small instances.
         min_component_length: Minimal length for filtering out connected components.
-        min_edge_distance: Minimal distance in micrometer between points to create edges for connected components.
+        min_edge_distance: Maximal distance in micrometer between points to create edges for connected components.
 
     Returns:
         List of component label for each point in dataframe. 0 - background, then in descending order of size
@@ -600,7 +600,7 @@ def postprocess_ihc_seg(
         table: Dataframe of segmentation table.
         min_size: Minimal number of pixels for filtering small instances.
         min_component_length: Minimal length for filtering out connected components.
-        min_edge_distance: Minimal distance in micrometer between points to create edges for connected components.
+        min_edge_distance: Maximal distance in micrometer between points to create edges for connected components.
 
     Returns:
         Dataframe with component labels.

reproducibility/postprocess_sgn/SGN_v1_postprocess.json

@@ -12,7 +12,7 @@
 	{
 		"cochlea": "M_LR_000144_L",
 		"image_channel": "PV_resized",
-		"min_edge_distance": 70,
+		"max_edge_distance": 70,
 		"iterations_erode": 1,
 		"unet_version": "v1"
 	},

reproducibility/postprocess_sgn/repro_postprocess_sgn_v1.py

@@ -18,7 +18,7 @@ def repro_postprocess_sgn_v1(
     min_size = 1000
     default_threshold_erode = None
     default_min_length = 50
-    default_min_edge_distance = 30
+    default_max_edge_distance = 30
     default_iterations_erode = None
 
     with open(ddict, 'r') as myfile:
@@ -36,18 +36,18 @@ def repro_postprocess_sgn_v1(
 
         threshold_erode = dic["threshold_erode"] if "threshold_erode" in dic else default_threshold_erode
         min_component_length = dic["min_component_length"] if "min_component_length" in dic else default_min_length
-        min_edge_distance = dic["min_edge_distance"] if "min_edge_distance" in dic else default_min_edge_distance
+        max_edge_distance = dic["max_edge_distance"] if "max_edge_distance" in dic else default_max_edge_distance
         iterations_erode = dic["iterations_erode"] if "iterations_erode" in dic else default_iterations_erode
 
         print("threshold_erode", threshold_erode)
         print("min_component_length", min_component_length)
-        print("min_edge", min_edge_distance)
+        print("max_edge", max_edge_distance)
         print("iterations_erode", iterations_erode)
 
         tsv_table = postprocess_sgn_seg(table, min_size=min_size,
                                         threshold_erode=threshold_erode,
                                         min_component_length=min_component_length,
-                                        min_edge_distance=min_edge_distance,
+                                        max_edge_distance=max_edge_distance,
                                         iterations_erode=iterations_erode)
 
         largest_comp = len(tsv_table[tsv_table["component_labels"] == 1])

scripts/prediction/postprocess_seg.py

@@ -37,8 +37,8 @@ def main():
                         help="Threshold for spatial statistics.")
     parser.add_argument("--min_component_length", type=int, default=50,
                         help="Minimal length for filtering out connected components.")
-    parser.add_argument("--min_edge_dist", type=float, default=30,
-                        help="Minimal distance in micrometer between points to create edges for connected components.")
+    parser.add_argument("--max_edge_dist", type=float, default=30,
+                        help="Maximal distance in micrometer between points to create edges for connected components.")
     parser.add_argument("--iterations_erode", type=int, default=None,
                         help="Number of iterations for erosion, normally determined automatically.")
 
@@ -126,7 +126,7 @@ def create_spatial_statistics_dict(functions, keyword, options, threshold):
     if seg_path is None:
         post_table = postprocess_sgn_seg(
             tsv_table.copy(), min_size=args.min_size, threshold_erode=args.threshold,
-            min_component_length=args.min_component_length, min_edge_distance=args.min_edge_dist,
+            min_component_length=args.min_component_length, max_edge_distance=args.max_edge_dist,
             iterations_erode=args.iterations_erode,
         )