Refactor data challenge (#145)

* bug: swc reader

* refactor: updated results file

* refactor: change default param

---------

Co-authored-by: anna-grim <[email protected]>

Author: anna-grim

src/segmentation_skeleton_metrics/skeleton_metric.py

@@ -100,6 +100,10 @@ def __init__(
             Segment IDs that can be assigned to nodes. This argument accounts
             for segments that were been removed due to some type of filtering.
             Default is None.
+        use_anisotropy : bool, optional
+            Indication of whether coordinates in fragment SWC files should be
+            converted from physical to image coordinates using the given
+            anisotropy. Default is False.
         verbose : bool, optional
             Indication of whether to printout updates. Default is True.
         """
@@ -343,9 +347,10 @@ def detect_splits(self):
                 p_split = 100 * n_split_edges / n_before
                 rl = np.sum(self.graphs[key].run_lengths())
                 gt_rl = self.graphs[key].run_length
+                split_rate = rl / n_splits if n_splits > 0 else np.nan
 
                 self.metrics.at[key, "# Splits"] = n_splits
-                self.metrics.at[key, "Split Rate"] = rl / max(n_splits, 1)
+                self.metrics.at[key, "Split Rate"] = split_rate
                 self.metrics.loc[key, "% Split Edges"] = round(p_split, 2)
                 self.metrics.at[key, "% Omit Edges"] = round(p_omit, 2)
                 self.metrics.loc[key, "SWC Run Length"] = round(gt_rl, 2)
@@ -428,7 +433,7 @@ def is_fragment_merge(self, key, label, kdtree):
                 for leaf in gutil.get_leafs(fragment_graph):
                     voxel = fragment_graph.voxels[leaf]
                     gt_voxel = util.kdtree_query(kdtree, voxel)
-                    if self.physical_dist(gt_voxel, voxel) > 50:
+                    if self.physical_dist(gt_voxel, voxel) > 40:
                         self.find_merge_site(
                             key, kdtree, fragment_graph, leaf, visited
                         )

src/segmentation_skeleton_metrics/utils/graph_util.py

@@ -52,8 +52,9 @@ def __init__(
             Only SWC files with an swc_id contained in this set are read.
             Default is None.
         use_anisotropy : bool, optional
-            Indication of whether to apply anisotropy to coordinates in SWC
-            files. Default is True.
+            Indication of whether coordinates in SWC files should be converted
+            from physical to image coordinates using the given anisotropy.
+            Default is True.
         """
         # Instance attributes
         self.anisotropy = anisotropy