bug: added use_anisotropy back

src/neuron_proofreader/merge_proofreading/merge_dataloading.py

@@ -44,7 +44,9 @@ def load_fragments(dataset, is_test=False):
         for segmentation_id in sub_df["segmentation_id"].unique():
             if (brain_id, segmentation_id) in target_pairs:
                 swc_pointer = f"{root}/{brain_id}/{segmentation_id}/merged_fragments.zip"
-                dataset.load_fragment_graphs(brain_id, swc_pointer)
+                dataset.load_fragment_graphs(
+                    brain_id, swc_pointer, use_anisotropy=False
+                )
 
 
 def load_groundtruth(dataset, is_test=False):
@@ -62,7 +64,7 @@ def load_groundtruth(dataset, is_test=False):
     print("\nLoading Ground Truth")
     root = "gs://allen-nd-goog/ground_truth_tracings"
     for brain_id in get_brain_ids(dataset.merge_sites_df, is_test):
-        swc_pointer = f"{root}/{brain_id}/world"
+        swc_pointer = f"{root}/{brain_id}/voxel"
         dataset.load_gt_graphs(brain_id, swc_pointer)
 
 

src/neuron_proofreader/merge_proofreading/merge_datasets.py

@@ -121,7 +121,9 @@ def __init__(
         self.merge_site_kdtrees = dict()
 
     # --- Load Data ---
-    def load_fragment_graphs(self, brain_id, swc_pointer):
+    def load_fragment_graphs(
+        self, brain_id, swc_pointer, use_anisotropy=True
+    ):
         """
         Loads fragments containing merge mistakes for a whole-brain dataset,
         then stores them in the "graphs" attribute.
@@ -137,7 +139,7 @@ def load_fragment_graphs(self, brain_id, swc_pointer):
         graph = SkeletonGraph(
             anisotropy=self.anisotropy,
             node_spacing=self.node_spacing,
-            use_anisotropy=False
+            use_anisotropy=use_anisotropy
         )
         graph.load(swc_pointer)
 
@@ -184,7 +186,6 @@ def load_gt_graphs(self, brain_id, swc_pointer):
         self.gt_graphs[brain_id] = SkeletonGraph(
             anisotropy=self.anisotropy,
             node_spacing=self.node_spacing,
-            use_anisotropy=False
         )
         self.gt_graphs[brain_id].load(swc_pointer)
         self.gt_graphs[brain_id].set_kdtree()

src/neuron_proofreader/skeleton_graph.py

@@ -46,6 +46,7 @@ def __init__(
         min_size=0,
         node_spacing=1,
         prune_depth=20,
+        use_anisotropy=True,
         verbose=False,
     ):
         """
@@ -63,6 +64,10 @@ def __init__(
         prune_depth : float, optional
             Branches with length less than "prune_depth" microns are removed.
             Default is 20μm.
+        use_anisotropy : bool, optional
+            Indication of whether to apply anisotropy to SWC files. Note: set
+            to False if the SWC files are saved in physical coordinates.
+            Default is False.
         verbose : bool, optional
             Indication of whether to display a progress bar while building
             graph. Default is True.
@@ -77,6 +82,7 @@ def __init__(
         self.node_spacing = node_spacing
 
         # Graph Loader
+        anisotropy = anisotropy if use_anisotropy else (1.0, 1.0, 1.0)
         self.graph_loader = gutil.GraphLoader(
             anisotropy=anisotropy,
             min_size=min_size,

src/neuron_proofreader/utils/graph_util.py

@@ -127,6 +127,7 @@ def ingest_somas(self, segmentation_path):
             # Assign threads
             threads = list()
             for xyz in self.soma_centroids:
+                # CHANGE THIS
                 voxel = img_util.to_voxels(xyz, (0.748, 0.748, 1.0))
                 threads.append(executor.submit(reader.read_voxel, voxel, xyz))