Working in serial

Hjorthmedh · Oct 20, 2023 · 236f473 · 236f473
1 parent 305f2ab
commit 236f473
Show file tree

Hide file tree

Showing 3 changed files with 32 additions and 18 deletions.
diff --git a/examples/notebooks/bend_morphologies.ipynb b/examples/notebooks/bend_morphologies.ipynb
diff --git a/snudda/place/bend_morphologies.py b/snudda/place/bend_morphologies.py
@@ -90,6 +90,7 @@ def bend_morphology(self, morphology: NeuronMorphologyExtended, k=30e-6, n_rando
 
                 # Cache the random numbers for segments in the section...
                 if dist > parent_dist and self.rng.uniform() < P_move:
+                #  if self.rng.uniform() < P_move:
 
                     morphology_changed = True
                     parent_moved = True
@@ -340,9 +341,10 @@ def write_swc(self, morphology: MorphologyData, output_file, comment=None):
 
         print(f"Wrote {output_file}")
 
-    def edge_avoiding_morphology(self, swc_file, new_file):
+    def edge_avoiding_morphology(self, swc_file, new_file, original_position, original_rotation):
 
         md = MorphologyData(swc_file=swc_file)
+        md.place(rotation=original_rotation, position=original_position)
         rot_rep, morphology_changed = self.bend_morphology(md)
 
         if morphology_changed:

diff --git a/snudda/place/place.py b/snudda/place/place.py
@@ -624,7 +624,9 @@ def avoid_edges(self, neuron_id=None):
                 # Returns None if unchanged
                 new_morph_name = os.path.join(bend_morph_path, f"{neuron.name}-{neuron.neuron_id}.swc")
                 new_morphology = bend_morph[volume_id].edge_avoiding_morphology(swc_file=neuron.swc_filename,
-                                                                                new_file=new_morph_name)
+                                                                                new_file=new_morph_name,
+                                                                                original_position=neuron.position,
+                                                                                original_rotation=neuron.rotation)
 
                 if new_morphology:
                     # Replace the original morphology with the warped morphology, morphology includes rotation