Merge pull request #397 from Hjorthmedh/region_mesh_redux

Added parameters to config file
Hjorthmedh · Oct 26, 2023 · 4f9e989 · 4f9e989
2 parents 26b96df + 03ed349
commit 4f9e989
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Showing 4 changed files with 63 additions and 224 deletions.
diff --git a/examples/notebooks/bend_morphologies.ipynb b/examples/notebooks/bend_morphologies.ipynb
diff --git a/snudda/init/init.py b/snudda/init/init.py
@@ -416,7 +416,10 @@ def add_neurons(self, name,
                     model_type="neuron",
                     volume_id=None,
                     rotation_mode="random",
-                    stay_inside=False):
+                    stay_inside=False,
+                    k_dist=30e-6,
+                    n_random=5,
+                    max_angle=0.1):
 
         if num_neurons <= 0:
             return
@@ -571,7 +574,7 @@ def add_neurons(self, name,
                 cell_data["axonConfig"] = axon_config
 
             if stay_inside:
-                cell_data["stayInsideMesh"] = True
+                cell_data["stayInsideMesh"] = {"k_dist": k_dist, "n_random": n_random, "max_angle": max_angle}
 
             self.network_data["Neurons"][unique_name] = cell_data
 

diff --git a/snudda/place/bend_morphologies.py b/snudda/place/bend_morphologies.py
@@ -24,7 +24,9 @@ def check_if_inside(self, morphology: NeuronMorphologyExtended):
 
         return inside_flag
 
-    def bend_morphology(self, morphology: NeuronMorphologyExtended, k=30e-6, n_random=5, random_seed=None):
+    def bend_morphology(self, morphology: NeuronMorphologyExtended,
+                        k_dist=30e-6, max_angle=0.1,  # angle in radians
+                        n_random=5, random_seed=None):
 
         # k -- how early will the neuron start bending when it approaches the border
 
@@ -93,7 +95,7 @@ def bend_morphology(self, morphology: NeuronMorphologyExtended, k=30e-6, n_rando
                     # Parent has not moved, so use stored original distance
                     dist = section_dist[idx]
 
-                P_move = 1 / (1 + np.exp(-dist/k))
+                P_move = 1 / (1 + np.exp(-dist/k_dist))
 
                 # Cache the random numbers for segments in the section...
                 if dist > parent_dist and rng.uniform() < P_move:
@@ -103,7 +105,7 @@ def bend_morphology(self, morphology: NeuronMorphologyExtended, k=30e-6, n_rando
 
                     # We need to randomize new rotation matrix
                     # https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.transform.Rotation.html
-                    angles = rng.uniform(size=(n_random, 3), low=-0.1, high=0.1)  # Angles in radians
+                    angles = rng.uniform(size=(n_random, 3), low=-max_angle, high=max_angle)  # Angles in radians
                     avoidance_rotations = Rotation.from_euler(seq="XYZ", angles=angles)
 
                     for idx2, av_rot in enumerate(avoidance_rotations):
@@ -342,11 +344,16 @@ def write_swc(self, morphology: MorphologyData, output_file, comment=None):
 
         print(f"Wrote {output_file}")
 
-    def edge_avoiding_morphology(self, swc_file, new_file, original_position, original_rotation, random_seed=None):
+    def edge_avoiding_morphology(self, swc_file, new_file, original_position, original_rotation,
+                                 k_dist=30e-6, max_angle=0.1, n_random=5,
+                                 random_seed=None):
 
         md = MorphologyData(swc_file=swc_file)
         md.place(rotation=original_rotation, position=original_position)
-        rot_rep, morphology_changed = self.bend_morphology(md, random_seed=random_seed)
+        rot_rep, morphology_changed = self.bend_morphology(md,
+                                                           k_dist=k_dist, max_angle=max_angle,
+                                                           n_random=n_random,
+                                                           random_seed=random_seed)
 
         if morphology_changed:
             new_coord = self.apply_rotation(md, rot_rep)

diff --git a/snudda/place/place.py b/snudda/place/place.py
@@ -569,10 +569,31 @@ def avoid_edges_parallel(self):
             if "stayInsideMesh" in config and config["stayInsideMesh"]:
                 volume_id = config["volumeID"]
                 mesh_file = self.config["Volume"][volume_id]["meshFile"]
+
+                if type(config["stayInsideMesh"]) in (dict, OrderedDict):
+                    if "k_dist" in config["stayInsideMesh"]:
+                        k_dist = config["stayInsideMesh"]["k_dist"]
+                    else:
+                        k_dist = 30e-6
+
+                    if "n_random" in config["stayInsideMesh"]:
+                        n_random = config["stayInsideMesh"]["n_random"]
+                    else:
+                        n_random = 5
+
+                    if "max_angle" in config["stayInsideMesh"]:
+                        max_angle = config["stayInsideMesh"]["max_angle"]
+                    else:
+                        max_angle = 0.1  # radians
+                else:
+                    k_dist = 30e-6
+                    n_random = 5
+                    max_angle = 0.1  # radians
+
                 bend_neuron_info.append((neuron.neuron_id, neuron.name, neuron.swc_filename,
                                          neuron.position, neuron.rotation,
                                          neuron_random_seed[neuron.neuron_id],
-                                         volume_id, mesh_file))
+                                         volume_id, mesh_file, k_dist, n_random, max_angle))
 
         bend_morph_path = os.path.join(self.network_path, "modified_morphologies")
 
@@ -625,8 +646,8 @@ def avoid_edges_helper(bend_neuron_info, network_path):
 
         modified_morphologies = []
 
-        for neuron_id, neuron_name, swc_filename, position, rotation, random_seed, volume_id, mesh_file \
-                in bend_neuron_info:
+        for neuron_id, neuron_name, swc_filename, position, rotation, random_seed, volume_id, mesh_file,\
+            k_dist, n_random, max_angle in bend_neuron_info:
 
             if volume_id not in bend_morph:
                 bend_morph[volume_id] = BendMorphologies(region_mesh=mesh_file, rng=None)
@@ -637,7 +658,10 @@ def avoid_edges_helper(bend_neuron_info, network_path):
                                                                             new_file=new_morph_name,
                                                                             original_position=position,
                                                                             original_rotation=rotation,
-                                                                            random_seed=random_seed)
+                                                                            random_seed=random_seed,
+                                                                            k_dist=k_dist,
+                                                                            n_random=n_random,
+                                                                            max_angle=max_angle)
 
             if new_morphology:
                 modified_morphologies.append((neuron_id, new_morphology))