Fixed bend morphology load for simulations

snudda/cli.py

@@ -54,9 +54,7 @@ def snudda_cli():
     place_parser = sub_parsers.add_parser("place")
     place_parser.add_argument("path", help="Location of network")
     place_parser.add_argument("-randomseed", "--randomseed", "--seed", default=None, help="Random seed", type=int)
-    place_parser.add_argument("--raytraceBorders", help="Ray traces for more precise mesh edge detection",
-                              action="store_true", dest="raytrace_borders", default=False)
-    place_parser.add_argument("--honorStayInside", dest="stay_inside", default=False)
+    place_parser.add_argument("--honorStayInside", "--stayInside", dest="stay_inside", default=False, action="store_true")
     place_parser.add_argument("--profile", help="Run python cProfile", action="store_true")
     place_parser.add_argument("--verbose", action="store_true")
     place_parser.add_argument("--h5legacy", help="Use legacy hdf5 support", action="store_true")

snudda/core.py

@@ -164,7 +164,7 @@ def place_neurons_wrapper(self, args):
             args : command line arguments from argparse
 
         Example:
-            snudda place [--raytraceBorders] [--profile] [--verbose] [--h5legacy] [-parallel] path
+            snudda place [--profile] [--verbose] [--h5legacy] [-parallel] path
 
         """
 
@@ -176,7 +176,6 @@ def place_neurons_wrapper(self, args):
         self.place_neurons(random_seed=args.randomseed,
                            parallel=args.parallel,
                            ipython_profile=args.ipython_profile,
-                           raytrace_borders=args.raytrace_borders,
                            h5libver=h5libver,
                            verbose=args.verbose,
                            honor_stay_inside=args.stay_inside)
@@ -185,7 +184,6 @@ def place_neurons(self,
                       random_seed=None,
                       parallel=False,
                       ipython_profile=None,
-                      raytrace_borders=False,
                       h5libver="latest",
                       verbose=False,
                       honor_stay_inside=False):
@@ -208,7 +206,6 @@ def place_neurons(self,
                          verbose=verbose,
                          d_view=self.d_view,
                          h5libver=h5libver,
-                         raytrace_borders=raytrace_borders,
                          random_seed=random_seed,
                          morphologies_stay_inside=honor_stay_inside)
 

snudda/detect/detect.py

@@ -2301,6 +2301,7 @@ def load_neuron(self, neuron_info, use_cache=True):
         """
 
         neuron_id = neuron_info["neuronID"]
+
         if use_cache and neuron_id in self.neuron_cache:
             return self.neuron_cache[neuron_id]
 
@@ -2310,7 +2311,7 @@ def load_neuron(self, neuron_info, use_cache=True):
         else:
             morphology_path = None  # Get morpholog automatically from morphology_key
 
-        print(f"morphology_path = {morphology_path}")
+        # print(f"morphology_path = {morphology_path}")
 
         # Clone prototype neuron (it is centred, and not rotated)
         neuron = self.prototype_neurons[neuron_info["name"]].clone(parameter_key=neuron_info["parameterKey"],

snudda/neurons/neuron_model_extended.py

@@ -59,33 +59,39 @@ def __init__(self,
         self.script_dir = os.path.dirname(__file__)
         self.config_dir = os.path.join(self.script_dir, 'config')
 
-        morph_file = None
-        if parameter_key is not None and morphology_key is not None and param_file is not None:
-            meta_file = os.path.join(os.path.dirname(param_file), "meta.json")
-            if os.path.isfile(meta_file):
-                with open(meta_file, "r") as f:
-                    meta_data = json.load(f, object_pairs_hook=OrderedDict)
-                    morph_file = os.path.join(morph_path, meta_data[parameter_key][morphology_key]["morphology"])
-
-        if not morph_file:
-            # We now allow multiple variations of morphologies for a given neuron name, so here NeuronPrototype
-            # is used to acquire the actual morphology file we will use for this particular neuron
-            # based on parameter_id and morphology_id.
-            neuron_prototype = NeuronPrototype(neuron_name=cell_name,
-                                               neuron_path=None,
-                                               morphology_path=morph_path,
-                                               parameter_path=param_file,
-                                               mechanism_path=mech_file,
-                                               modulation_path=modulation_file)
-
-            morph_file, _ = neuron_prototype.get_morphology(parameter_id=parameter_id,
-                                                            morphology_id=morphology_id,
-                                                            parameter_key=parameter_key,
-                                                            morphology_key=morphology_key)
-
-        assert morph_file, (f"Neuron {cell_name} with morph_path = {morph_path} ({morphology_id}, "
-                            f"parameter_path = {param_file} ({parameter_id}) "
-                            f"has morph_file = {morph_file} (Should not be None)")
+        if os.path.isfile(morph_path):
+            # If morph_path is a swc file, use it directly
+            morph_file = morph_path
+        else:
+            # Figure out what file in the morphology path we should use
+
+            morph_file = None
+            if parameter_key is not None and morphology_key is not None and param_file is not None:
+                meta_file = os.path.join(os.path.dirname(param_file), "meta.json")
+                if os.path.isfile(meta_file):
+                    with open(meta_file, "r") as f:
+                        meta_data = json.load(f, object_pairs_hook=OrderedDict)
+                        morph_file = os.path.join(morph_path, meta_data[parameter_key][morphology_key]["morphology"])
+
+            if not morph_file:
+                # We now allow multiple variations of morphologies for a given neuron name, so here NeuronPrototype
+                # is used to acquire the actual morphology file we will use for this particular neuron
+                # based on parameter_id and morphology_id.
+                neuron_prototype = NeuronPrototype(neuron_name=cell_name,
+                                                   neuron_path=None,
+                                                   morphology_path=morph_path,
+                                                   parameter_path=param_file,
+                                                   mechanism_path=mech_file,
+                                                   modulation_path=modulation_file)
+
+                morph_file, _ = neuron_prototype.get_morphology(parameter_id=parameter_id,
+                                                                morphology_id=morphology_id,
+                                                                parameter_key=parameter_key,
+                                                                morphology_key=morphology_key)
+
+            assert morph_file, (f"Neuron {cell_name} with morph_path = {morph_path} ({morphology_id}, "
+                                f"parameter_path = {param_file} ({parameter_id}) "
+                                f"has morph_file = {morph_file} (Should not be None)")
 
         self.morph_file = morph_file
 

snudda/simulate/simulate.py

@@ -463,7 +463,9 @@ def setup_neurons(self):
 
             config = self.config["Neurons"][name]
 
-            morph = snudda_parse_path(config["morphology"], self.snudda_data)
+            # We need to get morphology from network_info, since it can now be redefined for bent morphologies
+            morph = snudda_parse_path(self.network_info["neurons"][ID]["morphology"], self.snudda_data)
+            # morph = snudda_parse_path(config["morphology"], self.snudda_data)
             param = snudda_parse_path(config["parameters"], self.snudda_data)
             mech = snudda_parse_path(config["mechanisms"], self.snudda_data)
 

tests/test_cli.py

@@ -68,11 +68,11 @@ def test_workflow(self):
             config_name = os.path.join("tiny_parallel", "network-config.json")
             cnc = SnuddaInit(struct_def={}, config_file=config_name, random_seed=123456)
             cnc.define_striatum(num_dSPN=4, num_iSPN=4, num_FS=2, num_LTS=2, num_ChIN=2,
-                                volume_type="cube")
+                                volume_type="cube", stay_inside=True)
             cnc.write_json(config_name)
 
         with self.subTest(stage="place-parallel"):
-            run_cli_command("place tiny_parallel --parallel --raytraceBorders")
+            run_cli_command("place tiny_parallel --parallel --stayInside")
 
         with self.subTest(stage="detect-parallel"):
             run_cli_command("detect tiny_parallel --parallel")