Added honorStayInside option to init

snudda/cli.py

@@ -46,6 +46,7 @@ def snudda_cli():
                              action="store_true")
     init_parser.add_argument("-connectionFile", "--connectionFile", default=None, dest="connection_file",
                              help="Use connectivity from user specified JSON file")
+    init_parser.add_argument("--honorStayInside", "--stayInside", default=False, dest="stay_inside", action="store_true")
     init_parser.add_argument("-randomseed", "--randomseed", "--seed", default=None, help="Random seed", type=int)
     init_parser.add_argument("--profile", help="Run python cProfile", action="store_true")
     init_parser.add_argument("--verbose", action="store_true")
@@ -55,6 +56,7 @@ def snudda_cli():
     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("--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

@@ -109,12 +109,14 @@ def init_config_wrapper(self, args):
                          neurons_dir=args.neurons_dir,
                          connection_file=args.connection_file,
                          overwrite=args.overwrite,
-                         random_seed=args.randomseed)
+                         random_seed=args.randomseed,
+                         honor_stay_inside=args.stay_inside)
 
     def init_config(self, network_size,
                     snudda_data=None,
                     neurons_dir=None,
                     connection_file=None,
+                    honor_stay_inside=True,   # currently the cli.py defaults to sending False
                     overwrite=False,
                     random_seed=None):
 
@@ -144,6 +146,7 @@ def init_config(self, network_size,
                    neurons_dir=neurons_dir,
                    snudda_data=snudda_data,
                    config_file=config_file,
+                   honor_stay_inside=honor_stay_inside,
                    random_seed=random_seed,
                    connection_override_file=connection_file)
 
@@ -175,15 +178,17 @@ def place_neurons_wrapper(self, args):
                            ipython_profile=args.ipython_profile,
                            raytrace_borders=args.raytrace_borders,
                            h5libver=h5libver,
-                           verbose=args.verbose)
+                           verbose=args.verbose,
+                           honor_stay_inside=args.stay_inside)
 
     def place_neurons(self,
                       random_seed=None,
                       parallel=False,
                       ipython_profile=None,
                       raytrace_borders=False,
                       h5libver="latest",
-                      verbose=False):
+                      verbose=False,
+                      honor_stay_inside=False):
 
         # self.networkPath = args.path
         print("Placing neurons")
@@ -204,7 +209,8 @@ def place_neurons(self,
                          d_view=self.d_view,
                          h5libver=h5libver,
                          raytrace_borders=raytrace_borders,
-                         random_seed=random_seed)
+                         random_seed=random_seed,
+                         morphologies_stay_inside=honor_stay_inside)
 
         sp.place()
 

snudda/init/init.py

@@ -8,6 +8,7 @@
 import json
 import os.path
 import sys
+import inspect
 
 import numexpr
 #
@@ -34,7 +35,8 @@ def __init__(self,
                  neurons_dir=None,
                  config_file=None,
                  random_seed=None,
-                 connection_override_file=None):
+                 connection_override_file=None,
+                 honor_stay_inside=False):
 
         """Constructor
 
@@ -99,8 +101,12 @@ def __init__(self,
 
         if struct_def:
             for sn in struct_def:
-                print(f"Adding {sn} with {struct_def[sn]} neurons")
-                struct_func[sn](num_neurons=struct_def[sn], neurons_dir=neurons_dir)
+                if "stay_inside" in inspect.getargspec(struct_func[sn]).args:
+                    print(f"Adding {sn} with {struct_def[sn]} neurons (stay_inside={honor_stay_inside})")
+                    struct_func[sn](num_neurons=struct_def[sn], neurons_dir=neurons_dir, stay_inside=honor_stay_inside)
+                else:
+                    print(f"Adding {sn} with {struct_def[sn]} neurons")
+                    struct_func[sn](num_neurons=struct_def[sn], neurons_dir=neurons_dir)
 
             if connection_override_file:
                 self.replace_connectivity(connection_file=connection_override_file)

snudda/place/place.py

@@ -50,10 +50,9 @@ def __init__(self,
                  rc=None,
                  d_view=None,
                  h5libver=None,
-                 raytrace_borders=False,
                  random_seed=None,
                  griddata_interpolation=False,
-                 morphologies_stay_inside=True):  # Setting this to true is 5x slower -- obsolete?
+                 morphologies_stay_inside=True):
 
         """
         Constructor.
@@ -67,7 +66,6 @@ def __init__(self,
             rc : ipyparallel remote client
             d_view : ipyparallel direct view object
             h5libver : Version of h5py library
-            raytrace_borders (bool) : Should positions in border voxels be raytraces, slower but more accurate
             random_seed (int) : Numpy random seed
             griddata_interpolation (bool) : Should we interpolate density data (5x slower)
 
@@ -126,8 +124,6 @@ def __init__(self,
         self.random_generator = None
         self.rotate_helper = None
 
-        self.raytrace_borders = raytrace_borders
-
         # This defines the neuron units/channels. The dictionary lists all the
         # members of each unit, the neuronChannel gives the individual neurons
         # channel membership
@@ -404,15 +400,6 @@ def parse_config(self, config_file=None, resort_neurons=True):
                     self.write_log(f"Unable to find mesh file {vol_def['meshFile']}")
                     sys.exit(-1)
 
-                # self.volume[volume_id]["mesh"] \
-                #     = RegionMesh(mesh_file,
-                #                  d_view=d_view,
-                #                  raytrace_borders=self.raytrace_borders,
-                #                  d_min=vol_def["dMin"],
-                #                  bin_width=mesh_bin_width,
-                #                  log_file=mesh_logfile,
-                #                  random_seed=vol_seed[volume_id])
-
                 if "n_putative_points" in self.volume[volume_id]:
                     n_putative_points = int(self.volume[volume_id]["n_putative_points"])
                 else: