Updated DA simulation

examples/notebooks/neuromodulation/data/connectivity_v2.json

@@ -0,0 +1,28 @@
+{
+    "regions": {
+        "Cube": {
+	    "connectivity": {
+		"dspn,dspn": {
+		    "GABA": {
+			"conductance": [
+			    1e-9,
+			    1e-3
+			],
+			"channel_parameters": {
+			    "mod_file": "tmGabaA"
+			},			
+			"cluster_size": 1,
+			"cluster_spread": null,
+			"pruning": {
+			    "f1": null,
+			    "soft_max": null,
+			    "mu2": null,
+			    "a3": null,
+			    "cluster_pruning": false
+			}
+		    }
+		}
+	    }
+	}
+    }
+}

examples/notebooks/neuromodulation/data/input_v4.json

@@ -0,0 +1,31 @@
+{
+    "0": {
+        "cortical" : {
+            "generator" : "poisson",
+            "start" : [0],
+            "end" : [2],
+            "frequency" : [5],
+            "conductance" : 0.5e-9,
+	    "input_correlation": 0.5,
+            "num_inputs" : 50,
+	    "parameter_file": "data/tmglut_DA_parameters.json",
+            "mod_file": "tmGlut"
+        },
+	"DA" : {
+            "generator" : "poisson",
+            "start" : [0.3],
+            "end" : [1.3],
+            "frequency" : [20],
+            "conductance" : 0.5e-9,
+            "num_inputs" : 200,
+	    "num_soma_synapses" : 10,
+            "mod_file": "DASyn",
+	    "RxD": {
+		"species_name": "DA",
+		"flux_variable": "open",
+		"region": "internal",
+		"weight_scale": 1e18
+	    }
+	}
+    }
+}

snudda/cli.py

@@ -144,12 +144,13 @@ def snudda_cli():
     simulate_parser.add_argument("--disableGJ", "--disableGapJunctions", action="store_true", dest="disable_gj", default=None,
                                  help="Disable gap junctions")
 
-    simulate_parser.add_argument("-mechdir", "--mechDir", dest="mech_dir",
+    simulate_parser.add_argument("--mechdir", "--mechDir", dest="mech_dir",
                                  help="mechanism directory if not default", default=None)
     simulate_parser.add_argument("--profile", help="Run python cProfile", action="store_true")
     simulate_parser.add_argument("--verbose", action="store_true")
     simulate_parser.add_argument("--exportCoreNeuron", action="store_true")
     simulate_parser.add_argument("--recordALL", dest="record_all", type=str, default=None)
+    simulate_parser.add_argument("--disable_rxd_neuromodulation", dest="use_rxd_neuromodulation", action="store_false", default=True)
 
     export_parser = sub_parsers.add_parser("export")
     export_parser.add_argument("path", help="Location of network")

snudda/core.py

@@ -716,6 +716,7 @@ def simulate_wrapper(self, args):
                             record_all=args.record_all,
                             simulation_config=args.simulation_config,
                             export_core_neuron=args.exportCoreNeuron,
+                            use_rxd_neuromodulation=args.use_rxd_neuromodulation,
                             verbose=args.verbose)
 
         sim.clear_neuron()
@@ -735,6 +736,7 @@ def simulate(self,
                  sample_dt=None,
                  simulation_config=None,
                  export_core_neuron=False,
+                 use_rxd_neuromodulation=True,
                  verbose=False):
 
         start = timeit.default_timer()
@@ -811,6 +813,7 @@ def simulate(self,
                              log_file=log_file,
                              simulation_config=simulation_config,
                              sample_dt=sample_dt,
+                             use_rxd_neuromodulation=use_rxd_neuromodulation,
                              verbose=verbose)
         sim.setup()
         sim.add_external_input()

snudda/neurons/neuron_model_extended.py

@@ -31,7 +31,8 @@ def __init__(self,
                  modulation_id=None,
                  parameter_key=None,
                  morphology_key=None,
-                 modulation_key=None):
+                 modulation_key=None,
+                 use_rxd_neuromodulation=True):
 
         """
         Constructor
@@ -61,6 +62,7 @@ def __init__(self,
 
         self.script_dir = os.path.dirname(__file__)
         self.config_dir = os.path.join(self.script_dir, 'config')
+        self.use_rxd_neuromodulation = use_rxd_neuromodulation
 
         if os.path.isfile(morph_path):
             # If morph_path is a swc file, use it directly
@@ -114,7 +116,7 @@ def __init__(self,
         super(NeuronModel, self).__init__(name=cell_name, morph=morph,
                                           mechs=mechs, params=params)
 
-        if reaction_diffusion_file:
+        if reaction_diffusion_file and self.use_rxd_neuromodulation:
             self.modulation = NeuronModulation(neuron=self)
             self.modulation.config_file = reaction_diffusion_file
         else:

snudda/neurons/neuron_modulation.py

@@ -6,7 +6,7 @@
 # TODO: Move DA species to external compartment. IMPORTANT.
 
 import numpy as np
-import neuron.crxd as rxd
+import neuron.rxd as rxd
 import json
 from itertools import chain
 

snudda/simulate/simulate.py

@@ -59,6 +59,7 @@ def __init__(self,
                  disable_synapses=None,
                  disable_gap_junctions=None,
                  sample_dt=None,
+                 use_rxd_neuromodulation=True,
                  simulation_config=None):
 
         """
@@ -124,6 +125,7 @@ def __init__(self,
         self.neuron_id = None
         self.neuron_id_on_node = None
         self.synapse_parameters = None
+        self.use_rxd_neuromodulation = use_rxd_neuromodulation
 
         self.sim_start_time = 0
         self.fih_time = None
@@ -293,7 +295,7 @@ def setup_parse_sim_info(self):
                 self.add_volt_recording_soma(cell_id=record_soma_cell_id)
 
             if "record_all_compartments" in self.sim_info:
-                raise DeprecationWarning("record_all_compartments depricated, please use record_voltate_all_compartments")
+                raise DeprecationWarning("record_all_compartments deprecated, please use record_voltate_all_compartments")
                 record_comp_cell_id = np.array(self.sim_info["record_all_compartments"], dtype=int)
                 self.add_volt_recording_all(cell_id=record_comp_cell_id)
 
@@ -302,15 +304,19 @@ def setup_parse_sim_info(self):
                 self.add_volt_recording_all(cell_id=record_comp_cell_id)
 
             if "record_all_synapses" in self.sim_info:
-                raise DeprecationWarning("record_all_synapses depricated, please use record_current_all_synapses")
+                raise DeprecationWarning("record_all_synapses deprecated, please use record_current_all_synapses")
                 record_syn_cell_id = np.array(self.sim_info["record_all_synapses"], dtype=int)
                 self.add_synapse_current_recording_all(record_syn_cell_id)
 
             if "record_current_all_synapses" in self.sim_info:
                 record_syn_cell_id = np.array(self.sim_info["record_current_all_synapses"], dtype=int)
                 self.add_synapse_current_recording_all(record_syn_cell_id)
 
-            if "record_rxd_species_concentration_all_compartments" in self.sim_info:
+            if "rxd_enable_extracellular" in self.sim_info:
+                import neuron.rxd as rxd
+                rxd.options.enable.extracellular = self.sim_info["rxd_enable_extracellular"]
+
+            if "record_rxd_species_concentration_all_compartments" in self.sim_info and self.use_rxd_neuromodulation:
 
                 rec_info = self.sim_info["record_rxd_species_concentration_all_compartments"]
 
@@ -323,6 +329,11 @@ def setup_parse_sim_info(self):
                     for rxd_neuron_id in record_rxd_neuron_id:
                         self.add_rxd_internal_concentration_recording_all(record_rx_species, rxd_neuron_id)
 
+            if "record_rxd_species_all" in self.sim_info and self.use_rxd_neuromodulation:
+                rxd_record_neuron_id = self.sim_info["record_rxd_species_all"]
+
+                self.add_rxd_internal_concentration_recording_all_species(neuron_id=rxd_record_neuron_id)
+
             if "record_density_mechanism" in self.sim_info:
                 record_info = self.sim_info["record_density_mechanism"]
 
@@ -648,7 +659,8 @@ def setup_neurons(self):
                                                reaction_diffusion_file=reaction_diffusion_file,
                                                parameter_key=parameter_key,
                                                morphology_key=morphology_key,
-                                               modulation_key=modulation_key)
+                                               modulation_key=modulation_key,
+                                               use_rxd_neuromodulation=self.use_rxd_neuromodulation)
 
                 # Register ID as belonging to this worker node
                 try:
@@ -1190,7 +1202,7 @@ def add_synapse(self, cell_id_source, cell_id_dest, dend_compartment, section_id
                     import pdb
                     pdb.set_trace()
 
-            if "RxD" in par_set:
+            if "RxD" in par_set and self.use_rxd_neuromodulation:
                 species_name = par_set["RxD"]["species_name"]
                 region = par_set["RxD"]["region"]
 
@@ -1412,7 +1424,7 @@ def add_external_input(self, input_file=None):
 
     def get_rxd_external_input_parameters(self, neuron_input):
 
-        if "RxD" in neuron_input.attrs.keys():
+        if "RxD" in neuron_input.attrs.keys() and self.use_rxd_neuromodulation:
 
             rxd_dict = json.loads(neuron_input.attrs["RxD"])
 
@@ -1849,6 +1861,10 @@ def add_synapse_current_recording(self, source_id, dest_id):
 
     def add_rxd_concentration_recording(self, species: str, neuron_id: int, region, sec_id, sec_x):
 
+        if not self.use_rxd_neuromodulation:
+            print(f"add_rxd_concentration_recording:  not enabled, ignoring recording of {species} in neuron {neuron_id}")
+            return
+
         if sec_id == -1:
             sec_type = "soma"
         elif sec_id >= 0:
@@ -1881,6 +1897,10 @@ def add_rxd_internal_concentration_recording_all(self, species, neuron_id):
         if neuron_id not in self.neuron_id:
             return
 
+        if not self.use_rxd_neuromodulation:
+            print(f"add_rxd_internal_concentration_recording_all:  not enabled, ignoring recording of {species} in neuron {neuron_id}")
+            return
+
         # Add soma
         self.add_rxd_concentration_recording(species, neuron_id, "soma_internal", "soma", -1, 0.5)
 
@@ -1889,11 +1909,23 @@ def add_rxd_internal_concentration_recording_all(self, species, neuron_id):
                 f"Internal error, assumed {sid} was section id of {sec.name()}"
             self.add_rxd_concentration_recording(species, neuron_id, "dend_internal", "dend", sid, 0.5)
 
-    def add_rxd_internal_concentration_recording_all_species(self, neuron_id):
+    def add_rxd_internal_concentration_recording_all_species(self, neuron_id, quiet=False):
+
+        if not quiet:
+            self.write_log(f"Recording all RxD species from neurons: {neuron_id}")
+
+        if isinstance(neuron_id, (list, np.ndarray)):
+            for nid in neuron_id:
+                self.add_rxd_internal_concentration_recording_all_species(neuron_id=nid, quiet=True)
+            return
 
         if neuron_id not in self.neuron_id:
             return
 
+        if not self.use_rxd_neuromodulation:
+            print(f"add_rxd_internal_concentration_recording_all_species:  not enabled, ignoring recording of neuron {neuron_id}")
+            return
+
         for species in self.neurons[neuron_id].modulation.species.keys():
 
             # Add soma