temporary PR before moving ET branch

examples/tvb_netpyne/__init__.py

@@ -0,0 +1 @@
+pip3 import tvb

examples/tvb_netpyne/models/ET_wilson_cowan.py

@@ -0,0 +1,167 @@
+# -*- coding: utf-8 -*-
+
+from tvb_multiscale.tvb_netpyne.interfaces.models.wilson_cowan import WilsonCowanTVBNetpyneInterfaceBuilder
+from tvb_multiscale.tvb_netpyne.netpyne_models.models.wilson_cowan import WilsonCowanBuilder
+from tvb_multiscale.tvb_netpyne.netpyne_models.models.thalamic_VIM_exc_io_inh_i import WilsonCowanThalamicVIMBuilder
+
+from examples.tvb_netpyne.example import main_example
+from examples.models.wilson_cowan import wilson_cowan_example as wilson_cowan_example_base
+# 0------
+from IPython.display import Image, display
+import os
+from collections import OrderedDict
+import time
+import numpy as np
+from tvb.basic.profile import TvbProfile
+TvbProfile.set_profile(TvbProfile.LIBRARY_PROFILE)
+# 1  ------
+from tvb.datatypes.connectivity import Connectivity
+from tvb.simulator.integrators import HeunStochastic
+from tvb.simulator.monitors import Raw  # , Bold, EEG
+
+from tvb_multiscale.tvb_netpyne.config import *
+
+def wilson_cowan_example(**kwargs):
+    params = {
+        "simulation_length": 500,
+        # "model_params": {"lamda": 0.5}
+    }
+
+    #(0) Setup stuff
+    # For a minimal example, select:
+    N_REGIONS = None # total TVB brain regions
+    NETPYNE_NODES_INDS = np.array([0, 1])  # the brain region nodes to place spiking networks from [0, N_REGIONS-1] interval
+    N_NEURONS = 100 # number of neurons per spiking population
+
+    # Interface basic configurations:
+    INTERFACE_MODEL = "RATE"  # The only available option for NetPyNE so far
+    INTERFACE_COUPLING_MODE = "spikeNet"  # "spikeNet" # "TVB"
+    # -----------------------------------------------
+    work_path = os.getcwd()
+    outputs_path = os.path.join(work_path, "outputs/NetPyNE_wilsoncowan_%s_%s" % (INTERFACE_MODEL, INTERFACE_COUPLING_MODE))
+
+    config = Config(output_base=outputs_path)
+    config.figures.SHOW_FLAG = True 
+    config.figures.SAVE_FLAG = True
+    config.figures.FIG_FORMAT = 'png'
+    config.figures.DEFAULT_SIZE= config.figures.NOTEBOOK_SIZE
+    FIGSIZE = config.figures.DEFAULT_SIZE
+
+    from tvb_multiscale.core.plot.plotter import Plotter
+    plotter = Plotter(config.figures)
+
+    #1. Load structural data (minimally a TVB connectivity) & prepare TVB simulator (region mean field model, integrator, monitors etc)
+    # This would run on TVB only before creating any multiscale cosimulation interface connections.
+    from tvb_multiscale.core.tvb.cosimulator.models.reduced_wong_wang_exc_io_inh_i import ReducedWongWangExcIOInhI
+
+    # Load full TVB connectome connectivity: Glasser parcellation
+    data_path = os.path.expanduser("~/packages/tvb-multiscale/examples/tvb_netpyne/models")
+    conn_path = os.path.join(data_path, "temp_connectivity_Glasser")
+
+    w = np.loadtxt(os.path.join(conn_path, "weights.txt")) #np.zeros((11,11))
+    c = np.loadtxt(os.path.join(conn_path, "centres.txt"), usecols=range(1,3))
+    rl = np.loadtxt(os.path.join(conn_path, "region_labels.txt"), dtype="str", usecols = 1)
+    t = np.loadtxt(os.path.join(conn_path, "tract_lengths.txt"))
+
+    ######## PETERSEN ATLAS ############
+    #doesn't do anything for now, except change variable name used from this point onwards
+    # later, if we add additional connections from e.g. another atlas, we can add/modify/merge the values/labels and specify the new filenames here
+    wTVB = w 
+    cTVB = c
+    rlTVB = rl
+    tTVB = t
+    #####################################
+
+    number_of_regions = len(rlTVB)
+    speed = np.array([4.0])
+
+    connTVB = Connectivity(region_labels=rlTVB, weights=wTVB, centres=cTVB, tract_lengths=tTVB, speed=speed)
+
+    # -------------- Pick a minimal brain of only the first N_REGIONS regions: ----------------
+    if N_REGIONS is not None:
+        connTVB.number_of_regions = N_REGIONS
+        connTVB.region_labels = connTVB.region_labels[:N_REGIONS]
+        connTVB.centres = connTVB.centres[:N_REGIONS]
+        connTVB.areas = connTVB.areas[:N_REGIONS]
+        connTVB.orientations = connTVB.orientations[:N_REGIONS]
+        connTVB.hemispheres = connTVB.hemispheres[:N_REGIONS]
+        connTVB.cortical = connTVB.cortical[:N_REGIONS]
+        connTVB.weights = connTVB.weights[:N_REGIONS][:, :N_REGIONS]
+        connTVB.tract_lengths = connTVB.tract_lengths[:N_REGIONS][:, :N_REGIONS]
+    # -----------------------------------------------------------------------------------------
+
+    # Remove diagonal self-connections:
+    np.fill_diagonal(connTVB.weights, 0.0)
+
+    # Normalize connectivity weights
+    connTVB.weights = connTVB.scaled_weights(mode="region")
+    connTVB.weights /= np.percentile(connTVB.weights, 99)
+
+    # CoSimulator builder--------------------------------
+    from tvb_multiscale.core.tvb.cosimulator.cosimulator_builder import CoSimulatorSerialBuilder
+
+    simulator_builder = CoSimulatorSerialBuilder()
+    simulator_builder.config = config
+    simulator_builder.model = ThalamicVIMBuilder()
+    simulator_builder.connectivity = connTVB
+    simulator_builder.model_params = model_params
+    simulator_builder.initial_conditions = np.array([0.0])
+
+    simulator_builder.configure()
+    simulator_builder.print_summary_info_details(recursive=1)
+
+    simulator = simulator_builder.build()
+    # -----
+
+    simulator.configure()
+
+
+    simulator.print_summary_info_details(recursive=1)
+
+    # Plot TVB connectome:
+    plotter.plot_tvb_connectivity(simulator.connectivity)
+
+
+    #(2) NetPyNE Network Builder
+    netpyne_network_builder = WilsonCowanThalamicVIMBuilder()
+
+    #change connectivity to Glasser
+    kwargs['connectivity']='/home/docker/packages/tvb_data/tvb_data/connectivity/connectivity_Glasser.zip'
+    kwargs.update(params)
+
+    netpyne_network_builder.tvb_to_spiking_dt_ratio = 2 # 2 NetPyNE integration steps for 1 TVB integration step
+    netpyne_network_builder.monitor_period = 1.0
+
+    #TVB (Glasser parcellation) regions to be substituted with spiking populations (netpyne pops)
+    #M1R (8), PMC (8), brainstem (379), thalamusR (371), cerebellumL (361), muscle (NA)   ###DEFAULT[50, 58,] #50:precentral_R, 58:superiofrontal_R (taken as temp proxy for premotor cortex)
+
+    netpyne_network_builder.primary_motor_cortex_R = 8
+    netpyne_network_builder.cerebellar_cortex_L = 361
+    netpyne_network_builder.thalamus_R = 371
+    netpyne_network_builder.brainstem = 379
+
+    params["spiking_proxy_inds"] = [
+        netpyne_network_builder.primary_motor_cortex_R,
+        netpyne_network_builder.cerebellar_cortex_L,
+        netpyne_network_builder.thalamus_R,
+        netpyne_network_builder.brainstem,
+    ]
+    kwargs.update(params)
+
+    tvb_netpyne_interface_builder = WilsonCowanTVBNetpyneInterfaceBuilder()
+
+    # input/output interfaces
+    import numpy as np
+    tvb_netpyne_interface_builder.default_coupling_mode == "spikeNet"
+    if tvb_netpyne_interface_builder.default_coupling_mode == "spikeNet":
+        pass
+        # coupling is computing in NetPyNE, we need as many TVB proxies 
+        # as TVB regions coupling to STN and Striatum
+        #??? proxy_inds = np.unique(np.concatenate([CTXtoSTNinds, CTXtoSNinds]))    
+
+
+    return main_example(wilson_cowan_example_base, netpyne_network_builder, tvb_netpyne_interface_builder, **kwargs)
+
+
+if __name__ == "__main__":
+    wilson_cowan_example()

examples/tvb_netpyne/models/red_wong_wang.py

@@ -1,4 +1,5 @@
 from tvb_multiscale.tvb_netpyne.netpyne_models.models.default_exc_io_inh_i import DefaultExcIOInhIBuilder
+from tvb_multiscale.tvb_netpyne.netpyne_models.models.thalamic_VIM_exc_io_inh_i import ThalamicVIMBuilder
 from tvb_multiscale.tvb_netpyne.interfaces.models.default import RedWongWangExcIOInhITVBNetpyneInterfaceBuilder
 
 from examples.tvb_netpyne.example import main_example
@@ -10,8 +11,12 @@ def excio_inhi_example(**kwargs):
         # "model_params": {"lamda": 0.5}
     }
 
-    netpyne_network_builder = DefaultExcIOInhIBuilder()
-    params["spiking_proxy_inds"] = [0, 1]
+    # netpyne_network_builder = DefaultExcIOInhIBuilder()
+    # params["spiking_proxy_inds"] = [0, 1]
+
+    netpyne_network_builder = ThalamicVIMBuilder()
+    params["spiking_proxy_inds"] = [46]
+
 
     kwargs.update(params)