/

figures/MAM2EBRAINS/.ipynb_checkpoints/M2E_visualize_interareal_connectivity-checkpoint.py

@@ -18,59 +18,8 @@ from scipy import stats
 # rc_file('plotstyle.rc')
 
 def visualize_interareal_connectivity(M):
-    scale_down_to = 1
-    cc_weights_factor = 1.0
-    areas_simulated = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 
-                       'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 
-                       'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 
-                       'STPa', '46', 'AITd', 'TH']
-    replace_non_simulated_areas = 'het_poisson_stat'
-    
-    conn_params = {
-        'replace_non_simulated_areas': 'het_poisson_stat',
-        'g': -11.,
-        'K_stable': 'K_stable.npy',
-        'fac_nu_ext_TH': 1.2,
-        'fac_nu_ext_5E': 1.125,
-        'fac_nu_ext_6E': 1.41666667,
-        'av_indegree_V1': 3950.
-    }
-
-    input_params = {
-        'rate_ext': 10.
-    } 
-
-    neuron_params = {
-        'V0_mean': -150.,
-        'V0_sd': 50.}
-
-    network_params = {
-        'N_scaling': scale_down_to, # Scaling of population sizes, by default: 1.
-        'K_scaling': scale_down_to, # Scaling of indegrees, by default: 1.
-        'fullscale_rates': 'tests/fullscale_rates.json',
-        'input_params': input_params, # Input parameters
-        'connection_params': conn_params, # Connection parameters
-        'neuron_params': neuron_params # Neuron parameters
-    } 
-
-    sim_params = {
-        'areas_simulated': areas_simulated,
-        't_sim': 2000., # Simulated time (in ms), by default: 10.0
-        'num_processes': 1, # The number of MPI processes, by default: 1
-        'local_num_threads': 1, # The number of threads per MPI process, by default: 1
-        'recording_dict': {'record_vm': False},
-        'rng_seed': 1  # global random seed
-    }
-
-    theory_params = {
-        'dt': 0.1 # The time step of the mean-field theory integration, by default: 0.01
-    } 
-
-    M_full_scale = MultiAreaModel(network_params, 
-                                  simulation=True,
-                                  sim_spec=sim_params,
-                                  theory=True,
-                                  theory_spec=theory_params)
+    # full-scale model
+    M_full_scale = MultiAreaModel()
     
     """
     Figure layout

figures/MAM2EBRAINS/M2E_visualize_interareal_connectivity.py

@@ -18,59 +18,8 @@ from scipy import stats
 # rc_file('plotstyle.rc')
 
 def visualize_interareal_connectivity(M):
-    scale_down_to = 1
-    cc_weights_factor = 1.0
-    areas_simulated = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 
-                       'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 
-                       'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 
-                       'STPa', '46', 'AITd', 'TH']
-    replace_non_simulated_areas = 'het_poisson_stat'
-    
-    conn_params = {
-        'replace_non_simulated_areas': 'het_poisson_stat',
-        'g': -11.,
-        'K_stable': 'K_stable.npy',
-        'fac_nu_ext_TH': 1.2,
-        'fac_nu_ext_5E': 1.125,
-        'fac_nu_ext_6E': 1.41666667,
-        'av_indegree_V1': 3950.
-    }
-
-    input_params = {
-        'rate_ext': 10.
-    } 
-
-    neuron_params = {
-        'V0_mean': -150.,
-        'V0_sd': 50.}
-
-    network_params = {
-        'N_scaling': scale_down_to, # Scaling of population sizes, by default: 1.
-        'K_scaling': scale_down_to, # Scaling of indegrees, by default: 1.
-        'fullscale_rates': 'tests/fullscale_rates.json',
-        'input_params': input_params, # Input parameters
-        'connection_params': conn_params, # Connection parameters
-        'neuron_params': neuron_params # Neuron parameters
-    } 
-
-    sim_params = {
-        'areas_simulated': areas_simulated,
-        't_sim': 2000., # Simulated time (in ms), by default: 10.0
-        'num_processes': 1, # The number of MPI processes, by default: 1
-        'local_num_threads': 1, # The number of threads per MPI process, by default: 1
-        'recording_dict': {'record_vm': False},
-        'rng_seed': 1  # global random seed
-    }
-
-    theory_params = {
-        'dt': 0.1 # The time step of the mean-field theory integration, by default: 0.01
-    } 
-
-    M_full_scale = MultiAreaModel(network_params, 
-                                  simulation=True,
-                                  sim_spec=sim_params,
-                                  theory=True,
-                                  theory_spec=theory_params)
+    # full-scale model
+    M_full_scale = MultiAreaModel()
     
     """
     Figure layout