/

.ipynb_checkpoints/run_simulation-checkpoint.py

+"""
+This script is used to run a simulation from the given command-line
+arguments:
+1. Label of the simulation
+2. Label of the network to be simulated
+
+It initializes the network class and then runs the simulate method of
+the simulation class instance.
+
+This script should be used in the `jobscript_template` defined in the
+config.py file. See config_template.py.
+"""
+
+import json
+import nest
+import os
+import sys
+
+from config import data_path
+from multiarea_model import MultiAreaModel
+
+label = sys.argv[1]
+network_label = sys.argv[2]
+fn = os.path.join(data_path,
+                  label,
+                  '_'.join(('custom_params',
+                            label,
+                           str(nest.Rank()))))
+with open(fn, 'r') as f:
+    custom_params = json.load(f)
+
+os.remove(fn)
+
+M = MultiAreaModel(network_label,
+                   simulation=True,
+                   sim_spec=custom_params['sim_params'])
+M.simulation.simulate()

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

@@ -189,10 +189,12 @@ def visualize_interareal_connectivity(M):
     y = np.arange(0, len(area_list[::-1]) + 1)
     X, Y = np.meshgrid(x, y)
 
-    ax.set_xticks([i + 0.5 for i in np.arange(0, len(area_list) + 1, 1)])
+    # ax.set_xticks([i + 0.5 for i in np.arange(0, len(area_list) + 1, 1)])
+    ax.set_xticks([i + 0.5 for i in np.arange(0, len(area_list), 1)])
     # ax.set_xticklabels(area_list, rotation=90, size=6.)
 
-    ax.set_yticks([i + 0.5 for i in np.arange(0, len(area_list) + 1, 1)])
+    # ax.set_yticks([i + 0.5 for i in np.arange(0, len(area_list) + 1, 1)])
+    ax.set_yticks([i + 0.5 for i in np.arange(0, len(area_list), 1)])
     # ax.set_yticklabels(area_list[::-1], size=6.)
 
     ax.set_ylabel('Target area')

figures/MAM2EBRAINS/M2E_visualize_interareal_connectivity.py

@@ -189,10 +189,12 @@ def visualize_interareal_connectivity(M):
     y = np.arange(0, len(area_list[::-1]) + 1)
     X, Y = np.meshgrid(x, y)
 
-    ax.set_xticks([i + 0.5 for i in np.arange(0, len(area_list) + 1, 1)])
+    # ax.set_xticks([i + 0.5 for i in np.arange(0, len(area_list) + 1, 1)])
+    ax.set_xticks([i + 0.5 for i in np.arange(0, len(area_list), 1)])
     # ax.set_xticklabels(area_list, rotation=90, size=6.)
 
-    ax.set_yticks([i + 0.5 for i in np.arange(0, len(area_list) + 1, 1)])
+    # ax.set_yticks([i + 0.5 for i in np.arange(0, len(area_list) + 1, 1)])
+    ax.set_yticks([i + 0.5 for i in np.arange(0, len(area_list), 1)])
     # ax.set_yticklabels(area_list[::-1], size=6.)
 
     ax.set_ylabel('Target area')