Comment out unnecessary stuff

demos/brunel_simulation/brunel_example.py

@@ -11,11 +11,10 @@ is not structured spatially.
 from copy import deepcopy
 from math import sqrt
 import numpy as np
-from mpl_toolkits.mplot3d import Axes3D
-import matplotlib.pyplot as plt
+# from mpl_toolkits.mplot3d import Axes3D
+# import matplotlib.pyplot as plt
 
 import nest
-import nest.raster_plot
 import nest.topology as tp
 
 
@@ -23,6 +22,7 @@ class Brunel3D:
 
     def __init__(self):
         self.layer_dict = {}
+        nest.SetKernelStatus({"local_num_threads": 1})
         nest.Install("streamingmodule")
         # nest.SetKernelStatus({'print_time': True})
 
@@ -196,70 +196,70 @@ class Brunel3D:
     def simulate(self):
         nest.Simulate(1000)
 
-    def plot_positions(self):
-        ex_pos = self.layers[0][1]['positions']
-        in_pos = self.layers[1][1]['positions']
-        fig = plt.figure()
-        ax = Axes3D(fig)
-        for c, m, positions in [('b', 'o', ex_pos), ('r', '^', in_pos)]:
-            ax.scatter([x for x, y, z in positions],
-                       [y for x, y, z in positions],
-                       [z for x, y, z in positions],
-                       c=c, marker=m)
-
-    def get_results(self):
-        mm = (self.layer_dict['Multimeter'][0] + 1,)
-        sd = (self.layer_dict['SpikeDetector'][0] + 1,)
-        mm_status = nest.GetStatus(mm)[0]
-        sd_status = nest.GetStatus(sd)[0]
-
-        nest.raster_plot.from_device(sd, hist=True)
-
-        senders = mm_status['events']['senders']
-        times = mm_status['events']['times']
-        v_m = mm_status['events']['V_m']
-        v_th = mm_status['events']['V_th']
-        step = int(max(senders)/100 + 1)  # Only plot results from some GIDs
-
-        mm_events = []
-        for i in range(1, max(senders) + 1, step):
-            if i in senders:
-                indices = np.argwhere(senders == i)
-                mm_events.append({'GID': i,
-                      'times': [times[n] for n in indices],
-                      'V_m': [v_m[n] for n in indices],
-                      'V_th': [v_th[n] for n in indices]})
-
-        return {'multimeter': mm_events,
-                'spike_detector': nest.GetStatus(sd)[0]}
-
-
-if __name__ == '__main__':
-    nest.ResetKernel()
-
-    print('Making specifications')
-    brunel = Brunel3D()
-    brunel.make_layer_specs()
-    brunel.make_connection_specs()
-
-    print('Making layers')
-    brunel.make_layers()
-    nest.topology.DumpLayerNodes([l[0] for l in brunel.layer_dict.values()][:2],
-                                     'brunel_nodes.txt')
-
-    print('Making connections')
-    brunel.make_connections()
-
-    brunel.simulate()
-
-    print('Getting results')
-    brunel.plot_positions()
-    results = brunel.get_results()
-
-    for value in ['V_m', 'V_th']:
-        plt.figure()
-        for n in results['multimeter'][::20]:
-            plt.plot(n['times'], n[value], label='{}'.format(n['GID']))
-            plt.legend()
-        plt.title(value)
-    plt.show()
+    # def plot_positions(self):
+    #     ex_pos = self.layers[0][1]['positions']
+    #     in_pos = self.layers[1][1]['positions']
+    #     fig = plt.figure()
+    #     ax = Axes3D(fig)
+    #     for c, m, positions in [('b', 'o', ex_pos), ('r', '^', in_pos)]:
+    #         ax.scatter([x for x, y, z in positions],
+    #                    [y for x, y, z in positions],
+    #                    [z for x, y, z in positions],
+    #                    c=c, marker=m)
+
+    # def get_results(self):
+    #     mm = (self.layer_dict['Multimeter'][0] + 1,)
+    #     sd = (self.layer_dict['SpikeDetector'][0] + 1,)
+    #     mm_status = nest.GetStatus(mm)[0]
+    #     sd_status = nest.GetStatus(sd)[0]
+
+    #     nest.raster_plot.from_device(sd, hist=True)
+
+    #     senders = mm_status['events']['senders']
+    #     times = mm_status['events']['times']
+    #     v_m = mm_status['events']['V_m']
+    #     v_th = mm_status['events']['V_th']
+    #     step = int(max(senders)/100 + 1)  # Only plot results from some GIDs
+
+    #     mm_events = []
+    #     for i in range(1, max(senders) + 1, step):
+    #         if i in senders:
+    #             indices = np.argwhere(senders == i)
+    #             mm_events.append({'GID': i,
+    #                   'times': [times[n] for n in indices],
+    #                   'V_m': [v_m[n] for n in indices],
+    #                   'V_th': [v_th[n] for n in indices]})
+
+    #     return {'multimeter': mm_events,
+    #             'spike_detector': nest.GetStatus(sd)[0]}
+
+
+# if __name__ == '__main__':
+#     nest.ResetKernel()
+
+#     print('Making specifications')
+#     brunel = Brunel3D()
+#     brunel.make_layer_specs()
+#     brunel.make_connection_specs()
+
+#     print('Making layers')
+#     brunel.make_layers()
+#     nest.topology.DumpLayerNodes([l[0] for l in brunel.layer_dict.values()][:2],
+#                                      'brunel_nodes.txt')
+
+#     print('Making connections')
+#     brunel.make_connections()
+
+#     brunel.simulate()
+
+#     print('Getting results')
+#     brunel.plot_positions()
+#     results = brunel.get_results()
+
+#     for value in ['V_m', 'V_th']:
+#         plt.figure()
+#         for n in results['multimeter'][::20]:
+#             plt.plot(n['times'], n[value], label='{}'.format(n['GID']))
+#             plt.legend()
+#         plt.title(value)
+#     plt.show()