Added test for net after simulation and resolved bug in cell response

hnn_core/network.py

@@ -1467,8 +1467,16 @@ def _get_cell_response_as_dict(cell_response):
     cell_response_data['spike_times'] = cell_response.spike_times
     cell_response_data['spike_gids'] = cell_response.spike_gids
     cell_response_data['spike_types'] = cell_response.spike_types
-    cell_response_data['vsec'] = cell_response.vsec
-    cell_response_data['isec'] = cell_response.isec
+    vsec_data = cell_response.vsec
+    cell_response_data['vsec'] = list()
+    for trial in vsec_data:
+        trial = dict((str(key), val) for key, val in trial.items())
+        cell_response_data['vsec'].append(trial)
+    isec_data = cell_response.isec
+    cell_response_data['isec'] = list()
+    for trial in isec_data:
+        trial = dict((str(key), val) for key, val in trial.items())
+        cell_response_data['isec'].append(trial)
     cell_response_data['times'] = cell_response.times
     return cell_response_data
 
@@ -1524,6 +1532,15 @@ def _read_cell_response(cell_response_data):
                                  spike_gids=cell_response_data['spike_gids'],
                                  spike_types=cell_response_data['spike_types'])
 
+    cell_response._times = cell_response_data['times']
+    cell_response._vsec = list()
+    for trial in cell_response_data['vsec']:
+        trial = dict((int(key), val) for key, val in trial.items())
+        cell_response._vsec.append(trial)
+    cell_response._isec = list()
+    for trial in cell_response_data['isec']:
+        trial = dict((int(key), val) for key, val in trial.items())
+        cell_response._isec.append(trial)
     return cell_response
 
 

hnn_core/tests/test_network.py

@@ -20,12 +20,26 @@
 def test_network_io(tmpdir):
     net_jones = jones_2009_model()
     add_erp_drives_to_jones_model(net_jones)
+    net_jones.add_tonic_bias(cell_type='L2_pyramidal', amplitude=1.0)
     # Writing network
     net_jones.write(tmpdir.join('net_jones.hdf5'))
     # Reading network
     net_jones_read = read_network(tmpdir.join('net_jones.hdf5'))
     assert net_jones == net_jones_read
 
+    # Add test to check weights are equal in connections and drives
+    # Run simulation and simulation output should be same (dipole)
+
+    # Simulating network
+    simulate_dipole(net_jones, tstop=5)
+    # Writing network
+    net_jones.write(tmpdir.join('net_jones_sim.hdf5'))
+    # Reading network
+    net_jones_sim = read_network(tmpdir.join('net_jones_sim.hdf5'))
+    assert net_jones == net_jones_sim
+    # For cell response vsec isec bug
+    assert net_jones.cell_response.vsec == net_jones_sim.cell_response.vsec
+
 
 def test_network_models():
     """"Test instantiations of the network object"""