Changeset 506

Timestamp:

11/19/08 16:08:43 (2 months ago)

Author:

apdavison

Message:

Added a measure of the difference between Vm traces to the test_synaptic_integration.py script.

Files:

• trunk/test/explore_space.py (modified) (2 diffs)
• trunk/test/simple_network.py (modified) (1 diff)
• trunk/test/test_synaptic_integration.py (modified) (3 diffs)

trunk/test/explore_space.py

@@ -3 +3 @@
-object. If run on a cluster, the runs will be distributed across different nodes.
-
-R
+For a full description of usage, r
-
-python3 explore_space.py --help
-
-for a full description of usage.
-
-"""
@@ -77 +75 @@
-    test_module.parameters = test_module.load_parameters(job.args[0])
-    print ds.retrieve(test_module, 'distances')
+    print ds.retrieve(test_module, 'vm_diff')
-    ds.store(test_module, 'output', job.output)
-

trunk/test/simple_network.py

@@ -115 +115 @@
-                                           dt=self.parameters.system.timestep,
-                                           t_start=min(vm_arr[:,1]),
-
++self.parameters.system.timestep
-        return vm
-    

trunk/test/test_synaptic_integration.py

@@ -35 +35 @@
-from NeuroTools.stgen import StGen
-from NeuroTools.plotting import SimpleMultiplot
+from NeuroTools.signals import VmList
-from pyNN.utility import MultiSim, init_logging
-from simple_network import SimpleNetwork
@@ -81 +82 @@
-    return distances
-
+def calc_Vm_diff(vm_data):
+    mean_stdev = {}
+    for sim1 in sim_list:
+        mean_stdev[sim1.__name__] = {}
+        v1 = vm_data[sim1.__name__]['post'][0]
+        for sim2 in sim_list:
+            v2 = vm_data[sim2.__name__]['post'][0]
+            vmlist = VmList([],[], dt=v1.dt)
+            # NEST seems to be missing some values at the start and end of the trace,
+            # so we trim all signals to the minimum length. This should be fixed in PyNN
+            t_start = max(v1.t_start, v2.t_start)
+            t_stop = min(v1.t_stop, v2.t_stop)
+            v1 = v1.time_slice(t_start, t_stop)
+            v2 = v2.time_slice(t_start, t_stop)
+            
+            vmlist.append(0, v1)
+            vmlist.append(1, v2)
+            mean_stdev[sim1.__name__][sim2.__name__] = vmlist.std().mean()
+    return mean_stdev
+
-def plot_figure(spike_data, vm_data, model_parameters):
-    fig = SimpleMultiplot(2, 1, xlabel="Time (ms)")
@@ -121 +142 @@
-    distances = calc_distances(spike_data)
-    print distances
+    vm_diff = calc_Vm_diff(vm_data)
+    print vm_diff
-
-    ds = datastore.ShelveDataStore(root_dir=parameters.results_dir, key_generator=datastore.keygenerators.hash_pickle)
-    this = sys.modules[__name__]
-    ds.store(this, 'distances', distances)
+    ds.store(this, 'vm_diff', vm_diff)
-    ds.store(this, 'spike_data', spike_data)
-    ds.store(this, 'vm_data', vm_data)