Merge 4003741 into ad00b7a

NeuralEnsemble · Aug 4, 2017 · a369762 · a369762
2 parents ad00b7a + 4003741
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diff --git a/doc/backends/NeuroML.txt b/doc/backends/NeuroML.txt
@@ -2,3 +2,6 @@
 NeuroML
 =======
 
+A subset of models specified in PyNN can be exported into NeuroML 2 format.
+
+See https://github.com/NeuroML/NeuroML2/issues/73 for latest status.
diff --git a/examples/Potjans2014/network.py b/examples/Potjans2014/network.py
@@ -35,15 +35,15 @@ def setup(self, sim) :
 
                 # Spike recording
                 if record_fraction:
-                    num_spikes = round(this_pop.size * frac_record_spikes)
+                    num_spikes = int(round(this_pop.size * frac_record_spikes))
                 else:
                     num_spikes = n_record
                 this_pop[0:num_spikes].record('spikes')
 
                 # Membrane potential recording
                 if record_v:
                     if record_fraction:
-                        num_v = round(this_pop.size * frac_record_v)
+                        num_v = int(round(this_pop.size * frac_record_v))
 
                     else:
                         num_v = n_record_v

diff --git a/examples/Potjans2014/plotting.py b/examples/Potjans2014/plotting.py
@@ -53,7 +53,7 @@ def show_raster_bars(t_start, t_stop, n_rec, frac_to_plot, path):
         # Compute rates with all neurons
         rate = 1000 * len(t_spikes) / (t_stop - t_start) * 1 / float(n_rec[layer][pop])
         rates[i] = rate
-        print(pops[-i] + np.round(rate, 2))
+        #print(pops[-i] + np.round(rate, 2))
         # Reduce data for raster plot
         num_neurons = frac_to_plot * np.unique(ids).size
         t_spikes = t_spikes[np.where(ids < num_neurons + id_count + 1)[0]]

diff --git a/examples/Potjans2014/sim_params.py b/examples/Potjans2014/sim_params.py
@@ -8,7 +8,6 @@
       'timestep'        : 0.1,    # ms
       'threads'         : 1,
       'sim_duration'    : 1000.,  # ms
-      'min_delay'       : 0.1     # ms
     }
 }
 

diff --git a/pyNN/neuroml/__init__.py b/pyNN/neuroml/__init__.py
@@ -36,13 +36,13 @@ def list_standard_models():
 
 
 def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
-          max_delay=DEFAULT_MAX_DELAY, **extra_params):
+          **extra_params):
     """ Set up for saving cell models and network structure to NeuroML """
-    common.setup(timestep, min_delay, max_delay, **extra_params)
+    common.setup(timestep, min_delay, **extra_params)
     simulator.state.clear()
     simulator.state.dt = timestep  # move to common.setup?
     simulator.state.min_delay = min_delay
-    simulator.state.max_delay = max_delay
+    simulator.state.max_delay =  extra_params.get('max_delay', DEFAULT_MAX_DELAY)
     simulator.state.mpi_rank = extra_params.get('rank', 0)
     simulator.state.num_processes = extra_params.get('num_processes', 1)