Changeset 1030

Timestamp:

12/13/11 15:04:42 (5 months ago)

Author:

apdavison

Message:

In neo_output branch, fixed some bugs, started updating examples

Location:

branches/neo_output

Files:

• examples/IF_cond_exp.py (modified) (1 diff)
• examples/VAbenchmarks.py (modified) (2 diffs)
• examples/VAbenchmarks2.py (modified) (3 diffs)
• examples/VAbenchmarks3.py (modified) (3 diffs)
• examples/simpleNetwork.py (modified) (1 diff)
• examples/simpleRandomNetwork.py (modified) (2 diffs)
• src/common/populations.py (modified) (2 diffs)
• src/common/projections.py (modified) (1 diff)
• src/connectors.py (modified) (1 diff)
• src/neuron/cells.py (modified) (2 diffs)
• src/neuron/recording.py (modified) (2 diffs)
• src/recording/__init__.py (modified) (3 diffs)

branches/neo_output/examples/IF_cond_exp.py

@@ -35 +35 @@
 connI = connect(spike_sourceI, ifcell, weight=0.02, synapse_type ='inhibitory',delay=4.0)
     
-record_v(ifcell, "Results/IF_cond_exp_%s.v" % simulator_name)
+record_v(ifcell, "Results/IF_cond_exp_%s.h5" % simulator_name)
 #try:
-record_gsyn(ifcell, "Results/IF_cond_exp_%s.gsyn" % simulator_name)
+#record_gsyn(ifcell, "Results/IF_cond_exp_%s.gsyn" % simulator_name)
 #except (NotImplementedError, RecordingError):
 #    pass

branches/neo_output/examples/VAbenchmarks.py

@@ -168 +168 @@
 simCPUTime = timer.diff()
 
-E_count = exc_cells.meanSpikeCount()
-I_count = inh_cells.meanSpikeCount()
+E_count = exc_cells.mean_spike_count()
+I_count = inh_cells.mean_spike_count()
 
 # === Print results to file ====================================================
@@ -178 +178 @@
     os.mkdir('Results')
 
-exc_cells.write_data(PyNNTextIO("Results/VAbenchmark_%s_exc_%s_np%d.ras" % (benchmark, simulator_name, np)), 'spikes')
-inh_cells.write_data(PyNNTextIO("Results/VAbenchmark_%s_inh_%s_np%d.ras" % (benchmark, simulator_name, np)), 'spikes')
-exc_cells[[0, 1]].write_data(PyNNTextIO("Results/VAbenchmark_%s_exc_%s_np%d.v" % (benchmark, simulator_name, np)), 'v')
+exc_cells.write_data("Results/VAbenchmark_%s_exc_%s_np%d.txt" % (benchmark, simulator_name, np))
+inh_cells.write_data("Results/VAbenchmark_%s_inh_%s_np%d.txt" % (benchmark, simulator_name, np))
 writeCPUTime = timer.diff()
 

branches/neo_output/examples/VAbenchmarks2.py

@@ -148 +148 @@
 # === Setup recording ==========================================================
 print "%s Setting up recording..." % node_id
-all_cells.record()
-exc_cells[[0, 1]].record_v()
+all_cells.record('spikes')
+exc_cells[[0, 1]].record('v')
 
 buildCPUTime = timer.diff()
@@ -167 +167 @@
 simCPUTime = timer.diff()
 
-E_count = exc_cells.meanSpikeCount()
-I_count = inh_cells.meanSpikeCount()
+E_count = exc_cells.mean_spike_count()
+I_count = inh_cells.mean_spike_count()
 
 # === Print results to file ====================================================
@@ -177 +177 @@
     os.mkdir('Results')
 
-exc_cells.printSpikes("Results/VAbenchmark_%s_exc_%s_np%d.ras" % (benchmark, simulator_name, np))
-inh_cells.printSpikes("Results/VAbenchmark_%s_inh_%s_np%d.ras" % (benchmark, simulator_name, np))
-exc_cells[[0, 1]].print_v("Results/VAbenchmark_%s_exc_%s_np%d.v" % (benchmark, simulator_name, np))
+all_cells.write_data("Results/VAbenchmark_%s_%s_np%d.txt" % (benchmark, simulator_name, np))
+
 writeCPUTime = timer.diff()
 

branches/neo_output/examples/VAbenchmarks3.py

@@ -149 +149 @@
 # === Setup recording ==========================================================
 print "%s Setting up recording..." % node_id
-all_cells.record()
-exc_cells[[0, 1]].record_v()
+all_cells.record('spikes')
+exc_cells[[0, 1]].record('v')
 
 buildCPUTime = timer.diff()
@@ -168 +168 @@
 simCPUTime = timer.diff()
 
-E_count = exc_cells.meanSpikeCount()
-I_count = inh_cells.meanSpikeCount()
+E_count = exc_cells.mean_spike_count()
+I_count = inh_cells.mean_spike_count()
 
 # === Print results to file ====================================================
@@ -178 +178 @@
     os.mkdir('Results')
 
-exc_cells.printSpikes("Results/VAbenchmark_%s_exc_%s_np%d.ras" % (benchmark, simulator_name, np))
-inh_cells.printSpikes("Results/VAbenchmark_%s_inh_%s_np%d.ras" % (benchmark, simulator_name, np))
-exc_cells[[0, 1]].print_v("Results/VAbenchmark_%s_exc_%s_np%d.v" % (benchmark, simulator_name, np))
+all_cells.write_data("Results/VAbenchmark_%s_%s_np%d.txt" % (benchmark, simulator_name, np))
+
 writeCPUTime = timer.diff()
 

branches/neo_output/examples/simpleNetwork.py

@@ -33 +33 @@
 projection.setWeights(1.0)
 
-input_population.record()
-output_population.record()
-output_population.record_v()
+input_population.record('spikes')
+output_population.record(('spikes', 'v'))
 
 run(tstop)
 
-output_population.printSpikes("Results/simpleNetwork_output_%s.ras" % simulator_name)
-input_population.printSpikes("Results/simpleNetwork_input_%s.ras" % simulator_name)
-output_population.print_v("Results/simpleNetwork_%s.v" % simulator_name)
+output_population.write_data("Results/simpleNetwork_output_%s.h5" % simulator_name)
+input_population.write_data("Results/simpleNetwork_input_%s.h5" % simulator_name)
 
 end()

branches/neo_output/examples/simpleRandomNetwork.py

@@ -50 +50 @@
 projection.saveConnections('%s.conn' % file_stem)
 
-input_population.record()
-output_population.record()
-output_population.sample(n_record, rng).record_v()
+input_population.record('spikes')
+output_population.record('spikes')
+output_population.sample(n_record, rng).record('v')
 
 print "[%d] Running simulation" % node
@@ -58 +58 @@
 
 print "[%d] Writing spikes to disk" % node
-output_population.printSpikes('%s_output.ras' % file_stem)
-input_population.printSpikes('%s_input.ras' % file_stem)
+output_population.write_data('%s_output.ras' % file_stem, 'spikes')
+input_population.write_data('%s_input.ras' % file_stem)
 print "[%d] Writing Vm to disk" % node
-output_population.print_v('%s.v' % file_stem)
+output_population.write_data('%s.v' % file_stem, 'v')
 
 print "[%d] Finishing" % node

branches/neo_output/src/common/populations.py

@@ -14 +14 @@
 import tempfile
 from pyNN import random, recording, errors, standardmodels, core, space, descriptions
-from pyNN.recording import files
 from itertools import chain
 
@@ -501 +500 @@
         simulated on the local node.
         """
-        self.recorder.get(variables, gather, self.record_filter)
+        return self.recorder.get(variables, gather, self.record_filter)
 
     @deprecated("write_data(file, 'spikes')")

branches/neo_output/src/common/projections.py

@@ -11 +11 @@
 import operator
 from pyNN import random, recording, errors, models, core, descriptions
-from pyNN.recording import files
 from populations import BasePopulation, Assembly, is_conductance
 

branches/neo_output/src/connectors.py

@@ -12 +12 @@
 from pyNN import errors, common, core, random, utility, recording, descriptions
 from pyNN.space import Space
-from pyNN.recording import files
+#from pyNN.recording import files
 from pyNN.random import RandomDistribution
 from numpy import arccos, arcsin, arctan, arctan2, ceil, cos, cosh, e, exp, \

branches/neo_output/src/neuron/cells.py

@@ -288 +288 @@
         # insert Brette-Gerstner spike mechanism
         self.adexp = h.AdExpIF(0.5, sec=self)
-        self.source = self.seg._ref_v
+        self.source = self.adexp
         
         self.parameter_names = ['c_m', 'tau_m', 'v_rest', 'v_thresh', 't_refrac',
@@ -330 +330 @@
     def record(self, active):
         if active:
-            self.rec = h.NetCon(self.source, None,
+            self.rec = h.NetCon(self.seg._ref_v, None,
                                 self.get_threshold(), 0.0, 0.0,
                                 sec=self)

branches/neo_output/src/neuron/recording.py

@@ -144 +144 @@
                     get_signal = lambda id: id._cell.gsyn_trace['inhibitory']
                 else:
-                    signal = lambda id: id._cell.traces[variable]
+                    get_signal = lambda id: id._cell.traces[variable]
                 segment.analogsignals.extend(
                     neo.AnalogSignal(get_signal(id), # assuming not using cvode, otherwise need to use IrregularlySampledAnalogSignal
@@ -154 +154 @@
                                      source_id=int(id))
                     for id in self.filter_recorded(variable, filter_ids))
-                assert segment.analogsignals[0].t_stop - simulator.state.t*pq.ms < simulator.state.dt*pq.ms
+                assert segment.analogsignals[0].t_stop - simulator.state.t*pq.ms < 2*simulator.state.dt*pq.ms
                 # need to add `Unit` and `RecordingChannel` objects
         return segment

branches/neo_output/src/recording/__init__.py

@@ -90 +90 @@
 def normalize_variables_arg(variables):
     """If variables is a single string, encapsulate it in a list."""
-    if isinstance(variables, basestring):
+    if isinstance(variables, basestring) and variables != 'all':
         return [variables]
     else:
@@ -99 +99 @@
     Return a Neo IO instance, guessing the type based on the filename suffix.
     """
-    if os.path.splitext(filename)[0] in ('.txt', '.ras', '.v', '.gsyn'):
-        return neo.io.PyNNTextIO(filename)
+    extension = os.path.splitext(filename)[1]
+    if extension in ('.txt', '.ras', '.v', '.gsyn'):
+        return neo.io.PyNNTextIO(filename=filename)
+    elif extension in ('.h5',):
+        return neo.io.NeoHdf5IO(filename=filename)
     else: # function to be improved later
-        return neo.io.PyNNTextIO(filename)
+        raise Exception("file extension %s not supported" % extension)
 
 
@@ -167 +170 @@
         if self._simulator.state.mpi_rank == 0 or gather == False:
             # Open the output file, if necessary and write the data
-            logger.debug("Writing data to file %s" % file)
-            file.write(data)
+            logger.debug("Writing data to file %s" % io)
+            io.write(data)
     
     @property