updated README

examples/pattern_matching_showcase/experiment.py

@@ -29,7 +29,7 @@
 plotter = None
 exitcode = -1
 
-if not "TEST_MODE" in sys.argv[1:]:
+if "TEST_MODE" not in sys.argv[1:]:
     # don't create plotter in test mode
     try:
         dev0 = open("/dev/null", "w")

examples/pattern_matching_showcase/python/config.py

@@ -23,10 +23,7 @@
 #           GLOBAL CONFIGURATION FILE
 # ##########################################################
 
-import os
-import math
 import logging
-import time
 import sys
 
 

examples/pattern_matching_showcase/python/control_node.py

@@ -5,7 +5,6 @@
 
 import music
 import numpy as np
-from itertools import takewhile, dropwhile
 
 import experiment_utils.reward as reward
 
@@ -92,7 +91,7 @@ def _run_single_cycle(self, curr_time):
             self._current_pattern_id = self._next_pattern[1]
             try:
                 self._next_pattern = next(self._pattern_switch_gen)
-            except StopIteration as e:
+            except StopIteration:
                 self._next_pattern = None
 
             if spike_rate_buffer_clear_on_phase_change:

examples/pattern_matching_showcase/python/interface.py

@@ -46,9 +46,9 @@ def configure_detail_plot(data_source):
                      label="Output Activity (#neurons = {})".format(n_hidden_neurons))
 
     c1.add_plot(plots.AnalogSignalPlot(data_source,
-                                       ['activity_rate_{}'.format(i) for i in range(n_patterns)], label='Activity Rates',
+                                       ['activity_rate_{}'.format(i) for i in range(n_patterns)],
+                                       label='Activity Rates', colors=pattern_colors,
                                        legend=["Population #{}".format(i + 1) for i in range(n_patterns)],
-                                       colors=pattern_colors,
                                        y_ticks=[], y_lim=(0.0, 1000.0 / hidden_neuron_properties['dead_time'])))
 
     c1.add_plot(plots.AnalogSignalPlot(data_source,

examples/pattern_matching_showcase/python/network_node.py

@@ -5,7 +5,6 @@
 from config import *
 
 import nest
-import numpy as np
 from mpi4py import MPI
 
 from snn_utils.comm.music.node.nest import PyNestNode

examples/pattern_matching_showcase/python/snn_utils/comm/music/__init__.py

@@ -146,8 +146,8 @@ def buffer_event_input(self, n_buffers):
 
     def pre_cycle(self, curr_sim_time):
         for buffers, array_buffer in self._cont_array_buffers:
-            for i, buffer in enumerate(buffers):
-                buffer.append_value(curr_sim_time, array_buffer[i])
+            for i, buffer_ in enumerate(buffers):
+                buffer_.append_value(curr_sim_time, array_buffer[i])
 
     def post_cycle(self, curr_sim_time):
         pass
@@ -165,11 +165,11 @@ def _create_event_buffer(self):
         return buffer.WindowedSpikeBuffer(self._time_window)
 
     def post_cycle(self, curr_sim_time):
-        for buffer in self._all_buffers:
-            buffer.update(curr_sim_time)
+        for buffer_ in self._all_buffers:
+            buffer_.update(curr_sim_time)
 
 
 class SingleStepBuffer(BaseBuffer):
     def post_cycle(self, curr_sim_time):
-        for buffer in self._all_buffers:
-            buffer.clear()
+        for buffer_ in self._all_buffers:
+            buffer_.clear()

examples/pattern_matching_showcase/python/snn_utils/comm/zmq/__init__.py

@@ -56,18 +56,23 @@ def add_subscriber(self, host, port, callback, transport="tcp", prefix=u"", dese
         sock.setsockopt_string(zmq.SUBSCRIBE, prefix)
 
         if multipart:
-            def receive(): return sock.recv_multipart(zmq.NOBLOCK)
+            def receive():
+                return sock.recv_multipart(zmq.NOBLOCK)
         else:
-            def receive(): return sock.recv(zmq.NOBLOCK)
+            def receive():
+                return sock.recv(zmq.NOBLOCK)
 
         if deserialize is None:
-            def handle(): return callback(receive())
+            def handle():
+                return callback(receive())
         else:
             if multipart:
-                def handle(): return callback([elem if i == 0 else deserialize(elem)
-                                               for i, elem in enumerate(receive())])
+                def handle():
+                    return callback([elem if i == 0 else deserialize(elem)
+                                     for i, elem in enumerate(receive())])
             else:
-                def handle(): return callback(deserialize(receive()))
+                def handle():
+                    return callback(deserialize(receive()))
 
         self._handler[sock] = handle
         self._poller.register(sock, zmq.POLLIN)

examples/pattern_matching_showcase/python/snn_utils/plotter/data_provider.py

@@ -49,7 +49,7 @@ def extend_weight_data(self, key, df):
             self._weight_map[key] = df.copy()
         else:
             self._weight_map[key] = df.copy()
-            #self._weight_map[key] = self._weight_map[key].append(df)
+            # self._weight_map[key] = self._weight_map[key].append(df)
 
     def get_cont_data(self, keys, time_window=None):
         return [self._map[key] for key in keys]

examples/pattern_matching_showcase/python/zmq_proxy_node.py

@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import time
-
 import snn_utils.comm.music
 from config import *
 from snn_utils.comm.music.node import PyMusicNode

unittests/test_dbl_exp_neuron.py

@@ -53,7 +53,9 @@ def test_spore_exp_poisson_neuron(self):
         I_e = -3.0
 
         n = nest.Create('poisson_dbl_exp_neuron',  params={
-                        'tau_rise_exc': tau_rise_exc, 'tau_fall_exc': tau_fall_exc, 'tau_rise_inh': tau_rise_inh, 'tau_fall_inh': tau_fall_inh, 'I_e': I_e})
+                        'tau_rise_exc': tau_rise_exc, 'tau_fall_exc': tau_fall_exc,
+                        'tau_rise_inh': tau_rise_inh, 'tau_fall_inh': tau_fall_inh,
+                        'I_e': I_e})
 
         m = nest.Create('multimeter', params={'withtime': True, 'interval': 0.1, 'record_from': ['V_m']})
 
@@ -86,8 +88,11 @@ def test_spore_exp_poisson_neuron(self):
                 u_rise_inh += w_inh
                 u_fall_inh += w_inh
 
-            u_gd[int(t * (1.0 / delta_t))] = (tau_fall_exc / (tau_fall_exc - tau_rise_exc)) * (u_fall_exc -
-                                                                                               u_rise_exc) + (tau_fall_inh / (tau_fall_inh - tau_rise_inh)) * (u_fall_inh - u_rise_inh) + I_e
+            u_gd[int(t * (1.0 / delta_t))] = ((tau_fall_exc / (tau_fall_exc - tau_rise_exc)) *
+                                              (u_fall_exc - u_rise_exc) +
+                                              (tau_fall_inh / (tau_fall_inh - tau_rise_inh)) *
+                                              (u_fall_inh - u_rise_inh) +
+                                              I_e)
 
         # simulate
         nest.Simulate(100)

unittests/test_dbl_exp_neuron_rate.py

@@ -39,7 +39,9 @@ def do_exp_poisson_neuron_rate_test(self, I_e, target_rate):
         tau_fall_inh = 10.0
 
         n = nest.Create('poisson_dbl_exp_neuron',  params={
-                        'tau_rise_exc': tau_rise_exc, 'tau_fall_exc': tau_fall_exc, 'tau_rise_inh': tau_rise_inh, 'tau_fall_inh': tau_fall_inh, 'I_e': I_e})
+                        'tau_rise_exc': tau_rise_exc, 'tau_fall_exc': tau_fall_exc,
+                        'tau_rise_inh': tau_rise_inh, 'tau_fall_inh': tau_fall_inh,
+                        'I_e': I_e})
 
         m = nest.Create('spike_detector')
 

unittests/test_garbage_collector.py

@@ -132,6 +132,8 @@ def test_garbage_collector_2(self):
                          0.,    0.,    0.,    0.,    0.,    0.,    0.,    0.,    0.,
                          0.,    0.,    0.,    0.,    0.]
 
+        self.spore_connection_test(p_sim, synapse_properties, target_values)
+
     def test_garbage_collector_3(self):
         p_sim = {"resolution": 0.2, "interval": 500, "delay": 500,
                  "exp_len": 5000.0, "num_synapses": 100, "frame": 30.0}