def _store(self):
store_dict = {}
for key in self._data:
val = self._data[key]
if isinstance(val, Quantity):
if self._storage_mode == BrianResult.STRING_MODE:
valstr = val.in_best_unit(python_code=True)
store_dict[key + BrianResult.IDENTIFIER] = ObjectTable(
data={'data': [valstr]})
elif self._storage_mode == BrianResult.FLOAT_MODE:
unitstr = repr(get_unit_fast(val))
value = float(val)
store_dict[key + BrianResult.IDENTIFIER] = ObjectTable(
data={'value': [value], 'unit': [unitstr]})
else:
raise RuntimeError('You shall not pass!')
else:
store_dict[key] = val
return store_dict
def check_state_spike_monitor(self, res, monitor):
self.assertTrue(comp.nested_equal(monitor.delay, res.delay))
self.assertTrue(comp.nested_equal(monitor.nspikes, res.nspikes))
self.assertTrue(comp.nested_equal(str(monitor.source), res.source))
self.assertTrue(comp.nested_equal(monitor._varnames, res.varnames))
self.assertEqual('second', res.spiketimes_unit)
if res.v_storage_mode == BrianMonitorResult.TABLE_MODE:
spike_frame = res.spikes
spiked_list=sorted(list(set(spike_frame['neuron'].to_dict().values())))
self.assertEqual(spiked_list, res.neurons_with_spikes)
for idx,val_tuple in enumerate(monitor.spikes):
neuron = val_tuple[0]
time = val_tuple[1]
vals = val_tuple[2:]
self.assertEqual(neuron, spike_frame['neuron'][idx])
self.assertEqual(float(time), spike_frame['spiketimes'][idx])
for idx_var, varname in enumerate(res.varnames):
val = vals[idx_var]
self.assertEqual(float(val),spike_frame[varname][idx])
elif res.v_storage_mode == BrianMonitorResult.ARRAY_MODE:
self.assertTrue('%0' in res.format_string and 'd' in res.format_string)
spiked_set=set()
for item_name in res:
if item_name.startswith('spiketimes') and not item_name.endswith('unit'):
neuron_id = int(item_name.split('_')[-1])
spiked_set.add(neuron_id)
times = monitor.times(neuron_id)
self.assertTrue(comp.nested_equal(times,res[item_name]))
for varname in res.varnames:
if item_name.startswith(varname) and not item_name.endswith('unit'):
neuron_id =int(item_name.split('_')[-1])
values = monitor.values(varname,neuron_id)
# Remove units:
self.assertTrue(comp.nested_equal(values,res[item_name]))
spiked_list = sorted(list(spiked_set))
self.assertEqual(spiked_list, res.neurons_with_spikes)
else:
raise RuntimeError('You shall not pass!')
# Check Units
for idx,varname in enumerate(monitor._varnames):
unit = repr(get_unit_fast(monitor.spikes[0][idx+2]))
self.assertTrue(unit,res[varname+'_unit'])
def _store(self):
if isinstance(self._data,Quantity):
store_dict={}
if self._storage_mode == BrianParameter.STRING_MODE:
valstr = self._data.in_best_unit(python_code=True)
store_dict['data'+BrianParameter.IDENTIFIER] = ObjectTable(data={'data':[valstr]})
if self.f_has_range():
valstr_list = []
for val in self._explored_range:
valstr = val.in_best_unit(python_code=True)
valstr_list.append(valstr)
store_dict['explored_data'+BrianParameter.IDENTIFIER] = \
ObjectTable(data={'data':valstr_list})
elif self._storage_mode == BrianParameter.FLOAT_MODE:
unitstr = repr(get_unit_fast(self._data))
value = float(self._data)
store_dict['data'+BrianParameter.IDENTIFIER] = ObjectTable(data={'value':[value],
'unit':[unitstr]})
if self.f_has_range():
value_list = []
for val in self._explored_range:
value = float(val)
value_list.append(value)
store_dict['explored_data'+BrianParameter.IDENTIFIER] = \
ObjectTable(data={'value':value_list})
else:
raise RuntimeError('You shall not pass!')
self._locked = True
return store_dict
else:
return super(BrianParameter,self)._store()
def _store(self):
if isinstance(self._data, Quantity):
store_dict = {}
if self._storage_mode == BrianParameter.STRING_MODE:
valstr = self._data.in_best_unit(python_code=True)
store_dict['data' + BrianParameter.IDENTIFIER] = ObjectTable(
data={'data': [valstr]})
if self.f_has_range():
valstr_list = []
for val in self._explored_range:
valstr = val.in_best_unit(python_code=True)
valstr_list.append(valstr)
store_dict['explored_data' + BrianParameter.IDENTIFIER] = \
ObjectTable(data={'data': valstr_list})
elif self._storage_mode == BrianParameter.FLOAT_MODE:
unitstr = repr(get_unit_fast(self._data))
value = float(self._data)
store_dict['data' + BrianParameter.IDENTIFIER] = ObjectTable(
data={'value': [value], 'unit': [unitstr]})
if self.f_has_range():
value_list = []
for val in self._explored_range:
value = float(val)
value_list.append(value)
store_dict['explored_data' + BrianParameter.IDENTIFIER] = \
ObjectTable(data={'value': value_list})
else:
raise RuntimeError('You shall not pass!')
self._locked = True
return store_dict
else:
return super(BrianParameter, self)._store()
def _extract_state_spike_monitor(self,monitor):
self.f_set(source = str(monitor.source))
varnames = monitor._varnames
if not isinstance(varnames, tuple) :
varnames = (varnames,)
for idx,varname in enumerate(varnames):
unit = repr(get_unit_fast(monitor.spikes[0][idx+2]))
self.f_set(**{varname+'_unit':unit})
self.f_set(varnames = varnames)
#self.f_set(record = monitor.record)
self.f_set(delay=monitor.delay)
self.f_set(nspikes = monitor.nspikes)
self.f_set(spiketimes_unit = 'second')
if self._storage_mode==BrianMonitorResult.TABLE_MODE:
spike_dict={}
if len(monitor.spikes)>0:
zip_lists = zip(*monitor.spikes)
time_list = zip_lists[1]
nounit_list = [np.float64(time) for time in time_list]
spike_dict['spiketimes'] = nounit_list
spike_dict['neuron'] = list(zip_lists[0])
spiked_neurons = sorted(list(set(spike_dict['neuron'])))
if spiked_neurons:
self.f_set(neurons_with_spikes=spiked_neurons)
count = 2
for varname in varnames:
var_list = list(zip_lists[count])
nounit_list = [np.float64(var) for var in var_list]
spike_dict[varname] = nounit_list
count += 1
self.f_set(spikes=pd.DataFrame(data=spike_dict))
elif self._storage_mode==BrianMonitorResult.ARRAY_MODE:
format_string = self._get_format_string(monitor)
self.f_set(format_string=format_string)
spiked_neurons = set()
for neuron in range(len(monitor.source)):
spikes = monitor.times(neuron)
if len(spikes)>0:
spiked_neurons.add(neuron)
key = 'spiketimes_' + format_string % neuron
self.f_set(**{key:spikes})
spiked_neurons = sorted(list(spiked_neurons))
if spiked_neurons:
self.f_set(neurons_with_spikes=spiked_neurons)
for varname in varnames:
for neuron in range(len(monitor.source)):
values = monitor.values(varname,neuron)
if len(values)>0:
key = varname+'_' + format_string % neuron
self.f_set(**{key:values})
else:
raise RuntimeError('You shall not pass!')
def _extract_state_spike_monitor(self, monitor):
self.f_set(source=str(monitor.source))
varnames = monitor._varnames
if not isinstance(varnames, tuple):
varnames = (varnames,)
for idx, varname in enumerate(varnames):
unit = repr(get_unit_fast(monitor.spikes[0][idx + 2]))
self.f_set(**{varname + '_unit': unit})
self.f_set(varnames=varnames)
#self.f_set(record = monitor.record)
self.f_set(delay=monitor.delay)
self.f_set(nspikes=monitor.nspikes)
self.f_set(spiketimes_unit='second')
if self._storage_mode == BrianMonitorResult.TABLE_MODE:
spike_dict = {}
if len(monitor.spikes) > 0:
zip_lists = list(zip(*monitor.spikes))
time_list = zip_lists[1]
nounit_list = [np.float64(time) for time in time_list]
spike_dict['spiketimes'] = nounit_list
spike_dict['neuron'] = list(zip_lists[0])
spiked_neurons = sorted(list(set(spike_dict['neuron'])))
if spiked_neurons:
self.f_set(neurons_with_spikes=spiked_neurons)
count = 2
for varname in varnames:
var_list = list(zip_lists[count])
nounit_list = [np.float64(var) for var in var_list]
spike_dict[varname] = nounit_list
count += 1
self.f_set(spikes=pd.DataFrame(data=spike_dict))
elif self._storage_mode == BrianMonitorResult.ARRAY_MODE:
format_string = self._get_format_string(monitor)
self.f_set(format_string=format_string)
spiked_neurons = set()
for neuron in range(len(monitor.source)):
spikes = monitor.times(neuron)
if len(spikes) > 0:
spiked_neurons.add(neuron)
key = 'spiketimes_' + format_string % neuron
self.f_set(**{key: spikes})
spiked_neurons = sorted(list(spiked_neurons))
if spiked_neurons:
self.f_set(neurons_with_spikes=spiked_neurons)
for varname in varnames:
for neuron in range(len(monitor.source)):
values = monitor.values(varname, neuron)
if len(values) > 0:
key = varname + '_' + format_string % neuron
self.f_set(**{key: values})
else:
raise RuntimeError('You shall not pass!')
def check_state_spike_monitor(self, res, monitor):
self.assertTrue(comp.nested_equal(monitor.delay, res.delay))
self.assertTrue(comp.nested_equal(monitor.nspikes, res.nspikes))
self.assertTrue(comp.nested_equal(str(monitor.source), res.source))
self.assertTrue(comp.nested_equal(monitor._varnames, res.varnames))
self.assertEqual('second', res.spiketimes_unit)
if res.v_storage_mode == BrianMonitorResult.TABLE_MODE:
spike_frame = res.spikes
spiked_list = sorted(
list(set(spike_frame['neuron'].to_dict().values())))
self.assertEqual(spiked_list, res.neurons_with_spikes)
for idx, val_tuple in enumerate(monitor.spikes):
neuron = val_tuple[0]
time = val_tuple[1]
vals = val_tuple[2:]
self.assertEqual(neuron, spike_frame['neuron'][idx])
self.assertEqual(float(time), spike_frame['spiketimes'][idx])
for idx_var, varname in enumerate(res.varnames):
val = vals[idx_var]
self.assertEqual(float(val), spike_frame[varname][idx])
elif res.v_storage_mode == BrianMonitorResult.ARRAY_MODE:
self.assertTrue('%0' in res.format_string
and 'd' in res.format_string)
spiked_set = set()
for item_name in res:
if item_name.startswith(
'spiketimes') and not item_name.endswith('unit'):
neuron_id = int(item_name.split('_')[-1])
spiked_set.add(neuron_id)
times = monitor.times(neuron_id)
self.assertTrue(comp.nested_equal(times, res[item_name]))
for varname in res.varnames:
if item_name.startswith(
varname) and not item_name.endswith('unit'):
neuron_id = int(item_name.split('_')[-1])
values = monitor.values(varname, neuron_id)
# Remove units:
self.assertTrue(
comp.nested_equal(values, res[item_name]))
spiked_list = sorted(list(spiked_set))
self.assertEqual(spiked_list, res.neurons_with_spikes)
else:
raise RuntimeError('You shall not pass!')
# Check Units
for idx, varname in enumerate(monitor._varnames):
unit = repr(get_unit_fast(monitor.spikes[0][idx + 2]))
self.assertTrue(unit, res[varname + '_unit'])
