def printSpikes(self, filename, gather=True):
"""
Write spike time information from the population to a given file.
:param filename: the absoluete file path for where the spikes are to be
printed in
:param gather: Supported from the PyNN language, but Spinnaker only does
gather = True.
"""
if not gather:
logger.warn("Spynnaker only supports gather = true, will execute"
" as if gather was true anyhow")
spikes = self.getSpikes(compatible_output=True)
if spikes is not None:
first_id = 0
num_neurons = self._vertex.n_atoms
dimensions = self._vertex.n_atoms
last_id = self._vertex.n_atoms - 1
utility_calls.check_directory_exists_and_create_if_not(filename)
spike_file = open(filename, "w")
spike_file.write("# first_id = {}\n".format(first_id))
spike_file.write("# n = {}\n".format(num_neurons))
spike_file.write("# dimensions = [{}]\n".format(dimensions))
spike_file.write("# last_id = {}\n".format(last_id))
for (neuronId, time) in spikes:
spike_file.write("{}\t{}\n".format(time, neuronId))
spike_file.close()
def print_gsyn(self, filename, gather=True):
""" Write conductance information from the population to a given file.
:param filename: the absolute file path for where the gsyn are to be\
printed in
:param gather: Supported from the PyNN language, but ignored here
"""
time_step = (self._spinnaker_control.machine_time_step * 1.0) / 1000.0
gsyn_exc = self._get_recorded_variable('gsyn_exc')
gsyn_inh = self._get_recorded_variable('gsyn_inh')
first_id = 0
num_neurons = self._vertex.n_atoms
dimensions = self._vertex.n_atoms
utility_calls.check_directory_exists_and_create_if_not(filename)
file_handle = open(filename, "w")
file_handle.write("# first_id = {}\n".format(first_id))
file_handle.write("# n = {}\n".format(num_neurons))
file_handle.write("# dt = {}\n".format(time_step))
file_handle.write("# dimensions = [{}]\n".format(dimensions))
file_handle.write("# last_id = {{}}\n".format(num_neurons - 1))
file_handle = open(filename, "w")
# TODO will need adjusting when filters and views assemblies work
for ((neuronId, time, value_e), (_, _, value_i)) in zip(
gsyn_exc, gsyn_inh):
file_handle.write("{}\t{}\t{}\t{}\n".format(
time, neuronId, value_e, value_i))
file_handle.close()
def printSpikes(self, filename, gather=True):
""" Write spike time information from the population to a given file.
:param filename: the absolute file path for where the spikes are to\
be printed in
:param gather: Supported from the PyNN language, but ignored here
"""
if not gather:
logger.warn("Spynnaker only supports gather = true, will execute"
" as if gather was true anyhow")
spikes = self._get_recorded_variable('spikes')
if spikes is not None:
first_id = 0
num_neurons = self._vertex.n_atoms
dimensions = self._vertex.n_atoms
last_id = self._vertex.n_atoms - 1
utility_calls.check_directory_exists_and_create_if_not(filename)
spike_file = open(filename, "w")
spike_file.write("# first_id = {}\n".format(first_id))
spike_file.write("# n = {}\n".format(num_neurons))
spike_file.write("# dimensions = [{}]\n".format(dimensions))
spike_file.write("# last_id = {}\n".format(last_id))
for (neuronId, time) in spikes:
spike_file.write("{}\t{}\n".format(time, neuronId))
spike_file.close()
def test_check_directory_not_exists(self):
test_dir = os.path.join(os.path.dirname(__file__), "test_utility_call")
test_file = os.path.join(test_dir, "test")
if os.path.exists(test_dir):
shutil.rmtree(test_dir)
print("Directory existed. Deleting...")
utility_calls.check_directory_exists_and_create_if_not(test_file)
if not os.path.exists(test_dir):
raise AssertionError("Directory was not created")
print("Directory created successfully. Deleting...")
os.rmdir(test_dir)
def test_check_directory_not_exists(self):
test_dir = os.path.join(os.path.dirname(__file__),
"test_utility_call")
test_file = os.path.join(test_dir, "test")
if os.path.exists(test_dir):
shutil.rmtree(test_dir)
print "Directory existed. Deleting..."
utility_calls.check_directory_exists_and_create_if_not(test_file)
if os.path.exists(test_dir):
os.rmdir(test_dir)
print "Directory created successfully. Deleting..."
else:
raise AssertionError("Directory was not created")
def _get_io(filename):
""" Return a Neo IO instance, guessing the type based on the filename\
suffix.
"""
logger.debug("Creating Neo IO for filename {}", filename)
directory = os.path.dirname(filename)
utility_calls.check_directory_exists_and_create_if_not(directory)
extension = os.path.splitext(filename)[1]
if extension in ('.txt', '.ras', '.v', '.gsyn'):
raise IOError(
"ASCII-based formats are not currently supported for output"
" data. Try using the file extension '.pkl' or '.h5'")
elif extension in ('.h5', ):
return NeoHdf5IO(filename=filename)
elif extension in ('.pkl', '.pickle'):
return PickleIO(filename=filename)
elif extension == '.mat':
return NeoMatlabIO(filename=filename)
else: # function to be improved later
raise Exception("file extension %s not supported" % extension)
def print_v(self, filename, gather=True):
""" Write membrane potential information from the population to a\
given file.
:param filename: the absolute file path for where the voltage are to\
be printed in
:param gather: Supported from the PyNN language, but ignored here
"""
time_step = (self._spinnaker.machine_time_step * 1.0) / 1000.0
v = self.get_v(gather, compatible_output=True)
utility_calls.check_directory_exists_and_create_if_not(filename)
file_handle = open(filename, "w")
first_id = 0
num_neurons = self._vertex.n_atoms
dimensions = self._vertex.n_atoms
file_handle.write("# first_id = {}\n".format(first_id))
file_handle.write("# n = {}\n".format(num_neurons))
file_handle.write("# dt = {}\n".format(time_step))
file_handle.write("# dimensions = [{}]\n".format(dimensions))
file_handle.write("# last_id = {}\n".format(num_neurons - 1))
for (neuronId, time, value) in v:
file_handle.write("{}\t{}\t{}\n".format(time, neuronId, value))
file_handle.close()
def print_v(self, filename, gather=True):
""" Write membrane potential information from the population to a\
given file.
:param filename: the absolute file path for where the voltage are to\
be printed in
:param gather: Supported from the PyNN language, but ignored here
"""
time_step = (self._spinnaker.machine_time_step * 1.0) / 1000.0
v = self.get_v(gather, compatible_output=True)
utility_calls.check_directory_exists_and_create_if_not(filename)
file_handle = open(filename, "w")
first_id = 0
num_neurons = self._vertex.n_atoms
dimensions = self._vertex.n_atoms
file_handle.write("# first_id = {}\n".format(first_id))
file_handle.write("# n = {}\n".format(num_neurons))
file_handle.write("# dt = {}\n".format(time_step))
file_handle.write("# dimensions = [{}]\n".format(dimensions))
file_handle.write("# last_id = {}\n".format(num_neurons - 1))
for (neuronId, time, value) in v:
file_handle.write("{}\t{}\t{}\n".format(time, neuronId, value))
file_handle.close()
def print_gsyn(self, filename, gather=True):
""" Write conductance information from the population to a given file.
:param filename: the absoluete file path for where the gsyn are to be\
printed in
:param gather: Supported from the PyNN language, but ignored here
"""
time_step = (self._spinnaker.machine_time_step * 1.0) / 1000.0
gsyn = self.get_gsyn(gather, compatible_output=True)
first_id = 0
num_neurons = self._vertex.n_atoms
dimensions = self._vertex.n_atoms
utility_calls.check_directory_exists_and_create_if_not(filename)
file_handle = open(filename, "w")
file_handle.write("# first_id = {}\n".format(first_id))
file_handle.write("# n = {}\n".format(num_neurons))
file_handle.write("# dt = {}\n".format(time_step))
file_handle.write("# dimensions = [{}]\n".format(dimensions))
file_handle.write("# last_id = {{}}\n".format(num_neurons - 1))
file_handle = open(filename, "w")
for (neuronId, time, value_e, value_i) in gsyn:
file_handle.write("{}\t{}\t{}\t{}\n".format(
time, neuronId, value_e, value_i))
file_handle.close()
def test_check_directory_exists(self):
utility_calls.check_directory_exists_and_create_if_not(
os.path.dirname(os.path.realpath(__file__)))
self.assertTrue(
os.path.exists(os.path.dirname(os.path.realpath(__file__))))
def test_check_directory_exists(self):
utility_calls.check_directory_exists_and_create_if_not(os.path.dirname(
os.path.realpath(__file__)))
self.assertTrue(os.path.exists(os.path.dirname(
os.path.realpath(__file__))))
