def getWeights(self, format='list'):
"""
Get synaptic weights for all connections in this Projection.
(pyNN gather parameter not supported from the signiture
getWeights(self, format='list', gather=True):)
Possible formats are: a list of length equal to the number of connections
in the projection, a 2D weight array (with NaN for non-existent
connections). Note that for the array format, if there is more than
one connection between two cells, the summed weight will be given.
"""
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
synapse_list = self._get_synaptic_data()
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
if format == 'list':
weights = list()
for row in synapse_list.get_rows():
weights.extend(row.weights)
return weights
elif format == 'array':
weights = numpy.zeros((self.projection_edge.prevertex.atoms,
self.projection_edge.postvertex.atoms))
rows = synapse_list.get_rows()
for pre_atom, row in enumerate(rows):
for post_atom, weight in zip(row.target_indices, row.weights):
weights[pre_atom][post_atom] = weight
return weights
def getDelays(self, format='list', gather=True):
"""
Get synaptic delays for all connections in this Projection.
Possible formats are: a list of length equal to the number of connections
in the projection, a 2D delay array (with NaN for non-existent
connections).
"""
global controller
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
synapse_list = self._get_synaptic_data()
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
if format == 'list':
delays = list()
for row in synapse_list.get_rows():
delays.extend(row.delays
* (float(controller.dao.machineTimeStep) / 1000.0))
return delays
delays = numpy.zeros((self.projection_edge.prevertex.atoms,
self.projection_edge.postvertex.atoms))
rows = synapse_list.get_rows()
for pre_atom in range(len(rows)):
row = rows[pre_atom]
for i in len(row.target_indices):
post_atom = row.target_indices[i]
delay = (float(row.delays[i])
* (float(controller.dao.machineTimeStep) / 1000.0))
delays[pre_atom][post_atom] = delay
return delays
def get_gsyn(self, gather=True, compatible_output=False):
"""
Return a 3-column numpy array containing cell ids and synaptic conductances for recorded cells.
"""
global controller
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
gsyn = self.vertex.get_gsyn(controller, gather=gather, compatible_output=compatible_output)
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
return gsyn
def getSpikes(self, compatible_output=False, gather=True):
"""
Return a 2-column numpy array containing cell ids and spike times for
recorded cells. This is read directly from the memory for the board.
"""
global controller
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
spikes = self.vertex.getSpikes(controller, controller.dao.run_time, compatible_output)
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
return spikes
def get_v(self, gather=True, compatible_output=False):
"""
Return a 3-column numpy array containing cell ids, time, and Vm for recorded cells.
:param bool gather:
not used - inserted to match PyNN specs
:param bool compatible_output:
not used - inserted to match PyNN specs
"""
global controller
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
v = self.vertex.get_v(controller, gather=gather, compatible_output=compatible_output)
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
return v
def getWeights(self, format='list'):
"""
Get synaptic weights for all connections in this Projection.
(pyNN gather parameter not supported from the signiture
getWeights(self, format='list', gather=True):)
Possible formats are: a list of length equal to the number of connections
in the projection, a 2D weight array (with NaN for non-existent
connections). Note that for the array format, if there is more than
one connection between two cells, the summed weight will be given.
"""
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
synapse_list = self._get_synaptic_data()
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
if format == 'list':
weights = list()
for row in synapse_list.get_rows():
weights.extend(row.weights)
return weights
elif format == 'array':
weights = numpy.zeros((self.projection_edge.prevertex.atoms,
self.projection_edge.postvertex.atoms))
rows = synapse_list.get_rows()
for pre_atom, row in enumerate(rows):
for post_atom, weight in zip(row.target_indices, row.weights):
weights[pre_atom][post_atom] = weight
return weights
def getDelays(self, format='list', gather=True):
"""
Get synaptic delays for all connections in this Projection.
Possible formats are: a list of length equal to the number of connections
in the projection, a 2D delay array (with NaN for non-existent
connections).
"""
global controller
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
synapse_list = self._get_synaptic_data()
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
if format == 'list':
delays = list()
for row in synapse_list.get_rows():
delays.extend(row.delays *
(float(controller.dao.machineTimeStep) / 1000.0))
return delays
delays = numpy.zeros((self.projection_edge.prevertex.atoms,
self.projection_edge.postvertex.atoms))
rows = synapse_list.get_rows()
for pre_atom in range(len(rows)):
row = rows[pre_atom]
for i in len(row.target_indices):
post_atom = row.target_indices[i]
delay = (float(row.delays[i]) *
(float(controller.dao.machineTimeStep) / 1000.0))
delays[pre_atom][post_atom] = delay
return delays
def get_gsyn(self, gather=True, compatible_output=False):
"""
Return a 3-column numpy array containing cell ids and synaptic conductances for recorded cells.
"""
global controller
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
gsyn = self.vertex.get_gsyn(controller,
gather=gather,
compatible_output=compatible_output)
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
return gsyn
def getSpikes(self, compatible_output=False, gather=True):
"""
Return a 2-column numpy array containing cell ids and spike times for
recorded cells. This is read directly from the memory for the board.
"""
global controller
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
spikes = self.vertex.getSpikes(controller, controller.dao.run_time,
compatible_output)
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
return spikes
def get_v(self, gather=True, compatible_output=False):
"""
Return a 3-column numpy array containing cell ids, time, and Vm for recorded cells.
:param bool gather:
not used - inserted to match PyNN specs
:param bool compatible_output:
not used - inserted to match PyNN specs
"""
global controller
timer = None
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer = Timer()
timer.start_timing()
v = self.vertex.get_v(controller,
gather=gather,
compatible_output=compatible_output)
if conf.config.getboolean("Reports", "outputTimesForSections"):
timer.take_sample()
return v
def run(run_time=None, do_load=None, do_run=None):
"""
Run the simulation for run_time ms.
:param int run_time:
simulation length (in ms)
On run the following :py:class:`pacman103.core.control.Controller` functions are called:
- :py:mod:`pacman103.core.control.Controller.map_model`
- :py:mod:`pacman103.core.control.Controller.specify_output`
- :py:mod:`pacman103.core.control.Controller.generate_output`
- :py:mod:`pacman103.core.control.Controller.load_executables`
- :py:mod:`pacman103.core.control.Controller.run`
"""
global controller
do_timing = conf.config.getboolean("Reports", "outputTimesForSections")
if do_timing:
timer = Timer()
if do_load == None:
do_load = True
if conf.config.has_option("Execute", "load"):
do_load = conf.config.getboolean("Execute", "load")
if do_run == None:
do_run = True
if conf.config.has_option("Execute", "run"):
do_run = conf.config.getboolean("Execute", "run")
controller.dao.run_time = run_time
logger.info("*** Running Mapper *** ")
if do_timing:
timer.start_timing()
controller.map_model()
if do_timing:
timer.take_sample()
if do_timing:
timer.start_timing()
logger.info("*** Generating Output *** ")
logger.debug("")
controller.generate_output()
if do_timing:
timer.take_sample()
controller.start_visualiser()
if do_timing:
timer.start_timing()
if (conf.config.getboolean("Execute", "run_simulation")):
if do_load == True:
logger.info("*** Loading data ***")
controller.load_targets()
controller.load_write_mem()
if do_timing:
timer.take_sample()
if do_run == True:
logger.info("*** Running simulation... *** ")
controller.run(controller.dao.app_id)
else:
logger.info("*** No simulation requested: Stopping. ***")
return run_time
def run(run_time = None, do_load = None, do_run = None):
"""
Run the simulation for run_time ms.
:param int run_time:
simulation length (in ms)
On run the following :py:class:`pacman103.core.control.Controller` functions are called:
- :py:mod:`pacman103.core.control.Controller.map_model`
- :py:mod:`pacman103.core.control.Controller.specify_output`
- :py:mod:`pacman103.core.control.Controller.generate_output`
- :py:mod:`pacman103.core.control.Controller.load_executables`
- :py:mod:`pacman103.core.control.Controller.run`
"""
global controller
do_timing = conf.config.getboolean("Reports", "outputTimesForSections")
if do_timing:
timer = Timer()
if do_load == None:
do_load = True
if conf.config.has_option("Execute", "load"):
do_load = conf.config.getboolean("Execute", "load")
if do_run == None:
do_run = True
if conf.config.has_option("Execute", "run"):
do_run = conf.config.getboolean("Execute", "run")
controller.dao.run_time = run_time
logger.info("*** Running Mapper *** ")
if do_timing:
timer.start_timing()
controller.map_model()
if do_timing:
timer.take_sample()
if do_timing:
timer.start_timing()
logger.info("*** Generating Output *** ")
logger.debug("")
controller.generate_output()
if do_timing:
timer.take_sample()
controller.start_visualiser()
if do_timing:
timer.start_timing()
if(conf.config.getboolean("Execute", "run_simulation")):
if do_load == True:
logger.info("*** Loading data ***")
controller.load_targets()
controller.load_write_mem()
if do_timing:
timer.take_sample()
if do_run == True:
logger.info("*** Running simulation... *** ")
controller.run(controller.dao.app_id)
else:
logger.info("*** No simulation requested: Stopping. ***")
return run_time