def __init__(self, **kwargs):
"""
:Parameters:
kwargs : dict
Keyword arguments, see Keywords.
:Keywords:
debug : bool
Debug output toggle.
Default=False
externals : list
A list of SimExternalDelegate instances. Internal state changes
will be propagated to the delegates.
Default=False
sample_rate : float
Sample rate.
frame : int
Frame to start at.
frame_size : int
Frame size.
cfg : str
Path to a config file, readable by a ConfigParser instance.
"""
# private property members
self._cfg = None
self._externals = []
self._frame = None
self._frame_size = None
self._sample_rate = None
self._status = None
# public members
self.cls_dyn = ClusterDynamics()
self.io_man = SimIOManager()
self.neuron_data = NeuronDataContainer()
self.debug = kwargs.get('debug', False)
# externals
for ext in kwargs.get('externals', []):
if not isinstance(ext, SimExternalDelegate):
continue
self._externals.append(ext)
def __init__(self, **kwargs):
"""
:Parameters:
kwargs : dict
Keyword arguments, see Keywords.
:Keywords:
debug : bool
Debug output toggle.
Default=False
externals : list
A list of SimExternalDelegate instances. Internal state changes
will be propagated to the delegates.
Default=False
sample_rate : float
Sample rate.
frame : int
Frame to start at.
frame_size : int
Frame size.
cfg : str
Path to a config file, readable by a ConfigParser instance.
"""
# private property members
self._cfg = None
self._externals = []
self._frame = None
self._frame_size = None
self._sample_rate = None
self._status = None
# public members
self.cls_dyn = ClusterDynamics()
self.io_man = SimIOManager()
self.neuron_data = NeuronDataContainer()
self.debug = kwargs.get("debug", False)
# externals
for ext in kwargs.get("externals", []):
if not isinstance(ext, SimExternalDelegate):
continue
self._externals.append(ext)
class BaseSimulation(dict):
"""simulation class controlling the scene"""
## constructor
def __init__(self, **kwargs):
"""
:Parameters:
kwargs : dict
Keyword arguments, see Keywords.
:Keywords:
debug : bool
Debug output toggle.
Default=False
externals : list
A list of SimExternalDelegate instances. Internal state changes
will be propagated to the delegates.
Default=False
sample_rate : float
Sample rate.
frame : int
Frame to start at.
frame_size : int
Frame size.
cfg : str
Path to a config file, readable by a ConfigParser instance.
"""
# private property members
self._cfg = None
self._externals = []
self._frame = None
self._frame_size = None
self._sample_rate = None
self._status = None
# public members
self.cls_dyn = ClusterDynamics()
self.io_man = SimIOManager()
self.neuron_data = NeuronDataContainer()
self.debug = kwargs.get("debug", False)
# externals
for ext in kwargs.get("externals", []):
if not isinstance(ext, SimExternalDelegate):
continue
self._externals.append(ext)
def initialize(self, **kwargs):
"""initialize the simulation
:Keywords:
debug : bool
Debug flag, enables verbose output.
Default=False
frame : long
Frame id to start at.
Default=0
frame_size : int
The frame size.
Default=16
sample_rate : float
Sample rate to operate.
Default=16000.0
"""
self.clear()
# reset private members
self.sample_rate = kwargs.get("sample_rate", 16000.0)
self.frame = kwargs.get("frame", 0)
self.frame_size = kwargs.get("frame_size", 1024)
self.status
# reset pubic members
self.cls_dyn.clear()
self.io_man.initialize()
self.neuron_data.clear()
def finalize(self):
"""finalize the simulation"""
self.clear()
# reset pubic members
self.cls_dyn.clear()
self.io_man.finalize()
self.neuron_data.clear()
## properties
def get_frame(self):
return self._frame
def set_frame(self, value):
self._frame = long(value)
for ext in self._externals:
ext.frame(self._frame)
frame = property(get_frame, set_frame)
def get_frame_size(self):
return self._frame_size
def set_frame_size(self, value):
self._frame_size = int(value)
for ext in self._externals:
ext.frame_size(self._frame_size)
self.status
frame_size = property(get_frame_size, set_frame_size)
def get_sample_rate(self):
return self._sample_rate
def set_sample_rate(self, value):
self._sample_rate = float(value)
self.cls_dyn.sample_rate = self._sample_rate
for ext in self._externals:
ext.sample_rate(self._sample_rate)
self.status
sample_rate = property(get_sample_rate, set_sample_rate)
def get_status(self):
self._status = {
"frame_size": self.frame_size,
"sample_rate": self.sample_rate,
"neurons": self.neuron_keys,
"recorders": self.recorder_keys,
}
if self.io_man.is_initialized:
self.io_man.status = self._status
return self._status
status = property(get_status)
def get_neuron_keys(self):
return [idx for idx in self if isinstance(self[idx], Neuron)]
neuron_keys = property(get_neuron_keys)
def get_recorder_keys(self):
return [idx for idx in self if isinstance(self[idx], Recorder)]
recorder_keys = property(get_recorder_keys)
## simulation control methods
def simulate(self):
"""advance the simulation by one frame"""
# inc frame counter
self.frame += 1
# process events
self._simulate_io_tick()
# process units
self._simulate_neuron_tick()
# record for recorders
self._simulate_recorder_tick()
def _simulate_io_tick(self):
"""process io loop for the current frame
This will tick the SimIOManager and process all queued events.
"""
# get events
events = self.io_man.tick()
while len(events) > 0:
pkg = events.pop(0)
print pkg
log_str = ">>> "
if pkg.ident in self:
# recorder event
if isinstance(self[pkg.ident], Recorder):
log_str += "R[%s]:" % pkg.ident
# position event
if pkg.tid == SimPkg.T_POS:
# position request
if pkg.nitems == 0:
log_str += "MOVE[%s] - request" % (self[pkg.ident].name)
# reposition request
elif pkg.nitems == 1:
pos, vel = pkg.cont[0].cont[:2]
log_str += "MOVE: %s, %s" % (pos, vel)
self[pkg.ident].trajectory_pos = pos
# TODO: implementation of the velocity component
# weird position event
else:
print "weird event, was T_POS with:", pkg.cont
continue
# send position acknowledgement
self.io_man.send_package(SimPkg.T_POS, pkg.ident, self._frame, self[pkg.ident].trajectory_pos)
# neuron event
elif isinstance(self[pkg.ident], Neuron):
log_str += "N:[%s] neuron event" % pkg.ident
else:
log_str += "ANY:[%s] unknown" % pkg.ident
# other event
else:
log_str += "O[%s]:" % pkg.ident
if pkg.tid == SimPkg.T_CON:
log_str += "CONNECT from %s" % str(pkg.cont)
elif pkg.tid == SimPkg.T_END:
log_str += "DISCONNECT from %s" % str(pkg.cont)
else:
log_str += "unknown"
# log
self.log(log_str)
def _simulate_neuron_tick(self):
"""process neurons for current frame
This will generate spike trains and configure the neuronal firing
behavior for the current frame.
"""
# generate spike trains for the scene
self.cls_dyn.generate(self.frame_size)
# propagate spike trains to neurons
for nrn_k in self.neuron_keys:
self[nrn_k].simulate(frame_size=self.frame_size, firing_times=self.cls_dyn.get_spike_train(nrn_k))
def _simulate_recorder_tick(self):
"""process recorders for the current frame
This will record waveforms and grountruth for the current frame.
"""
# list of all neurons
nlist = [self[nrn_k] for nrn_k in self.neuron_keys]
# record per recorder
for rec_k in self.recorder_keys:
self.io_man.send_package(
SimPkg.T_REC, rec_k, self._frame, self[rec_k].simulate(nlist=nlist, frame_size=self.frame_size)
)
## methods logging
def log(self, log_str):
"""log a string"""
for ext in self._externals:
ext.log("[#%09d] %s" % (self.frame, log_str))
def log_d(self, log_str):
"""log a string"""
if self.debug is True:
for ext in self._externals:
ext.log("[DEBUG] %s" % log_str)
## methods object management
def register_neuron(self, **kwargs):
"""register a neuron to the simulation
:Keywords:
neuron_data : NeuronData or path or None
Reference to a NeuronData object or a path to the HDF5 archive
where the data can be load from.
CAUTION! str != QString etc.. use str(neuron_data)!
position : arraylike
Position in the scene (x,y,z).
Default=[0,0,0]
orientation : arraylike
Orientation of the object. If ndarray it is interpreted as
direction of orientation relative to the scene's positive
z-axis. If its a list or tuple, it is interpreted as a triple of
euler angles relative to the scene's positive z-axis. If it is
True a random rotation is created.
Default=False
rate_of_fire : float
Rate of fire in Hz.
Default=50.0
amplitude : float
Amplitude of the waveform.
Default=1.0
cluster : int
The cluster idx
:Raises:
some error .. mostly ValueErrors for invalid parameters.
:Returns:
The string representation of the registered Neuron.
"""
# check neuron data
try:
neuron_data = kwargs.pop("neuron_data")
except:
raise ValueError('No "neuron_data" given!')
if neuron_data in self.neuron_data:
ndata = self.neuron_data[neuron_data]
else:
if not self.neuron_data.insert(neuron_data):
raise ValueError("Unknown neuron_data: %s" % str(neuron_data))
else:
ndata = self.neuron_data[neuron_data]
kwargs.update(neuron_data=ndata)
# build neuron
neuron = Neuron(**kwargs)
self[id(neuron)] = neuron
# register in cluster dynamics
cls_idx = kwargs.get("cluster", None)
if cls_idx is not None:
cls_idx = int(cls_idx)
self.cls_dyn.add_neuron(neuron, cls_idx=cls_idx)
# log and return
self.log(">> %s created!" % neuron)
self.status
return str(neuron)
def register_recorder(self, **kwargs):
"""register a recorder for simulation
:Keywords:
position : array like
Position in scene (x,y,z).
Default=[0,0,0]
orientation : arraylike or bool
Orientation of the object. If ndarray it is interpreted as
direction of orientation relative to the scene's positive
z-axis. If its a list or tuple, it is interpreted as a triple of
euler angles relative to the scene's positive z-axis. If it is
True a random rotation is created.
Default=False
scale : float
Scale factor for the Tetrahedron height. The default uses values
from the Thomas Recording GmbH website, with a tetrode of about
40µm height and 20µm for the basis triangle. Note that negative
values invert the tetrode direction with respect to
self.position.
Default=1.0
snr : float
Signal to Noise Ratio (SNR) for the noise process.
Default=1.0
TODO: fix this value to be congruent with the neuron amplitudes.
noise_params : list
The noise generator parameters.
Default=None
:Raises:
some error ..mostly ValueError for invalid parameters.
:Returns:
The string representation of the registered Recorder.
"""
# build tetrode
tetrode = Tetrode(**kwargs)
self[id(tetrode)] = tetrode
# connect and return
self.log(">> %s created!" % tetrode)
self.status
return str(tetrode)
def remove_object(self, key):
"""remove the SimObject with objectName 'key'
:Parameters:
key : SimObject or int/long
A SimObject or the id of a SimObject attached (as int/long/str).
:Returns:
True on successful removal, False else.
"""
# convert the key
if isinstance(key, SimObject):
lookup = id(key)
elif isinstance(key, (str, unicode, int, long)):
try:
lookup = long(key)
except:
try:
lookup = long(key, 16)
except:
return False
else:
return False
# remove item
try:
item = self.pop(lookup)
self.log(">> %s destroyed!" % item)
self.status
return True
except:
return False
def scene_config_load(self, fname):
"""load a scene configuration file
:Parameters:
fname : str
Path to the scene configuration file.
"""
# checks and inits
cfg = ConfigParser()
cfg_check = cfg.read(fname)
if fname not in cfg_check:
raise IOError("could not load scene from %s" % fname)
# check for config
ndata_paths = cfg.get("CONFIG", "neuron_data_dir")
ndata_paths = ndata_paths.strip().split("\n")
# read per section
for sec in cfg.sections():
# check section
sec_str = sec.split()
cls = sec_str[0]
if cls not in ["Neuron", "Tetrode"]:
continue
kwargs = {}
if len(sec_str) > 1:
kwargs["name"] = " ".join(sec_str[1:])
# elaborate class and keyword arguments
bad_ndata = False
for k, v in cfg.items(sec):
# read items
if k is None or v is None or k == "" or v == "":
continue
elif k in ["position", "orientation", "trajectory"]:
if v == "False":
kwargs[k] = False
elif v == "Truse":
kwargs[k] = True
else:
kwargs[k] = map(float, v.split())
elif k in ["neuron_data"]:
kwargs[k] = v
ndata_path_list = [osp.join(path, v) for path in ndata_paths]
added_ndata = self.neuron_data.insert(ndata_path_list)
if added_ndata == 0:
bad_ndata = True
else:
kwargs[k] = v
# delegate action
if bad_ndata:
continue
elif cls == "Neuron":
self.register_neuron(**kwargs)
elif cls == "Tetrode":
self.register_recorder(**kwargs)
def scene_config_save(self, fname):
"""save the current scene configuration to a file
:Parameters:
fname : str
Path to save tha cfg to.
"""
# checks and inits
cfg = ConfigParser()
# write CONFIG section
cfg.add_section("CONFIG")
cfg.set("CONFIG", "frame_size", self.frame_size)
cfg.set("CONFIG", "sample_rate", self.sample_rate)
ndata_paths = "\t\n".join(self.neuron_data.paths)
cfg.set("CONFIG", "neuron_data_dir", ndata_paths)
# helper functions
npy2cfg = lambda x: " ".join(map(str, x.tolist()))
# add per SimObject
for obj in self.values():
if isinstance(obj, Neuron):
name = "Neuron %s" % obj.name
cfg.add_section(name)
cfg.set(name, "cluster", str(self.cls_dyn.get_cls_for_nrn(obj)))
cfg.set(name, "position", npy2cfg(obj.position))
if obj.orientation is True or obj.orientation is False:
cfg.set(name, "orientation", obj.orientation)
else:
cfg.set(name, "orientation", npy2cfg(obj.orientation))
cfg.set(name, "rate_of_fire", str(obj.rate_of_fire))
cfg.set(name, "amplitude", str(obj.amplitude))
cfg.set(name, "neuron_data", str(obj._neuron_data.filename))
elif isinstance(obj, Recorder):
name = "Tetrode %s" % obj.name
cfg.add_section(name)
cfg.set(name, "position", npy2cfg(obj.position))
cfg.set(name, "orientation", npy2cfg(obj._trajectory))
cfg.set(name, "snr", str(obj.snr))
# save
save_file = open(fname, "w")
cfg.write(save_file)
save_file.close()
## methods config loading
def load_config(self, cfg_path=None):
"""loads initialization values from file
:Parameters:
cfg_file : str
Path to the config file. Should be readable by a ConfigParser.
"""
# TODO: implement config file handling
## special methods
def __len__(self):
return len(filter(lambda x: isinstance(x, Neuron), self.values()))
def __str__(self):
return "BaseSimulation :: %d items" % len(self)
class BaseSimulation(dict):
"""simulation class controlling the scene"""
## constructor
def __init__(self, **kwargs):
"""
:Parameters:
kwargs : dict
Keyword arguments, see Keywords.
:Keywords:
debug : bool
Debug output toggle.
Default=False
externals : list
A list of SimExternalDelegate instances. Internal state changes
will be propagated to the delegates.
Default=False
sample_rate : float
Sample rate.
frame : int
Frame to start at.
frame_size : int
Frame size.
cfg : str
Path to a config file, readable by a ConfigParser instance.
"""
# private property members
self._cfg = None
self._externals = []
self._frame = None
self._frame_size = None
self._sample_rate = None
self._status = None
# public members
self.cls_dyn = ClusterDynamics()
self.io_man = SimIOManager()
self.neuron_data = NeuronDataContainer()
self.debug = kwargs.get('debug', False)
# externals
for ext in kwargs.get('externals', []):
if not isinstance(ext, SimExternalDelegate):
continue
self._externals.append(ext)
def initialize(self, **kwargs):
"""initialize the simulation
:Keywords:
debug : bool
Debug flag, enables verbose output.
Default=False
frame : long
Frame id to start at.
Default=0
frame_size : int
The frame size.
Default=16
sample_rate : float
Sample rate to operate.
Default=16000.0
"""
self.clear()
# reset private members
self.sample_rate = kwargs.get('sample_rate', 16000.0)
self.frame = kwargs.get('frame', 0)
self.frame_size = kwargs.get('frame_size', 1024)
self.status
# reset pubic members
self.cls_dyn.clear()
self.io_man.initialize()
self.neuron_data.clear()
def finalize(self):
"""finalize the simulation"""
self.clear()
# reset pubic members
self.cls_dyn.clear()
self.io_man.finalize()
self.neuron_data.clear()
## properties
def get_frame(self):
return self._frame
def set_frame(self, value):
self._frame = long(value)
for ext in self._externals:
ext.frame(self._frame)
frame = property(get_frame, set_frame)
def get_frame_size(self):
return self._frame_size
def set_frame_size(self, value):
self._frame_size = int(value)
for ext in self._externals:
ext.frame_size(self._frame_size)
self.status
frame_size = property(get_frame_size, set_frame_size)
def get_sample_rate(self):
return self._sample_rate
def set_sample_rate(self, value):
self._sample_rate = float(value)
self.cls_dyn.sample_rate = self._sample_rate
for ext in self._externals:
ext.sample_rate(self._sample_rate)
self.status
sample_rate = property(get_sample_rate, set_sample_rate)
def get_status(self):
self._status = {
'frame_size': self.frame_size,
'sample_rate': self.sample_rate,
'neurons': self.neuron_keys,
'recorders': self.recorder_keys,
}
if self.io_man.is_initialized:
self.io_man.status = self._status
return self._status
status = property(get_status)
def get_neuron_keys(self):
return [idx for idx in self if isinstance(self[idx], Neuron)]
neuron_keys = property(get_neuron_keys)
def get_recorder_keys(self):
return [idx for idx in self if isinstance(self[idx], Recorder)]
recorder_keys = property(get_recorder_keys)
## simulation control methods
def simulate(self):
"""advance the simulation by one frame"""
# inc frame counter
self.frame += 1
# process events
self._simulate_io_tick()
# process units
self._simulate_neuron_tick()
# record for recorders
self._simulate_recorder_tick()
def _simulate_io_tick(self):
"""process io loop for the current frame
This will tick the SimIOManager and process all queued events.
"""
# get events
events = self.io_man.tick()
while len(events) > 0:
pkg = events.pop(0)
print pkg
log_str = '>>> '
if pkg.ident in self:
# recorder event
if isinstance(self[pkg.ident], Recorder):
log_str += 'R[%s]:' % pkg.ident
# position event
if pkg.tid == SimPkg.T_POS:
# position request
if pkg.nitems == 0:
log_str += 'MOVE[%s] - request' % (
self[pkg.ident].name)
# reposition request
elif pkg.nitems == 1:
pos, vel = pkg.cont[0].cont[:2]
log_str += 'MOVE: %s, %s' % (pos, vel)
self[pkg.ident].trajectory_pos = pos
# TODO: implementation of the velocity component
# weird position event
else:
print 'weird event, was T_POS with:', pkg.cont
continue
# send position acknowledgement
self.io_man.send_package(
SimPkg.T_POS, pkg.ident, self._frame,
self[pkg.ident].trajectory_pos)
# neuron event
elif isinstance(self[pkg.ident], Neuron):
log_str += 'N:[%s] neuron event' % pkg.ident
else:
log_str += 'ANY:[%s] unknown' % pkg.ident
# other event
else:
log_str += 'O[%s]:' % pkg.ident
if pkg.tid == SimPkg.T_CON:
log_str += 'CONNECT from %s' % str(pkg.cont)
elif pkg.tid == SimPkg.T_END:
log_str += 'DISCONNECT from %s' % str(pkg.cont)
else:
log_str += 'unknown'
# log
self.log(log_str)
def _simulate_neuron_tick(self):
"""process neurons for current frame
This will generate spike trains and configure the neuronal firing
behavior for the current frame.
"""
# generate spike trains for the scene
self.cls_dyn.generate(self.frame_size)
# propagate spike trains to neurons
for nrn_k in self.neuron_keys:
self[nrn_k].simulate(
frame_size=self.frame_size,
firing_times=self.cls_dyn.get_spike_train(nrn_k))
def _simulate_recorder_tick(self):
"""process recorders for the current frame
This will record waveforms and grountruth for the current frame.
"""
# list of all neurons
nlist = [self[nrn_k] for nrn_k in self.neuron_keys]
# record per recorder
for rec_k in self.recorder_keys:
self.io_man.send_package(
SimPkg.T_REC, rec_k, self._frame,
self[rec_k].simulate(nlist=nlist, frame_size=self.frame_size))
## methods logging
def log(self, log_str):
"""log a string"""
for ext in self._externals:
ext.log('[#%09d] %s' % (self.frame, log_str))
def log_d(self, log_str):
"""log a string"""
if self.debug is True:
for ext in self._externals:
ext.log('[DEBUG] %s' % log_str)
## methods object management
def register_neuron(self, **kwargs):
"""register a neuron to the simulation
:Keywords:
neuron_data : NeuronData or path or None
Reference to a NeuronData object or a path to the HDF5 archive
where the data can be load from.
CAUTION! str != QString etc.. use str(neuron_data)!
position : arraylike
Position in the scene (x,y,z).
Default=[0,0,0]
orientation : arraylike
Orientation of the object. If ndarray it is interpreted as
direction of orientation relative to the scene's positive
z-axis. If its a list or tuple, it is interpreted as a triple of
euler angles relative to the scene's positive z-axis. If it is
True a random rotation is created.
Default=False
rate_of_fire : float
Rate of fire in Hz.
Default=50.0
amplitude : float
Amplitude of the waveform.
Default=1.0
cluster : int
The cluster idx
:Raises:
some error .. mostly ValueErrors for invalid parameters.
:Returns:
The string representation of the registered Neuron.
"""
# check neuron data
try:
neuron_data = kwargs.pop('neuron_data')
except:
raise ValueError('No "neuron_data" given!')
if neuron_data in self.neuron_data:
ndata = self.neuron_data[neuron_data]
else:
if not self.neuron_data.insert(neuron_data):
raise ValueError('Unknown neuron_data: %s' % str(neuron_data))
else:
ndata = self.neuron_data[neuron_data]
kwargs.update(neuron_data=ndata)
# build neuron
neuron = Neuron(**kwargs)
self[id(neuron)] = neuron
# register in cluster dynamics
cls_idx = kwargs.get('cluster', None)
if cls_idx is not None:
cls_idx = int(cls_idx)
self.cls_dyn.add_neuron(neuron, cls_idx=cls_idx)
# log and return
self.log('>> %s created!' % neuron)
self.status
return str(neuron)
def register_recorder(self, **kwargs):
"""register a recorder for simulation
:Keywords:
position : array like
Position in scene (x,y,z).
Default=[0,0,0]
orientation : arraylike or bool
Orientation of the object. If ndarray it is interpreted as
direction of orientation relative to the scene's positive
z-axis. If its a list or tuple, it is interpreted as a triple of
euler angles relative to the scene's positive z-axis. If it is
True a random rotation is created.
Default=False
scale : float
Scale factor for the Tetrahedron height. The default uses values
from the Thomas Recording GmbH website, with a tetrode of about
40µm height and 20µm for the basis triangle. Note that negative
values invert the tetrode direction with respect to
self.position.
Default=1.0
snr : float
Signal to Noise Ratio (SNR) for the noise process.
Default=1.0
TODO: fix this value to be congruent with the neuron amplitudes.
noise_params : list
The noise generator parameters.
Default=None
:Raises:
some error ..mostly ValueError for invalid parameters.
:Returns:
The string representation of the registered Recorder.
"""
# build tetrode
tetrode = Tetrode(**kwargs)
self[id(tetrode)] = tetrode
# connect and return
self.log('>> %s created!' % tetrode)
self.status
return str(tetrode)
def remove_object(self, key):
"""remove the SimObject with objectName 'key'
:Parameters:
key : SimObject or int/long
A SimObject or the id of a SimObject attached (as int/long/str).
:Returns:
True on successful removal, False else.
"""
# convert the key
if isinstance(key, SimObject):
lookup = id(key)
elif isinstance(key, (str, unicode, int, long)):
try:
lookup = long(key)
except:
try:
lookup = long(key, 16)
except:
return False
else:
return False
# remove item
try:
item = self.pop(lookup)
self.log('>> %s destroyed!' % item)
self.status
return True
except:
return False
def scene_config_load(self, fname):
"""load a scene configuration file
:Parameters:
fname : str
Path to the scene configuration file.
"""
# checks and inits
cfg = ConfigParser()
cfg_check = cfg.read(fname)
if fname not in cfg_check:
raise IOError('could not load scene from %s' % fname)
# check for config
ndata_paths = cfg.get('CONFIG', 'neuron_data_dir')
ndata_paths = ndata_paths.strip().split('\n')
# read per section
for sec in cfg.sections():
# check section
sec_str = sec.split()
cls = sec_str[0]
if cls not in ['Neuron', 'Tetrode']:
continue
kwargs = {}
if len(sec_str) > 1:
kwargs['name'] = ' '.join(sec_str[1:])
# elaborate class and keyword arguments
bad_ndata = False
for k, v in cfg.items(sec):
# read items
if k is None or v is None or k == '' or v == '':
continue
elif k in ['position', 'orientation', 'trajectory']:
if v == 'False':
kwargs[k] = False
elif v == 'Truse':
kwargs[k] = True
else:
kwargs[k] = map(float, v.split())
elif k in ['neuron_data']:
kwargs[k] = v
ndata_path_list = [
osp.join(path, v) for path in ndata_paths
]
added_ndata = self.neuron_data.insert(ndata_path_list)
if added_ndata == 0:
bad_ndata = True
else:
kwargs[k] = v
# delegate action
if bad_ndata:
continue
elif cls == 'Neuron':
self.register_neuron(**kwargs)
elif cls == 'Tetrode':
self.register_recorder(**kwargs)
def scene_config_save(self, fname):
"""save the current scene configuration to a file
:Parameters:
fname : str
Path to save tha cfg to.
"""
# checks and inits
cfg = ConfigParser()
# write CONFIG section
cfg.add_section('CONFIG')
cfg.set('CONFIG', 'frame_size', self.frame_size)
cfg.set('CONFIG', 'sample_rate', self.sample_rate)
ndata_paths = '\t\n'.join(self.neuron_data.paths)
cfg.set('CONFIG', 'neuron_data_dir', ndata_paths)
# helper functions
npy2cfg = lambda x: ' '.join(map(str, x.tolist()))
# add per SimObject
for obj in self.values():
if isinstance(obj, Neuron):
name = 'Neuron %s' % obj.name
cfg.add_section(name)
cfg.set(name, 'cluster',
str(self.cls_dyn.get_cls_for_nrn(obj)))
cfg.set(name, 'position', npy2cfg(obj.position))
if obj.orientation is True or obj.orientation is False:
cfg.set(name, 'orientation', obj.orientation)
else:
cfg.set(name, 'orientation', npy2cfg(obj.orientation))
cfg.set(name, 'rate_of_fire', str(obj.rate_of_fire))
cfg.set(name, 'amplitude', str(obj.amplitude))
cfg.set(name, 'neuron_data', str(obj._neuron_data.filename))
elif isinstance(obj, Recorder):
name = 'Tetrode %s' % obj.name
cfg.add_section(name)
cfg.set(name, 'position', npy2cfg(obj.position))
cfg.set(name, 'orientation', npy2cfg(obj._trajectory))
cfg.set(name, 'snr', str(obj.snr))
# save
save_file = open(fname, 'w')
cfg.write(save_file)
save_file.close()
## methods config loading
def load_config(self, cfg_path=None):
"""loads initialization values from file
:Parameters:
cfg_file : str
Path to the config file. Should be readable by a ConfigParser.
"""
# TODO: implement config file handling
## special methods
def __len__(self):
return len(filter(lambda x: isinstance(x, Neuron), self.values()))
def __str__(self):
return 'BaseSimulation :: %d items' % len(self)