def reset(self, attributes=-1, synapses=False):
"""
Resets all parameters and variables of the projection to the value they had before the call to compile.
*Parameters:*
* **attributes**: list of attributes (parameter or variable) which should be reinitialized. Default: all attributes.
.. note::
Only parameters and variables are reinitialized, not the connectivity structure (including the weights and delays).
The parameter ``synapses`` will be used in a future release to also reinitialize the connectivity structure.
"""
if attributes == -1:
attributes = self.attributes
for var in attributes:
# Skip w
if var=='w':
continue
# check it exists
if not var in self.attributes:
Global._warning("Projection.reset():", var, "is not an attribute of the population, won't reset.")
continue
# Set the value
try:
self.__setattr__(var, self.init[var])
except Exception as e:
Global._print(e)
Global._warning("Projection.reset(): something went wrong while resetting", var)
def histogram(data, binsize=Global.config['dt']):
"""
**Deprecated!!**
Returns for each recorded simulation step the number of spikes occuring in the population.
*Parameters*:
* **data**: the dictionary returned by the get_record() method for the population.
* **binsize**: the duration in milliseconds where spikes are averaged (default: dt).
"""
Global._warning("histogram() is deprecated, use a Monitor instead.")
if isinstance(data['start'], int): # only one recording
duration = data['stop'] - data['start']
else:
duration = 0
for t in range(len(data['start'])):
duration += data['stop'][t] - data['start'][t]
nb_neurons = len(data['data'])
nb_bins = int(duration * Global.config['dt'] / binsize)
spikes = [0 for t in xrange(nb_bins)]
for neuron in range(nb_neurons):
for t in data['data'][neuron]:
spikes[int(t / float(binsize / Global.config['dt']))] += 1
return np.array(spikes)
def sum(self, target):
"""
Returns the array of weighted sums corresponding to the target:
```python
excitatory = pop.sum('exc')
```
For spiking networks, this is equivalent to accessing the conductances directly:
```python
excitatory = pop.g_exc
```
If no incoming projection has the given target, the method returns zeros.
**Note:** it is not possible to distinguish the original population when the same target is used.
:param target: the desired projection target.
"""
# Check if the network is initialized
if not self.initialized:
Global._warning('sum(): the population', self.name,
'is not initialized yet.')
return np.zeros(self.geometry)
# Check if a projection has this type
if not target in self.targets:
Global._warning('sum(): the population', self.name,
'receives no projection with the target', target)
return np.zeros(self.geometry)
# Spiking neurons already have conductances available
if self.neuron_type.type == 'spike':
return getattr(self, 'g_' + target)
# Otherwise, call the Cython method
return getattr(self.cyInstance, 'get_sum_' + target)()
def sum(self, target):
"""
Returns the array of weighted sums corresponding to the target::
excitatory = pop.sum('exc')
For spiking networks, this is equivalent to accessing the conductances directly::
excitatory = pop.g_exc
If no incoming projection has the given target, the method returns zeros.
*Parameter:*
* **target**: the desired projection target.
**Note:** it is not possible to distinguish the original population when the same target is used.
"""
# Check if the network is initialized
if not self.initialized:
Global._warning('sum(): the population', self.name, 'is not initialized yet.')
return np.zeros(self.geometry)
# Check if a projection has this type
if not target in self.targets:
Global._warning('sum(): the population', self.name, 'receives no projection with the target', target)
return np.zeros(self.geometry)
# Spiking neurons already have conductances available
if self.neuron_type.type == 'spike':
return getattr(self, 'g_'+target)
# Otherwise, call the Cython method
return getattr(self.cyInstance, 'get_sum_'+target)()
def _data(self):
"Returns a dictionary containing all information about the population. Used for saving."
desc = {}
desc['name'] = self.name
desc['geometry'] = self.geometry
desc['size'] = self.size
# Attributes
desc['attributes'] = self.attributes
desc['parameters'] = self.parameters
desc['variables'] = self.variables
# Save all attributes
for var in self.attributes:
try:
ctype = self._get_attribute_cpp_type(var)
if var in self.neuron_type.description['local']:
data = self.cyInstance.get_local_attribute_all(var, ctype)
desc[var] = data.reshape(self.geometry)
else:
desc[var] = self.cyInstance.get_global_attribute(
var, ctype)
except:
Global._warning('Can not save the attribute ' + var +
' in the population ' + self.name + '.')
return desc
def __init__(self, rates, schedule=0., period= -1., name=None, copied=False):
neuron = Neuron(
parameters="",
equations=" r = 0.0",
name="Timed Array",
description="Timed array source."
)
# Geometry of the population
geometry = rates.shape[1:]
# Check the schedule
if isinstance(schedule, (int, float)):
if float(schedule) <= 0.0:
schedule = Global.config['dt']
schedule = [ float(schedule*i) for i in range(rates.shape[0])]
if len(schedule) > rates.shape[0]:
Global._error('TimedArray: the length of the schedule parameter cannot exceed the first dimension of the rates parameter.')
if len(schedule) < rates.shape[0]:
Global._warning('TimedArray: the length of the schedule parameter is smaller than the first dimension of the rates parameter (more data than time points). Make sure it is what you expect.')
SpecificPopulation.__init__(self, geometry=geometry, neuron=neuron, name=name, copied=copied)
self.init['schedule'] = schedule
self.init['rates'] = rates
self.init['period'] = period
def set_image(self, image_name):
"""
Sets an image (.png, .jpg or whatever is supported by PIL) into the firing rate of the population.
If the image has a different size from the population, it will be resized.
"""
try:
im = Image.open(image_name)
except : # image does not exist
Global._error('The image ' + image_name + ' does not exist.')
exit(0)
# Resize the image if needed
(width, height) = (self.geometry[1], self.geometry[0])
if im.size != (width, height):
Global._warning('The image ' + image_name + ' does not have the same size '+str(im.size)+' as the population ' + str((width, height)) + '. It will be resized.')
im = im.resize((width, height))
# Check if only the luminance should be extracted
if self.dimension == 2 or self.geometry[2] == 1:
im=im.convert("L")
# Set the rate of the population
if not Global._network[0]['compiled']:
self.r = (np.array(im))/255.
else:
self.cyInstance.set_r(np.array(im).reshape(self.size)/255.)
def histogram(data, binsize=Global.config['dt']):
"""
**Deprecated!!**
Returns for each recorded simulation step the number of spikes occuring in the population.
*Parameters*:
* **data**: the dictionary returned by the get_record() method for the population.
* **binsize**: the duration in milliseconds where spikes are averaged (default: dt).
"""
Global._warning("histogram() is deprecated, use a Monitor instead.")
if isinstance(data['start'], int): # only one recording
duration = data['stop'] - data['start']
else:
duration = 0
for t in range(len(data['start'])):
duration += data['stop'][t] - data['start'][t]
nb_neurons = len(data['data'])
nb_bins = int(duration*Global.config['dt']/binsize)
spikes = [0 for t in xrange(nb_bins)]
for neuron in range(nb_neurons):
for t in data['data'][neuron]:
spikes[int(t/float(binsize/Global.config['dt']))] += 1
return np.array(spikes)
def set_image(self, image_name):
"""
Sets an image (.png, .jpg or whatever is supported by PIL) into the firing rate of the population.
If the image has a different size from the population, it will be resized.
"""
try:
im = Image.open(image_name)
except: # image does not exist
Global._error('The image ' + image_name + ' does not exist.')
exit(0)
# Resize the image if needed
(width, height) = (self.geometry[1], self.geometry[0])
if im.size != (width, height):
Global._warning('The image ' + image_name +
' does not have the same size ' + str(im.size) +
' as the population ' + str((width, height)) +
'. It will be resized.')
im = im.resize((width, height))
# Check if only the luminance should be extracted
if self.dimension == 2 or self.geometry[2] == 1:
im = im.convert("L")
# Set the rate of the population
if not Global._network[0]['compiled']:
self.r = (np.array(im)) / 255.
else:
self.cyInstance.set_r(np.array(im).reshape(self.size) / 255.)
def _data(self):
"Method gathering all info about the projection when calling save()"
if not self.initialized:
Global._error('save_connectivity(): the network has not been compiled yet.')
desc = {}
desc['name'] = self.name
desc['pre'] = self.pre.name
desc['post'] = self.post.name
desc['target'] = self.target
desc['post_ranks'] = self.post_ranks
desc['attributes'] = self.attributes
desc['parameters'] = self.parameters
desc['variables'] = self.variables
desc['pre_ranks'] = self.cyInstance.pre_rank_all()
desc['delays'] = self._get_delay()
# Attributes to save
attributes = self.attributes
if not 'w' in self.attributes:
attributes.append('w')
# Save all attributes
for var in attributes:
try:
desc[var] = getattr(self.cyInstance, 'get_'+var)()
except:
Global._warning('Can not save the attribute ' + var + ' in the projection.')
return desc
def reset(self, attributes=-1):
"""
Resets all parameters and variables of the population to the value they had before the call to compile().
*Parameters:*
* **attributes**: list of attributes (parameter or variable) which should be reinitialized. Default: all attributes.
"""
if attributes == -1:
try:
self.set(self.init)
except Exception as e:
Global._print(e)
Global._error("Population.reset(): something went wrong while resetting", var)
else: # only some of them
for var in attributes:
# check it exists
if not var in self.attributes:
Global._warning("Population.reset():", var, "is not an attribute of the population, skipping.")
continue
try:
self.__setattr__(var, self.init[var])
except Exception as e:
Global._print(e)
Global._warning("Population.reset(): something went wrong while resetting", var)
self.cyInstance.activate(self.enabled)
self.cyInstance.reset()
def start_record(self, variable, period=None, ranks='all'):
"""
**Deprecated!!**
Start recording neural variables.
Parameter:
* **variable**: single variable name or list of variable names.
* **period**: delay in ms between two recording (default: dt). Not valid for the ``spike`` variable.
* **ranks**: list of ranks of the neurons to record (default: 'all').
Example::
pop1.start_record('r')
pop2.start_record(['mp', 'r'], period=10.0)
pop3.start_record(['spike'])
pop4.start_record(['r'], ranks=range(10, 100))
"""
Global._warning(
"recording from a Population is deprecated, use a Monitor instead."
)
from .Record import Monitor
if ranks == 'all':
self._monitor = Monitor(self, variable, period=period)
else:
self._monitor = Monitor(PopulationView(self, ranks),
variable,
period=period)
def reset(self, attributes=-1):
"""
Resets all parameters and variables of the population to the value they had before the call to compile().
:param attributes: list of attributes (parameter or variable) which should be reinitialized. Default: all attributes.
"""
if attributes == -1:
try:
self.set(self.init)
except Exception as e:
Global._print(e)
Global._error(
"Population.reset(): something went wrong while resetting."
)
else: # only some of them
for var in attributes:
# check it exists
if not var in self.attributes:
Global._warning(
"Population.reset():", var,
"is not an attribute of the population, skipping.")
continue
try:
self.__setattr__(var, self.init[var])
except Exception as e:
Global._print(e)
Global._warning(
"Population.reset(): something went wrong while resetting",
var)
self.cyInstance.activate(self.enabled)
self.cyInstance.reset()
def get_populations(self):
"""
Returns a list of all declared populations in this network.
"""
if self.populations == []:
Global._warning("Network.get_populations(): no populations attached to this network.")
return self.populations
def _function(self, func):
"Access a user defined function"
if not self.initialized:
Global._warning('the network is not compiled yet, cannot access the function ' + func)
return
return getattr(self.cyInstance, func)
def refractory(self, value):
if self.neuron_type.description['type'] == 'spike':
if isinstance(self.neuron_type.description['refractory'], str):
Global._warning(
"The refractory period is linked to the neural variable",
self.neuron_type.description['refractory'],
", doing nothing... Change its value instead.")
return
if self.initialized:
if isinstance(value, RandomDistribution):
refs = (value.get_values(self.size) /
Global.config['dt']).astype(int)
elif isinstance(value, np.ndarray):
refs = (value / Global.config['dt']).astype(int).reshape(
self.size)
else:
refs = (value / Global.config['dt'] *
np.ones(self.size)).astype(int)
# TODO cast into int
self.cyInstance.set_refractory(refs)
else: # not initialized yet, saving for later
self.neuron_type.description['refractory'] = value
else:
Global._warning(
'Rate-coded neurons do not have refractory periods...')
def __getattr__(self, name):
" Method called when accessing an attribute."
if name == 'proj':
return object.__getattribute__(self, name)
elif hasattr(self, 'proj'):
if name == 'rank': # TODO: remove 'rank' in a future version
Global._warning(
"Dendrite.rank: the attribute is deprecated, use Dendrite.pre_ranks instead."
)
return self.proj.cyInstance.pre_rank(self.idx)
elif name == 'pre_rank':
return self.proj.cyInstance.pre_rank(self.idx)
elif name == 'delay':
if self.proj.uniform_delay == -1:
return [
d * Global.config['dt'] for d in
self.proj.cyInstance.get_dendrite_delay(self.idx)
]
else:
return self.proj.max_delay * Global.config['dt']
elif name in self.proj.attributes:
return getattr(self.proj.cyInstance,
'get_dendrite_' + name)(self.idx)
else:
return object.__getattribute__(self, name)
else:
return object.__getattribute__(self, name)
def start_record(self, variable, period=None, ranks="all"):
"""
**Deprecated!!**
Start recording neural variables.
Parameter:
* **variable**: single variable name or list of variable names.
* **period**: delay in ms between two recording (default: dt). Not valid for the ``spike`` variable.
* **ranks**: list of ranks of the neurons to record (default: 'all').
Example::
pop1.start_record('r')
pop2.start_record(['mp', 'r'], period=10.0)
pop3.start_record(['spike'])
pop4.start_record(['r'], ranks=range(10, 100))
"""
Global._warning("recording from a Population is deprecated, use a Monitor instead.")
from .Record import Monitor
if ranks == "all":
self._monitor = Monitor(self, variable, period=period)
else:
self._monitor = Monitor(PopulationView(self, ranks), variable, period=period)
def pause_record(self):
"""
**Deprecated!!**
Pause in recording the defined variables.
"""
Global._warning("recording from a Dendrite is deprecated, use a Monitor instead.")
self.proj.recorded_variables[self.post_rank].pause()
def resume_record(self):
"""
**Deprecated!!**
Resume recording the previous defined variables.
"""
Global._warning("recording from a Dendrite is deprecated, use a Monitor instead.")
self.proj.recorded_variables[self.post_rank].resume()
def get_populations(self):
"""
Returns a list of all declared populations in this network.
"""
if self.populations == []:
Global._warning(
"Network.get_populations(): no populations attached to this network."
)
return self.populations
def resume_record(self):
"""
**Deprecated!!**
Resume recording the previous defined variables.
"""
Global._warning(
"recording from a Dendrite is deprecated, use a Monitor instead.")
self.proj.recorded_variables[self.post_rank].resume()
def refractory(self):
if self.neuron_type.description["type"] == "spike":
if self.initialized:
return Global.config["dt"] * self.cyInstance.get_refractory()
else:
return self.neuron_type.description["refractory"]
else:
Global._warning("rate-coded neurons do not have refractory periods...")
return None
def _function(self, func):
"Access a user defined function"
if not self.initialized:
Global._warning(
'the network is not compiled yet, cannot access the function '
+ func)
return
return getattr(self.cyInstance, func)
def pause_record(self):
"""
**Deprecated!!**
Pause in recording the defined variables.
"""
Global._warning(
"recording from a Dendrite is deprecated, use a Monitor instead.")
self.proj.recorded_variables[self.post_rank].pause()
def refractory(self):
if self.neuron_type.description['type'] == 'spike':
if self.initialized:
return Global.config['dt']*self.cyInstance.get_refractory()
else :
return self.neuron_type.description['refractory']
else:
Global._warning('rate-coded neurons do not have refractory periods...')
return None
def refractory(self):
if self.neuron_type.description['type'] == 'spike':
if self.initialized:
return Global.config['dt'] * self.cyInstance.get_refractory()
else:
return self.neuron_type.description['refractory']
else:
Global._warning(
'rate-coded neurons do not have refractory periods...')
return None
def _proj_recorder_class(self, proj):
"""
Generate the code for the recorder object.
Returns:
* complete code as string
Templates:
record
"""
if Global.config['paradigm'] == "openmp":
template = RecTemplate.omp_projection
elif Global.config['paradigm'] == "cuda":
template = RecTemplate.cuda_projection
else:
raise NotImplementedError
# Specific template
if 'monitor_class' in proj._specific_template.keys():
return proj._specific_template['monitor_class']
init_code = ""
recording_code = ""
struct_code = ""
attributes = []
for var in proj.synapse_type.description['parameters'] + proj.synapse_type.description['variables']:
# Avoid doublons
if var['name'] in attributes:
continue
attributes.append(var['name'])
# Get the locality
locality = var['locality']
# Special case for single weights
if var['name'] == "w" and proj._has_single_weight():
locality = 'global'
# Get the template for the structure declaration
struct_code += template[locality]['struct'] % {'type' : var['ctype'], 'name': var['name']}
# Get the initialization code
init_code += template[locality]['init'] % {'type' : var['ctype'], 'name': var['name']}
# Get the recording code
if proj._storage_format == "lil":
recording_code += template[locality]['recording'] % {'id': proj.id, 'type' : var['ctype'], 'name': var['name']}
else:
Global._warning("Monitor: variable "+ var['name'] + " cannot be recorded for a projection using the csr format...")
return template['struct'] % {'id': proj.id, 'init_code': init_code, 'recording_code': recording_code, 'struct_code': struct_code}
def _load_pop_data(pop, desc):
"""
Update a population with the stored data set.
"""
if not 'attributes' in desc.keys():
_error('Saved with a too old version of ANNarchy (< 4.2).', exit=True)
for var in desc['attributes']:
try:
getattr(pop.cyInstance, 'set_'+var)(desc[var])
except:
Global._warning('Can not load the variable ' + var + ' in the population ' + pop.name)
Global._print('Skipping this variable.')
continue
def stop_record(self):
"""
**Deprecated!!**
Stops recording all the previously defined variables.
Example::
pop1.stop_record()
"""
Global._warning("recording from a Population is deprecated, use a Monitor instead.")
if self._monitor:
self._monitor.stop()
self._monitor = None
def __getattr__(self, name):
# Method called when accessing an attribute.
if name == 'proj':
return object.__getattribute__(self, name)
elif hasattr(self, 'proj'):
if name == 'rank': # TODO: remove 'rank' in a future version
Global._warning(
"Dendrite.rank: the attribute is deprecated, use Dendrite.pre_ranks instead."
)
return self.proj.cyInstance.pre_rank(self.idx)
elif name == 'pre_rank':
return self.proj.cyInstance.pre_rank(self.idx)
elif name == 'delay':
if self.proj.uniform_delay == -1:
return [
d * Global.config['dt'] for d in
self.proj.cyInstance.get_dendrite_delay(self.idx)
]
else:
return self.proj.max_delay * Global.config['dt']
elif name == "w" and self.proj._has_single_weight():
return self.proj.cyInstance.get_global_attribute(
name, Global.config["precision"])
elif name in self.proj.attributes:
# Determine C++ data type
ctype = None
for var in self.proj.synapse_type.description[
'variables'] + self.proj.synapse_type.description[
'parameters']:
if var['name'] == name:
ctype = var['ctype']
if name in self.proj.synapse_type.description['local']:
return self.proj.cyInstance.get_local_attribute_row(
name, self.idx, ctype)
elif name in self.proj.synapse_type.description['semiglobal']:
return self.proj.cyInstance.get_semiglobal_attribute(
name, self.idx, ctype)
else:
return self.proj.cyInstance.get_global_attribute(
name, ctype)
else:
return object.__getattribute__(self, name)
else:
return object.__getattribute__(self, name)
def reset(self, synapses=False):
"""
Resets all parameters and variables to the value they had before the call to compile.
*Parameters*:
* **synapses**: if True, the connections will also be erased (default: False).
.. note::
Not implemented yet...
"""
self._init_attributes()
if synapses:
Global._warning('Resetting synapses is not implemented yet...')
def start_record(self, variable, period=None):
"""
**Deprecated!!**
Starts recording the given variables.
*Parameter*:
* **variable**: single variable name or list of variable names.
* **period**: period of recording in milliseconds.
"""
Global._warning("recording from a Dendrite is deprecated, use a Monitor instead.")
from .Record import Monitor
self.proj.recorded_variables[self.post_rank] = Monitor(self, variable, period)
def refractory(self, value):
if self.neuron_type.description['type'] == 'spike':
if self.initialized:
if isinstance(value, RandomDistribution):
refs = (value.get_values(self.size)/Global.config['dt']).astype(int)
elif isinstance(value, np.ndarray):
refs = (value / Global.config['dt']).astype(int).reshape(self.size)
else:
refs = (value/ Global.config['dt']*np.ones(self.size)).astype(int)
# TODO cast into int
self.cyInstance.set_refractory(refs)
else: # not initialized yet, saving for later
self.neuron_type.description['refractory'] = value
else:
Global._warning('rate-coded neurons do not have refractory periods...')
def population_rate(data, smooth=Global.config['dt']):
"""
**Deprecated!!**
Takes the recorded spikes of a population and returns a smoothed firing rate for the whole population.
*Parameters*:
* **data**: the dictionary returned by ``get_record()[pop]['spike']``
* **smooth**: the smoothing time constant (default: dt)
"""
Global._warning("population_rate() is deprecated, use a Monitor instead.")
import ANNarchy.core.cython_ext.Transformations as Transformations
return Transformations.population_rate(data, smooth)
def population_rate(data, smooth=Global.config['dt']):
"""
**Deprecated!!**
Takes the recorded spikes of a population and returns a smoothed firing rate for the whole population.
*Parameters*:
* **data**: the dictionary returned by ``get_record()[pop]['spike']``
* **smooth**: the smoothing time constant (default: dt)
"""
Global._warning("population_rate() is deprecated, use a Monitor instead.")
import ANNarchy.core.cython_ext.Transformations as Transformations
return Transformations.population_rate(data, smooth)
def get_record(self, variable=None):
"""
**Deprecated!!**
Returns the recorded data as one matrix or a dictionary if more then one variable is requested.
The first dimension is the neuron index, the last dimension represents the number of simulation steps.
*Parameter*:
* **variable**: single variable name or list of variable names. If no argument provided, all recorded data is returned.
"""
Global._warning("recording from a Dendrite is deprecated, use a Monitor instead.")
data_dict = self.proj.recorded_variables[self.post_rank].get(variable)
return data_dict
def stop_record(self):
"""
**Deprecated!!**
Stops recording all the previously defined variables.
Example::
pop1.stop_record()
"""
Global._warning(
"recording from a Population is deprecated, use a Monitor instead."
)
if self._monitor:
self._monitor.stop()
self._monitor = None
def get_record(self, variable=None):
"""
**Deprecated!!**
Returns the recorded data as one matrix or a dictionary if more then one variable is requested.
The first dimension is the neuron index, the last dimension represents the number of simulation steps.
*Parameter*:
* **variable**: single variable name or list of variable names. If no argument provided, all recorded data is returned.
"""
Global._warning(
"recording from a Dendrite is deprecated, use a Monitor instead.")
data_dict = self.proj.recorded_variables[self.post_rank].get(variable)
return data_dict
def start_record(self, variable, period=None):
"""
**Deprecated!!**
Starts recording the given variables.
*Parameter*:
* **variable**: single variable name or list of variable names.
* **period**: period of recording in milliseconds.
"""
Global._warning(
"recording from a Dendrite is deprecated, use a Monitor instead.")
from .Record import Monitor
self.proj.recorded_variables[self.post_rank] = Monitor(
self, variable, period)
def sparse_random_matrix(pre, post, p, weight, delay=0):
"""
Returns a sparse (lil) matrix to connect the pre and post populations with the probability p and the value weight.
"""
try:
from scipy.sparse import lil_matrix
except:
Global._warning("scipy is not installed, sparse matrices won't work")
return None
from random import sample
W=lil_matrix((pre, post))
for i in xrange(pre):
k=np.random.binomial(post,p,1)[0]
W.rows[i]=sample(xrange(post),k)
W.data[i]=[weight]*k
return W
def sparse_random_matrix(pre, post, p, weight, delay=0):
"""
Returns a sparse (lil) matrix to connect the pre and post populations with the probability p and the value weight.
"""
try:
from scipy.sparse import lil_matrix
except:
Global._warning("scipy is not installed, sparse matrices won't work")
return None
from random import sample
W = lil_matrix((pre, post))
for i in range(pre):
k = np.random.binomial(post, p, 1)[0]
W.rows[i] = sample(range(post), k)
W.data[i] = [weight] * k
return W
def resume_record(self, variable=None):
"""
**Deprecated!!**
Resume recording the previous defined variables.
*Parameter*:
* **variable**: single variable name or list of variable names.
Example::
pop1.resume_record('r')
pop2.resume_record(['mp', 'r'])
"""
Global._warning("recording from a Population is deprecated, use a Monitor instead.")
if self._monitor:
self._monitor.resume(variable)
def _load_pop_data(self, desc):
"""
Updates the population with the stored data set.
"""
if not 'attributes' in desc.keys():
Global._error('Saved with a too old version of ANNarchy (< 4.2).',
exit=True)
for var in desc['attributes']:
try:
self._set_cython_attribute(var, desc[var])
except Exception as e:
Global._print(e)
Global._warning('Can not load the variable ' + var +
' in the population ' + self.name)
Global._print('Skipping this variable.')
continue
def pause_record(self, variable=None):
"""
**Deprecated!!**
Pauses the recording of variables (can be resumed later with resume_record()).
*Parameter*:
* **variable**: single variable name or list of variable names. If no argument is provided all recordings will pause.
Example::
pop1.pause_record('r')
pop2.pause_record(['mp', 'r'])
"""
Global._warning("recording from a Population is deprecated, use a Monitor instead.")
if self._monitor:
self._monitor.pause(variable)
def _data(self):
"Returns a dictionary containing all information about the population. Used for saving."
desc = {}
desc['name'] = self.name
desc['geometry'] = self.geometry
desc['size'] = self.size
# Attributes
desc['attributes'] = self.attributes
desc['parameters'] = self.parameters
desc['variables'] = self.variables
# Save all attributes
for var in self.attributes:
try:
desc[var] = getattr(self.cyInstance, 'get_'+var)()
except:
Global._warning('Can not save the attribute ' + var + 'in the population ' + self.name + '.')
return desc
def _data(self):
"Returns a dictionary containing all information about the population. Used for saving."
desc = {}
desc["name"] = self.name
desc["geometry"] = self.geometry
desc["size"] = self.size
# Attributes
desc["attributes"] = self.attributes
desc["parameters"] = self.parameters
desc["variables"] = self.variables
# Save all attributes
for var in self.attributes:
try:
desc[var] = getattr(self.cyInstance, "get_" + var)()
except:
Global._warning("Can not save the attribute " + var + "in the population " + self.name + ".")
return desc
def disable_learning(self, update=None):
"""
Disables learning for all synapses of this projection.
The effect depends on the rate-coded or spiking nature of the projection:
* **Rate-coded**: the updating of all synaptic variables is disabled (including the weights ``w``). This is equivalent to ``proj.update = False``.
* **Spiking**: the updating of the weights ``w`` is disabled, but all other variables are updated. This is equivalent to ``proj.plasticity = False``.
This method is useful when performing some tests on a trained network without messing with the learned weights.
"""
try:
if self.synapse_type.type == 'rate':
self.cyInstance._set_update(False)
else:
self.cyInstance._set_plasticity(False)
except:
Global._warning('disabling learning is only possible after compile().')
def rank_from_coordinates(self, coord):
"""
Returns the rank of a neuron based on coordinates.
*Parameter*:
* **coord**: coordinate tuple, can be multidimensional.
"""
try:
rank = self._rank_from_coord( coord, self.geometry )
except:
Global._error('There is no neuron of coordinates', coord, 'in the population', self.name, self.geometry)
exit(0)
if rank > self.size:
Global._warning('Error when accessing neuron', str(coord), ': the population' , self.name , 'has only', self.size, 'neurons (geometry '+ str(self.geometry) +').')
exit(0)
else:
return rank
def refractory(self, value):
if self.neuron_type.description['type'] == 'spike':
if self.initialized:
if isinstance(value, RandomDistribution):
refs = (value.get_values(self.size) /
Global.config['dt']).astype(int)
elif isinstance(value, np.ndarray):
refs = (value / Global.config['dt']).astype(int).reshape(
self.size)
else:
refs = (value / Global.config['dt'] *
np.ones(self.size)).astype(int)
# TODO cast into int
self.cyInstance.set_refractory(refs)
else: # not initialized yet, saving for later
self.neuron_type.description['refractory'] = value
else:
Global._warning(
'rate-coded neurons do not have refractory periods...')
def _data(self):
"Returns a dictionary containing all information about the population. Used for saving."
desc = {}
desc['name'] = self.name
desc['geometry'] = self.geometry
desc['size'] = self.size
# Attributes
desc['attributes'] = self.attributes
desc['parameters'] = self.parameters
desc['variables'] = self.variables
# Save all attributes
for var in self.attributes:
try:
desc[var] = getattr(self.cyInstance, 'get_' + var)()
except:
Global._warning('Can not save the attribute ' + var +
'in the population ' + self.name + '.')
return desc
def get(self, name):
"""
Returns the value of a variable/parameter.
*Parameter*:
* *name*: name of the parameter/variable::
dendrite.get('w')
"""
if name == 'rank':
Global._warning("Dendrite.get('rank'): the attribute is deprecated, use Dendrite.pre_ranks instead.")
return self.proj.cyInstance.pre_rank(self.idx)
elif name == 'pre_ranks':
return self.proj.cyInstance.pre_rank(self.idx)
elif name in self.attributes:
return getattr(self.proj.cyInstance, 'get_dendrite_'+name)(self.idx)
else:
Global._error("Dendrite has no parameter/variable called", name)
def _store_connectivity(self, method, args, delay, storage_format="lil", storage_order="post_to_pre"):
"""
Store connectivity data. This function is called from cython_ext.Connectors module.
"""
if self._connection_method != None:
Global._warning("Projection ", self.proj.name, " was already connected ... data will be overwritten.")
# Store connectivity pattern parameters
self._connection_method = method
self._connection_args = args
self._connection_delay = delay
self._storage_format = storage_format
self._storage_order = storage_order
# Analyse the delay
if isinstance(delay, (int, float)): # Uniform delay
self.max_delay = round(delay/Global.config['dt'])
self.uniform_delay = round(delay/Global.config['dt'])
elif isinstance(delay, RandomDistribution): # Non-uniform delay
self.uniform_delay = -1
# Ensure no negative delays are generated
if delay.min is None or delay.min < Global.config['dt']:
delay.min = Global.config['dt']
# The user needs to provide a max in order to compute max_delay
if delay.max is None:
Global._error('Projection.connect_xxx(): if you use a non-bounded random distribution for the delays (e.g. Normal), you need to set the max argument to limit the maximal delay.')
self.max_delay = round(delay.max/Global.config['dt'])
elif isinstance(delay, (list, np.ndarray)): # connect_from_matrix/sparse
if len(delay) > 0:
self.uniform_delay = -1
self.max_delay = round(max([max(l) for l in delay])/Global.config['dt'])
else: # list is empty, no delay
self.max_delay = -1
self.uniform_delay = -1
else:
Global._error('Projection.connect_xxx(): delays are not valid!')
# Transmit the max delay to the pre pop
if isinstance(self.pre, PopulationView):
self.pre.population.max_delay = max(self.max_delay, self.pre.population.max_delay)
else:
self.pre.max_delay = max(self.max_delay, self.pre.max_delay)
def disable_learning(self, update=None):
"""
Disables learning for all synapses of this projection.
The effect depends on the rate-coded or spiking nature of the projection:
* **Rate-coded**: the updating of all synaptic variables is disabled (including the weights ``w``). This is equivalent to ``proj.update = False``.
* **Spiking**: the updating of the weights ``w`` is disabled, but all other variables are updated. This is equivalent to ``proj.plasticity = False``.
This method is useful when performing some tests on a trained network without messing with the learned weights.
"""
try:
if self.synapse_type.type == 'rate':
self.cyInstance._set_update(False)
else:
self.cyInstance._set_plasticity(False)
except Exception as e:
Global._warning('disabling learning is only possible after compile().')
def pause_record(self, variable=None):
"""
**Deprecated!!**
Pauses the recording of variables (can be resumed later with resume_record()).
*Parameter*:
* **variable**: single variable name or list of variable names. If no argument is provided all recordings will pause.
Example::
pop1.pause_record('r')
pop2.pause_record(['mp', 'r'])
"""
Global._warning(
"recording from a Population is deprecated, use a Monitor instead."
)
if self._monitor:
self._monitor.pause(variable)
def resume_record(self, variable=None):
"""
**Deprecated!!**
Resume recording the previous defined variables.
*Parameter*:
* **variable**: single variable name or list of variable names.
Example::
pop1.resume_record('r')
pop2.resume_record(['mp', 'r'])
"""
Global._warning(
"recording from a Population is deprecated, use a Monitor instead."
)
if self._monitor:
self._monitor.resume(variable)