Population

core.Population.Population(
    self,
    geometry,
    neuron,
    name=None,
    stop_condition=None,
    storage_order='post_to_pre',
    copied=False,
)

Structure for a population of homogeneous neurons.

Example:

pop = ann.Population(100, neuron=ann.Izhikevich, name="Excitatory population")

Parameters

Name	Type	Description	Default
geometry	tuple \| int	population geometry as tuple. If an integer is given, it is the size of the population.	required
neuron	Neuron	`Neuron`instance. It can be user-defined or a built-in model.	required
name	str	unique name of the population (optional, it defaults to `pop0`, `pop1`, etc).	`None`
stop_condition	str	a single condition on a neural variable which can stop the simulation whenever it is true.	`None`

Attributes

Name	Description
attributes	List of attribute names.
depth	Depth of the population.
dimension	Number of dimensions of the population.
functions	List of declared functions.
geometry	Geometry of the population.
height	Height of the population.
name	Name of the population
neurons	Returns iteratively each neuron in the population.
parameters	List of parameter names.
ranks	Array of ranks in the population (between 0 and `size - 1`).
refractory	Refractory period (in ms).
size	Size of the population.
targets	List of connected targets.
variables	List of variable names.
width	Width of the population.

Methods

Name	Description
clear	Clears all spiking events previously emitted (history of spikes, delayed spikes).
compute_firing_rate	Tells spiking neurons in the population to compute their mean firing rate over the given window and store the values in the variable `r`.
coordinates_from_rank	Returns the coordinates of a neuron based on its rank.
disable	Temporarily disables computations in this population (including the projections leading to it).
enable	(Re)-enables computations in this population, after they were disabled by the `disable()` method.
get	Returns the value of neural variables and parameters.
load	Load the saved state of the population by `Population.save()`.
neuron	Returns an `IndividualNeuron` object wrapping the neuron with the provided rank or coordinates.
normalized_coordinates_from_rank	Returns normalized coordinates of a neuron based on its rank.
rank_from_coordinates	Returns the rank of a neuron based on coordinates.
reset	Resets all parameters and variables of the population to the value they had before the call to compile().
save	Saves all information about the population (structure, current value of parameters and variables) into a file.
set	Sets the value of neural variables and parameters.
size_in_bytes	Returns the size of allocated memory on the C++ side. Please note that this does not contain monitored data and works only if compile() has been invoked.
sum	Returns the array of weighted sums corresponding to the target:

clear

core.Population.Population.clear()

Clears all spiking events previously emitted (history of spikes, delayed spikes).

Can be useful if you do not want to totally reset a population (i.e. all variables), only to clear the spiking history between two trials.

Note: does nothing for rate-coded networks.

compute_firing_rate

core.Population.Population.compute_firing_rate(window)

Tells spiking neurons in the population to compute their mean firing rate over the given window and store the values in the variable r.

This method has an effect on spiking neurons only.

If this method is not called, r will always be 0.0. r can of course be accessed and recorded as any other variable.

Parameters

Name	Type	Description	Default
window	float	window in ms over which the spikes will be counted.	required

coordinates_from_rank

core.Population.Population.coordinates_from_rank(rank)

Returns the coordinates of a neuron based on its rank.

Parameters

Name	Type	Description	Default
rank	int	Rank of the neuron.	required

Returns

Name	Type	Description
	tuple	Coordinates.

disable

core.Population.Population.disable()

Temporarily disables computations in this population (including the projections leading to it).

You can re-enable it with the enable() method.

enable

core.Population.Population.enable()

(Re)-enables computations in this population, after they were disabled by the disable() method.

The status of the population is accessible through the enabled flag.

get

core.Population.Population.get(name)

Returns the value of neural variables and parameters.

Parameters

Name	Type	Description	Default
name	str	attribute name as a string.	required

load

core.Population.Population.load(filename, pickle_encoding=None)

Load the saved state of the population by Population.save().

Warning: Matlab data can not be loaded.

Example:

pop.load('pop1.npz')
pop.load('pop1.txt')
pop.load('pop1.txt.gz')

Parameters

Name	Type	Description	Default
filename		the filename with relative or absolute path.	required

neuron

core.Population.Population.neuron(*coord)

Returns an IndividualNeuron object wrapping the neuron with the provided rank or coordinates.

Returns

Name	Type	Description
	IndividualNeuron	IndividualNeuron instance.

normalized_coordinates_from_rank

core.Population.Population.normalized_coordinates_from_rank(rank, norm=1.0)

Returns normalized coordinates of a neuron based on its rank. The geometry of the population is mapped to the hypercube [0, 1]^d

Parameters

Name	Type	Description	Default
rank	int	Rank of the neuron	required
norm	float	Norm of the cube (default = 1.0)	`1.0`

Returns

Name	Type	Description
	tuple	Coordinates.

rank_from_coordinates

core.Population.Population.rank_from_coordinates(coord)

Returns the rank of a neuron based on coordinates.

Parameters

Name	Type	Description	Default
coord	tuple	Coordinate tuple, can be multidimensional.	required

Returns

Name	Type	Description
	int	Rank.

reset

core.Population.Population.reset(attributes=None)

Resets all parameters and variables of the population to the value they had before the call to compile().

Parameters

Name	Type	Description	Default
attributes	list	list of attributes (parameter or variable) which should be reinitialized. Default: all attributes.	`None`

save

core.Population.Population.save(filename)

Saves all information about the population (structure, current value of parameters and variables) into a file.

If the file name is ‘.npz’, the data will be saved and compressed using np.savez_compressed (recommended).
If the file name ends with ‘.gz’, the data will be pickled into a binary file and compressed using gzip.
If the file name is ‘.mat’, the data will be saved as a Matlab 7.2 file. Scipy must be installed.
Otherwise, the data will be pickled into a simple binary text file using pickle.

Warning: The ‘.mat’ data will not be loadable by ANNarchy, it is only for external analysis purpose.

Example:

pop.save('pop1.npz')
pop.save('pop1.txt')
pop.save('pop1.txt.gz')
pop.save('pop1.mat')

Parameters

Name	Type	Description	Default
filename	str	Filename, may contain relative or absolute path.	required

set

core.Population.Population.set(values)

Sets the value of neural variables and parameters.

Example:

pop.set({'tau': 20.0, 'r': np.random.rand((8,8)) } )

Parameters

Name	Type	Description	Default
values	dict	dictionary of attributes to be updated.	required

size_in_bytes

core.Population.Population.size_in_bytes()

Returns the size of allocated memory on the C++ side. Please note that this does not contain monitored data and works only if compile() has been invoked.

Returns

Name	Type	Description
	int	Size.

sum

core.Population.Population.sum(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.

Note: it is not possible to distinguish the original population when the same target is used.

Parameters

Name	Type	Description	Default
target	str	the desired projection target.	required