Spatial structure

Structure classes

Structure classes all inherit from the following base class, and inherit its methods:

class BaseStructure

Bases: object

get_parameters()

Return a dict containing the parameters of the Structure.

describe(template='structure_default.txt', engine='default')

Returns a human-readable description of the network structure.

The output may be customized by specifying a different template togther with an associated template engine (see pyNN.descriptions).

If template is None, then a dictionary containing the template context will be returned.

generate_positions(n)

Calculate and return the positions of n neurons positioned according to this structure.

class Line(dx=1.0, x0=0.0, y=0.0, z=0.0)

Bases: pyNN.space.BaseStructure

Represents a structure with neurons distributed evenly on a straight line.

Arguments:

dx:

distance between points in the line.

y, z,:

y- and z-coordinates of all points in the line.

x0:

x-coordinate of the first point in the line.

parameter_names = ('dx', 'x0', 'y', 'z')

generate_positions(n)

Calculate and return the positions of n neurons positioned according to this structure.

class Grid2D(aspect_ratio=1.0, dx=1.0, dy=1.0, x0=0.0, y0=0.0, z=0, fill_order='sequential', rng=None)

Bases: pyNN.space.BaseStructure

Represents a structure with neurons distributed on a 2D grid.

Arguments:

dx, dy:

distances between points in the x, y directions.

x0, y0:

coordinates of the starting corner of the grid.

z:

the z-coordinate of all points in the grid.

aspect_ratio:

ratio of the number of grid points per side (not the ratio of the side lengths, unless dx == dy)

fill_order:

may be ‘sequential’ or ‘random’

parameter_names = ('aspect_ratio', 'dx', 'dy', 'x0', 'y0', 'z', 'fill_order')

calculate_size(n)

docstring goes here

generate_positions(n)

Calculate and return the positions of n neurons positioned according to this structure.

class Grid3D(aspect_ratioXY=1.0, aspect_ratioXZ=1.0, dx=1.0, dy=1.0, dz=1.0, x0=0.0, y0=0.0, z0=0, fill_order='sequential', rng=None)

Bases: pyNN.space.BaseStructure

Represents a structure with neurons distributed on a 3D grid.

Arguments:

dx, dy, dz:

distances between points in the x, y, z directions.

x0, y0. z0:

coordinates of the starting corner of the grid.

aspect_ratioXY, aspect_ratioXZ:

ratios of the number of grid points per side (not the ratio of the side lengths, unless dx == dy == dz)

fill_order:

may be ‘sequential’ or ‘random’.

If fill_order is ‘sequential’, the z-index will be filled first, then y then x, i.e. the first cell will be at (0,0,0) (given default values for the other arguments), the second at (0,0,1), etc.

parameter_names = ('aspect_ratios', 'dx', 'dy', 'dz', 'x0', 'y0', 'z0', 'fill_order')

calculate_size(n)

docstring goes here

generate_positions(n)

Calculate and return the positions of n neurons positioned according to this structure.

class RandomStructure(boundary, origin=(0.0, 0.0, 0.0), rng=None)

Bases: pyNN.space.BaseStructure

Represents a structure with neurons distributed randomly within a given volume.

Arguments:

boundary - a subclass of Shape. origin - the coordinates (x,y,z) of the centre of the volume.

parameter_names = ('boundary', 'origin', 'rng')

generate_positions(n)

Calculate and return the positions of n neurons positioned according to this structure.

Shape classes

class Cuboid(width, height, depth)

Bases: pyNN.space.Shape

Represents a cuboidal volume within which neurons may be distributed.

Arguments:

height:

extent in y direction

width:

extent in x direction

depth:

extent in z direction

sample(n, rng)

Return n points distributed randomly with uniform density within the cuboid.

class Sphere(radius)

Bases: pyNN.space.Shape

Represents a spherical volume within which neurons may be distributed.

sample(n, rng)

Return n points distributed randomly with uniform density within the sphere.

The Space class

class Space(axes=None, scale_factor=1.0, offset=0.0, periodic_boundaries=None)

Class representing a space within distances can be calculated. The space is Cartesian, may be 1-, 2- or 3-dimensional, and may have periodic boundaries in any of the dimensions.

Arguments:

axes:

if not supplied, then the 3D distance is calculated. If supplied, axes should be a string containing the axes to be used, e.g. ‘x’, or ‘yz’. axes=’xyz’ is the same as axes=None.

scale_factor:

it may be that the pre and post populations use different units for position, e.g. degrees and µm. In this case, scale_factor can be specified, which is applied to the positions in the post-synaptic population.

offset:

if the origins of the coordinate systems of the pre- and post- synaptic populations are different, offset can be used to adjust for this difference. The offset is applied before any scaling.

periodic_boundaries:

either None, or a tuple giving the boundaries for each dimension, e.g. ((x_min, x_max), None, (z_min, z_max)).

AXES = {'x': [0], 'y': [1], 'z': [2], 'xy': [0, 1], 'yz': [1, 2], 'xz': [0, 2], 'xyz': range(0, 3), None: range(0, 3)}

distances(A, B, expand=False)

Calculate the distance matrix between two sets of coordinates, given the topology of the current space. From http://projects.scipy.org/pipermail/numpy-discussion/2007-April/027203.html

distance_generator(f, g)

Implementing your own Shape

Todo

write this

Implementing your own Structure

Todo

write this