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

class
BaseStructure
[source]¶ Bases:
object

describe
(template='structure_default.txt', engine='default')[source]¶ Returns a humanreadable 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.


class
Line
(dx=1.0, x0=0.0, y=0.0, z=0.0)[source]¶ 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 zcoordinates of all points in the line.
 x0:
 xcoordinate of the first point in the line.

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

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)[source]¶ 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 zcoordinate 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')¶

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)[source]¶ 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 zindex 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')¶

class
RandomStructure
(boundary, origin=(0.0, 0.0, 0.0), rng=None)[source]¶ 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')¶
Shape classes¶
The Space class¶

class
Space
(axes=None, scale_factor=1.0, offset=0.0, periodic_boundaries=None)[source]¶ Class representing a space within distances can be calculated. The space is Cartesian, may be 1, 2 or 3dimensional, 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 postsynaptic 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
= {'xz': [0, 2], 'yz': [1, 2], 'x': [0], 'xy': [0, 1], None: range(0, 3), 'xyz': range(0, 3), 'z': [2], 'y': [1]}¶

distances
(A, B, expand=False)[source]¶ Calculate the distance matrix between two sets of coordinates, given the topology of the current space. From http://projects.scipy.org/pipermail/numpydiscussion/2007April/027203.html
Implementing your own Shape¶
Todo
write this
Implementing your own Structure¶
Todo
write this