core.reference.slices

Module: core.reference.slices

A set of methods to get coordinate maps which represent slices in space.

Functions

nipy.core.reference.slices.bounding_box(coordmap, shape)

Determine a valid bounding box from a CoordinateMap and a shape.

Parameters:

coordmap : CoordinateMap or AffineTransform

shape : (int)

Tuple of ints.

Returns:

limits : (float)

Tuple of floats.

Examples

>>> A = AffineTransform.from_start_step('ijk', lps_output_coordnames, [2,4,6], [1,3,5])
>>> bounding_box(A, (30,40,20))
([2.0, 31.0], [4.0, 121.0], [6.0, 101.0])
>>> 

nipy.core.reference.slices.xslice(x, y_spec, z_spec, output_space='')

Return an LPS slice through a 3d box with x fixed.

Parameters:

x : float

The value at which x is fixed.

yspec : ([float,float], int)

Tuple representing the y-limits of the bounding box and the number of points.

zspec : ([float,float], int)

Tuple representing the z-limits of the bounding box and the number of points.

output_space : str, optional

Origin of the range CoordinateSystem.

Returns:

affine_transform : AffineTransform

An affine transform that describes an plane in LPS coordinates with x fixed.

Examples

>>> y_spec = ([-114,114], 115) # voxels of size 2 in y, starting at -114, ending at 114
>>> z_spec = ([-70,100], 86) # voxels of size 2 in z, starting at -70, ending at 100
>>> x30 = xslice(30, y_spec, z_spec)
>>> x30([0,0])
array([  30., -114.,  -70.])
>>> x30([114,85])
array([  30.,  114.,  100.])
>>> x30
AffineTransform(
   function_domain=CoordinateSystem(coord_names=('i_y', 'i_z'), name='slice', coord_dtype=float64),
   function_range=CoordinateSystem(coord_names=('x+LR', 'y+PA', 'z+SI'), name='', coord_dtype=float64),
   affine=array([[   0.,    0.,   30.],
                 [   2.,    0., -114.],
                 [   0.,    2.,  -70.],
                 [   0.,    0.,    1.]])
)
>>> bounding_box(x30, (y_spec[1], z_spec[1]))
([30.0, 30.0], [-114.0, 114.0], [-70.0, 100.0])

nipy.core.reference.slices.yslice(y, x_spec, z_spec, output_space='')

Return a slice through a 3d box with y fixed.

Parameters:

y : float

The value at which y is fixed.

xspec : ([float,float], int)

Tuple representing the x-limits of the bounding box and the number of points.

zspec : ([float,float], int)

Tuple representing the z-limits of the bounding box and the number of points.

output_space : str, optional

Origin of the range CoordinateSystem.

Returns:

affine_transform : AffineTransform

An affine transform that describes an plane in LPS coordinates with y fixed.

Examples

>>> x_spec = ([-92,92], 93) # voxels of size 2 in x, starting at -92, ending at 92
>>> z_spec = ([-70,100], 86) # voxels of size 2 in z, starting at -70, ending at 100
>>> 

>>> y70 = yslice(70, x_spec, z_spec)
>>> y70
AffineTransform(
   function_domain=CoordinateSystem(coord_names=('i_x', 'i_z'), name='slice', coord_dtype=float64),
   function_range=CoordinateSystem(coord_names=('x+LR', 'y+PA', 'z+SI'), name='', coord_dtype=float64),
   affine=array([[  2.,   0., -92.],
                 [  0.,   0.,  70.],
                 [  0.,   2., -70.],
                 [  0.,   0.,   1.]])
)
>>> y70([0,0])
array([-92.,  70., -70.])
>>> y70([92,85])
array([  92.,   70.,  100.])
>>> 
>>> bounding_box(y70, (x_spec[1], z_spec[1]))
([-92.0, 92.0], [70.0, 70.0], [-70.0, 100.0])

nipy.core.reference.slices.zslice(z, x_spec, y_spec, output_space='')

Return a slice through a 3d box with z fixed.

Parameters:

z : float

The value at which z is fixed.

x_spec : ([float,float], int)

Tuple representing the x-limits of the bounding box and the number of points.

y_spec : ([float,float], int)

Tuple representing the y-limits of the bounding box and the number of points.

output_space : str, optional

Origin of the range CoordinateSystem.

Returns:

affine_transform : AffineTransform

An affine transform that describes an plane in LPS coordinates with z fixed.

Examples

>>> x_spec = ([-92,92], 93) # voxels of size 2 in x, starting at -92, ending at 92
>>> y_spec = ([-114,114], 115) # voxels of size 2 in y, starting at -114, ending at 114
>>> z40 = zslice(40, x_spec, y_spec)
>>> z40
AffineTransform(
   function_domain=CoordinateSystem(coord_names=('i_x', 'i_y'), name='slice', coord_dtype=float64),
   function_range=CoordinateSystem(coord_names=('x+LR', 'y+PA', 'z+SI'), name='', coord_dtype=float64),
   affine=array([[   2.,    0.,  -92.],
                 [   0.,    2., -114.],
                 [   0.,    0.,   40.],
                 [   0.,    0.,    1.]])
)
>>> 
>>> z40([0,0])
array([ -92., -114.,   40.])
>>> z40([92,114])
array([  92.,  114.,   40.])

>>> bounding_box(z40, (x_spec[1], y_spec[1]))
([-92.0, 92.0], [-114.0, 114.0], [40.0, 40.0])