# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
A set of methods to get coordinate maps which represent slices in space.
"""
from __future__ import absolute_import
import numpy as np
from nibabel.affines import from_matvec
from .coordinate_system import CoordinateSystem
from .coordinate_map import AffineTransform
from .array_coords import ArrayCoordMap
from .spaces import get_world_cs
[docs]def xslice(x, y_spec, z_spec, world):
"""
Return an LPS slice through a 3d box with x fixed.
Parameters
----------
x : float
The value at which x is fixed.
y_spec : sequence
A sequence with 2 values of form ((float, float), int). The
(float, float) components are the min and max y values; the int
is the number of points.
z_spec : sequence
As for `y_spec` but for z
world : str or CoordinateSystem CoordSysMaker or XYZSpace
World 3D space to which resulting coordmap refers
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, 'scanner')
>>> 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=('scanner-x=L->R', 'scanner-y=P->A', 'scanner-z=I->S'), name='scanner', 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))
"""
affine_range = get_world_cs(world)
(ymin, ymax), yno = y_spec
y_tick = (ymax-ymin) / (yno - 1.0)
(zmin, zmax), zno = z_spec
z_tick = (zmax-zmin) / (zno - 1.0)
origin = [x, ymin, zmin]
colvectors = np.asarray([[0, 0],
[y_tick, 0],
[0, z_tick]])
T = from_matvec(colvectors, origin)
affine_domain = CoordinateSystem(['i_y', 'i_z'], 'slice')
return AffineTransform(affine_domain,
affine_range,
T)
[docs]def yslice(y, x_spec, z_spec, world):
""" Return a slice through a 3d box with y fixed.
Parameters
----------
y : float
The value at which y is fixed.
x_spec : sequence
A sequence with 2 values of form ((float, float), int). The
(float, float) components are the min and max x values; the int
is the number of points.
z_spec : sequence
As for `x_spec` but for z
world : str or CoordinateSystem CoordSysMaker or XYZSpace
World 3D space to which resulting coordmap refers
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, 'mni')
>>> y70
AffineTransform(
function_domain=CoordinateSystem(coord_names=('i_x', 'i_z'), name='slice', coord_dtype=float64),
function_range=CoordinateSystem(coord_names=('mni-x=L->R', 'mni-y=P->A', 'mni-z=I->S'), name='mni', 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))
"""
affine_range = get_world_cs(world)
(xmin, xmax), xno = x_spec
x_tick = (xmax-xmin) / (xno - 1.0)
(zmin, zmax), zno = z_spec
z_tick = (zmax-zmin) / (zno - 1.0)
origin = [xmin, y, zmin]
colvectors = np.asarray([[x_tick, 0],
[0, 0],
[0, z_tick]])
T = from_matvec(colvectors, origin)
affine_domain = CoordinateSystem(['i_x', 'i_z'], 'slice')
return AffineTransform(affine_domain,
affine_range,
T)
[docs]def zslice(z, x_spec, y_spec, world):
""" Return a slice through a 3d box with z fixed.
Parameters
----------
z : float
The value at which z is fixed.
x_spec : sequence
A sequence with 2 values of form ((float, float), int). The
(float, float) components are the min and max x values; the int
is the number of points.
y_spec : sequence
As for `x_spec` but for y
world : str or CoordinateSystem CoordSysMaker or XYZSpace
World 3D space to which resulting coordmap refers
Returns
-------
affine_transform : AffineTransform
An affine transform that describes a 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, 'unknown')
>>> z40
AffineTransform(
function_domain=CoordinateSystem(coord_names=('i_x', 'i_y'), name='slice', coord_dtype=float64),
function_range=CoordinateSystem(coord_names=('unknown-x=L->R', 'unknown-y=P->A', 'unknown-z=I->S'), name='unknown', 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))
"""
affine_range = get_world_cs(world)
(xmin, xmax), xno = x_spec
x_tick = (xmax-xmin) / (xno - 1.0)
(ymin, ymax), yno = y_spec
y_tick = (ymax-ymin) / (yno - 1.0)
origin = [xmin, ymin, z]
colvectors = np.asarray([[x_tick, 0],
[0, y_tick],
[0, 0]])
T = from_matvec(colvectors, origin)
affine_domain = CoordinateSystem(['i_x', 'i_y'], 'slice')
return AffineTransform(affine_domain,
affine_range,
T)
[docs]def bounding_box(coordmap, shape):
"""
Determine a valid bounding box from a CoordinateMap
and a shape.
Parameters
----------
coordmap : CoordinateMap or AffineTransform
Containing mapping between voxel coordinates implied by `shape` and
physical coordinates.
shape : sequence of int
shape implying array
Returns
-------
limits : (N,) tuple of (2,) tuples of float
minimum and maximum coordinate values in output space (range) of
`coordmap`. N is given by coordmap.ndim[1].
Examples
--------
Make a 3D voxel to mni coordmap
>>> from nipy.core.api import vox2mni
>>> affine = np.array([[1, 0, 0, 2],
... [0, 3, 0, 4],
... [0, 0, 5, 6],
... [0, 0, 0, 1]], dtype=np.float64)
>>> A = vox2mni(affine)
>>> bounding_box(A, (30,40,20))
((2.0, 31.0), (4.0, 121.0), (6.0, 101.0))
"""
e = ArrayCoordMap.from_shape(coordmap, shape)
return tuple([(r.min(), r.max()) for r in e.transposed_values])