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:
- coordmapCoordinateMap or AffineTransform
Containing mapping between voxel coordinates implied by shape and physical coordinates.
- shapesequence 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))
- nipy.core.reference.slices.xslice(x, y_spec, z_spec, world)¶
Return an LPS slice through a 3d box with x fixed.
- Parameters:
- xfloat
The value at which x is fixed.
- y_specsequence
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_specsequence
As for y_spec but for z
- worldstr or CoordinateSystem CoordSysMaker or XYZSpace
World 3D space to which resulting coordmap refers
- Returns:
- affine_transformAffineTransform
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))
- nipy.core.reference.slices.yslice(y, x_spec, z_spec, world)¶
Return a slice through a 3d box with y fixed.
- Parameters:
- yfloat
The value at which y is fixed.
- x_specsequence
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_specsequence
As for x_spec but for z
- worldstr or CoordinateSystem CoordSysMaker or XYZSpace
World 3D space to which resulting coordmap refers
- Returns:
- affine_transformAffineTransform
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))
- nipy.core.reference.slices.zslice(z, x_spec, y_spec, world)¶
Return a slice through a 3d box with z fixed.
- Parameters:
- zfloat
The value at which z is fixed.
- x_specsequence
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_specsequence
As for x_spec but for y
- worldstr or CoordinateSystem CoordSysMaker or XYZSpace
World 3D space to which resulting coordmap refers
- Returns:
- affine_transformAffineTransform
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))