def from_origin_and_columns(origin, colvectors, shape, output_coords):
"""
Return a CoordinateMap representing a slice based on a given origin,
a pair of direction vectors which span the slice, and a shape.
:Parameters:
origin : the corner of the output coordinates, i.e. the [0]*ndimin
point
colvectors : the steps in each voxel direction
shape : how many steps in each voxel direction
output_coords : a CoordinateSystem for the output
:Returns: `CoordinateMap`
"""
colvectors = np.asarray(colvectors)
nout = colvectors.shape[1]
nin = colvectors.shape[0]
f = np.zeros((nout+1,nin+1))
for i in range(nin):
f[0:nout,i] = colvectors[i]
f[0:nout,-1] = origin
f[nout, nin] = 1.
input_coords = CoordinateSystem(['i%d' % d for d in range(len(shape))],
'slice', output_coords.coord_dtype)
g = Affine(f, input_coords, output_coords)
return ArrayCoordMap.from_shape(g, shape)
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
--------
>>> 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))
"""
e = ArrayCoordMap.from_shape(coordmap, shape)
return tuple([(r.min(), r.max()) for r in e.transposed_values])
def 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])
>>>
"""
e = ArrayCoordMap.from_shape(coordmap, shape)
return tuple([[r.min(), r.max()] for r in e.transposed_values])
def bounding_box(coordmap, shape):
"""
Determine a valid bounding box from a CoordinateMap instance.
:Parameters:
coordmap : `CoordinateMap`
"""
e = ArrayCoordMap.from_shape(coordmap, shape)
return [[r.min(), r.max()] for r in e.transposed_values]
def get_coordmap_array(coordmap, shape):
'''
See: http://nipy.org/nipy/stable/api/generated/nipy.core.reference.array_coords.html?highlight=grid#nipy.core.reference.array_coords.Grid
'''
return ArrayCoordMap(coordmap, shape)