def test_reorder(self):
(vox_array,
affine,
aff_trans,
ornt_trans) = dcmstack.reorder_voxels(self.vox_array,
self.affine,
'PRS')
ok_(np.all(vox_array == np.array([[[[4, 5],
[6, 7]],
[[12, 13],
[14,15]]
],
[[[0, 1],
[2, 3]],
[[8, 9],
[10, 11]]
]
]
)
)
)
ok_(np.allclose(affine,
np.array([[0,1,0,0],
[-1,0,0,1],
[0,0,1,0],
[0,0,0,1]])
)
)
def test_reorder(self):
(vox_array,
affine,
aff_trans,
ornt_trans) = dcmstack.reorder_voxels(self.vox_array,
self.affine,
'PRS')
ok_(np.all(vox_array == np.array([[[[4, 5],
[6, 7]],
[[12, 13],
[14,15]]
],
[[[0, 1],
[2, 3]],
[[8, 9],
[10, 11]]
]
]
)
)
)
ok_(np.allclose(affine,
np.array([[0,1,0,0],
[-1,0,0,1],
[0,0,1,0],
[0,0,0,1]])
)
)
def test_no_op(self):
vox_order = [dcmstack.closest_ortho_pat_axis(self.affine[:3, idx])[0] for idx in range(3)]
vox_order = "".join(vox_order)
vox_array, affine, perm = dcmstack.reorder_voxels(self.vox_array, self.affine, vox_order)
ok_((vox_array == self.vox_array).all())
ok_((affine == self.affine).all())
eq_(perm, (0, 1, 2))
eq_(np.may_share_memory(affine, self.affine), False)
def test_no_op(self):
vox_order = ''.join(aff2axcodes(self.affine))
(vox_array, affine, aff_trans,
ornt_trans) = dcmstack.reorder_voxels(self.vox_array, self.affine,
vox_order)
ok_((vox_array == self.vox_array).all())
ok_((affine == self.affine).all())
ok_((aff_trans == np.eye(4)).all())
ok_(np.allclose(ornt_trans, [[0, 1], [1, 1], [2, 1]]))
eq_(np.may_share_memory(affine, self.affine), False)
def test_aniso_reorder(self):
self.vox_array = self.vox_array.reshape(2, 4, 2)
self.affine = np.eye(4)
(vox_array, affine, aff_trans,
ornt_trans) = dcmstack.reorder_voxels(self.vox_array, self.affine,
'PLS')
ok_(
np.allclose(
affine,
np.array([[0, -1, 0, 1], [-1, 0, 0, 3], [0, 0, 1, 0],
[0, 0, 0, 1]])))
def test_no_op(self):
vox_order = [
dcmstack.closest_ortho_pat_axis(self.affine[:3, idx])[0]
for idx in range(3)
]
vox_order = ''.join(vox_order)
vox_array, affine, perm = dcmstack.reorder_voxels(
self.vox_array, self.affine, vox_order)
ok_((vox_array == self.vox_array).all())
ok_((affine == self.affine).all())
eq_(perm, (0, 1, 2))
eq_(np.may_share_memory(affine, self.affine), False)
def test_no_op(self):
vox_order = ''.join(aff2axcodes(self.affine))
(vox_array,
affine,
aff_trans,
ornt_trans) = dcmstack.reorder_voxels(self.vox_array,
self.affine,
vox_order)
ok_((vox_array == self.vox_array).all())
ok_((affine == self.affine).all())
ok_((aff_trans == np.eye(4)).all())
ok_(np.allclose(ornt_trans, [[0, 1], [1, 1], [2, 1]]))
eq_(np.may_share_memory(affine, self.affine), False)
def test_aniso_reorder(self):
self.vox_array = self.vox_array.reshape(2, 4, 2)
self.affine = np.eye(4)
(vox_array,
affine,
aff_trans,
ornt_trans) = dcmstack.reorder_voxels(self.vox_array,
self.affine,
'PLS')
ok_(np.allclose(affine,
np.array([[0,-1,0,1],
[-1,0,0,3],
[0,0,1,0],
[0,0,0,1]])
)
)
def reorder_voxels(imagedata, qto_xyz, voxel_order):
"""
Reorder voxel data to the specified voxel_order.
Does not directly manipulate imagedata or qto_xyz.
Returns manipulated copies of imagedata and qto_xyz.
Parameters
----------
imagedata : np.array
single np.array of image data
qto_xyz : np.matrix, 4x4
patient space
voxel_order : str, 3 char
3 character voxel order string, such as 'LPS' or 'RAI'
"""
log.debug('reorienting to voxel order %s' % voxel_order)
new_data, new_qto_xyz, _, _ = dcmstack.reorder_voxels(imagedata, qto_xyz, voxel_order)
return new_data, new_qto_xyz
def reorder_voxels(imagedata, qto_xyz, voxel_order):
"""
Reorder voxel data to the specified voxel_order.
Does not directly manipulate imagedata or qto_xyz.
Returns manipulated copies of imagedata and qto_xyz.
Parameters
----------
imagedata : np.array
single np.array of image data
qto_xyz : np.matrix, 4x4
patient space
voxel_order : str, 3 char
3 character voxel order string, such as 'LPS' or 'RAI'
"""
log.debug('reorienting to voxel order %s' % voxel_order)
new_data, new_qto_xyz, _, _ = dcmstack.reorder_voxels(
imagedata, qto_xyz, voxel_order)
return new_data, new_qto_xyz