def test_AvScale_inputs():
input_map = dict(
args=dict(argstr='%s', ),
environ=dict(
nohash=True,
usedefault=True,
),
ignore_exception=dict(
nohash=True,
usedefault=True,
),
mat_file=dict(
argstr='%s',
position=0,
),
output_type=dict(),
terminal_output=dict(
mandatory=True,
nohash=True,
),
)
inputs = AvScale.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def rotate_bvecs(bvecs, motion_vecs, rotate):
if not rotate:
rotated_bvecs = bvecs
else:
import numpy as np
import os
from nipype.interfaces.fsl.utils import AvScale
bvecs = np.genfromtxt(bvecs)
rotated_bvecs = open(os.path.abspath('rotated_bvecs.txt'),'w')
for i,r in enumerate(motion_vecs):
avscale = AvScale()
avscale.inputs.mat_file = r
res = avscale.run()
mat = np.asarray(res.outputs.rotation_translation_matrix)
rot = np.dot(mat,np.hstack((bvecs[i,:],1)))
for point in rot[:-1]:
rotated_bvecs.write('%f '%point)
rotated_bvecs.write('\n')
rotated_bvecs.close()
rotated_bvecs = os.path.abspath('rotated_bvecs.txt')
return rotated_bvecs
def test_AvScale_outputs():
output_map = dict(average_scaling=dict(),
backward_half_transform=dict(),
determinant=dict(),
forward_half_transform=dict(),
left_right_orientation_preserved=dict(),
rotation_translation_matrix=dict(),
scales=dict(),
skews=dict(),
)
outputs = AvScale.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_AvScale_outputs():
output_map = dict(
average_scaling=dict(),
backward_half_transform=dict(),
determinant=dict(),
forward_half_transform=dict(),
left_right_orientation_preserved=dict(),
rotation_translation_matrix=dict(),
scales=dict(),
skews=dict(),
)
outputs = AvScale.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def get_flirt_motion_parameters(flirt_out_mats):
def get_params(A):
"""This is a copy of spm's spm_imatrix where
we already know the rotations and translations matrix,
shears and zooms (as outputs from fsl FLIRT/avscale)
Let A = the 4x4 rotation and translation matrix
R = [ c5*c6, c5*s6, s5]
[-s4*s5*c6-c4*s6, -s4*s5*s6+c4*c6, s4*c5]
[-c4*s5*c6+s4*s6, -c4*s5*s6-s4*c6, c4*c5]
"""
def rang(b):
a = min(max(b, -1), 1)
return a
Ry = np.arcsin(A[0, 2])
# Rx = np.arcsin(A[1, 2] / np.cos(Ry))
# Rz = np.arccos(A[0, 1] / np.sin(Ry))
if (abs(Ry) - np.pi / 2)**2 < 1e-9:
Rx = 0
Rz = np.arctan2(-rang(A[1, 0]), rang(-A[2, 0] / A[0, 2]))
else:
c = np.cos(Ry)
Rx = np.arctan2(rang(A[1, 2] / c), rang(A[2, 2] / c))
Rz = np.arctan2(rang(A[0, 1] / c), rang(A[0, 0] / c))
rotations = [Rx, Ry, Rz]
translations = [A[0, 3], A[1, 3], A[2, 3]]
return rotations, translations
motion_params = open(op.abspath('motion_parameters.par'), 'w')
for mat in flirt_out_mats:
res = AvScale(mat_file=mat).run()
A = np.asarray(res.outputs.rotation_translation_matrix)
rotations, translations = get_params(A)
for i in rotations + translations:
motion_params.write('%f ' % i)
motion_params.write('\n')
motion_params.close()
motion_params = op.abspath('motion_parameters.par')
return motion_params
def test_AvScale_inputs():
input_map = dict(args=dict(argstr='%s',
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
mat_file=dict(argstr='%s',
position=0,
),
output_type=dict(),
terminal_output=dict(nohash=True,
),
)
inputs = AvScale.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
