def test_mcflirt_run_copy_image(image_fmri_nii, image_copy_fmri_nii, tmpdir):
file_inp, image_inp, data_inp = image_fmri_nii
filename_copy, data_copy = image_copy_fmri_nii
mcflt = MCFLIRT()
#pdb.set_trace()
mcflt.inputs.in_file = filename_copy
mcflt.inputs.out_file = str(tmpdir.join("output_mcf_copy_im.nii.gz"))
mcflt.basedir = "test"
mcflt.run()
img_out = nb.load(mcflt.inputs.out_file)
data_out = img_out.get_data()
#pdb.set_trace()
# since all images are the same mcflirt shouldn't do anything
assert (data_copy == data_out).all()
def test_mcflirt_run(image_fmri_nii, cost_function, tmpdir):
file_inp, _, data_inp = image_fmri_nii
mcflt = MCFLIRT()
mcflt.inputs.in_file = file_inp
mcflt.inputs.out_file = str(tmpdir.join("output_mcf.nii.gz"))
mcflt.basedir = "test"
setattr(mcflt.inputs, "cost", cost_function)
mcflt.run()
data_out = nb.load(mcflt.inputs.out_file).get_data()
# the middle image shouldn't change
assert (data_inp[:, :, :, data_inp.shape[3] //
2] == data_out[:, :, :, data_inp.shape[3] // 2]).all()
# i'm assuming that the sum shouldn't change "too much"
for i in range(data_inp.shape[3]):
assert np.allclose(data_inp[:, :, :, i].sum(),
data_out[:, :, :, i].sum(),
rtol=5e-3)
def test_mcflirt_translate_image(image_fmri_nii, tmpdir):
file_inp, image_inp, data_inp = image_fmri_nii
mcflt = MCFLIRT()
filename_trans, data_trans = image_translate_nii(data_inp, image_inp)
mcflt.inputs.in_file = filename_trans
mcflt.inputs.out_file = str(tmpdir.join("output_mcf_translate.nii.gz"))
mcflt.basedir = "test"
mcflt.inputs.smooth = 0.
mcflt.run()
img_out = nb.load(mcflt.inputs.out_file)
data_out = img_out.get_data()
# should think about some other error metric
# this one gives a big error
# mcflt.inputs.smooth = 0. doesn't really change
for i in [0, 2]:
assert np.allclose(data_out[:, :, :, i],
data_out[:, :, :, 1],
rtol=1e-1)
