def test_sct_register_multimodal_with_softmask(tmp_path):
"""
Verify that softmask is actually applied during registration.
NB: For 'gaussian', ANTs binaries can't handle softmasks natively, so SCT should be applying
the mask directly to the image. Related links:
* https://github.com/ivadomed/pipeline-hemis/issues/3.
* https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3075
"""
fname_mask = str(tmp_path / 'mask_t2.nii.gz')
fname_t2 = sct_test_path('t2', 't2.nii.gz')
fname_t1 = sct_test_path('t1', 't1w.nii.gz')
fname_warp = str(tmp_path / "warp_t1w2t2.nii.gz")
sct_create_mask.main([
'-i', fname_t2, '-p',
f"centerline,{sct_test_path('t2', 't2_centerline-manual.nii.gz')}",
'-o', fname_mask, '-f', 'gaussian'
])
sct_register_multimodal.main([
'-i', fname_t1, '-d', fname_t2, '-dseg',
sct_test_path('t2', 't2_seg-manual.nii.gz'), '-param',
"step=1,type=im,algo=slicereg,metric=CC", '-m', fname_mask, '-ofolder',
str(tmp_path), '-r', '0', '-v', '2'
])
# If registration was successful, the warping field should be non-empty
assert np.any(Image(fname_warp).data)
def test_sct_register_multimodal_mask_files_exist(tmp_path):
"""
Run the script without validating results.
- TODO: Write a check that verifies the registration results.
- TODO: Parametrize this test to add '-initwarpinv warp_anat2template.nii.gz',
after the file is added to sct_testing_data:
https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3407#discussion_r646895013
"""
fname_mask = str(tmp_path / 'mask_mt1.nii.gz')
sct_create_mask.main([
'-i',
sct_test_path('mt', 'mt1.nii.gz'), '-p',
f"centerline,{sct_test_path('mt', 'mt1_seg.nii.gz')}", '-size', '35mm',
'-f', 'cylinder', '-o', fname_mask
])
sct_register_multimodal.main([
'-i',
sct_dir_local_path('data/PAM50/template/', 'PAM50_t2.nii.gz'), '-iseg',
sct_dir_local_path('data/PAM50/template/', 'PAM50_cord.nii.gz'), '-d',
sct_test_path('mt', 'mt1.nii.gz'), '-dseg',
sct_test_path('mt', 'mt1_seg.nii.gz'), '-param',
'step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3',
'-m', fname_mask, '-initwarp',
sct_test_path('t2', 'warp_template2anat.nii.gz'), '-ofolder',
str(tmp_path)
])
for path in ["PAM50_t2_reg.nii.gz", "warp_PAM50_t22mt1.nii.gz"]:
assert os.path.exists(tmp_path / path)
# Because `-initwarp` was specified (but `-initwarpinv` wasn't) the dest->seg files should NOT exist
for path in ["mt1_reg.nii.gz", "warp_mt12PAM50_t2.nii.gz"]:
assert not os.path.exists(tmp_path / path)
def register_data(im_src, im_dest, param_reg, path_copy_warp=None, rm_tmp=True):
'''
Parameters
----------
im_src: class Image: source image
im_dest: class Image: destination image
param_reg: str: registration parameter
path_copy_warp: path: path to copy the warping fields
Returns: im_src_reg: class Image: source image registered on destination image
-------
'''
# im_src and im_dest are already preprocessed (in theory: im_dest = mean_image)
# binarize images to get seg
im_src_seg = binarize(im_src, thr_min=1, thr_max=1)
im_dest_seg = binarize(im_dest)
# create tmp dir and go in it
tmp_dir = tmp_create()
curdir = os.getcwd()
os.chdir(tmp_dir)
# save image and seg
fname_src = 'src.nii.gz'
im_src.save(fname_src)
fname_src_seg = 'src_seg.nii.gz'
im_src_seg.save(fname_src_seg)
fname_dest = 'dest.nii.gz'
im_dest.save(fname_dest)
fname_dest_seg = 'dest_seg.nii.gz'
im_dest_seg.save(fname_dest_seg)
# do registration using param_reg
sct_register_multimodal.main(args=['-i', fname_src,
'-d', fname_dest,
'-iseg', fname_src_seg,
'-dseg', fname_dest_seg,
'-param', param_reg])
# get registration result
fname_src_reg = add_suffix(fname_src, '_reg')
im_src_reg = Image(fname_src_reg)
# get out of tmp dir
os.chdir(curdir)
# copy warping fields
if path_copy_warp is not None and os.path.isdir(os.path.abspath(path_copy_warp)):
path_copy_warp = os.path.abspath(path_copy_warp)
file_src = extract_fname(fname_src)[1]
file_dest = extract_fname(fname_dest)[1]
fname_src2dest = 'warp_' + file_src + '2' + file_dest + '.nii.gz'
fname_dest2src = 'warp_' + file_dest + '2' + file_src + '.nii.gz'
copy(os.path.join(tmp_dir, fname_src2dest), path_copy_warp)
copy(os.path.join(tmp_dir, fname_dest2src), path_copy_warp)
if rm_tmp:
# remove tmp dir
rmtree(tmp_dir)
# return res image
return im_src_reg, fname_src2dest, fname_dest2src
def test_sct_register_multimodal_mt0_image_data_within_threshold(
use_seg, param, fname_gt, tmp_path):
"""Run the CLI script and verify that the output image data is close to a reference image (within threshold)."""
fname_out_src = str(tmp_path / 'mt0_reg.nii.gz')
fname_out_dest = str(tmp_path / 'mt0_reg_inv.nii.gz')
fname_owarp = str(tmp_path / 'warp_mt02mt1.nii.gz')
fname_owarpinv = str(tmp_path / 'warp_mt12mt0.nii.gz')
argv = [
'-i', 'mt/mt0.nii.gz', '-d', 'mt/mt1.nii.gz', '-x', 'linear', '-r',
'0', '-param', param, '-o', fname_out_src, '-owarp', fname_owarp,
'-owarpinv', fname_owarpinv
]
seg_argv = ['-iseg', 'mt/mt0_seg.nii.gz', '-dseg', 'mt/mt1_seg.nii.gz']
sct_register_multimodal.main(argv=(argv + seg_argv) if use_seg else argv)
for f in [fname_out_src, fname_out_dest, fname_owarp, fname_owarpinv]:
assert os.path.isfile(f)
def test_sct_register_multimodal_mask_no_checks(tmp_path):
"""Run the script without validating results.
TODO: Write a check that verifies the registration results as part of
https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3246."""
fname_mask = str(tmp_path / 'mask_mt1.nii.gz')
sct_create_mask.main([
'-i',
sct_test_path('mt', 'mt1.nii.gz'), '-p',
f"centerline,{sct_test_path('mt', 'mt1_seg.nii.gz')}", '-size', '35mm',
'-f', 'cylinder', '-o', fname_mask
])
sct_register_multimodal.main([
'-i',
sct_dir_local_path('data/PAM50/template/', 'PAM50_t2.nii.gz'), '-iseg',
sct_dir_local_path('data/PAM50/template/', 'PAM50_cord.nii.gz'), '-d',
sct_test_path('mt', 'mt1.nii.gz'), '-dseg',
sct_test_path('mt', 'mt1_seg.nii.gz'), '-param',
'step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3',
'-m', fname_mask, '-initwarp',
sct_test_path('t2', 'warp_template2anat.nii.gz')
])