def test_concat_niimgs():
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
concatenated = _utils.concat_niimgs((img1, img3, img1))
concatenate_true = np.ones(shape + (3,))
concatenate_true[..., 1] = 0
np.testing.assert_almost_equal(concatenated.get_data(), concatenate_true)
assert_raises(ValueError, _utils.concat_niimgs, [img1, img2])
# Smoke-test the accept_4d
assert_raises(ValueError, _utils.concat_niimgs, [img1, img4d])
concatenated = _utils.concat_niimgs([img1, img4d], accept_4d=True)
assert_equal(concatenated.shape[3], 3)
_, tmpimg1 = tempfile.mkstemp(suffix='.nii')
_, tmpimg2 = tempfile.mkstemp(suffix='.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img2, tmpimg2)
nose.tools.assert_raises(ValueError, _utils.concat_niimgs,
[tmpimg1, tmpimg2])
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
def test_iterator_generator():
# Create a list of random images
rng = np.random.RandomState(42)
list_images = [
Nifti1Image(
rng.random_sample((10, 10, 10)), np.eye(4)
)
for i in range(10)
]
cc = _utils.concat_niimgs(list_images)
assert cc.shape[-1] == 10
assert_array_almost_equal(get_data(cc)[..., 0], get_data(list_images[0]))
# Same with iteration
i = image.iter_img(list_images)
cc = _utils.concat_niimgs(i)
assert cc.shape[-1] == 10
assert_array_almost_equal(get_data(cc)[..., 0], get_data(list_images[0]))
# Now, a generator
b = []
g = nifti_generator(b)
cc = _utils.concat_niimgs(g)
assert cc.shape[-1] == 10
assert len(b) == 10
def test_concat_niimgs():
shape = (10, 11, 12)
affine = np.eye(4)
niimg1 = Nifti1Image(np.ones(shape), affine)
niimg2 = Nifti1Image(np.ones(shape), 2 * affine)
niimg3 = Nifti1Image(np.zeros(shape), affine)
niimg4d = Nifti1Image(np.ones(shape + (2, )), affine)
concatenated = _utils.concat_niimgs((niimg1, niimg3, niimg1))
concatenate_true = np.ones(shape + (3, ))
concatenate_true[..., 1] = 0
np.testing.assert_almost_equal(concatenated.get_data(), concatenate_true)
assert_raises(ValueError, _utils.concat_niimgs, [niimg1, niimg2])
# Smoke-test the accept_4d
assert_raises(ValueError, _utils.concat_niimgs, [niimg1, niimg4d])
concatenated = _utils.concat_niimgs([niimg1, niimg4d], accept_4d=True)
assert_equal(concatenated.shape[3], 3)
_, tmpimg1 = tempfile.mkstemp(suffix='.nii')
_, tmpimg2 = tempfile.mkstemp(suffix='.nii')
try:
nibabel.save(niimg1, tmpimg1)
nibabel.save(niimg2, tmpimg2)
nose.tools.assert_raises(ValueError, _utils.concat_niimgs,
[tmpimg1, tmpimg2])
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
def test_concat_niimgs():
# create images different in affine and 3D/4D shape
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
shape2 = (12, 11, 10)
img1b = Nifti1Image(np.ones(shape2), affine)
shape3 = (11, 22, 33)
img1c = Nifti1Image(np.ones(shape3), affine)
# Regression test for #601. Dimensionality of first image was not checked
# properly
_dimension_error_msg = ("Input data has incompatible dimensionality: "
"Expected dimension is 4D and you provided "
"a list of 4D images \(5D\)")
assert_raises_regex(DimensionError,
_dimension_error_msg,
_utils.concat_niimgs, [img4d],
ensure_ndim=4)
# check basic concatenation with equal shape/affine
concatenated = _utils.concat_niimgs((img1, img3, img1))
assert_raises_regex(DimensionError, _dimension_error_msg,
_utils.concat_niimgs, [img1, img4d])
# smoke-test auto_resample
concatenated = _utils.concat_niimgs((img1, img1b, img1c),
auto_resample=True)
assert_true(concatenated.shape == img1.shape + (3, ))
# check error for non-forced but necessary resampling
assert_raises_regex(ValueError,
'Field of view of image',
_utils.concat_niimgs, [img1, img2],
auto_resample=False)
# test list of 4D niimgs as input
tmpimg1 = tempfile.mktemp(suffix='.nii')
tmpimg2 = tempfile.mktemp(suffix='.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img3, tmpimg2)
concatenated = _utils.concat_niimgs([tmpimg1, tmpimg2])
assert_array_equal(concatenated.get_data()[..., 0], img1.get_data())
assert_array_equal(concatenated.get_data()[..., 1], img3.get_data())
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
img5d = Nifti1Image(np.ones((2, 2, 2, 2, 2)), affine)
assert_raises_regex(
TypeError, 'Concatenated images must be 3D or 4D. '
'You gave a list of 5D images', _utils.concat_niimgs, [img5d, img5d])
def test_concat_niimgs():
# create images different in affine and 3D/4D shape
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
shape2 = (12, 11, 10)
img1b = Nifti1Image(np.ones(shape2), affine)
shape3 = (11, 22, 33)
img1c = Nifti1Image(np.ones(shape3), affine)
# Regression test for #601. Dimensionality of first image was not checked
# properly
_dimension_error_msg = ("Input data has incompatible dimensionality: "
"Expected dimension is 4D and you provided "
"a list of 4D images \(5D\)")
assert_raises_regex(DimensionError, _dimension_error_msg,
_utils.concat_niimgs, [img4d], ensure_ndim=4)
# check basic concatenation with equal shape/affine
concatenated = _utils.concat_niimgs((img1, img3, img1))
assert_raises_regex(DimensionError, _dimension_error_msg,
_utils.concat_niimgs, [img1, img4d])
# smoke-test auto_resample
concatenated = _utils.concat_niimgs((img1, img1b, img1c),
auto_resample=True)
assert_true(concatenated.shape == img1.shape + (3, ))
# check error for non-forced but necessary resampling
assert_raises_regex(ValueError, 'Field of view of image',
_utils.concat_niimgs, [img1, img2],
auto_resample=False)
# test list of 4D niimgs as input
tmpimg1 = tempfile.mktemp(suffix='.nii')
tmpimg2 = tempfile.mktemp(suffix='.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img3, tmpimg2)
concatenated = _utils.concat_niimgs([tmpimg1, tmpimg2])
assert_array_equal(
concatenated.get_data()[..., 0], img1.get_data())
assert_array_equal(
concatenated.get_data()[..., 1], img3.get_data())
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
img5d = Nifti1Image(np.ones((2, 2, 2, 2, 2)), affine)
assert_raises_regex(TypeError, 'Concatenated images must be 3D or 4D. '
'You gave a list of 5D images', _utils.concat_niimgs,
[img5d, img5d])
def test_concat_niimg_dtype():
shape = [2, 3, 4]
vols = [nibabel.Nifti1Image(
np.zeros(shape + [n_scans]).astype(np.int16), np.eye(4))
for n_scans in [1, 5]]
nimg = _utils.concat_niimgs(vols)
assert_equal(nimg.get_data().dtype, np.float32)
nimg = _utils.concat_niimgs(vols, dtype=None)
assert_equal(nimg.get_data().dtype, np.int16)
def test_concat_niimg_dtype():
shape = [2, 3, 4]
vols = [nibabel.Nifti1Image(
np.zeros(shape + [n_scans]).astype(np.int16), np.eye(4))
for n_scans in [1, 5]]
nimg = _utils.concat_niimgs(vols)
assert get_data(nimg).dtype == np.float32
nimg = _utils.concat_niimgs(vols, dtype=None)
assert get_data(nimg).dtype == np.int16
def test_concat_niimgs():
# create images different in affine and 3D/4D shape
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
shape2 = (12, 11, 10)
img1b = Nifti1Image(np.ones(shape2), affine)
shape3 = (11, 22, 33)
img1c = Nifti1Image(np.ones(shape2), affine)
# check basic concatenation with equal shape/affine
concatenated = _utils.concat_niimgs((img1, img3, img1), accept_4d=False)
concatenate_true = np.ones(shape + (3, ))
# Smoke-test the accept_4d
assert_raises_regexp(ValueError, 'image', _utils.concat_niimgs,
[img1, img4d])
concatenated = _utils.concat_niimgs([img1, img4d], accept_4d=True)
np.testing.assert_equal(concatenated.get_data(),
concatenate_true,
verbose=0)
# smoke-test auto_resample
concatenated = _utils.concat_niimgs((img1, img1b, img1c),
accept_4d=False,
auto_resample=True)
assert_true(concatenated.shape == img1.shape + (3, ))
# check error for non-forced but necessary resampling
assert_raises_regexp(ValueError,
'different from reference affine',
_utils.concat_niimgs, [img1, img2],
accept_4d=False)
# Smoke-test the 4d parsing
concatenated = _utils.concat_niimgs([img1, img4d], accept_4d=True)
assert_equal(concatenated.shape[3], 3)
# test list of 4D niimgs as input
_, tmpimg1 = tempfile.mkstemp(suffix='.nii')
_, tmpimg2 = tempfile.mkstemp(suffix='.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img3, tmpimg2)
concatenated = _utils.concat_niimgs([tmpimg1, tmpimg2],
accept_4d=False)
assert_array_equal(concatenated.get_data()[..., 0], img1.get_data())
assert_array_equal(concatenated.get_data()[..., 1], img3.get_data())
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
def test_concat_niimgs():
# create images different in affine and 3D/4D shape
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
shape2 = (12, 11, 10)
img1b = Nifti1Image(np.ones(shape2), affine)
shape3 = (11, 22, 33)
img1c = Nifti1Image(np.ones(shape2), affine)
# check basic concatenation with equal shape/affine
concatenated = _utils.concat_niimgs((img1, img3, img1),
accept_4d=False)
concatenate_true = np.ones(shape + (3,))
# Smoke-test the accept_4d
assert_raises_regexp(ValueError, 'image',
_utils.concat_niimgs, [img1, img4d])
concatenated = _utils.concat_niimgs([img1, img4d], accept_4d=True)
np.testing.assert_equal(concatenated.get_data(), concatenate_true,
verbose=0)
# smoke-test auto_resample
concatenated = _utils.concat_niimgs((img1, img1b, img1c), accept_4d=False,
auto_resample=True)
assert_true(concatenated.shape == img1.shape + (3, ))
# check error for non-forced but necessary resampling
assert_raises_regexp(ValueError, 'different from reference affine',
_utils.concat_niimgs, [img1, img2],
accept_4d=False)
# Smoke-test the 4d parsing
concatenated = _utils.concat_niimgs([img1, img4d], accept_4d=True)
assert_equal(concatenated.shape[3], 3)
# test list of 4D niimgs as input
_, tmpimg1 = tempfile.mkstemp(suffix='.nii')
_, tmpimg2 = tempfile.mkstemp(suffix='.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img3, tmpimg2)
concatenated = _utils.concat_niimgs([tmpimg1, tmpimg2],
accept_4d=False)
assert_array_equal(
concatenated.get_data()[..., 0], img1.get_data())
assert_array_equal(
concatenated.get_data()[..., 1], img3.get_data())
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
def test_concat_niimgs():
# create images different in affine and 3D/4D shape
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
shape2 = (12, 11, 10)
img1b = Nifti1Image(np.ones(shape2), affine)
shape3 = (11, 22, 33)
img1c = Nifti1Image(np.ones(shape3), affine)
# Regression test for #601. Dimensionality of first image was not checked
# properly
assert_raises_regex(DimensionError,
'Data must be a 4D Niimg-like object but '
'you provided',
_utils.concat_niimgs, [img4d],
ensure_ndim=4)
# check basic concatenation with equal shape/affine
concatenated = _utils.concat_niimgs((img1, img3, img1))
assert_raises_regex(
DimensionError, 'Data must be a 4D Niimg-like object but '
'you provided', _utils.concat_niimgs, [img1, img4d])
# smoke-test auto_resample
concatenated = _utils.concat_niimgs((img1, img1b, img1c),
auto_resample=True)
assert_true(concatenated.shape == img1.shape + (3, ))
# check error for non-forced but necessary resampling
assert_raises_regex(ValueError,
'Field of view of image',
_utils.concat_niimgs, [img1, img2],
auto_resample=False)
# test list of 4D niimgs as input
_, tmpimg1 = tempfile.mkstemp(suffix='.nii')
_, tmpimg2 = tempfile.mkstemp(suffix='.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img3, tmpimg2)
concatenated = _utils.concat_niimgs([tmpimg1, tmpimg2])
assert_array_equal(concatenated.get_data()[..., 0], img1.get_data())
assert_array_equal(concatenated.get_data()[..., 1], img3.get_data())
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
def test_concat_niimgs():
# create images different in affine and 3D/4D shape
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
shape2 = (12, 11, 10)
img1b = Nifti1Image(np.ones(shape2), affine)
shape3 = (11, 22, 33)
img1c = Nifti1Image(np.ones(shape3), affine)
# Regression test for #601. Dimensionality of first image was not checked
# properly
assert_raises_regex(TypeError, 'Data must be a 3D Niimg-like object but '
'you provided an image of shape',
_utils.concat_niimgs, [img4d], ensure_ndim=4)
# check basic concatenation with equal shape/affine
concatenated = _utils.concat_niimgs((img1, img3, img1))
assert_raises_regex(TypeError, 'Data must be a 3D Niimg-like object but '
'you provided an image of shape',
_utils.concat_niimgs, [img1, img4d])
# smoke-test auto_resample
concatenated = _utils.concat_niimgs((img1, img1b, img1c),
auto_resample=True)
assert_true(concatenated.shape == img1.shape + (3, ))
# check error for non-forced but necessary resampling
assert_raises_regex(ValueError, 'Field of view of image',
_utils.concat_niimgs, [img1, img2],
auto_resample=False)
# test list of 4D niimgs as input
_, tmpimg1 = tempfile.mkstemp(suffix='.nii')
_, tmpimg2 = tempfile.mkstemp(suffix='.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img3, tmpimg2)
concatenated = _utils.concat_niimgs([tmpimg1, tmpimg2])
assert_array_equal(
concatenated.get_data()[..., 0], img1.get_data())
assert_array_equal(
concatenated.get_data()[..., 1], img3.get_data())
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
def test_iterator_generator():
# Create a list of random images
l = [Nifti1Image(np.random.random((10, 10, 10)), np.eye(4)) for i in range(10)]
cc = _utils.concat_niimgs(l)
assert_equal(cc.shape[-1], 10)
assert_array_almost_equal(cc.get_data()[..., 0], l[0].get_data())
# Same with iteration
i = image.iter_img(l)
cc = _utils.concat_niimgs(i)
assert_equal(cc.shape[-1], 10)
assert_array_almost_equal(cc.get_data()[..., 0], l[0].get_data())
# Now, a generator
b = []
g = nifti_generator(b)
cc = _utils.concat_niimgs(g)
assert_equal(cc.shape[-1], 10)
assert_equal(len(b), 10)
def test_iterator_generator():
# Create a list of random images
l = [
Nifti1Image(np.random.random((10, 10, 10)), np.eye(4))
for i in range(10)
]
cc = _utils.concat_niimgs(l)
assert_equal(cc.shape[-1], 10)
assert_array_almost_equal(cc.get_data()[..., 0], l[0].get_data())
# Same with iteration
i = image.iter_img(l)
cc = _utils.concat_niimgs(i)
assert_equal(cc.shape[-1], 10)
assert_array_almost_equal(cc.get_data()[..., 0], l[0].get_data())
# Now, a generator
b = []
g = nifti_generator(b)
cc = _utils.concat_niimgs(g)
assert_equal(cc.shape[-1], 10)
assert_equal(len(b), 10)
def test_csf_wm_extracted_signal():
dlayo = params['layout']
nb_run = params['data']['nb_run']
sub, sess = 1,1
runs_dir = osp.join(base_dir, dlayo['dir']['sub+'].format(sub),
dlayo['dir']['sess+'].format(sess),
dlayo['dir']['runs'])
csf_dir = osp.join(runs_dir, dlayo['csf']['dir'])
wm_dir = osp.join(runs_dir, dlayo['wm']['dir'])
#print(csf_dir, ' + pat ', dlayo['csf']['roi_mask'])
csf_file = gb.glob(osp.join(csf_dir, dlayo['csf']['roi_mask']))
if not csf_file: print("glob empty: {} {}".format(
csf_dir, dlayo['csf']['roi_mask']))
csf_file = suf._check_glob_res(csf_file, ensure=1, files_only=True)
wm_file = gb.glob(osp.join(wm_dir, dlayo['wm']['roi_mask']))
if not wm_file: print("glob empty: {} {}".format(
wm_dir, dlayo['wm']['roi_mask']))
wm_file = suf._check_glob_res(wm_file, ensure=1, files_only=True)
dir_smooth_imgs = osp.join(runs_dir, dlayo['dir']['smooth'])
pat_imgs_files = dlayo['pat']['sub+sess+run+']+"*.nii*"
runs_pat = [pat_imgs_files.format(sub, sess, run_idx) \
for run_idx in range(1, nb_run+1)]
runs = [gb.glob(osp.join(dir_smooth_imgs, pat)) for pat in runs_pat]
for run in runs: run.sort()
#print("csf_file : ", csf_file)
#print("csf_dir : ", csf_dir)
#print("dir_smooth_imgs : ", dir_smooth_imgs)
#for k in arielle_runs[0].keys():
# print(k)
for idx, run in enumerate(runs):
run_4d = concat_niimgs(run, ensure_ndim=4)
#--- get CSF
csf_arr, csf_labs = ucr.extract_roi_run(csf_dir, csf_file,
run_4d, standardize=False, check_lengh=196, verbose=False)
csf_mat_arr = arielle_runs[idx]['csf_map_0.93_erode']
assert_allclose(csf_mat_arr, csf_arr)
#print(csf_labs)
#--- get WM
wm_arr, wm_labs = ucr.extract_roi_run(wm_dir, wm_file,
run_4d, standardize=False, check_lengh=196, verbose=False)
wm_mat_arr = arielle_runs[idx]['wm_map_0.99_erode']
assert_allclose(wm_mat_arr, wm_arr)
def do_one_run(run_curr, sess_curr, sub_curr, params, verbose=False):
"""
"""
run_info = {}
nvol = params['data']['nb_vol']
dt = params['data']['TR']
nb_run = params['data']['nb_run']
file_names = run_curr['file_names']
run_idx = run_curr['run_idx']
run_idx0 = run_idx - 1
assert run_idx0 >= 0
assert run_idx0 < nb_run
#sub_idx = sub_curr['sub_idx']
sess_idx = sess_curr['sess_idx']
mvt_cond = run_curr['motion']
dsig = sess_curr['dsig']
mask = sess_curr['mask']
low_freq = params['analysis']['filter']['low_freq']
high_freq = params['analysis']['filter']['high_freq']
# signal file names
#-------------------
_fn_sig = params['layout']['out']['signals']['signals+']
# _fn_fsig = params['layout']['out']['signals']['f_signals+']
fn_sig = osp.join(dsig, _fn_sig.format(sess_idx, run_idx) + mvt_cond)
# fn_fsig = osp.join(dsig, _fn_fsig.format(run_idx)+mvt_cond)
# extract signals and save them in preproc/roi_signals
#-----------------------------------------------------
min_vox_roi = params['analysis']['min_vox_in_roi']
run_4d = concat_niimgs(file_names, ensure_ndim=4)
signals, _issues, _info = ucr.extract_signals(sess_curr['droi'],
sess_curr['roi_prefix'], run_4d,
mask=mask, minvox=min_vox_roi)
# construct matrix of counfounds
#-----------------------------------------------------
arr_counf = []
labs_counf = []
#--- get WM
if params['analysis']['apply_wm']:
wm_arr, wm_labs = ucr.extract_roi_run(
sess_curr['wm_dir'], sess_curr['wm_filename'],
run_4d, check_lengh=nvol, verbose=verbose)
labs_counf = labs_counf + wm_labs
arr_counf.append(wm_arr)
if verbose: print("applying wm \n")
else:
wm_arr, wm_labs = None, None
#--- get CSF
if params['analysis']['apply_csf']:
csf_arr, csf_labs = ucr.extract_roi_run(
sess_curr['csf_dir'], sess_curr['csf_filename'],
run_4d, check_lengh=nvol, verbose=verbose)
labs_counf = labs_counf + csf_labs
arr_counf.append(csf_arr)
if verbose: print("applying csf \n")
else:
csf_arr, csf_labs = None, None
#--- get GR
if params['analysis']['apply_global_reg']:
gr_arr, gr_labs = ucr.extract_roi_run(
sess_curr['mask_dir'], sess_curr['mask_filename'],
run_4d, check_lengh=nvol, verbose=verbose)
labs_counf = labs_counf + gr_labs
arr_counf.append(gr_arr)
if verbose: print("applying GR \n")
else:
gr_arr, gr_labs = None, None
#--- get MVT
if params['analysis']['apply_mvt']:
mvt_arr, mvt_labs = ucr.extract_mvt(sess_curr['mvtfile'], run_idx0, nvol,
verbose=verbose)
labs_counf = labs_counf + mvt_labs
arr_counf.append(mvt_arr)
if verbose: print("applying mvt \n")
else:
mvt_arr, mvt_labs = None, None
#--- get cosine functions;
if params['analysis']['apply_filter']:
bf_arr, bf_labs = ucr.extract_bf(low_freq, high_freq, nvol, dt,
verbose=verbose)
labs_counf = labs_counf + bf_labs
arr_counf.append(bf_arr)
if verbose: print("applying filter \n")
else:
bf_arr, bf_labs = None, None
#--- put it together
# arr_counf = np.hstack((wm_arr, csf_arr, mvt_arr, bf_arr))
# labs_counf = wm_labs + csf_labs + mvt_labs + bf_labs
if arr_counf:
some_counfounds = True
arr_counf = np.hstack(tuple(arr_counf))
if verbose:
#print("wm.shape {}, csf.shape {}, mvt.shape {}, bf.shape {}".format(
# wm_arr.shape, csf_arr.shape, mvt_arr.shape, bf_arr.shape))
print(arr_counf.shape)
print(labs_counf[:17])
#run_info['shapes'] = (wm_arr.shape, csf_arr.shape, mvt_arr.shape, bf_arr.shape)
#run_info['mean_csf'] = csf_arr.mean(axis=0)
#run_info['mean_mvt'] = mvt_arr.mean(axis=0)
# filter and save
#-----------------------------------------------------
arr_sig, labels_sig = ucr._dict_signals_to_arr(signals)
if some_counfounds:
arr_sig_f = ucr.R_proj(arr_counf, arr_sig)
else:
arr_sig_f = arr_sig
run_info = dict(arr_sig=arr_sig, labels_sig=labels_sig, issues=_issues,
info=_info, arr_sig_f=arr_sig_f, arr_counf=arr_counf,
labs_counf=labs_counf)
# save filtered signals
save_is_true = params['analysis']['write_signals']
if save_is_true:
np.savez(fn_sig, arr_sig=arr_sig, labels_sig=labels_sig,
issues=_issues, info=_info, arr_sig_f=arr_sig_f,
arr_counf=arr_counf, labs_counf=labs_counf, params=params)
#np.savez(fn_fsig, arr_sig_f=arr_sig_f, arr_counf=arr_counf, labs_counf=labs_counf)
return run_info
def convert(subject_id, henson_base_dir, output_base_dir, run_ids=None,
resample_if_necessary=False):
if run_ids is None:
run_ids = range(1, 10)
henson_subject_dir = path(henson_base_dir) / ("Sub%02d" % subject_id)
openfmri_subject_dir = path(output_base_dir) / ("sub%03d" % subject_id)
# Take all fmri volumes and concatenate them into one
henson_bold_dir = henson_subject_dir / "BOLD"
openfmri_bold_dir = openfmri_subject_dir / "BOLD"
for run_id in run_ids:
print "run id %d" % run_id
henson_run_dir = henson_bold_dir / ("Run_%02d" % run_id)
openfmri_run_dir = openfmri_bold_dir / "task001_run001"
if not openfmri_run_dir.exists():
openfmri_run_dir.makedirs()
henson_run_files = sorted(henson_run_dir.glob(
"fMR09029-00??-00???-000???-01.nii"))
if subject_id == 14 and run_id == 2:
# File fMR09029-0004-00010-000010-01.nii is broken
henson_run_files.remove(henson_run_dir /
"fMR09029-0004-00010-000010-01.nii")
try:
# This only works if affines, shape, etc are equal
# it is actually not the case as I just saw
concatenated = concat_niimgs(henson_run_files)
except ValueError:
ref_affine = nb.load(henson_run_files[0]).get_affine()
niimgs = [nb.load(hrf) for hrf in henson_run_files]
for i, niimg in enumerate(niimgs):
aff = niimg.get_affine()
if np.abs(
np.linalg.norm(
np.linalg.inv(ref_affine).dot(aff)
- np.eye(4), 2)) > 1e-6:
warnings.warn("File %s has a significantly different affine %s from %s" % (hrf.basename(), str(aff), str(ref_affine)))
if resample_if_necessary:
niimgs[i] = resample_img(niimg, target_affine=ref_affine,
target_shape=niimg.shape)
else:
tmp = niimg.get_affine()
niimg._affine = ref_affine
concatenated = concat_niimgs(niimgs)
nb.save(concatenated, openfmri_run_dir / "bold.nii.gz")
keep_filenames_file = openfmri_run_dir / "original_files.json"
json.dump([hrf.basename() for hrf in henson_run_files],
open(keep_filenames_file, "w"))
# Copy anat file
henson_anat_file = henson_subject_dir / "T1" / "mprage.nii"
openfmri_anat_file = (openfmri_subject_dir / "anatomy" /
"highres001.nii.gz")
if not openfmri_anat_file.dirname().exists():
openfmri_anat_file.dirname().makedirs()
nb.save(nb.load(henson_anat_file), openfmri_anat_file)
def test_concat_niimgs():
# create images different in affine and 3D/4D shape
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
shape2 = (12, 11, 10)
img1b = Nifti1Image(np.ones(shape2), affine)
shape3 = (11, 22, 33)
img1c = Nifti1Image(np.ones(shape3), affine)
# Regression test for #601. Dimensionality of first image was not checked
# properly
_dimension_error_msg = ("Input data has incompatible dimensionality: "
"Expected dimension is 4D and you provided "
"a list of 4D images \\(5D\\)")
with pytest.raises(DimensionError, match=_dimension_error_msg):
_utils.concat_niimgs([img4d], ensure_ndim=4)
# check basic concatenation with equal shape/affine
concatenated = _utils.concat_niimgs((img1, img3, img1))
with pytest.raises(DimensionError, match=_dimension_error_msg):
_utils.concat_niimgs([img1, img4d])
# smoke-test auto_resample
concatenated = _utils.concat_niimgs((img1, img1b, img1c),
auto_resample=True)
assert concatenated.shape == img1.shape + (3, )
# check error for non-forced but necessary resampling
with pytest.raises(ValueError, match='Field of view of image'):
_utils.concat_niimgs([img1, img2], auto_resample=False)
# test list of 4D niimgs as input
tempdir = tempfile.mkdtemp()
tmpimg1 = os.path.join(tempdir, '1.nii')
tmpimg2 = os.path.join(tempdir, '2.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img3, tmpimg2)
concatenated = _utils.concat_niimgs(os.path.join(tempdir, '*'))
assert_array_equal(get_data(concatenated)[..., 0], get_data(img1))
assert_array_equal(get_data(concatenated)[..., 1], get_data(img3))
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
if os.path.exists(tempdir):
os.removedirs(tempdir)
img5d = Nifti1Image(np.ones((2, 2, 2, 2, 2)), affine)
with pytest.raises(TypeError,
match='Concatenated images must be 3D or 4D. '
'You gave a list of 5D images'):
_utils.concat_niimgs([img5d, img5d])
