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 gen_qc(path_qc):
t2_image = sct_test_path('t2', 't2.nii.gz')
t2_seg = sct_test_path('t2', 't2_seg-manual.nii.gz')
qc.generate_qc(fname_in1=t2_image,
fname_seg=t2_seg,
path_qc=path_qc,
process="sct_deepseg_gm")
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 dmri_single_volumes(tmp_path):
"""
Create .nii.gz, bvals, and bvecs files for individual dMRI volumes.
This prep is necessary because `sct_testing_data` lacks individual bvals
and bvecs files for the `dmri_T000#.nii.gz` files, and
sct_dmri_separate_b0_and_dwi won't generate new bvals/bvecs file either.
"""
# Get all bvals/bvecs corresponding to individual dMRI volumes
bvals, bvecs = read_bvals_bvecs(sct_test_path('dmri', 'bvals.txt'),
sct_test_path('dmri', 'bvecs.txt'))
fname_dmri_imgs, fname_bvals, fname_bvecs = [], [], []
for i, (bval, bvec) in enumerate(zip(bvals, bvecs)):
# 1. Use existing single-volume dMRI files from sct_testing_data
fname_dmri_imgs.append(sct_test_path('dmri', f'dmri_T000{i}.nii.gz'))
# 2. Copy bval into single-volume bvals file
fname_bval = str(tmp_path / f'bvals_T000{i}.txt')
fname_bvals.append(fname_bval)
with open(fname_bval, 'w') as f:
f.write(str(bval))
# 3. Copy bvec into single-volume bvecs file
fname_bvec = str(tmp_path / f'bvecs_T000{i}.txt')
fname_bvecs.append(fname_bvec)
with open(fname_bvec, 'w') as f:
f.write(' '.join(map(str, bvec)))
return fname_dmri_imgs, fname_bvals, fname_bvecs
def test_straighten():
"""Test straightening with default params"""
fname_t2 = sct_test_path('t2', 't2.nii.gz') # sct_download_data -d sct_testing_data
fname_t2_seg = sct_test_path('t2', 't2_seg-manual.nii.gz')
sc_straight = SpinalCordStraightener(fname_t2, fname_t2_seg)
sc_straight.accuracy_results = True
sc_straight.straighten()
assert sc_straight.mse_straightening < 0.8
assert sc_straight.max_distance_straightening < 1.2
def template_lpi(tmp_path_factory):
"""Change orientation of test data template to LPI."""
path_out = str(
tmp_path_factory.mktemp("tmp_data") /
'template_lpi') # tmp_path_factory is needed for module scope
shutil.copytree(sct_test_path('template'), path_out)
for file in glob.glob(sct_test_path('template_lpi', 'template',
'*.nii.gz')):
nii = Image(file)
nii.change_orientation('LPI')
nii.save(file)
return path_out
def test_deep_segmentation_spinalcord(params):
"""High level segmentation API"""
fname_im = sct_test_path('t2', 't2.nii.gz')
fname_centerline_manual = sct_test_path('t2', 't2_centerline-manual.nii.gz')
# Set at channels_first in test_deepseg_lesion.test_segment()
K.set_image_data_format("channels_last")
# Call segmentation function
im_seg, _, _ = sct.deepseg_sc.core.deep_segmentation_spinalcord(
Image(fname_im), params['contrast'], ctr_algo='file', ctr_file=fname_centerline_manual, brain_bool=False,
kernel_size=params['kernel'], threshold_seg=0.5)
assert im_seg.data.dtype == np.dtype('uint8')
# Compare with ground-truth segmentation
assert np.all(im_seg.data == Image(params['fname_seg_manual']).data)
def test_sct_deepseg_sc_check_output_exists(tmp_path):
fname_out = str(tmp_path / 'test_seg.nii.gz')
sct_deepseg_sc.main(argv=[
'-i',
sct_test_path('t2', 't2.nii.gz'), '-c', 't2', '-o', fname_out
])
assert os.path.isfile(fname_out)
def test_sct_analyze_lesion_matches_expected_dummy_lesion_measurements(dummy_lesion, rtol, tmp_path):
"""Run the CLI script and verify that the lesion measurements match
expected values."""
# Run the analysis on the dummy lesion file
path_lesion, expected_measurements = dummy_lesion
sct_analyze_lesion.main(argv=['-m', path_lesion,
'-s', sct_test_path("t2", "t2_seg-manual.nii.gz"),
'-ofolder', str(tmp_path)])
# Load analysis results from pickled pandas.Dataframe
_, fname, _ = extract_fname(path_lesion)
with open(tmp_path/f"{fname}_analyzis.pkl", 'rb') as f:
measurements = pickle.load(f)['measures']
# Validate analysis results
for key, expected_value in expected_measurements.items():
if key == 'volume [mm3]':
np.testing.assert_equal(measurements.at[0, key], expected_value)
else:
# The length/diameter won't match exactly due to angle adjustment
# from spinal cord centerline curvature
np.testing.assert_allclose(measurements.at[0, key],
expected_value, rtol=rtol)
# The values will be adjusted according to the cos of the angle
# between the spinal cord centerline and the S-I axis, as per:
# https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3681#discussion_r804822552
if key == 'max_equivalent_diameter [mm]':
assert measurements.at[0, key] < expected_value
elif key == 'length [mm]':
assert measurements.at[0, key] > expected_value
def check_testing_data_integrity(files_checksums: Mapping[os.PathLike, str]):
changed = []
new = []
missing = []
after = []
for root, _, files in os.walk(sct_test_path()):
for f in files:
fname = os.path.join(root, f)
chksum = checksum(fname)
after.append(fname)
if fname not in files_checksums:
logger.warning(
f"Discovered new file in sct_testing_data that didn't exist before: {(fname, chksum)}"
)
new.append((fname, chksum))
elif files_checksums[fname] != chksum:
logger.error(
f"Checksum mismatch for test data: {fname}. Got {chksum} instead of {files_checksums[fname]}"
)
changed.append((fname, chksum))
for fname, chksum in files_checksums.items():
if fname not in after:
logger.error(f"Test data missing after test:a: {fname}")
missing.append((fname, chksum))
assert not changed
# assert not new
assert not missing
def download_data(request):
# This is a hack because the capsys fixture can't be used with
# session scope at the moment.
# https://github.com/pytest-dev/pytest/issues/2704#issuecomment-603387680
capmanager = request.config.pluginmanager.getplugin("capturemanager")
with capmanager.global_and_fixture_disabled():
print('\nDownloading sct testing data.')
downloader.main(['-d', 'sct_testing_data', '-o', sct_test_path()])
def step_axial_data_in_same_space():
"""
"""
src = sct_test_path('mt', 'mt0_seg.nii.gz')
dest = sct_test_path('mt', 'mt1_seg.nii.gz')
step = Paramreg(
step='1',
type='seg',
algo='slicereg',
metric='MeanSquares',
iter='5',
)
cli_params = Param()
cli_params.debug = 2
return src, dest, step, cli_params
def test_sct_register_to_template_non_rpi_template(tmp_path, template_lpi):
"""Test registration with option -ref subject when template is not RPI orientation, causing #3300."""
# Run registration to template using the RPI template as input file
sct_register_to_template.main(argv=[
'-i',
sct_test_path('template', 'template', 'PAM50_small_t2.nii.gz'), '-s',
sct_test_path('template', 'template',
'PAM50_small_cord.nii.gz'), '-ldisc',
sct_test_path('template', 'template', 'PAM50_small_label_disc.nii.gz'),
'-c', 't2', '-t', template_lpi, '-ref', 'subject', '-param',
'step=1,type=seg,algo=centermass', '-ofolder',
str(tmp_path), '-r', '0', '-v', '2'
])
img_orig = Image(
sct_test_path('template', 'template', 'PAM50_small_t2.nii.gz'))
img_reg = Image(str(tmp_path / 'template2anat.nii.gz'))
# Check if both images almost overlap. If they are right-left flipped, distance should be above threshold
assert np.linalg.norm(img_orig.data - img_reg.data) < 1
def test_data_integrity(request):
files_checksums = dict()
for root, _, files in os.walk(sct_test_path()):
for f in files:
fname = os.path.join(root, f)
chksum = checksum(fname)
files_checksums[fname] = chksum
request.addfinalizer(lambda: check_testing_data_integrity(files_checksums))
def labeled_data_test_params(path_in=sct_test_path('t2', 't2.nii.gz'),
path_seg=sct_test_path('t2', 'labels.nii.gz')):
"""Generate image/label pairs for various test cases of
test_sagittal_slice_get_center_spit."""
im_in = Image(path_in) # Base anatomical image
im_seg_labeled = Image(path_seg) # Base labeled segmentation
assert np.count_nonzero(im_seg_labeled.data) >= 2, "Labeled segmentation image has fewer than 2 labels"
# Create image with all but one label removed
im_seg_one_label = im_seg_labeled.copy()
for x, y, z in np.argwhere(im_seg_one_label.data)[1:]:
im_seg_one_label.data[x, y, z] = 0
# Create image with no labels
im_seg_no_labels = im_seg_labeled.copy()
for x, y, z in np.argwhere(im_seg_no_labels.data):
im_seg_no_labels.data[x, y, z] = 0
return [pytest.param(im_in, im_seg_labeled, id='multiple_labels'),
pytest.param(im_in, im_seg_one_label, id='one_label'),
pytest.param(im_in, im_seg_no_labels, id='no_labels')]
def test_sct_maths_symmetrize(dim, tmp_path):
"""Run the CLI script, then verify that symmetrize properly flips and
averages the image data."""
path_in = sct_test_path('t2', 't2.nii.gz')
path_out = str(tmp_path / f't2_sym_{dim}.nii.gz')
sct_maths.main(
argv=['-i', path_in, '-symmetrize',
str(dim), '-o', path_out])
im_in = Image(path_out)
im_out = Image(path_out)
assert np.array_equal(
im_out.data, (im_in.data + np.flip(im_in.data, axis=int(dim))) / 2.0)
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')
])
def test_register_step_ants_slice_regularized_registration(
step_axial_data_in_same_space):
src, dest, step, cli_params = step_axial_data_in_same_space
warp_forward_out, warp_inverse_out = register_step_ants_slice_regularized_registration(
src=src, dest=dest, step=step, metricSize='4')
# Verify integrity of the output Tx Ty file
txty_result = np.genfromtxt('step1TxTy_poly.csv',
skip_header=1,
delimiter=',')
txty_groundtruth = np.genfromtxt(sct_test_path(
'mt', 'step1TxTy_poly_groundtruth.csv'),
skip_header=1,
delimiter=',')
assert txty_result == pytest.approx(txty_groundtruth, abs=1e-14)
def test_register_step_ants_slice_regularized_registration(
step_axial_data_in_same_space):
src, dest, step, cli_params = step_axial_data_in_same_space
outfiles = _, _, txty_csv_out = register_step_ants_slice_regularized_registration(
src, dest, step, metricSize='4')
# Verify integrity of the output Tx Ty file
txty_result = np.genfromtxt(txty_csv_out, skip_header=1, delimiter=',')
txty_groundtruth = np.genfromtxt(sct_test_path(
'mt', 'step1TxTy_poly_groundtruth.csv'),
skip_header=1,
delimiter=',')
assert txty_result == pytest.approx(txty_groundtruth, abs=1e-14)
# tmp_path can't be used here because the output files are generated by isct_antsSliceRegularizedRegistration,
# which doesn't easily allow the output filepaths to be modified. Instead, remove manually.
for file in outfiles:
os.unlink(file)
def test_create_seg_mid(tmp_path):
"""Test the '-create-seg-mid' option in sct_label_utils."""
input = sct_test_path('t2', 't2_seg-manual.nii.gz')
output = str(tmp_path / 't2_seg_labeled.nii.gz')
# Create a single label using the new syntax
sct_label_utils.main(['-i', input, '-create-seg-mid', '3', '-o', output])
output_img = Image(output)
labels = np.argwhere(output_img.data)
assert len(labels) == 1
# Ensure slice coordinate of label is centered at midpoint of I-S axis
for coord, axis, shape in zip(labels[0], output_img.orientation,
Image(output).data.shape):
if axis in ['I', 'S']:
assert coord == round(shape / 2)
# Old syntax for this behavior should not be allowed
with pytest.raises(DeprecationWarning):
sct_label_utils.main(
['-i', input, '-create-seg', '-1,3', '-o', output])
def dummy_lesion(request, tmp_path):
"""Define a fake voxel lesion using the specified dimensions."""
starting_coord, dim = request.param
# Format the coordinates into a str argument that `-create` can accept
coordinates = []
for x in range(starting_coord[0], starting_coord[0] + dim[0]):
for y in range(starting_coord[1], starting_coord[1] + dim[1]):
for z in range(starting_coord[2], starting_coord[2] + dim[2]):
coord = [str(x), str(y), str(z), "1"]
coordinates.append(",".join(coord))
create_arg = ":".join(coordinates)
# Create the lesion mask file and output to a temporary directory
path_ref = sct_test_path("t2", "t2.nii.gz")
path_out = str(tmp_path/"lesion.nii.gz")
sct_label_utils.main(argv=['-i', path_ref, '-o', path_out,
'-create', create_arg])
# Compute the expected (voxel) measurements from the provided dimensions
# NB: Actual measurements will differ slightly due to spine curvature
measurements = {
# NB: 'sct_analyze_lesion' treats lesions as cylinders. So:
# - Vertical axis: Length of the cylinder
'length [mm]': dim[1],
# - Horizontal plane: Cross-sectional slices of the cylinder.
# Specifically, 'max_equivalent_diameter' takes the
# cross-sectional area of the lesion (which is computed
# using square voxels), then finds the diameter of an
# equivalent *circle* with that same area:
# a = pi*r^2
# -> a = pi*(d/2)^2
# -> d = 2*sqrt(a/pi)
'max_equivalent_diameter [mm]': 2 * np.sqrt(dim[0] * dim[2] / np.pi),
'volume [mm3]': dim[0] * dim[1] * dim[2],
}
return path_out, measurements
def test_model_dict():
"""
Make sure all fields are present in each model.
:return:
"""
for key, value in sct.deepseg.models.MODELS.items():
assert('url' in value)
assert('description' in value)
assert('default' in value)
# noinspection 801,PyShadowingNames
@pytest.mark.parametrize('fname_image, fname_seg_manual, fname_out, task', [
(sct_test_path('t2s', 't2s.nii.gz'),
sct_test_path('t2s', 't2s_seg-deepseg.nii.gz'),
't2s_seg_deepseg.nii.gz',
'seg_sc_t2star'),
])
def test_segment_nifti(fname_image, fname_seg_manual, fname_out, task,
tmp_path):
"""
Uses the locally-installed sct_testing_data
"""
fname_out = str(tmp_path/fname_out) # tmp_path for automatic cleanup
sct_deepseg.main(['-i', fname_image, '-task', task, '-o', fname_out])
# TODO: implement integrity test (for now, just checking if output segmentation file exists)
# Make sure output file exists
assert os.path.isfile(fname_out)
# Compare with ground-truth segmentation
def setUp(self):
self.image = msct_image.Image(sct_test_path('t2', 't2.nii.gz'))
self.overlay = msct_image.Image(self.image)
self.params = base.AnatomicalParams()
from __future__ import print_function, absolute_import
import os
import pytest
from spinalcordtoolbox.utils import sct_test_path
import sct_compute_mtsat
out_mstat = "out_mtsat.nii.gz"
out_t1map = "out_t1map.nii.gz"
INPUT_PARAMS = [
[
'-mt',
sct_test_path('mt', 'mt1.nii.gz'), '-pd',
sct_test_path('mt', 'mt0.nii.gz'), '-t1',
sct_test_path('mt', 't1w.nii.gz'), '-omtsat', out_mstat, '-ot1map',
out_t1map
],
[
'-mt',
sct_test_path('mt', 'mt1.nii.gz'), '-pd',
sct_test_path('mt', 'mt0.nii.gz'), '-t1',
sct_test_path('mt', 't1w.nii.gz'), '-omtsat', out_mstat, '-ot1map',
out_t1map, '-trmt', '51', '-trpd', '52', '-trt1', '10', '-famt', '4',
'-fapd', '5', '-fat1', '14'
],
]
def test_sct_image_display_warp_check_output_exists():
"""Run the CLI script and check that the warp image file was created."""
fname_in = 'warp_template2anat.nii.gz'
fname_out = 'grid_3_resample_' + fname_in
sct_image.main(argv=['-i', sct_test_path('t2', fname_in), '-display-warp'])
assert os.path.exists(sct_test_path('t2', fname_out))
def test_sct_dmri_display_bvecs_png_exists_bvec_bval_inputs():
"""Run the CLI script."""
sct_dmri_display_bvecs.main(argv=['-bvec', sct_test_path('dmri', 'bvecs.txt'),
'-bval', sct_test_path('dmri', 'bvals.txt')])
assert os.path.exists('bvecs.png')
os.unlink('bvecs.png')
'rmse': 0.3,
'laplacian': 0.5,
'norm': 3.6
}, {}),
(dummy_centerline(size_arr=(30, 20, 50), subsampling=10), {
'median': 0,
'rmse': 0.1,
'laplacian': 0.5,
'norm': 3.8
}, {}),
]
param_optic = [
({
'fname_image':
sct_test_path('t2', 't2.nii.gz'),
'contrast':
't2',
'fname_centerline-optic':
sct_test_path('t2', 't2_centerline-optic.nii.gz')
}),
({
'fname_image': sct_test_path('t2s', 't2s.nii.gz'),
'contrast': 't2s',
'fname_centerline-optic':
sct_test_path('t2s/t2s_centerline-optic.nii.gz')
}),
({
'fname_image':
sct_test_path('dmri', 'dwi_mean.nii.gz'),
'contrast':
import logging
from time import time
import numpy as np
import pytest
import spinalcordtoolbox.labels as sct_labels
from spinalcordtoolbox.image import Image, zeros_like
from spinalcordtoolbox.utils import sct_test_path
from spinalcordtoolbox.types import Coordinate
from test_image import fake_3dimage, fake_3dimage2
logger = logging.getLogger(__name__)
seg_img = Image(sct_test_path('t2', 't2_seg-manual.nii.gz'))
t2_img = Image(sct_test_path('t2', 't2.nii.gz'))
labels_img = Image(sct_test_path('t2', 'labels.nii.gz'))
# TODO [AJ] investigate how to parametrize fixtures from test_image.py
# without redefining the function here
def fake_3dimage_sct2():
"""
:return: an Image (3D) in RAS+ (aka SCT LPI) space
shape = (1,2,3)
"""
i = fake_3dimage2()
img = Image(
i.get_data(),
hdr=i.header,
# pytest unit tests for spinalcordtoolbox.deepseg_sc
import pytest
import numpy as np
import nibabel as nib
from keras import backend as K
import spinalcordtoolbox as sct
from spinalcordtoolbox.image import Image
import spinalcordtoolbox.deepseg_sc.core
from spinalcordtoolbox.testing.create_test_data import dummy_centerline
from spinalcordtoolbox.utils import sct_test_path
param_deepseg = [
({
'fname_seg_manual': sct_test_path('t2', 't2_seg-deepseg_sc-2d.nii.gz'),
'contrast': 't2',
'kernel': '2d'
}),
({
'fname_seg_manual': sct_test_path('t2', 't2_seg-deepseg_sc-3d.nii.gz'),
'contrast': 't2',
'kernel': '3d'
}),
]
# noinspection 801,PyShadowingNames
@pytest.mark.parametrize('params', param_deepseg)
def test_deep_segmentation_spinalcord(params):
"""High level segmentation API"""
def test_sct_propseg_o_flag(tmp_path):
argv = ['-i', sct_test_path('t2', 't2.nii.gz'), '-c', 't2', '-ofolder', str(tmp_path), '-o', 'test_seg.nii.gz']
sct_propseg.main(argv)
output_files = sorted([f for f in os.listdir(tmp_path)
if os.path.isfile(os.path.join(tmp_path, f))])
assert output_files == ['t2_centerline.nii.gz', 'test_seg.nii.gz']