def pytest_sessionstart():
"""Perform actions that must be done prior to test collection."""
# Use a non-interactive backend so that no GUI plots will interrupt the test suite.
# (NB: We do this here to ensure it is set before `matplotlib` is first imported.)
if 'MPLBACKEND' not in os.environ:
os.environ["MPLBACKEND"] = 'Agg'
# Download sct_testing_data prior to test collection
if not os.path.exists(sct_test_path()):
logger.info("Downloading sct test data")
downloader.main(['-d', 'sct_testing_data', '-o', sct_test_path()])
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 run_in_sct_testing_data_dir():
"""Temporarily change the working directory to 'sct_testing_data'. This replicates the behavior of the old
`sct_testing`, and is needed to prevent tests from cluttering the working directory with output files."""
cwd = os.getcwd()
os.chdir(sct_test_path())
yield
os.chdir(cwd)
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 main():
# Initialization
fname_input = ''
fname_segmentation = ''
if param.debug:
printv('\n*** WARNING: DEBUG MODE ON ***\n')
fname_input = ''
fname_segmentation = sct_test_path('t2', 't2_seg.nii.gz')
else:
# Check input param
try:
opts, args = getopt.getopt(sys.argv[1:], 'hi:t:')
except getopt.GetoptError as err:
logger.error(str(err))
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-i'):
fname_input = arg
elif opt in ('-t'):
fname_segmentation = arg
# display usage if a mandatory argument is not provided
if fname_segmentation == '' or fname_input == '':
usage()
# check existence of input files
check_file_exist(fname_input)
check_file_exist(fname_segmentation)
# read nifti input file
img = nibabel.load(fname_input)
# 3d array for each x y z voxel values for the input nifti image
data = img.get_data()
# read nifti input file
img_seg = nibabel.load(fname_segmentation)
# 3d array for each x y z voxel values for the input nifti image
data_seg = img_seg.get_data()
X, Y, Z = (data > 0).nonzero()
status = 0
for i in range(0, len(X)):
if data_seg[X[i], Y[i], Z[i]] == 0:
status = 1
break
if status is not 0:
printv('ERROR: detected point is not in segmentation', 1, 'warning')
else:
printv('OK: detected point is in segmentation')
sys.exit(status)
def test_non_executable_task():
data_path = sct_test_path()
with \
NamedTemporaryFile('w', suffix='.sh') as script,\
TemporaryDirectory() as out:
script_text = """
#!/bin/bash
echo $SUBJECT
"""
script.write(
dedent(script_text)[1:]) #indexing removes beginning newline
script.flush()
assert not os.access(script.name, os.X_OK), "Script already executable"
sct_run_batch.main([
'-include', '^t.*', '-subject-prefix', '', '-path-data', data_path,
'-path-out', out, '-script', script.name, '-continue-on-error', 0
])
def pytest_sessionstart():
""" Download sct_testing_data prior to test collection. """
logger.info("Downloading sct test data")
downloader.main(['-d', 'sct_testing_data', '-o', sct_test_path()])
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))