def layout_ds005_multi_derivs():
data_dir = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(data_dir)
deriv_dir1 = join(get_test_data_path(), 'ds005_derivs')
deriv_dir2 = join(data_dir, 'derivatives', 'events')
layout.add_derivatives([deriv_dir1, deriv_dir2])
return layout
def test_parsing_dwi(testmeta, testconfig):
"""
parsing.dwi_info returns a str description of each diffusion scan
"""
bval_file = join(get_test_data_path(), 'images/4d.bval')
img = nib.load(join(get_test_data_path(), 'images/4d.nii.gz'))
desc = parsing.dwi_info(bval_file, testmeta, img, testconfig)
assert isinstance(desc, str)
def test_get_bidsfile_image_prop():
path = "synthetic/sub-01/ses-01/func/sub-01_ses-01_task-nback_run-01_bold.nii.gz"
path = path.split('/')
path = join(get_test_data_path(), *path)
bf = BIDSFile(path, None)
assert bf.image is not None
assert bf.image.shape == (64, 64, 64, 64)
def model():
layout_path = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(layout_path)
models = auto_model(layout, scan_length=480, one_vs_rest=True)
return models[0]
def test_auto_model_analysis(model):
layout_path = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(layout_path)
# Test to make sure an analaysis can be setup from the generated model
analysis = Analysis(layout, model)
analysis.setup(scan_length=480)
assert model['Name'] == 'ds005_mixedgamblestask'
# run level
block = model['Steps'][0]
assert block['Name'] == 'Run'
assert block['Level'] == 'Run'
assert block['Transformations'][0]['Name'] == 'Factor'
assert block['Contrasts'][0]['Name'] == 'run_parametric gain'
assert block['Contrasts'][0]['Weights'] == [1]
# subject level
block = model['Steps'][1]
assert block['Name'] == 'Subject'
assert block['Level'] == 'Subject'
assert block['Model']['X'][0] == 'run_parametric gain'
assert block['Contrasts'][0]['Name'] == 'subject_run_parametric gain'
# dataset level
block = model['Steps'][2]
assert block['Name'] == 'Dataset'
assert block['Level'] == 'Dataset'
assert block['Model']['X'][0] == 'subject_run_parametric gain'
assert block['Contrasts'][0]['Name'] == 'dataset_subject_run_parametric gain'
def test_derivative_getters():
synth_path = join(get_test_data_path(), 'synthetic')
bare_layout = BIDSLayout(synth_path, derivatives=False)
full_layout = BIDSLayout(synth_path, derivatives=True)
with pytest.raises(AttributeError):
bare_layout.get_spaces()
assert set(full_layout.get_spaces()) == {'MNI152NLin2009cAsym', 'T1w'}
def analysis():
layout_path = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(layout_path)
json_file = join(layout_path, 'models', 'ds-005_type-test_model.json')
analysis = Analysis(layout, json_file)
analysis.setup(scan_length=480, subject=['01', '02'])
return analysis
def test_bidsfile_image_property():
path = os.path.join(get_test_data_path(), 'synthetic', 'sub-01', 'ses-01',
'func', 'sub-01_ses-01_task-nback_run-01_bold.nii.gz')
bf = BIDSFile(path)
img = bf.image
assert img.__class__.__name__ == 'Nifti1Image'
assert img.header.get_data_shape() == (64, 64, 64, 64)
def test_parsing_anat(testmeta, testconfig):
"""
parsing.anat_info returns a str description of each structural scan
"""
type_ = 'T1w'
img = nib.load(join(get_test_data_path(), 'images/3d.nii.gz'))
desc = parsing.anat_info(type_, testmeta, img, testconfig)
assert isinstance(desc, str)
def test_parsing_func(testmeta, testconfig):
"""
parsing.func_info returns a str description of a set of functional scans
grouped by task
"""
img = nib.load(join(get_test_data_path(), 'images/4d.nii.gz'))
desc = parsing.func_info('nback', 3, testmeta, img, testconfig)
assert isinstance(desc, str)
def test_parsing_fmap(testlayout, testmeta, testconfig):
"""
parsing.fmap_info returns a str decsription of each field map
"""
testmeta['PhaseEncodingDirection'] = 'j-'
img = nib.load(join(get_test_data_path(), 'images/3d.nii.gz'))
desc = parsing.fmap_info(testmeta, img, testconfig, testlayout)
assert isinstance(desc, str)
def test_report_file_config(testlayout):
"""Report initialization should take in a config file and use that if
provided.
"""
config_file = abspath(
join(get_test_data_path(), '../../reports/config/converters.json'))
report = BIDSReport(testlayout, config=config_file)
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def test_force_index(layout_ds005):
data_dir = join(get_test_data_path(), 'ds005')
target = join(data_dir, 'models', 'ds-005_type-test_model.json')
model_layout = BIDSLayout(data_dir, validate=True, force_index=['models'])
assert target not in layout_ds005.files
assert target in model_layout.files
assert 'all' not in model_layout.get_subjects()
for f in model_layout.files.values():
assert 'derivatives' not in f.path
def test_layout_with_derivs(deriv_layout):
assert deriv_layout.root == join(get_test_data_path(), 'ds005')
assert isinstance(deriv_layout.files, dict)
assert set(deriv_layout.domains.keys()) == {'bids', 'derivatives'}
assert deriv_layout.domains['bids'].files
assert deriv_layout.domains['derivatives'].files
assert 'derivatives.roi' in deriv_layout.entities
assert 'bids.roi' not in deriv_layout.entities
assert 'bids.subject' in deriv_layout.entities
def tmp_bids(tmpdir_factory):
tmp_bids = tmpdir_factory.mktemp("tmp_bids")
yield tmp_bids
shutil.rmtree(str(tmp_bids))
# Ugly hack
try:
shutil.rmtree(join(get_test_data_path(), '7t_trt', 'sub-Bob'))
except:
pass
def test_layout_with_validation():
data_dir = join(get_test_data_path(), '7t_trt')
layout1 = BIDSLayout(data_dir, validate=True)
layout2 = BIDSLayout(data_dir, validate=False)
assert len(layout1.files) < len(layout2.files)
# Not a valid BIDS file
badfile = join(data_dir, 'test.bval')
assert (badfile not in layout1.files)
assert (badfile in layout2.files)
def test_layout_save(layout_7t_trt):
_, f = tempfile.mkstemp(suffix='.db')
layout_7t_trt.save(f, replace_connection=False)
data_dir = join(get_test_data_path(), '7t_trt')
layout = BIDSLayout(data_dir, database_file=f)
oldfies = set(layout_7t_trt.get(suffix='events', return_type='file'))
newfies = set(layout.get(suffix='events', return_type='file'))
assert oldfies == newfies
os.unlink(f)
def test_report_file_config(testlayout):
"""Report initialization should take in a config file and use that if
provided.
"""
config_file = abspath(join(get_test_data_path(),
'../../reports/config/converters.json'))
report = BIDSReport(testlayout, config=config_file)
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def collection():
layout_path = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(layout_path, exclude='derivatives/')
collection = layout.get_collections('run',
types=['events'],
scan_length=480,
merge=True,
sampling_rate=10)
return collection
def test_incremental_data_loading():
layout_path = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(layout_path)
json_file = join(layout_path, 'models', 'ds-005_type-test_model.json')
analysis = Analysis(layout, json_file)
analysis.setup(scan_length=480, subject=['01'], run=[1], finalize=False)
analysis.setup(scan_length=480, subject=['02'], run=[2], finalize=False)
analysis.finalize()
assert len(analysis['run'].get_collections()) == 2
def test_index_metadata(index_metadata, query, result):
data_dir = join(get_test_data_path(), '7t_trt')
layout = BIDSLayout(data_dir, index_metadata=index_metadata)
if not index_metadata and query is not None:
indexer = BIDSLayoutIndexer(layout)
indexer.index_metadata(**query)
sample_file = layout.get(task='rest', extension='nii.gz',
acq='fullbrain')[0]
metadata = sample_file.get_metadata()
assert metadata.get('RepetitionTime') == result
def test_parsing_anat():
"""
parsing.anat_info returns a str description of each structural scan
"""
type_ = 'T1w'
metadata = testmeta()
img = nib.load(join(get_test_data_path(), 'images/3d.nii.gz'))
config = testconfig()
desc = parsing.anat_info(type_, metadata, img, config)
assert isinstance(desc, str)
def synthetic(request):
root = join(get_test_data_path(), 'synthetic')
if request.param == 'preproc':
layout = BIDSLayout(root, derivatives=True)
dataset = load_variables(layout, skip_empty=True, desc='preproc',
space='T1w')
else:
layout = BIDSLayout(root)
dataset = load_variables(layout, skip_empty=True)
yield request.param, dataset
def test_layout_repr_overshadow_run(tmp_path):
"""A test creating a layout to replicate #681."""
shutil.copytree(join(get_test_data_path(), '7t_trt'), tmp_path / "7t_trt")
(tmp_path / "7t_trt" / "sub-01" / "ses-1" /
"sub-01_ses-1_scans.json").write_text(
json.dumps({"run": {
"Description": "metadata to cause #681"
}}))
assert "Subjects: 10 | Sessions: 20 | Runs: 20" in str(
BIDSLayout(tmp_path / "7t_trt"))
def test_report_dict_config():
"""Report initialization should take in a config dict and use that if provided.
"""
config_file = abspath(
join(get_test_data_path(), '../../reports/config/converters.json'))
with open(config_file, 'r') as fobj:
config = json.load(fobj)
report = BIDSReport(testlayout(), config=config)
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def test_parsing_func():
"""
parsing.func_info returns a str description of a set of functional scans
grouped by task
"""
metadata = testmeta()
img = nib.load(join(get_test_data_path(), 'images/4d.nii.gz'))
config = testconfig()
desc = parsing.func_info('nback', 3, metadata, img, config)
assert isinstance(desc, str)
def test_report_dict_config(testlayout):
"""Report initialization should take in a config dict and use that if
provided.
"""
config_file = abspath(join(get_test_data_path(),
'../../reports/config/converters.json'))
with open(config_file, 'r') as fobj:
config = json.load(fobj)
report = BIDSReport(testlayout, config=config)
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def synthetic(request):
root = join(get_test_data_path(), 'synthetic')
default_preproc = get_option('loop_preproc')
if request.param == 'preproc':
set_option('loop_preproc', True)
layout = BIDSLayout((root, ['bids', 'derivatives']))
else:
set_option('loop_preproc', default_preproc)
layout = BIDSLayout(root, exclude='derivatives')
yield request.param, load_variables(layout, skip_empty=True)
set_option('loop_preproc', default_preproc)
def test_load_description(testlayout1):
with pytest.raises(ValueError) as e:
data_dir = join(get_test_data_path(), 'images')
layout = BIDSLayout(data_dir)
assert e.value.message.startswith("Mandatory 'dataset_description'")
# Should not raise an error
layout = BIDSLayout(data_dir, config='derivatives')
assert hasattr(testlayout1, 'description')
assert testlayout1.description['Name'] == '7t_trt'
assert testlayout1.description['BIDSVersion'] == "1.0.0rc3"
def test_get_metadata_caches_in_index(layout):
targ = 'sub-04/ses-1/func/sub-04_ses-1_task-rest_acq-fullbrain_run-1_bold.nii.gz'
targ = targ.split('/')
targ = join(get_test_data_path(), '7t_trt', *targ)
mdi = layout.metadata_index
assert not mdi.file_index
md = layout.get_metadata(targ)
assert targ in mdi.file_index
assert len(mdi.file_index) == 1
assert 'CogAtlasID' in mdi.key_index
assert 'RepetitionTime' in mdi.key_index
def test_parsing_fmap():
"""
parsing.fmap_info returns a str decsription of each field map
"""
metadata = testmeta()
metadata['PhaseEncodingDirection'] = 'j-'
img = nib.load(join(get_test_data_path(), 'images/3d.nii.gz'))
config = testconfig()
layout = testlayout()
desc = parsing.fmap_info(metadata, img, config, layout)
assert isinstance(desc, str)
def test_layout_with_derivs(layout_ds005_derivs):
assert layout_ds005_derivs.root == join(get_test_data_path(), 'ds005')
assert isinstance(layout_ds005_derivs.files, dict)
assert len(layout_ds005_derivs.derivatives) == 1
deriv = layout_ds005_derivs.derivatives['events']
assert deriv.files
assert len(deriv.files) == 2
event_file = "sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv"
deriv_files = [basename(f) for f in list(deriv.files.keys())]
assert event_file in deriv_files
assert 'roi' in deriv.entities
assert 'subject' in deriv.entities
def test_restricted_words_in_path(tmpdir):
orig_path = join(get_test_data_path(), 'synthetic')
parent_dir = str(tmpdir / 'derivatives' / 'pipeline')
os.makedirs(parent_dir)
new_path = join(parent_dir, 'sourcedata')
os.symlink(orig_path, new_path)
orig_layout = BIDSLayout(orig_path)
new_layout = BIDSLayout(new_path)
orig_files = set(f.replace(orig_path, '') for f in orig_layout.files)
new_files = set(f.replace(new_path, '') for f in new_layout.files)
assert orig_files == new_files
def synthetic(request):
root = join(get_test_data_path(), 'synthetic')
if request.param == 'preproc':
layout = BIDSLayout(root, derivatives=True)
dataset = load_variables(layout,
skip_empty=True,
desc='preproc',
space='T1w')
else:
layout = BIDSLayout(root)
dataset = load_variables(layout, skip_empty=True)
yield request.param, dataset
def test_layout_with_derivs(layout_ds005_derivs):
assert layout_ds005_derivs.root == join(get_test_data_path(), 'ds005')
assert isinstance(layout_ds005_derivs.files, dict)
assert len(layout_ds005_derivs.derivatives) == 1
deriv = layout_ds005_derivs.derivatives['events']
assert deriv.files
assert len(deriv.files) == 2
event_file = "sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv"
deriv_files = [basename(f) for f in list(deriv.files.keys())]
assert event_file in deriv_files
assert 'roi' in deriv.entities
assert 'subject' in deriv.entities
def test_restricted_words_in_path(tmpdir):
orig_path = join(get_test_data_path(), 'synthetic')
parent_dir = str(tmpdir / 'derivatives' / 'pipeline')
os.makedirs(parent_dir)
new_path = join(parent_dir, 'sourcedata')
os.symlink(orig_path, new_path)
orig_layout = BIDSLayout(orig_path)
new_layout = BIDSLayout(new_path)
orig_files = set(f.replace(orig_path, '') for f in orig_layout.files)
new_files = set(f.replace(new_path, '') for f in new_layout.files)
assert orig_files == new_files
def test_path_arguments():
data_dir = join(get_test_data_path(), 'ds005')
deriv_dir = join(data_dir, 'derivatives', 'events')
layout = BIDSLayout(Path(data_dir), derivatives=Path(deriv_dir))
assert layout.get(scope='derivatives')
assert layout.get(scope='events')
assert not layout.get(scope='nonexistent')
layout = BIDSLayout(Path(data_dir), derivatives=[Path(deriv_dir)])
assert layout.get(scope='derivatives')
assert layout.get(scope='events')
assert not layout.get(scope='nonexistent')
def collection():
if 'ds005' not in cached_collections:
layout_path = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(layout_path)
cached_collections['ds005'] = layout.get_collections(
'run',
types=['events'],
scan_length=SCAN_LENGTH,
merge=True,
sampling_rate=10,
subject=SUBJECTS)
# Always return a clone!
return cached_collections['ds005'].clone()
def test_deriv_indexing():
data_dir = join(get_test_data_path(), 'ds005')
deriv_dir = join(data_dir, 'derivatives', 'bbr')
# missing dataset_description.json
with pytest.warns(UserWarning):
layout = BIDSLayout(data_dir, derivatives=deriv_dir)
# Should work fine
deriv_dir = join(data_dir, 'derivatives', 'events')
layout = BIDSLayout(data_dir, derivatives=deriv_dir)
assert layout.get(scope='derivatives')
assert layout.get(scope='events')
assert not layout.get(scope='nonexistent')
def test_layout_with_multi_derivs(layout_ds005_multi_derivs):
assert layout_ds005_multi_derivs.root == join(get_test_data_path(), 'ds005')
assert isinstance(layout_ds005_multi_derivs.files, dict)
assert len(layout_ds005_multi_derivs.derivatives) == 2
deriv = layout_ds005_multi_derivs.derivatives['events']
assert deriv.files
assert len(deriv.files) == 2
deriv = layout_ds005_multi_derivs.derivatives['dummy']
assert deriv.files
assert len(deriv.files) == 4
assert 'roi' in deriv.entities
assert 'subject' in deriv.entities
preproc = layout_ds005_multi_derivs.get(desc='preproc')
assert len(preproc) == 3
def test_deriv_indexing():
data_dir = join(get_test_data_path(), 'ds005')
deriv_dir = join(data_dir, 'derivatives', 'bbr')
# missing dataset_description.json
with pytest.warns(UserWarning):
layout = BIDSLayout(data_dir, derivatives=deriv_dir)
# Should work fine
deriv_dir = join(data_dir, 'derivatives', 'events')
layout = BIDSLayout(data_dir, derivatives=deriv_dir)
assert layout.get(scope='derivatives')
assert layout.get(scope='events')
assert not layout.get(scope='nonexistent')
def test_layout_with_multi_derivs(layout_ds005_multi_derivs):
assert layout_ds005_multi_derivs.root == join(get_test_data_path(), 'ds005')
assert isinstance(layout_ds005_multi_derivs.files, dict)
assert len(layout_ds005_multi_derivs.derivatives) == 2
deriv = layout_ds005_multi_derivs.derivatives['events']
assert deriv.files
assert len(deriv.files) == 2
deriv = layout_ds005_multi_derivs.derivatives['dummy']
assert deriv.files
assert len(deriv.files) == 4
assert 'roi' in deriv.entities
assert 'subject' in deriv.entities
preproc = layout_ds005_multi_derivs.get(desc='preproc')
assert len(preproc) == 3
def collection():
if 'ds005' not in cached_collections:
layout_path = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(layout_path)
cached_collections['ds005'] = layout.get_collections(
'run',
types=['events'],
scan_length=SCAN_LENGTH,
merge=True,
sampling_rate=10,
subject=SUBJECTS
)
# Always return a clone!
return cached_collections['ds005'].clone()
def test_nested_include_exclude_with_regex():
# ~same as above test, but use regexps instead of strings
patt1 = re.compile('.*dels$')
patt2 = re.compile('xtra')
data_dir = join(get_test_data_path(), 'ds005')
target1 = join(data_dir, 'models', 'ds-005_type-test_model.json')
target2 = join(data_dir, 'models', 'extras', 'ds-005_type-test_model.json')
layout = BIDSLayout(data_dir, ignore=[patt2], force_index=[patt1])
assert layout.get_file(target1)
assert not layout.get_file(target2)
layout = BIDSLayout(data_dir, ignore=[patt1], force_index=[patt2])
assert not layout.get_file(target1)
assert layout.get_file(target2)
def test_ignore_files(layout_ds005):
data_dir = join(get_test_data_path(), 'ds005')
target1 = join(data_dir, 'models', 'ds-005_type-test_model.json')
target2 = join(data_dir, 'models', 'extras', 'ds-005_type-test_model.json')
layout1 = BIDSLayout(data_dir, validate=False)
assert target1 not in layout_ds005.files
assert target1 not in layout1.files
assert target2 not in layout1.files
# now the models/ dir should show up, because passing ignore explicitly
# overrides the default - but 'model/extras/' should still be ignored
# because of the regex.
ignore = [re.compile('xtra'), 'dummy']
layout2 = BIDSLayout(data_dir, validate=False, ignore=ignore)
assert target1 in layout2.files
assert target2 not in layout2.files
def test_searching_without_file_list_indexes_everything(index):
res = index.search(nonexistent_key=2)
assert not res
keys = {
'EchoTime2', 'EchoTime1', 'IntendedFor', 'CogAtlasID', 'EchoTime',
'EffectiveEchoSpacing', 'PhaseEncodingDirection', 'RepetitionTime',
'SliceEncodingDirection', 'SliceTiming', 'TaskName', 'StartTime',
'SamplingFrequency', 'Columns', 'BIDSVersion', 'Name'
}
assert keys == set(index.key_index.keys())
targ = 'sub-04/ses-1/func/sub-04_ses-1_task-rest_acq-fullbrain_run-1_bold.nii.gz'
targ = targ.split('/')
targ = join(get_test_data_path(), '7t_trt', *targ)
assert targ in index.file_index
assert index.file_index[targ]['EchoTime'] == 0.017
def test_layout(runner, tmp_path):
def is_success(res):
return res.stdout.startswith("Successfully generated database index")
res = runner.invoke(cli, ['layout', '--help'])
assert "Initialize a BIDSLayout" in res.stdout
bids_dir = os.path.join(get_test_data_path(), 'ds005')
db0 = tmp_path / "db0"
db0.mkdir()
res = runner.invoke(cli, ['layout', bids_dir, str(db0)],
catch_exceptions=False)
assert is_success(res)
# rerunning targeting the save directory should not generate a new index
res = runner.invoke(cli, ['layout', bids_dir, str(db0)],
catch_exceptions=False)
assert not is_success(res)
# but forcing it should
res = runner.invoke(
cli, ['layout', bids_dir, str(db0), '--reset-db'],
catch_exceptions=False)
assert is_success(res)
db1 = tmp_path / "db1"
db1.mkdir()
# throw the kitchen sink at it
res = runner.invoke(
cli,
[
'layout',
bids_dir,
str(db1),
'--validate',
'--no-index-metadata',
'--ignore',
'derivatives',
'--ignore',
'sourcedata',
'--ignore',
r'm/^\./',
'--force-index',
'test',
'--config',
'bids',
],
catch_exceptions=False,
)
assert is_success(res)
def synthetic(request):
import bids.config
# Not testing with/without here
with patch.dict('bids.config._settings'):
bids.config.set_option('extension_initial_dot', True)
root = join(get_test_data_path(), 'synthetic')
if request.param == 'preproc':
layout = BIDSLayout(root, derivatives=True)
dataset = load_variables(layout,
skip_empty=True,
desc='preproc',
space='T1w')
else:
layout = BIDSLayout(root)
dataset = load_variables(layout, skip_empty=True)
yield request.param, dataset
def test_automodel_runs(model):
layout_path = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(layout_path)
# Test to make sure an analaysis can be setup from the generated model
graph = BIDSStatsModelsGraph(layout, model)
graph.load_collections(scan_length=480, subject=["01", "02"])
outputs = graph["Run"].run()
assert len(outputs) == 6
cis = list(chain(*[op.contrasts for op in outputs]))
assert len(cis) == 6
outputs = graph["Subject"].run(cis)
# 2 subjects x 1 contrast
assert len(outputs) == 2
cis = list(chain(*[op.contrasts for op in outputs]))
assert len(cis) == 2
def test_get_return_type_dir(layout_7t_trt, layout_7t_trt_relpath):
query = dict(target='subject', return_type='dir')
# In case of relative paths
res_relpath = layout_7t_trt_relpath.get(**query)
# returned directories should be in sorted order so we can match exactly
target_relpath = ["sub-{:02d}".format(i) for i in range(1, 11)]
assert target_relpath == res_relpath
res = layout_7t_trt.get(**query)
target = [
os.path.join(get_test_data_path(), '7t_trt', p)
for p in target_relpath
]
assert target == res
# and we can overload the value for absolute_path in .get call
res_relpath2 = layout_7t_trt.get(absolute_paths=False, **query)
assert target_relpath == res_relpath2
res2 = layout_7t_trt_relpath.get(absolute_paths=True, **query)
assert target == res2
def layout1():
path = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(path)
return layout
def layout_ds005_models():
data_dir = join(get_test_data_path(), 'ds005')
return BIDSLayout(data_dir, validate=True, force_index=['models'])
def layout_ds117():
data_dir = join(get_test_data_path(), 'ds000117')
return BIDSLayout(data_dir)
def layout_7t_trt():
data_dir = join(get_test_data_path(), '7t_trt')
return BIDSLayout(data_dir)
def layout_7t_trt_relpath():
data_dir = join(get_test_data_path(), '7t_trt')
return BIDSLayout(data_dir, absolute_paths=False)
def layout_synthetic():
path = join(get_test_data_path(), 'synthetic')
return BIDSLayout(path, derivatives=True)
def layout2():
path = join(get_test_data_path(), '7t_trt')
layout = BIDSLayout(path)
return layout
def testconfig():
config_file = abspath(join(get_test_data_path(),
'../../reports/config/converters.json'))
with open(config_file, 'r') as fobj:
config = json.load(fobj)
return config
import sys
import pytest
from pathlib import Path
from bids.layout import BIDSLayout
from bids.tests import get_test_data_path
"""
test handling of pathlib Path file paths in place of old-style string type
"""
TESTPATH = Path(get_test_data_path()).joinpath("ds005")
TESTSTR = str(TESTPATH)
FALSEPATH = TESTPATH.joinpath("junk")
FALSESTR = str(FALSEPATH)
assert not FALSEPATH.exists()
def test_strroot_pos():
layout = BIDSLayout(TESTSTR)
def test_strroot_neg():
with pytest.raises(ValueError):
layout = BIDSLayout(FALSESTR)
def test_pathroot_pos():
layout = BIDSLayout(TESTPATH)
def test_pathroot_neg():
with pytest.raises(ValueError):
layout = BIDSLayout(FALSEPATH)
def testlayout():
data_dir = join(get_test_data_path(), 'synthetic')
return BIDSLayout(data_dir)
