def test_load_layout(layout_synthetic_nodb, db_dir):
db_path = str(db_dir / 'tmp_db')
layout_synthetic_nodb.save(db_path)
reloaded = BIDSLayout.load(db_path)
assert sorted(layout_synthetic_nodb.get(return_type='file')) == \
sorted(reloaded.get(return_type='file'))
assert layout_synthetic_nodb._init_args == reloaded._init_args
def test_load_layout(layout_synthetic_nodb, db_dir):
db_path = str(db_dir / 'tmp_db')
layout_synthetic_nodb.save(db_path)
reloaded = BIDSLayout.load(db_path)
assert sorted(layout_synthetic_nodb.get(return_type='file')) == \
sorted(reloaded.get(return_type='file'))
cm1 = layout_synthetic_nodb.connection_manager
cm2 = reloaded.connection_manager
for attr in ['root', 'absolute_paths', 'config', 'derivatives']:
assert getattr(cm1.layout_info, attr) == getattr(cm2.layout_info, attr)
def _run_interface(self, runtime):
from bids.layout import BIDSLayout
from bids.modeling import BIDSStatsModelsGraph
layout = BIDSLayout.load(database_path=self.inputs.database_path)
selectors = self.inputs.selectors
graph = BIDSStatsModelsGraph(layout, self.inputs.model)
graph.load_collections(**selectors)
self._results['all_specs'] = self._load_graph(runtime, graph)
return runtime
def _run_interface(self, runtime):
from bids.analysis import Analysis
from bids.layout import BIDSLayout
layout = BIDSLayout.load(database_path=self.inputs.database_path)
selectors = self.inputs.selectors
analysis = Analysis(model=self.inputs.model, layout=layout)
analysis.setup(drop_na=False, **selectors)
self._load_level1(runtime, analysis)
self._load_higher_level(runtime, analysis)
return runtime
def _run_interface(self, runtime):
from bids.layout import BIDSLayout
layout = BIDSLayout.load(database_path=self.inputs.database_path)
bold_files = []
mask_files = []
entities = []
for ents in self.inputs.entities:
selectors = {'desc': 'preproc', **ents, **self.inputs.selectors}
bold_file = layout.get(**selectors)
if len(bold_file) == 0:
raise FileNotFoundError(
"Could not find BOLD file in {} with entities {}"
"".format(layout.root, selectors)
)
elif len(bold_file) > 1:
raise ValueError(
"Non-unique BOLD file in {} with entities {}.\n"
"Matches:\n\t{}"
"".format(
layout.root,
selectors,
"\n\t".join(
'{} ({})'.format(f.path, layout.files[f.path].entities)
for f in bold_file
),
)
)
# Select exactly matching mask file (may be over-cautious)
bold_ents = layout.parse_file_entities(bold_file[0].path)
bold_ents['suffix'] = 'mask'
bold_ents['desc'] = 'brain'
bold_ents['extension'] = ['.nii', '.nii.gz']
mask_file = layout.get(**bold_ents)
bold_ents.pop('suffix')
bold_ents.pop('desc')
bold_files.append(bold_file[0].path)
mask_files.append(mask_file[0].path if mask_file else None)
entities.append(bold_ents)
self._results['bold_files'] = bold_files
self._results['mask_files'] = mask_files
self._results['entities'] = entities
return runtime
