def testGetSidecarMetadata(bidsArchive4D, imageMetadata):
# all entities in imageMetadata should be returned
EXTENSION = '.nii'
returnedMeta = bidsArchive4D.getSidecarMetadata(
bids_build_path(imageMetadata, BIDS_FILE_PATH_PATTERN) + EXTENSION,
includeEntities=True)
# 'TaskName' is parsed from 'task' by BIDS-I when being created, before an
# append, so it's not in the default imageMetadata test fixture
imageMetadata['TaskName'] = imageMetadata['task']
adjustTimeUnits(imageMetadata)
diff = symmetricDictDifference(returnedMeta, imageMetadata, opeq)
# Remove the file-name entities from comparison, as we're only concerned
# about the sidecar metadata
bidsEntities = loadBidsEntities()
diff = {key: diff[key] for key in diff.keys() if key not in bidsEntities}
assert diff == {}
invalidValues = [5, ["path1", "path2"]]
for v in invalidValues:
with pytest.raises(TypeError):
bidsArchive4D.getSidecarMetadata(v)
def testGetIncrementalNoMatchingMetadata(bidsArchive4D, imageMetadata, caplog,
tmpdir):
# Create path to sidecar metadata file
relPath = bids_build_path(imageMetadata, BIDS_FILE_PATH_PATTERN) + \
BidsFileExtension.METADATA.value
absPath = None
files = os.listdir(tmpdir)
for fname in files:
if "dataset" in fname:
absPath = Path(tmpdir, fname, relPath)
break
# Remove the sidecar metadata file
os.remove(absPath)
bidsArchive4D._updateLayout()
# Without the sidecar metadata, not enough information for an incremental
errorText = r"Archive lacks required metadata for BIDS Incremental " \
r"creation: .*"
with pytest.raises(MissingMetadataError, match=errorText):
bidsArchive4D.getIncremental(
subject=imageMetadata["subject"],
task=imageMetadata["task"],
suffix=imageMetadata["suffix"],
datatype="func",
session=imageMetadata["session"])
def makeBidsFileName(self, extension: BidsFileExtension) -> str:
"""
Create the a BIDS-compatible file name based on the metadata. General
format of the filename, per BIDS standard 1.4.1, is as follows (items in
[square brackets] are considered optional):
sub-<label>[_ses-<label>]_task-<label>[_acq-<label>] [_ce-<label>]
[_dir-<label>][_rec-<label>][_run-<index>]
[_echo-<index>]_<contrast_label >.ext
Args:
extension: The extension for the file, e.g., 'nii' for images or
'json' for metadata
Return:
Filename from metadata according to BIDS standard 1.4.1.
"""
entities = {key: self._imgMetadata[key] for key in self.ENTITIES.keys()
if self._imgMetadata.get(key, None) is not None}
entities["extension"] = extension.value
if extension == BidsFileExtension.EVENTS:
entities["suffix"] = "events"
else:
entities["suffix"] = self._imgMetadata["suffix"]
return bids_build_path(entities, BIDS_FILE_PATTERN)
def archiveWithImage(image, metadata: dict, tmpdir):
"""
Create an archive on disk by hand with the provided image and metadata
"""
# Create ensured empty directory
while True:
id = str(randint(0, 1e6))
rootPath = Path(tmpdir, f"dataset-{id}/")
if not Path.exists(rootPath):
rootPath.mkdir()
break
# Create the archive by hand, with default readme and dataset description
Path(rootPath, 'README').write_text("README for pytest")
Path(rootPath, 'dataset_description.json') \
.write_text(json.dumps(DEFAULT_DATASET_DESC))
# Write the nifti image & metadata
dataPath = Path(rootPath, bids_build_path(metadata, BIDS_DIR_PATH_PATTERN))
dataPath.mkdir(parents=True)
filenamePrefix = bids_build_path(metadata, BIDS_FILE_PATTERN)
imagePath = Path(dataPath, filenamePrefix + '.nii')
metadataPath = Path(dataPath, filenamePrefix + '.json')
nib.save(image, str(imagePath))
# BIDS-I's takes care of this automatically, but must be done manually here
metadata['TaskName'] = metadata['task']
metadataPath.write_text(json.dumps(metadata))
del metadata['TaskName']
# BIDS-I's takes care of event file creation automatically, but must be done
# manually here
metadata['suffix'] = 'events'
metadata['extension'] = '.tsv'
eventsPath = Path(dataPath, bids_build_path(metadata, BIDS_FILE_PATTERN))
with open(eventsPath, mode='w') as eventsFile:
eventDefaultHeaders = ['onset', 'duration', 'response_time']
pd.DataFrame(columns=eventDefaultHeaders).to_csv(eventsFile, sep='\t')
# Create an archive from the directory and return it
return BidsArchive(rootPath)
def getDataDirPath(self) -> str:
"""
Path to where this incremental's data would be in a BIDS archive,
relative to the archive root.
Returns:
Path string relative to root of the imaginary dataset.
Examples:
>>> print(bidsi.getDataDirPath())
sub-01/ses-2011/anat
"""
return bids_build_path(self._imgMetadata, BIDS_DIR_PATH_PATTERN)
def testFilenameConstruction(validBidsI, imageMetadata):
"""
General format:
sub-<label>[_ses-<label>]_task-<label>[_acq-<label>] [_ce-<label>]
[_dir-<label>][_rec-<label>][_run-<index>]
[_echo-<index>]_<contrast_label >.ext
"""
baseFilename = bids_build_path(imageMetadata, BIDS_FILE_PATTERN)
assert baseFilename + ".nii" == \
validBidsI.makeBidsFileName(BidsFileExtension.IMAGE)
assert baseFilename + ".json" == \
validBidsI.makeBidsFileName(BidsFileExtension.METADATA)
def testArchivePathConstruction(validBidsI, imageMetadata):
assert validBidsI.getDataDirPath() == \
bids_build_path(imageMetadata, BIDS_DIR_PATH_PATTERN)
