def test4DAppend(bidsArchive4D, validBidsI, imageMetadata):
incrementAcquisitionValues(validBidsI)
bidsArchive4D.appendIncremental(validBidsI)
assert archiveHasMetadata(bidsArchive4D, imageMetadata)
assert appendDataMatches(bidsArchive4D, validBidsI, startIndex=2)
assert isValidBidsArchive(bidsArchive4D.rootPath)
def testDiskOutput(validBidsI, tmpdir):
# Write the archive
datasetRoot = os.path.join(tmpdir, "bids-pytest-dataset")
validBidsI.writeToDisk(datasetRoot)
# Validate the output can be opened by BidsArchive and verified against the
# source BIDS-Incremental
archive = BidsArchive(datasetRoot)
archiveImage = archive.getImages()[0]
# Remove pseudo entities to avoid conflict with the validBidsI
metadata = archive.getSidecarMetadata(archiveImage, includeEntities=True)
for entity in PYBIDS_PSEUDO_ENTITIES:
metadata.pop(entity)
incrementalFromArchive = BidsIncremental(archiveImage, metadata)
assert incrementalFromArchive == validBidsI
assert isValidBidsArchive(archive.rootPath)
# Try only writing data
datasetRoot = os.path.join(tmpdir, "bids-pytest-dataset-2")
validBidsI.writeToDisk(datasetRoot, onlyData=True)
assert not os.path.exists(os.path.join(datasetRoot, "README"))
assert not os.path.exists(
os.path.join(datasetRoot, "dataset_description.json"))
def testAppendNewSubject(bidsArchive4D, validBidsI):
preSubjects = bidsArchive4D.getSubjects()
validBidsI.setMetadataField("subject", "02")
bidsArchive4D.appendIncremental(validBidsI)
assert len(bidsArchive4D.getSubjects()) == len(preSubjects) + 1
assert appendDataMatches(bidsArchive4D, validBidsI)
assert isValidBidsArchive(bidsArchive4D.rootPath)
def testEmptyArchiveAppend(validBidsI, imageMetadata, tmpdir):
# Create in root with no BIDS-I, then append to make non-empty archive
datasetRoot = Path(tmpdir, testEmptyArchiveAppend.__name__)
archive = BidsArchive(datasetRoot)
archive.appendIncremental(validBidsI)
assert not archive.isEmpty()
assert archiveHasMetadata(archive, imageMetadata)
assert appendDataMatches(archive, validBidsI)
assert isValidBidsArchive(datasetRoot)
def testSequenceAppend(bidsArchive4D, validBidsI, imageMetadata):
NUM_APPENDS = 2
BIDSI_LENGTH = 2
for i in range(NUM_APPENDS):
incrementAcquisitionValues(validBidsI)
bidsArchive4D.appendIncremental(validBidsI)
image = bidsArchive4D.getImages(
matchExact=False, **filterEntities(imageMetadata))[0].get_image()
shape = image.header.get_data_shape()
assert len(shape) == 4 and shape[3] == (BIDSI_LENGTH * (1 + NUM_APPENDS))
assert archiveHasMetadata(bidsArchive4D, imageMetadata)
assert appendDataMatches(bidsArchive4D, validBidsI,
startIndex=2, endIndex=4)
assert isValidBidsArchive(bidsArchive4D.rootPath)
def testBidsArchiveMultipleRun(bidsArchiveMultipleRuns):
assert isValidBidsArchive(bidsArchiveMultipleRuns.rootPath), \
"BIDS Archive Multiple Runs fixture is not a valid BIDS Archive " \
"(path: " + bidsArchiveMultipleRuns.rootPath + " )"
def testBidsArchive4D(bidsArchive4D):
assert isValidBidsArchive(bidsArchive4D.rootPath), \
"BIDS Archive 4D fixture is not a valid BIDS Archive"
