def testFailEmpty(tmpdir):
datasetRoot = Path(tmpdir, "bids-archive")
emptyArchive = BidsArchive(datasetRoot)
with pytest.raises(StateError):
emptyArchive.dirExistsInArchive("will fail anyway")
emptyArchive.getImages("will fail anyway")
emptyArchive.addImage(None, "will fall anyway")
emptyArchive.getSidecarMetadata("will fall anyway")
emptyArchive.addMetadata({"will": "fail"}, "will fall anyway")
emptyArchive.getIncremental(subject="will fall anyway",
session="will fall anyway",
task="will fall anyway",
suffix="will fall anyway",
datatype="will fall anyway")
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 appendDataMatches(archive: BidsArchive, reference: BidsIncremental,
startIndex: int = 0, endIndex: int = -1):
entities = filterEntities(reference.imageMetadata)
images = archive.getImages(**entities)
assert len(images) == 1
imageFromArchive = images[0].get_image()
fullImageData = getNiftiData(imageFromArchive)
if endIndex == -1:
endIndex = len(fullImageData)
appendedData = fullImageData[..., startIndex:endIndex]
appendedImage = nib.Nifti1Image(appendedData,
imageFromArchive.affine,
imageFromArchive.header)
return BidsIncremental(appendedImage, reference.imageMetadata) == reference
class BidsStream:
"""
A class that opens a BIDS archive and prepares to stream the data as
BIDS incrementals.
"""
def __init__(self, archivePath, **entities):
"""
Args:
archivePath: Absolute path of the BIDS archive.
entities: BIDS entities (subject, session, task, run, suffix, datatype) that
define the particular subject/run of the data to stream
"""
self.bidsArchive = BidsArchive(archivePath)
# TODO - when we have BidsRun
# self.bidsRun = self.bidsArchive.getBidsRun(**entities)
images = self.bidsArchive.getImages(**entities)
if len(images) == 0:
raise ValidationError('No matching images found')
if len(images) > 1:
raise ValidationError('More than one match, please give more specific subject/session/task/run')
self.bidsImage = images[0]
self.niftiImage = self.bidsImage.get_image()
self.filename = self.niftiImage.get_filename()
self.imgVolumes = nib.four_to_three(self.niftiImage)
self.metadata = self.bidsArchive.getSidecarMetadata(self.filename, includeEntities=True)
self.metadata.pop('extension')
self.numVolumes = len(self.imgVolumes)
self.nextVol = 0
def getNumVolumes(self) -> int:
"""Return the number of brain volumes in the run"""
# TODO - when we have BidsRun
# return self.bidsRun.getNumVolumes()
return self.numVolumes
def getIncremental(self, volIdx=-1) -> BidsIncremental:
"""
Get a BIDS incremental for the indicated index in the current subject/run
VolIdx acts similar to a file_seek pointer. If a volIdx >= 0 is supplied
the volume pointer is advanced to that position. If no volIdx or
a volIdx < 0 is supplied, then the next image volume after the previous
position is returned and the pointer is incremented.
Args:
volIdx: The volume index (or TR) within the run to retrieve.
Returns:
BidsIncremental of that volume index within this subject/run
"""
# TODO - when we have BidsRun
# return self.bidsRun.getIncremental(volIdx)
if volIdx >= 0:
# reset the next volume to the user specified volume
self.nextVol = volIdx
else:
# use the default next volume
pass
if self.nextVol < self.numVolumes:
incremental = BidsIncremental(self.imgVolumes[self.nextVol], self.metadata)
self.nextVol += 1
return incremental
else:
return None
