def testGetBidsRunInheritedEvents(tmpdir, validBidsI, sampleBidsEntities):
# Add an events file on the top level with data
rootPath = os.path.join(tmpdir, 'dataset')
incrementalDFDict = {col: [4] for col in DEFAULT_EVENTS_HEADERS}
incrementalDF = pd.DataFrame.from_dict(incrementalDFDict)
validBidsI.events = correctEventsFileDatatypes(incrementalDF)
validBidsI.writeToDisk(rootPath)
archive = BidsArchive(rootPath)
newDFDict = {col: [1, 2, 3] for col in DEFAULT_EVENTS_HEADERS}
newDF = pd.DataFrame.from_dict(newDFDict)
newDF = correctEventsFileDatatypes(newDF)
writeDataFrameToEvents(
newDF, '{dirPath}/task-{taskName}_events.tsv'.format(
dirPath=rootPath, taskName=sampleBidsEntities['task']))
archive._updateLayout()
# Get the BIDS run
run = archive.getBidsRun(**sampleBidsEntities)
# Ensure that the BIDS run has all of the data added at the top level
combinedDF = newDF.append(incrementalDF)
combinedDF.sort_values(by='onset', inplace=True, ignore_index=True)
assert combinedDF.equals(run._events)
def testAppendBidsRun(tmpdir, bidsArchive4D, bidsArchiveMultipleRuns,
sampleBidsEntities):
archivePath = Path(tmpdir, "appendBidsRunArchive")
archive = BidsArchive(archivePath)
emptyRun = BidsRun()
archive.appendBidsRun(emptyRun)
run = bidsArchive4D.getBidsRun(**sampleBidsEntities)
archive.appendBidsRun(run)
assert archive.getBidsRun(**sampleBidsEntities) == run
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)
self.bidsRun = self.bidsArchive.getBidsRun(**entities)
self.numVolumes = self.bidsRun.numIncrementals()
self.nextVol = 0
def getNumVolumes(self) -> int:
"""Return the number of brain volumes in the run"""
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
"""
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 = self.bidsRun.getIncremental(self.nextVol)
self.nextVol += 1
return incremental
else:
return None
def openNeuroStreamTest(bidsInterface):
dsAccessionNumber = 'ds002338'
dsSubject = 'xp201'
datasetDir = tmpDownloadOpenNeuro(dsAccessionNumber, dsSubject, 1)
localEntities = {'subject': dsSubject, 'run': 1, 'suffix': 'bold', 'datatype': 'func'}
remoteEntities = {'subject': dsSubject, 'run': 1}
localBidsArchive = BidsArchive(datasetDir)
streamId = bidsInterface.initOpenNeuroStream(dsAccessionNumber, **remoteEntities)
for idx in range(3):
streamIncremental = bidsInterface.getIncremental(streamId)
localIncremental = localBidsArchive._getIncremental(idx, **localEntities)
print(f"OpenNeuro stream check: image {idx}")
assert streamIncremental == localIncremental
for idx in [5, 2, 7]:
streamIncremental = bidsInterface.getIncremental(streamId, volIdx=idx)
localIncremental = localBidsArchive._getIncremental(idx, **localEntities)
print(f"OpenNeuro stream check: image {idx}")
assert streamIncremental == localIncremental
# Resume without specifying volumes
for idx in [*range(8, 10)]:
streamIncremental = bidsInterface.getIncremental(streamId)
localIncremental = localBidsArchive._getIncremental(idx, **localEntities)
print(f"OpenNeuro stream check: image {idx}")
assert streamIncremental == localIncremental
numVols = bidsInterface.getNumVolumes(streamId)
assert numVols > 0 and numVols < 1000
# Check with local bidsRun
localBidsRun = localBidsArchive.getBidsRun(**localEntities)
assert numVols == localBidsRun.numIncrementals()
assert numVols > 10
for idx in [*range(6, 10)]:
streamIncremental = bidsInterface.getIncremental(streamId, volIdx=idx)
localIncremental = localBidsRun.getIncremental(idx)
print(f"OpenNeuro bidsRun check: image {idx}")
assert streamIncremental == localIncremental