def testEquals(sample4DNifti1, sample3DNifti1, imageMetadata):
# Test images with different headers
assert BidsIncremental(sample4DNifti1, imageMetadata) != \
BidsIncremental(sample3DNifti1, imageMetadata)
# Test images with the same header, but different data
newData = 2 * getNiftiData(sample4DNifti1)
reversedNifti1 = nib.Nifti1Image(newData,
sample4DNifti1.affine,
header=sample4DNifti1.header)
assert BidsIncremental(sample4DNifti1, imageMetadata) != \
BidsIncremental(reversedNifti1, imageMetadata)
# Test different image metadata
modifiedImageMetadata = deepcopy(imageMetadata)
modifiedImageMetadata["subject"] = "newSubject"
assert BidsIncremental(sample4DNifti1, imageMetadata) != \
BidsIncremental(sample4DNifti1, modifiedImageMetadata)
# Test different dataset metadata
datasetMeta1 = {"Name": "Dataset_1", "BIDSVersion": "1.0"}
datasetMeta2 = {"Name": "Dataset_2", "BIDSVersion": "2.0"}
assert BidsIncremental(sample4DNifti1, imageMetadata, datasetMeta1) != \
BidsIncremental(sample4DNifti1, imageMetadata, datasetMeta2)
# Test different readme
incremental1 = BidsIncremental(sample4DNifti1, imageMetadata)
incremental2 = BidsIncremental(sample4DNifti1, imageMetadata)
readme1 = "README 1"
readme2 = "README 2"
incremental1.readme = readme1
incremental2.readme = readme2
assert incremental1 != incremental2
# Test different events file
incremental1 = BidsIncremental(sample4DNifti1, imageMetadata)
incremental2 = BidsIncremental(sample4DNifti1, imageMetadata)
events1 = {
'onset': [1, 25, 50],
'duration': [10, 10, 10],
'response_time': [15, 36, 70]
}
events2 = {key: [v + 5 for v in events1[key]] for key in events1.keys()}
incremental1.events = pd.DataFrame(data=events1)
incremental2.events = pd.DataFrame(data=events2)
assert incremental1 != incremental2
def getBidsRun(self, **entities) -> BidsRun:
"""
Get a BIDS Run from the archive.
Args:
entities: Entities defining a run in the archive.
Returns:
A BidsRun containing all the BidsIncrementals in the specified run.
Raises:
NoMatchError: If the entities don't match any runs in the archive.
QueryError: If the entities match more than one run in the archive.
Examples:
>>> archive = BidsArchive('/tmp/dataset')
>>> run = archive.getBidsRun(subject='01', session='02',
task='testTask', run=1)
>>> print(run.numIncrementals())
53
"""
images = self.getImages(**entities)
if len(images) == 0:
raise NoMatchError(f"Found no runs matching entities {entities}")
if len(images) > 1:
entities = [img.get_entities() for img in images]
raise QueryError("Provided entities were not unique to one run; "
"try specifying more entities "
f" (got runs with these entities: {entities}")
else:
bidsImage = images[0]
niftiImage = bidsImage.get_image()
# TODO: Add inheritance processing for higher-level metadata JSON
# files, in the style of the below events file inheritance
metadata = self.getSidecarMetadata(bidsImage)
metadata.pop('extension') # only used in PyBids
# This incremental will typically have a 4th (time) dimension > 1
incremental = BidsIncremental(niftiImage, metadata)
# Get dataset description, set
incremental.datasetDescription = self.getDatasetDescription()
# Get README, set
with open(self.getReadme().path) as readmeFile:
incremental.readme = readmeFile.read()
# Get events file, set
# Due to inheritance, must find and process all events files the
# target image inherits from to create the final events file for
# this run
# Parse out the events files that the image file inherits from
inheritedFiles = []
searchEntities = bidsImage.get_entities()
# only want to compare entities, not file type
searchEntities.pop('extension', None)
searchEntities.pop('suffix', None)
allEventsFiles = self.getEvents()
for eventFile in allEventsFiles:
fileEntities = eventFile.get_entities()
# only want to compare entities, not file type
fileEntities.pop('extension', None)
fileEntities.pop('suffix', None)
if all(item in searchEntities.items()
for item in fileEntities.items()):
inheritedFiles.append(eventFile)
# Sort the files by their position in the hierarchy.
# Metric: Files with shorter path lengths are higher in the
# inheritance hierarchy.
inheritedFiles.sort(key=lambda eventsFile: len(eventsFile.path))
# Merge every subsequent events file's DataFrame, in order of
# inheritance (from top level to bottom level)
# Using a dictionary representation of the DataFrame gives access to
# the dict.update() method, which has exactly the desired
# combination behavior for inheritance (replace conflicting values
# with the new values, keep any non-conflicting values)
def mergeEventsFiles(base: dict, eventsFile: BIDSDataFile):
# Set DataFrame to be indexed by 'onset' column to ensure
# dictionary update changes rows when onsets match
dfToAdd = eventsFile.get_df()
dfToAdd.set_index('onset', inplace=True, drop=False)
base.update(dfToAdd.to_dict(orient='index'))
return base
eventsDFDict = functools.reduce(mergeEventsFiles, inheritedFiles,
{})
eventsDF = pd.DataFrame.from_dict(eventsDFDict, orient='index')
# If there's no data in the DataFrame, create the default empty
# events file DataFrame
if eventsDF.empty:
eventsDF = pd.DataFrame(columns=DEFAULT_EVENTS_HEADERS)
# Ensure the events file order is the same as presentation/onset
# order
eventsDF.sort_values(by='onset', inplace=True, ignore_index=True)
incremental.events = correctEventsFileDatatypes(eventsDF)
run = BidsRun()
# appendIncremental will take care of splitting the BidsIncremental
# into its component 3-D images
run.appendIncremental(incremental, validateAppend=False)
return run