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More refactoring (reducing the need for creating DataSource())
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@marcelzwiers
marcelzwiers committed Sep 30, 2024
1 parent 92e49b3 commit f4f774e
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Showing 6 changed files with 182 additions and 198 deletions.
137 changes: 67 additions & 70 deletions bidscoin/bids.py
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4 changes: 2 additions & 2 deletions bidscoin/bidseditor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -236,7 +236,7 @@ def show_contextmenu(self, pos):
datasource = bids.DataSource(dataformat=dataformat)
for filename in filenames:
datasource = bids.DataSource(filename, self.output_bidsmap.plugins, dataformat, self.output_bidsmap.options)
if datasource.has_plugin():
if datasource.has_support():
runitem = self.template_bidsmap.get_run(datatype, 0, datasource)
runitem.properties['filepath'] = datasource.properties('filepath') # Make the added run a strict match (i.e. an exception)
runitem.properties['filename'] = datasource.properties('filename') # Make the added run a strict match (i.e. an exception)
Expand All @@ -248,7 +248,7 @@ def show_contextmenu(self, pos):
self.ordered_file_index[dataformat] = {datasource.path: 0}
else:
self.ordered_file_index[dataformat][datasource.path] = max(self.ordered_file_index[dataformat][fname] for fname in self.ordered_file_index[dataformat]) + 1
if datasource.has_plugin():
if datasource.has_support():
self.update_subses_samples(dataformat)

elif action == delete:
Expand Down
55 changes: 26 additions & 29 deletions bidscoin/plugins/dcm2niix2bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ def bidsmapper_plugin(session: Path, bidsmap_new: BidsMap, bidsmap_old: BidsMap,
for sourcedir in lsdirs(session, '**/*'):
for n in range(1): # Option: Use range(2) to scan two files and catch e.g. magnitude1/2 fieldmap files that are stored in one Series folder (but bidscoiner sees only the first file anyhow and it makes bidsmapper 2x slower :-()
sourcefile = bids.get_dicomfile(sourcedir, n)
if sourcefile.name and has_support(sourcefile):
if sourcefile.name:
sourcefiles.append(sourcefile)
elif dataformat == 'PAR':
sourcefiles = bids.get_parfiles(session)
Expand All @@ -150,21 +150,20 @@ def bidsmapper_plugin(session: Path, bidsmap_new: BidsMap, bidsmap_old: BidsMap,
break

# See if we can find a matching run in the old bidsmap
datasource = bids.DataSource(sourcefile, plugins, dataformat, bidsmap_new.options)
run, match = bidsmap_old.get_matching_run(datasource)
run, match = bidsmap_old.get_matching_run(sourcefile, dataformat)

# If not, see if we can find a matching run in the template
if not match:
LOGGER.bcdebug('No match found in the study bidsmap, now trying the template bidsmap')
run, _ = template.get_matching_run(datasource)
run, _ = template.get_matching_run(sourcefile, dataformat)

# See if we have collected the run somewhere in our new bidsmap
if not bidsmap_new.exist_run(run):

# Communicate with the user if the run was not present in bidsmap_old or in template, i.e. that we found a new sample
if not match:

LOGGER.info(f"Discovered sample: {datasource}")
LOGGER.info(f"Discovered sample: {run.datasource}")

# Try to automagically set the {part: phase/imag/real} (should work for Siemens data)
if not run.datatype == '' and 'part' in run.bids and not run.bids['part'][-1] and run.attributes.get('ImageType'): # part[-1]==0 -> part is not specified
Expand All @@ -181,13 +180,13 @@ def bidsmapper_plugin(session: Path, bidsmap_new: BidsMap, bidsmap_old: BidsMap,
LOGGER.verbose(f"Updated {run} entity: 'part' -> '{run.bids['part'][run.bids['part'][-1]]}' ({imagetype})")

else:
LOGGER.bcdebug(f"Known sample: {datasource}")
LOGGER.bcdebug(f"Known sample: {run.datasource}")

# Copy the filled-in run over to the new bidsmap
bidsmap_new.insert_run(run)

else:
LOGGER.bcdebug(f"Existing/duplicate sample: {datasource}")
LOGGER.bcdebug(f"Existing/duplicate sample: {run.datasource}")


@due.dcite(Doi('10.1016/j.jneumeth.2016.03.001'), description='dcm2niix: DICOM to NIfTI converter', tags=['reference-implementation'])
Expand Down Expand Up @@ -238,38 +237,36 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[N
scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
scans_table.index.name = 'filename'

# Process all the source files or run subfolders
sourcefile = Path()
# Process all the source files / folders
for source in sources:

# Get a sourcefile
if dataformat == 'DICOM':
sourcefile = bids.get_dicomfile(source)
elif dataformat == 'PAR':
else:
sourcefile = source
if not sourcefile.name or not has_support(sourcefile):
continue

# Get a matching run from the bidsmap
datasource = bids.DataSource(sourcefile, {'dcm2niix2bids': options}, dataformat, bidsmap.options)
run, runid = bidsmap.get_matching_run(datasource, runtime=True)
run, runid = bidsmap.get_matching_run(sourcefile, dataformat, runtime=True)

# Check if we should ignore this run
if run.datatype in bidsmap.options['ignoretypes']:
LOGGER.info(f"--> Leaving out: {source}")
bids.bidsprov(bidsses, source, runid, run.datatype) # Write out empty provenance data
LOGGER.info(f"--> Leaving out: {run.datasource}")
bids.bidsprov(bidsses, source, run) # Write out empty provenance data
continue

# Check if we already know this run
if not runid:
LOGGER.error(f"--> Skipping unknown '{run.datatype}' run: {sourcefile}\n-> Re-run the bidsmapper and delete {bidsses} to solve this warning")
LOGGER.error(f"--> Skipping unknown run: {run.datasource}\n-> Re-run the bidsmapper and delete {bidsses} to solve this warning")
bids.bidsprov(bidsses, source) # Write out empty provenance data
continue

LOGGER.info(f"--> Coining: {source}")
LOGGER.info(f"--> Coining: {run.datasource}")

# Create the BIDS session/datatype output folder
suffix = datasource.dynamicvalue(run.bids['suffix'], True, True)
suffix = run.datasource.dynamicvalue(run.bids['suffix'], True, True)
if suffix in bids.get_derivatives(run.datatype, exceptions):
outfolder = bidsfolder/'derivatives'/manufacturer.replace(' ','')/subid/sesid/run.datatype
else:
Expand Down Expand Up @@ -411,21 +408,21 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[N
newbidsname = newbidsname.replace('_phasediff_e1', '_phasediff') # Case 1
newbidsname = newbidsname.replace('_phasediff_e2', '_phasediff') # Case 1
newbidsname = newbidsname.replace('_phasediff_ph', '_phasediff') # Case 1
newbidsname = newbidsname.replace('_magnitude1_ph', '_phase1') # Case 2: One or two magnitude and phase images in one folder/datasource
newbidsname = newbidsname.replace('_magnitude2_ph', '_phase2') # Case 2: Two magnitude + two phase images in one folder/datasource
newbidsname = newbidsname.replace('_magnitude1_ph', '_phase1') # Case 2: One or two magnitude and phase images in one folder
newbidsname = newbidsname.replace('_magnitude2_ph', '_phase2') # Case 2: Two magnitude + two phase images in one folder
newbidsname = newbidsname.replace('_phase1_e1', '_phase1') # Case 2
newbidsname = newbidsname.replace('_phase1_e2', '_phase2') # Case 2: This can happen when the e2 image is stored in the same directory as the e1 image, but with the e2 listed first
newbidsname = newbidsname.replace('_phase2_e1', '_phase1') # Case 2: This can happen when the e2 image is stored in the same directory as the e1 image, but with the e2 listed first
newbidsname = newbidsname.replace('_phase2_e2', '_phase2') # Case 2
newbidsname = newbidsname.replace('_phase1_ph', '_phase1') # Case 2: One or two magnitude and phase images in one folder/datasource
newbidsname = newbidsname.replace('_phase2_ph', '_phase2') # Case 2: Two magnitude + two phase images in one folder/datasource
newbidsname = newbidsname.replace('_phase1_ph', '_phase1') # Case 2: One or two magnitude and phase images in one folder
newbidsname = newbidsname.replace('_phase2_ph', '_phase2') # Case 2: Two magnitude + two phase images in one folder
newbidsname = newbidsname.replace('_magnitude_e1', '_magnitude') # Case 3 = One magnitude + one fieldmap image
if len(dcm2niixfiles) == 2:
newbidsname = newbidsname.replace('_fieldmap_e1', '_magnitude') # Case 3: One magnitude + one fieldmap image in one folder/datasource
newbidsname = newbidsname.replace('_fieldmap_e1', '_magnitude') # Case 3: One magnitude + one fieldmap image in one folder
newbidsname = newbidsname.replace('_magnitude_fieldmaphz', '_fieldmap')
newbidsname = newbidsname.replace('_fieldmap_fieldmaphz', '_fieldmap')
newbidsname = newbidsname.replace('_fieldmap_e1', '_fieldmap') # Case 3
newbidsname = newbidsname.replace('_magnitude_ph', '_fieldmap') # Case 3: One magnitude + one fieldmap image in one folder/datasource
newbidsname = newbidsname.replace('_magnitude_ph', '_fieldmap') # Case 3: One magnitude + one fieldmap image in one folder
newbidsname = newbidsname.replace('_fieldmap_ph', '_fieldmap') # Case 3

# Append the dcm2niix info to the fallback-label, may need to be improved/elaborated for future BIDS standards, supporting multi-coil data
Expand Down Expand Up @@ -454,7 +451,7 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[N
oldfile.replace(newbidsfile.with_suffix('').with_suffix(''.join(oldfile.suffixes)))

# Write out provenance data
bids.bidsprov(bidsses, source, runid, run.datatype, targets)
bids.bidsprov(bidsses, source, run, targets)

# Loop over all non-derivative targets (i.e. the produced output files) and edit the json sidecar data
for target in sorted(targets):
Expand All @@ -467,7 +464,7 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[N
jsonfile = target.with_suffix('').with_suffix('.json')
if not jsonfile.is_file():
LOGGER.warning(f"Unexpected conversion result, could not find: {jsonfile}")
metadata = bids.updatemetadata(datasource, jsonfile, run.meta, options.get('meta',[]))
metadata = bids.updatemetadata(run.datasource, jsonfile, run.meta, options.get('meta',[]))

# Remove the bval/bvec files of sbref- and inv-images (produced by dcm2niix but not allowed by the BIDS specifications)
if ((run.datatype == 'dwi' and suffix == 'sbref') or
Expand All @@ -492,9 +489,9 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[N
if not ignore:
acq_time = ''
if dataformat == 'DICOM':
acq_time = f"{datasource.attributes('AcquisitionDate')}T{datasource.attributes('AcquisitionTime')}"
acq_time = f"{run.datasource.attributes('AcquisitionDate')}T{run.datasource.attributes('AcquisitionTime')}"
elif dataformat == 'PAR':
acq_time = datasource.attributes('exam_date')
acq_time = run.datasource.attributes('exam_date')
if not acq_time or acq_time == 'T':
acq_time = f"1925-01-01T{metadata.get('AcquisitionTime','')}"
try:
Expand All @@ -509,7 +506,7 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[N

# Check if the target output aligns with dcm2niix's "BidsGuess" datatype and filename entities
if not ignore:
typeguess, targetguess = metadata.get('BidsGuess') or ['', ''] # BidsGuess: [datatype, filename]
typeguess, targetguess = metadata.get('BidsGuess') or ['', ''] # BidsGuess: [datatype, filename]
LOGGER.bcdebug(f"BidsGuess: [{typeguess}, {targetguess}]")
if typeguess and run.datatype != typeguess:
LOGGER.info(f"The datatype of {target.relative_to(bidsses)} does not match with the datatype guessed by dcm2niix: {typeguess}")
Expand All @@ -527,7 +524,7 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[N
scans_table.replace('','n/a').to_csv(scans_tsv, sep='\t', encoding='utf-8', na_rep='n/a')

# Collect personal data for the participants.tsv file
if dataformat == 'DICOM': # PAR does not contain personal info
if dataformat == 'DICOM': # PAR does not contain personal info?
age = datasource.attributes('PatientAge') # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
try:
if age.endswith('D'): age = float(age.rstrip('D')) / 365.2524
Expand Down
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