示例#1
0
def coin_data2bids(dataformat: str, session: Path, bidsmap: dict,
                   bidsfolder: Path, personals: dict, subprefix: str,
                   sesprefix: str) -> None:
    """
    Converts the session source-files into BIDS-valid nifti-files in the corresponding bidsfolder and
    extracts personals (e.g. Age, Sex) from the source header

    :param dataformat:  The format of the raw input data that is to be coined (e.g. 'DICOM' or 'PAR', see bids.get_dataformat)
    :param session:     The full-path name of the subject/session source file/folder
    :param bidsmap:     The full mapping heuristics from the bidsmap YAML-file
    :param bidsfolder:  The full-path name of the BIDS root-folder
    :param personals:   The dictionary with the personal information
    :param subprefix:   The prefix common for all source subject-folders
    :param sesprefix:   The prefix common for all source session-folders
    :return:            Nothing
    """

    # Get valid BIDS subject/session identifiers from the (first) DICOM- or PAR/XML source file
    if dataformat == 'DICOM':
        sourcefile = Path()
        sources = bids.lsdirs(session)
        for source in sources:
            sourcefile = bids.get_dicomfile(source)
            manufacturer = bids.get_dicomfield('Manufacturer', sourcefile)
            if sourcefile.name:
                break

    elif dataformat == 'PAR':
        sources = bids.get_parfiles(session)
        manufacturer = 'Philips Medical Systems'
        if sources:
            sourcefile = sources[0]

    else:
        LOGGER.error(
            f"Unsupported data format: {dataformat}\nPlease report this bug")
        return

    if not sources:
        LOGGER.info(f"No data found for: {session}")
        return

    subid, sesid = bids.get_subid_sesid(sourcefile,
                                        bidsmap[dataformat]['subject'],
                                        bidsmap[dataformat]['session'],
                                        subprefix, sesprefix)

    if subid == subprefix:
        LOGGER.error(f"No valid subject identifier found for: {session}")
        return

    # Create the BIDS session-folder and a scans.tsv file
    bidsses = bidsfolder / subid / sesid
    if bidsses.is_dir():
        LOGGER.warning(
            f"Existing BIDS output-directory found, which may result in duplicate data (with increased run-index). Make sure {bidsses} was cleaned-up from old data before (re)running the bidscoiner"
        )
    bidsses.mkdir(parents=True, exist_ok=True)
    scans_tsv = bidsses / f"{subid}{bids.add_prefix('_',sesid)}_scans.tsv"
    if scans_tsv.is_file():
        scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
    else:
        scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
        scans_table.index.name = 'filename'

    # Process all the source files or run subfolders
    for source in sources:

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

        # Get a matching run from the bidsmap
        run, datatype, index = bids.get_matching_run(sourcefile, bidsmap,
                                                     dataformat)

        # Check if we should ignore this run
        if datatype == bids.ignoredatatype:
            LOGGER.info(f"Leaving out: {source}")
            continue

        # Check if we already know this run
        if index is None:
            LOGGER.error(
                f"Skipping unknown '{datatype}' run: {sourcefile}\n-> Re-run the bidsmapper and delete {bidsses} to solve this warning"
            )
            continue

        LOGGER.info(f"Processing: {source}")

        # Create the BIDS session/datatype output folder
        if run['bids']['suffix'] in bids.get_derivatives(datatype):
            outfolder = bidsfolder / 'derivatives' / manufacturer.replace(
                ' ', '') / subid / sesid / datatype
        else:
            outfolder = bidsses / datatype
        outfolder.mkdir(parents=True, exist_ok=True)

        # Compose the BIDS filename using the matched run
        bidsname = bids.get_bidsname(subid, sesid, run)
        runindex = run['bids'].get('run', '')
        if runindex.startswith('<<') and runindex.endswith('>>'):
            bidsname = bids.increment_runindex(outfolder, bidsname)
        jsonfiles = [
            (outfolder / bidsname).with_suffix('.json')
        ]  # List -> Collect the associated json-files (for updating them later) -- possibly > 1

        # Check if file already exists (-> e.g. when a static runindex is used)
        if (outfolder / bidsname).with_suffix('.json').is_file():
            LOGGER.warning(
                f"{outfolder/bidsname}.* already exists and will be deleted -- check your results carefully!"
            )
            for ext in ('.nii.gz', '.nii', '.json', '.bval', '.bvec',
                        'tsv.gz'):
                (outfolder / bidsname).with_suffix(ext).unlink(missing_ok=True)

        # Convert physiological log files (dcm2niix can't handle these)
        if run['bids']['suffix'] == 'physio':
            if bids.get_dicomfile(source, 2).name:
                LOGGER.warning(
                    f"Found > 1 DICOM file in {source}, using: {sourcefile}")
            physiodata = physio.readphysio(sourcefile)
            physio.physio2tsv(physiodata, outfolder / bidsname)

        # Convert the source-files in the run folder to nifti's in the BIDS-folder
        else:
            command = '{path}dcm2niix {args} -f "{filename}" -o "{outfolder}" "{source}"'.format(
                path=bidsmap['Options']['dcm2niix']['path'],
                args=bidsmap['Options']['dcm2niix']['args'],
                filename=bidsname,
                outfolder=outfolder,
                source=source)
            if not bids.run_command(command):
                continue

            # Replace uncropped output image with the cropped one
            if '-x y' in bidsmap['Options']['dcm2niix']['args']:
                for dcm2niixfile in sorted(
                        outfolder.glob(bidsname +
                                       '*_Crop_*')):  # e.g. *_Crop_1.nii.gz
                    ext = ''.join(dcm2niixfile.suffixes)
                    newbidsfile = str(dcm2niixfile).rsplit(ext, 1)[0].rsplit(
                        '_Crop_', 1)[0] + ext
                    LOGGER.info(
                        f"Found dcm2niix _Crop_ postfix, replacing original file\n{dcm2niixfile} ->\n{newbidsfile}"
                    )
                    dcm2niixfile.replace(newbidsfile)

            # Rename all files that got additional postfixes from dcm2niix. See: https://github.com/rordenlab/dcm2niix/blob/master/FILENAMING.md
            dcm2niixpostfixes = ('_c', '_i', '_Eq', '_real', '_imaginary',
                                 '_MoCo', '_t', '_Tilt', '_e', '_ph')
            dcm2niixfiles = sorted(
                set([
                    dcm2niixfile for dcm2niixpostfix in dcm2niixpostfixes
                    for dcm2niixfile in outfolder.glob(
                        f"{bidsname}*{dcm2niixpostfix}*")
                ]))
            for dcm2niixfile in dcm2niixfiles:
                ext = ''.join(dcm2niixfile.suffixes)
                postfixes = str(dcm2niixfile).split(bidsname)[1].rsplit(
                    ext)[0].split('_')[1:]
                newbidsname = dcm2niixfile.name  # Strip the additional postfixes and assign them to bids entities in the for-loop below
                for postfix in postfixes:  # dcm2niix postfixes _c%d, _e%d and _ph (and any combination of these in that order) are for multi-coil data, multi-echo data and phase data

                    # Patch the echo entity in the newbidsname with the dcm2niix echo info                      # NB: We can't rely on the bids-entity info here because manufacturers can e.g. put multiple echos in one series / run-folder
                    if postfix[0] == 'e' and bids.get_bidsvalue(
                            newbidsname, 'echo'
                    ):  # NB: Check if postfix[0]=='e' uniquely refers to the right dcm2niixpostfix
                        echonr = f"_{postfix}"  # E.g. echonr='_e1' or echonr='_pha'
                        for dcm2niixpostfix in dcm2niixpostfixes:
                            echonr = echonr.replace(
                                dcm2niixpostfix, ''
                            )  # Strip the dcm2niixpostfix to keep the echonr info. E.g. [echonr='_e1' or echonr='_pha'] -> [echonr='1' or echonr='a']
                        if echonr.isalpha():
                            echonr = ord(
                                echonr
                            ) - 95  # dcm2niix adds an alphabetically ordered character if it outputs more than one image with the same name. Convert character to echo-number: '' -> 1, 'a'->2, etc
                        elif not echonr:
                            echonr = 1
                        newbidsname = bids.get_bidsvalue(
                            newbidsname, 'echo', str(echonr)
                        )  # In contrast to other labels, run and echo labels MUST be integers. Those labels MAY include zero padding, but this is NOT RECOMMENDED to maintain their uniqueness

                    # Patch fieldmap images (NB: datatype=='fmap' is too broad, see the fmap.yaml file)
                    elif run['bids']['suffix'] in ('magnitude', 'magnitude1',
                                                   'magnitude2', 'phase1',
                                                   'phase2', 'phasediff',
                                                   'fieldmap'):
                        if len(dcm2niixfiles) not in (
                                0, 2, 4, 6, 8
                        ):  # Phase / echo data may be stored in the same data source / run folder
                            LOGGER.warning(
                                f"Unknown fieldmap {outfolder/bidsname} for '{postfix}'"
                            )
                        newbidsname = newbidsname.replace(
                            '_fieldmap_ph', '_fieldmap')
                        newbidsname = newbidsname.replace(
                            '_magnitude_e1', '_magnitude')
                        newbidsname = newbidsname.replace(
                            '_magnitude_ph', '_fieldmap')
                        newbidsname = newbidsname.replace(
                            '_magnitude1_e1', '_magnitude1')
                        newbidsname = newbidsname.replace(
                            '_magnitude2_e1', '_magnitude1'
                        )  # 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(
                            '_magnitude1_e2', '_magnitude2')
                        if len(dcm2niixfiles) == 8:
                            newbidsname = newbidsname.replace(
                                '_magnitude1_ph', '_phase1'
                            )  # Two magnitude + 2 phase images in one folder / datasource
                        else:
                            newbidsname = newbidsname.replace(
                                '_magnitude1_ph', '_phasediff'
                            )  # One or two magnitude + 1 phasediff image
                        newbidsname = newbidsname.replace(
                            '_magnitude1a', '_magnitude2')
                        newbidsname = newbidsname.replace(
                            '_magnitude1_pha', '_phase2')
                        newbidsname = newbidsname.replace(
                            '_magnitude2_e2', '_magnitude2')
                        newbidsname = newbidsname.replace(
                            '_magnitude2_ph', '_phase2')
                        newbidsname = newbidsname.replace(
                            '_phase1_e1', '_phase1')
                        newbidsname = newbidsname.replace(
                            '_phase2_e1', '_phase1'
                        )  # 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(
                            '_phase1_ph', '_phase1')
                        newbidsname = newbidsname.replace(
                            '_phase1_e2', '_phase2')
                        newbidsname = newbidsname.replace(
                            '_phase2_e2', '_phase2')
                        newbidsname = newbidsname.replace(
                            '_phase2_ph', '_phase2')

                    # Append the dcm2niix info to acq-label, may need to be improved / elaborated for future BIDS standards, supporting multi-coil data
                    else:
                        newbidsname = bids.get_bidsvalue(
                            newbidsname, 'dummy', postfix)

                    # Remove the added postfix from the new bidsname
                    newbidsname = newbidsname.replace(f"_{postfix}_",
                                                      '_')  # If it is not last
                    newbidsname = newbidsname.replace(f"_{postfix}.",
                                                      '.')  # If it is last

                # Save the file with a new name
                if runindex.startswith('<<') and runindex.endswith('>>'):
                    newbidsname = bids.increment_runindex(
                        outfolder, newbidsname, ''
                    )  # Update the runindex now that the acq-label has changed
                newbidsfile = outfolder / newbidsname
                LOGGER.info(
                    f"Found dcm2niix {postfixes} postfixes, renaming\n{dcm2niixfile} ->\n{newbidsfile}"
                )
                if newbidsfile.is_file():
                    LOGGER.warning(
                        f"Overwriting existing {newbidsfile} file -- check your results carefully!"
                    )
                dcm2niixfile.replace(newbidsfile)
                if ext == '.json':
                    oldjsonfile = (outfolder / bidsname).with_suffix('.json')
                    if oldjsonfile in jsonfiles and not oldjsonfile.is_file():
                        jsonfiles.remove(
                            (outfolder / bidsname).with_suffix('.json'))
                    jsonfiles.append(newbidsfile)

        # Loop over and adapt all the newly produced json files and write to the scans.tsv file (every nifti-file comes with a json-file)
        for jsonfile in sorted(set(jsonfiles)):

            # Check if dcm2niix behaved as expected
            if not jsonfile.is_file():
                LOGGER.error(
                    f"Unexpected file conversion result: {jsonfile} not found")
                continue

            # Add a dummy b0 bval- and bvec-file for any file without a bval/bvec file (e.g. sbref, b0 scans)
            if datatype == 'dwi':
                bvecfile = jsonfile.with_suffix('.bvec')
                bvalfile = jsonfile.with_suffix('.bval')
                if not bvecfile.is_file():
                    LOGGER.info(f"Adding dummy bvec file: {bvecfile}")
                    with bvecfile.open('w') as bvec_fid:
                        bvec_fid.write('0\n0\n0\n')
                if not bvalfile.is_file():
                    LOGGER.info(f"Adding dummy bval file: {bvalfile}")
                    with bvalfile.open('w') as bval_fid:
                        bval_fid.write('0\n')

            # Add the TaskName to the func json-file
            elif datatype == 'func':
                with jsonfile.open('r') as json_fid:
                    data = json.load(json_fid)
                if not 'TaskName' in data:
                    LOGGER.info(f"Adding TaskName to: {jsonfile}")
                    data['TaskName'] = run['bids']['task']
                    with jsonfile.open('w') as json_fid:
                        json.dump(data, json_fid, indent=4)

            # Parse the acquisition time from the json file or else from the source header (NB: assuming the source file represents the first acquisition)
            niifile = list(
                jsonfile.parent.glob(jsonfile.stem + '.nii*')
            )  # Find the corresponding nifti file (there should be only one, let's not make assumptions about the .gz extension)
            if niifile and datatype not in bidsmap['Options']['bidscoin'][
                    'bidsignore'] and not run['bids'][
                        'suffix'] in bids.get_derivatives(datatype):
                with jsonfile.open('r') as json_fid:
                    data = json.load(json_fid)
                if 'AcquisitionTime' not in data or not data['AcquisitionTime']:
                    data['AcquisitionTime'] = bids.get_sourcefield(
                        'AcquisitionTime', sourcefile)  # DICOM
                if not data['AcquisitionTime']:
                    data['AcquisitionTime'] = bids.get_sourcefield(
                        'exam_date', sourcefile)  # PAR/XML
                try:
                    acq_time = dateutil.parser.parse(data['AcquisitionTime'])
                except:
                    LOGGER.warning(
                        f"Could not parse the acquisition time from: '{data['AcquisitionTime']}' in {sourcefile}"
                    )
                    acq_time = dateutil.parser.parse('00:00:00')
                scanpath = niifile[0].relative_to(bidsses)
                scans_table.loc[
                    scanpath.as_posix(),
                    'acq_time'] = '1925-01-01T' + acq_time.strftime('%H:%M:%S')

    # Write the scans_table to disk
    LOGGER.info(f"Writing acquisition time data to: {scans_tsv}")
    scans_table.sort_values(by=['acq_time', 'filename'], inplace=True)
    scans_table.to_csv(scans_tsv, sep='\t', encoding='utf-8')

    # Add IntendedFor and TE1+TE2 meta-data to the fieldmap json-files. This has been postponed untill all datatypes have been processed (i.e. so that all target images are indeed on disk)
    if bidsmap[dataformat]['fmap'] is not None:
        for fieldmap in bidsmap[dataformat]['fmap']:
            bidsname = bids.get_bidsname(subid, sesid, fieldmap)
            niifiles = []
            intendedfor = fieldmap['bids']['IntendedFor']

            # Search for the imaging files that match the IntendedFor search criteria
            if intendedfor:
                if intendedfor.startswith('<<') and intendedfor.endswith('>>'):
                    intendedfor = intendedfor[2:-2].split('><')
                elif not isinstance(intendedfor, list):
                    intendedfor = [intendedfor]
                for selector in intendedfor:
                    niifiles.extend(
                        [
                            Path(niifile).relative_to(bidsfolder / subid)
                            for niifile in sorted(
                                bidsses.rglob(f"*{selector}*.nii*"))
                            if selector
                        ]
                    )  # Search in all runs using a relative path to the subject folder
            else:
                intendedfor = []

            # Get the set of json-files (account for multiple runs in one data source and dcm2niix postfixes inserted into the acquisition label)
            jsonfiles = []
            acqlabel = bids.get_bidsvalue(bidsname, 'acq')
            patterns = (bidsname.replace('_run-1_', '_run-[0-9]*_').replace(
                '_magnitude1',
                '_magnitude*').replace('_magnitude2', '_magnitude*').replace(
                    '_phase1', '_phase*').replace('_phase2', '_phase*'),
                        bidsname.replace('_run-1_', '_run-[0-9]*_').replace(
                            '_magnitude1',
                            '_phase*').replace('_magnitude2', '_phase*'))
            for pattern in patterns:
                jsonfiles.extend((bidsses / 'fmap').glob(pattern + '.json'))
                if acqlabel:
                    cepattern = bids.get_bidsvalue(pattern, 'acq',
                                                   acqlabel + '[CE][0-9]*')
                    jsonfiles.extend(
                        list((bidsses / 'fmap').glob(cepattern + '.json')))

            # Save the meta-data in the jsonfiles
            for jsonfile in sorted(set(jsonfiles)):

                # Add the IntendedFor data
                with jsonfile.open('r') as json_fid:
                    data = json.load(json_fid)
                if 'IntendedFor' not in data:
                    if niifiles:
                        LOGGER.info(f"Adding IntendedFor to: {jsonfile}")
                    elif intendedfor:
                        LOGGER.warning(
                            f"Empty 'IntendedFor' fieldmap value in {jsonfile}: the search for {intendedfor} gave no results"
                        )
                    else:
                        LOGGER.warning(
                            f"Empty 'IntendedFor' fieldmap value in {jsonfile}: the IntendedFor value of the bidsmap entry was empty"
                        )
                    data['IntendedFor'] = [
                        niifile.as_posix() for niifile in niifiles
                    ]  # The path needs to use forward slashes instead of backward slashes
                    with jsonfile.open('w') as json_fid:
                        json.dump(data, json_fid, indent=4)

                # Extract the echo times from magnitude1 and magnitude2 and add them to the phasediff json-file
                if jsonfile.name.endswith('phasediff.json'):
                    json_magnitude = [None, None]
                    TE = [None, None]
                    for n in (0, 1):
                        json_magnitude[
                            n] = jsonfile.parent / jsonfile.name.replace(
                                '_phasediff', f"_magnitude{n+1}")
                        if not json_magnitude[n].is_file():
                            LOGGER.error(
                                f"Could not find expected magnitude{n+1} image associated with: {jsonfile}"
                            )
                        else:
                            with json_magnitude[n].open('r') as json_fid:
                                data = json.load(json_fid)
                            TE[n] = data['EchoTime']
                    if None in TE:
                        LOGGER.error(
                            f"Cannot find and add valid EchoTime1={TE[0]} and EchoTime2={TE[1]} data to: {jsonfile}"
                        )
                    elif TE[0] > TE[1]:
                        LOGGER.error(
                            f"Found invalid EchoTime1={TE[0]} > EchoTime2={TE[1]} for: {jsonfile}"
                        )
                    else:
                        with jsonfile.open('r') as json_fid:
                            data = json.load(json_fid)
                        data['EchoTime1'] = TE[0]
                        data['EchoTime2'] = TE[1]
                        LOGGER.info(
                            f"Adding EchoTime1: {TE[0]} and EchoTime2: {TE[1]} to {jsonfile}"
                        )
                        with jsonfile.open('w') as json_fid:
                            json.dump(data, json_fid, indent=4)

    # Collect personal data from a source header (PAR/XML does not contain personal info)
    if dataformat == 'DICOM' and sourcefile.name:
        personals['participant_id'] = subid
        if sesid:
            if 'session_id' not in personals:
                personals['session_id'] = sesid
            else:
                return  # Only take data from the first session -> BIDS specification
        age = bids.get_dicomfield(
            'PatientAge', sourcefile
        )  # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
        if age.endswith('D'):
            personals['age'] = str(int(float(age.rstrip('D')) / 365.2524))
        elif age.endswith('W'):
            personals['age'] = str(int(float(age.rstrip('W')) / 52.1775))
        elif age.endswith('M'):
            personals['age'] = str(int(float(age.rstrip('M')) / 12))
        elif age.endswith('Y'):
            personals['age'] = str(int(float(age.rstrip('Y'))))
        elif age:
            personals['age'] = age
        personals['sex'] = bids.get_dicomfield('PatientSex', sourcefile)
        personals['size'] = bids.get_dicomfield('PatientSize', sourcefile)
        personals['weight'] = bids.get_dicomfield('PatientWeight', sourcefile)
示例#2
0
def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> None:
    """
    The bidscoiner plugin to convert the session DICOM and PAR/REC source-files into BIDS-valid nifti-files in the
    corresponding bids session-folder and extract personals (e.g. Age, Sex) from the source header

    :param session:     The full-path name of the subject/session source folder
    :param bidsmap:     The full mapping heuristics from the bidsmap YAML-file
    :param bidsses:     The full-path name of the BIDS output `sub-/ses-` folder
    :return:            Nothing
    """

    # Get the subject identifiers and the BIDS root folder from the bidsses folder
    if bidsses.name.startswith('ses-'):
        bidsfolder = bidsses.parent.parent
        subid = bidsses.parent.name
        sesid = bidsses.name
    else:
        bidsfolder = bidsses.parent
        subid = bidsses.name
        sesid = ''

    # Get started and see what dataformat we have
    options = bidsmap['Options']['plugins']['dcm2niix2bids']
    datasource = bids.get_datasource(session, {'dcm2niix2bids': options})
    dataformat = datasource.dataformat
    if not dataformat:
        LOGGER.info(f"No {__name__} sourcedata found in: {session}")
        return

    # Make a list of all the data sources / runs
    manufacturer = 'UNKNOWN'
    sources = []
    if dataformat == 'DICOM':
        sources = bidscoin.lsdirs(session)
        manufacturer = datasource.attributes('Manufacturer')
    elif dataformat == 'PAR':
        sources = bids.get_parfiles(session)
        manufacturer = 'Philips Medical Systems'
    else:
        LOGGER.exception(f"Unsupported dataformat '{dataformat}'")

    # Read or create a scans_table and tsv-file
    scans_tsv = bidsses / f"{subid}{bids.add_prefix('_',sesid)}_scans.tsv"
    if scans_tsv.is_file():
        scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
    else:
        scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
        scans_table.index.name = 'filename'

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

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

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

        # Check if we should ignore this run
        if datasource.datatype in bidsmap['Options']['bidscoin'][
                'ignoretypes']:
            LOGGER.info(f"Leaving out: {source}")
            continue

        # Check if we already know this run
        if not match:
            LOGGER.error(
                f"Skipping unknown '{datasource.datatype}' run: {sourcefile}\n-> Re-run the bidsmapper and delete {bidsses} to solve this warning"
            )
            continue

        LOGGER.info(f"Processing: {source}")

        # Create the BIDS session/datatype output folder
        if run['bids']['suffix'] in bids.get_derivatives(datasource.datatype):
            outfolder = bidsfolder / 'derivatives' / manufacturer.replace(
                ' ', '') / subid / sesid / datasource.datatype
        else:
            outfolder = bidsses / datasource.datatype
        outfolder.mkdir(parents=True, exist_ok=True)

        # Compose the BIDS filename using the matched run
        bidsname = bids.get_bidsname(subid, sesid, run, runtime=True)
        runindex = run['bids'].get('run', '')
        if runindex.startswith('<<') and runindex.endswith('>>'):
            bidsname = bids.increment_runindex(outfolder, bidsname)
        jsonfiles = [
            (outfolder / bidsname).with_suffix('.json')
        ]  # List -> Collect the associated json-files (for updating them later) -- possibly > 1

        # Check if file already exists (-> e.g. when a static runindex is used)
        if (outfolder / bidsname).with_suffix('.json').is_file():
            LOGGER.warning(
                f"{outfolder/bidsname}.* already exists and will be deleted -- check your results carefully!"
            )
            for ext in ('.nii.gz', '.nii', '.json', '.tsv', '.tsv.gz', '.bval',
                        '.bvec'):
                (outfolder / bidsname).with_suffix(ext).unlink(missing_ok=True)

        # Convert physiological log files (dcm2niix can't handle these)
        if run['bids']['suffix'] == 'physio':
            if bids.get_dicomfile(
                    source, 2).name:  # TODO: issue warning or support PAR
                LOGGER.warning(
                    f"Found > 1 DICOM file in {source}, using: {sourcefile}")
            physiodata = physio.readphysio(sourcefile)
            physio.physio2tsv(physiodata, outfolder / bidsname)

        # Convert the source-files in the run folder to nifti's in the BIDS-folder
        else:
            command = '{command} {args} -f "{filename}" -o "{outfolder}" "{source}"'.format(
                command=options['command'],
                args=options.get('args', ''),
                filename=bidsname,
                outfolder=outfolder,
                source=source)
            if not bidscoin.run_command(command):
                if not list(outfolder.glob(f"{bidsname}.nii*")): continue
            if list(outfolder.glob(f"{bidsname}a.nii*")):
                LOGGER.warning(
                    f"Unexpected variants of {outfolder/bidsname}* were produced by dcm2niix. Possibly this can be remedied by using the dcm2niix -i option (to ignore derived, localizer and 2D images)"
                )

            # Replace uncropped output image with the cropped one
            if '-x y' in options.get('args', ''):
                for dcm2niixfile in sorted(
                        outfolder.glob(bidsname +
                                       '*_Crop_*')):  # e.g. *_Crop_1.nii.gz
                    ext = ''.join(dcm2niixfile.suffixes)
                    newbidsfile = str(dcm2niixfile).rsplit(ext, 1)[0].rsplit(
                        '_Crop_', 1)[0] + ext
                    LOGGER.info(
                        f"Found dcm2niix _Crop_ postfix, replacing original file\n{dcm2niixfile} ->\n{newbidsfile}"
                    )
                    dcm2niixfile.replace(newbidsfile)

            # Rename all files that got additional postfixes from dcm2niix. See: https://github.com/rordenlab/dcm2niix/blob/master/FILENAMING.md
            dcm2niixpostfixes = ('_c', '_i', '_Eq', '_real', '_imaginary',
                                 '_MoCo', '_t', '_Tilt', '_e', '_ph', '_ADC',
                                 '_fieldmaphz')
            dcm2niixfiles = sorted(
                set([
                    dcm2niixfile for dcm2niixpostfix in dcm2niixpostfixes
                    for dcm2niixfile in outfolder.glob(
                        f"{bidsname}*{dcm2niixpostfix}*.nii*")
                ]))
            if not jsonfiles[0].is_file(
            ) and dcm2niixfiles:  # Possibly renamed by dcm2niix, e.g. with multi-echo data (but not always for the first echo)
                jsonfiles.pop(0)
            for dcm2niixfile in dcm2niixfiles:
                ext = ''.join(dcm2niixfile.suffixes)
                postfixes = str(dcm2niixfile).split(bidsname)[1].rsplit(
                    ext)[0].split('_')[1:]
                newbidsname = dcm2niixfile.name  # Strip the additional postfixes and assign them to bids entities in the for-loop below
                for postfix in postfixes:  # dcm2niix postfixes _c%d, _e%d and _ph (and any combination of these in that order) are for multi-coil data, multi-echo data and phase data

                    # Patch the echo entity in the newbidsname with the dcm2niix echo info                      # NB: We can't rely on the bids-entity info here because manufacturers can e.g. put multiple echos in one series / run-folder
                    if 'echo' in run['bids'] and postfix.startswith('e'):
                        echonr = f"_{postfix}".replace('_e',
                                                       '')  # E.g. postfix='e1'
                        if not echonr:
                            echonr = '1'
                        if echonr.isnumeric():
                            newbidsname = bids.insert_bidskeyval(
                                newbidsname, 'echo', echonr.lstrip('0')
                            )  # In contrast to other labels, run and echo labels MUST be integers. Those labels MAY include zero padding, but this is NOT RECOMMENDED to maintain their uniqueness
                        else:
                            LOGGER.error(
                                f"Unexpected postix '{postfix}' found in {dcm2niixfile}"
                            )
                            newbidsname = bids.get_bidsvalue(
                                newbidsname, 'dummy', postfix
                            )  # Append the unknown postfix to the acq-label

                    # Patch the phase entity in the newbidsname with the dcm2niix mag/phase info
                    elif 'part' in run['bids'] and postfix in (
                            'ph', 'real', 'imaginary'
                    ):  # e.g. part: ['', 'mag', 'phase', 'real', 'imag', 0]
                        if postfix == 'ph':
                            newbidsname = bids.insert_bidskeyval(
                                newbidsname, 'part', 'phase')
                        if postfix == 'real':
                            newbidsname = bids.insert_bidskeyval(
                                newbidsname, 'part', 'real')
                        if postfix == 'imaginary':
                            newbidsname = bids.insert_bidskeyval(
                                newbidsname, 'part', 'imag')

                    # Patch fieldmap images (NB: datatype=='fmap' is too broad, see the fmap.yaml file)
                    elif run['bids']['suffix'] in bids.bidsdatatypes['fmap'][0][
                            'suffixes']:  # i.e. in ('magnitude','magnitude1','magnitude2','phase1','phase2','phasediff','fieldmap'). TODO: Make this robust for future BIDS versions
                        if len(dcm2niixfiles) not in (
                                1, 2, 3, 4
                        ):  # Phase / echo data may be stored in the same data source / run folder
                            LOGGER.debug(
                                f"Unknown fieldmap {outfolder/bidsname} for '{postfix}'"
                            )
                        newbidsname = newbidsname.replace(
                            '_magnitude1a', '_magnitude2'
                        )  # First catch this potential weird / rare case
                        newbidsname = newbidsname.replace(
                            '_magnitude1_pha', '_phase2'
                        )  # First catch this potential weird / rare case
                        newbidsname = newbidsname.replace(
                            '_magnitude1_e1', '_magnitude1'
                        )  # Case 2 = Two phase and magnitude images
                        newbidsname = newbidsname.replace(
                            '_magnitude1_e2', '_magnitude2'
                        )  # 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(
                            '_magnitude2_e1', '_magnitude1'
                        )  # 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(
                            '_magnitude2_e2', '_magnitude2')  # Case 2
                        if len(dcm2niixfiles) in (
                                2, 3
                        ):  # Case 1 = One or two magnitude + one phasediff image
                            newbidsname = newbidsname.replace(
                                '_magnitude1_ph', '_phasediff')
                            newbidsname = newbidsname.replace(
                                '_magnitude2_ph', '_phasediff')
                        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(
                            '_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(
                            '_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', '_fieldmap')  # Case 3
                        newbidsname = newbidsname.replace(
                            '_magnitude_ph', '_fieldmap'
                        )  # Case 3: One magnitude + one fieldmap image in one folder / datasource
                        newbidsname = newbidsname.replace(
                            '_fieldmap_ph', '_fieldmap')  # Case 3

                    # Append the dcm2niix info to acq-label, may need to be improved / elaborated for future BIDS standards, supporting multi-coil data
                    else:
                        newbidsname = bids.get_bidsvalue(
                            newbidsname, 'dummy', postfix)

                    # Remove the added postfix from the new bidsname
                    newbidsname = newbidsname.replace(f"_{postfix}_",
                                                      '_')  # If it is not last
                    newbidsname = newbidsname.replace(f"_{postfix}.",
                                                      '.')  # If it is last

                    # The ADC images are not BIDS compliant
                    if postfix == 'ADC':
                        LOGGER.warning(
                            f"The {newbidsname} image is most likely not BIDS-compliant -- you can probably delete it safely and update the scants.tsv file"
                        )

                # Save the nifti file with a new name
                if runindex.startswith('<<') and runindex.endswith('>>'):
                    newbidsname = bids.increment_runindex(
                        outfolder, newbidsname, ''
                    )  # Update the runindex now that the acq-label has changed
                newbidsfile = outfolder / newbidsname
                LOGGER.info(
                    f"Found dcm2niix {postfixes} postfixes, renaming\n{dcm2niixfile} ->\n{newbidsfile}"
                )
                if newbidsfile.is_file():
                    LOGGER.warning(
                        f"Overwriting existing {newbidsfile} file -- check your results carefully!"
                    )
                dcm2niixfile.replace(newbidsfile)

                # Rename all associated files (i.e. the json-, bval- and bvec-files)
                oldjsonfile = dcm2niixfile.with_suffix('').with_suffix('.json')
                newjsonfile = newbidsfile.with_suffix('').with_suffix('.json')
                if not oldjsonfile.is_file():
                    LOGGER.warning(
                        f"Unexpected file conversion result: {oldjsonfile} not found"
                    )
                else:
                    if oldjsonfile in jsonfiles:
                        jsonfiles.remove(oldjsonfile)
                    if newjsonfile not in jsonfiles:
                        jsonfiles.append(newjsonfile)
                for oldfile in outfolder.glob(
                        dcm2niixfile.with_suffix('').stem + '.*'):
                    oldfile.replace(
                        newjsonfile.with_suffix(''.join(oldfile.suffixes)))

        # Copy over the source meta-data
        metadata = bids.copymetadata(sourcefile, outfolder / bidsname,
                                     options.get('meta', []))

        # Loop over and adapt all the newly produced json sidecar-files and write to the scans.tsv file (NB: assumes every nifti-file comes with a json-file)
        for jsonfile in sorted(set(jsonfiles)):

            # Load the json meta-data
            with jsonfile.open('r') as json_fid:
                jsondata = json.load(json_fid)

            # Add all the source meta data to the meta-data
            for metakey, metaval in metadata.items():
                if jsondata.get(metakey) == metaval:
                    LOGGER.warning(
                        f"Replacing {metakey} values in {jsonfile}: {jsondata[metakey]} -> {metaval}"
                    )
                jsondata[metakey] = metaval

            # Add all the run meta data to the meta-data. NB: the dynamic `IntendedFor` value is handled separately later
            for metakey, metaval in run['meta'].items():
                if metakey != 'IntendedFor':
                    metaval = datasource.dynamicvalue(metaval,
                                                      cleanup=False,
                                                      runtime=True)
                    try:
                        metaval = ast.literal_eval(str(metaval))
                    except (ValueError, SyntaxError):
                        pass
                    LOGGER.info(
                        f"Adding '{metakey}: {metaval}' to: {jsonfile}")
                if not metaval:
                    metaval = None
                jsondata[metakey] = metaval

            # Remove unused (but added from the template) B0FieldIdentifiers/Sources
            if not jsondata.get('B0FieldSource'):
                jsondata.pop('B0FieldSource', None)
            if not jsondata.get('B0FieldIdentifier'):
                jsondata.pop('B0FieldIdentifier', None)

            # Save the meta-data to the json sidecar-file
            with jsonfile.open('w') as json_fid:
                json.dump(jsondata, json_fid, indent=4)

            # Parse the acquisition time from the source header or else from the json file (NB: assuming the source file represents the first acquisition)
            outputfile = [
                file for file in jsonfile.parent.glob(jsonfile.stem + '.*')
                if file.suffix in ('.nii', '.gz')
            ]  # Find the corresponding nifti/tsv.gz file (there should be only one, let's not make assumptions about the .gz extension)
            if not outputfile:
                LOGGER.exception(
                    f"No data-file found with {jsonfile} when updating {scans_tsv}"
                )
            elif datasource.datatype not in bidsmap['Options']['bidscoin'][
                    'bidsignore'] and not run['bids'][
                        'suffix'] in bids.get_derivatives(datasource.datatype):
                acq_time = ''
                if dataformat == 'DICOM':
                    acq_time = f"{datasource.attributes('AcquisitionDate')}T{datasource.attributes('AcquisitionTime')}"
                elif dataformat == 'PAR':
                    acq_time = datasource.attributes('exam_date')
                if not acq_time or acq_time == 'T':
                    acq_time = f"1925-01-01T{jsondata.get('AcquisitionTime','')}"
                try:
                    acq_time = dateutil.parser.parse(acq_time)
                    if options.get('anon', 'y') in ('y', 'yes'):
                        acq_time = acq_time.replace(
                            year=1925, month=1, day=1
                        )  # Privacy protection (see BIDS specification)
                    acq_time = acq_time.isoformat()
                except Exception as jsonerror:
                    LOGGER.warning(
                        f"Could not parse the acquisition time from: {sourcefile}\n{jsonerror}"
                    )
                    acq_time = 'n/a'
                scanpath = outputfile[0].relative_to(bidsses)
                scans_table.loc[scanpath.as_posix(), 'acq_time'] = acq_time

    # Write the scans_table to disk
    LOGGER.info(f"Writing acquisition time data to: {scans_tsv}")
    scans_table.sort_values(by=['acq_time', 'filename'], inplace=True)
    scans_table.replace('', 'n/a').to_csv(scans_tsv,
                                          sep='\t',
                                          encoding='utf-8',
                                          na_rep='n/a')

    # Collect personal data from a source header (PAR/XML does not contain personal info)
    personals = {}
    if sesid and 'session_id' not in personals:
        personals['session_id'] = sesid
    personals['age'] = ''
    if dataformat == 'DICOM':
        age = datasource.attributes(
            'PatientAge'
        )  # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
        if age.endswith('D'): age = float(age.rstrip('D')) / 365.2524
        elif age.endswith('W'): age = float(age.rstrip('W')) / 52.1775
        elif age.endswith('M'): age = float(age.rstrip('M')) / 12
        elif age.endswith('Y'): age = float(age.rstrip('Y'))
        if age:
            if options.get('anon', 'y') in ('y', 'yes'):
                age = int(float(age))
            personals['age'] = str(age)
        personals['sex'] = datasource.attributes('PatientSex')
        personals['size'] = datasource.attributes('PatientSize')
        personals['weight'] = datasource.attributes('PatientWeight')

    # Store the collected personals in the participants_table
    participants_tsv = bidsfolder / 'participants.tsv'
    if participants_tsv.is_file():
        participants_table = pd.read_csv(participants_tsv, sep='\t', dtype=str)
        participants_table.set_index(['participant_id'],
                                     verify_integrity=True,
                                     inplace=True)
    else:
        participants_table = pd.DataFrame()
        participants_table.index.name = 'participant_id'
    if subid in participants_table.index and 'session_id' in participants_table.keys(
    ) and participants_table.loc[subid, 'session_id']:
        return  # Only take data from the first session -> BIDS specification
    for key in personals:  # TODO: Check that only values that are consistent over sessions go in the participants.tsv file, otherwise put them in a sessions.tsv file
        if key not in participants_table or participants_table[key].isnull(
        ).get(subid, True) or participants_table[key].get(subid) == 'n/a':
            participants_table.loc[subid, key] = personals[key]

    # Write the collected data to the participants tsv-file
    LOGGER.info(f"Writing {subid} subject data to: {participants_tsv}")
    participants_table.replace('', 'n/a').to_csv(participants_tsv,
                                                 sep='\t',
                                                 encoding='utf-8',
                                                 na_rep='n/a')
示例#3
0
def coin_dicom(session: str, bidsmap: dict, bidsfolder: str, personals: dict,
               subprefix: str, sesprefix: str) -> None:
    """
    Converts the session dicom-files into BIDS-valid nifti-files in the corresponding bidsfolder and
    extracts personals (e.g. Age, Sex) from the dicom header

    :param session:     The full-path name of the subject/session source folder
    :param bidsmap:     The full mapping heuristics from the bidsmap YAML-file
    :param bidsfolder:  The full-path name of the BIDS root-folder
    :param personals:   The dictionary with the personal information
    :param subprefix:   The prefix common for all source subject-folders
    :param sesprefix:   The prefix common for all source session-folders
    :return:            Nothing
    """

    if not bids.lsdirs(session):
        logger.warning('No series subfolder(s) found in: ' + session)
        return

    TE = [None, None]

    # Get a valid BIDS subject identifier from the (first) dicom-header or from the session source folder
    if bidsmap['DICOM']['participant_label'] and bidsmap['DICOM'][
            'participant_label'].startswith(
                '<<') and bidsmap['DICOM']['participant_label'].endswith('>>'):
        subid = bids.get_dicomfield(
            bidsmap['DICOM']['participant_label'][2:-2],
            bids.get_dicomfile(bids.lsdirs(session)[0]))
    elif bidsmap['DICOM']['participant_label']:
        subid = bidsmap['DICOM']['participant_label']
    else:
        subid = session.rsplit(os.sep + subprefix,
                               1)[1].split(os.sep + sesprefix, 1)[0]
    subid = 'sub-' + bids.cleanup_label(subid.lstrip(subprefix))
    if subid == subprefix:
        logger.error('Error: No valid subject identifier found for: ' +
                     session)
        return

    # Get a valid or empty BIDS session identifier from the (first) dicom-header or from the session source folder
    if bidsmap['DICOM']['session_label'] and bidsmap['DICOM'][
            'session_label'].startswith(
                '<<') and bidsmap['DICOM']['session_label'].endswith('>>'):
        sesid = bids.get_dicomfield(
            bidsmap['DICOM']['session_label'][2:-2],
            bids.get_dicomfile(bids.lsdirs(session)[0]))
    elif bidsmap['DICOM']['session_label']:
        sesid = bidsmap['DICOM']['session_label']
    elif os.sep + sesprefix in session:
        sesid = session.rsplit(os.sep + sesprefix)[1]
    else:
        sesid = ''
    if sesid:
        sesid = 'ses-' + bids.cleanup_label(sesid.lstrip(sesprefix))

    # Create the BIDS session-folder and a scans.tsv file
    bidsses = os.path.join(
        bidsfolder, subid, sesid
    )  # NB: This gives a trailing '/' if ses=='', but that should be ok
    os.makedirs(bidsses, exist_ok=True)
    scans_tsv = os.path.join(bidsses,
                             f'{subid}{bids.add_prefix("_",sesid)}_scans.tsv')
    if os.path.exists(scans_tsv):
        scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
    else:
        scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
        scans_table.index.name = 'filename'

    # Process all the dicom series subfolders
    for series in bids.lsdirs(session):

        if series.startswith('.'):
            logger.info('Ignoring hidden dicom-folder: ' + series)
            continue
        else:
            logger.info('Processing dicom-folder: ' + series)

        # Get the cleaned-up bids labels from a dicom-file and bidsmap
        dicomfile = bids.get_dicomfile(series)
        if not dicomfile: continue
        result = bids.get_matching_dicomseries(dicomfile, bidsmap)
        series_ = result['series']
        modality = result['modality']

        # Create the BIDS session/modality folder
        bidsmodality = os.path.join(bidsses, modality)
        os.makedirs(bidsmodality, exist_ok=True)

        # Compose the BIDS filename using the bids labels and run-index
        runindex = series_['bids']['run_index']
        if runindex.startswith('<<') and runindex.endswith('>>'):
            bidsname = bids.get_bidsname(subid, sesid, modality, series_,
                                         runindex[2:-2])
            bidsname = bids.increment_runindex(bidsmodality, bidsname)
        else:
            bidsname = bids.get_bidsname(subid, sesid, modality, series_,
                                         runindex)

        # Convert the dicom-files in the series folder to nifti's in the BIDS-folder
        command = '{path}dcm2niix {args} -f "{filename}" -o "{outfolder}" "{infolder}"'.format(
            path=bidsmap['Options']['dcm2niix']['path'],
            args=bidsmap['Options']['dcm2niix']['args'],
            filename=bidsname,
            outfolder=bidsmodality,
            infolder=series)
        logger.info('$ ' + command)
        process = subprocess.run(
            command,
            shell=True,
            stdout=subprocess.PIPE,
            stderr=subprocess.STDOUT
        )  # TODO: investigate shell=False and capture_output=True
        logger.info(process.stdout.decode('utf-8'))
        if process.returncode != 0:
            errormsg = f'Error: Failed to process {series} (errorcode {process.returncode})'
            logger.error(errormsg)
            continue

        # Replace uncropped output image with the cropped one
        if '-x y' in bidsmap['Options']['dcm2niix']['args']:
            for filename in sorted(
                    glob.glob(os.path.join(
                        bidsmodality,
                        bidsname + '*_Crop_*'))):  # e.g. *_Crop_1.nii.gz
                basepath, ext1 = os.path.splitext(filename)
                basepath, ext2 = os.path.splitext(
                    basepath)  # Account for .nii.gz files
                basepath = basepath.rsplit('_Crop_', 1)[0]
                newfilename = basepath + ext2 + ext1
                logger.info(
                    f'Found dcm2niix _Crop_ suffix, replacing original file\n{filename} ->\n{newfilename}'
                )
                os.replace(filename, newfilename)

        # Rename all files ending with _c%d, _e%d and _ph (and any combination of these): These are produced by dcm2niix for multi-coil data, multi-echo data and phase data, respectively
        jsonfiles = [
        ]  # Collect the associated json-files (for updating them later) -- possibly > 1
        for suffix in ('_c', '_e', '_ph', '_i'):
            for filename in sorted(
                    glob.glob(
                        os.path.join(bidsmodality,
                                     bidsname + suffix + '[0-9]*'))):
                basepath, ext1 = os.path.splitext(filename)
                basepath, ext2 = os.path.splitext(
                    basepath)  # Account for .nii.gz files
                basepath, index = basepath.rsplit(suffix, 1)
                index = index.split('_')[0].zfill(
                    2
                )  # Zero padd as specified in the BIDS-standard (assuming two digits is sufficient); strip following suffices (fieldmaps produce *_e2_ph files)

                # This is a special hack: dcm2niix does not always add a _c/_e suffix for the first(?) coil/echo image -> add it when we encounter a **_e2/_c2 file
                if suffix in (
                        '_c', '_e'
                ) and int(index) == 2 and basepath.rsplit(
                        '_', 1
                )[1] != 'magnitude1':  # For fieldmaps: *_magnitude1_e[index] -> *_magnitude[index] (This is handled below)
                    filename_ce = basepath + ext2 + ext1  # The file without the _c1/_e1 suffix
                    if suffix == '_e' and bids.set_bidslabel(basepath, 'echo'):
                        newbasepath_ce = bids.set_bidslabel(
                            basepath, 'echo', '1')
                    else:
                        newbasepath_ce = bids.set_bidslabel(
                            basepath, 'dummy',
                            suffix.upper() + '1'.zfill(len(index))
                        )  # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data
                    newfilename_ce = newbasepath_ce + ext2 + ext1  # The file as it should have been
                    if os.path.isfile(filename_ce):
                        if filename_ce != newfilename_ce:
                            logger.info(
                                f'Found no dcm2niix {suffix} suffix for image instance 1, renaming\n{filename_ce} ->\n{newfilename_ce}'
                            )
                            os.rename(filename_ce, newfilename_ce)
                        if ext1 == '.json':
                            jsonfiles.append(newbasepath_ce + '.json')

                # Patch the basepath with the suffix info
                if suffix == '_e' and bids.set_bidslabel(basepath,
                                                         'echo') and index:
                    basepath = bids.set_bidslabel(
                        basepath, 'echo', str(int(index))
                    )  # In contrast to other labels, run and echo labels MUST be integers. Those labels MAY include zero padding, but this is NOT RECOMMENDED to maintain their uniqueness

                elif suffix == '_e' and basepath.rsplit('_', 1)[1] in (
                        'magnitude1',
                        'magnitude2') and index:  # i.e. modality == 'fmap'
                    basepath = basepath[0:-1] + str(
                        int(index)
                    )  # basepath: *_magnitude1_e[index] -> *_magnitude[index]
                    # Read the echo times that need to be added to the json-file (see below)
                    if os.path.splitext(filename)[1] == '.json':
                        with open(filename, 'r') as json_fid:
                            data = json.load(json_fid)
                        TE[int(index) - 1] = data['EchoTime']
                        logger.info(
                            f"Reading EchoTime{index} = {data['EchoTime']} from: {filename}"
                        )
                elif suffix == '_e' and basepath.rsplit(
                        '_', 1
                )[1] == 'phasediff' and index:  # i.e. modality == 'fmap'
                    pass

                elif suffix == '_ph' and basepath.rsplit('_', 1)[1] in [
                        'phase1', 'phase2'
                ] and index:  # i.e. modality == 'fmap' (TODO: untested)
                    basepath = basepath[0:-1] + str(
                        int(index
                            ))  # basepath: *_phase1_e[index] -> *_phase[index]
                    logger.warning('Untested dcm2niix "_ph"-filetype: ' +
                                   basepath)

                else:
                    basepath = bids.set_bidslabel(
                        basepath, 'dummy',
                        suffix.upper() + index
                    )  # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data

                # Save the file with a new name
                if runindex.startswith('<<') and runindex.endswith('>>'):
                    newbidsname = bids.increment_runindex(
                        bidsmodality, os.path.basename(basepath), ext2 + ext1
                    )  # Update the runindex now that the acq-label has changed
                else:
                    newbidsname = os.path.basename(basepath)
                newfilename = os.path.join(bidsmodality,
                                           newbidsname + ext2 + ext1)
                logger.info(
                    f'Found dcm2niix {suffix} suffix, renaming\n{filename} ->\n{newfilename}'
                )
                os.rename(filename, newfilename)
                if ext1 == '.json':
                    jsonfiles.append(
                        os.path.join(bidsmodality, newbidsname + '.json'))

        # Loop over and adapt all the newly produced json files and write to the scans.tsv file (every nifti-file comes with a json-file)
        if not jsonfiles:
            jsonfiles = [os.path.join(bidsmodality, bidsname + '.json')]
        for jsonfile in set(jsonfiles):

            # Check if dcm2niix behaved as expected
            if not os.path.isfile(jsonfile):
                logger.warning(
                    f'Unexpected file conbids.version result: {jsonfile} not found'
                )
                continue

            # Add a dummy b0 bval- and bvec-file for any file without a bval/bvec file (e.g. sbref, b0 scans)
            if modality == 'dwi':
                bvecfile = os.path.splitext(jsonfile)[0] + '.bvec'
                bvalfile = os.path.splitext(jsonfile)[0] + '.bval'
                if not os.path.isfile(bvecfile):
                    logger.info('Adding dummy bvec file: ' + bvecfile)
                    with open(bvecfile, 'w') as bvec_fid:
                        bvec_fid.write('0\n0\n0\n')
                if not os.path.isfile(bvalfile):
                    logger.info('Adding dummy bval file: ' + bvalfile)
                    with open(bvalfile, 'w') as bval_fid:
                        bval_fid.write('0\n')

            # Add the TaskName to the func json-file
            elif modality == 'func':
                with open(jsonfile, 'r') as json_fid:
                    data = json.load(json_fid)
                if not 'TaskName' in data:
                    logger.info('Adding TaskName to: ' + jsonfile)
                    data['TaskName'] = series_['bids']['task_label']
                    with open(jsonfile, 'w') as json_fid:
                        json.dump(data, json_fid, indent=4)

            # Add the EchoTime(s) used to create the difference image to the fmap json-file. NB: This assumes the magnitude series have already been parsed (i.e. their nifti's had an _e suffix) -- This is normally the case for Siemens (phase-series being saved after the magnitude series
            elif modality == 'fmap':
                if series_['bids']['suffix'] == 'phasediff':
                    logger.info('Adding EchoTime1 and EchoTime2 to: ' +
                                jsonfile)
                    with open(jsonfile, 'r') as json_fid:
                        data = json.load(json_fid)
                    data['EchoTime1'] = TE[0]
                    data['EchoTime2'] = TE[1]
                    with open(jsonfile, 'w') as json_fid:
                        json.dump(data, json_fid, indent=4)
                    if TE[0] > TE[1]:
                        logger.warning('EchoTime1 > EchoTime2 in: ' + jsonfile)

            # Parse the acquisition time from the json file
            with open(jsonfile, 'r') as json_fid:
                data = json.load(json_fid)
            acq_time = dateutil.parser.parse(data['AcquisitionTime'])
            niipath = glob.glob(
                os.path.splitext(jsonfile)[0] + '.nii*'
            )[0]  # Find the corresponding nifti file (there should be only one, let's not make assumptions about the .gz extension)
            niipath = niipath.replace(
                bidsses + os.sep, ''
            )  # Use a relative path. Somehow .strip(bidsses) instead of replace(bidsses,'') does not work properly
            scans_table.loc[
                niipath,
                'acq_time'] = '1900-01-01T' + acq_time.strftime('%H:%M:%S')

    # Write the scans_table to disk
    logger.info('Writing acquisition time data to: ' + scans_tsv)
    scans_table.to_csv(scans_tsv, sep='\t', encoding='utf-8')

    # Search for the IntendedFor images and add them to the json-files. This has been postponed untill all modalities have been processed (i.e. so that all target images are indeed on disk)
    if bidsmap['DICOM']['fmap'] is not None:
        for fieldmap in bidsmap['DICOM']['fmap']:
            if 'IntendedFor' in fieldmap['bids'] and fieldmap['bids'][
                    'IntendedFor']:
                bidsname = bids.get_bidsname(subid, sesid, 'fmap', fieldmap,
                                             '1')
                acqlabel = bids.set_bidslabel(bidsname, 'acq')
                for jsonfile in glob.glob(
                        os.path.join(
                            bidsses, 'fmap',
                            bidsname.replace(
                                '_run-1_', '_run-[0-9]*_').replace(
                                    acqlabel, acqlabel + '[CE][0-9]*') +
                            '.json')
                ):  # Account for multiple runs and dcm2niix suffixes inserted into the acquisition label

                    intendedfor = fieldmap['bids']['IntendedFor']
                    if intendedfor.startswith('<<') and intendedfor.endswith(
                            '>>'):
                        intendedfor = intendedfor[2:-2].split('><')
                    else:
                        intendedfor = [intendedfor]

                    niifiles = []
                    for selector in intendedfor:
                        niifiles.extend([
                            niifile.split(os.sep + subid + os.sep,
                                          1)[1].replace('\\', '/')
                            for niifile in sorted(
                                glob.glob(
                                    os.path.join(
                                        bidsses,
                                        f'**{os.sep}*{selector}*.nii*')))
                        ])  # Search in all series using a relative path

                    with open(jsonfile, 'r') as json_fid:
                        data = json.load(json_fid)
                    data['IntendedFor'] = niifiles
                    logger.info('Adding IntendedFor to: ' + jsonfile)
                    with open(jsonfile, 'w') as json_fid:
                        json.dump(data, json_fid, indent=4)

                # Catch magnitude2 files produced by dcm2niix (i.e. magnitude1 & magnitude2 both in the same seriesfolder)
                if jsonfile.endswith('magnitude1.json'):
                    jsonfile2 = jsonfile.rsplit('1.json', 1)[0] + '2.json'
                    if os.path.isfile(jsonfile2):

                        with open(jsonfile2, 'r') as json_fid:
                            data = json.load(json_fid)
                        if 'IntendedFor' not in data:
                            data['IntendedFor'] = niifiles
                            logger.info('Adding IntendedFor to: ' + jsonfile2)
                            with open(jsonfile2, 'w') as json_fid:
                                json.dump(data, json_fid, indent=4)

    # Collect personal data from the DICOM header
    dicomfile = bids.get_dicomfile(series)
    personals['participant_id'] = subid
    if sesid:
        personals['session_id'] = sesid
    personals['age'] = bids.get_dicomfield('PatientAge', dicomfile)
    personals['sex'] = bids.get_dicomfield('PatientSex', dicomfile)
    personals['size'] = bids.get_dicomfield('PatientSize', dicomfile)
    personals['weight'] = bids.get_dicomfield('PatientWeight', dicomfile)
示例#4
0
def coin_dicom(session: Path, bidsmap: dict, bidsfolder: Path, personals: dict,
               subprefix: str, sesprefix: str) -> None:
    """
    Converts the session dicom-files into BIDS-valid nifti-files in the corresponding bidsfolder and
    extracts personals (e.g. Age, Sex) from the dicom header

    :param session:     The full-path name of the subject/session source folder
    :param bidsmap:     The full mapping heuristics from the bidsmap YAML-file
    :param bidsfolder:  The full-path name of the BIDS root-folder
    :param personals:   The dictionary with the personal information
    :param subprefix:   The prefix common for all source subject-folders
    :param sesprefix:   The prefix common for all source session-folders
    :return:            Nothing
    """

    if not bids.lsdirs(session):
        LOGGER.warning(f"No run subfolder(s) found in: {session}")
        return

    TE = [None, None]

    # Get valid BIDS subject/session identifiers from the (first) dicom-header or from the session source folder
    subid, sesid = bids.get_subid_sesid(
        bids.get_dicomfile(bids.lsdirs(session)[0]),
        bidsmap['DICOM']['subject'], bidsmap['DICOM']['session'], subprefix,
        sesprefix)
    if subid == subprefix:
        LOGGER.error(f"No valid subject identifier found for: {session}")
        return

    # Create the BIDS session-folder and a scans.tsv file
    bidsses = bidsfolder / subid / sesid
    if bidsses.is_dir():
        LOGGER.warning(
            f"Existing BIDS output-directory found, which may result in duplicate data (with increased run-index). Make sure {bidsses} was cleaned-up from old data before (re)running the bidscoiner"
        )
    bidsses.mkdir(parents=True, exist_ok=True)
    scans_tsv = bidsses / f"{subid}{bids.add_prefix('_',sesid)}_scans.tsv"
    if scans_tsv.is_file():
        scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
    else:
        scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
        scans_table.index.name = 'filename'

    # Process all the dicom run subfolders
    for runfolder in bids.lsdirs(session):

        # Get a dicom-file
        dicomfile = bids.get_dicomfile(runfolder)
        if not dicomfile.name: continue

        # Get a matching run from the bidsmap
        run, modality, index = bids.get_matching_run(dicomfile, bidsmap)

        # Check if we should ignore this run
        if modality == bids.ignoremodality:
            LOGGER.info(f"Leaving out: {runfolder}")
            continue

        # Check if we already know this run
        if index is None:
            LOGGER.warning(
                f"Skipping unknown '{modality}': {dicomfile}\n-> re-run the bidsmapper and delete {session} to solve this warning"
            )
            continue

        LOGGER.info(f"Processing: {runfolder}")

        # Create the BIDS session/modality folder
        bidsmodality = bidsses / modality
        bidsmodality.mkdir(parents=True, exist_ok=True)

        # Compose the BIDS filename using the matched run
        bidsname = bids.get_bidsname(subid, sesid, modality, run)
        runindex = run['bids']['run']
        if runindex.startswith('<<') and runindex.endswith('>>'):
            bidsname = bids.increment_runindex(bidsmodality, bidsname)

        # Check if file already exists (-> e.g. when a static runindex is used)
        if (bidsmodality / bidsname).with_suffix('.json').is_file():
            LOGGER.warning(
                f"{bidsmodality/bidsname}.* already exists -- check your results carefully!"
            )

        # Convert the dicom-files in the run folder to nifti's in the BIDS-folder
        command = '{path}dcm2niix {args} -f "{filename}" -o "{outfolder}" "{infolder}"'.format(
            path=bidsmap['Options']['dcm2niix']['path'],
            args=bidsmap['Options']['dcm2niix']['args'],
            filename=bidsname,
            outfolder=bidsmodality,
            infolder=runfolder)
        if not bids.run_command(command):
            continue

        # Replace uncropped output image with the cropped one
        if '-x y' in bidsmap['Options']['dcm2niix']['args']:
            for filename in sorted(
                    bidsmodality.glob(bidsname +
                                      '*_Crop_*')):  # e.g. *_Crop_1.nii.gz
                ext = ''.join(filename.suffixes)
                newfilename = str(filename).rsplit(ext, 1)[0].rsplit(
                    '_Crop_', 1)[0] + ext
                LOGGER.info(
                    f"Found dcm2niix _Crop_ suffix, replacing original file\n{filename} ->\n{newfilename}"
                )
                filename.replace(newfilename)

        # Rename all files ending with _c%d, _e%d and _ph (and any combination of these): These are produced by dcm2niix for multi-coil data, multi-echo data and phase data, respectively
        jsonfiles = [
        ]  # Collect the associated json-files (for updating them later) -- possibly > 1
        for dcm2niisuffix in ('_c', '_e', '_ph', '_i'):
            for filename in sorted(
                    bidsmodality.glob(bidsname + dcm2niisuffix + '*')):
                ext = ''.join(filename.suffixes)
                basepath, index = str(filename).rsplit(ext, 1)[0].rsplit(
                    dcm2niisuffix, 1
                )  # basepath = the name without the added stuff (i.e. bidsmodality/bidsname), index = added dcm2niix index (e.g. _c1 -> index=1)
                basesuffix = basepath.rsplit(
                    '_', 1
                )[1]  # The BIDS suffix, e.g. basepath = *_magnitude1 -> basesuffix=magnitude1
                index = index.split('_')[0].zfill(
                    2
                )  # Zero padd as specified in the BIDS-standard (assuming two digits is sufficient); strip following suffices (fieldmaps produce *_e2_ph files)

                # This is a special hack: dcm2niix does not always add a _c/_e suffix for the first(?) coil/echo image -> add it when we encounter a **_e2/_c2 file
                if dcm2niisuffix in (
                        '_c', '_e'
                ) and int(index) == 2 and basesuffix not in [
                        'magnitude1', 'phase1'
                ]:  # For fieldmaps: *_magnitude1_e[index] -> *_magnitude[index] (This is handled below)
                    filename_ce = Path(
                        basepath + ext)  # The file without the _c1/_e1 suffix
                    if dcm2niisuffix == '_e' and bids.get_bidsvalue(
                            basepath, 'echo'):
                        newbasepath_ce = Path(
                            bids.get_bidsvalue(basepath, 'echo', '1'))
                    else:
                        newbasepath_ce = Path(
                            bids.get_bidsvalue(
                                basepath, 'dummy',
                                dcm2niisuffix.upper() + '1'.zfill(len(index)))
                        )  # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data
                    newfilename_ce = newbasepath_ce.with_suffix(
                        ext)  # The file as it should have been
                    if filename_ce.is_file():
                        if filename_ce != newfilename_ce:
                            LOGGER.info(
                                f"Found no dcm2niix {dcm2niisuffix} suffix for image instance 1, renaming\n{filename_ce} ->\n{newfilename_ce}"
                            )
                            filename_ce.replace(newfilename_ce)
                        if ext == '.json':
                            jsonfiles.append(
                                newbasepath_ce.with_suffix('.json'))

                # Patch the basepath with the dcm2niix suffix info (we can't rely on the basepath info here because Siemens can e.g. put multiple echos in one series / run-folder)
                if dcm2niisuffix == '_e' and bids.get_bidsvalue(
                        basepath, 'echo') and index:
                    basepath = bids.get_bidsvalue(
                        basepath, 'echo', str(int(index))
                    )  # In contrast to other labels, run and echo labels MUST be integers. Those labels MAY include zero padding, but this is NOT RECOMMENDED to maintain their uniqueness

                elif dcm2niisuffix == '_e' and basesuffix in (
                        'magnitude1',
                        'magnitude2') and index:  # i.e. modality == 'fmap'
                    basepath = basepath[0:-1] + str(
                        int(index)
                    )  # basepath: *_magnitude1_e[index] -> *_magnitude[index]
                    # Collect the echo times that need to be added to the json-file (see below)
                    if filename.suffix == '.json':
                        with filename.open('r') as json_fid:
                            data = json.load(json_fid)
                        TE[int(index) - 1] = data['EchoTime']
                        LOGGER.info(
                            f"Collected EchoTime{index} = {data['EchoTime']} from: {filename}"
                        )
                elif dcm2niisuffix == '_e' and basesuffix == 'phasediff' and index:  # i.e. modality == 'fmap'
                    pass

                elif dcm2niisuffix == '_e' and basesuffix in [
                        'phase1', 'phase2'
                ] and index:  # i.e. modality == 'fmap'
                    basepath = basepath[0:-1] + str(
                        int(index)
                    )  # basepath: *_phase1_e[index]_ph -> *_phase[index]

                else:
                    basepath = bids.get_bidsvalue(
                        basepath, 'dummy',
                        dcm2niisuffix.upper() + index
                    )  # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data

                # Save the file with a new name
                newbidsname = str(Path(basepath).name)
                if runindex.startswith('<<') and runindex.endswith('>>'):
                    newbidsname = bids.increment_runindex(
                        bidsmodality, newbidsname, ext
                    )  # Update the runindex now that the acq-label has changed
                newfilename = (bidsmodality / newbidsname).with_suffix(ext)
                LOGGER.info(
                    f"Found dcm2niix {dcm2niisuffix} suffix, renaming\n{filename} ->\n{newfilename}"
                )
                filename.replace(newfilename)
                if ext == '.json':
                    jsonfiles.append(
                        (bidsmodality / newbidsname).with_suffix('.json'))

        # Loop over and adapt all the newly produced json files and write to the scans.tsv file (every nifti-file comes with a json-file)
        if not jsonfiles:
            jsonfiles = [(bidsmodality / bidsname).with_suffix('.json')]
        for jsonfile in set(jsonfiles):

            # Check if dcm2niix behaved as expected
            if not jsonfile.is_file():
                LOGGER.error(
                    f"Unexpected file conversion result: {jsonfile} not found")
                continue

            # Add a dummy b0 bval- and bvec-file for any file without a bval/bvec file (e.g. sbref, b0 scans)
            if modality == 'dwi':
                bvecfile = jsonfile.with_suffix('.bvec')
                bvalfile = jsonfile.with_suffix('.bval')
                if not bvecfile.is_file():
                    LOGGER.info(f"Adding dummy bvec file: {bvecfile}")
                    with bvecfile.open('w') as bvec_fid:
                        bvec_fid.write('0\n0\n0\n')
                if not bvalfile.is_file():
                    LOGGER.info(f"Adding dummy bval file: {bvalfile}")
                    with bvalfile.open('w') as bval_fid:
                        bval_fid.write('0\n')

            # Add the TaskName to the func json-file
            elif modality == 'func':
                with jsonfile.open('r') as json_fid:
                    data = json.load(json_fid)
                if not 'TaskName' in data:
                    LOGGER.info(f"Adding TaskName to: {jsonfile}")
                    data['TaskName'] = run['bids']['task']
                    with jsonfile.open('w') as json_fid:
                        json.dump(data, json_fid, indent=4)

            # Add the EchoTime(s) used to create the difference image to the fmap json-file. NB: This assumes the magnitude runs have already been parsed (i.e. their nifti's had an _e suffix) -- This is normally the case for Siemens (phase-runs being saved after the magnitude runs
            elif modality == 'fmap':
                if run['bids']['suffix'] == 'phasediff':
                    LOGGER.info(
                        f"Adding EchoTime1: {TE[0]} and EchoTime2: {TE[1]} to {jsonfile}"
                    )
                    if TE[0] is None or TE[1] is None:
                        LOGGER.warning(
                            f"Missing Echo-Time data for: {jsonfile}")
                    elif TE[0] > TE[1]:
                        LOGGER.warning(
                            f"EchoTime1 > EchoTime2 for: {jsonfile}")
                    with jsonfile.open('r') as json_fid:
                        data = json.load(json_fid)
                    data['EchoTime1'] = TE[0]
                    data['EchoTime2'] = TE[1]
                    with jsonfile.open('w') as json_fid:
                        json.dump(data, json_fid, indent=4)

            # Parse the acquisition time from the json file or else from the dicom header (NB: assuming the dicom file represents the first aqcuisition)
            with jsonfile.open('r') as json_fid:
                data = json.load(json_fid)
            if 'AcquisitionTime' not in data:
                data['AcquisitionTime'] = bids.get_dicomfield(
                    'AcquisitionTime', dicomfile)
            acq_time = dateutil.parser.parse(data['AcquisitionTime'])
            scanpath = list(
                jsonfile.parent.glob(jsonfile.stem + '.nii*')
            )[0].relative_to(
                bidsses
            )  # Find the corresponding nifti file (there should be only one, let's not make assumptions about the .gz extension)
            scans_table.loc[
                scanpath.as_posix(),
                'acq_time'] = '1900-01-01T' + acq_time.strftime('%H:%M:%S')

    # Write the scans_table to disk
    LOGGER.info(f"Writing acquisition time data to: {scans_tsv}")
    scans_table.sort_values(by=['acq_time', 'filename'], inplace=True)
    scans_table.to_csv(scans_tsv, sep='\t', encoding='utf-8')

    # Search for the IntendedFor images and add them to the json-files. This has been postponed untill all modalities have been processed (i.e. so that all target images are indeed on disk)
    if bidsmap['DICOM']['fmap'] is not None:
        for fieldmap in bidsmap['DICOM']['fmap']:
            bidsname = bids.get_bidsname(subid, sesid, 'fmap', fieldmap)
            niifiles = []
            intendedfor = fieldmap['bids']['IntendedFor']

            # Search for the imaging files that match the IntendedFor search criteria
            if intendedfor:
                if intendedfor.startswith('<<') and intendedfor.endswith('>>'):
                    intendedfor = intendedfor[2:-2].split('><')
                elif not isinstance(intendedfor, list):
                    intendedfor = [intendedfor]
                for selector in intendedfor:
                    niifiles.extend(
                        [
                            Path(niifile).relative_to(bidsfolder / subid)
                            for niifile in sorted(
                                bidsses.rglob(f"*{selector}*.nii*"))
                            if selector
                        ]
                    )  # Search in all runs using a relative path to the subject folder
            else:
                intendedfor = []

            # Save the IntendedFor data in the json-files (account for multiple runs and dcm2niix suffixes inserted into the acquisition label)
            acqlabel = bids.get_bidsvalue(bidsname, 'acq')
            for jsonfile in list((bidsses/'fmap').glob(bidsname.replace('_run-1_', '_run-[0-9]*_') + '.json')) + \
                            list((bidsses/'fmap').glob(bidsname.replace('_run-1_', '_run-[0-9]*_').replace(acqlabel, acqlabel+'[CE][0-9]*') + '.json')):

                if niifiles:
                    LOGGER.info(f"Adding IntendedFor to: {jsonfile}")
                elif intendedfor:
                    LOGGER.warning(
                        f"Empty 'IntendedFor' fieldmap value in {jsonfile}: the search for {intendedfor} gave no results"
                    )
                else:
                    LOGGER.warning(
                        f"Empty 'IntendedFor' fieldmap value in {jsonfile}: the IntendedFor value of the bidsmap entry was empty"
                    )
                with jsonfile.open('r') as json_fid:
                    data = json.load(json_fid)
                data['IntendedFor'] = [
                    niifile.as_posix() for niifile in niifiles
                ]  # The path needs to use forward slashes instead of backward slashes
                with jsonfile.open('w') as json_fid:
                    json.dump(data, json_fid, indent=4)

                # Catch magnitude2 and phase2 files produced by dcm2niix (i.e. magnitude1 & magnitude2 both in the same runfolder)
                if jsonfile.name.endswith(
                        'magnitude1.json') or jsonfile.name.endswith(
                            'phase1.json'):
                    jsonfile2 = jsonfile.with_name(
                        jsonfile.name.rsplit('1.json', 1)[0] + '2.json')
                    if jsonfile2.is_file():
                        with jsonfile2.open('r') as json_fid:
                            data = json.load(json_fid)
                        if 'IntendedFor' not in data:
                            if niifiles:
                                LOGGER.info(
                                    f"Adding IntendedFor to: {jsonfile2}")
                            else:
                                LOGGER.warning(
                                    f"Empty 'IntendedFor' fieldmap value in {jsonfile2}: the search for {intendedfor} gave no results"
                                )
                            data['IntendedFor'] = [
                                niifile.as_posix() for niifile in niifiles
                            ]  # The path needs to use forward slashes instead of backward slashes
                            with jsonfile2.open('w') as json_fid:
                                json.dump(data, json_fid, indent=4)

    # Collect personal data from the DICOM header: only from the first session (-> BIDS specification)
    if 'runfolder' in locals():
        dicomfile = bids.get_dicomfile(runfolder)
        personals['participant_id'] = subid
        if sesid:
            if 'session_id' not in personals:
                personals['session_id'] = sesid
            else:
                return
        age = bids.get_dicomfield(
            'PatientAge', dicomfile
        )  # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
        if age.endswith('D'):
            personals['age'] = str(int(float(age.rstrip('D')) / 365.2524))
        elif age.endswith('W'):
            personals['age'] = str(int(float(age.rstrip('W')) / 52.1775))
        elif age.endswith('M'):
            personals['age'] = str(int(float(age.rstrip('M')) / 12))
        elif age.endswith('Y'):
            personals['age'] = str(int(float(age.rstrip('Y'))))
        elif age:
            personals['age'] = age
        personals['sex'] = bids.get_dicomfield('PatientSex', dicomfile)
        personals['size'] = bids.get_dicomfield('PatientSize', dicomfile)
        personals['weight'] = bids.get_dicomfield('PatientWeight', dicomfile)
示例#5
0
def coin_dicom(session, bidsmap, bidsfolder, personals):
    """
    Converts the session dicom-files into BIDS-valid nifti-files in the corresponding bidsfolder and
    extracts personals (e.g. Age, Sex) from the dicom header

    :param str session:    The full-path name of the subject/session source folder
    :param dict bidsmap:   The full mapping heuristics from the bidsmap YAML-file
    :param str bidsfolder: The full-path name of the BIDS root-folder
    :param dict personals: The dictionary with the personal information
    :return:               Nothing
    :rtype: NoneType
    """

    global logfile
    TE = [None, None]

    # Get a valid BIDS subject identifier from the (first) dicom-header or from the session source folder
    if bidsmap['DICOM']['participant_label'] and bidsmap['DICOM'][
            'participant_label'].startswith(
                '<<') and bidsmap['DICOM']['participant_label'].endswith('>>'):
        subid = 'sub-' + bids.get_dicomfield(
            bidsmap['DICOM']['participant_label'][2:-2],
            bids.get_dicomfile(bids.lsdirs(session)[0]))
    elif bidsmap['DICOM']['participant_label']:
        subid = 'sub-' + bidsmap['DICOM']['participant_label']
    else:
        subid = 'sub-' + session.rsplit(os.sep + 'sub-', 1)[1].split(
            os.sep + 'ses-', 1)[0]
    if subid == 'sub-':
        bids.printlog(
            'Error: No valid subject identifier found for: ' + session,
            logfile)
        return

    # Get a BIDS session identifier from the (first) dicom-header or from the session source folder
    if bidsmap['DICOM']['session_label'] and bidsmap['DICOM'][
            'session_label'].startswith(
                '<<') and bidsmap['DICOM']['session_label'].endswith('>>'):
        sesid = 'ses-' + bids.get_dicomfield(
            bidsmap['DICOM']['session_label'][2:-2],
            bids.get_dicomfile(bids.lsdirs(session)[0]))
    elif bidsmap['DICOM']['session_label']:
        sesid = 'ses-' + bidsmap['DICOM']['session_label']
    elif os.sep + 'ses-' in session:
        sesid = 'ses-' + session.rsplit(os.sep + 'ses-')[1]
    else:
        sesid = ''

    # Create the BIDS session-folder
    bidsses = os.path.join(
        bidsfolder, subid, sesid
    )  # NB: This gives a trailing '/' if ses=='', but that should be ok
    os.makedirs(bidsses, exist_ok=True)

    # Process all the dicom series subfolders
    for series in bids.lsdirs(session):

        bids.printlog('Processing dicom-folder: ' + series, logfile)

        # Get the cleaned-up bids labels from a dicom-file and bidsmap
        dicomfile = bids.get_dicomfile(series)
        result = bids.get_matching_dicomseries(dicomfile, bidsmap)
        series_ = result['series']
        modality = result['modality']

        # Create the BIDS session/modality folder
        bidsmodality = os.path.join(bidsses, modality)
        os.makedirs(bidsmodality, exist_ok=True)

        # Compose the BIDS filename using the bids labels and run-index
        runindex = series_['run_index']
        if runindex.startswith('<<') and runindex.endswith('>>'):
            bidsname = bids.get_bidsname(subid, sesid, modality, series_,
                                         runindex[2:-2])
            bidsname = bids.increment_runindex(bidsmodality, bidsname)
        else:
            bidsname = bids.get_bidsname(subid, sesid, modality, series_,
                                         runindex)

        # Convert the dicom-files in the series folder to nifti's in the BIDS-folder
        command = '{path}dcm2niix {args} -f "{filename}" -o "{outfolder}" "{infolder}"'.format(
            path=bidsmap['Options']['dcm2niix']['path'],
            args=bidsmap['Options']['dcm2niix']['args'],
            filename=bidsname,
            outfolder=bidsmodality,
            infolder=series)
        bids.printlog('$ ' + command, logfile)
        process = subprocess.run(
            command,
            shell=True,
            stdout=subprocess.PIPE,
            stderr=subprocess.STDOUT
        )  # TODO: investigate shell=False and capture_output=True
        bids.printlog(process.stdout.decode('utf-8'), logfile)
        if process.returncode != 0:
            errormsg = 'Error: Failed to process {} (errorcode {})'.format(
                series, process.returncode)
            bids.printlog(errormsg, logfile)
            continue

        # Rename all files ending with _c%d, _e%d and _ph: These are produced by dcm2niix for multi-coil data, multi-echo data and phase data, respectively
        jsonfiles = [
        ]  # Collect the associated json-files (for updating them later)
        for suffix in ('_c', '_e', '_ph'):
            for filename in sorted(
                    glob.glob(
                        os.path.join(bidsmodality, bidsname + suffix + '*'))):
                basepath, ext1 = os.path.splitext(filename)
                basepath, ext2 = os.path.splitext(
                    basepath)  # Account for .nii.gz files
                basepath, index = basepath.rsplit(suffix, 1)

                if suffix == '_e' and bids.set_bidslabel(basepath,
                                                         'echo') and index:
                    basepath = bids.set_bidslabel(basepath, 'echo', index)

                elif suffix == '_e' and basepath.rsplit('_', 1)[1] in [
                        'magnitude1', 'magnitude2'
                ] and index:  # i.e. modality == 'fmap'
                    basepath = basepath[0:-1] + index
                    # Read the echo times that need to be added to the json-file (see below)
                    if os.path.splitext(filename)[1] == '.json':
                        with open(filename, 'r') as json_fid:
                            data = json.load(json_fid)
                        TE[int(index) - 1] = data['EchoTime']
                        bids.printlog(
                            'Reading EchoTime{} = {} from: {}'.format(
                                index, data['EchoTime'], filename), logfile)
                elif suffix == '_e' and basepath.rsplit(
                        '_', 1
                )[1] == 'phasediff' and index:  # i.e. modality == 'fmap'
                    pass

                elif suffix == '_ph' and basepath.rsplit('_', 1)[1] in [
                        'phase1', 'phase2'
                ] and index:  # i.e. modality == 'fmap' (TODO: untested)
                    basepath = basepath[0:-1] + index
                    bids.printlog(
                        'WARNING: Untested dcm2niix "_ph"-filetype: ' +
                        basepath, logfile)

                else:
                    basepath = bids.set_bidslabel(
                        basepath, 'dummy',
                        suffix.upper() + index
                    )  # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data

                if runindex.startswith('<<') and runindex.endswith('>>'):
                    newbidsname = bids.increment_runindex(
                        bidsmodality, os.path.basename(basepath), ext2 + ext1
                    )  # Update the runindex now that the acq-label has changed
                else:
                    newbidsname = os.path.basename(basepath)
                newfilename = os.path.join(bidsmodality,
                                           newbidsname + ext2 + ext1)
                bids.printlog(
                    'Found dcm2niix {} suffix, renaming\n{} ->\n{}'.format(
                        suffix, filename, newfilename), logfile)
                os.rename(filename, newfilename)
                if ext1 == '.json':
                    jsonfiles.append(
                        os.path.join(bidsmodality, newbidsname + '.json'))

        # Loop over and adapt all the newly produced json files (every nifti file comes with a json file)
        if not jsonfiles:
            jsonfiles = [os.path.join(bidsmodality, bidsname + '.json')]

        for jsonfile in jsonfiles:

            # Add a dummy b0 bval- and bvec-file for any file without a bval/bvec file (e.g. sbref, b0 scans)
            if modality == 'dwi':
                bvecfile = os.path.splitext(jsonfile)[0] + '.bvec'
                bvalfile = os.path.splitext(jsonfile)[0] + '.bval'
                if not os.path.isfile(bvecfile):
                    with open(bvecfile, 'w') as bvec_fid:
                        bids.printlog('Adding dummy bvec file: ' + bvecfile,
                                      logfile)
                        bvec_fid.write('0\n0\n0\n')
                if not os.path.isfile(bvalfile):
                    with open(bvalfile, 'w') as bval_fid:
                        bids.printlog('Adding dummy bval file: ' + bvalfile,
                                      logfile)
                        bval_fid.write('0\n')

            # Add the TaskName to the func json-file
            elif modality == 'func':
                with open(jsonfile, 'r') as json_fid:
                    data = json.load(json_fid)
                if not 'TaskName' in data:
                    bids.printlog('Adding TaskName to: ' + jsonfile, logfile)
                    with open(jsonfile, 'w') as json_fid:
                        data['TaskName'] = series_['task_label']
                        json.dump(data, json_fid, indent=4)

            # Add the EchoTime(s) used to create the difference image to the fmap json-file. NB: This assumes the magnitude series have already been parsed (i.e. their nifti's had an _e suffix) -- This is normally the case for Siemens (phase-series being saved after the magnitude series
            elif modality == 'fmap':
                if series_['suffix'] == 'phasediff':
                    bids.printlog(
                        'Adding EchoTime1 and EchoTime2 to: ' + jsonfile,
                        logfile)
                    with open(jsonfile, 'r') as json_fid:
                        data = json.load(json_fid)
                    data['EchoTime1'] = TE[0]
                    data['EchoTime2'] = TE[1]
                    with open(jsonfile, 'w') as json_fid:
                        json.dump(data, json_fid, indent=4)
                    if TE[0] > TE[1]:
                        bids.printlog(
                            'WARNING: EchoTime1 > EchoTime2 in: ' + jsonfile,
                            logfile)

    # Search for the IntendedFor images and add them to the json-files. This has been postponed untill all modalities have been processed (i.e. so that all target images are indeed on disk)
    if bidsmap['DICOM']['fmap'] is not None:
        for fieldmap in bidsmap['DICOM']['fmap']:
            if 'IntendedFor' in fieldmap and fieldmap['IntendedFor']:
                jsonfile = os.path.join(
                    bidsses, 'fmap',
                    bids.get_bidsname(subid, sesid, 'fmap', fieldmap, '1') +
                    '.json'
                )  # TODO: Assumes that there is only 1 fieldmap acquired for each bidsmap entry / series
                if not os.path.isfile(jsonfile):
                    continue
                intendedfor = fieldmap['IntendedFor']
                if intendedfor.startswith('<<') and intendedfor.endswith('>>'):
                    intendedfor = intendedfor[2:-2].split('><')
                else:
                    intendedfor = [intendedfor]
                with open(jsonfile, 'r') as json_fid:
                    data = json.load(json_fid)
                niifiles = [
                    niifile.split(os.sep + subid + os.sep, 1)[1]
                    for niifile in sorted(
                        glob.glob(
                            os.path.join(
                                bidsses, '**' + os.sep + '*' +
                                '*'.join(intendedfor) + '*.nii*')))
                ]  # Use a relative path
                data['IntendedFor'] = niifiles
                bids.printlog('Adding IntendedFor to: ' + jsonfile, logfile)
                with open(jsonfile, 'w') as json_fid:
                    json.dump(data, json_fid, indent=4)

                # Catch magnitude2 files produced by dcm2niix
                if jsonfile.endswith('magnitude1.json'):
                    jsonfile2 = jsonfile.rsplit('1.json', 1)[0] + '2.json'
                    if os.path.isfile(jsonfile2):
                        with open(jsonfile2, 'r') as json_fid:
                            data = json.load(json_fid)
                        data['IntendedFor'] = niifiles
                        bids.printlog('Adding IntendedFor to: ' + jsonfile2,
                                      logfile)
                        with open(jsonfile2, 'w') as json_fid:
                            json.dump(data, json_fid, indent=4)

    # Collect personal data from the DICOM header
    dicomfile = bids.get_dicomfile(series)
    personals['participant_id'] = subid
    if sesid:
        personals[
            'session_id'] = sesid  # TODO: Check if this can be in the participants.tsv file according to BIDS
    personals['age'] = bids.get_dicomfield('PatientAge', dicomfile)
    personals['sex'] = bids.get_dicomfield('PatientSex', dicomfile)
    personals['size'] = bids.get_dicomfield('PatientSize', dicomfile)
    personals['weight'] = bids.get_dicomfield('PatientWeight', dicomfile)
def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> None:
    """
    This wrapper funtion around spec2nii converts the MRS data in the session folder and saves it in the bidsfolder.
    Each saved datafile should be accompanied with a json sidecar file. The bidsmap options for this plugin can be found in:

    bidsmap_new['Options']['plugins']['spec2nii2bids']

    :param session:     The full-path name of the subject/session raw data source folder
    :param bidsmap:     The full mapping heuristics from the bidsmap YAML-file
    :param bidsses:     The full-path name of the BIDS output `sub-/ses-` folder
    :return:            Nothing
    """

    # Get the subject identifiers and the BIDS root folder from the bidsses folder
    if bidsses.name.startswith('ses-'):
        bidsfolder = bidsses.parent.parent
        subid = bidsses.parent.name
        sesid = bidsses.name
    else:
        bidsfolder = bidsses.parent
        subid = bidsses.name
        sesid = ''

    # Get started and see what dataformat we have
    options = bidsmap['Options']['plugins']['spec2nii2bids']
    datasource = bids.get_datasource(session, {'spec2nii2bids': options})
    dataformat = datasource.dataformat
    sourcefiles = [file for file in session.rglob('*') if is_sourcefile(file)]
    if not sourcefiles:
        LOGGER.info(f"No {__name__} sourcedata found in: {session}")
        return

    # Read or create a scans_table and tsv-file
    scans_tsv = bidsses / f"{subid}{bids.add_prefix('_',sesid)}_scans.tsv"
    if scans_tsv.is_file():
        scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
    else:
        scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
        scans_table.index.name = 'filename'

    # Loop over all MRS source data files and convert them to BIDS
    for sourcefile in sourcefiles:

        # Get a data source, a matching run from the bidsmap
        datasource = bids.DataSource(sourcefile, {'spec2nii2bids': options})
        run, index = bids.get_matching_run(datasource, bidsmap, runtime=True)

        # Check if we should ignore this run
        if datasource.datatype in bidsmap['Options']['bidscoin'][
                'ignoretypes']:
            LOGGER.info(f"Leaving out: {sourcefile}")
            continue

        # Check that we know this run
        if index is None:
            LOGGER.error(
                f"Skipping unknown '{datasource.datatype}' run: {sourcefile}\n-> Re-run the bidsmapper and delete the MRS output data in {bidsses} to solve this warning"
            )
            continue

        LOGGER.info(f"Processing: {sourcefile}")

        # Create the BIDS session/datatype output folder
        outfolder = bidsses / datasource.datatype
        outfolder.mkdir(parents=True, exist_ok=True)

        # Compose the BIDS filename using the matched run
        bidsname = bids.get_bidsname(subid, sesid, run, runtime=True)
        runindex = run['bids'].get('run', '')
        if runindex.startswith('<<') and runindex.endswith('>>'):
            bidsname = bids.increment_runindex(outfolder, bidsname)
        jsonfile = (outfolder / bidsname).with_suffix('.json')

        # Check if file already exists (-> e.g. when a static runindex is used)
        if jsonfile.is_file():
            LOGGER.warning(
                f"{outfolder/bidsname}.* already exists and will be deleted -- check your results carefully!"
            )
            for ext in ('.nii.gz', '.nii', '.json', '.bval', '.bvec',
                        '.tsv.gz'):
                (outfolder / bidsname).with_suffix(ext).unlink(missing_ok=True)

        # Run spec2nii to convert the source-files in the run folder to nifti's in the BIDS-folder
        arg = ''
        args = options.get('args', OPTIONS['args'])
        if args is None:
            args = ''
        if dataformat == 'SPAR':
            dformat = 'philips'
            arg = f'"{sourcefile.with_suffix(".SDAT")}"'
        elif dataformat == 'Twix':
            dformat = 'twix'
            arg = '-e image'
        elif dataformat == 'Pfile':
            dformat = 'ge'
        else:
            LOGGER.exception(f"Unsupported dataformat: {dataformat}")
        command = options.get("command", "spec2nii")
        if not bidscoin.run_command(
                f'{command} {dformat} -j -f "{bidsname}" -o "{outfolder}" {args} {arg} "{sourcefile}"'
        ):
            if not list(outfolder.glob(f"{bidsname}.nii*")): continue

        # Load and adapt the newly produced json sidecar-file (NB: assumes every nifti-file comes with a json-file)
        with jsonfile.open('r') as json_fid:
            jsondata = json.load(json_fid)

        # Copy over the source meta-data
        metadata = bids.copymetadata(sourcefile, outfolder / bidsname,
                                     options.get('meta', []))
        for metakey, metaval in metadata.items():
            if jsondata.get(metakey) == metaval:
                LOGGER.warning(
                    f"Replacing {metakey} values in {jsonfile}: {jsondata[metakey]} -> {metaval}"
                )
            jsondata[metakey] = metaval

        # Add all the meta data to the json-file
        for metakey, metaval in run['meta'].items():
            metaval = datasource.dynamicvalue(metaval,
                                              cleanup=False,
                                              runtime=True)
            try:
                metaval = ast.literal_eval(str(metaval))
            except (ValueError, SyntaxError):
                pass
            LOGGER.info(f"Adding '{metakey}: {metaval}' to: {jsonfile}")
            if not metaval:
                metaval = None
            jsondata[metakey] = metaval

        # Save the meta data to disk
        with jsonfile.open('w') as json_fid:
            json.dump(jsondata, json_fid, indent=4)

        # Parse the acquisition time from the source header or else from the json file (NB: assuming the source file represents the first acquisition)
        if datasource.datatype not in bidsmap['Options']['bidscoin'][
                'bidsignore'] and not run['bids'][
                    'suffix'] in bids.get_derivatives(datasource.datatype):
            acq_time = ''
            if dataformat == 'SPAR':
                acq_time = datasource.attributes('scan_date')
            elif dataformat == 'Twix':
                acq_time = f"{datasource.attributes('AcquisitionDate')}T{datasource.attributes('AcquisitionTime')}"
            elif dataformat == 'Pfile':
                acq_time = f"{datasource.attributes('rhr_rh_scan_date')}T{datasource.attributes('rhr_rh_scan_time')}"
            if not acq_time or acq_time == 'T':
                acq_time = f"1925-01-01T{jsondata.get('AcquisitionTime','')}"
            try:
                acq_time = dateutil.parser.parse(acq_time)
                if options.get('anon', OPTIONS['anon']) in ('y', 'yes'):
                    acq_time = acq_time.replace(
                        year=1925, month=1,
                        day=1)  # Privacy protection (see BIDS specification)
                acq_time = acq_time.isoformat()
            except Exception as jsonerror:
                LOGGER.warning(
                    f"Could not parse the acquisition time from: {sourcefile}\n{jsonerror}"
                )
                acq_time = 'n/a'
            scans_table.loc[jsonfile.with_suffix('.nii.gz').
                            relative_to(bidsses).as_posix(),
                            'acq_time'] = acq_time

    # Write the scans_table to disk
    LOGGER.info(f"Writing acquisition time data to: {scans_tsv}")
    scans_table.sort_values(by=['acq_time', 'filename'], inplace=True)
    scans_table.replace('', 'n/a').to_csv(scans_tsv,
                                          sep='\t',
                                          encoding='utf-8',
                                          na_rep='n/a')

    # Collect personal data from a source header
    personals = {}
    if sesid and 'session_id' not in personals:
        personals['session_id'] = sesid
    age = ''
    if sesid and 'session_id' not in personals:
        personals['session_id'] = sesid
    if dataformat == 'Twix':
        personals['sex'] = datasource.attributes('PatientSex')
        personals['size'] = datasource.attributes('PatientSize')
        personals['weight'] = datasource.attributes('PatientWeight')
        age = datasource.attributes(
            'PatientAge'
        )  # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
    elif dataformat == 'Pfile':
        sex = datasource.attributes('rhe_patsex')
        if sex == '0': personals['sex'] = 'O'
        elif sex == '1': personals['sex'] = 'M'
        elif sex == '2': personals['sex'] = 'F'
        age = dateutil.parser.parse(
            datasource.attributes('rhr_rh_scan_date')) - dateutil.parser.parse(
                datasource.attributes('rhe_dateofbirth'))
        age = str(age.days) + 'D'
    if age.endswith('D'): age = float(age.rstrip('D')) / 365.2524
    elif age.endswith('W'): age = float(age.rstrip('W')) / 52.1775
    elif age.endswith('M'): age = float(age.rstrip('M')) / 12
    elif age.endswith('Y'): age = float(age.rstrip('Y'))
    if age and options.get('anon', OPTIONS['anon']) in ('y', 'yes'):
        age = int(float(age))
    personals['age'] = str(age)

    # Store the collected personals in the participants_table
    participants_tsv = bidsfolder / 'participants.tsv'
    if participants_tsv.is_file():
        participants_table = pd.read_csv(participants_tsv, sep='\t', dtype=str)
        participants_table.set_index(['participant_id'],
                                     verify_integrity=True,
                                     inplace=True)
    else:
        participants_table = pd.DataFrame()
        participants_table.index.name = 'participant_id'
    if subid in participants_table.index and 'session_id' in participants_table.keys(
    ) and participants_table.loc[subid, 'session_id']:
        return  # Only take data from the first session -> BIDS specification
    for key in personals:  # TODO: Check that only values that are consistent over sessions go in the participants.tsv file, otherwise put them in a sessions.tsv file
        if key not in participants_table or participants_table[key].isnull(
        ).get(subid, True) or participants_table[key].get(subid) == 'n/a':
            participants_table.loc[subid, key] = personals[key]

    # Write the collected data to the participants tsv-file
    LOGGER.info(f"Writing {subid} subject data to: {participants_tsv}")
    participants_table.replace('', 'n/a').to_csv(participants_tsv,
                                                 sep='\t',
                                                 encoding='utf-8',
                                                 na_rep='n/a')
def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> None:
    """
    The bidscoiner plugin to convert the session Nibabel source-files into BIDS-valid nifti-files in the
    corresponding bids session-folder

    :param session:     The full-path name of the subject/session source folder
    :param bidsmap:     The full mapping heuristics from the bidsmap YAML-file
    :param bidsses:     The full-path name of the BIDS output `sub-/ses-` folder
    :return:            Nothing
    """

    # Get the subject identifiers and the BIDS root folder from the bidsses folder
    if bidsses.name.startswith('ses-'):
        bidsfolder = bidsses.parent.parent
        subid = bidsses.parent.name
        sesid = bidsses.name
    else:
        bidsfolder = bidsses.parent
        subid = bidsses.name
        sesid = ''

    # Get started
    options = bidsmap['Options']['plugins']['nibabel2bids']
    ext = options.get('ext', OPTIONS['ext'])
    meta = options.get('meta', [])
    sourcefiles = [file for file in session.rglob('*') if is_sourcefile(file)]
    if not sourcefiles:
        LOGGER.info(f"No {__name__} sourcedata found in: {session}")
        return

    # Read or create a scans_table and tsv-file
    scans_tsv = bidsses / f"{subid}{bids.add_prefix('_', sesid)}_scans.tsv"
    if scans_tsv.is_file():
        scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
    else:
        scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
        scans_table.index.name = 'filename'

    # Collect the different Nibabel source files for all files in the session
    for sourcefile in sourcefiles:

        datasource = bids.DataSource(sourcefile, {'nibabel2bids': options})
        run, match = bids.get_matching_run(datasource, bidsmap, runtime=True)

        # Check if we should ignore this run
        if datasource.datatype in bidsmap['Options']['bidscoin'][
                'ignoretypes']:
            LOGGER.info(f"Leaving out: {sourcefile}")
            continue

        # Check if we already know this run
        if not match:
            LOGGER.error(
                f"Skipping unknown '{datasource.datatype}' run: {sourcefile}\n-> Re-run the bidsmapper and delete {bidsses} to solve this warning"
            )
            continue

        LOGGER.info(f"Processing: {sourcefile}")

        # Create the BIDS session/datatype output folder
        outfolder = bidsses / datasource.datatype
        outfolder.mkdir(parents=True, exist_ok=True)

        # Compose the BIDS filename using the matched run
        bidsname = bids.get_bidsname(subid, sesid, run, runtime=True)
        runindex = run['bids'].get('run', '')
        if runindex.startswith('<<') and runindex.endswith('>>'):
            bidsname = bids.increment_runindex(outfolder, bidsname)
        bidsfile = (outfolder / bidsname).with_suffix(ext)

        # Check if file already exists (-> e.g. when a static runindex is used)
        if bidsfile.is_file():
            LOGGER.warning(
                f"{bidsfile}.* already exists and will be deleted -- check your results carefully!"
            )
            bidsfile.with_suffix('').with_suffix(ext).unlink()

        # Save the sourcefile as a BIDS nifti file
        nib.save(nib.load(sourcefile), bidsfile)

        # Copy over the source meta-data
        jsonfile = bidsfile.with_suffix('').with_suffix('.json')
        jsondata = bids.copymetadata(sourcefile, bidsfile, meta)

        # Add all the meta data to the meta-data. NB: the dynamic `IntendedFor` value is handled separately later
        for metakey, metaval in run['meta'].items():
            if metakey != 'IntendedFor':
                metaval = datasource.dynamicvalue(metaval,
                                                  cleanup=False,
                                                  runtime=True)
                try:
                    metaval = ast.literal_eval(str(metaval))
                except (ValueError, SyntaxError):
                    pass
                LOGGER.info(f"Adding '{metakey}: {metaval}' to: {jsonfile}")
            if not metaval:
                metaval = None
            jsondata[metakey] = metaval

        # Remove unused (but added from the template) B0FieldIdentifiers/Sources
        if not jsondata.get('B0FieldSource'):
            jsondata.pop('B0FieldSource', None)
        if not jsondata.get('B0FieldIdentifier'):
            jsondata.pop('B0FieldIdentifier', None)

        # Save the meta-data to the json sidecar-file
        with jsonfile.open('w') as json_fid:
            json.dump(jsondata, json_fid, indent=4)

        # Add an entry to the scans_table (we typically don't have useful data to put there)
        acq_time = dateutil.parser.parse(
            f"1925-01-01T{jsondata.get('AcquisitionTime', '')}")
        scans_table.loc[bidsfile.relative_to(bidsses).as_posix(),
                        'acq_time'] = acq_time.isoformat()

    # Write the scans_table to disk
    LOGGER.info(f"Writing data to: {scans_tsv}")
    scans_table.replace('', 'n/a').to_csv(scans_tsv,
                                          sep='\t',
                                          encoding='utf-8',
                                          na_rep='n/a')

    # Add an (empty) entry to the participants_table (we don't have useful data to put there)
    participants_tsv = bidsfolder / 'participants.tsv'
    if participants_tsv.is_file():
        participants_table = pd.read_csv(participants_tsv, sep='\t', dtype=str)
        participants_table.set_index(['participant_id'],
                                     verify_integrity=True,
                                     inplace=True)
    else:
        participants_table = pd.DataFrame()
        participants_table.index.name = 'participant_id'
    if subid in participants_table.index and 'session_id' in participants_table.keys(
    ) and participants_table.loc[subid, 'session_id']:
        return  # Only take data from the first session -> BIDS specification
    participants_table.loc[subid, 'session_id'] = sesid if sesid else None

    # Write the collected data to the participants tsv-file
    LOGGER.info(f"Writing {subid} subject data to: {participants_tsv}")
    participants_table.replace('', 'n/a').to_csv(participants_tsv,
                                                 sep='\t',
                                                 encoding='utf-8',
                                                 na_rep='n/a')