How to use niworkflows - 10 common examples

wf = init_single_subject_wf(
    anat_only=False,
    debug=False,
    force_syn=True,
    freesurfer=True,
    hires=True,
    ignore=[],
    layout=BIDSLayout('.'),
    longitudinal=False,
    low_mem=False,
    name='single_subject_wf',
    omp_nthreads=1,
    output_dir='.',
    reportlets_dir='.',
    skull_strip_fixed_seed=False,
    skull_strip_template=Reference('OASIS30ANTs'),
    spaces=SpatialReferences(
        spaces=['MNI152Lin',
                ('fsaverage', {'density': '10k'}),
                'T1w',
                'fsnative'],
        checkpoint=True),
    subject_id='test',
    use_syn=True,
)

"""

    dataset_folder = dataset_name if not dataset_prefix \
        else '%s%s' % (dataset_prefix, dataset_name)
    default_paths = default_paths or ''
    paths = [p / dataset_folder for p in _get_data_path(data_dir)]
    all_paths = [Path(p) / dataset_folder
                 for p in default_paths.split(os.pathsep)] + paths

    # Check if the dataset folder exists somewhere and is not empty
    for path in all_paths:
        if path.is_dir() and list(path.iterdir()):
            if verbose > 1:
                NIWORKFLOWS_LOG.info(
                    'Dataset "%s" already cached in %s', dataset_name, path)
            return path, True

    for path in paths:
        if verbose > 0:
            NIWORKFLOWS_LOG.info(
                'Dataset "%s" not cached, downloading to %s', dataset_name, path)
        path.mkdir(parents=True, exist_ok=True)
        return path, False

default_paths = default_paths or ''
    paths = [p / dataset_folder for p in _get_data_path(data_dir)]
    all_paths = [Path(p) / dataset_folder
                 for p in default_paths.split(os.pathsep)] + paths

    # Check if the dataset folder exists somewhere and is not empty
    for path in all_paths:
        if path.is_dir() and list(path.iterdir()):
            if verbose > 1:
                NIWORKFLOWS_LOG.info(
                    'Dataset "%s" already cached in %s', dataset_name, path)
            return path, True

    for path in paths:
        if verbose > 0:
            NIWORKFLOWS_LOG.info(
                'Dataset "%s" not cached, downloading to %s', dataset_name, path)
        path.mkdir(parents=True, exist_ok=True)
        return path, False

def init_spaces(checkpoint=True):
    """Initialize the :attr:`~workflow.spaces` setting."""
    from niworkflows.utils.spaces import Reference, SpatialReferences

    spaces = execution.output_spaces or SpatialReferences()
    if not isinstance(spaces, SpatialReferences):
        spaces = SpatialReferences(
            [ref for s in spaces.split(" ") for ref in Reference.from_string(s)]
        )

    if checkpoint and not spaces.is_cached():
        spaces.checkpoint()

    # Make the SpatialReferences object available
    workflow.spaces = spaces

def parse_args(args=None, namespace=None):
    """Parse args and run further checks on the command line."""
    import logging
    from niworkflows.utils.spaces import Reference, SpatialReferences

    parser = _build_parser()
    opts = parser.parse_args(args, namespace)
    config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
    config.from_dict(vars(opts))
    config.loggers.init()

    # Initialize --output-spaces if not defined
    if config.execution.output_spaces is None:
        config.execution.output_spaces = SpatialReferences([Reference("run")])

    # Retrieve logging level
    build_log = config.loggers.cli

    if config.execution.fs_license_file is None:
        raise RuntimeError(
            """\
ERROR: a valid license file is required for FreeSurfer to run. dMRIPrep looked for an existing \
license file at several paths, in this order: 1) command line argument ``--fs-license-file``; \
2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it \
(for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html"""
        )
    os.environ["FS_LICENSE"] = str(config.execution.fs_license_file)

    # Load base plugin_settings from file if --use-plugin
    if opts.use_plugin is not None:

current_palette = sns.color_palette()
    in_nii = nb.load(in_file)
    if not tr:
        tr = in_nii.header.get_zooms()[3]
        units = in_nii.header.get_xyzt_units()
        if units:
            if units[-1] == "msec":
                tr = tr / 1000.0
            elif units[-1] == "usec":
                tr = tr / 1000000.0
            elif units[-1] != "sec":
                NIWORKFLOWS_LOG.warning(
                    "Unknown repetition time units " "specified - assuming seconds"
                )
        else:
            NIWORKFLOWS_LOG.warning(
                "Repetition time units not specified - assuming seconds"
            )

    from nilearn.input_data import NiftiMasker
    from nilearn.plotting import cm

    if not report_mask:
        nifti_masker = NiftiMasker(mask_strategy="epi")
        nifti_masker.fit(index_img(in_nii, range(2)))
        mask_img = nifti_masker.mask_img_
    else:
        mask_img = nb.load(report_mask)

    mask_sl = []
    for j in range(3):
        mask_sl.append(transform_to_2d(mask_img.get_fdata(), j))

if not keywords:
        raise NotThisMethod("no keywords at all, weird")
    date = keywords.get("date")
    if date is not None:
        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
        # -like" string, which we must then edit to make compliant), because
        # it's been around since git-1.5.3, and it's too difficult to
        # discover which version we're using, or to work around using an
        # older one.
        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
    refnames = keywords["refnames"].strip()
    if refnames.startswith("$Format"):
        if verbose:
            print("keywords are unexpanded, not using")
        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
    refs = set([r.strip() for r in refnames.strip("()").split(",")])
    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
    TAG = "tag: "
    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
    if not tags:
        # Either we're using git < 1.8.3, or there really are no tags. We use
        # a heuristic: assume all version tags have a digit. The old git %d
        # expansion behaves like git log --decorate=short and strips out the
        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
        # between branches and tags. By ignoring refnames without digits, we
        # filter out many common branch names like "release" and
        # "stabilization", as well as "HEAD" and "master".
        tags = set([r for r in refs if re.search(r'\d', r)])
        if verbose:
            print("discarding '%s', no digits" % ",".join(refs - tags))

def git_versions_from_keywords(keywords, tag_prefix, verbose):
    """Get version information from git keywords."""
    if not keywords:
        raise NotThisMethod("no keywords at all, weird")
    date = keywords.get("date")
    if date is not None:
        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
        # -like" string, which we must then edit to make compliant), because
        # it's been around since git-1.5.3, and it's too difficult to
        # discover which version we're using, or to work around using an
        # older one.
        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
    refnames = keywords["refnames"].strip()
    if refnames.startswith("$Format"):
        if verbose:
            print("keywords are unexpanded, not using")
        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
    refs = set([r.strip() for r in refnames.strip("()").split(",")])
    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of

from matplotlib.gridspec import GridSpec
    import os

    sns.set_style("white")
    current_palette = sns.color_palette()
    in_nii = nb.load(in_file)
    if not tr:
        tr = in_nii.header.get_zooms()[3]
        units = in_nii.header.get_xyzt_units()
        if units:
            if units[-1] == "msec":
                tr = tr / 1000.0
            elif units[-1] == "usec":
                tr = tr / 1000000.0
            elif units[-1] != "sec":
                NIWORKFLOWS_LOG.warning(
                    "Unknown repetition time units " "specified - assuming seconds"
                )
        else:
            NIWORKFLOWS_LOG.warning(
                "Repetition time units not specified - assuming seconds"
            )

    from nilearn.input_data import NiftiMasker
    from nilearn.plotting import cm

    if not report_mask:
        nifti_masker = NiftiMasker(mask_strategy="epi")
        nifti_masker.fit(index_img(in_nii, range(2)))
        mask_img = nifti_masker.mask_img_
    else:
        mask_img = nb.load(report_mask)

# option was called without any output spaces, so user does not want outputs
            spaces.checkpoint()
        for val in values:
            val = val.rstrip(":")
            if (
                val not in NONSTANDARD_REFERENCES
                and not val.split(":")[0].startswith("fs")
                and ":res-" not in val
                and ":resolution-" not in val
            ):
                # by default, explicitly set volumetric resolution to native
                # relevant discussions:
                # https://github.com/nipreps/niworkflows/pull/457#discussion_r375510227
                # https://github.com/nipreps/niworkflows/pull/494
                val = ":".join((val, "res-native"))
            for sp in Reference.from_string(val):
                spaces.add(sp)
        setattr(namespace, self.dest, spaces)