Python utils.get_subjects_dir函数代码示例

def test_datasets_basic(tmpdir):
    """Test simple dataset functions."""
    # XXX 'hf_sef' and 'misc' do not conform to these standards
    for dname in ('sample', 'somato', 'spm_face', 'testing', 'opm',
                  'bst_raw', 'bst_auditory', 'bst_resting', 'multimodal',
                  'bst_phantom_ctf', 'bst_phantom_elekta', 'kiloword',
                  'mtrf', 'phantom_4dbti',
                  'visual_92_categories', 'fieldtrip_cmc'):
        if dname.startswith('bst'):
            dataset = getattr(datasets.brainstorm, dname)
            check_name = 'brainstorm.%s' % (dname,)
        else:
            dataset = getattr(datasets, dname)
            check_name = dname
        if dataset.data_path(download=False) != '':
            assert isinstance(dataset.get_version(), str)
            assert datasets.utils.has_dataset(check_name)
        else:
            assert dataset.get_version() is None
            assert not datasets.utils.has_dataset(check_name)
        print('%s: %s' % (dname, datasets.utils.has_dataset(check_name)))
    tempdir = str(tmpdir)
    # don't let it read from the config file to get the directory,
    # force it to look for the default
    with modified_env(**{'_MNE_FAKE_HOME_DIR': tempdir, 'SUBJECTS_DIR': None}):
        assert (datasets.utils._get_path(None, 'foo', 'bar') ==
                op.join(tempdir, 'mne_data'))
        assert get_subjects_dir(None) is None
        _set_montage_coreg_path()
        sd = get_subjects_dir()
        assert sd.endswith('MNE-fsaverage-data')

def dissolve_label(labels, source, targets, subjects_dir=None,
                   hemi='both'):
    """
    Assign every point from source to the target that is closest to it.

    Parameters
    ----------
    labels : list
        List of labels (as returned by mne.read_annot).
    source : str
        Name of the source label (without hemi affix).
    targets : list of str
        List of target label names (without hemi affix).
    subjects_dir : str
        subjects_dir.
    hemi : 'both', 'lh', 'rh'
        Hemisphere(s) for which to dissolve the label.

    Notes
    -----
    Modifies ``labels`` in-place, returns None.
    """
    subjects_dir = get_subjects_dir(subjects_dir)
    subject = labels[0].subject
    if hemi == 'both':
        hemis = ('lh', 'rh')
    elif hemi == 'lh' or hemi == 'rh':
        hemis = (hemi,)
    else:
        raise ValueError("hemi=%r" % hemi)

    idx = {l.name: i for i, l in enumerate(labels)}

    rm = set()
    for hemi in hemis:
        fpath = os.path.join(subjects_dir, subject, 'surf', hemi + '.inflated')
        points, _ = mne.read_surface(fpath)

        src_name = '-'.join((source, hemi))
        src_idx = idx[src_name]
        rm.add(src_idx)
        src_label = labels[src_idx]
        tgt_names = ['-'.join((name, hemi)) for name in targets]
        tgt_idxs = [idx[name] for name in tgt_names]
        tgt_labels = [labels[i] for i in tgt_idxs]
        tgt_points = [points[label.vertices] for label in tgt_labels]

        vert_by_tgt = {i: [] for i in xrange(len(targets))}
        for src_vert in src_label.vertices:
            point = points[src_vert:src_vert + 1]
            dist = [cdist(point, pts).min() for pts in tgt_points]
            tgt = np.argmin(dist)
            vert_by_tgt[tgt].append(src_vert)

        for i, label in enumerate(tgt_labels):
            new_vertices = vert_by_tgt[i]
            label.vertices = np.union1d(label.vertices, new_vertices)

    for i in sorted(rm, reverse=True):
        del labels[i]

def fix_annot_names(subject, parc, clean_subject=None, clean_parc=None, hemi="both", subjects_dir=None):
    """Fix for Freesurfer's mri_surf2surf corrupting label names in annot files

    Notes
    -----
    Requires nibabel > 1.3.0 for annot file I/O
    """
    # process args
    subjects_dir = get_subjects_dir(subjects_dir)
    if clean_subject is None:
        clean_subject = subject
    if clean_parc is None:
        clean_parc = parc

    fpaths, hemis = _get_annot_fname(None, subject, hemi, parc, subjects_dir)
    clean_fpaths, _ = _get_annot_fname(None, clean_subject, hemi, clean_parc, subjects_dir)

    for fpath, clean_fpath, hemi in izip(fpaths, clean_fpaths, hemis):
        labels, ctab, names = read_annot(fpath)
        _, _, clean_names = read_annot(clean_fpath)
        if all(n == nc for n, nc in izip(names, clean_names)):
            continue

        if len(clean_names) != len(names):
            err = "Different names in %s annot files: %s vs. " "%s" % (hemi, str(names), str(clean_names))
            raise ValueError(err)

        for clean_name, name in izip(clean_names, names):
            if not name.startswith(clean_name):
                err = "%s does not start with %s" % (str(name), clean_name)
                raise ValueError(err)

        write_annot(fpath, labels, ctab, clean_names)

def freeview_bem_surfaces(subject, subjects_dir, method):
    """View 3-Layers BEM model with Freeview.

    Parameters
    ----------
    subject : string
        Subject name
    subjects_dir : string
        Directory containing subjects data (Freesurfer SUBJECTS_DIR)
    method : string
        Can be 'flash' or 'watershed'.
    """
    subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)

    if subject is None:
        raise ValueError("subject argument is None.")

    subject_dir = op.join(subjects_dir, subject)

    if not op.isdir(subject_dir):
        raise ValueError("Wrong path: '{}'. Check subjects-dir or"
                         "subject argument.".format(subject_dir))

    env = os.environ.copy()
    env['SUBJECT'] = subject
    env['SUBJECTS_DIR'] = subjects_dir

    if 'FREESURFER_HOME' not in env:
        raise RuntimeError('The FreeSurfer environment needs to be set up.')

    mri_dir = op.join(subject_dir, 'mri')
    bem_dir = op.join(subject_dir, 'bem')
    mri = op.join(mri_dir, 'T1.mgz')

    if method == 'watershed':
        bem_dir = op.join(bem_dir, 'watershed')
        outer_skin = op.join(bem_dir, '%s_outer_skin_surface' % subject)
        outer_skull = op.join(bem_dir, '%s_outer_skull_surface' % subject)
        inner_skull = op.join(bem_dir, '%s_inner_skull_surface' % subject)
    else:
        if method == 'flash':
            bem_dir = op.join(bem_dir, 'flash')
        outer_skin = op.join(bem_dir, 'outer_skin.surf')
        outer_skull = op.join(bem_dir, 'outer_skull.surf')
        inner_skull = op.join(bem_dir, 'inner_skull.surf')

    # put together the command
    cmd = ['freeview']
    cmd += ["--volume", mri]
    cmd += ["--surface", "%s:color=red:edgecolor=red" % inner_skull]
    cmd += ["--surface", "%s:color=yellow:edgecolor=yellow" % outer_skull]
    cmd += ["--surface",
            "%s:color=255,170,127:edgecolor=255,170,127" % outer_skin]

    run_subprocess(cmd, env=env, stdout=sys.stdout)
    print("[done]")

def _fs_subjects(arg, exclude=[], subjects_dir=None):
    if '*' in arg:
        subjects_dir = get_subjects_dir(subjects_dir)
        subjects = fnmatch.filter(os.listdir(subjects_dir), arg)
        subjects = filter(os.path.isdir, subjects)
        for subject in exclude:
            if subject in subjects:
                subjects.remove(subject)
    else:
        subjects = [arg]
    return subjects

def plot_stc_time_point(stc, subject, limits=[5, 10, 15], time_index=0,
                        surf='inflated', measure='dSPM', subjects_dir=None):
    """Plot a time instant from a SourceEstimate using matplotlib

    The same could be done with mayavi using proper 3D.

    Parameters
    ----------
    stc : instance of SourceEstimate
        The SourceEstimate to plot.
    subject : string
        The subject name (only needed if surf is a string).
    time_index : int
        Time index to plot.
    surf : str, or instance of surfaces
        Surface to use (e.g., 'inflated' or 'white'), or pre-loaded surfaces.
    measure : str
        The label for the colorbar. None turns the colorbar off.
    subjects_dir : str, or None
        Path to the SUBJECTS_DIR. If None, the path is obtained by using
        the environment variable SUBJECTS_DIR.
    """
    subjects_dir = get_subjects_dir(subjects_dir)
    pl.figure(facecolor='k', figsize=(8, 5))
    hemis = ['lh', 'rh']
    if isinstance(surf, str):
        surf = [read_surface(op.join(subjects_dir, subject, 'surf',
                                     '%s.%s' % (h, surf))) for h in hemis]
    my_cmap = mne_analyze_colormap(limits)
    for hi, h in enumerate(hemis):
        coords = surf[hi][0][stc.vertno[hi]]
        if hi == 0:
            vals = stc_all_cluster_vis.lh_data[:, time_index]
        else:
            vals = stc_all_cluster_vis.rh_data[:, time_index]
        ax = pl.subplot(1, 2, 1 - hi, axis_bgcolor='none')
        pl.tick_params(labelbottom='off', labelleft='off')
        flipper = -1 if hi == 1 else 1
        sc = ax.scatter(flipper * coords[:, 1], coords[:, 2], c=vals,
                        vmin=-limits[2], vmax=limits[2], cmap=my_cmap,
                        edgecolors='none', s=5)
        ax.set_aspect('equal')
        pl.axis('off')
    try:
        pl.tight_layout(0)
    except:
        pass
    if measure is not None:
        cax = pl.axes([0.85, 0.15, 0.025, 0.15], axisbg='k')
        cb = pl.colorbar(sc, cax, ticks=[-limits[2], 0, limits[2]])
        cb.set_label(measure, color='w')
    pl.setp(pl.getp(cb.ax, 'yticklabels'), color='w')
    pl.draw()
    pl.show()

def mri_annotation2label(subject='*', annot='aparc',
                         dest=os.path.join("{sdir}", "label", "{annot}"),
                         hemi='*', subjects_dir=None):
    """
    Calls ``mri_annotation2label`` (`freesurfer wiki
    <http://surfer.nmr.mgh.harvard.edu/fswiki/mri_annotation2label>`_)

    mri_dir : str(path)
        Path containing mri subject directories (freesurfer's ``SUBJECTS_DIR``).

    subject : str
        Name of the subject ('*' uses fnmatch to find folders in ``mri_dir``).

    annot : str
        Name of the annotation file (e.g., ``'aparc'``, ...).

    dest : str(path)
        Destination for the label files. {sdir}" and "{annot}" are filled in
        appropriately.

    hemi : 'lh' | 'rh' | '*'
        Hemisphere to process; '*' proceses both.

    """
    hemis = _fs_hemis(hemi)
    subjects = _fs_subjects(subject)
    subjects_dir = get_subjects_dir(subjects_dir)

    # progress monitor
    i_max = len(subjects) * len(hemis)
    if len(subjects) > 1:
        prog = ui.progress_monitor(i_max, "mri_annotation2label", "")
    else:
        prog = None

    for subject in subjects:
        sdir = os.path.join(subjects_dir, subject)
        outdir = dest.format(sdir=sdir, annot=annot)

        for hemi in hemis:
            if prog:
                prog.message("Processing: %s - %s" % (subject, hemi))

            cmd = [get_bin("freesurfer", "mri_annotation2label"),
                   '--annotation', annot,
                   '--subject', subject,
                   '--hemi', hemi,
                   '--outdir', outdir,
                   ]

            _run(cmd, cwd=subjects_dir)
            if prog:
                prog.advance()

def run():
    from mne.commands.utils import get_optparser

    parser = get_optparser(__file__)

    subject = os.environ.get('SUBJECT')
    subjects_dir = get_subjects_dir()

    parser.add_option("-s", "--subject", dest="subject",
                      help="Subject name", default=subject)
    parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
                      help="Subjects directory", default=subjects_dir)
    parser.add_option("-m", "--method", dest="method",
                      help=("Method used to generate the BEM model. "
                            "Can be flash or watershed."), metavar="FILE")

    options, args = parser.parse_args()

    subject = options.subject
    subjects_dir = options.subjects_dir
    method = options.method

    freeview_bem_surfaces(subject, subjects_dir, method)

def _run(subjects_dir, subject, force, overwrite, no_decimate, verbose=None):
    this_env = copy.copy(os.environ)
    subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
    this_env['SUBJECTS_DIR'] = subjects_dir
    this_env['SUBJECT'] = subject
    if 'FREESURFER_HOME' not in this_env:
        raise RuntimeError('The FreeSurfer environment needs to be set up '
                           'for this script')
    incomplete = 'warn' if force else 'raise'
    subj_path = op.join(subjects_dir, subject)
    if not op.exists(subj_path):
        raise RuntimeError('%s does not exist. Please check your subject '
                           'directory path.' % subj_path)

    mri = 'T1.mgz' if op.exists(op.join(subj_path, 'mri', 'T1.mgz')) else 'T1'

    logger.info('1. Creating a dense scalp tessellation with mkheadsurf...')

    def check_seghead(surf_path=op.join(subj_path, 'surf')):
        surf = None
        for k in ['lh.seghead', 'lh.smseghead']:
            this_surf = op.join(surf_path, k)
            if op.exists(this_surf):
                surf = this_surf
                break
        return surf

    my_seghead = check_seghead()
    if my_seghead is None:
        run_subprocess(['mkheadsurf', '-subjid', subject, '-srcvol', mri],
                       env=this_env)

    surf = check_seghead()
    if surf is None:
        raise RuntimeError('mkheadsurf did not produce the standard output '
                           'file.')

    bem_dir = op.join(subjects_dir, subject, 'bem')
    if not op.isdir(bem_dir):
        os.mkdir(bem_dir)
    dense_fname = op.join(bem_dir, '%s-head-dense.fif' % subject)
    logger.info('2. Creating %s ...' % dense_fname)
    _check_file(dense_fname, overwrite)
    surf = mne.bem._surfaces_to_bem(
        [surf], [mne.io.constants.FIFF.FIFFV_BEM_SURF_ID_HEAD], [1],
        incomplete=incomplete)[0]
    mne.write_bem_surfaces(dense_fname, surf)
    levels = 'medium', 'sparse'
    tris = [] if no_decimate else [30000, 2500]
    if os.getenv('_MNE_TESTING_SCALP', 'false') == 'true':
        tris = [len(surf['tris'])]  # don't actually decimate
    for ii, (n_tri, level) in enumerate(zip(tris, levels), 3):
        logger.info('%i. Creating %s tessellation...' % (ii, level))
        logger.info('%i.1 Decimating the dense tessellation...' % ii)
        with ETSContext():
            points, tris = mne.decimate_surface(points=surf['rr'],
                                                triangles=surf['tris'],
                                                n_triangles=n_tri)
        dec_fname = dense_fname.replace('dense', level)
        logger.info('%i.2 Creating %s' % (ii, dec_fname))
        _check_file(dec_fname, overwrite)
        dec_surf = mne.bem._surfaces_to_bem(
            [dict(rr=points, tris=tris)],
            [mne.io.constants.FIFF.FIFFV_BEM_SURF_ID_HEAD], [1], rescale=False,
            incomplete=incomplete)
        mne.write_bem_surfaces(dec_fname, dec_surf)

def _stc_to_label(stc, src, smooth, subjects_dir=None):
    """Compute a label from the non-zero sources in an stc object.

    Parameters
    ----------
    stc : SourceEstimate
        The source estimates.
    src : SourceSpaces | str | None
        The source space over which the source estimates are defined.
        If it's a string it should the subject name (e.g. fsaverage).
        Can be None if stc.subject is not None.
    smooth : int
        Number of smoothing iterations.
    subjects_dir : str | None
        Path to SUBJECTS_DIR if it is not set in the environment.

    Returns
    -------
    labels : list of Labels | list of list of Labels
        The generated labels. If connected is False, it returns
        a list of Labels (one per hemisphere). If no Label is available
        in a hemisphere, None is returned. If connected is True,
        it returns for each hemisphere a list of connected labels
        ordered in decreasing order depending of the maximum value in the stc.
        If no Label is available in an hemisphere, an empty list is returned.
    """
    src = stc.subject if src is None else src

    if isinstance(src, string_types):
        subject = src
    else:
        subject = stc.subject

    if isinstance(src, string_types):
        subjects_dir = get_subjects_dir(subjects_dir)
        surf_path_from = op.join(subjects_dir, src, 'surf')
        rr_lh, tris_lh = read_surface(op.join(surf_path_from,
                                      'lh.white'))
        rr_rh, tris_rh = read_surface(op.join(surf_path_from,
                                      'rh.white'))
        rr = [rr_lh, rr_rh]
        tris = [tris_lh, tris_rh]
    else:
        if not isinstance(src, SourceSpaces):
            raise TypeError('src must be a string or a set of source spaces')
        if len(src) != 2:
            raise ValueError('source space should contain the 2 hemispheres')
        rr = [1e3 * src[0]['rr'], 1e3 * src[1]['rr']]
        tris = [src[0]['tris'], src[1]['tris']]

    labels = []
    cnt = 0
    for hemi_idx, (hemi, this_vertno, this_tris, this_rr) in enumerate(
            zip(['lh', 'rh'], stc.vertices, tris, rr)):
        this_data = stc.data[cnt:cnt + len(this_vertno)]
        e = mesh_edges(this_tris)
        e.data[e.data == 2] = 1
        n_vertices = e.shape[0]
        e = e + sparse.eye(n_vertices, n_vertices)

        clusters = [this_vertno[np.any(this_data, axis=1)]]

        cnt += len(this_vertno)

        clusters = [c for c in clusters if len(c) > 0]

        if len(clusters) == 0:
            this_labels = None
        else:
            this_labels = []
            colors = _n_colors(len(clusters))
            for c, color in zip(clusters, colors):
                idx_use = c
                for k in range(smooth):
                    e_use = e[:, idx_use]
                    data1 = e_use * np.ones(len(idx_use))
                    idx_use = np.where(data1)[0]

                label = Label(idx_use, this_rr[idx_use], None, hemi,
                              'Label from stc', subject=subject,
                              color=color)

                this_labels.append(label)

            this_labels = this_labels[0]

        labels.append(this_labels)

    return labels

def labels_from_mni_coords(seeds, extent=30., subject='fsaverage',
                           surface='white', mask=None, subjects_dir=None,
                           parc=None):
    """Create a parcellation from seed coordinates in MNI space

    Parameters
    ----------
    seeds : dict
        Seed coordinates. Keys are label names, including -hemi tags. values
        are seeds (array_like of shape (3,) or (3, n_seeds)).
    extent : scalar
        Extent of the label in millimeters (maximum distance from the seed).
    subject : str
        MRI-subject to use (default 'fsaverage').
    surface : str
        Surface to use (default 'white').
    mask : None | str
        A parcellation used to mask the parcellation under construction.
    subjects_dir : str
        SUBJECTS_DIR.
    parc : None | str
        Name of the parcellation under construction (only used for error
        messages).
    """
    name_re = re.compile("\w+-(lh|rh)$")
    if not all(name.endswith(('lh', 'rh')) for name in seeds):
        err = ("Names need to end in 'lh' or 'rh' so that the proper "
               "hemisphere can be selected")
        raise ValueError(err)

    # load surfaces
    subjects_dir = get_subjects_dir(subjects_dir)
    fpath = os.path.join(subjects_dir, subject, 'surf', '.'.join(('%s', surface)))
    surfs = {hemi: mne.read_surface(fpath % hemi) for hemi in ('lh', 'rh')}

    # prepare seed properties for mne.grow_labels
    vertices = []
    names = []
    hemis = []
    for name, coords_ in seeds.iteritems():
        m = name_re.match(name)
        if not m:
            raise ValueError("Invalid seed name in %r parc: %r. Names must "
                             "conform to the 'xxx-lh' or 'xxx-rh' scheme."
                             % (parc, name))
        coords = np.atleast_2d(coords_)
        if coords.ndim != 2 or coords.shape[1] != 3:
            raise ValueError("Invalid coordinate specification for seed %r in "
                             "parc %r: %r. Seeds need to be specified as "
                             "arrays with shape (3,) or (n_seeds, 3)."
                             % (name, parc, coords_))
        hemi = m.group(1)
        seed_verts = []
        for coord in coords:
            dist = np.sqrt(np.sum((surfs[hemi][0] - coord) ** 2, axis=1))
            seed_verts.append(np.argmin(dist))
        vertices.append(seed_verts)
        names.append(name)
        hemis.append(hemi == 'rh')

    # grow labels
    labels = mne.grow_labels(subject, vertices, extent, hemis, subjects_dir,
                             1, False, names, surface)

    # apply mask
    if mask is not None:
        mlabels = mne.read_labels_from_annot(subject, mask,
                                             subjects_dir=subjects_dir)
        unknown = {l.hemi: l for l in mlabels if l.name.startswith('unknown-')}

        for label in labels:
            rm = unknown[label.hemi]
            if np.any(np.in1d(label.vertices, rm.vertices)):
                label.vertices = np.setdiff1d(label.vertices, rm.vertices, True)

    return labels

def write_labels_to_annot(labels, subject=None, parc=None, overwrite=False,
                          subjects_dir=None, annot_fname=None,
                          colormap='hsv', hemi='both'):
    """Create a FreeSurfer annotation from a list of labels

    FIX: always write both hemispheres

    Parameters
    ----------
    labels : list with instances of mne.Label
        The labels to create a parcellation from.
    subject : str | None
        The subject for which to write the parcellation for.
    parc : str | None
        The parcellation name to use.
    overwrite : bool
        Overwrite files if they already exist.
    subjects_dir : string, or None
        Path to SUBJECTS_DIR if it is not set in the environment.
    annot_fname : str | None
        Filename of the .annot file. If not None, only this file is written
        and 'parc' and 'subject' are ignored.
    colormap : str
        Colormap to use to generate label colors for labels that do not
        have a color specified.
    hemi : 'both' | 'lh' | 'rh'
        The hemisphere(s) for which to write *.annot files (only applies if
        annot_fname is not specified; default is 'both').
    verbose : bool, str, int, or None
        If not None, override default verbose level (see mne.verbose).

    Notes
    -----
    Vertices that are not covered by any of the labels are assigned to a label
    named "unknown".
    """
    subjects_dir = get_subjects_dir(subjects_dir)

    # get the .annot filenames and hemispheres
    annot_fname, hemis = _get_annot_fname(annot_fname, subject, hemi, parc,
                                          subjects_dir)

    if not overwrite:
        for fname in annot_fname:
            if op.exists(fname):
                raise ValueError('File %s exists. Use "overwrite=True" to '
                                 'overwrite it' % fname)

    # prepare container for data to save:
    to_save = []
    # keep track of issues found in the labels
    duplicate_colors = []
    invalid_colors = []
    overlap = []
    no_color = (-1, -1, -1, -1)
    no_color_rgb = (-1, -1, -1)
    for hemi, fname in zip(hemis, annot_fname):
        hemi_labels = [label for label in labels if label.hemi == hemi]
        n_hemi_labels = len(hemi_labels)

        if n_hemi_labels == 0:
            ctab = np.empty((0, 4), dtype=np.int32)
            ctab_rgb = ctab[:, :3]
        else:
            hemi_labels.sort(key=lambda label: label.name)

            # convert colors to 0-255 RGBA tuples
            hemi_colors = [no_color if label.color is None else
                           tuple(int(round(255 * i)) for i in label.color)
                           for label in hemi_labels]
            ctab = np.array(hemi_colors, dtype=np.int32)
            ctab_rgb = ctab[:, :3]

            # make color dict (for annot ID, only R, G and B count)
            labels_by_color = defaultdict(list)
            for label, color in zip(hemi_labels, ctab_rgb):
                labels_by_color[tuple(color)].append(label.name)

            # check label colors
            for color, names in labels_by_color.items():
                if color == no_color_rgb:
                    continue

                if color == (0, 0, 0):
                    # we cannot have an all-zero color, otherw. e.g. tksurfer
                    # refuses to read the parcellation
                    msg = ('At least one label contains a color with, "r=0, '
                           'g=0, b=0" value. Some FreeSurfer tools may fail '
                           'to read the parcellation')
                    logger.warning(msg)

                if any(i > 255 for i in color):
                    msg = ("%s: %s (%s)" % (color, ', '.join(names), hemi))
                    invalid_colors.append(msg)

                if len(names) > 1:
                    msg = "%s: %s (%s)" % (color, ', '.join(names), hemi)
                    duplicate_colors.append(msg)

            # replace None values (labels with unspecified color)
#.........这里部分代码省略.........