Python Brain.set_time方法代码示例

# 需要导入模块: from surfer import Brain [as 别名]
# 或者: from surfer.Brain import set_time [as 别名]
def test_meg_inverse():
    """Test plotting of MEG inverse solution."""
    _set_backend()
    brain = Brain(*std_args)
    stc_fname = os.path.join(data_dir, 'meg_source_estimate-lh.stc')
    stc = io.read_stc(stc_fname)
    vertices = stc['vertices']
    colormap = 'hot'
    data = stc['data']
    data_full = (brain.geo['lh'].nn[vertices][..., np.newaxis] *
                 data[:, np.newaxis])
    time = np.linspace(stc['tmin'], stc['tmin'] + data.shape[1] * stc['tstep'],
                       data.shape[1], endpoint=False)

    def time_label(t):
        return 'time=%0.2f ms' % (1e3 * t)

    for use_data in (data, data_full):
        brain.add_data(use_data, colormap=colormap, vertices=vertices,
                       smoothing_steps=1, time=time, time_label=time_label)

    brain.scale_data_colormap(fmin=13, fmid=18, fmax=22, transparent=True)
    assert_equal(brain.data_dict['lh']['time_idx'], 0)

    brain.set_time(.1)
    assert_equal(brain.data_dict['lh']['time_idx'], 2)
    # viewer = TimeViewer(brain)

    # multiple data layers
    assert_raises(ValueError, brain.add_data, data, vertices=vertices,
                  time=time[:-1])
    brain.add_data(data, colormap=colormap, vertices=vertices,
                   smoothing_steps=1, time=time, time_label=time_label,
                   initial_time=.09)
    assert_equal(brain.data_dict['lh']['time_idx'], 1)
    data_dicts = brain._data_dicts['lh']
    assert_equal(len(data_dicts), 3)
    assert_equal(data_dicts[0]['time_idx'], 1)
    assert_equal(data_dicts[1]['time_idx'], 1)

    # shift time in both layers
    brain.set_data_time_index(0)
    assert_equal(data_dicts[0]['time_idx'], 0)
    assert_equal(data_dicts[1]['time_idx'], 0)
    brain.set_data_smoothing_steps(2)

    # add second data-layer without time axis
    brain.add_data(data[:, 1], colormap=colormap, vertices=vertices,
                   smoothing_steps=2)
    brain.set_data_time_index(2)
    assert_equal(len(data_dicts), 4)

    # change surface
    brain.set_surf('white')

    # remove all layers
    brain.remove_data()
    assert_equal(brain._data_dicts['lh'], [])

    brain.close()

# 需要导入模块: from surfer import Brain [as 别名]
# 或者: from surfer.Brain import set_time [as 别名]
def test_meg_inverse():
    """Test plotting of MEG inverse solution
    """
    mlab.options.backend = 'test'
    brain = Brain(*std_args)
    stc_fname = os.path.join(data_dir, 'meg_source_estimate-lh.stc')
    stc = io.read_stc(stc_fname)
    data = stc['data']
    vertices = stc['vertices']
    time = np.linspace(stc['tmin'], stc['tmin'] + data.shape[1] * stc['tstep'],
                       data.shape[1], endpoint=False)
    colormap = 'hot'

    def time_label(t):
        return 'time=%0.2f ms' % (1e3 * t)

    brain.add_data(data, colormap=colormap, vertices=vertices,
                   smoothing_steps=10, time=time, time_label=time_label)
    brain.scale_data_colormap(fmin=13, fmid=18, fmax=22, transparent=True)
    assert_equal(brain.data_dict['lh']['time_idx'], 0)

    brain.set_time(.1)
    assert_equal(brain.data_dict['lh']['time_idx'], 2)
    # viewer = TimeViewer(brain)

    brain.add_data(data, colormap=colormap, vertices=vertices,
                   smoothing_steps=10, time=time, time_label=time_label,
                   initial_time=.09, remove_existing=True)
    assert_equal(brain.data_dict['lh']['time_idx'], 1)
    brain.close()

# 需要导入模块: from surfer import Brain [as 别名]
# 或者: from surfer.Brain import set_time [as 别名]

#.........这里部分代码省略.........
    if surfer_version < v06:
        raise ImportError("This function requires PySurfer 0.6 (you are "
                          "running version %s). You can update PySurfer "
                          "using:\n\n    $ pip install -U pysurfer" %
                          surfer.__version__)

    if initial_time is not None and surfer_version > v06:
        kwargs = {'initial_time': initial_time}
        initial_time = None  # don't set it twice
    else:
        kwargs = {}

    if time_unit is None:
        warn("The time_unit parameter default will change from 'ms' to 's' "
             "in MNE 0.14. To avoid this warning specify the parameter "
             "explicitly.", DeprecationWarning)
        time_unit = 'ms'
    elif time_unit not in ('s', 'ms'):
        raise ValueError("time_unit needs to be 's' or 'ms', got %r" %
                         (time_unit,))

    if time_label == 'auto':
        if time_unit == 'ms':
            time_label = 'time=%0.2f ms'
        else:
            def time_label(t):
                return 'time=%0.2f ms' % (t * 1e3)

    if not isinstance(stc, SourceEstimate):
        raise ValueError('stc has to be a surface source estimate')

    if hemi not in ['lh', 'rh', 'split', 'both']:
        raise ValueError('hemi has to be either "lh", "rh", "split", '
                         'or "both"')

    # check `figure` parameter (This will be performed by PySurfer > 0.6)
    if figure is not None:
        if isinstance(figure, int):
            # use figure with specified id
            size_ = size if isinstance(size, (tuple, list)) else (size, size)
            figure = [mayavi.mlab.figure(figure, size=size_)]
        elif not isinstance(figure, (list, tuple)):
            figure = [figure]
        if not all(isinstance(f, mayavi.core.scene.Scene) for f in figure):
            raise TypeError('figure must be a mayavi scene or list of scenes')

    # convert control points to locations in colormap
    ctrl_pts, colormap = _limits_to_control_points(clim, stc.data, colormap)

    # Construct cmap manually if 'mne' and get cmap bounds
    # and triage transparent argument
    if colormap in ('mne', 'mne_analyze'):
        colormap = mne_analyze_colormap(ctrl_pts)
        scale_pts = [-1 * ctrl_pts[-1], 0, ctrl_pts[-1]]
        transparent = False if transparent is None else transparent
    else:
        scale_pts = ctrl_pts
        transparent = True if transparent is None else transparent

    subjects_dir = get_subjects_dir(subjects_dir=subjects_dir,
                                    raise_error=True)
    subject = _check_subject(stc.subject, subject, True)
    if hemi in ['both', 'split']:
        hemis = ['lh', 'rh']
    else:
        hemis = [hemi]

    title = subject if len(hemis) > 1 else '%s - %s' % (subject, hemis[0])
    with warnings.catch_warnings(record=True):  # traits warnings
        brain = Brain(subject, hemi, surface, True, title, cortex, size,
                      background, foreground, figure, subjects_dir, views,
                      config_opts=config_opts)

    if time_unit == 's':
        times = stc.times
    else:  # time_unit == 'ms'
        times = 1e3 * stc.times

    for hemi in hemis:
        hemi_idx = 0 if hemi == 'lh' else 1
        if hemi_idx == 0:
            data = stc.data[:len(stc.vertices[0])]
        else:
            data = stc.data[len(stc.vertices[0]):]
        vertices = stc.vertices[hemi_idx]
        with warnings.catch_warnings(record=True):  # traits warnings
            brain.add_data(data, colormap=colormap, vertices=vertices,
                           smoothing_steps=smoothing_steps, time=times,
                           time_label=time_label, alpha=alpha, hemi=hemi,
                           colorbar=colorbar, **kwargs)

        # scale colormap and set time (index) to display
        brain.scale_data_colormap(fmin=scale_pts[0], fmid=scale_pts[1],
                                  fmax=scale_pts[2], transparent=transparent)

    if initial_time is not None:
        brain.set_time(initial_time)
    if time_viewer:
        TimeViewer(brain)
    return brain