Example #1
0
def demo_plot_map():
    map = np.zeros((182, 218, 182))
    # Color a asymetric rectangle around Broadman area 26:
    x, y, z = -6, -53, 9
    x_map, y_map, z_map = coord_transform(x, y, z, mni_sform_inv)
    map[x_map-30:x_map+30, y_map-3:y_map+3, z_map-10:z_map+10] = 1
    plot_map(map, mni_sform, cut_coords=(x, y, z), vmin=0.5,
                                figure_num=512)
Example #2
0
def auto_plot_map(map, sform, vmin=None, cut_coords=None, do3d=False, 
                    anat=None, anat_sform=None, title='',
                    figure_num=None, mask=None, auto_sign=True):
    """ Automatic plotting of an activation map.

        Plot a together a 3D volume rendering view of the activation, with an
        outline of the brain, and 2D cuts. If Mayavi is not installed,
        falls back to 2D views only.

        Parameters
        ----------
        map : 3D ndarray
            The activation map, as a 3D image.
        sform : 4x4 ndarray
            The affine matrix going from image voxel space to MNI space.
        vmin : float, optional
            The lower threshold of the positive activation. This
            parameter is used to threshold the activation map.
        cut_coords: 3-tuple of floats, optional
            The MNI coordinates of the point where the cut is performed, in 
            MNI coordinates and order. If None is given, the cut_coords are 
            automaticaly estimated.
        do3d : boolean, optional
            If do3d is True, a 3D plot is created if Mayavi is installed.
        anat : 3D ndarray, optional
            The anatomical image to be used as a background. If None, the 
            MNI152 T1 1mm template is used.
        anat_sform : 4x4 ndarray, optional
            The affine matrix going from the anatomical image voxel space to 
            MNI space. This parameter is not used when the default 
            anatomical is used, but it is compulsory when using an
            explicite anatomical image.
        title : string, optional
            The title dispayed on the figure.
        figure_num : integer, optional
            The number of the matplotlib and Mayavi figures used. If None is 
            given, a new figure is created.
        mask : 3D ndarray, boolean, optional
            The brain mask. If None, the mask is computed from the map.
        auto_sign : boolean, optional
            If auto_sign is True, the sign of the activation is
            automaticaly computed: negative activation can thus be
            plotted.

        Returns
        -------
        vmin : float
            The lower threshold of the activation used.
        cut_coords : 3-tuple of floats
            The Talairach coordinates of the cut performed for the 2D
            view.

        Notes
        -----
        All the 3D arrays are in numpy convention: (x, y, z)

        Cut coordinates are in Talairach coordinates. Warning: Talairach
        coordinates are (y, x, z), if (x, y, z) are in voxel-ordering
        convention.
    """
    if do3d:
        if do3d == 'offscreen':
            try:
                from enthought.mayavi import mlab
                mlab.options.offscreen = True
            except:
                pass
        plotter = plot_map
    else:
        plotter = plot_map_2d
    if mask is None:
        mask = compute_mask(map)
    if vmin is None:
        vmin = np.inf
        pvalue = 0.04
        while not np.isfinite(vmin):
            pvalue *= 1.25
            vmax, vmin = find_activation(map, mask=mask, pvalue=pvalue)
            if not np.isfinite(vmin) and auto_sign:
                if np.isfinite(vmax):
                    vmin = -vmax
                    if mask is not None:
                        map[mask] *= -1
                    else:
                        map *= -1
    if cut_coords is None:
        x, y, z = find_cut_coords(map, activation_threshold=vmin)
        # XXX: Careful with Voxel/MNI ordering
        y, x, z = coord_transform(x, y, z, sform)
        cut_coords = (x, y, z)
    plotter(map, sform, vmin=vmin, cut_coords=cut_coords,
                anat=anat, anat_sform=anat_sform, title=title,
                figure_num=figure_num, mask=mask)
    return vmin, cut_coords
Example #3
0
def plot_map_2d(map, sform, cut_coords, anat=None, anat_sform=None,
                    vmin=None, figure_num=None, axes=None, title='',
                    mask=None, **kwargs):
    """ Plot three cuts of a given activation map (Frontal, Axial, and Lateral)

        Parameters
        ----------
        map : 3D ndarray
            The activation map, as a 3D image.
        sform : 4x4 ndarray
            The affine matrix going from image voxel space to MNI space.
        cut_coords: 3-tuple of floats
            The MNI coordinates of the point where the cut is performed, in 
            MNI coordinates and order.
        anat : 3D ndarray, optional or False
            The anatomical image to be used as a background. If None, the 
            MNI152 T1 1mm template is used. If False, no anat is displayed.
        anat_sform : 4x4 ndarray, optional
            The affine matrix going from the anatomical image voxel space to 
            MNI space. This parameter is not used when the default 
            anatomical is used, but it is compulsory when using an
            explicite anatomical image.
        vmin : float, optional
            The lower threshold of the positive activation. This
            parameter is used to threshold the activation map.
        figure_num : integer, optional
            The number of the matplotlib figure used. If None is given, a
            new figure is created.
        axes : 4 tuple of float: (xmin, xmax, ymin, ymin), optional
            The coordinates, in matplotlib figure space, of the axes
            used to display the plot. If None, the complete figure is 
            used.
        title : string, optional
            The title dispayed on the figure.
        mask : 3D ndarray, boolean, optional
            The brain mask. If None, the mask is computed from the map.*
        kwargs: extra keyword arguments, optional
            Extra keyword arguments passed to pylab.imshow

        Notes
        -----
        All the 3D arrays are in numpy convention: (x, y, z)

        Cut coordinates are in Talairach coordinates. Warning: Talairach
        coordinates are (y, x, z), if (x, y, z) are in voxel-ordering
        convention.
    """
    if anat is None:
        anat, anat_sform, vmax_anat = _AnatCache.get_anat()
    elif anat is not False:
        vmax_anat = anat.max()

    if mask is not None and (
                    np.all(mask) or np.all(np.logical_not(mask))):
        mask = None

    vmin_map  = map.min()
    vmax_map  = map.max()
    if vmin is not None and np.isfinite(vmin):
        map = np.ma.masked_less(map, vmin)
    elif mask is not None and not isinstance(map, np.ma.masked_array):
        map = np.ma.masked_array(map, np.logical_not(mask))
        vmin_map  = map.min()
        vmax_map  = map.max()

    if isinstance(map, np.ma.core.MaskedArray):
        use_mask = False
        if map._mask is False or np.all(np.logical_not(map._mask)):
            map = np.asarray(map)
        elif map._mask is True or np.all(map._mask):
            map = np.asarray(map)
        if use_mask and mask is not None:
            map = np.ma.masked_array(map, np.logical_not(mask))

    # Calculate the bounds
    if anat is not False:
        anat_bounds = np.zeros((4, 6))
        anat_bounds[:3, -3:] = np.identity(3)*anat.shape
        anat_bounds[-1, :] = 1
        anat_bounds = np.dot(anat_sform, anat_bounds)

    map_bounds = np.zeros((4, 6))
    map_bounds[:3, -3:] = np.identity(3)*map.shape
    map_bounds[-1, :] = 1
    map_bounds = np.dot(sform, map_bounds)

    # The coordinates of the center of the cut in different spaces.
    y, x, z = cut_coords
    x_map, y_map, z_map = [int(round(c)) for c in 
                            coord_transform(x, y, z,
                                    np.linalg.inv(sform))]
    if anat is not False:
        x_anat, y_anat, z_anat = [int(round(c)) for c in 
                            coord_transform(x, y, z,
                                    np.linalg.inv(anat_sform))]


    fig = pl.figure(figure_num, figsize=(6.6, 2.6))
    if axes is None:
        axes = (0., 1., 0., 1.)
        pl.clf()
    ax_xmin, ax_xmax, ax_ymin, ax_ymax = axes
    ax_width = ax_xmax - ax_xmin
    ax_height = ax_ymax - ax_ymin
    
    # Calculate the axes ratio size in a 'clever' way
    if anat is not False:
        shapes = np.array(anat.shape, 'f')
    else:
        shapes = np.array(map.shape, 'f')
    shapes *= ax_width/shapes.sum()
    
    ###########################################################################
    # Frontal
    pl.axes([ax_xmin, ax_ymin, shapes[0], ax_height])
    if anat is not False:
        if y_anat < anat.shape[1]:
            pl.imshow(np.rot90(anat[:, y_anat, :]), 
                                    cmap=pl.cm.gray,
                                    vmin=-.5*vmax_anat,
                                    vmax=vmax_anat, 
                                    extent=(anat_bounds[0, 3],
                                            anat_bounds[0, 0],
                                            anat_bounds[2, 0],
                                            anat_bounds[2, 5]))
    if y_map < map.shape[1]:
        pl.imshow(np.rot90(map[:, y_map, :]),
                                vmin=vmin_map,
                                vmax=vmax_map,
                                extent=(map_bounds[0, 3],
                                        map_bounds[0, 0],
                                        map_bounds[2, 0],
                                        map_bounds[2, 5]),
                                **kwargs)
    pl.text(ax_xmin +shapes[0] + shapes[1] - 0.01, ax_ymin + 0.07, '%i' % x,
             horizontalalignment='right',
             verticalalignment='bottom',
             transform=fig.transFigure)
    
    xmin, xmax = pl.xlim()
    ymin, ymax = pl.ylim()
    pl.hlines(z, xmin, xmax, color=(.5, .5, .5))
    pl.vlines(-x, ymin, ymax, color=(.5, .5, .5))
    pl.axis('off')
    
    ###########################################################################
    # Lateral
    pl.axes([ax_xmin + shapes[0], ax_ymin, shapes[1], ax_height])
    if anat is not False:
        if x_anat < anat.shape[0]:
            pl.imshow(np.rot90(anat[x_anat, ...]), cmap=pl.cm.gray,
                                    vmin=-.5*vmax_anat,
                                    vmax=vmax_anat, 
                                    extent=(anat_bounds[1, 0],
                                            anat_bounds[1, 4],
                                            anat_bounds[2, 0],
                                            anat_bounds[2, 5]))
    if x_map < map.shape[0]:
        pl.imshow(np.rot90(map[x_map, ...]),
                                vmin=vmin_map,
                                vmax=vmax_map,
                                extent=(map_bounds[1, 0],
                                        map_bounds[1, 4],
                                        map_bounds[2, 0],
                                        map_bounds[2, 5]),
                                **kwargs)
    pl.text(ax_xmin + shapes[-1] - 0.01, ax_ymin + 0.07, '%i' % y, 
             horizontalalignment='right',
             verticalalignment='bottom',
             transform=fig.transFigure)
    
    xmin, xmax = pl.xlim()
    ymin, ymax = pl.ylim()
    pl.hlines(z, xmin, xmax, color=(.5, .5, .5))
    pl.vlines(y, ymin, ymax, color=(.5, .5, .5))
    pl.axis('off')

    ###########################################################################
    # Axial
    pl.axes([ax_xmin + shapes[0] + shapes[1], ax_ymin, shapes[-1],
                ax_height])
    if anat is not False:
        if z_anat < anat.shape[2]:
            pl.imshow(np.rot90(anat[..., z_anat]), 
                                    cmap=pl.cm.gray,
                                    vmin=-.5*vmax_anat,
                                    vmax=vmax_anat, 
                                    extent=(anat_bounds[0, 0],
                                            anat_bounds[0, 3],
                                            anat_bounds[1, 0],
                                            anat_bounds[1, 4]))
    if z_map < map.shape[2]:
        pl.imshow(np.rot90(map[..., z_map]),
                                vmin=vmin_map,
                                vmax=vmax_map,
                                extent=(map_bounds[0, 0],
                                        map_bounds[0, 3],
                                        map_bounds[1, 0],
                                        map_bounds[1, 4]),
                                **kwargs)
    pl.text(ax_xmax - 0.01, ax_ymin + 0.07, '%i' % z, 
             horizontalalignment='right',
             verticalalignment='bottom',
             transform=fig.transFigure)
    
    xmin, xmax = pl.xlim()
    ymin, ymax = pl.ylim()
    pl.hlines(y,  xmin, xmax, color=(.5, .5, .5))
    pl.vlines(x, ymin, ymax, color=(.5, .5, .5))
    pl.axis('off')
    
    pl.text(ax_xmin + 0.01, ax_ymax - 0.01, title, 
             horizontalalignment='left',
             verticalalignment='top',
             transform=fig.transFigure)

    pl.axis('off')