Note

This page is a reference documentation. It only explains the class signature, and not how to use it. Please refer to the user guide for the big picture.

8.10.32. nilearn.plotting.displays.OrthoSlicer

class nilearn.plotting.displays.OrthoSlicer(cut_coords, axes=None, black_bg=False, brain_color=(0.5, 0.5, 0.5), **kwargs)

A class to create 3 linked axes for plotting orthogonal cuts of 3D maps.

Notes

The extent of the different axes are adjusted to fit the data best in the viewing area.

Attributes
axesdictionary of axes

The 3 axes used to plot each view.

frame_axesaxes

The axes framing the whole set of views.

__init__(cut_coords, axes=None, black_bg=False, brain_color=(0.5, 0.5, 0.5), **kwargs)

Create 3 linked axes for plotting orthogonal cuts.

Parameters
cut_coords3 tuple of ints

The cut position, in world space.

axesmatplotlib axes object, optional

The axes that will be subdivided in 3.

black_bgboolean, optional

If True, the background of the figure will be put to black. If you wish to save figures with a black background, you will need to pass “facecolor=’k’, edgecolor=’k’” to matplotlib.pyplot.savefig. Default=False.

brain_colortuple, optional

The brain color to use as the background color (e.g., for transparent colorbars). Default=(0.5, 0.5, 0.5)

classmethod find_cut_coords(img=None, threshold=None, cut_coords=None)

Instantiate the slicer and find cut coordinates

draw_cross(cut_coords=None, **kwargs)

Draw a crossbar on the plot to show where the cut is performed.

Parameters
cut_coords3-tuple of floats, optional

The position of the cross to draw. If none is passed, the ortho_slicer’s cut coordinates are used.

kwargs :

Extra keyword arguments are passed to axhline

add_contours(img, threshold=1e-06, filled=False, **kwargs)

Contour a 3D map in all the views.

Parameters
imgNiimg-like object

See http://nilearn.github.io/manipulating_images/input_output.html Provides image to plot.

thresholdInt or Float or None, optional

If None is given, the maps are not thresholded. If a number is given, it is used to threshold the maps, values below the threshold (in absolute value) are plotted as transparent. Default=1e-6.

filledboolean, optional

If filled=True, contours are displayed with color fillings. Default=False.

kwargs :

Extra keyword arguments are passed to contour, see the documentation of pylab.contour and see pylab.contourf documentation for arguments related to contours with fillings. Useful, arguments are typical “levels”, which is a list of values to use for plotting a contour or contour fillings (if filled=True), and “colors”, which is one color or a list of colors for these contours.

Notes

If colors are not specified, default coloring choices (from matplotlib) for contours and contour_fillings can be different.

add_edges(img, color='r')

Plot the edges of a 3D map in all the views.

Parameters
imgNiimg-like object

See http://nilearn.github.io/manipulating_images/input_output.html The 3D map to be plotted. If it is a masked array, only the non-masked part will be plotted.

colormatplotlib color: string or (r, g, b) value

The color used to display the edge map. Default=’r’.

add_markers(marker_coords, marker_color='r', marker_size=30, **kwargs)

Add markers to the plot.

Parameters
marker_coordsarray of size (n_markers, 3)

Coordinates of the markers to plot. For each slice, only markers that are 2 millimeters away from the slice are plotted.

marker_colorpyplot compatible color or list of shape (n_markers,), optional

List of colors for each marker that can be string or matplotlib colors. Default=’r’.

marker_sizesingle float or list of shape (n_markers,), optional

Size in pixel for each marker. Default=30.

add_overlay(img, threshold=1e-06, colorbar=False, **kwargs)

Plot a 3D map in all the views.

Parameters
imgNiimg-like object

See http://nilearn.github.io/manipulating_images/input_output.html If it is a masked array, only the non-masked part will be plotted.

thresholdInt or Float or None, optional

If None is given, the maps are not thresholded. If a number is given, it is used to threshold the maps: values below the threshold (in absolute value) are plotted as transparent. Default=1e-6.

colorbarboolean, optional

If True, display a colorbar on the right of the plots. Default=False.

kwargs :

Extra keyword arguments are passed to imshow.

annotate(left_right=True, positions=True, scalebar=False, size=12, scale_size=5.0, scale_units='cm', scale_loc=4, decimals=0, **kwargs)

Add annotations to the plot.

Parameters
left_rightboolean, optional

If left_right is True, annotations indicating which side is left and which side is right are drawn. Default=True.

positionsboolean, optional

If positions is True, annotations indicating the positions of the cuts are drawn. Default=True.

scalebarboolean, optional

If True, cuts are annotated with a reference scale bar. For finer control of the scale bar, please check out the draw_scale_bar method on the axes in “axes” attribute of this object. Default=False.

sizeinteger, optional

The size of the text used. Default=12.

scale_sizenumber, optional

The length of the scalebar, in units of scale_units. Default=5.0.

scale_units{‘cm’, ‘mm’}, optional

The units for the scalebar. Default=’cm’.

scale_locinteger, optional

The positioning for the scalebar. Default=4. Valid location codes are:

  • ‘upper right’ : 1

  • ‘upper left’ : 2

  • ‘lower left’ : 3

  • ‘lower right’ : 4

  • ‘right’ : 5

  • ‘center left’ : 6

  • ‘center right’ : 7

  • ‘lower center’ : 8

  • ‘upper center’ : 9

  • ‘center’ : 10

decimalsinteger, optional

Number of decimal places on slice position annotation. If zero, the slice position is integer without decimal point. Default=0.

kwargs :

Extra keyword arguments are passed to matplotlib’s text function.

close()

Close the figure. This is necessary to avoid leaking memory.

classmethod init_with_figure(img, threshold=None, cut_coords=None, figure=None, axes=None, black_bg=False, leave_space=False, colorbar=False, brain_color=(0.5, 0.5, 0.5), **kwargs)

Initialize the slicer with an image

savefig(filename, dpi=None)

Save the figure to a file

Parameters
filenamestring

The file name to save to. Its extension determines the file type, typically ‘.png’, ‘.svg’ or ‘.pdf’.

dpiNone or scalar, optional

The resolution in dots per inch.

title(text, x=0.01, y=0.99, size=15, color=None, bgcolor=None, alpha=1, **kwargs)

Write a title to the view.

Parameters
textstring

The text of the title.

xfloat, optional

The horizontal position of the title on the frame in fraction of the frame width. Default=0.01.

yfloat, optional

The vertical position of the title on the frame in fraction of the frame height. Default=0.99.

sizeinteger, optional

The size of the title text. Default=15.

colormatplotlib color specifier, optional

The color of the font of the title.

bgcolormatplotlib color specifier, optional

The color of the background of the title.

alphafloat, optional

The alpha value for the background. Default=1.

kwargs :

Extra keyword arguments are passed to matplotlib’s text function.