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
axes: dictionary of axes The 3 axes used to plot each view. frame_axes: axes 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_coords: 3 tuple of ints
The cut position, in world space.
axes: matplotlib axes object, optional
The axes that will be subdivided in 3.
black_bg: boolean, 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.
brain_color : tuple
The brain color to use as the background color (e.g., for transparent colorbars).
add_contours(img, threshold=1e-06, filled=False, **kwargs)¶Contour a 3D map in all the views.
Parameters: img: Niimg-like object
See http://nilearn.github.io/manipulating_images/input_output.html Provides image to plot.
threshold: a number, None
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.
filled: boolean, optional
If filled=True, contours are displayed with color fillings.
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. Note: 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: img: Niimg-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.
color: matplotlib color: string or (r, g, b) value
The color used to display the edge map
add_markers(marker_coords, marker_color='r', marker_size=30, **kwargs)¶Add markers to the plot.
Parameters: marker_coords: array 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_color: pyplot compatible color or list of shape (n_markers,)
List of colors for each marker that can be string or matplotlib colors
marker_size: single float or list of shape (n_markers,)
Size in pixel for each marker
add_overlay(img, threshold=1e-06, colorbar=False, **kwargs)¶Plot a 3D map in all the views.
Parameters: img: Niimg-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.
threshold : a number, None
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.
colorbar: boolean, optional
If True, display a colorbar on the right of the plots.
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_right: boolean, optional
If left_right is True, annotations indicating which side is left and which side is right are drawn.
positions: boolean, optional
If positions is True, annotations indicating the positions of the cuts are drawn.
scalebar: boolean, 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.size: integer, optional
The size of the text used.
scale_size: number, optional
The length of the scalebar, in units of scale_units
scale_units: {‘mm’, ‘cm’}
The units for the scalebar
scale_loc: integer
- The positioning for the scalebar, 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
decimals: integer, optional
Number of decimal places on slice position annotation. If False (default), the slice position is integer without decimal point.
kwargs:
Extra keyword arguments are passed to matplotlib’s text function.
close()¶Close the figure. This is necessary to avoid leaking memory.
draw_cross(cut_coords=None, **kwargs)¶Draw a crossbar on the plot to show where the cut is performed.
Parameters: cut_coords: 3-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
- classmethod
find_cut_coords(img=None, threshold=None, cut_coords=None)¶ Instantiate the slicer and find cut coordinates
- 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: filename: string
The file name to save to. Its extension determines the file type, typically ‘.png’, ‘.svg’ or ‘.pdf’.
dpi: None or scalar
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: text: string
The text of the title
x: float, optional
The horizontal position of the title on the frame in fraction of the frame width.
y: float, optional
The vertical position of the title on the frame in fraction of the frame height.
size: integer, optional
The size of the title text.
color: matplotlib color specifier, optional
The color of the font of the title.
bgcolor: matplotlib color specifier, optional
The color of the background of the title.
alpha: float, optional
The alpha value for the background.
kwargs:
Extra keyword arguments are passed to matplotlib’s text function.
