neurospin.viz_tools.ortho_slicer

Module: neurospin.viz_tools.ortho_slicer

Inheritance diagram for nipy.neurospin.viz_tools.ortho_slicer:

The OrthoSlicer class.

The main purpose of this class is to have auto adjust of axes size to the data.

OrthoSlicer

class nipy.neurospin.viz_tools.ortho_slicer.OrthoSlicer(cut_coords, axes=None)

Bases: object

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: dictionnary of axes	The 3 axes used to plot each view.
frame_axes: axes	The axes framing the whole set of views.

Methods

annotate
draw_cross
plot_map
title

__init__(cut_coords, axes=None)

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.

annotate(left_right=True, positions=True, size=12, **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.

size: integer, optional :

The size of the text used.

kwargs: :

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

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 coordinnates are used.

kwargs: :

Extra keyword arguments are passed to axhline

plot_map(map, affine, **kwargs)

Plot a 3D map in all the views.

Parameters:

map: 3D ndarray :

The 3D map to be plotted. If it is a masked array, only the non-masked part will be plotted.

affine: 4x4 ndarray :

The affine matrix giving the transformation from voxel indices to world space.

kwargs: :

Extra keyword arguments are passed to imshow.

title(text, x=0.01, y=0.98999999999999999, size=15, color='w', bgcolor='k', alpha=0.90000000000000002, **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.

nipy.neurospin.viz_tools.ortho_slicer.demo_ortho_slicer()

A small demo of the OrthoSlicer functionality.