labs.viz_tools.slicers

Module: labs.viz_tools.slicers

Inheritance diagram for nipy.labs.viz_tools.slicers:

The Slicer classes.

The main purpose of these classes is to have auto adjust of axes size to the data with different layout of cuts.

Classes

BaseSlicer

class nipy.labs.viz_tools.slicers.BaseSlicer(cut_coords, axes=None, black_bg=False)

Bases: object

The main purpose of these class is to have auto adjust of axes size to the data with different layout of cuts.

__init__(cut_coords, axes=None, black_bg=False)

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 pyplot’s savefig.

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.

contour_map(map, affine, **kwargs)

Contour 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 contour.

edge_map(map, affine, color='r')

Plot the edges of 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.

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

The color used to display the edge map

static find_cut_coords(data=None, affine=None, threshold=None, cut_coords=None)

classmethod init_with_figure(data=None, affine=None, threshold=None, cut_coords=None, figure=None, axes=None, black_bg=False, leave_space=False)

plot_map(map, affine, threshold=None, **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.

thresholda number, None, or ‘auto’

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 are plotted as transparent.

kwargs:

Extra keyword arguments are passed to imshow.

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.

BaseStackedSlicer

class nipy.labs.viz_tools.slicers.BaseStackedSlicer(cut_coords, axes=None, black_bg=False)

Bases: BaseSlicer

A class to create linked axes for plotting stacked 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 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)

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 pyplot’s savefig.

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.

contour_map(map, affine, **kwargs)

Contour 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 contour.

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

edge_map(map, affine, color='r')

Plot the edges of 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.

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

The color used to display the edge map

classmethod find_cut_coords(data=None, affine=None, threshold=None, cut_coords=None)

classmethod init_with_figure(data=None, affine=None, threshold=None, cut_coords=None, figure=None, axes=None, black_bg=False, leave_space=False)

plot_map(map, affine, threshold=None, **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.

thresholda number, None, or ‘auto’

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 are plotted as transparent.

kwargs:

Extra keyword arguments are passed to imshow.

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.

CutAxes

class nipy.labs.viz_tools.slicers.CutAxes(ax, direction, coord)

Bases: object

An MPL axis-like object that displays a cut of 3D volumes

__init__(ax, direction, coord)

An MPL axis-like object that displays a cut of 3D volumes

Parameters:

ax: a MPL axes instance

The axes in which the plots will be drawn

direction: {‘x’, ‘y’, ‘z’}

The directions of the cut

coord: float

The coordinate along the direction of the cut

do_cut(map, affine)

Cut the 3D volume into a 2D slice

Parameters:

map: 3D ndarray

The 3D volume to cut

affine: 4x4 ndarray

The affine of the volume

draw_cut(cut, data_bounds, bounding_box, type='imshow', **kwargs)

draw_left_right(size, bg_color, **kwargs)

draw_position(size, bg_color, **kwargs)

get_object_bounds()

Return the bounds of the objects on this axes.

OrthoSlicer

class nipy.labs.viz_tools.slicers.OrthoSlicer(cut_coords, axes=None, black_bg=False)

Bases: BaseSlicer

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)

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 pyplot’s savefig.

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.

contour_map(map, affine, **kwargs)

Contour 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 contour.

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

edge_map(map, affine, color='r')

Plot the edges of 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.

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

The color used to display the edge map

static find_cut_coords(data=None, affine=None, threshold=None, cut_coords=None)

classmethod init_with_figure(data=None, affine=None, threshold=None, cut_coords=None, figure=None, axes=None, black_bg=False, leave_space=False)

plot_map(map, affine, threshold=None, **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.

thresholda number, None, or ‘auto’

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 are plotted as transparent.

kwargs:

Extra keyword arguments are passed to imshow.

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.

XSlicer

class nipy.labs.viz_tools.slicers.XSlicer(cut_coords, axes=None, black_bg=False)

Bases: BaseStackedSlicer

__init__(cut_coords, axes=None, black_bg=False)

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 pyplot’s savefig.

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.

contour_map(map, affine, **kwargs)

Contour 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 contour.

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

edge_map(map, affine, color='r')

Plot the edges of 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.

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

The color used to display the edge map

classmethod find_cut_coords(data=None, affine=None, threshold=None, cut_coords=None)

classmethod init_with_figure(data=None, affine=None, threshold=None, cut_coords=None, figure=None, axes=None, black_bg=False, leave_space=False)

plot_map(map, affine, threshold=None, **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.

thresholda number, None, or ‘auto’

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 are plotted as transparent.

kwargs:

Extra keyword arguments are passed to imshow.

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.

YSlicer

class nipy.labs.viz_tools.slicers.YSlicer(cut_coords, axes=None, black_bg=False)

Bases: BaseStackedSlicer

__init__(cut_coords, axes=None, black_bg=False)

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 pyplot’s savefig.

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.

contour_map(map, affine, **kwargs)

Contour 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 contour.

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

edge_map(map, affine, color='r')

Plot the edges of 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.

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

The color used to display the edge map

classmethod find_cut_coords(data=None, affine=None, threshold=None, cut_coords=None)

classmethod init_with_figure(data=None, affine=None, threshold=None, cut_coords=None, figure=None, axes=None, black_bg=False, leave_space=False)

plot_map(map, affine, threshold=None, **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.

thresholda number, None, or ‘auto’

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 are plotted as transparent.

kwargs:

Extra keyword arguments are passed to imshow.

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.

ZSlicer

class nipy.labs.viz_tools.slicers.ZSlicer(cut_coords, axes=None, black_bg=False)

Bases: BaseStackedSlicer

__init__(cut_coords, axes=None, black_bg=False)

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 pyplot’s savefig.

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.

contour_map(map, affine, **kwargs)

Contour 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 contour.

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

edge_map(map, affine, color='r')

Plot the edges of 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.

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

The color used to display the edge map

classmethod find_cut_coords(data=None, affine=None, threshold=None, cut_coords=None)

classmethod init_with_figure(data=None, affine=None, threshold=None, cut_coords=None, figure=None, axes=None, black_bg=False, leave_space=False)

plot_map(map, affine, threshold=None, **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.

thresholda number, None, or ‘auto’

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 are plotted as transparent.

kwargs:

Extra keyword arguments are passed to imshow.

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.

Function

nipy.labs.viz_tools.slicers.demo_ortho_slicer()

A small demo of the OrthoSlicer functionality.