viewers

Utilities for viewing images

Includes version of OrthoSlicer3D code originally written by our own Paul Ivanov.

OrthoSlicer3D(data[, affine, axes, title])

Orthogonal-plane slice viewer.

OrthoSlicer3D

class nibabel.viewers.OrthoSlicer3D(data, affine=None, axes=None, title=None)

Bases: object

Orthogonal-plane slice viewer.

OrthoSlicer3d expects 3- or 4-dimensional array data. It treats 4D data as a sequence of 3D spatial volumes, where a slice over the final array axis gives a single 3D spatial volume.

For 3D data, the default behavior is to create a figure with 3 axes, one for each slice orientation of the spatial volume.

Clicking and dragging the mouse in any one axis will select out the corresponding slices in the other two. Scrolling up and down moves the slice up and down in the current axis.

For 4D data, the fourth figure axis can be used to control which 3D volume is displayed. Alternatively, the - key can be used to decrement the displayed volume and the + or = keys can be used to increment it.

Examples

>>> import numpy as np
>>> a = np.sin(np.linspace(0, np.pi, 20))
>>> b = np.sin(np.linspace(0, np.pi*5, 20))
>>> data = np.outer(a, b)[..., np.newaxis] * a
>>> OrthoSlicer3D(data).show()
Parameters:
dataarray-like

The data that will be displayed by the slicer. Should have 3+ dimensions.

affinearray-like or None, optional

Affine transform for the data. This is used to determine how the data should be sliced for plotting into the sagittal, coronal, and axial view axes. If None, identity is assumed. The aspect ratio of the data are inferred from the affine transform.

axestuple of mpl.Axes or None, optional

3 or 4 axes instances for the 3 slices plus volumes, or None (default).

titlestr or None, optional

The title to display. Can be None (default) to display no title.

__init__(data, affine=None, axes=None, title=None)
Parameters:
dataarray-like

The data that will be displayed by the slicer. Should have 3+ dimensions.

affinearray-like or None, optional

Affine transform for the data. This is used to determine how the data should be sliced for plotting into the sagittal, coronal, and axial view axes. If None, identity is assumed. The aspect ratio of the data are inferred from the affine transform.

axestuple of mpl.Axes or None, optional

3 or 4 axes instances for the 3 slices plus volumes, or None (default).

titlestr or None, optional

The title to display. Can be None (default) to display no title.

property clim

The current color limits

close()

Close the viewer figures

property cmap

The current colormap

draw()

Redraw the current image

property figs

A tuple of the figure(s) containing the axes

Link positional changes between two canvases

Parameters:
otherinstance of OrthoSlicer3D

Other viewer to use to link movements.

property n_volumes

Number of volumes in the data

property position

The current coordinates

set_position(x=None, y=None, z=None)

Set current displayed slice indices

Parameters:
xfloat | None

X coordinate to use. If None, do not change.

yfloat | None

Y coordinate to use. If None, do not change.

zfloat | None

Z coordinate to use. If None, do not change.

set_volume_idx(v)

Set current displayed volume index

Parameters:
vint

Volume index.

show()

Show the slicer in blocking mode; convenience for plt.show()