visbrain.objects.VolumeObj

class visbrain.objects.VolumeObj(name, vol=None, hdr=None, method='mip', threshold=0.0, cmap='OpaqueGrays', select=None, transform=None, parent=None, preload=True, verbose=None, **kw)

Create a 3-D volume object.

Parameters:

namestring

Name of the volume object. If name is ‘brodmann’, ‘aal’ or ‘talairach’ a predefined volume object is used and vol, index and label are ignored. The name input can also be the path to an nii.gz file.

volarray_like

The volume to use. Should be a 3-d array.

hdrarray_like | None

Matrix transformation to apply. hdr should be a (4, 4) array.

method{‘mip’, ‘translucent’, ‘additive’, ‘iso’}

Volume rendering method. Default is ‘mip’.

thresholdfloat | 0.

Threshold value for iso rendering method.

cmap{‘OpaqueGrays’, ‘TransFire’, ‘OpaqueFire’, ‘TransGrays’}

Colormap to use.

selectlist | None

Select some structures in the volume.

transformVisPy.visuals.transforms | None

VisPy transformation to set to the parent node.

parentVisPy.parent | None

Volume object parent.

kwdict | {}

Optional arguments are used to control the colorbar (See ColorbarObj).

Notes

List of supported shortcuts :

• s : save the figure

• <delete> : reset camera

Examples

>>> from visbrain.objects import VolumeObj
>>> select = [4, 6]  # select Brodmann area 4 and 6
>>> v = VolumeObj('brodmann', method='iso', select=select)
>>> v.preview(axis=True)

Methods

__init__(name[, vol, hdr, method, ...])	Init.
animate([step, interval, iterations])	Animate the object.
copy()	Get a copy of the object.
describe_tree()	Tree description.
extract_activity(xyz[, radius])	Extract activity of a volume around (x, y, z) points.
list([file])	Get the list of installed volumes.
pos_to_slice(pos[, axis, hdr])	Return the slice from position.
preview([bgcolor, axis, xyz, show, obj, ...])	Previsualize the result.
record_animation(name[, n_pic, bgcolor])	Record an animated object and save as a *.gif file.
remove()	Remove the volume template.
render()	Render the canvas.
save([tmpfile])	Save the volume template.
screenshot(saveas[, print_size, dpi, unit, ...])	Take a screeshot of the scene.
set_data(vol[, hdr, threshold, cmap, ...])	Set data to the volume.
set_shortcuts_to_canvas(canvas)	Set shortcuts to a VisbrainCanvas.
slice_to_pos(sl[, axis, hdr])	Return the position from slice in the volume space.
to_dict()	Return a dictionary of all colorbar args.
to_kwargs([addisminmax])	Return a dictionary for input arguments.
update()	Update the volume.
update_from_dict(kwargs)	Update attributes from a dictionary.

Examples using visbrain.objects.VolumeObj

Volume object (VolumeObj) : complete tutorial

Volume object (VolumeObj) : complete tutorial

Cross-sections and volume control

Cross-sections and volume control

Add Nifti volume

Add Nifti volume