visbrain.objects.Picture3DObj

class visbrain.objects.Picture3DObj(name, data, xyz, select=None, pic_width=7.0, pic_height=7.0, alpha=1.0, cmap='viridis', clim=None, vmin=None, vmax=None, under='gray', over='red', translate=(0.0, 0.0, 1.0), transform=None, parent=None, verbose=None, _z=-10.0, **kw)[source][source]

Create a 3-D picture object.

Parameters
namestring

The name of the connectivity object.

dataarray_like

Array of data pictures of shape (n_sources, n_rows, n_columns).

xyzarray_like

The 3-d position of each picture of shape (n_sources, 3).

selectarray_like | None

Select the pictures to display. Should be a vector of bolean values of shape (n_sources,).

pic_widthfloat | 7.

Width of each picture.

pic_heightfloat | 7.

Height of each picture.

alphafloat | 1.

Image transparency.

cmapstring | ‘viridis’

Colormap to use.

vminfloat | None

Lower threshold of the colormap.

understring | None

Color to use for values under vmin.

vminfloat | None

Higher threshold of the colormap.

overstring | None

Color to use for values over vmax.

translatetuple | (0., 0., 1.)

Translation over the (x, y, z) axis.

transformVisPy.visuals.transforms | None

VisPy transformation to set to the parent node.

parentVisPy.parent | None

Line object parent.

verbosestring

Verbosity level.

_zfloat | 10.

In case of (n_sources, 2) use _z to specify the elevation.

kwdict | {}

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

Notes

List of supported shortcuts :

  • s : save the figure

  • <delete> : reset camera

Examples

>>> import numpy as np
>>> from visbrain.objects import Picture3DObj
>>> n_rows, n_cols, n_pic = 10, 20, 5
>>> data = np.random.rand(n_pic, n_rows, n_cols)
>>> xyz = np.random.uniform(-10, 10, (n_pic, 3))
>>> pic = Picture3DObj('Pic', data, xyz, cmap='plasma')
>>> pic.preview(axis=True)

Methods

__init__(name, data, xyz[, select, …])

Init.

animate([step, interval, iterations])

Animate the object.

copy()

Get a copy of the object.

describe_tree()

Tree description.

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.

render()

Render the canvas.

screenshot(saveas[, print_size, dpi, unit, …])

Take a screeshot of the scene.

set_shortcuts_to_canvas(canvas)

Set shortcuts to a VisbrainCanvas.

to_dict()

Return a dictionary of all colorbar args.

to_kwargs([addisminmax])

Return a dictionary for input arguments.

update()

Update image.

update_from_dict(kwargs)

Update attributes from a dictionary.

alpha

Get the alpha value.

animate(step=1.0, interval='auto', iterations=-1)[source]

Animate the object.

Note that this method can only be used with 3D objects.

Parameters
stepfloat | 1.

Rotation step.

intervalfloat | ‘auto’

Time between events in seconds. The default is ‘auto’, which attempts to find the interval that matches the refresh rate of the current monitor. Currently this is simply 1/60.

iterationsint | -1

Number of iterations. Can be -1 for infinite.

cmap

Get the cmap value.

copy()[source]

Get a copy of the object.

data_folder

Get the data_folder value.

name

Get the name value.

parent

Get the parent value.

pic_height

Get the height value.

pic_width

Get the pic_width value.

preview(bgcolor='black', axis=False, xyz=False, show=True, obj=None, size=(1200, 800), mpl=False, **kwargs)[source]

Previsualize the result.

Parameters
bgcolorarray_like/string/tuple | ‘black’

Background color for the preview.

axisbool | False

Add x and y axis with ticks.

xyzbool | False

Add an (x, y, z) axis to the scene.

objVisbrainObj | None

Pass a Visbrain object if you want to use the camera of an other object.

sizetuple | (1200, 800)

Default size of the window.

mplbool | False

Use Matplotlib to display the object. This result in a non interactive figure.

kwargsdict | {}

Optional arguments are passed to the VisbrainCanvas class.

record_animation(name, n_pic=10, bgcolor=None)[source]

Record an animated object and save as a *.gif file.

Note that this method :

  • Can only be used with 3D objects.

  • Requires the python package imageio

Parameters
namestring

Name of the gif file (e.g ‘myfile.gif’)

n_picint | 10

Number of pictures to use to render the gif.

bgcolorstring, tuple, list | None

Background color.

render()[source]

Render the canvas.

Returns
imgarray_like

Array of shape (n_rows, n_columns, 4) where 4 describes the RGBA components.

screenshot(saveas, print_size=None, dpi=300.0, unit='centimeter', factor=None, region=None, autocrop=False, bgcolor=None, transparent=False, obj=None, line_width=1.0, **kwargs)[source]

Take a screeshot of the scene.

By default, the rendered canvas will have the size of your screen. The screenshot() method provides two ways to increase to exported image resolution :

  • Using print_size, unit and dpi inputs : specify the size of the image at a specific dpi level. For example, you might want to have an (10cm, 15cm) image at 300 dpi.

  • Using the factor input : multiply the default image size by this factor. For example, if you have a (1920, 1080) monitor and if factor is 2, the exported image should have a shape of (3840, 2160) pixels.

Parameters
saveasstr

The name of the file to be saved. This file must contains a extension like .png, .tiff, .jpg…

print_sizetuple | None

The desired print size. This argument should be used in association with the dpi and unit inputs. print_size describe should be a tuple of two floats describing (width, height) of the exported image for a specific dpi level. The final image might not have the exact desired size but will try instead to find a compromize regarding to the proportion of width/height of the original image.

dpifloat | 300.

Dots per inch for printing the image.

unit{‘centimeter’, ‘millimeter’, ‘pixel’, ‘inch’}

Unit of the printed size.

factorfloat | None

If you don’t want to use the print_size input, factor simply multiply the resolution of your screen.

regiontuple | None

Select a specific region. Must be a tuple of four integers each one describing (x_start, y_start, width, height).

autocropbool | False

Automaticaly crop the figure in order to have the smallest space between the brain and the border of the picture.

bgcolorarray_like/string | None

The background color of the image.

transparentbool | False

Specify if the exported figure have to contains a transparent background.

objVisbrainObj | None

Pass a Visbrain object if you want to use the camera of an other object for the sceen rendering.

kwargsdict | {}

Optional arguments are passed to the VisbrainCanvas class.

transform

Get the transform value.

translate

Get the translate value.

visible_obj

Get the visible_obj value.