visbrain.objects.TopoObj¶
-
class
visbrain.objects.
TopoObj
(name, data, xyz=None, channels=None, system='cartesian', levels=None, level_colors='white', unit='degree', line_color='black', line_width=3.0, chan_size=12.0, chan_offset=(0.0, 0.0, 0.0), chan_mark_color='white', chan_mark_symbol='disc', chan_txt_color='black', cmap='viridis', clim=None, vmin=None, under='gray', vmax=None, over='red', margin=0.05, transform=None, parent=None, verbose=None, **kw)[source][source]¶ Create a topoplot object.
- Parameters
- namestring
The name of the connectivity object.
- dataarray_like
Array of data of shape (n_channels)
- xyzarray_like | None
Array of source’s coordinates.
- channelslist | None
List of channel names.
- system{‘cartesian’, ‘spherical’}
Coordinate system.
- levelsarray_like/int | None
The levels at which the isocurve is constructed.
- level_colorsstring/array_like | ‘white’
The color to use when drawing the line. If a list is given, it must be of shape (Nlev), if an array is given, it must be of shape (Nlev, …). and provide one color per level (rgba, colorname). By default, all levels are whites.
- unit{‘degree’, ‘rad’}
If system is ‘spherical’, specify if angles are in degrees or radians.
- line_colorarray_like/string | ‘black’
Color of lines for the head, nose and eras.
- line_widthfloat | 4.
Line width for the head, nose and eras.
- chan_sizefloat | 12.
Size of channel names text.
- chan_mark_colorarray_like/string | ‘white’
Color of channel markers.
- chan_mark_symbolstring | ‘disc’
Symbol to use for markers. Use disc, arrow, ring, clobber, square, diamond, vbar, hbar, cross, tailed_arrow, x, triangle_up, triangle_down, and star.
- chan_txt_colorarray_like/string | ‘black’
Color of channel names.
- cmapstring | None
Matplotlib colormap (like ‘viridis’, ‘inferno’…).
- climtuple/list | None
Colorbar limit. Every values under / over clim will clip.
- vminfloat | None
Every values under vmin will have the color defined using the under parameter.
- vmaxfloat | None
Every values over vmin will have the color defined using the over parameter.
- undertuple/string | None
Matplotlib color under vmin.
- overtuple/string | None
Matplotlib color over vmax.
- transformVisPy.visuals.transforms | None
VisPy transformation to set to the parent node.
- parentVisPy.parent | None
Line object parent.
- verbosestring
Verbosity level.
- kwdict | {}
Optional arguments are used to control the colorbar (See
ColorbarObj
).
Notes
List of supported shortcuts :
s : save the figure
<delete> : reset camera
Methods
__init__
(self, name, data[, xyz, channels, …])Init.
animate
(self[, step, interval, iterations])Animate the object.
connect
(self, connect, \*\*kwargs)Draw connectivity lines between channels.
copy
(self)Get a copy of the object.
describe_tree
(self)Tree description.
preview
(self[, bgcolor, axis, xyz, show, …])Previsualize the result.
record_animation
(self, name[, n_pic, bgcolor])Record an animated object and save as a *.gif file.
render
(self)Render the canvas.
screenshot
(self, saveas[, print_size, dpi, …])Take a screeshot of the scene.
set_data
(self, data[, levels, level_colors, …])Set data to the topoplot.
set_shortcuts_to_canvas
(self, canvas)Set shortcuts to a VisbrainCanvas.
to_dict
(self)Return a dictionary of all colorbar args.
to_kwargs
(self[, addisminmax])Return a dictionary for input arguments.
update
(self)Fonction to run when an update is needed.
update_from_dict
(self, kwargs)Update attributes from a dictionary.
-
animate
(self, 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.
-
property
cmap
¶ Get the cmap value.
-
connect
(self, connect, **kwargs)[source][source]¶ Draw connectivity lines between channels.
- Parameters
- connectarray_like
A 2D array of connectivity links of shape (n_channels, n_channels).
- kwargsdict | {}
Optional arguments are passed to the visbrain.objects.ConnectObj object.
-
property
data_folder
¶ Get the data_folder value.
-
property
name
¶ Get the name value.
-
property
parent
¶ Get the parent value.
-
preview
(self, 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
(self, 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
(self)[source]¶ Render the canvas.
- Returns
- imgarray_like
Array of shape (n_rows, n_columns, 4) where 4 describes the RGBA components.
-
screenshot
(self, 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.
-
set_data
(self, data, levels=None, level_colors='white', cmap='viridis', clim=None, vmin=None, under='gray', vmax=None, over='red')[source][source]¶ Set data to the topoplot.
- Parameters
- dataarray_like
Array of data of shape (n_channels)
- levelsarray_like/int | None
The levels at which the isocurve is constructed.
- level_colorsstring/array_like | ‘white’
The color to use when drawing the line. If a list is given, it must be of shape (Nlev), if an array is given, it must be of shape (Nlev, …). and provide one color per level (rgba, colorname). By default, all levels are whites.
- cmapstring | None
Matplotlib colormap (like ‘viridis’, ‘inferno’…).
- climtuple/list | None
Colorbar limit. Every values under / over clim will clip.
- vminfloat | None
Every values under vmin will have the color defined using the under parameter.
- vmaxfloat | None
Every values over vmin will have the color defined using the over parameter.
- undertuple/string | None
Matplotlib color under vmin.
- overtuple/string | None
Matplotlib color over vmax.
-
property
transform
¶ Get the transform value.
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property
visible_obj
¶ Get the visible_obj value.