Wiki source code of Widget 3D Head

Version 25.1 by reginafilange on 2025/05/30 13:47

version	line-number	content
15.1	1	Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
3.1	2
22.1	3	This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>https://pypi.org/project/tvb-widgets/]]
11.1	4
22.1	5	//tvb-widgets// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
	6
3.1	7	== Purpose ==
	8
12.1	9	It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
3.1	10
	11	* surfaces of different types (cortex, face, skull, etc)
25.1	12	* connectivity region centers and edges
3.1	13	* sensors locations (SEEG, MEG, EEG)
	14
25.1	15	On cortical surfaces, it can also display region parcellation.
	16
3.1	17	== Inputs ==
	18
	19	It supports the above data in the form of their corresponding TVB datatypes:
	20
	21	* Surface (CorticalSurface, FaceSurface, etc)
25.1	22	* Parcellation (RegionMapping)
3.1	23	* Connectivity
	24	* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
	25
	26	== Installation ==
	27
	28	(% class="box" %)
	29	(((
	30	pip install tvb-widgets
	31	)))
	32
	33	== API usage ==
	34
	35	We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
	36
	37	(% class="box" %)
	38	(((
	39	import tvbwidgets.api as api
	40
	41	from tvb.simulator.lab import *
	42
	43	from IPython.core.display_functions import display
	44	)))
	45
18.1	46	Then, there are 2 options to work with the widget:
3.1	47
18.1	48	1. Use a file browser to load the data and automatically display it
	49	1. Use directly the API to load the data and display it
	50
	51	For the first option, you have to run the following 2 lines of code in a notebook cell and then just use the UI controls:
	52
3.1	53	(% class="box" %)
	54	(((
18.1	55	widget = api.HeadBrowser()
	56	display(widget)
	57	)))
	58
21.1	59	{{html}}
24.1	60	<iframe width="840" height="480" src="https://www.youtube.com/embed/BCCh-wdcnVo" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
	61	{{/html}}
18.1	62
21.1	63
18.1	64	For the second option, the API is described below:
	65
	66	In a new cell, we instantiate the HeadWidget and a FaceSurface datatype that we want to visualize. Using the //add_datatype// method we add the surface to our widget and __display__ the widget:
	67
	68	(% class="box" %)
	69	(((
12.1	70	widget = api.HeadWidget()
3.1	71
	72	face = surfaces.FaceSurface().from_file()
	73
	74	face.configure()
	75
9.1	76	widget.add_datatype(face)
	77	display(widget)
3.1	78	)))
	79
	80	{{html}}
23.1	81	<iframe width="840" height="480" src="https://www.youtube.com/embed/8bmjKp3BYFA" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
3.1	82	{{/html}}
	83
25.1	84	Next, we can continue adding other datatypes to this widget, by calling //add_datatype// multiple times.
3.1	85
	86	In the code below, we add a Connectivity and SEEG Sensors:
	87
	88	(% class="box" %)
	89	(((
	90	conn = connectivity.Connectivity().from_file()
	91
	92	conn.configure()
	93
9.1	94	widget.add_datatype(conn)
3.1	95
	96
	97	seeg = sensors.SensorsInternal().from_file()
	98
	99	seeg.configure()
	100
25.1	101	widget.add_datatype(seeg)
3.1	102	)))
	103
6.1	104	{{html}}
23.1	105	<iframe width="840" height="480" src="https://www.youtube.com/embed/6UQhL9gd1HM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
6.1	106	{{/html}}
	107
25.1	108	We can also provide a RegionMapping to be used as parcellation for a surface:
3.1	109
	110	(% class="box" %)
	111	(((
	112	reg_map = region_mapping.RegionMapping.from_file()
	113
	114
	115	cortex = surfaces.CorticalSurface().from_file()
	116
	117	cortex.configure()
	118
16.2	119
25.1	120	widget.add_datatype(cortex, reg_map)
16.2	121
	122	display(widget)
8.1	123	)))
3.1	124
	125	{{html}}
24.1	126	<iframe width="840" height="480" src="https://www.youtube.com/embed/aDC2TJm2NxM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
3.1	127	{{/html}}

Wiki source code of Widget 3D Head

TVB Widgets