Wiki source code of Widget 3D Head

Version 22.1 by ldomide on 2023/03/08 17:28

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)
	12	* connectivity region centers
	13	* sensors locations (SEEG, MEG, EEG)
	14
	15	== Inputs ==
	16
	17	It supports the above data in the form of their corresponding TVB datatypes:
	18
	19	* Surface (CorticalSurface, FaceSurface, etc)
	20	* Connectivity
	21	* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
	22
	23	== Installation ==
	24
	25	(% class="box" %)
	26	(((
	27	pip install tvb-widgets
	28	)))
	29
	30	== API usage ==
	31
	32	We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
	33
	34	(% class="box" %)
	35	(((
	36	import tvbwidgets.api as api
	37
	38	from tvb.simulator.lab import *
	39
	40	from IPython.core.display_functions import display
	41	)))
	42
18.1	43	Then, there are 2 options to work with the widget:
3.1	44
18.1	45	1. Use a file browser to load the data and automatically display it
	46	1. Use directly the API to load the data and display it
	47
	48	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:
	49
3.1	50	(% class="box" %)
	51	(((
18.1	52	widget = api.HeadBrowser()
	53	display(widget)
	54	)))
	55
21.1	56	{{html}}
	57	<iframe src="https://drive.google.com/file/d/1lY3X5eqJfOLmkmHuBa2iq_Aas8mDPa1e/preview" width="840" height="480" allow="autoplay"></iframe>
	58	{{/html}}
18.1	59
21.1	60
18.1	61	For the second option, the API is described below:
	62
	63	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:
	64
	65	(% class="box" %)
	66	(((
12.1	67	widget = api.HeadWidget()
3.1	68
	69	face = surfaces.FaceSurface().from_file()
	70
	71	face.configure()
	72
9.1	73	widget.add_datatype(face)
	74	display(widget)
3.1	75	)))
	76
	77	{{html}}
5.1	78	<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
3.1	79	{{/html}}
	80
	81	Next, we can continue adding other datatypes to this widget, by calling //add_datatype// multiple times. A maximum of 10 datatypes are supported by this widget.
	82
	83	The Config object can be used to tweak the display options for each datatype.
	84
	85	In the code below, we add a Connectivity and SEEG Sensors:
	86
	87	(% class="box" %)
	88	(((
	89	conn = connectivity.Connectivity().from_file()
	90
	91	conn.configure()
	92
9.1	93	widget.add_datatype(conn)
3.1	94
	95
	96	seeg = sensors.SensorsInternal().from_file()
	97
	98	seeg.configure()
	99
13.1	100	widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
3.1	101	)))
	102
6.1	103	{{html}}
16.2	104	<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
6.1	105	{{/html}}
	106
3.1	107	We can also provide a RegionMapping to be used as colormap for a surface:
	108
	109	(% class="box" %)
	110	(((
	111	reg_map = region_mapping.RegionMapping.from_file()
	112
13.1	113	config = api.HeadWidgetConfig(name='Cortex')
3.1	114
	115	config.add_region_mapping_as_cmap(reg_map)
	116
	117
	118	cortex = surfaces.CorticalSurface().from_file()
	119
	120	cortex.configure()
	121
16.2	122
	123	widget = api.HeadWidget()
	124
9.1	125	widget.add_datatype(cortex, config)
16.2	126
	127	display(widget)
8.1	128	)))
3.1	129
	130	{{html}}
16.2	131	<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
3.1	132	{{/html}}

Wiki source code of Widget 3D Head

TVB Widgets