Wiki source code of Widget 3D Head

Version 15.1 by ldomide on 2022/05/24 09:19

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
15.1	3	Immediate testing here: [[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks]]
11.1	4
3.1	5	== Purpose ==
	6
12.1	7	It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
3.1	8
	9	* surfaces of different types (cortex, face, skull, etc)
	10	* connectivity region centers
	11	* sensors locations (SEEG, MEG, EEG)
	12
	13	== Inputs ==
	14
	15	It supports the above data in the form of their corresponding TVB datatypes:
	16
	17	* Surface (CorticalSurface, FaceSurface, etc)
	18	* Connectivity
	19	* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
	20
	21	== Installation ==
	22
	23	(% class="box" %)
	24	(((
	25	pip install tvb-widgets
	26	)))
	27
	28	== API usage ==
	29
	30	We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
	31
	32	(% class="box" %)
	33	(((
	34	import tvbwidgets.api as api
	35
	36	from tvb.simulator.lab import *
	37
	38	from IPython.core.display_functions import display
	39	)))
	40
12.1	41	Then, 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:
3.1	42
	43	(% class="box" %)
	44	(((
12.1	45	widget = api.HeadWidget()
3.1	46
	47	face = surfaces.FaceSurface().from_file()
	48
	49	face.configure()
	50
9.1	51	widget.add_datatype(face)
	52	display(widget)
3.1	53	)))
	54
	55	{{html}}
5.1	56	<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
3.1	57	{{/html}}
	58
	59	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.
	60
	61	The Config object can be used to tweak the display options for each datatype.
	62
	63	In the code below, we add a Connectivity and SEEG Sensors:
	64
	65	(% class="box" %)
	66	(((
	67	conn = connectivity.Connectivity().from_file()
	68
	69	conn.configure()
	70
9.1	71	widget.add_datatype(conn)
3.1	72
	73
	74	seeg = sensors.SensorsInternal().from_file()
	75
	76	seeg.configure()
	77
13.1	78	widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
3.1	79	)))
	80
6.1	81	{{html}}
	82	<iframe src="https://drive.google.com/file/d/1vFqqzXle8VGcHaLB-OdE-6BdetK9aJ1T/preview" width="840" height="480" allow="autoplay"></iframe>
	83	{{/html}}
	84
3.1	85	We can also provide a RegionMapping to be used as colormap for a surface:
	86
	87	(% class="box" %)
	88	(((
	89	reg_map = region_mapping.RegionMapping.from_file()
	90
13.1	91	config = api.HeadWidgetConfig(name='Cortex')
3.1	92
	93	config.add_region_mapping_as_cmap(reg_map)
	94
	95
	96	cortex = surfaces.CorticalSurface().from_file()
	97
	98	cortex.configure()
	99
9.1	100	widget.add_datatype(cortex, config)
8.1	101	)))
3.1	102
	103	{{html}}
6.1	104	<iframe src="https://drive.google.com/file/d/1z2yEuQWUT2Poxh63adYbBdhKPcWGskex/preview" width="840" height="480" allow="autoplay"></iframe>
3.1	105	{{/html}}

Wiki source code of Widget 3D Head

TVB Widgets