Wiki source code of Widget 3D Head

Version 21.1 by paulapopa on 2023/03/01 17:12

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
16.1	3	Immediate testing: [[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb]]
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
18.1	41	Then, there are 2 options to work with the widget:
3.1	42
18.1	43	1. Use a file browser to load the data and automatically display it
	44	1. Use directly the API to load the data and display it
	45
	46
	47	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:
	48
3.1	49	(% class="box" %)
	50	(((
18.1	51	widget = api.HeadBrowser()
	52	display(widget)
	53	)))
	54
21.1	55	{{html}}
	56	<iframe src="https://drive.google.com/file/d/1lY3X5eqJfOLmkmHuBa2iq_Aas8mDPa1e/preview" width="840" height="480" allow="autoplay"></iframe>
	57	{{/html}}
18.1	58
21.1	59
18.1	60	For the second option, the API is described below:
	61
	62	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:
	63
	64	(% class="box" %)
	65	(((
12.1	66	widget = api.HeadWidget()
3.1	67
	68	face = surfaces.FaceSurface().from_file()
	69
	70	face.configure()
	71
9.1	72	widget.add_datatype(face)
	73	display(widget)
3.1	74	)))
	75
	76	{{html}}
5.1	77	<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
3.1	78	{{/html}}
	79
	80	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.
	81
	82	The Config object can be used to tweak the display options for each datatype.
	83
	84	In the code below, we add a Connectivity and SEEG Sensors:
	85
	86	(% class="box" %)
	87	(((
	88	conn = connectivity.Connectivity().from_file()
	89
	90	conn.configure()
	91
9.1	92	widget.add_datatype(conn)
3.1	93
	94
	95	seeg = sensors.SensorsInternal().from_file()
	96
	97	seeg.configure()
	98
13.1	99	widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
3.1	100	)))
	101
6.1	102	{{html}}
16.2	103	<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
6.1	104	{{/html}}
	105
3.1	106	We can also provide a RegionMapping to be used as colormap for a surface:
	107
	108	(% class="box" %)
	109	(((
	110	reg_map = region_mapping.RegionMapping.from_file()
	111
13.1	112	config = api.HeadWidgetConfig(name='Cortex')
3.1	113
	114	config.add_region_mapping_as_cmap(reg_map)
	115
	116
	117	cortex = surfaces.CorticalSurface().from_file()
	118
	119	cortex.configure()
	120
16.2	121
	122	widget = api.HeadWidget()
	123
9.1	124	widget.add_datatype(cortex, config)
16.2	125
	126	display(widget)
8.1	127	)))
3.1	128
	129	{{html}}
16.2	130	<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
3.1	131	{{/html}}

Wiki source code of Widget 3D Head

TVB Widgets