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Author

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1		-XWiki.reginafilange
	1	+XWiki.paulapopa

Content

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1	1	Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
2	2
3		-This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>https://pypi.org/project/tvb-widgets/]]
	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]]
4	4
5		-//**tvb-widgets**// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
6		-
7	7	== Purpose ==
8	8
9	9	It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
10	10
11	11	* surfaces of different types (cortex, face, skull, etc)
12		-* connectivity region centers and edges
	10	+* connectivity region centers
13	13	* sensors locations (SEEG, MEG, EEG)
14	14
15		-On cortical surfaces, it can also display region parcellation.
16		-
17	17	== Inputs ==
18	18
19	19	It supports the above data in the form of their corresponding TVB datatypes:
20	20
21	21	* Surface (CorticalSurface, FaceSurface, etc)
22		-* Parcellation (RegionMapping)
23	23	* Connectivity
24	24	* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
25	25
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48	48	1. Use a file browser to load the data and automatically display it
49	49	1. Use directly the API to load the data and display it
50	50
	46	+
51	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	52
53	53	(% class="box" %)
...	...	@@ -56,11 +56,7 @@
56	56	display(widget)
57	57	)))
58	58
59		-{{html}}
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}}
62	62
63		-
64	64	For the second option, the API is described below:
65	65
66	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:
...	...	@@ -78,11 +78,13 @@
78	78	)))
79	79
80	80	{{html}}
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>
	73	+<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
82	82	{{/html}}
83	83
84		-Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
	76	+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.
85	85
	78	+The **Config** object can be used to tweak the display options for each datatype.
	79	+
86	86	In the code below, we add a **Connectivity** and SEEG **Sensors:**
87	87
88	88	(% class="box" %)
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98	98
99	99	seeg.configure()
100	100
101		-widget.add_datatype(seeg)
	95	+widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
102	102	)))
103	103
104	104	{{html}}
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>
	99	+<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
106	106	{{/html}}
107	107
108		-We can also provide a **RegionMapping** to be used as parcellation for a surface:
	102	+We can also provide a **RegionMapping** to be used as colormap for a surface:
109	109
110	110	(% class="box" %)
111	111	(((
112	112	reg_map = region_mapping.RegionMapping.from_file()
113	113
	108	+config = api.HeadWidgetConfig(name='Cortex')
114	114
	110	+config.add_region_mapping_as_cmap(reg_map)
	111	+
	112	+
115	115	cortex = surfaces.CorticalSurface().from_file()
116	116
117	117	cortex.configure()
118	118
119	119
120		-widget.add_datatype(cortex, reg_map)
	118	+widget = api.HeadWidget()
121	121
	120	+widget.add_datatype(cortex, config)
	121	+
122	122	display(widget)
123	123	)))
124	124
125	125	{{html}}
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>
	126	+<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
127	127	{{/html}}