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Author

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1		-XWiki.paulapopa
	1	+XWiki.reginafilange

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		-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]]
	3	+This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>https://pypi.org/project/tvb-widgets/]]
4	4
	5	+//**tvb-widgets**// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
	6	+
5	5	== Purpose ==
6	6
7	7	It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
8	8
9	9	* surfaces of different types (cortex, face, skull, etc)
10		-* connectivity region centers
	12	+* connectivity region centers and edges
11	11	* sensors locations (SEEG, MEG, EEG)
12	12
	15	+On cortical surfaces, it can also display region parcellation.
	16	+
13	13	== Inputs ==
14	14
15	15	It supports the above data in the form of their corresponding TVB datatypes:
16	16
17	17	* Surface (CorticalSurface, FaceSurface, etc)
	22	+* Parcellation (RegionMapping)
18	18	* Connectivity
19	19	* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
20	20
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38	38	from IPython.core.display_functions import display
39	39	)))
40	40
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:
	46	+Then, there are 2 options to work with the widget:
42	42
	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	+
43	43	(% class="box" %)
44	44	(((
	55	+widget = api.HeadBrowser()
	56	+display(widget)
	57	+)))
	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	+
	63	+
	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	+(((
45	45	widget = api.HeadWidget()
46	46
47	47	face = surfaces.FaceSurface().from_file()
...	...	@@ -53,13 +53,11 @@
53	53	)))
54	54
55	55	{{html}}
56		-<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
	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>
57	57	{{/html}}
58	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.
	84	+Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
60	60
61		-The **Config** object can be used to tweak the display options for each datatype.
62		-
63	63	In the code below, we add a **Connectivity** and SEEG **Sensors:**
64	64
65	65	(% class="box" %)
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75	75
76	76	seeg.configure()
77	77
78		-widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
	101	+widget.add_datatype(seeg)
79	79	)))
80	80
81	81	{{html}}
82		-<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
	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>
83	83	{{/html}}
84	84
85		-We can also provide a **RegionMapping** to be used as colormap for a surface:
	108	+We can also provide a **RegionMapping** to be used as parcellation for a surface:
86	86
87	87	(% class="box" %)
88	88	(((
89	89	reg_map = region_mapping.RegionMapping.from_file()
90	90
91		-config = api.HeadWidgetConfig(name='Cortex')
92	92
93		-config.add_region_mapping_as_cmap(reg_map)
94		-
95		-
96	96	cortex = surfaces.CorticalSurface().from_file()
97	97
98	98	cortex.configure()
99	99
100	100
101		-widget = api.HeadWidget()
	120	+widget.add_datatype(cortex, reg_map)
102	102
103		-widget.add_datatype(cortex, config)
104		-
105	105	display(widget)
106	106	)))
107	107
108	108	{{html}}
109		-<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
	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>
110	110	{{/html}}