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1		-XWiki.paulapopa
	1	+XWiki.reginafilange

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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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29	29
30	30	We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
31	31
32		-(% class="box" %)
33		-(((
	37	+{{code language="python" layout="LINENUMBERS"}}
34	34	import tvbwidgets.api as api
35		-
36	36	from tvb.simulator.lab import *
	40	+from IPython.core.display_functions import display
	41	+{{/code}}
37	37
38		-from IPython.core.display_functions import display
39		-)))
40		-
41	41	Then, there are 2 options to work with the widget:
42	42
43	43	1. Use a file browser to load the data and automatically display it
44	44	1. Use directly the API to load the data and display it
45	45
46		-
47		-
48	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	49
50		-(% class="box" %)
51		-(((
	50	+{{code language="python" layout="LINENUMBERS"}}
52	52	widget = api.HeadBrowser()
53	53	display(widget)
54		-)))
	53	+{{/code}}
55	55
56	56
57	57	For the second option, the API is described below:
58	58
59		-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:
	58	+In a cell, we load the data using the TVB API:
60	60
61		-(% class="box" %)
62		-(((
63		-widget = api.HeadWidget()
	60	+{{code language="python" layout="LINENUMBERS"}}
	61	+surface = surfaces.Surface.from_file()
	62	+surface.configure()
64	64
65		-face = surfaces.FaceSurface().from_file()
66		-
	64	+face = surfaces.Surface.from_file('face_8614.zip')
67	67	face.configure()
68	68
69		-widget.add_datatype(face)
70		-display(widget)
71		-)))
	67	+reg_map = region_mapping.RegionMapping.from_file()
72	72
73		-{{html}}
74		-<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
75		-{{/html}}
76		-
77		-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.
78		-
79		-The **Config** object can be used to tweak the display options for each datatype.
80		-
81		-In the code below, we add a **Connectivity** and SEEG **Sensors:**
82		-
83		-(% class="box" %)
84		-(((
85		-conn = connectivity.Connectivity().from_file()
86		-
	69	+conn = connectivity.Connectivity.from_file()
87	87	conn.configure()
88	88
89		-widget.add_datatype(conn)
90		-
91		-
92		-seeg = sensors.SensorsInternal().from_file()
93		-
	72	+seeg = sensors.SensorsInternal.from_file()
94	94	seeg.configure()
	74	+{{/code}}
95	95
96		-widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
97		-)))
	76	+Then we prepare the **HeadWidget** for display:
98	98
99		-{{html}}
100		-<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
101		-{{/html}}
	78	+{{code language="python" layout="LINENUMBERS"}}
	79	+widget = api.HeadWidget([face, conn, seeg])
	80	+display(widget)
	81	+{{/code}}
102	102
103		-We can also provide a **RegionMapping** to be used as colormap for a surface:
104	104
105		-(% class="box" %)
106		-(((
107		-reg_map = region_mapping.RegionMapping.from_file()
	84	+Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
108	108
109		-config = api.HeadWidgetConfig(name='Cortex')
	86	+In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
110	110
111		-config.add_region_mapping_as_cmap(reg_map)
	88	+{{code language="python" layout="LINENUMBERS"}}
	89	+widget.add_datatype(surface, reg_map)
	90	+{{/code}}
112	112
113		-
114		-cortex = surfaces.CorticalSurface().from_file()
115		-
116		-cortex.configure()
117		-
118		-
119		-widget = api.HeadWidget()
120		-
121		-widget.add_datatype(cortex, config)
122		-
123		-display(widget)
124		-)))
125		-
126	126	{{html}}
127		-<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
	93	+<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>
128	128	{{/html}}

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	1	+XWiki.reginafilange

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