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Author

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1		-XWiki.reginafilange
	1	+XWiki.paulapopa

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

head.png

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1		-XWiki.reginafilange

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