Summary

• Page properties (3 modified, 0 added, 0 removed)

Details

Page properties

Title

...	...	@@ -1,1 +1,1 @@
1		-Widget 3D Head
	1	+Widget 3D

Author

...	...	@@ -1,1 +1,1 @@
1		-XWiki.reginafilange
	1	+XWiki.ldomide

Content

...	...	@@ -1,127 +1,10 @@
1		-Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
2		-
3		-This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>https://pypi.org/project/tvb-widgets/]]
4		-
5		-//**tvb-widgets**// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
6		-
7		-== Purpose ==
8		-
9		-It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
10		-
11		-* surfaces of different types (cortex, face, skull, etc)
12		-* connectivity region centers and edges
13		-* sensors locations (SEEG, MEG, EEG)
14		-
15		-On cortical surfaces, it can also display region parcellation.
16		-
17		-== Inputs ==
18		-
19		-It supports the above data in the form of their corresponding TVB datatypes:
20		-
21		-* Surface (CorticalSurface, FaceSurface, etc)
22		-* Parcellation (RegionMapping)
23		-* Connectivity
24		-* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
25		-
26		-== Installation ==
27		-
28		-(% class="box" %)
29		-(((
30		-pip install tvb-widgets
31		-)))
32		-
33		-== API usage ==
34		-
35		-We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
36		-
37		-(% class="box" %)
38		-(((
39		-import tvbwidgets.api as api
40		-
41		-from tvb.simulator.lab import *
42		-
43		-from IPython.core.display_functions import display
44		-)))
45		-
46		-Then, there are 2 options to work with the widget:
47		-
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		-
53		-(% class="box" %)
54		-(((
55		-widget = api.HeadBrowser()
56		-display(widget)
57		-)))
58		-
	1	+TODO
	2	+! pip install -i tvb-widgets
	3	+from tvbwidgets.api import SurfaceWidget
	4	+from IPython.core.display_functions import display
	5	+w3d = SurfaceWidget(...)
	6	+display(w3d)
	7	+
59	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>
	9	+<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/preview" width="640" height="480" allow="autoplay"></iframe>
61	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		-(((
70		-widget = api.HeadWidget()
71		-
72		-face = surfaces.FaceSurface().from_file()
73		-
74		-face.configure()
75		-
76		-widget.add_datatype(face)
77		-display(widget)
78		-)))
79		-
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>
82		-{{/html}}
83		-
84		-Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
85		-
86		-In the code below, we add a **Connectivity** and SEEG **Sensors:**
87		-
88		-(% class="box" %)
89		-(((
90		-conn = connectivity.Connectivity().from_file()
91		-
92		-conn.configure()
93		-
94		-widget.add_datatype(conn)
95		-
96		-
97		-seeg = sensors.SensorsInternal().from_file()
98		-
99		-seeg.configure()
100		-
101		-widget.add_datatype(seeg)
102		-)))
103		-
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>
106		-{{/html}}
107		-
108		-We can also provide a **RegionMapping** to be used as parcellation for a surface:
109		-
110		-(% class="box" %)
111		-(((
112		-reg_map = region_mapping.RegionMapping.from_file()
113		-
114		-
115		-cortex = surfaces.CorticalSurface().from_file()
116		-
117		-cortex.configure()
118		-
119		-
120		-widget.add_datatype(cortex, reg_map)
121		-
122		-display(widget)
123		-)))
124		-
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>
127		-{{/html}}