Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 25.1
edited by reginafilange
on 2025/05/30 13:47
Change comment: There is no comment for this version
To version 2.1
edited by ldomide
on 2022/03/23 21:43
Change comment: There is no comment for this version

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -Widget 3D Head
1 +Widget 3D
Author
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1 -XWiki.reginafilange
1 +XWiki.ldomide
Content
... ... @@ -1,127 +1,8 @@
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 -
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 -(((
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}}
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 +
8 +{{html}}<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/preview" width="840" height="480" allow="autoplay"></iframe>{{/html}}
Public

TVB Widgets