Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 2.1
edited by ldomide
on 2022/03/23 21:43
Change comment: There is no comment for this version
To version 23.1
edited by paulapopa
on 2023/03/23 13:16
Change comment: There is no comment for this version

Summary

Details

Page properties
Title
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1 -Widget 3D
1 +Widget 3D Head
Author
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1 -XWiki.ldomide
1 +XWiki.paulapopa
Content
... ... @@ -1,8 +1,131 @@
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}}
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
13 +* sensors locations (SEEG, MEG, EEG)
14 +
15 +== Inputs ==
16 +
17 +It supports the above data in the form of their corresponding TVB datatypes:
18 +
19 +* Surface (CorticalSurface, FaceSurface, etc)
20 +* Connectivity
21 +* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
22 +
23 +== Installation ==
24 +
25 +(% class="box" %)
26 +(((
27 +pip install tvb-widgets
28 +)))
29 +
30 +== API usage ==
31 +
32 +We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
33 +
34 +(% class="box" %)
35 +(((
36 +import tvbwidgets.api as api
37 +
38 +from tvb.simulator.lab import *
39 +
40 +from IPython.core.display_functions import display
41 +)))
42 +
43 +Then, there are 2 options to work with the widget:
44 +
45 +1. Use a file browser to load the data and automatically display it
46 +1. Use directly the API to load the data and display it
47 +
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 +
50 +(% class="box" %)
51 +(((
52 +widget = api.HeadBrowser()
53 +display(widget)
54 +)))
55 +
56 +{{html}}
57 +<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>{{/html}}
58 +
59 +
60 +For the second option, the API is described below:
61 +
62 +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:
63 +
64 +(% class="box" %)
65 +(((
66 +widget = api.HeadWidget()
67 +
68 +face = surfaces.FaceSurface().from_file()
69 +
70 +face.configure()
71 +
72 +widget.add_datatype(face)
73 +display(widget)
74 +)))
75 +
76 +{{html}}
77 +<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>
78 +{{/html}}
79 +
80 +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.
81 +
82 +The **Config** object can be used to tweak the display options for each datatype.
83 +
84 +In the code below, we add a **Connectivity** and SEEG **Sensors:**
85 +
86 +(% class="box" %)
87 +(((
88 +conn = connectivity.Connectivity().from_file()
89 +
90 +conn.configure()
91 +
92 +widget.add_datatype(conn)
93 +
94 +
95 +seeg = sensors.SensorsInternal().from_file()
96 +
97 +seeg.configure()
98 +
99 +widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
100 +)))
101 +
102 +{{html}}
103 +<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>
104 +{{/html}}
105 +
106 +We can also provide a **RegionMapping** to be used as colormap for a surface:
107 +
108 +(% class="box" %)
109 +(((
110 +reg_map = region_mapping.RegionMapping.from_file()
111 +
112 +config = api.HeadWidgetConfig(name='Cortex')
113 +
114 +config.add_region_mapping_as_cmap(reg_map)
115 +
116 +
117 +cortex = surfaces.CorticalSurface().from_file()
118 +
119 +cortex.configure()
120 +
121 +
122 +widget = api.HeadWidget()
123 +
124 +widget.add_datatype(cortex, config)
125 +
126 +display(widget)
127 +)))
128 +
129 +{{html}}
130 +<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
131 +{{/html}}
Public

TVB Widgets