Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 24.1
edited by paulapopa
on 2023/03/24 07:58
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
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1 -Widget 3D Head
1 +Widget 3D
Author
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1 -XWiki.paulapopa
1 +XWiki.ldomide
Content
... ... @@ -1,132 +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
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>
58 -{{/html}}
59 -
60 -
61 -For the second option, the API is described below:
62 -
63 -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:
64 -
65 -(% class="box" %)
66 -(((
67 -widget = api.HeadWidget()
68 -
69 -face = surfaces.FaceSurface().from_file()
70 -
71 -face.configure()
72 -
73 -widget.add_datatype(face)
74 -display(widget)
75 -)))
76 -
77 -{{html}}
78 -<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>
79 -{{/html}}
80 -
81 -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.
82 -
83 -The **Config** object can be used to tweak the display options for each datatype.
84 -
85 -In the code below, we add a **Connectivity** and SEEG **Sensors:**
86 -
87 -(% class="box" %)
88 -(((
89 -conn = connectivity.Connectivity().from_file()
90 -
91 -conn.configure()
92 -
93 -widget.add_datatype(conn)
94 -
95 -
96 -seeg = sensors.SensorsInternal().from_file()
97 -
98 -seeg.configure()
99 -
100 -widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
101 -)))
102 -
103 -{{html}}
104 -<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>
105 -{{/html}}
106 -
107 -We can also provide a **RegionMapping** to be used as colormap for a surface:
108 -
109 -(% class="box" %)
110 -(((
111 -reg_map = region_mapping.RegionMapping.from_file()
112 -
113 -config = api.HeadWidgetConfig(name='Cortex')
114 -
115 -config.add_region_mapping_as_cmap(reg_map)
116 -
117 -
118 -cortex = surfaces.CorticalSurface().from_file()
119 -
120 -cortex.configure()
121 -
122 -
123 -widget = api.HeadWidget()
124 -
125 -widget.add_datatype(cortex, config)
126 -
127 -display(widget)
128 -)))
129 -
130 -{{html}}
131 -<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>
132 -{{/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