Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 23.1
edited by paulapopa
on 2023/03/23 13:16
Change comment: There is no comment for this version
To version 1.1
edited by ldomide
on 2022/03/23 21:41
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
... ... @@ -1,131 +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
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 -
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 + 
56 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>
9 +<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/preview" width="640" height="480" allow="autoplay"></iframe>
78 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