Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 20.1
edited by paulapopa
on 2023/03/01 14:12
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
... ... @@ -1,128 +1,8 @@
1 -Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
2 -
3 -Immediate testing: [[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb]]
4 -
5 -== Purpose ==
6 -
7 -It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
8 -
9 -* surfaces of different types (cortex, face, skull, etc)
10 -* connectivity region centers
11 -* sensors locations (SEEG, MEG, EEG)
12 -
13 -== Inputs ==
14 -
15 -It supports the above data in the form of their corresponding TVB datatypes:
16 -
17 -* Surface (CorticalSurface, FaceSurface, etc)
18 -* Connectivity
19 -* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
20 -
21 -== Installation ==
22 -
23 -(% class="box" %)
24 -(((
25 -pip install tvb-widgets
26 -)))
27 -
28 -== API usage ==
29 -
30 -We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
31 -
32 -(% class="box" %)
33 -(((
34 -import tvbwidgets.api as api
35 -
36 -from tvb.simulator.lab import *
37 -
38 -from IPython.core.display_functions import display
39 -)))
40 -
41 -Then, there are 2 options to work with the widget:
42 -
43 -1. Use a file browser to load the data and automatically display it
44 -1. Use directly the API to load the data and display it
45 -
46 -
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 -
57 -For the second option, the API is described below:
58 -
59 -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:
60 -
61 -(% class="box" %)
62 -(((
63 -widget = api.HeadWidget()
64 -
65 -face = surfaces.FaceSurface().from_file()
66 -
67 -face.configure()
68 -
69 -widget.add_datatype(face)
70 -display(widget)
71 -)))
72 -
73 -{{html}}
74 -<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
75 -{{/html}}
76 -
77 -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.
78 -
79 -The **Config** object can be used to tweak the display options for each datatype.
80 -
81 -In the code below, we add a **Connectivity** and SEEG **Sensors:**
82 -
83 -(% class="box" %)
84 -(((
85 -conn = connectivity.Connectivity().from_file()
86 -
87 -conn.configure()
88 -
89 -widget.add_datatype(conn)
90 -
91 -
92 -seeg = sensors.SensorsInternal().from_file()
93 -
94 -seeg.configure()
95 -
96 -widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
97 -)))
98 -
99 -{{html}}
100 -<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
101 -{{/html}}
102 -
103 -We can also provide a **RegionMapping** to be used as colormap for a surface:
104 -
105 -(% class="box" %)
106 -(((
107 -reg_map = region_mapping.RegionMapping.from_file()
108 -
109 -config = api.HeadWidgetConfig(name='Cortex')
110 -
111 -config.add_region_mapping_as_cmap(reg_map)
112 -
113 -
114 -cortex = surfaces.CorticalSurface().from_file()
115 -
116 -cortex.configure()
117 -
118 -
119 -widget = api.HeadWidget()
120 -
121 -widget.add_datatype(cortex, config)
122 -
123 -display(widget)
124 -)))
125 -
126 -{{html}}
127 -<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
128 -{{/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