Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 19.1
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
... ... @@ -1,127 +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 -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:
48 -
49 -(% class="box" %)
50 -(((
51 -widget = api.HeadBrowser()
52 -display(widget)
53 -)))
54 -
55 -
56 -For the second option, the API is described below:
57 -
58 -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:
59 -
60 -(% class="box" %)
61 -(((
62 -widget = api.HeadWidget()
63 -
64 -face = surfaces.FaceSurface().from_file()
65 -
66 -face.configure()
67 -
68 -widget.add_datatype(face)
69 -display(widget)
70 -)))
71 -
72 -{{html}}
73 -<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
74 -{{/html}}
75 -
76 -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.
77 -
78 -The **Config** object can be used to tweak the display options for each datatype.
79 -
80 -In the code below, we add a **Connectivity** and SEEG **Sensors:**
81 -
82 -(% class="box" %)
83 -(((
84 -conn = connectivity.Connectivity().from_file()
85 -
86 -conn.configure()
87 -
88 -widget.add_datatype(conn)
89 -
90 -
91 -seeg = sensors.SensorsInternal().from_file()
92 -
93 -seeg.configure()
94 -
95 -widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
96 -)))
97 -
98 -{{html}}
99 -<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
100 -{{/html}}
101 -
102 -We can also provide a **RegionMapping** to be used as colormap for a surface:
103 -
104 -(% class="box" %)
105 -(((
106 -reg_map = region_mapping.RegionMapping.from_file()
107 -
108 -config = api.HeadWidgetConfig(name='Cortex')
109 -
110 -config.add_region_mapping_as_cmap(reg_map)
111 -
112 -
113 -cortex = surfaces.CorticalSurface().from_file()
114 -
115 -cortex.configure()
116 -
117 -
118 -widget = api.HeadWidget()
119 -
120 -widget.add_datatype(cortex, config)
121 -
122 -display(widget)
123 -)))
124 -
125 -{{html}}
126 -<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></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