Wiki source code of Widget 3D Head

Version 18.1 by paulapopa on 2023/03/01 14:12
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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()
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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()
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108 config = api.HeadWidgetConfig(name='Cortex')
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110 config.add_region_mapping_as_cmap(reg_map)
111
112
113 cortex = surfaces.CorticalSurface().from_file()
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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}}
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TVB Widgets