Wiki source code of Widget 3D Head

Version 22.1 by ldomide on 2023/03/08 17:28
Show last authors
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 src="https://drive.google.com/file/d/1lY3X5eqJfOLmkmHuBa2iq_Aas8mDPa1e/preview" width="840" height="480" allow="autoplay"></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 src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></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 src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></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 src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
132 {{/html}}
Public

TVB Widgets