Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 27.1
edited by paulapopa
on 2025/05/30 14:45
Change comment: There is no comment for this version
To version 21.1
edited by paulapopa
on 2023/03/01 17:12
Change comment: There is no comment for this version

Summary

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1 1  Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
2 2  
3 -This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>https://pypi.org/project/tvb-widgets/]]
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 4  
5 -//**tvb-widgets**// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
6 -
7 7  == Purpose ==
8 8  
9 9  It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
10 10  
11 11  * surfaces of different types (cortex, face, skull, etc)
12 -* connectivity region centers and edges
10 +* connectivity region centers
13 13  * sensors locations (SEEG, MEG, EEG)
14 14  
15 -On cortical surfaces, it can also display region parcellation. 
16 -
17 17  == Inputs ==
18 18  
19 19  It supports the above data in the form of their corresponding TVB datatypes:
20 20  
21 21  * Surface (CorticalSurface, FaceSurface, etc)
22 -* Parcellation (RegionMapping)
23 23  * Connectivity
24 24  * Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
25 25  
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34 34  
35 35  We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
36 36  
37 -{{code language="python" layout="LINENUMBERS"}}
32 +(% class="box" %)
33 +(((
38 38  import tvbwidgets.api as api
35 +
39 39  from tvb.simulator.lab import *
40 -from IPython.core.display_functions import display 
41 -{{/code}}
42 42  
38 +from IPython.core.display_functions import display
39 +)))
40 +
43 43  Then, there are 2 options to work with the widget:
44 44  
45 45  1. Use a file browser to load the data and automatically display it
46 46  1. Use directly the API to load the data and display it
47 47  
46 +
48 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 49  
50 -{{code language="python" layout="LINENUMBERS"}}
49 +(% class="box" %)
50 +(((
51 51  widget = api.HeadBrowser()
52 52  display(widget)
53 -{{/code}}
53 +)))
54 54  
55 +{{html}}
56 +<iframe src="https://drive.google.com/file/d/1lY3X5eqJfOLmkmHuBa2iq_Aas8mDPa1e/preview" width="840" height="480" allow="autoplay"></iframe>
57 +{{/html}}
55 55  
59 +
56 56  For the second option, the API is described below:
57 57  
58 -In a cell, we load the data using the TVB API:
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:
59 59  
60 -{{code language="python" layout="LINENUMBERS"}}
61 -surface = surfaces.Surface.from_file()
62 -surface.configure()
64 +(% class="box" %)
65 +(((
66 +widget = api.HeadWidget()
63 63  
64 -face = surfaces.Surface.from_file('face_8614.zip')
68 +face = surfaces.FaceSurface().from_file()
69 +
65 65  face.configure()
66 66  
67 -reg_map = region_mapping.RegionMapping.from_file()
72 +widget.add_datatype(face)
73 +display(widget)
74 +)))
68 68  
69 -conn = connectivity.Connectivity.from_file()
76 +{{html}}
77 +<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
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 +
70 70  conn.configure()
71 71  
72 -seeg = sensors.SensorsInternal.from_file()
92 +widget.add_datatype(conn)
93 +
94 +
95 +seeg = sensors.SensorsInternal().from_file()
96 +
73 73  seeg.configure()
74 -{{/code}}
75 75  
76 -Then we prepare the **HeadWidget** for display:
99 +widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
100 +)))
77 77  
78 -{{code language="python" layout="LINENUMBERS"}}
79 -widget = api.HeadWidget([face, conn, seeg])
80 -display(widget)
81 -{{/code}}
102 +{{html}}
103 +<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
104 +{{/html}}
82 82  
83 -[[image:head.png]]
106 +We can also provide a **RegionMapping** to be used as colormap for a surface:
84 84  
85 -Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
108 +(% class="box" %)
109 +(((
110 +reg_map = region_mapping.RegionMapping.from_file()
86 86  
87 -In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
112 +config = api.HeadWidgetConfig(name='Cortex')
88 88  
89 -{{code language="python" layout="LINENUMBERS"}}
90 -widget.add_datatype(surface, reg_map)
91 -{{/code}}
114 +config.add_region_mapping_as_cmap(reg_map)
92 92  
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 +
93 93  {{html}}
94 -<iframe width="840" height="480" src="https://www.youtube.com/embed/aDC2TJm2NxM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
130 +<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
95 95  {{/html}}
conncenters.png
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cort.png
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head.png
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TVB Widgets