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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 25.1
edited by reginafilange
on 2025/05/30 13:47
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.paulapopa
1 +XWiki.reginafilange
Content
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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 -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]]
3 +This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>https://pypi.org/project/tvb-widgets/]]
4 4  
5 +//**tvb-widgets**// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
6 +
5 5  == Purpose ==
6 6  
7 7  It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
8 8  
9 9  * surfaces of different types (cortex, face, skull, etc)
10 -* connectivity region centers
12 +* connectivity region centers and edges
11 11  * sensors locations (SEEG, MEG, EEG)
12 12  
15 +On cortical surfaces, it can also display region parcellation. 
16 +
13 13  == Inputs ==
14 14  
15 15  It supports the above data in the form of their corresponding TVB datatypes:
16 16  
17 17  * Surface (CorticalSurface, FaceSurface, etc)
22 +* Parcellation (RegionMapping)
18 18  * Connectivity
19 19  * Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
20 20  
... ... @@ -43,8 +43,6 @@
43 43  1. Use a file browser to load the data and automatically display it
44 44  1. Use directly the API to load the data and display it
45 45  
46 -
47 -
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 50  (% class="box" %)
... ... @@ -53,7 +53,11 @@
53 53  display(widget)
54 54  )))
55 55  
59 +{{html}}
60 +<iframe width="840" height="480" src="https://www.youtube.com/embed/BCCh-wdcnVo" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
61 +{{/html}}
56 56  
63 +
57 57  For the second option, the API is described below:
58 58  
59 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:
... ... @@ -71,13 +71,11 @@
71 71  )))
72 72  
73 73  {{html}}
74 -<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
81 +<iframe width="840" height="480" src="https://www.youtube.com/embed/8bmjKp3BYFA" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
75 75  {{/html}}
76 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.
84 +Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
78 78  
79 -The **Config** object can be used to tweak the display options for each datatype.
80 -
81 81  In the code below, we add a **Connectivity** and SEEG **Sensors:**
82 82  
83 83  (% class="box" %)
... ... @@ -93,36 +93,30 @@
93 93  
94 94  seeg.configure()
95 95  
96 -widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
101 +widget.add_datatype(seeg)
97 97  )))
98 98  
99 99  {{html}}
100 -<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
105 +<iframe width="840" height="480" src="https://www.youtube.com/embed/6UQhL9gd1HM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
101 101  {{/html}}
102 102  
103 -We can also provide a **RegionMapping** to be used as colormap for a surface:
108 +We can also provide a **RegionMapping** to be used as parcellation for a surface:
104 104  
105 105  (% class="box" %)
106 106  (((
107 107  reg_map = region_mapping.RegionMapping.from_file()
108 108  
109 -config = api.HeadWidgetConfig(name='Cortex')
110 110  
111 -config.add_region_mapping_as_cmap(reg_map)
112 -
113 -
114 114  cortex = surfaces.CorticalSurface().from_file()
115 115  
116 116  cortex.configure()
117 117  
118 118  
119 -widget = api.HeadWidget()
120 +widget.add_datatype(cortex, reg_map)
120 120  
121 -widget.add_datatype(cortex, config)
122 -
123 123  display(widget)
124 124  )))
125 125  
126 126  {{html}}
127 -<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
126 +<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>
128 128  {{/html}}
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TVB Widgets