Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 8.1
edited by paulapopa
on 2022/03/30 15:27
Change comment: There is no comment for this version
To version 29.1
edited by paulapopa
on 2025/05/30 14:55
Change comment: There is no comment for this version

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -Widget 3D
1 +Widget 3D Head
Content
... ... @@ -1,18 +1,25 @@
1 -TODO - Not yet released!
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/]]
4 +
5 +//**tvb-widgets**// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
6 +
3 3  == Purpose ==
4 4  
5 -It is a Jupyter widget intended for visualization of the 3D data available for a patient:
9 +It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
6 6  
7 7  * surfaces of different types (cortex, face, skull, etc)
8 -* connectivity region centers
12 +* connectivity region centers and edges
9 9  * sensors locations (SEEG, MEG, EEG)
10 10  
15 +On cortical surfaces, it can also display region parcellation. 
16 +
11 11  == Inputs ==
12 12  
13 13  It supports the above data in the form of their corresponding TVB datatypes:
14 14  
15 15  * Surface (CorticalSurface, FaceSurface, etc)
22 +* Parcellation (RegionMapping)
16 16  * Connectivity
17 17  * Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
18 18  
... ... @@ -27,77 +27,77 @@
27 27  
28 28  We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
29 29  
30 -(% class="box" %)
31 -(((
37 +{{code language="python" layout="LINENUMBERS"}}
32 32  import tvbwidgets.api as api
33 -
34 34  from tvb.simulator.lab import *
40 +from IPython.core.display_functions import display 
41 +{{/code}}
35 35  
36 -from IPython.core.display_functions import display
37 -)))
43 +Then, there are 2 options to work with the widget:
38 38  
39 -Then, we instantiate the **ThreeDWidget** 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:
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
40 40  
41 -(% class="box" %)
42 -(((
43 -widget_3d = api.ThreeDWidget()
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:
44 44  
45 -face = surfaces.FaceSurface().from_file()
50 +{{code language="python" layout="LINENUMBERS"}}
51 +widget = api.HeadBrowser()
52 +display(widget)
53 +{{/code}}
46 46  
47 -face.configure()
48 48  
49 -widget_3d.add_datatype(face)
50 -display(widget_3d)
51 -)))
56 +For the second option, the API is described below:
52 52  
53 -{{html}}
54 -<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
55 -{{/html}}
58 +In a cell, we load the data using the TVB API:
56 56  
57 -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.
60 +{{code language="python" layout="LINENUMBERS"}}
61 +surface = surfaces.Surface.from_file()
62 +surface.configure()
58 58  
59 -The **Config** object can be used to tweak the display options for each datatype.
64 +face = surfaces.Surface.from_file('face_8614.zip')
65 +face.configure()
60 60  
61 -In the code below, we add a **Connectivity** and SEEG **Sensors:**
67 +reg_map = region_mapping.RegionMapping.from_file()
62 62  
63 -(% class="box" %)
64 -(((
65 -conn = connectivity.Connectivity().from_file()
66 -
69 +conn = connectivity.Connectivity.from_file()
67 67  conn.configure()
68 68  
69 -widget_3d.add_datatype(conn)
72 +seeg = sensors.SensorsInternal.from_file()
73 +seeg.configure()
74 +{{/code}}
70 70  
76 +Then we prepare the **HeadWidget** for display:
71 71  
72 -seeg = sensors.SensorsInternal().from_file()
78 +{{code language="python" layout="LINENUMBERS"}}
79 +widget = api.HeadWidget([face, conn, seeg])
80 +display(widget)
81 +{{/code}}
73 73  
74 -seeg.configure()
83 +[[image:head.png]]
75 75  
76 -widget_3d.add_datatype(seeg, api.Config(name='SEEG'))
77 -)))
85 +Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
78 78  
79 -{{html}}
80 -<iframe src="https://drive.google.com/file/d/1vFqqzXle8VGcHaLB-OdE-6BdetK9aJ1T/preview" width="840" height="480" allow="autoplay"></iframe>
81 -{{/html}}
87 +In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
82 82  
83 -We can also provide a **RegionMapping** to be used as colormap for a surface:
89 +{{code language="python" layout="LINENUMBERS"}}
90 +widget.add_datatype(surface, reg_map)
91 +{{/code}}
84 84  
85 -(% class="box" %)
86 -(((
87 -reg_map = region_mapping.RegionMapping.from_file()
93 +[[image:cort.png]]
88 88  
89 -config = api.Config(name='Cortex')
90 90  
91 -config.add_region_mapping_as_cmap(reg_map)
96 +In the upper-right corner, a menu is displayed. This will allow us to control what we want to visualize. For example, I can hide the head in order to get a better view of the cortical surface:
92 92  
93 93  
94 -cortex = surfaces.CorticalSurface().from_file()
95 95  
96 -cortex.configure()
100 +I can rotate the surface and zoom in/out:
97 97  
98 -widget_3d.add_datatype(cortex, config)
99 -)))
102 +[[image:parcel.png]]
100 100  
101 -{{html}}
102 -<iframe src="https://drive.google.com/file/d/1z2yEuQWUT2Poxh63adYbBdhKPcWGskex/preview" width="840" height="480" allow="autoplay"></iframe>
103 -{{/html}}
104 +I could also make it transparent to visualize the connectivity centers and their edges:
105 +
106 +[[image:conncenters.png]]
107 +
108 +Also, I can hide the connectivity and display only the SEEG sensors:
109 +
110 +[[image:seeg.png]]
conncenters.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +509.5 KB
Content
cort.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +308.8 KB
Content
head.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.reginafilange
Size
... ... @@ -1,0 +1,1 @@
1 +245.6 KB
Content
menu.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +241.0 KB
Content
mm.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +242.7 KB
Content
parcel.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +273.8 KB
Content
seeg.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +415.0 KB
Content
Public

TVB Widgets