Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 3.1
edited by paulapopa
on 2022/03/30 15:16
Change comment: There is no comment for this version
To version 20.1
edited by paulapopa
on 2023/03/01 14:12
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
... ... @@ -1,8 +1,10 @@
1 -TODO
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]]
4 +
3 3  == Purpose ==
4 4  
5 -It is a Jupyter widget intended for visualization of the 3D data available for a patient:
7 +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 8  * connectivity region centers
... ... @@ -36,22 +36,40 @@
36 36  from IPython.core.display_functions import display
37 37  )))
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:
41 +Then, there are 2 options to work with the widget:
40 40  
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 +
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 +
41 41  (% class="box" %)
42 42  (((
43 -widget_3d = api.ThreeDWidget()
52 +widget = api.HeadBrowser()
53 +display(widget)
54 +)))
44 44  
56 +
57 +For the second option, the API is described below:
58 +
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:
60 +
61 +(% class="box" %)
62 +(((
63 +widget = api.HeadWidget()
64 +
45 45  face = surfaces.FaceSurface().from_file()
46 46  
47 47  face.configure()
48 48  
49 -widget_3d.add_datatype(face)
50 -display(widget_3d)
69 +widget.add_datatype(face)
70 +display(widget)
51 51  )))
52 52  
53 53  {{html}}
54 -<iframe src="https://drive.google.com/drive/folders/1Q9oTEqoqMRwjzJpngSCNRAIbJzDfUh4q/preview" width="840" height="480" allow="autoplay"></iframe>
74 +<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
55 55  {{/html}}
56 56  
57 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.
... ... @@ -66,7 +66,7 @@
66 66  
67 67  conn.configure()
68 68  
69 -widget_3d.add_datatype(conn)
89 +widget.add_datatype(conn)
70 70  
71 71  
72 72  seeg = sensors.SensorsInternal().from_file()
... ... @@ -73,9 +73,13 @@
73 73  
74 74  seeg.configure()
75 75  
76 -widget_3d.add_datatype(seeg, api.Config(name='SEEG'))
96 +widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
77 77  )))
78 78  
99 +{{html}}
100 +<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
101 +{{/html}}
102 +
79 79  We can also provide a **RegionMapping** to be used as colormap for a surface:
80 80  
81 81  (% class="box" %)
... ... @@ -82,7 +82,7 @@
82 82  (((
83 83  reg_map = region_mapping.RegionMapping.from_file()
84 84  
85 -config = api.Config(name='Cortex')
109 +config = api.HeadWidgetConfig(name='Cortex')
86 86  
87 87  config.add_region_mapping_as_cmap(reg_map)
88 88  
... ... @@ -91,9 +91,14 @@
91 91  
92 92  cortex.configure()
93 93  
94 -widget_3d.add_datatype(cortex, config)
95 95  
119 +widget = api.HeadWidget()
120 +
121 +widget.add_datatype(cortex, config)
122 +
123 +display(widget)
124 +)))
125 +
96 96  {{html}}
97 -<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/preview" width="840" height="480" allow="autoplay"></iframe>
127 +<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
98 98  {{/html}}
99 -)))
Public

TVB Widgets