Summary

• Page properties (3 modified, 0 added, 0 removed)

Details

Page properties

Title

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1		-Widget 3D
	1	+Widget 3D Head

Author

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1		-XWiki.ldomide
	1	+XWiki.paulapopa

Content

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1		-NOTE - Not yet released, but testable here
	1	+Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
2	2
3		-[[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks]]
	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	5	== Purpose ==
6	6
7		-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:
8	8
9	9	* surfaces of different types (cortex, face, skull, etc)
10	10	* connectivity region centers
...	...	@@ -38,12 +38,33 @@
38	38	from IPython.core.display_functions import display
39	39	)))
40	40
41		-Then, we instantiate the **SurfaceWidget** 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:
42	42
	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	+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:
	48	+
43	43	(% class="box" %)
44	44	(((
45		-widget = api.SurfaceWidget()
	51	+widget = api.HeadBrowser()
	52	+display(widget)
	53	+)))
46	46
	55	+{{html}}
	56	+<iframe src="https://drive.google.com/file/d/1lY3X5eqJfOLmkmHuBa2iq_Aas8mDPa1e/preview" width="840" height="480" allow="autoplay"></iframe>
	57	+{{/html}}
	58	+
	59	+
	60	+For the second option, the API is described below:
	61	+
	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:
	63	+
	64	+(% class="box" %)
	65	+(((
	66	+widget = api.HeadWidget()
	67	+
47	47	face = surfaces.FaceSurface().from_file()
48	48
49	49	face.configure()
...	...	@@ -75,11 +75,11 @@
75	75
76	76	seeg.configure()
77	77
78		-widget.add_datatype(seeg, api.SurfaceWidgetConfig(name='SEEG'))
	99	+widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
79	79	)))
80	80
81	81	{{html}}
82		-<iframe src="https://drive.google.com/file/d/1vFqqzXle8VGcHaLB-OdE-6BdetK9aJ1T/preview" width="840" height="480" allow="autoplay"></iframe>
	103	+<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
83	83	{{/html}}
84	84
85	85	We can also provide a **RegionMapping** to be used as colormap for a surface:
...	...	@@ -88,7 +88,7 @@
88	88	(((
89	89	reg_map = region_mapping.RegionMapping.from_file()
90	90
91		-config = api.SurfaceWidgetConfig(name='Cortex')
	112	+config = api.HeadWidgetConfig(name='Cortex')
92	92
93	93	config.add_region_mapping_as_cmap(reg_map)
94	94
...	...	@@ -97,9 +97,14 @@
97	97
98	98	cortex.configure()
99	99
	121	+
	122	+widget = api.HeadWidget()
	123	+
100	100	widget.add_datatype(cortex, config)
	125	+
	126	+display(widget)
101	101	)))
102	102
103	103	{{html}}
104		-<iframe src="https://drive.google.com/file/d/1z2yEuQWUT2Poxh63adYbBdhKPcWGskex/preview" width="840" height="480" allow="autoplay"></iframe>
	130	+<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
105	105	{{/html}}