Summary

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

Details

Page properties

Title

...	...	@@ -1,1 +1,1 @@
1		-Widget 3D
	1	+Widget 3D Head

Author

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1		-XWiki.paulapopa
	1	+XWiki.reginafilange

Content

...	...	@@ -1,18 +1,25 @@
1		-TODO
	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
...	...	@@ -36,28 +36,46 @@
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:
	46	+Then, there are 2 options to work with the widget:
40	40
	48	+1. Use a file browser to load the data and automatically display it
	49	+1. Use directly the API to load the data and display it
	50	+
	51	+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:
	52	+
41	41	(% class="box" %)
42	42	(((
43		-widget_3d = api.ThreeDWidget()
	55	+widget = api.HeadBrowser()
	56	+display(widget)
	57	+)))
44	44
	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}}
	62	+
	63	+
	64	+For the second option, the API is described below:
	65	+
	66	+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:
	67	+
	68	+(% class="box" %)
	69	+(((
	70	+widget = api.HeadWidget()
	71	+
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)
	76	+widget.add_datatype(face)
	77	+display(widget)
51	51	)))
52	52
53	53	{{html}}
54		-<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>
55	55	{{/html}}
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.
	84	+Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
58	58
59		-The **Config** object can be used to tweak the display options for each datatype.
60		-
61	61	In the code below, we add a **Connectivity** and SEEG **Sensors:**
62	62
63	63	(% class="box" %)
...	...	@@ -66,7 +66,7 @@
66	66
67	67	conn.configure()
68	68
69		-widget_3d.add_datatype(conn)
	94	+widget.add_datatype(conn)
70	70
71	71
72	72	seeg = sensors.SensorsInternal().from_file()
...	...	@@ -73,27 +73,30 @@
73	73
74	74	seeg.configure()
75	75
76		-widget_3d.add_datatype(seeg, api.Config(name='SEEG'))
	101	+widget.add_datatype(seeg)
77	77	)))
78	78
79		-We can also provide a **RegionMapping** to be used as colormap for a surface:
	104	+{{html}}
	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>
	106	+{{/html}}
80	80
	108	+We can also provide a **RegionMapping** to be used as parcellation for a surface:
	109	+
81	81	(% class="box" %)
82	82	(((
83	83	reg_map = region_mapping.RegionMapping.from_file()
84	84
85		-config = api.Config(name='Cortex')
86	86
87		-config.add_region_mapping_as_cmap(reg_map)
88		-
89		-
90	90	cortex = surfaces.CorticalSurface().from_file()
91	91
92	92	cortex.configure()
93	93
94		-widget_3d.add_datatype(cortex, config)
95	95
	120	+widget.add_datatype(cortex, reg_map)
	121	+
	122	+display(widget)
	123	+)))
	124	+
96	96	{{html}}
97		-<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/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>
98	98	{{/html}}
99		-)))