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

...	...	@@ -1,1 +1,1 @@
1		-XWiki.ldomide
	1	+XWiki.reginafilange

Content

...	...	@@ -1,10 +1,127 @@
1		-TODO
2		-! pip install -i tvb-widgets
3		-from tvbwidgets.api import SurfaceWidget
4		-from IPython.core.display_functions import display
5		-w3d = SurfaceWidget(...)
6		-display(w3d)
7		-
	1	+Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
	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	+
	7	+== Purpose ==
	8	+
	9	+It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
	10	+
	11	+* surfaces of different types (cortex, face, skull, etc)
	12	+* connectivity region centers and edges
	13	+* sensors locations (SEEG, MEG, EEG)
	14	+
	15	+On cortical surfaces, it can also display region parcellation.
	16	+
	17	+== Inputs ==
	18	+
	19	+It supports the above data in the form of their corresponding TVB datatypes:
	20	+
	21	+* Surface (CorticalSurface, FaceSurface, etc)
	22	+* Parcellation (RegionMapping)
	23	+* Connectivity
	24	+* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
	25	+
	26	+== Installation ==
	27	+
	28	+(% class="box" %)
	29	+(((
	30	+pip install tvb-widgets
	31	+)))
	32	+
	33	+== API usage ==
	34	+
	35	+We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
	36	+
	37	+(% class="box" %)
	38	+(((
	39	+import tvbwidgets.api as api
	40	+
	41	+from tvb.simulator.lab import *
	42	+
	43	+from IPython.core.display_functions import display
	44	+)))
	45	+
	46	+Then, there are 2 options to work with the widget:
	47	+
	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	+
	53	+(% class="box" %)
	54	+(((
	55	+widget = api.HeadBrowser()
	56	+display(widget)
	57	+)))
	58	+
8	8	{{html}}
9		-<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/preview" width="640" height="480" allow="autoplay"></iframe>
	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>
10	10	{{/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	+
	72	+face = surfaces.FaceSurface().from_file()
	73	+
	74	+face.configure()
	75	+
	76	+widget.add_datatype(face)
	77	+display(widget)
	78	+)))
	79	+
	80	+{{html}}
	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>
	82	+{{/html}}
	83	+
	84	+Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
	85	+
	86	+In the code below, we add a **Connectivity** and SEEG **Sensors:**
	87	+
	88	+(% class="box" %)
	89	+(((
	90	+conn = connectivity.Connectivity().from_file()
	91	+
	92	+conn.configure()
	93	+
	94	+widget.add_datatype(conn)
	95	+
	96	+
	97	+seeg = sensors.SensorsInternal().from_file()
	98	+
	99	+seeg.configure()
	100	+
	101	+widget.add_datatype(seeg)
	102	+)))
	103	+
	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}}
	107	+
	108	+We can also provide a **RegionMapping** to be used as parcellation for a surface:
	109	+
	110	+(% class="box" %)
	111	+(((
	112	+reg_map = region_mapping.RegionMapping.from_file()
	113	+
	114	+
	115	+cortex = surfaces.CorticalSurface().from_file()
	116	+
	117	+cortex.configure()
	118	+
	119	+
	120	+widget.add_datatype(cortex, reg_map)
	121	+
	122	+display(widget)
	123	+)))
	124	+
	125	+{{html}}
	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>
	127	+{{/html}}