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Title

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1		-Widget 3D
	1	+Widget 3D Head

Author

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1		-XWiki.ldomide
	1	+XWiki.reginafilange

Content

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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	+{{code language="python" layout="LINENUMBERS"}}
	38	+import tvbwidgets.api as api
	39	+from tvb.simulator.lab import *
	40	+from IPython.core.display_functions import display
	41	+{{/code}}
	42	+
	43	+Then, there are 2 options to work with the widget:
	44	+
	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
	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	+
	50	+{{code language="python" layout="LINENUMBERS"}}
	51	+widget = api.HeadBrowser()
	52	+display(widget)
	53	+{{/code}}
	54	+
	55	+
	56	+For the second option, the API is described below:
	57	+
	58	+In a cell, we load the data using the TVB API:
	59	+
	60	+{{code language="python" layout="LINENUMBERS"}}
	61	+surface = surfaces.Surface.from_file()
	62	+surface.configure()
	63	+
	64	+face = surfaces.Surface.from_file('face_8614.zip')
	65	+face.configure()
	66	+
	67	+reg_map = region_mapping.RegionMapping.from_file()
	68	+
	69	+conn = connectivity.Connectivity.from_file()
	70	+conn.configure()
	71	+
	72	+seeg = sensors.SensorsInternal.from_file()
	73	+seeg.configure()
	74	+{{/code}}
	75	+
	76	+Then we prepare the **HeadWidget** for display:
	77	+
	78	+{{code language="python" layout="LINENUMBERS"}}
	79	+widget = api.HeadWidget([face, conn, seeg])
	80	+display(widget)
	81	+{{/code}}
	82	+
	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 the **CorticalSurface** with a **RegionMapping** as parcellation**:**
	87	+
	88	+{{code language="python" layout="LINENUMBERS"}}
	89	+widget.add_datatype(surface, reg_map)
	90	+{{/code}}
	91	+
8	8	{{html}}
9		-<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/preview" width="640" height="480" allow="autoplay"></iframe>
	93	+<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>
10	10	{{/html}}

head.png

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	1	+XWiki.reginafilange

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	1	+245.6 KB

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