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Title

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1		-Widget 3D
	1	+Widget 3D Head

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
	13	+* sensors locations (SEEG, MEG, EEG)
	14	+
	15	+== Inputs ==
	16	+
	17	+It supports the above data in the form of their corresponding TVB datatypes:
	18	+
	19	+* Surface (CorticalSurface, FaceSurface, etc)
	20	+* Connectivity
	21	+* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
	22	+
	23	+== Installation ==
	24	+
	25	+(% class="box" %)
	26	+(((
	27	+pip install tvb-widgets
	28	+)))
	29	+
	30	+== API usage ==
	31	+
	32	+We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
	33	+
	34	+(% class="box" %)
	35	+(((
	36	+import tvbwidgets.api as api
	37	+
	38	+from tvb.simulator.lab import *
	39	+
	40	+from IPython.core.display_functions import display
	41	+)))
	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	+(% class="box" %)
	51	+(((
	52	+widget = api.HeadBrowser()
	53	+display(widget)
	54	+)))
	55	+
8	8	{{html}}
9		-<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/preview" width="640" height="480" allow="autoplay"></iframe>
	57	+<iframe src="https://drive.google.com/file/d/1lY3X5eqJfOLmkmHuBa2iq_Aas8mDPa1e/preview" width="840" height="480" allow="autoplay"></iframe>
10	10	{{/html}}
	59	+
	60	+
	61	+For the second option, the API is described below:
	62	+
	63	+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:
	64	+
	65	+(% class="box" %)
	66	+(((
	67	+widget = api.HeadWidget()
	68	+
	69	+face = surfaces.FaceSurface().from_file()
	70	+
	71	+face.configure()
	72	+
	73	+widget.add_datatype(face)
	74	+display(widget)
	75	+)))
	76	+
	77	+{{html}}
	78	+<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
	79	+{{/html}}
	80	+
	81	+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.
	82	+
	83	+The **Config** object can be used to tweak the display options for each datatype.
	84	+
	85	+In the code below, we add a **Connectivity** and SEEG **Sensors:**
	86	+
	87	+(% class="box" %)
	88	+(((
	89	+conn = connectivity.Connectivity().from_file()
	90	+
	91	+conn.configure()
	92	+
	93	+widget.add_datatype(conn)
	94	+
	95	+
	96	+seeg = sensors.SensorsInternal().from_file()
	97	+
	98	+seeg.configure()
	99	+
	100	+widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
	101	+)))
	102	+
	103	+{{html}}
	104	+<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
	105	+{{/html}}
	106	+
	107	+We can also provide a **RegionMapping** to be used as colormap for a surface:
	108	+
	109	+(% class="box" %)
	110	+(((
	111	+reg_map = region_mapping.RegionMapping.from_file()
	112	+
	113	+config = api.HeadWidgetConfig(name='Cortex')
	114	+
	115	+config.add_region_mapping_as_cmap(reg_map)
	116	+
	117	+
	118	+cortex = surfaces.CorticalSurface().from_file()
	119	+
	120	+cortex.configure()
	121	+
	122	+
	123	+widget = api.HeadWidget()
	124	+
	125	+widget.add_datatype(cortex, config)
	126	+
	127	+display(widget)
	128	+)))
	129	+
	130	+{{html}}
	131	+<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
	132	+{{/html}}