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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		-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	+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	+
	5	+== Purpose ==
	6	+
	7	+It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
	8	+
	9	+* surfaces of different types (cortex, face, skull, etc)
	10	+* connectivity region centers
	11	+* sensors locations (SEEG, MEG, EEG)
	12	+
	13	+== Inputs ==
	14	+
	15	+It supports the above data in the form of their corresponding TVB datatypes:
	16	+
	17	+* Surface (CorticalSurface, FaceSurface, etc)
	18	+* Connectivity
	19	+* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
	20	+
	21	+== Installation ==
	22	+
	23	+(% class="box" %)
	24	+(((
	25	+pip install tvb-widgets
	26	+)))
	27	+
	28	+== API usage ==
	29	+
	30	+We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
	31	+
	32	+(% class="box" %)
	33	+(((
	34	+import tvbwidgets.api as api
	35	+
	36	+from tvb.simulator.lab import *
	37	+
	38	+from IPython.core.display_functions import display
	39	+)))
	40	+
	41	+Then, there are 2 options to work with the widget:
	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	+
	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	+
	56	+
	57	+For the second option, the API is described below:
	58	+
	59	+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:
	60	+
	61	+(% class="box" %)
	62	+(((
	63	+widget = api.HeadWidget()
	64	+
	65	+face = surfaces.FaceSurface().from_file()
	66	+
	67	+face.configure()
	68	+
	69	+widget.add_datatype(face)
	70	+display(widget)
	71	+)))
	72	+
8	8	{{html}}
9		-<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/preview" width="640" height="480" allow="autoplay"></iframe>
	74	+<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
10	10	{{/html}}
	76	+
	77	+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.
	78	+
	79	+The **Config** object can be used to tweak the display options for each datatype.
	80	+
	81	+In the code below, we add a **Connectivity** and SEEG **Sensors:**
	82	+
	83	+(% class="box" %)
	84	+(((
	85	+conn = connectivity.Connectivity().from_file()
	86	+
	87	+conn.configure()
	88	+
	89	+widget.add_datatype(conn)
	90	+
	91	+
	92	+seeg = sensors.SensorsInternal().from_file()
	93	+
	94	+seeg.configure()
	95	+
	96	+widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
	97	+)))
	98	+
	99	+{{html}}
	100	+<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
	101	+{{/html}}
	102	+
	103	+We can also provide a **RegionMapping** to be used as colormap for a surface:
	104	+
	105	+(% class="box" %)
	106	+(((
	107	+reg_map = region_mapping.RegionMapping.from_file()
	108	+
	109	+config = api.HeadWidgetConfig(name='Cortex')
	110	+
	111	+config.add_region_mapping_as_cmap(reg_map)
	112	+
	113	+
	114	+cortex = surfaces.CorticalSurface().from_file()
	115	+
	116	+cortex.configure()
	117	+
	118	+
	119	+widget = api.HeadWidget()
	120	+
	121	+widget.add_datatype(cortex, config)
	122	+
	123	+display(widget)
	124	+)))
	125	+
	126	+{{html}}
	127	+<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
	128	+{{/html}}