Summary

• Page properties (2 modified, 0 added, 0 removed)
• Attachments (0 modified, 0 added, 7 removed)
  • conncenters.png
  • cort.png
  • head.png
  • menu.png
  • mm.png
  • parcel.png
  • seeg.png

Details

Page properties

Author

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1		-XWiki.paulapopa
	1	+XWiki.reginafilange

Content

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34	34
35	35	We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
36	36
37		-{{code language="python" layout="LINENUMBERS"}}
	37	+(% class="box" %)
	38	+(((
38	38	import tvbwidgets.api as api
	40	+
39	39	from tvb.simulator.lab import *
40		-from IPython.core.display_functions import display
41		-{{/code}}
42	42
	43	+from IPython.core.display_functions import display
	44	+)))
	45	+
43	43	Then, there are 2 options to work with the widget:
44	44
45	45	1. Use a file browser to load the data and automatically display it
...	...	@@ -47,64 +47,78 @@
47	47
48	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	49
50		-{{code language="python" layout="LINENUMBERS"}}
	53	+(% class="box" %)
	54	+(((
51	51	widget = api.HeadBrowser()
52	52	display(widget)
53		-{{/code}}
	57	+)))
54	54
	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}}
55	55
	63	+
56	56	For the second option, the API is described below:
57	57
58		-In a cell, we load the data using the TVB API:
	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:
59	59
60		-{{code language="python" layout="LINENUMBERS"}}
61		-surface = surfaces.Surface.from_file()
62		-surface.configure()
	68	+(% class="box" %)
	69	+(((
	70	+widget = api.HeadWidget()
63	63
64		-face = surfaces.Surface.from_file('face_8614.zip')
	72	+face = surfaces.FaceSurface().from_file()
	73	+
65	65	face.configure()
66	66
67		-reg_map = region_mapping.RegionMapping.from_file()
	76	+widget.add_datatype(face)
	77	+display(widget)
	78	+)))
68	68
69		-conn = connectivity.Connectivity.from_file()
70		-conn.configure()
	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}}
71	71
72		-seeg = sensors.SensorsInternal.from_file()
73		-seeg.configure()
74		-{{/code}}
	84	+Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
75	75
76		-Then we prepare the **HeadWidget** for display:
	86	+In the code below, we add a **Connectivity** and SEEG **Sensors:**
77	77
78		-{{code language="python" layout="LINENUMBERS"}}
79		-widget = api.HeadWidget([face, conn, seeg])
80		-display(widget)
81		-{{/code}}
	88	+(% class="box" %)
	89	+(((
	90	+conn = connectivity.Connectivity().from_file()
82	82
83		-[[image:head.png]]
	92	+conn.configure()
84	84
85		-Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
	94	+widget.add_datatype(conn)
86	86
87		-In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
88	88
89		-{{code language="python" layout="LINENUMBERS"}}
90		-widget.add_datatype(surface, reg_map)
91		-{{/code}}
	97	+seeg = sensors.SensorsInternal().from_file()
92	92
93		-[[image:cort.png]]
	99	+seeg.configure()
94	94
	101	+widget.add_datatype(seeg)
	102	+)))
95	95
96		-In the upper-right corner, a menu is displayed. This will allow us to control what we want to visualize. For example, I can hide the head in order to get a better view of the cortical 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}}
97	97
	108	+We can also provide a **RegionMapping** to be used as parcellation for a surface:
98	98
	110	+(% class="box" %)
	111	+(((
	112	+reg_map = region_mapping.RegionMapping.from_file()
99	99
100		-I can rotate the surface and zoom in/out:
101	101
102		-[[image:parcel.png]]
	115	+cortex = surfaces.CorticalSurface().from_file()
103	103
104		-I could also make it transparent to visualize the connectivity centers and their edges:
	117	+cortex.configure()
105	105
106		-[[image:conncenters.png]]
107	107
108		-Also, I can hide the connectivity and display only the SEEG sensors:
	120	+widget.add_datatype(cortex, reg_map)
109	109
110		-[[image:seeg.png]]
	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}}

conncenters.png

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1		-XWiki.paulapopa

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cort.png

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1		-XWiki.paulapopa

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head.png

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1		-XWiki.reginafilange

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menu.png

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mm.png

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parcel.png

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seeg.png

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1		-XWiki.paulapopa

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