Wiki source code of Widget 3D Head
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| author | version | line-number | content |
|---|---|---|---|
| 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 | [[image:head.png]] | ||
| 84 | |||
| 85 | Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times. | ||
| 86 | |||
| 87 | In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:** | ||
| 88 | |||
| 89 | {{code language="python" layout="LINENUMBERS"}} | ||
| 90 | widget.add_datatype(surface, reg_map) | ||
| 91 | {{/code}} | ||
| 92 | |||
| 93 | {{html}} | ||
| 94 | <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> | ||
| 95 | {{/html}} |