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Changes for page Widget TimeSeries

Last modified by ldomide on 2023/05/23 14:34
From version 33.1
edited by rominabaila
on 2023/05/15 11:06
Change comment: There is no comment for this version
To version 9.1
edited by rominabaila
on 2022/04/12 09:30
Change comment: Uploaded new attachment "image-20220412103041-1.png", version {1}

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1 -Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>url:https://github.com/the-virtual-brain/tvb-widgets]]
2 -
3 -This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>url: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 7  == Purpose ==
8 8  
9 -It is a Jupyter Widget intended for the visualization of brain signals represented as time series.
3 +It is a Jupyter widget intended for the visualization of brain signals represented as time series.
10 10  
11 -== Backends ==
12 12  
13 -Starting with //**tvb-widgets 1.5.0**, //the TS widget comes in 2 forms, corresponding to the 2 different libraries (we called them backends) used for plotting: **matplotlib **and **plotly**. The matplotlib backend, build on top of the **mne** library, offers more advanced scientifical features, while the plotly backend has a more appealing look and moves faster when talking about the basic interactions.
14 -
15 -Below you can see the TS widget with each backend option (first one using the matplotlib backend, the second one using the plotly backend).
16 -
17 -(% style="text-align:center" %)
18 -[[image:matplotlib.png]]
19 -
20 -(% style="text-align:center" %)
21 -[[image:plotly.png]]
22 -
23 23  == Inputs ==
24 24  
25 -Time series can be given as inputs in two forms:
8 +It supports time series inputs of two types:
26 26  
27 27  * TVB TimeSeries datatype
28 28  * Numpy arrays
29 29  
30 -This widget supports 2D, 3D, and 4D arrays. In all three cases, there is a fixed shape that the TimeSeries widget expects:
13 +The widget supports 2-, 3-, and 4-dimensional arrays. In all three cases, there is a fixed shape that the TimeSeries widget expects:
31 31  
32 32  * for **2D**: (no_timepoints, no_channels)
33 33  * for **3D**: (no_timepoints, state_variable/mode, no_channels)
34 34  * for **4D**: (no_timepoints, state_variable, no_channels, mode)
35 35  
36 -~* Note that the TVB TimeSeries datatype is always 4D and already has the expected shape.
19 +~* Note that the TVB TimeSeries datatype is always is always 4D and already has the expected shape.
37 37  
21 +
38 38  == Requirements and installation ==
39 39  
24 +Before installing the tvb-widgets library containing the TimeSeries widget, the following python libraries and  Jupyter Notebook extensions should be installed:
40 40  
41 -Before installing the tvb-widgets library containing the TimeSeries widget, the following python libraries and Jupyter extensions should be installed:
42 -
43 43  * **Libraries:**
44 -** [[mne>>https://mne.tools/stable/index.html]] >= 1.0
45 -** [[matplotlib>>https://matplotlib.org/3.5.0/index.html]]
46 -** [[plotly>>https://plotly.com/python/]] == 5.14.0
47 -** [[ipywidgets>>https://ipywidgets.readthedocs.io/en/7.x/]] == 7.7.2
48 -** [[ipympl>>https://github.com/matplotlib/ipympl#installation]] >= 0.8.5
27 +** [[ipympl>>https://github.com/matplotlib/ipympl#installation]]
49 49  * (((
50 -**Extensions:**
29 +**Extensions:***
51 51  
52 52  (% class="box" %)
53 53  (((
54 54  jupyter labextension install @jupyter-widgets/jupyterlab-manager
34 +)))
55 55  
36 +* (% class="box" %)
37 +(((
56 56  jupyter labextension install jupyter-matplotlib
57 -
58 -jupyter labextension install jupyterlab-plotly
59 59  )))
60 60  )))
61 61  
62 -Then, to install the tvb-widgets library, just type:
42 +Then, to install the tvb-widgets library just type:
63 63  
64 64  (% class="box" %)
65 65  (((
66 66  pip install tvb-widgets
67 67  )))
68 -
69 -== API usage ==
70 -
71 -First, the correct matplotlib backend must be set, which enables the interaction with the TimeSeries widget, by running the following command:
72 -
73 -(% class="box" %)
74 -(((
75 -%matplotlib widget
76 -)))
77 -
78 - Then, the **TimeSeriesWidget** (from the tvb-widgets API) and the **//display//** function should be imported:
79 -
80 -(% class="box" %)
81 -(((
82 -from tvbwidgets.api import TimeSeriesWidget
83 -from IPython.core.display_functions import display
84 -)))
85 -
86 -Assuming that the user has already created or imported a valid input, this is how the widget can be initialized and how an input can be assigned to it, using the //**add_datatype** //method (example below assumes that **//tsr//  **is a TVB TimeSeries datatype):
87 -
88 -(% class="box" %)
89 -(((
90 -tsw = TimeSeriesWidget()
91 -tsw.add_datatype(tsr)
92 -)))
93 -
94 -Finally, to display and interact with the TimeSeries widget, the **//get_widget//**// //method is used inside the //**display **//function:
95 -
96 -(% class="box" %)
97 -(((
98 -display(tsw)
99 -)))
100 -
101 -{{html}}
102 -<iframe width="840" height="480" src="https://www.youtube.com/embed/VmueiXMxbVk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
103 -{{/html}}
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TVB Widgets