Wiki source code of Widget PhasePlane
Version 2.1 by teodoramisan on 2023/01/03 13:34
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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 | Immediate testing: [[https:~~/~~/lab.ch.ebrains.eu/user/teodoramisan/lab/workspaces/auto-3/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/PhasePlane.ipynb>>https://lab.ch.ebrains.eu/user/teodoramisan/lab/workspaces/auto-3/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/PhasePlane.ipynb]] | ||
| 4 | |||
| 5 | == Purpose == | ||
| 6 | |||
| 7 | It is a Jupyter Widget intended for the visualization of the interactive phase-plane. | ||
| 8 | |||
| 9 | It provides sliders for setting: | ||
| 10 | |||
| 11 | * ((( | ||
| 12 | The value of all parameters of the Model. | ||
| 13 | ))) | ||
| 14 | * ((( | ||
| 15 | The extent of the axes. | ||
| 16 | ))) | ||
| 17 | * ((( | ||
| 18 | A fixed value for the state-variables which aren't currently selected. | ||
| 19 | ))) | ||
| 20 | * ((( | ||
| 21 | The noise strength, if a stochastic integrator is specified. | ||
| 22 | ))) | ||
| 23 | |||
| 24 | and dropdown lists for selecting: | ||
| 25 | |||
| 26 | * ((( | ||
| 27 | Which state-variables to show on each axis. | ||
| 28 | ))) | ||
| 29 | * ((( | ||
| 30 | Which mode to show, if the Model has them. | ||
| 31 | ))) | ||
| 32 | |||
| 33 | Entering the coordinates in the X,Y Coordinate Boxes will generate a sample | ||
| 34 | trajectory, originating from the coordinates entered. | ||
| 35 | |||
| 36 | == Inputs == | ||
| 37 | |||
| 38 | Phase-Plane viewer will be represented in the beginning based on the parameters that it receives: | ||
| 39 | |||
| 40 | * Model (Generic2dOscillator, Epileptor, Hopfield, etc.) | ||
| 41 | * Integrator (HeunDeterministic, HeunStochastic, Identity, etc.) | ||
| 42 | |||
| 43 | == Requirements and installation == | ||
| 44 | |||
| 45 | Before installing the tvb-widgets library containing the PhasePlane widget, the following python libraries and Jupyter extensions should be installed: | ||
| 46 | |||
| 47 | * **Libraries:** | ||
| 48 | ** [[ipympl>>https://github.com/matplotlib/ipympl#installation]] | ||
| 49 | * **Extensions:** | ||
| 50 | |||
| 51 | (% class="box" %) | ||
| 52 | ((( | ||
| 53 | jupyter labextension install @jupyter-widgets/jupyterlab-manager | ||
| 54 | |||
| 55 | jupyter labextension install jupyter-matplotlib | ||
| 56 | ))) | ||
| 57 | |||
| 58 | Then, to install the tvb-widgets library, just type: | ||
| 59 | |||
| 60 | (% class="box" %) | ||
| 61 | ((( | ||
| 62 | pip install tvb-widgets | ||
| 63 | ))) | ||
| 64 | |||
| 65 | == API usage == | ||
| 66 | |||
| 67 | First, the correct matplotlib backend must be set, which enables the interaction with the TimeSeries widget, by running the following command: | ||
| 68 | |||
| 69 | (% class="box" %) | ||
| 70 | ((( | ||
| 71 | %matplotlib widget | ||
| 72 | ))) | ||
| 73 | |||
| 74 | Then, the PhasePlaneWidget (from the tvb-widgets API), the package lab (from tvb simulator) and the display function should be imported: | ||
| 75 | |||
| 76 | (% class="box" %) | ||
| 77 | ((( | ||
| 78 | {{{from tvbwidgets.api import PhasePlaneWidget | ||
| 79 | from tvb.simulator.lab import * | ||
| 80 | }}} | ||
| 81 | |||
| 82 | {{{from IPython.core.display_functions import display}}} | ||
| 83 | ))) | ||
| 84 | |||
| 85 | The widget can be initialized with the required parameters (Model and Integrator) as it shows below: | ||
| 86 | |||
| 87 | (% class="box" %) | ||
| 88 | ((( | ||
| 89 | {{{w = PhasePlaneWidget(model=models.Generic2dOscillator(), | ||
| 90 | integrator=integrators.HeunDeterministic())}}} | ||
| 91 | ))) | ||
| 92 | |||
| 93 | Finally, to display and interact with the PhasePlane widget, the **//get_widget//**// //method is used inside the //**display **//function: | ||
| 94 | |||
| 95 | (% class="box" %) | ||
| 96 | ((( | ||
| 97 | {{{display(w.get_widget(plot_size=(6,7)))}}} | ||
| 98 | ))) |