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1		-XWiki.ldomide
	1	+XWiki.teodoramisan

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2	2
3	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	4
	5	+
5	5	== Purpose ==
6	6
7		-It is a Jupyter Widget intended for the visualization of the interactive phase-plane for TVB math models ([[https:~~/~~/docs.thevirtualbrain.org/api/tvb.simulator.models.html#module-tvb.simulator.models>>https://docs.thevirtualbrain.org/api/tvb.simulator.models.html#module-tvb.simulator.models]]).
	8	+It is a Jupyter Widget intended for the visualization of the interactive phase-plane.
8	8
9		-It provides **//sliders//** for setting:
	10	+It provides sliders for setting:
10	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		-)))
	12	+*
23	23
24		-and **//dropdown lists//** for selecting:
	14	+{{{ The value of all parameters of the Model.}}}
	15	+*
25	25
26		-* (((
27		- Which state-variables to show on each axis.
28		-)))
29		-* (((
30		- Which mode to show, if the Model has them.
31		-)))
	17	+{{{ The extent of the axes.}}}
	18	+*
32	32
33		-Entering the coordinates in the X,Y Coordinate Boxes will generate a sample
34		-trajectory, originating from the coordinates entered.
	20	+{{{ A fixed value for the state-variables which aren't currently selected.}}}
	21	+*
35	35
36		-== Inputs ==
	23	+{{{ The noise strength, if a stochastic integrator is specified.}}}
37	37
38		-Phase-Plane viewer will be represented in the beginning based on the parameters that it receives:
	25	+and dropdown lists for selecting:
39	39
40		-* Model (Generic2dOscillator, Epileptor, Hopfield, etc.)
41		-* Integrator (HeunDeterministic, HeunStochastic, Identity, etc.)
	27	+*
42	42
43		-== Requirements and installation ==
44		-
45		-Before installing the tvb-widgets library containing the PhasePlane widget, the following python library 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 PhasePlane 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 *
	29	+{{{ Which state-variables to show on each axis.
80	80	}}}
	31	+*
81	81
82		-{{{from IPython.core.display_functions import display}}}
83		-)))
	33	+{{{ Which mode to show, if the Model has them.}}}
84	84
85		-The widget can be initialized with the required parameters (Model and Integrator) as it shows below:
86	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		-}}}
99		-)))
100		-
101		-The outcome will be something like in the image bellow.
102		-You can explore the inputs in the TAB on the left, and click on the canvas in the right to select initial conditions for evaluating the Model equations from that point onward (no structural connectivity, as is the eq are solved for a single node, in isolation).
103		-
104		-
	36	+{{{Entering the coordinates in the X,Y Coordinate Boxes will generate a sample
	37	+trajectory, originating from the coordinates entered.}}}

Screenshot 2023-01-09 at 20.39.52.png

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Screenshot 2023-01-09 at 20.42.00.png

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