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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	7	It is a Jupyter Widget intended for the visualization of the interactive phase-plane.
...	...	@@ -8,91 +8,29 @@
8	8
9	9	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 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 *
	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		-)))
	36	+{{{Entering the coordinates in the X,Y Coordinate Boxes will generate a sample
	37	+trajectory, originating from the coordinates entered.}}}