Wiki source code of Widget PSE

Version 17.1 by teodoramisan on 2023/07/21 12:15

version	line-number	content
7.1	1	(% class="wikigeneratedid" id="HWidgetPSE" %)
6.1	2	Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
	3
	4	== Purpose ==
	5
	6
11.1	7	It is composed of two separate Jupyter Widgets(PSE Launcher and PSE Visualizer) intended for the visualization of launching custom simulations. The launcher works locally and on HPC.
6.1	8
	9	The simulation can be customized by:
	10
12.1	11	* Getting a list of connectivities and an HPC configuration given as APIs
6.1	12	* Setting up parameters and ranges
	13	* Selecting multiple metrics
11.1	14	* Observing the progress of the launch by a monitor progress bar
6.1	15
	16	== Inputs ==
	17
13.1	18	* PSELauncher(Simulator, List of Connectivities, HPC Configuration)
6.1	19	* PSEVisualizer(Filename), the file will contain all the customized parameters from the launcher
	20
	21	== Requirements and installation ==
	22
	23	Before installing the tvb-widgets library containing the PSE widgets, the following python library and Jupyter extensions should be installed:
	24
	25	* Libraries
	26	** [[plotly>>https://plotly.com/python/getting-started/#installation]]
	27	* Extensions
	28
	29	(% class="box" %)
	30	(((
	31	jupyter labextension install @jupyter-widgets/jupyterlab-manager
	32
	33	jupyter labextension install jupyter-matplotlib
	34	)))
	35
	36	Then, to install the tvb-widgets library, just type:
	37
	38	(% class="box" %)
	39	(((
	40	pip install tvb-widgets
	41	)))
	42
	43	== API usage ==
	44
	45	First, the correct matplotlib backend must be set, which enables the interaction with the PSE widgets, by running the following command:
	46
	47	(% class="box" %)
	48	(((
	49	%matplotlib widget
	50	)))
	51
	52	Then, the PSELauncher and PSEWidget(from the tvb-widgets API) and the package lab(from tvb simulator) should be imported:
	53
	54	(% class="box" %)
	55	(((
	56	from tvbwidgets.api import PSELauncher, PSEWidget
	57	from tvb.simulator.lab import *
	58	)))
	59
17.1	60	The launcher widget can be initialized with more parameters: a simulator, a list of connectivities and an HPC configuration (only the simulator being a required argument). For HPC launch, besides the configuration part, an EBrains token needs to be stored. A custom initialization, which includes the HPC launch, is shown below:
6.1	61
	62	(% class="box" %)
	63	(((
17.1	64	os.environ['CLB_AUTH'] = 'PUT YOUR EBRAINS TOKEN HERE IF YOU WANT HPC RUNS'
	65
	66	from pyunicore.helpers.jobs import Resources
	67	res = Resources(cpus_per_node=4)
	68
	69	# !! Pay attention to env name and dir you might need to change if in conflict on the SAME project with another colleague of yours!!
	70
	71	hpc_config = HPCConfig(site="JUSUF", project="icei-hbp-2021-0007",
	72	env_dir="tvb_widget", env_name="venv_tvb", n_threads=None, resources=res)
	73	)))
	74
	75	(% class="box" %)
	76	(((
6.1	77	sim = simulator.Simulator(connectivity = connectivity.Connectivity.from_file())
	78	conn_66 = connectivity.Connectivity.from_file("connectivity_66.zip")
	79	conn_68 = connectivity.Connectivity.from_file("connectivity_68.zip")
	80	conn_76 = connectivity.Connectivity.from_file()
17.1	81	launch = PSELauncher(sim, [conn_66, conn_68, conn_76], hpc_config)
6.1	82	)))
	83
	84	The outcome will be something like in the image bellow.
	85	You can create a customized simulation by choosing different values for parameters, by setting ranges for them and by selecting the metrics for the simulation.
	86
10.1	87	[[image:setup_parameters.png\|\|alt="setup_parameters" style="float:left"]]
6.1	88
17.1	89
	90
	91
	92
	93
	94
	95
	96
	97
	98
6.1	99	Then, a file name has to be inserted in the indicated box(for storing the data) and as a last set-up, a launch type has to be chosen.
	100
	101
17.1	102	The progress of the launch can be monitored by a progress bar, as shown below:
6.1	103
17.1	104	(% style="text-align:center" %)
	105	[[image:image-20230721150554-1.png]]
	106
	107	A file with the name you specified will be generated in both approaches, HPC or local launch.
	108
6.1	109	Then, the PSEVisualizer can be called with the required parameter(file_name) as it shows below:
	110
	111	(% class="box" %)
	112	(((
	113	pse = PSEWidget("test.h5")
	114	)))
	115
	116	The outcome will be something like in the image bellow.
	117
	118	There will be a representation for every metric that was chosen before, in the launcher. The widget has some features for the type of visualization, the change of color and the option for choosing between metrics.
	119
10.1	120	[[image:result.png\|\|alt="result" style="float:left"]]

Wiki source code of Widget PSE

TVB Widgets