helios.layouts.mde

IPC-PyMDE: Minimum-Distortion Embedding Network Layout

This module implements a IPC Network Layout to be used with PyMDE[1]. The IPC layout grants a non-blocking behavior for PyMDE. PyMDE solves minimum-distortion embedding problem using pytorch.

References

[1] A. Agrawal, A. Ali, and S. Boyd, “Minimum-Distortion Embedding,” arXiv:2103.02559 [cs, math, stat], Mar. 2021, Accessed: Jul. 24, 2021. http://arxiv.org/abs/2103.02559

Notes

Python 3.8 or greater is a requirement for this module.

ivar ~helios.layouts.mde._CONSTRAINTS

vartype ~helios.layouts.mde._CONSTRAINTS

dict

ivar ~helios.layouts.mde._PENALTIES

vartype ~helios.layouts.mde._PENALTIES

dict

List of Objects

MDE

class helios.layouts.mde.MDE(edges, network_draw, weights=None, use_shortest_path=True, constraint_name=None, anchors=None, anchors_pos=None, penalty_name=None, penalty_parameters=None, attractive_penalty_name='log1p', repulsive_penalty_name='log')[source]

Bases: helios.layouts.base.NetworkLayoutIPCRender

Minimum Distortion Embedding algorithm running on IPC

This call the PyMDE lib running in a different process which comunicates with this object through SharedMemory from python>=3.8.

References

[1] A. Agrawal, A. Ali, and S. Boyd, “Minimum-Distortion Embedding,” arXiv:2103.02559 [cs, math, stat], Mar. 2021, Accessed: Jul. 24, 2021. http://arxiv.org/abs/2103.02559

Notes

Python 3.8+ is required to use this

Parameters

  • edges (ndarray) – the edges of the graph. A numpy array of shape (n_edges, 2)

  • network_draw (NetworkDraw) – a NetworkDraw object

  • weights (array, optional) – edge weights. A one dimensional array of shape (n_edges, )

  • use_shortest_path (bool, optional) – If set to True, shortest path is used to compute the layout

  • constraint_name (str, optional) – centered, standardized or anchored

  • anchors (array, optional) – a list of vertex that will be anchored

  • anchors_pos (ndarray, optional) – The positions of the anchored vertex

  • penalty_name (str, optional) – cubic, huber, invpower, linear, log, log1p, logratio, logistic, power, pushandpull or quadratic

  • penalty_parameters (array, optional) – the parameters of the penalty function

  • attractive_penalty_name (str, optional) – cubic, huber, invpower, linear, log, log1p, logratio, logistic, power, pushandpull or quadratic

  • repulsive_penalty_name (str, optional) – cubic, huber, invpower, linear, log, log1p, logratio, logistic, power, pushandpull or quadratic

cleanup()

Release the shared memory resources

start(ms=30, steps=100, iters_by_step=2, record_positions=False, without_iren_start=True)

This method starts the network layout algorithm creating a new subprocess.

Right after the network layout algorithm finish the computation (ending of the related subprocess), the stop method will be called automatically.

Parameters

  • ms (float) – time interval in milleseconds to update the positions inside of the NetworkDraw

  • steps (int) – number of steps; snapshots. For example, if you set steps=3 that means the positions will be updated three times.

  • iters_by_step (int) – number of interations in each step

  • record_positions (bool, optional, default True) – Record the positions of the network

  • without_iren_start (bool, optional, default True) – Set this to False if you will start the ShowManager. That is, if you will invoke the following commands

Examples

>>> network_draw.initialize()
>>> network_draw.start()
stop()

Stop the layout algorithm

update()

This method updates the position of the network actor and right after that refresh the network draw

MDEServerCalc

class helios.layouts.mde.MDEServerCalc(num_nodes, num_edges, edges_buffer_name, positions_buffer_name, info_buffer_name, dimension=3, weights_buffer_name=None, snapshots_buffer_name=None, num_snapshots=0, penalty_name=None, penalty_parameters_buffer_name=None, num_penalty_parameters=None, attractive_penalty_name='log1p', repulsive_penalty_name='log', use_shortest_path=False, constraint_name=None, constraint_anchors_buffer_name=None, num_anchors=None)[source]

Bases: helios.layouts.base.NetworkLayoutIPCServerCalc

This Obj. reads the network information stored in a shared memory resource and execute the MDE layout algorithm

Parameters

  • num_nodes (int) –

  • num_edges (int) –

  • edges_buffer_name (str) –

  • positions_buffer_name (str) –

  • info_buffer_name (str) –

  • weights_buffer_name (str, optional) –

  • snapshots_buffer_name (str, optional) –

  • num_snapshots (int, optional) –

  • dimension=3 (int, optional) – layout dimension

  • penalty_name (str, optional) –

  • penalty_parameters_buffer_name (str, optional) –

  • num_penalty_parameters (int, optional) –

  • attractive_penalty_name (str, optional) –

  • repulsive_penalty_name (str, optional) –

  • use_shortest_path (str, optional) –

  • constraint_name (str, optional) –

  • constraint_anchors_buffer_name (str, optional) –

  • num_anchors (int, optional) –

start(steps=100, iters_by_step=3)[source]

This method starts the network layout algorithm.

Parameters

  • steps (int) – number of iterations

  • iters_by_step (int) – number of iterations per step