Reproducing Time–Frequency Plots for Paper: 'Time–frequency processing of non-stationary signals to aid diagnosis', IEEE Signal Processing Magazine, Nov. 2013

This collection of M-files (computer code) generates the figures in

• B. Boashash, G. Azemi, and J.M. O’ Toole, “Time–frequency processing of nonstationary signals: advanced TFD design to aid diagnosis with highlights from medical applications,” IEEE Signal Process. Mag., vol. 30, no. 6, pp. 108–119, Nov. 2013. DOI: 10.1109/MSP.2013.2265914

Requires Matlab or Octave programming environments.

Files:

• reproduce_figures.m : main function to generate the plots
• load_paths_all.m : loads all sub-directories into the path
• generate_FigX.m : file to generate Fig. X (either: 1,2,3,4, or 5) only

Directories:

• data/ : contains Matlab files (.mat) with short epochs of biomedical signals.
• fastTFDs_v0.23/ : contains files to efficiently generate time-frequency distributions. More up-to-date versions of this code is available at fast_TFDs
• IF_est/ : contains code to estimate the instantaneous frequency of the signal. Similar code is available at time_frequency_tracks
• PLED_IFest/ : contains code to again estimate the instantaneous frequency, but this time specifically for epileptiform discharges; up-to-date code available at IF_estimation_PLEDs
• utils/ : miscellaneous files.

Requirements

Either Matlab (R2012 or newer, Mathworks) or Octave (v3.6 or newer, GNU Octave, with the 'octave-signal' add-on package). In addition, some figures require the 'time–frequency signal analysis (TFSA)' package, available for free download at http://time-frequency.net/. (Please note however that Figs. 1. and 2. cannot be generated with Octave (Matlab only), as these figures require the TFSA package.)

Start

Set paths in Matlab, or do so using the load_paths_all function:

  load_paths_all;

To reproduce the figures, open Matlab (or Octave) and run as follows:

 reproduce_figures(1);
 %% to plot Fig. 1, and similarly for Fig. 2
 reproduce_figures(2);
 %% and so on.

Version

• Version: 0.1
• Last update: 2013-05-16.

Copyright

Copyright (c) 2013 John M. O' Toole, University College Cork, and Ghasem Azemi, The University of Queensland. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
• Neither the name of the University College Cork nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY JOHN M. O' TOOLE ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL JOHN M. O' TOOLE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Test computer setup

• hardware: Intel(R) Xeon(R) CPU @ 2.80GHz; 8GB RAM.
• operating system: Ubuntu GNU/Linux x86_64 distribution (Raring, 13.04), with Linux kernel 3.5.0-28-generic
• software: Octave 3.6.4 (using Gnuplot 4.6 patchlevel 1), with 'octave-signal' toolbox and Matlab (R2009b, R2012a, and R2013a), with 'signal processing' toolbox

References

1. B. Boashash, G. Azemi, and J.M. O’ Toole, “Time–frequency processing of nonstationary signals: advanced TFD design to aid diagnosis with highlights from medical applications,” IEEE Signal Process. Mag., vol. 30, no. 6, pp. 108–119, Nov. 2013. DOI: 10.1109/MSP.2013.2265914

Contact

• John M. O' Toole,
• Neonatal Brain Research Group,
  Irish Centre for Fetal and Neonatal Translational Research (INFANT),
  Department of Paediatrics and Child Health,
  Room 2.19 Paediatrics Bld, Cork University Hospital,
  University College Cork,
  Ireland
• Email j.otoole AT ieee.org; jotoole AT ucc.ie