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- /symbolise_ed_vectorised.m
- /symbolise_ed_iter.m
- /LICENSE
- /generate_tiemask_ed.m
- /README.md
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Copyright (c) 2024, Alexander Edthofer.
Copyright (c) 2024, Alexander Edthofer, Dina Ettel.
Institute of Analysis and Scientific Computing
Technischen Universitaet Wien
......
# entropycalculation
# symbdiffpat
Das ist das ReadMe file zur Publikation xy
Hier sind die Codes zur Symbolisation der Difference Patterns, welche für die Berechnung der Entropy of Difference (EoD) benötigt werden. Für die Symbolisation der Permutation Entropy (PeEn) wird auf [1], [2] verwiesen.
Copyright (c) 2024, Alexander Edthofer
Sollten Sie weitere Fragen zur publizierten Implementation haben, bitte um Kontaktaufnahme mit alexander.edthofer@tuwien.ac.at.
A. Edthofer, D. Ettel, G. Schneider, A. Körner, and M. Kreuzer
Entropy of difference works similarly to permutation entropy for the assessment of sleep and anesthesia EEG despite the lower computational effort
## Getting started
## Changelog
To make it easy for you to get started with GitLab, here's a list of recommended next steps.
Version 0.1.0
This is the initial version.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
## Content
## Add your files
This is the supplementary MATLAB code to the above open-access publication for the symbolisation of the difference patterns, which are needed for the Entropy of Difference (EoD) [1]. In the publication it is shown that the EoD has a similar characterization performance of vigilance states during sleep and anesthesia to the Permutation Entropy (PeEn) [2] but with a faster computation time. The encoding of the ordinale patterns used for the PeEn is already discussed in [3], the implementations were taken from S. Berger.
The function symbolise_ed_iter.m encodes difference patterns iteratively, for faster computation time the further function generate_tiemask_ed.m is given as well.
The function symbolise_ed_vectorised.m uses vectorisation for this process.
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## Literature
```
cd existing_repo
git remote add origin https://gitlab.tuwien.ac.at/alexander.edthofer/entropycalculation.git
git branch -M main
git push -uf origin main
```
[1] P. Nardone, ''Entropy of Difference'', arXiv preprint arXiv:1411.0506, Nov. 2014, DOI: 10.48550/arXiv.1411.0506.
[2] C. Bandt and B. Pompe ''Permutation entropy: a natural complexity measure for time series'', Physical review letters, vol. 88, no. 17, pp. 174102, Apr. 2002, DOI: 10.1103/PhysRevLett.88.174102.
[3] S. Berger, A. Kravtsiv, G. Schneider, and D. Jordan, ''Teaching ordinal patterns to a computer: Efficient encoding algorithms based on the Lehmer code'', Entropy, vol. 21, no. 10, p. 1023, Oct. 2019, DOI: 10.3390/e21101023.
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## Test and Deploy
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***
# Editing this README
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
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function tiemask = generate_tiemask_ed(x, dim, dly, differences)
% TIEMASK(X, DIM, DLY, DIFFERENCES) returns a matrix that masks difference
% GENERATE_TIEMASK_ED(X, DIM, DLY, DIFFERENCES) returns a matrix that masks difference
% patterns that contain ties.
%
% The function returns a matrix of the size of the matrix of columnwise
......@@ -14,6 +14,41 @@ function tiemask = generate_tiemask_ed(x, dim, dly, differences)
% data points of the original data needed for determining the difference
% patterns.
% Copyright (c) 2024, Alexander Edthofer, Dina Ettel.
%
% Institute of Analysis and Scientific Computing
% Technischen Universitaet Wien
% Vienna, Austria
%
% 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 names of the copyright holders 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 THE COPYRIGHT HOLDERS AND CONTRIBUTORS
% "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 THE AUTHOR OR
% THE KLINIKUM RECHTS DER ISAR 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.
if (~isfloat(x) || ~isreal(x)) && ~isinteger(x)
error('X must contain real floating point values or integer values.');
end
......
......@@ -16,11 +16,45 @@ function y = symbolise_ed_iter(x, dim, dly, ties)
% Y = SYMBOLISE_ED_ITER(X, DIM, DLY, TIES) replaces ties by the value 0
% if TIES is set to TRUE. Otherwise (the default), if i<j and
% X(i) == X(j) this comparison is evaluated as if X(i) < X(j).
%
% The implementation of the tie mask in this function is not very
% efficient in terms of computation time. It is therefore more advisable
% to use the function GENERATE_TIEMASK_ED instead.
% Copyright (c) 2024, Alexander Edthofer, Dina Ettel.
%
% Institute of Analysis and Scientific Computing
% Technischen Universitaet Wien
% Vienna, Austria
%
% 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 names of the copyright holders 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 THE COPYRIGHT HOLDERS AND CONTRIBUTORS
% "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 THE AUTHOR OR
% THE KLINIKUM RECHTS DER ISAR 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.
narginchk(2, 4);
......
......@@ -17,6 +17,39 @@ function y = symbolise_ed_vectorised(x, dim, dly, ties)
% value 0 if TIES is set to TRUE. Otherwise (the default), if
% X(i) == X(j) this comparison is evaluated as if X(i) < X(j).
% Copyright (c) 2024, Alexander Edthofer, Dina Ettel.
%
% Institute of Analysis and Scientific Computing
% Technischen Universitaet Wien
% Vienna, Austria
%
% 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 names of the copyright holders 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 THE COPYRIGHT HOLDERS AND CONTRIBUTORS
% "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 THE AUTHOR OR
% THE KLINIKUM RECHTS DER ISAR 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.
narginchk(2, 4);
......
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