mirror of https://github.com/jlizier/jidt
87 lines
4.0 KiB
Matlab
Executable File
87 lines
4.0 KiB
Matlab
Executable File
%%
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%% Java Information Dynamics Toolkit (JIDT)
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%% Copyright (C) 2012, Joseph T. Lizier
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%%
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%% This program is free software: you can redistribute it and/or modify
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%% it under the terms of the GNU General Public License as published by
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%% the Free Software Foundation, either version 3 of the License, or
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%% (at your option) any later version.
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%%
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%% This program is distributed in the hope that it will be useful,
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%% but WITHOUT ANY WARRANTY; without even the implied warranty of
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%% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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%% GNU General Public License for more details.
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%%
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%% You should have received a copy of the GNU General Public License
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%% along with this program. If not, see <http://www.gnu.org/licenses/>.
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%%
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% To recreate the plots in:
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% J.T. Lizier and J.R. Mahoney, "Moving frames of reference, relativity and invariance in transfer entropy and information dynamics", Entropy, vol. 15, no. 1, p. 177-197, 2013; doi: 10.3390/e15010177
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clear all;
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% Set up options for TE j=-1 cell to the right, and which segment of the CA to plot
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measureParams.k=16;
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measureParams.j = -1;
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options.plotOptions.plotRows = 60;
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options.plotOptions.plotCols = 60;
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options.plotOptions.plotStartRow = 125;
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options.plotOptions.plotStartCol = 125;
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options.seed = 1;
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if (exist('initialStates/MovingFrameDemo2013-initialState.txt', 'file'))
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% A file specifying the initial state exists -- this
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% ensures that Matlab and Octave use the same initial state
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% (otherwise only Octave recreates the same initial state used in our chapter).
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% (You can delete/move the initial state file if you want them generated from scratch.)
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options.initialState = load('initialStates/MovingFrameDemo2013-initialState.txt');
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elseif (isfield(options, 'initialState'))
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options = rmfield(options, 'initialState');
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end
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options.saveImages = true;
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options.plotOptions.scaleColoursToSubsetOfPlot = true;
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% Turn up the contrast so that the small values aren't disproportionately visible:
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options.plotOptions.scalingMainComponent = 0.1;
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options.plotOptions.scalingScdryComponent = 0.15;
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options.movingFrameSpeed = 0;
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% Examining rule 54, stationary frame:
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'active', measureParams, options);
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fprintf('\nPress any key when ready for apparent transfer entropy ...\n');
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pause
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measureParams.j = -1;
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'transfer', measureParams, options);
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fprintf('\nPress any key when ready for complete transfer entropy ...\n');
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pause
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'transfercomplete', measureParams, options);
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fprintf('\nPress any key when ready for apparent transfer entropy j=1 channel...\n');
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pause
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measureParams.j = 1;
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'transfer', measureParams, options);
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fprintf('\nPress any key when ready for complete transfer entropy ...\n');
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pause
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'transfercomplete', measureParams, options);
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fprintf('\nCopy the figures from the figures directory, then press any key')
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fprintf('\nwhen ready for the measures in a moving frame of reference\n')
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pause
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options.movingFrameSpeed = 1;
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% Examining rule 54, f=1 frame:
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'active', measureParams, options);
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fprintf('\nPress any key when ready for apparent transfer entropy ...\n');
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pause
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measureParams.j = -1;
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'transfer', measureParams, options);
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fprintf('\nPress any key when ready for complete transfer entropy ...\n');
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pause
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'transfercomplete', measureParams, options);
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% Also plot TE for channel j=0 in the moving frame:
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measureParams.j = 0;
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fprintf('\nPress any key when ready for apparent transfer entropy with j=0...\n');
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pause
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'transfer', measureParams, options);
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fprintf('\nPress any key when ready for complete transfer entropy with j=0...\n');
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pause
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plotLocalInfoMeasureForCA(3, 2, 54, 10000, 600, 'transfercomplete', measureParams, options);
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