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+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  GNU General Public License for more details.
+%%  
+%%  You should have received a copy of the GNU General Public License
+%%  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+%%
+
+% To recreate the plots in:
+% Michael Wibral, Joseph T. Lizier and Viola Priesemann, "Bits from Biology for Computational Intelligence", submitted to Frontiers in Robotics and AI, 2014.
+% 
+% This is similar to one used in:
+% J.T. Lizier, M. Prokopenko and A.Y. Zomaya, "A framework for the local information dynamics of distributed computation in complex systems", in Guided self-organisation: Inception, ed. M. Prokopenko, pp. 115-158, Springer, Berlin/Heidelberg, 2014; doi: 10.1007/978-3-642-53734-9_5, arXiv:0811.2690.
+% but with slightly different number of cells and offset to make it technically a different figure.
+
+clear all;
+
+% Set up simulation options:
+cells = 10000;
+timeSteps = 600;
+neighbourhood = 3;
+caStates = 2;
+
+% Set up options for information dynamics analysis, and which segment of the CA to plot
+measureParams.k=16;
+options.saveImages = true;
+options.saveImagesFormat = 'eps';
+options.plotOptions.scaleColoursToSubsetOfPlot = true;
+scaleColoursToExtremesDefault = false;
+options.plotOptions.scaleColoursToExtremes = scaleColoursToExtremesDefault;
+% Turn up the contrast so that the small values aren't disproportionately visible: (0.15, 0.30 was good, except for separable which was better with 0.15, 0.35)
+options.plotOptions.scalingMainComponent = 0.15;
+options.plotOptions.scalingScdryComponent = 0.30;
+options.plotOptions.gammaPower = 0.5;
+
+
+%%%%%%%%%
+% Examining rule phi_par:
+% (70, 70, 17, 585) - was used in the above GSO paper
+% (75, 75, 12, 300 - is ok, but another collision would be good)
+% (100, 100, 12, 500 - is very interesting, but perhaps slightly too complicated. Dynamics will lead to some strange colouring also)
+options.plotRawCa = true;
+options.plotOptions.plotRows = 75;
+options.plotOptions.plotCols = 75;
+options.plotOptions.plotStartRow = 1;
+options.plotOptions.plotStartCol = 585;
+options.seed = 2;
+if (exist('initialStates/GsoChapterDemo2013-initialState-phipar.txt', 'file'))
+	% A file specifying the initial state exists -- this
+	%  ensures that Matlab and Octave use the same initial state
+	%  (otherwise only Octave recreates the same initial state used in our chapter).
+	%  (You can delete/move the initial state file if you want them generated from scratch.)
+	options.initialState = load('initialStates/GsoChapterDemo2013-initialState-phipar.txt');
+elseif (isfield(options, 'initialState'))
+	options = rmfield(options, 'initialState');
+end
+phi_par = 'feedffdec1aaeec0eef000a0e1a020a0';
+phi_par_neighbourhood = 7;
+phi_par_cells = 30000;
+phi_par_timeSteps = 200;
+measureParams.k=10; % Shorter for phi_par
+fprintf('\nStarting rule phi_par ...\n');
+fprintf('\nPlotting active info storage ...\n');
+plotLocalInfoMeasureForCA(phi_par_neighbourhood, caStates, phi_par, phi_par_cells, phi_par_timeSteps, 'active', measureParams, options);
+options.plotRawCa = false;
+fprintf('\nPress any key when ready for apparent transfer entropy j = -1 ...\n');
+pause
+% Use the full red scale for transfer and separable info, since we need to see the extreme negative values properly
+options.plotOptions.scaleColoursToExtremes = true;
+measureParams.j = -1;
+plotLocalInfoMeasureForCA(phi_par_neighbourhood, caStates, phi_par, phi_par_cells, phi_par_timeSteps, 'transfer', measureParams, options);
+fprintf('\nPress any key when ready for complete transfer entropy j = -1 ...\n');
+pause
+plotLocalInfoMeasureForCA(phi_par_neighbourhood, caStates, phi_par, phi_par_cells, phi_par_timeSteps, 'transfercomplete', measureParams, options);
+fprintf('\nPress any key when ready for apparent transfer entropy j = -3 ...\n');
+pause
+measureParams.j = -3;
+plotLocalInfoMeasureForCA(phi_par_neighbourhood, caStates, phi_par, phi_par_cells, phi_par_timeSteps, 'transfer', measureParams, options);
+fprintf('\nPress any key when ready for the separable information ...\n');
+pause
+options.plotOptions.scalingMainComponent = 0.35; % Make it easier to see stronger negatives
+options.plotOptions.scalingScdryComponent = 0.45;
+plotLocalInfoMeasureForCA(phi_par_neighbourhood, caStates, phi_par, phi_par_cells, phi_par_timeSteps, 'separable', measureParams, options);
+fprintf('\nPress any key when ready to apply to the next rule\n')
+pause
+options.plotOptions.scaleColoursToExtremes = scaleColoursToExtremesDefault; % return to default value 
+options.plotOptions.scalingScdryComponent = 0.30; % return to previous value
+options.plotOptions.scalingMainComponent = 0.15; % Return to previous value
+measureParams.k=16; % back to default
+