From e6242a544c9590a8ad2c2e2beae49d2e85f28619 Mon Sep 17 00:00:00 2001 From: "joseph.lizier" Date: Wed, 6 Aug 2014 06:52:59 +0000 Subject: [PATCH] Adding GPLv3 license statement to all code headers in the demos; also adding readme for use of octave-java code; correcting references to papers from CA code --- .../demos/Example1TeBinaryData.java | 18 +++++++++++++++ .../demos/Example2TeMultidimBinaryData.java | 18 +++++++++++++++ .../demos/Example3TeContinuousDataKernel.java | 18 +++++++++++++++ .../Example4TeContinuousDataKraskov.java | 18 +++++++++++++++ .../Example5TeBinaryMultivarTransfer.java | 18 +++++++++++++++ .../demos/Example6LateBindingMutualInfo.java | 18 +++++++++++++++ ...EnsembleMethodTeContinuousDataKraskov.java | 18 +++++++++++++++ .../Example8TeContinuousDataByBinning.java | 18 +++++++++++++++ .../DirectedMeasuresChapterDemo2013.m | 21 ++++++++++++++++- .../CellularAutomata/GsoChapterDemo2013.m | 21 +++++++++++++++-- demos/octave/CellularAutomata/TeBook2013.m | 23 ++++++++++++++++--- demos/octave/CellularAutomata/movingFrame.m | 21 +++++++++++++++-- .../plotLocalInfoMeasureForCA.m | 18 +++++++++++++++ .../CellularAutomata/plotLocalInfoValues.m | 18 +++++++++++++++ demos/octave/CellularAutomata/plotRawCa.m | 18 +++++++++++++++ .../CellularAutomata/prepareColourmap.m | 19 ++++++++++++++- demos/octave/CellularAutomata/runCA.m | 21 ++++++++++++++--- .../coupledLogisticMap.m | 18 +++++++++++++++ .../transferWithSourceMemory.m | 18 +++++++++++++++ ...activeInfoStorageHeartBreathRatesKraskov.m | 18 +++++++++++++++ .../runHeartBreathRateKernel.m | 18 +++++++++++++++ .../runHeartBreathRateKraskov.m | 18 +++++++++++++++ .../runTentMap.m | 18 +++++++++++++++ .../runUlamMap.m | 18 +++++++++++++++ demos/octave/example1TeBinaryData.m | 18 +++++++++++++++ demos/octave/example2TeMultidimBinaryData.m | 18 +++++++++++++++ demos/octave/example3TeContinuousDataKernel.m | 18 +++++++++++++++ .../octave/example4TeContinuousDataKraskov.m | 18 +++++++++++++++ .../octave/example5TeBinaryMultivarTransfer.m | 18 +++++++++++++++ .../octave/example6DynamicCallingMutualInfo.m | 18 +++++++++++++++ demos/octave/javaMatrixToOctave.m | 18 +++++++++++++++ demos/octave/octaveToJavaDoubleArray.m | 18 +++++++++++++++ demos/octave/octaveToJavaDoubleMatrix.m | 18 +++++++++++++++ demos/octave/octaveToJavaIntArray.m | 18 +++++++++++++++ demos/octave/octaveToJavaIntMatrix.m | 18 +++++++++++++++ demos/python/example1TeBinaryData.py | 18 +++++++++++++++ demos/python/example2TeMultidimBinaryData.py | 18 +++++++++++++++ .../python/example3TeContinuousDataKernel.py | 18 +++++++++++++++ .../python/example4TeContinuousDataKraskov.py | 18 +++++++++++++++ .../example5TeBinaryMultivarTransfer.py | 18 +++++++++++++++ .../example6DynamicCallingMutualInfo.py | 18 +++++++++++++++ notices/octave-java/readme.txt | 7 ++++++ readme-template.txt | 6 ++++- 43 files changed, 756 insertions(+), 13 deletions(-) create mode 100755 notices/octave-java/readme.txt diff --git a/demos/java/infodynamics/demos/Example1TeBinaryData.java b/demos/java/infodynamics/demos/Example1TeBinaryData.java index 3ef114a..cafa892 100755 --- a/demos/java/infodynamics/demos/Example1TeBinaryData.java +++ b/demos/java/infodynamics/demos/Example1TeBinaryData.java @@ -1,3 +1,21 @@ +/* + * 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 . + */ + package infodynamics.demos; import infodynamics.utils.RandomGenerator; diff --git a/demos/java/infodynamics/demos/Example2TeMultidimBinaryData.java b/demos/java/infodynamics/demos/Example2TeMultidimBinaryData.java index fe759c8..d70897b 100755 --- a/demos/java/infodynamics/demos/Example2TeMultidimBinaryData.java +++ b/demos/java/infodynamics/demos/Example2TeMultidimBinaryData.java @@ -1,3 +1,21 @@ +/* + * 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 . + */ + package infodynamics.demos; import infodynamics.utils.RandomGenerator; diff --git a/demos/java/infodynamics/demos/Example3TeContinuousDataKernel.java b/demos/java/infodynamics/demos/Example3TeContinuousDataKernel.java index ab6b160..c65595b 100755 --- a/demos/java/infodynamics/demos/Example3TeContinuousDataKernel.java +++ b/demos/java/infodynamics/demos/Example3TeContinuousDataKernel.java @@ -1,3 +1,21 @@ +/* + * 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 . + */ + package infodynamics.demos; import infodynamics.utils.EmpiricalMeasurementDistribution; diff --git a/demos/java/infodynamics/demos/Example4TeContinuousDataKraskov.java b/demos/java/infodynamics/demos/Example4TeContinuousDataKraskov.java index 1b9d837..16bb593 100755 --- a/demos/java/infodynamics/demos/Example4TeContinuousDataKraskov.java +++ b/demos/java/infodynamics/demos/Example4TeContinuousDataKraskov.java @@ -1,3 +1,21 @@ +/* + * 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 . + */ + package infodynamics.demos; import infodynamics.utils.RandomGenerator; diff --git a/demos/java/infodynamics/demos/Example5TeBinaryMultivarTransfer.java b/demos/java/infodynamics/demos/Example5TeBinaryMultivarTransfer.java index 68711e2..d4348c1 100755 --- a/demos/java/infodynamics/demos/Example5TeBinaryMultivarTransfer.java +++ b/demos/java/infodynamics/demos/Example5TeBinaryMultivarTransfer.java @@ -1,3 +1,21 @@ +/* + * 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 . + */ + package infodynamics.demos; import infodynamics.utils.MatrixUtils; diff --git a/demos/java/infodynamics/demos/Example6LateBindingMutualInfo.java b/demos/java/infodynamics/demos/Example6LateBindingMutualInfo.java index af3a153..2aa1e66 100755 --- a/demos/java/infodynamics/demos/Example6LateBindingMutualInfo.java +++ b/demos/java/infodynamics/demos/Example6LateBindingMutualInfo.java @@ -1,3 +1,21 @@ +/* + * 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 . + */ + package infodynamics.demos; import infodynamics.measures.continuous.MutualInfoCalculatorMultiVariate; diff --git a/demos/java/infodynamics/demos/Example7EnsembleMethodTeContinuousDataKraskov.java b/demos/java/infodynamics/demos/Example7EnsembleMethodTeContinuousDataKraskov.java index 35a3ec6..fc1da7c 100755 --- a/demos/java/infodynamics/demos/Example7EnsembleMethodTeContinuousDataKraskov.java +++ b/demos/java/infodynamics/demos/Example7EnsembleMethodTeContinuousDataKraskov.java @@ -1,3 +1,21 @@ +/* + * 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 . + */ + package infodynamics.demos; import infodynamics.utils.RandomGenerator; diff --git a/demos/java/infodynamics/demos/Example8TeContinuousDataByBinning.java b/demos/java/infodynamics/demos/Example8TeContinuousDataByBinning.java index d8cdbf4..38c3760 100755 --- a/demos/java/infodynamics/demos/Example8TeContinuousDataByBinning.java +++ b/demos/java/infodynamics/demos/Example8TeContinuousDataByBinning.java @@ -1,3 +1,21 @@ +/* + * 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 . + */ + package infodynamics.demos; import infodynamics.utils.MatrixUtils; diff --git a/demos/octave/CellularAutomata/DirectedMeasuresChapterDemo2013.m b/demos/octave/CellularAutomata/DirectedMeasuresChapterDemo2013.m index f6ba7aa..c472d22 100755 --- a/demos/octave/CellularAutomata/DirectedMeasuresChapterDemo2013.m +++ b/demos/octave/CellularAutomata/DirectedMeasuresChapterDemo2013.m @@ -1,6 +1,25 @@ +%% +%% 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 . +%% + % To recreate the plots in: % J. T. Lizier, "Measuring the dynamics of information processing on a local scale in time and space", -% accepted for "Directed Information Measures in Neuroscience", edited by M. Wibral, R. Vicente, J. T. Lizier, to be published by Springer, 2013 +% in "Directed Information Measures in Neuroscience", edited by M. Wibral, R. Vicente, J. T. Lizier, +% pp. 161-193, Springer, Berlin/Heidelberg, 2014; doi: 10.1007/978-3-642-54474-3_7 clear all; diff --git a/demos/octave/CellularAutomata/GsoChapterDemo2013.m b/demos/octave/CellularAutomata/GsoChapterDemo2013.m index bf3ef1c..73031a1 100755 --- a/demos/octave/CellularAutomata/GsoChapterDemo2013.m +++ b/demos/octave/CellularAutomata/GsoChapterDemo2013.m @@ -1,6 +1,23 @@ +%% +%% 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 . +%% + % To recreate the plots in: -% Lizier, Prokopenko and Zomaya, "A framework for the local information dynamics of distributed computation in complex systems", -% accepted for "Guided Self-Organization: Inception", edited by M. Prokopenko, to be published by Springer, 2013 +% 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. clear all; diff --git a/demos/octave/CellularAutomata/TeBook2013.m b/demos/octave/CellularAutomata/TeBook2013.m index c24c2c3..add0553 100755 --- a/demos/octave/CellularAutomata/TeBook2013.m +++ b/demos/octave/CellularAutomata/TeBook2013.m @@ -1,8 +1,25 @@ +%% +%% 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 . +%% + % To recreate the plots in: -% chapter 5 of T. Bossomaier, L. Barnett, M. Harré and J.T. Lizier, "An Introduction to Transfer Entropy: Information Flow in Complex Systems", Springer, to be published, 2013. +% chapter 5 of T. Bossomaier, L. Barnett, M. Harré and J.T. Lizier, "An Introduction to Transfer Entropy: Information Flow in Complex Systems", Springer, to be published, 2014. % These plots were first published in (see DirectedMeasuresChapterDemo2013.m): -% J. T. Lizier, "Measuring the dynamics of information processing on a local scale in time and space", -% accepted for "Directed Information Measures in Neuroscience", edited by M. Wibral, R. Vicente, J. T. Lizier, to be published by Springer, 2013 +% J.T. Lizier, "Measuring the dynamics of information processing on a local scale in time and space", in Directed information measures in Neuroscience, ed. M. Wibral, R. Vicente and J.T. Lizier, pp. 161-193, Springer, Berlin/Heidelberg, 2014; doi: 10.1007/978-3-642-54474-3_7 clear all; diff --git a/demos/octave/CellularAutomata/movingFrame.m b/demos/octave/CellularAutomata/movingFrame.m index d803fda..89e4fe6 100755 --- a/demos/octave/CellularAutomata/movingFrame.m +++ b/demos/octave/CellularAutomata/movingFrame.m @@ -1,6 +1,23 @@ +%% +%% 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 . +%% + % To recreate the plots in: -% Lizier and Mahoney, "Moving Frames of Reference, Relativity and Invariance in Transfer Entropy and Information Dynamics", -% submitted to Entropy, 2012 +% 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 clear all; diff --git a/demos/octave/CellularAutomata/plotLocalInfoMeasureForCA.m b/demos/octave/CellularAutomata/plotLocalInfoMeasureForCA.m index ba3289b..80efec0 100755 --- a/demos/octave/CellularAutomata/plotLocalInfoMeasureForCA.m +++ b/demos/octave/CellularAutomata/plotLocalInfoMeasureForCA.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function plotLocalInfoMeasureForCA(neighbourhood, base, rule, cells, timeSteps, measureId, measureParams, options) % % Plot one run of the given CA and compute and plot a local information dynamics profile for it diff --git a/demos/octave/CellularAutomata/plotLocalInfoValues.m b/demos/octave/CellularAutomata/plotLocalInfoValues.m index 31cdd28..18212dc 100755 --- a/demos/octave/CellularAutomata/plotLocalInfoValues.m +++ b/demos/octave/CellularAutomata/plotLocalInfoValues.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function h = plotLocalInfoValues(localResults, plotOptions) % % J. Lizier, 2012. diff --git a/demos/octave/CellularAutomata/plotRawCa.m b/demos/octave/CellularAutomata/plotRawCa.m index 7ac0ef0..d3bcb61 100755 --- a/demos/octave/CellularAutomata/plotRawCa.m +++ b/demos/octave/CellularAutomata/plotRawCa.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function plotRawCa(states, saveIt) % % Plot the given raw values of a cellular automata run diff --git a/demos/octave/CellularAutomata/prepareColourmap.m b/demos/octave/CellularAutomata/prepareColourmap.m index 42dbbae..eb5356f 100755 --- a/demos/octave/CellularAutomata/prepareColourmap.m +++ b/demos/octave/CellularAutomata/prepareColourmap.m @@ -1,4 +1,21 @@ -% J. Lizier, 2012. +%% +%% 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 . +%% + % % Function to create a colourmap of a given length. % diff --git a/demos/octave/CellularAutomata/runCA.m b/demos/octave/CellularAutomata/runCA.m index d7a6c6d..969cc8a 100755 --- a/demos/octave/CellularAutomata/runCA.m +++ b/demos/octave/CellularAutomata/runCA.m @@ -1,8 +1,23 @@ +%% +%% 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 . +%% + % function [caStates, ruleTable, executedRules] = runCA(neighbourhood, base, rule, cells, steps, debug, seedOrState) % -% Joseph Lizier -% 2012 -% Distributed under GPLv3 (see distribution of license with the code) % % Please cite: % Joseph T. Lizier, "JIDT: An information-theoretic toolkit for studying the dynamics of complex systems", 2012, https://code.google.com/p/information-dynamics-toolkit/ diff --git a/demos/octave/DetectingInteractionLags/coupledLogisticMap.m b/demos/octave/DetectingInteractionLags/coupledLogisticMap.m index faee0c5..33e1b0a 100755 --- a/demos/octave/DetectingInteractionLags/coupledLogisticMap.m +++ b/demos/octave/DetectingInteractionLags/coupledLogisticMap.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % Examine transfer entropy from variable X to Y for coupled logistic maps X and Y % where the process is as defined in Example V.A of: % Pompe and Runge, Momentary information transfer as a coupling measure of time series, diff --git a/demos/octave/DetectingInteractionLags/transferWithSourceMemory.m b/demos/octave/DetectingInteractionLags/transferWithSourceMemory.m index 3262cdc..423dd23 100755 --- a/demos/octave/DetectingInteractionLags/transferWithSourceMemory.m +++ b/demos/octave/DetectingInteractionLags/transferWithSourceMemory.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % Compute the transfer entropy (te) and the Pompe-Runge Momentary information transfer (mit) % in an example where we have short-term source memory (with decay). % diff --git a/demos/octave/SchreiberTransferEntropyExamples/activeInfoStorageHeartBreathRatesKraskov.m b/demos/octave/SchreiberTransferEntropyExamples/activeInfoStorageHeartBreathRatesKraskov.m index 9188b82..d87b641 100755 --- a/demos/octave/SchreiberTransferEntropyExamples/activeInfoStorageHeartBreathRatesKraskov.m +++ b/demos/octave/SchreiberTransferEntropyExamples/activeInfoStorageHeartBreathRatesKraskov.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function [aisHeart, aisBreath] = activeInfoStorageHeartBreathRatesKraskov(kHistories, knn, numSurrogates) % % activeInfoStorageHeartBreathRatesKraskov diff --git a/demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKernel.m b/demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKernel.m index 70b5633..22e0761 100755 --- a/demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKernel.m +++ b/demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKernel.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function [teHeartToBreath, teBreathToHeart] = runHeartBreathRateKernel(rs) % % runHeartBreathRateKernel diff --git a/demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKraskov.m b/demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKraskov.m index 1449fcd..dbc4d76 100755 --- a/demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKraskov.m +++ b/demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKraskov.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function [teHeartToBreath, teBreathToHeart] = runHeartBreathRateKraskov(kHistory, lHistory, knns, numSurrogates) % % runHeartBreathRateKraskov diff --git a/demos/octave/SchreiberTransferEntropyExamples/runTentMap.m b/demos/octave/SchreiberTransferEntropyExamples/runTentMap.m index 618a446..372d7f0 100755 --- a/demos/octave/SchreiberTransferEntropyExamples/runTentMap.m +++ b/demos/octave/SchreiberTransferEntropyExamples/runTentMap.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function Values = runTentMap() % % Version 1.0 diff --git a/demos/octave/SchreiberTransferEntropyExamples/runUlamMap.m b/demos/octave/SchreiberTransferEntropyExamples/runUlamMap.m index 88c500c..25179e1 100755 --- a/demos/octave/SchreiberTransferEntropyExamples/runUlamMap.m +++ b/demos/octave/SchreiberTransferEntropyExamples/runUlamMap.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function [teValues1to2, teValues2to1] = runUlamMap() % % Version 1.0 diff --git a/demos/octave/example1TeBinaryData.m b/demos/octave/example1TeBinaryData.m index 1f87a57..e6ecb85 100755 --- a/demos/octave/example1TeBinaryData.m +++ b/demos/octave/example1TeBinaryData.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % = Example 1 - Transfer entropy on binary data = % Simple transfer entropy (TE) calculation on binary data using the discrete TE calculator: diff --git a/demos/octave/example2TeMultidimBinaryData.m b/demos/octave/example2TeMultidimBinaryData.m index 92e347c..9d9fbaf 100755 --- a/demos/octave/example2TeMultidimBinaryData.m +++ b/demos/octave/example2TeMultidimBinaryData.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % = Example 2 - Transfer entropy on multidimensional binary data = % Simple transfer entropy (TE) calculation on multidimensional binary data using the discrete TE calculator. diff --git a/demos/octave/example3TeContinuousDataKernel.m b/demos/octave/example3TeContinuousDataKernel.m index 55368b1..c1855f6 100755 --- a/demos/octave/example3TeContinuousDataKernel.m +++ b/demos/octave/example3TeContinuousDataKernel.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % = Example 3 - Transfer entropy on continuous data using kernel estimators = % Simple transfer entropy (TE) calculation on continuous-valued data using the (box) kernel-estimator TE calculator. diff --git a/demos/octave/example4TeContinuousDataKraskov.m b/demos/octave/example4TeContinuousDataKraskov.m index 4e274ac..97e987f 100755 --- a/demos/octave/example4TeContinuousDataKraskov.m +++ b/demos/octave/example4TeContinuousDataKraskov.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % = Example 4 - Transfer entropy on continuous data using Kraskov estimators = % Simple transfer entropy (TE) calculation on continuous-valued data using the Kraskov-estimator TE calculator. diff --git a/demos/octave/example5TeBinaryMultivarTransfer.m b/demos/octave/example5TeBinaryMultivarTransfer.m index ac79a11..9fedf52 100755 --- a/demos/octave/example5TeBinaryMultivarTransfer.m +++ b/demos/octave/example5TeBinaryMultivarTransfer.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % = Example 5 - Multivariate transfer entropy on binary data = % Multivariate transfer entropy (TE) calculation on binary data using the discrete TE calculator: diff --git a/demos/octave/example6DynamicCallingMutualInfo.m b/demos/octave/example6DynamicCallingMutualInfo.m index 8053794..0d10f38 100755 --- a/demos/octave/example6DynamicCallingMutualInfo.m +++ b/demos/octave/example6DynamicCallingMutualInfo.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % Example 6 - Mutual information calculation with dynamic specification of calculator % This example shows how to write Matlab/Octave code to take advantage of the diff --git a/demos/octave/javaMatrixToOctave.m b/demos/octave/javaMatrixToOctave.m index e7aaab6..89206e1 100755 --- a/demos/octave/javaMatrixToOctave.m +++ b/demos/octave/javaMatrixToOctave.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function octaveMatrix = javaMatrixToOctave(javaMatrix) % % Convert a java matrix (1 or 2D, double or int - but not Integer!!) to an octave or matlab matrix diff --git a/demos/octave/octaveToJavaDoubleArray.m b/demos/octave/octaveToJavaDoubleArray.m index e8e6436..897d41a 100755 --- a/demos/octave/octaveToJavaDoubleArray.m +++ b/demos/octave/octaveToJavaDoubleArray.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function jDoubleArray = octaveToJavaDoubleArray(octaveArray) % % Convert a native octave array to a java double 1D array diff --git a/demos/octave/octaveToJavaDoubleMatrix.m b/demos/octave/octaveToJavaDoubleMatrix.m index cbc1f71..641d0cb 100755 --- a/demos/octave/octaveToJavaDoubleMatrix.m +++ b/demos/octave/octaveToJavaDoubleMatrix.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function jDoubleMatrix = octaveToJavaDoubleMatrix(octaveMatrix) % % Convert a native octave/matlab matrix to a java double 2D array diff --git a/demos/octave/octaveToJavaIntArray.m b/demos/octave/octaveToJavaIntArray.m index d1e885f..8692a0e 100755 --- a/demos/octave/octaveToJavaIntArray.m +++ b/demos/octave/octaveToJavaIntArray.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function jIntArray = octaveToJavaIntArray(octaveArray) % % Convert a native octave array to a java int 1D array. diff --git a/demos/octave/octaveToJavaIntMatrix.m b/demos/octave/octaveToJavaIntMatrix.m index cecf181..77bd55b 100755 --- a/demos/octave/octaveToJavaIntMatrix.m +++ b/demos/octave/octaveToJavaIntMatrix.m @@ -1,3 +1,21 @@ +%% +%% 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 . +%% + % function jIntMatrix = octaveToJavaIntMatrix(octaveMatrix) % % Convert a native octave matrix to a java int 2D array. diff --git a/demos/python/example1TeBinaryData.py b/demos/python/example1TeBinaryData.py index f2401a0..38f4ea9 100755 --- a/demos/python/example1TeBinaryData.py +++ b/demos/python/example1TeBinaryData.py @@ -1,3 +1,21 @@ +## +## 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 . +## + # = Example 1 - Transfer entropy on binary data = # Simple transfer entropy (TE) calculation on binary data using the discrete TE calculator: diff --git a/demos/python/example2TeMultidimBinaryData.py b/demos/python/example2TeMultidimBinaryData.py index 0670b65..31300c3 100755 --- a/demos/python/example2TeMultidimBinaryData.py +++ b/demos/python/example2TeMultidimBinaryData.py @@ -1,3 +1,21 @@ +## +## 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 . +## + # = Example 2 - Transfer entropy on multidimensional binary data = # Simple transfer entropy (TE) calculation on multidimensional binary data using the discrete TE calculator. diff --git a/demos/python/example3TeContinuousDataKernel.py b/demos/python/example3TeContinuousDataKernel.py index cbc4b70..67a10cb 100755 --- a/demos/python/example3TeContinuousDataKernel.py +++ b/demos/python/example3TeContinuousDataKernel.py @@ -1,3 +1,21 @@ +## +## 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 . +## + # = Example 3 - Transfer entropy on continuous data using kernel estimators = # Simple transfer entropy (TE) calculation on continuous-valued data using the (box) kernel-estimator TE calculator. diff --git a/demos/python/example4TeContinuousDataKraskov.py b/demos/python/example4TeContinuousDataKraskov.py index d078419..c2fb33b 100755 --- a/demos/python/example4TeContinuousDataKraskov.py +++ b/demos/python/example4TeContinuousDataKraskov.py @@ -1,3 +1,21 @@ +## +## 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 . +## + # = Example 4 - Transfer entropy on continuous data using Kraskov estimators = # Simple transfer entropy (TE) calculation on continuous-valued data using the Kraskov-estimator TE calculator. diff --git a/demos/python/example5TeBinaryMultivarTransfer.py b/demos/python/example5TeBinaryMultivarTransfer.py index 1c66e0d..ee6802d 100755 --- a/demos/python/example5TeBinaryMultivarTransfer.py +++ b/demos/python/example5TeBinaryMultivarTransfer.py @@ -1,3 +1,21 @@ +## +## 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 . +## + # = Example 5 - Multivariate transfer entropy on binary data = # Multivariate transfer entropy (TE) calculation on binary data using the discrete TE calculator: diff --git a/demos/python/example6DynamicCallingMutualInfo.py b/demos/python/example6DynamicCallingMutualInfo.py index e847737..8867085 100755 --- a/demos/python/example6DynamicCallingMutualInfo.py +++ b/demos/python/example6DynamicCallingMutualInfo.py @@ -1,3 +1,21 @@ +## +## 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 . +## + # = Example 6 - Mutual information calculation with dynamic specification of calculator = # This example shows how to write Python code to take advantage of the diff --git a/notices/octave-java/readme.txt b/notices/octave-java/readme.txt new file mode 100755 index 0000000..4e9e7e0 --- /dev/null +++ b/notices/octave-java/readme.txt @@ -0,0 +1,7 @@ +octave-java package of the Octave-Forge project -- http://octave.sourceforge.net/java/ + +This project is distributed under GPLv3 also; see the license file in the top level of this distribution. + +The code in infodynamics.utils.OctaveMatrix was adapted from this source. + + diff --git a/readme-template.txt b/readme-template.txt index ea6913c..c37f249 100755 --- a/readme-template.txt +++ b/readme-template.txt @@ -93,9 +93,13 @@ This project includes modified files from the Apache Commons Math library -- htt This Apache 2 software is now included as a derivative work in this GPLv3 licensed JIDT project, as per: http://www.apache.org/licenses/GPL-compatibility.html Notices and license for this software are found in the notices/commons-math directory. -The project also contains adapted code from the JAMA project -- http://math.nist.gov/javanumerics/jama/ +The project includes adapted code from the JAMA project -- http://math.nist.gov/javanumerics/jama/ Notices and license for this software are found in the notices/JAMA directory. +The project includes adapted code from the octave-java package of the Octave-Forge project -- http://octave.sourceforge.net/java/ +Notices for this software are found in the notices/JAMA directory. + + ============= Joseph T. Lizier, @DATE@