mirror of https://github.com/jlizier/jidt
50 lines
2.5 KiB
Matlab
Executable File
50 lines
2.5 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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% = Example 2 - Transfer entropy on multidimensional binary data =
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% Simple transfer entropy (TE) calculation on multidimensional binary data using the discrete TE calculator.
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% This example is important for Octave users, because it shows how to handle multidimensional arrays from Octave to Java (this is not as simple as single dimensional arrays in example 1 - it requires using supplied scripts to convert the array).
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% Change location of jar to match yours:
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javaaddpath('../../infodynamics.jar');
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% Create many columns in a multidimensional array (2 rows by 100 columns),
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% where the next time step (row 2) copies the value of the column on the left
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% from the previous time step (row 1):
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twoDTimeSeriesOctave = (rand(1, 100)>0.5)*1;
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twoDTimeSeriesOctave(2, :) = [twoDTimeSeriesOctave(1,100), twoDTimeSeriesOctave(1, 1:99)];
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% Things get a little tricky if we want to pass 2D arrays into Java.
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% Unlike native Octave 1D arrays in Example 1,
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% native Octave 2D+ arrays do not seem to get directly converted to java arrays,
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% so we use the supplied scripts to make the conversion (via org.octave.Matrix class in octave)
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% Matlab handles the conversion automatically, so in Matlab this script just returns
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% the array that was passed in.
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twoDTimeSeriesJavaInt = octaveToJavaIntMatrix(twoDTimeSeriesOctave);
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% Create a TE calculator and run it:
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teCalc=javaObject('infodynamics.measures.discrete.TransferEntropyCalculatorDiscrete', 2, 1);
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teCalc.initialise();
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% Add observations of transfer across one cell to the right per time step:
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teCalc.addObservations(twoDTimeSeriesJavaInt, 1);
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fprintf('The result should be close to 1 bit here, since we are executing copy operations of what is effectively a random bit to each cell here: ');
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result2D = teCalc.computeAverageLocalOfObservations()
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