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Updates to flocking demo including plotting local TEs per individual per time frame

This commit is contained in:
Joseph Lizier 2022-03-31 12:14:16 +11:00
parent b02760ddd3
commit 41361417ae
5 changed files with 198 additions and 26 deletions
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BIN
demos/octave/FlockingAnalysis/README-Flocking.pdf Normal file
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24
demos/octave/FlockingAnalysis/generateObservations.m
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@ -35,7 +35,7 @@ function [D, Dpast, S, RelSourcePos, safeDynamicCorrelationExclusionSamples] = g
%% along with this program. If not, see <http://www.gnu.org/licenses/>.
%%
% Call internal utility to put filename lists in a common format
% Call utility to put filename lists in a common format
files = processFilenames(properties.files);
% initialize series for storing the samples:
@ -455,25 +455,3 @@ function [diff] = angleDifferencePiOn2(angleA, angleB)
end
end
% Turns the fileList into a cell array of file names. The fileList can be either:
% a. a cell array of file names, e.g.: {'file1.xlsx', 'file2.xlsx'}
% b. a call to ls or ls with an argument, e.g. ls('*.xlsx')
% c. a space or tab separated character row vector of file names
% d. a character matrix of filenames (each filename on a separate row)
function fileCellArray = processFilenames(fileList)
if (iscell(fileList))
% We're done already:
fileCellArray = fileList;
elseif (isvector(fileList))
% We have a row vector of space/tab separate filenames:
fileCellArray = strsplit(strtrim(fileList)); % extra strtrim to remove trailing \n's
elseif (ismatrix(fileList))
fileCellArray = {};
for r = 1 : size(fileList, 1)
fileCellArray{r} = strtrim(fileList(r,:));
end
else
error('fileList appears to be of an incorrect format\n');
end
end

8
demos/octave/FlockingAnalysis/plotLocalTEs.m
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@ -4,7 +4,7 @@ function plotLocalTEs(properties)
% Author: Joseph T. Lizier, 2019
%
% Inputs:
% - properties (required) - object with properties for the calculations,
% - properties - object with properties for the calculations,
% with sub-members as specificied in the loadProperties.m file. If not supplied
% the properties are loaded from loadProperties.m
@ -66,8 +66,8 @@ function plotLocalTEs(properties)
else
distXY = relDistance;
end
distInFront = distXY .* cos(relTheta);
distToLeft = distXY .* sin(relTheta);
distInFront = distXY .* cos(relTheta); % X coordinate
distToLeft = distXY .* sin(relTheta); % Y coordinate
% Plot where all the raw positions are:
% Will need to turn this off when we have too many
@ -98,6 +98,8 @@ function plotLocalTEs(properties)
% Plot the TE in distance-phi plane
makePolarBinnedPlot(relPhi, relDistance, localTranEntropy, 12, 10, true, true);
title('Average TE in each bin (r, \phi)');
xlabel('r_{XY} [mm]');
ylabel('z [mm]');
end
end

41
demos/octave/FlockingAnalysis/processFilenames.m Normal file
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@ -0,0 +1,41 @@
function fileCellArray = processFilenames(fileList)
%
% Turns the fileList from the properties file (usually properties.files) into a cell array of file names. The fileList can be either:
% a. a cell array of file names, e.g.: {'file1.xlsx', 'file2.xlsx'}
% b. a call to ls or ls with an argument, e.g. ls('*.xlsx')
% c. a space or tab separated character row vector of file names
% d. a character matrix of filenames (each filename on a separate row)
%%
%% Java Information Dynamics Toolkit (JIDT)
%% Copyright (C) 2022, Joseph T. Lizier et al.
%%
%% 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/>.
%%
if (iscell(fileList))
% We're done already:
fileCellArray = fileList;
elseif (isvector(fileList))
% We have a row vector of space/tab separate filenames:
fileCellArray = strsplit(strtrim(fileList)); % extra strtrim to remove trailing \n's
elseif (ismatrix(fileList))
fileCellArray = {};
for r = 1 : size(fileList, 1)
fileCellArray{r} = strtrim(fileList(r,:));
end
else
error('fileList appears to be of an incorrect format\n');
end
end

151
demos/octave/FlockingAnalysis/watchLocalTEs.m Normal file
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@ -0,0 +1,151 @@
function watchLocalTEs(dataFileIndex, properties, refreshRate, zoomIn, plotTEIn)
% Plots a movie of local TEs in the swarm from the given input file
%
% Author: Joseph T. Lizier, 2020
%
% Inputs:
% - dataFileIndex - the index of the file to load, from the list of files listed in the properties file. Default 1.
% - properties - object with properties for the calculations,
% with sub-members as specificied in the loadProperties.m file. If not supplied
% the properties are loaded from loadProperties.m
% - refreshRate - how often to change the plotted data (default 0.1 sec)
% - zoomIn - whether to zoom into the individuals (default), or have plot take in whole field
% - plotTEIn - whether to plot the average TE into a target (true, default) or average TE out from a source (false)
%%
%% Java Information Dynamics Toolkit (JIDT)
%% Copyright (C) 2019, Joseph T. Lizier et al.
%%
%% 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/>.
%%
if (nargin < 1)
dataFileIndex = 1;
end
if (nargin < 2)
fprintf('No properties object supplied, attempting to load properties via a loadProperties script ...\n');
% By default, just try to load properties locally
if (exist('loadProperties') == 2)
% there is a loadProperties script
loadProperties;
else
% there is not a loadProperties script
error('No properties object supplied, and no loadProperties script found.');
end
end
load(properties.resultsFile);
% Loads:
% S -- source samples
% D -- target samples
% Dpast -- target past samples (embedded up to k previous samples)
% files -- cell array of file names that we took samples from
% fileTimeAndPair -- each row holds file index, time index, target index, source index
% RelSourcePos -- each row holds distance between the pair for this sample,
% their xyRelativeAngleOfSource, and zRelativeAngleOfSource
% lag -- source-target lag that is in use
% k -- embedding length for target that is in use
% tau -- embedding delay for target that is in use
% pairRange -- range within which we've pulled source-target interactions
% tranEntropy -- average transfer entropy
% localTranEntropy -- local TE for each sample
fprintf('%d samples in total for %d fish\n', length(S), length(unique(fileTimeAndPair(:,3))));
if (nargin < 3)
refreshRate = 0.1;
end
% Call utility to put filename lists in a common format
files = processFilenames(properties.files);
dataFileName = files{dataFileIndex};
% load preprocessed data using the function specified in properties.loadScript
if (properties.data3d)
[x,y,z] = feval(properties.loadScript, dataFileName, properties);
numMissing = sum(sum(isnan([x,y,z])));
maxZ = max(z(:));
minZ = min(z(:));
else
[x,y] = feval(properties.loadScript, dataFileName, properties);
numMissing = sum(sum(isnan([x,y])));
end
maxX = max(x(:));
minX = min(x(:));
maxY = max(y(:));
minY = min(y(:));
if (nargin < 4)
zoomIn = true;
end
figure()
if (~zoomIn)
fprintf('Focussing...\n');
if (properties.data3d)
axis([minX, maxX, minY, maxY, minZ, maxZ]);
else
axis([minX, maxX, minY, maxY]);
end
% Need to set this so that the axes don't keep updating
end
fprintf('%d missing values\n', numMissing);
if (nargin < 5)
plotTEIn = true;
end
% Work out the range of TEs for this data file:
teMin = min(localTranEntropy(find(fileTimeAndPair(:,1) == dataFileIndex)));
teMax = max(localTranEntropy(find(fileTimeAndPair(:,1) == dataFileIndex)));
% Loop over all the time steps in this data file
numFish = size(x,2);
cb = colorbar;
xlabel('x');
ylabel('y');
cb.Label.String = 'Av local TE';
% caxis([teMin teMax]); % These are likely too extreme for the averages
for t = 1:size(x, 1)
set(gca,'NextPlot','replacechildren') ;
% Now loop over all fish as either source or target:
averageTEs = zeros(1,numFish);
for f = 1:numFish
% Find which interactions involve TE into or out from this fish at this time step
if (plotTEIn)
% For TE in, match the target:
rowIDs = find((fileTimeAndPair(:,1) == dataFileIndex) & (fileTimeAndPair(:,2) == t) & ...
(fileTimeAndPair(:,3) == f));
else
% For TE out, match the source:
rowIDs = find((fileTimeAndPair(:,1) == dataFileIndex) & (fileTimeAndPair(:,2) == t) & ...
(fileTimeAndPair(:,4) == f));
end
% Now average the TE into or out of this fish:
averageTEs(f) = mean(localTranEntropy(rowIDs));
end
if (properties.data3d)
scatter3(x(t,:), y(t,:), z(t,:), 5, averageTEs);
else
scatter(x(t,:), y(t,:), 5, averageTEs)
end
if (plotTEIn)
title(sprintf('Average TEs into each individual at time %d, coloured for TE', t));
else
title(sprintf('Average TEs out from each individual at time %d, coloured for TE', t));
end
pause(refreshRate)
end
end