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read_microenvironment.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% If you use PhysiCell in your project, please cite PhysiCell and the version %
% number, such as below: %
% %
% We implemented and solved the model using PhysiCell (Version x.y.z) [1]. %
% %
% [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, %
% PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- %
% lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 %
% DOI: 10.1371/journal.pcbi.1005991 %
% %
% See VERSION.txt or call get_PhysiCell_version() to get the current version %
% x.y.z. Call display_citations() to get detailed information on all cite-%
% able software used in your PhysiCell application. %
% %
% Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM %
% as below: %
% %
% We implemented and solved the model using PhysiCell (Version x.y.z) [1], %
% with BioFVM [2] to solve the transport equations. %
% %
% [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, %
% PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- %
% lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 %
% DOI: 10.1371/journal.pcbi.1005991 %
% %
% [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- %
% llelized diffusive transport solver for 3-D biological simulations, %
% Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) %
% %
% Copyright (c) 2015-2018, Paul Macklin and the PhysiCell Project %
% All rights reserved. %
% %
% Redistribution and use in source and binary forms, with or without %
% modification, are permitted provided that the following conditions are met: %
% %
% 1. Redistributions of source code must retain the above copyright notice, %
% this list of conditions and the following disclaimer. %
% %
% 2. Redistributions in binary form must reproduce the above copyright %
% notice, this list of conditions and the following disclaimer in the %
% documentation and/or other materials provided with the distribution. %
% %
% 3. Neither the name of the copyright holder nor the names of its %
% contributors may be used to endorse or promote products derived from this %
% software without specific prior written permission. %
% %
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" %
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE %
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE %
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE %
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR %
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF %
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS %
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN %
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) %
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE %
% POSSIBILITY OF SUCH DAMAGE. %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Usage:
%
% out = read_microenvironment( filename )
%
% The data in filename must be a BioFVM .mat file (not MultiCellDS)
%
% Note: This will eventually be deprecated.
%
% Copyright 2015-2017 Paul Macklin / BioFVM project
% Licensed under 3-Clause BSD
%
function out = read_microenvironment( filename )
str = sprintf('Reading microenvironment scale stored in %s.\n\tTo access data field (n) at (i,j,k), use out.data{n}(i,j,k). \n' , filename);
disp(str);
A = struct2array( load( filename ) );
% figure out X, Y, Z, and size
% out = struct([]);
xmin = A(1,1);
ymin = A(2,1);
zmin = A(3,1);
n = size(A,2);
xmax = A(1,n);
ymax = A(2,n);
zmax = A(3,n);
% figure out number of x nodes
xnodes = 1;
while( A(1,xnodes) < xmax - eps )
xnodes = xnodes+1;
end
out.X = A(1,1:xnodes);
% figure out number of y nodes
ynodes = 1;
while( A(2,ynodes*xnodes) < ymax - eps )
ynodes = ynodes + 1;
end
out.Y = A(2,1:xnodes:xnodes*ynodes);
% figure out number of z nodes
znodes = 1;
while( A(3,ynodes*xnodes*znodes) < zmax - eps )
znodes = znodes + 1;
end
out.Z = A(3,1:xnodes*ynodes:xnodes*ynodes*znodes);
% read in data
temp = zeros(xnodes,ynodes,znodes);
% out.data = [] ;
% out.data = temp;
% out.data(1) = {temp};
% out.data = struct([]);
% to access x(i),y(k),z(k) of data field n:
% out.data{n}(i,j,k)
for n=5:size(A,1)
% fill in the data
m = 1;
for k=1:znodes
for j=1:ynodes
for i=1:xnodes
temp(i,j,k) = A(n,m);
m = m+1;
end
end
end
% allocate the spot
out.data(n-4) = {temp}; % {temp};
end
return ;