%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MCXLAB - Monte Carlo eXtreme for MATLAB/Octave by Qianqina Fang
%
% In this example, we show how to define continuously varying media
% (i.e. media optical properties vary from voxel to voxel)
%
% This file is part of Monte Carlo eXtreme (MCX) URL:http://mcx.sf.net
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% only clear cfg to avoid accidentally clearing other useful data
clear cfg cfgs;
cfg.nphoton = 1e8;
cfg.vol = uint8(ones(60, 60, 60));
cfg.srcpos = [30 30 1];
cfg.srcdir = [0 0 1];
cfg.gpuid = 1;
% cfg.gpuid='11'; % use two GPUs together
cfg.autopilot = 1;
cfg.prop = [0 0 1 1; 0.005 1 0 1.37];
cfg.tstart = 0;
cfg.tend = 5e-9;
cfg.tstep = 5e-9;
% calculate the flux distribution with the given config

%% Approach #1: a 1 x Nx x Ny x Nz floating-point array defines mua(x,y,z)
% define continuously varying media - use a 4D array - 1st dimension defines
% the optical property components of each spatial position

mua1 = 0.003;
mua2 = 0.1;
mua = single(reshape(repmat([mua1:(mua2 - mua1) / (60 - 1):mua2]', 60, 60), 60, 60, 60));
cfg.vol = permute(mua, [4, 1, 2, 3]); % make 1st dimension the property dimension

flux = mcxlabcl(cfg);

mcxplotvol(squeeze(cfg.vol));
title('continuously varying absorption coeff \mu_a (1/mm)');
view([-25.5, 21.2]);

mcxplotvol(log10(flux.data));
colormap(jet);
title('fluence in continuously varying media (1/mm^2)');
view([-25.5, 21.2]);

%% Approach #2: a 2 x Nx x Ny x Nz float32 array defines [mua,mus] per voxel

mus1 = 1.0;
mus2 = 5.0;
mus = single(reshape(repmat([mus1:(mus2 - mus1) / (60 - 1):mus2]', 60, 60), 60, 60, 60));
cfg.vol = reshape([mua(:)'; mus(:)'], [2 60 60 60]);

flux = mcxlabcl(cfg);

mcxplotvol(squeeze(cfg.vol(2, :, :, :)));
title('continuously varying scattering coeff \mu_s (1/mm)');
view([-25.5, 21.2]);

mcxplotvol(log10(flux.data));
colormap(jet);
title('fluence in continuously varying media (1/mm^2)');
view([-25.5, 21.2]);
