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% MCXLAB - Monte Carlo eXtreme for MATLAB/Octave by Qianqina Fang
%
% In this example, we show the most basic usage of MCXLAB.
%
% 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 0];
cfg.srcdir = [0 0 1];
cfg.gpuid = 1;
% cfg.gpuid='11'; % use two GPUs together
cfg.autopilot = 1;
cfg.issrcfrom0 = 1;
cfg.prop = [0 0 1 1; 0.005 1 0 1.37];
cfg.tstart = 0;
cfg.tend = 5e-9;
cfg.tstep = 5e-10;
% calculate the flux distribution with the given config
cfg.detpos = [15 30 0 2];
% cfg.savedetflag='dsp';
[flux, detp, vol, seeds] = mcxlabcl(cfg);

newcfg = cfg;
newcfg.seed = seeds.data;
newcfg.outputtype = 'jacobian';
newcfg.detphotons = detp.data;
[flux2, detp2, vol2, seeds2] = mcxlabcl(newcfg);
jac = sum(flux2.data, 4);
imagesc(log10(abs(squeeze(jac(:, 30, :)))));
