monte carlo photon transport in matlab

% Define input parameters
distance_to_center = 1; % in cm
tissue_properties = [0.01 1000 0.9]; % absorption, scattering coef, anisotrpy factor
num_photons = 1e6;

% Define geometry and optical properties of the model
geom = createGeometricModel('sphere','radius',distance_to_center);
tissue = createMedium('non-fluorophore','ScatteringCoefficient',tissue_properties(2),...
                      'AbsorptionCoefficient',tissue_properties(1),'Anisotropy',tissue_properties(3));

% Define input parameters for photon packets
x = 0*ones(num_photons,1); y = 0*ones(num_phots,1); z = distance_to_center*ones(num_photons,1);
direction = rand(num_photons,3); 

% Run Monte Carlo photon transport simulation
while num_photons ~= 0
  % Calculate the probability of interaction for each photon packet
  probs = calculateProbs(geom, tissue, [x y z], direction);
  
  % Sample the fate of each photon packet based on the probabilities
  [absorption,scattering,survival] = sampleFates(probs);
  
  % Update the photon packets' location and direction based on their fate
  [x,y,z,direction] = movePhotons(absorption,scattering,geom,direction,x,y,z);
  
  % Record the number of photons that suffered absorption or exited from the tissue
  absorbed_photons = sum(absorption);
  escaped_photons = sum(survival & (z<0));
  num_photons = num_photons - absorbed_photons - escaped_photons;
  
  % Optional: track the location and fate of each photon packet to visualize the results
  photonHist = [photonHist; [x,y,z,absorption,scattering,survival]];
end 

% Calculate the fluence rate and/or other relevant parameters of interest
fluenceRate = calculateFluence(geom,tissue,photonHist(:,1:3));
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