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ArteryVeinDetectionClassification.m
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ArteryVeinDetectionClassification.m
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% -------------------------------------------------------------------------
% Artery Vein Detection and Classification
% -------------------------------------------------------------------------
% Author: Seonyeong Park (sp33@illinois.edu)
% Date: Jan. 24, 2022
%
% This project is to detect blood vessels via estimation of total
% hemoglobin concentration and to classify them into arteries and veins via
% estimation of oxygen saturation, from three-dimensional (3D) optoacoustic
% tomography (OAT) images of the breast at two and three illumination
% wavelengths. The total hemoglobin concentration and oxygen saturation are
% estimated using spectral linear unmixing. The molar extinction
% coefficients of deoxy- and oxyhemoglobin used in the spectral linear
% unmixing are from the reference [OMLC]. Multiscale vessel enhancement
% filtering, also known as Frangi filtering [Frangi], and Otsu thresholding
% are applied to the estimate of total hemoglobin concentration to detect
% the blood vessels. Before running this code, the function package
% of the multiscale vessel enhancement filter [Fraingi] should be
% downloaded, and the 'eig3volume.c' file should be compiled ('mex
% eig3volume.c'). The method of the software is detailed in [Park2022].
%
% Reference:
% [Park2022] Seonyeong Park, Frank J. Brooks, Umberto Villa, Richard Su,
% Mark A. Anastasio, Alexander A. Oraevsky, "Normalization of
% optical fluence distribution for three-dimensional functional
% optoacoustic tomography of the breast," J. Biomed. Opt. 27(3)
% 036001 (16 March 2022)
% https://doi.org/10.1117/1.JBO.27.3.036001
%
% [OMLC] https://omlc.org/spectra/hemoglobin/summary.html
%
% [Frangi] Dirk-Jan Kroon (2022). Hessian based Frangi Vesselness filter
% (https://www.mathworks.com/matlabcentral/fileexchange/24409-
% hessian-based-frangi-vesselness-filter), MATLAB Central File
% Exchange. Retrieved April 15, 2022.
%
% Copyright (C) 2022 Seonyeong Park
% License: GNU General Public License version 3, Please see 'LICENSE' for
% details.
%
addpath('functions'); % Add a path of functions
addpath('frangi_filter_version2a'); % Add a path of vessel enhancement filter
flag_fig = true; % Flag to plot
% flag_fig = false; % Flag to plot
% Molar extinction coffient matix
eps = [156.048, 56.8; ... % 757 nm
76.172, 81.6; ... % 800 nm
69.132, 105.8]; % 850 nm
% True oxygen saturation
s_artery = 0.97; % Artery
s_vein = 0.7; % Vein
threshold = mean([s_artery, s_vein]);
% File name
filename_p0_w757 = fullfile('data', 'RECON_NOISY_w757_FBP.mat');
filename_p0_w800 = fullfile('data', 'RECON_NOISY_w800_FBP.mat');
filename_p0_w850 = fullfile('data', 'RECON_NOISY_w850_FBP.mat');
filename_phi0_est_w757 = fullfile('data', 'phi0_est_w757.mat');
filename_phi0_est_w800 = fullfile('data', 'phi0_est_w800.mat');
filename_phi0_est_w850 = fullfile('data', 'phi0_est_w850.mat');
filename_phia_est_w757 = fullfile('data', 'phia_est_w757.mat');
filename_phia_est_w800 = fullfile('data', 'phia_est_w800.mat');
filename_phia_est_w850 = fullfile('data', 'phia_est_w850.mat');
% No optical fluence normalization
filename_vessel_filter_non_w757_w800 = ...
fullfile('data', 'vessel_filter_non_w757_w800.mat');
filename_vessel_filter_non_w757_w850 = ...
fullfile('data', 'vessel_filter_non_w757_w850.mat');
filename_vessel_filter_non_w800_w850 = ...
fullfile('data', 'vessel_filter_non_w800_w850.mat');
filename_vessel_filter_non_w757_w800_w850 = ...
fullfile('data', 'vessel_filter_non_w757_w800_w850.mat');
% Optical fluence normalization
filename_vessel_filter_on_w757_w800 = ...
fullfile('data', 'vessel_filter_on_w757_w800.mat');
filename_vessel_filter_on_w757_w850 = ...
fullfile('data', 'vessel_filter_on_w757_w850.mat');
filename_vessel_filter_on_w800_w850 = ...
fullfile('data', 'vessel_filter_on_w800_w850.mat');
filename_vessel_filter_on_w757_w800_w850 = ...
fullfile('data', 'vessel_filter_on_w757_w800_w850.mat');
% Load estimated intial pressure, reconstructed image
fprintf('Loading reconstructed images...\n');
load(filename_p0_w757, 'recon'); p0_est_w757 = recon;
load(filename_p0_w800, 'recon'); p0_est_w800 = recon;
load(filename_p0_w850, 'recon'); p0_est_w850 = recon;
clear recon;
% Load estimated incident optical fluence and optical attenuation
fprintf('Loading estimated incident optical fluence...\n');
load(filename_phi0_est_w757); phi0_est_w757 = phi0_est;
load(filename_phi0_est_w800); phi0_est_w800 = phi0_est;
load(filename_phi0_est_w850); phi0_est_w850 = phi0_est;
clear phi0_est;
fprintf('Loading estimated optical attenuation...\n');
load(filename_phia_est_w757); phia_est_w757 = phia_est;
load(filename_phia_est_w800); phia_est_w800 = phia_est;
load(filename_phia_est_w850); phia_est_w850 = phia_est;
clear phia_est;
% Estimate optical absorption coefficient
fprintf('Estimating optical absorption coefficient...\n');
mu_a_est_w757 = smooth3(p0_est_w757./phi0_est_w757./phia_est_w757);
mu_a_est_w800 = smooth3(p0_est_w800./phi0_est_w800./phia_est_w800);
mu_a_est_w850 = smooth3(p0_est_w850./phi0_est_w850./phia_est_w850);
%% Spectral linear unmixing
fprintf('Computing Spectral linear unmixing...\n');
% No optical normalization
fprintf(' With no optical normaliation...\n');
[s_est_non_w757_w800, c_thb_est_non_w757_w800] = ... % 757, 800 nm
LinearUnmixing2([eps(1, :); eps(2, :)], p0_est_w757, p0_est_w800);
[s_est_non_w757_w850, c_thb_est_non_w757_w850] = ... % 757, 850 nm
LinearUnmixing2([eps(1, :); eps(3, :)], p0_est_w757, p0_est_w850);
[s_est_non_w800_w850, c_thb_est_non_w800_w850] = ... % 800, 850 nm
LinearUnmixing2([eps(2, :); eps(3, :)], p0_est_w800, p0_est_w850);
[s_est_non_w757_w800_w850, c_thb_est_non_w757_w800_w850] = ... % 757, 800, 850 nm
LinearUnmixing3(eps, p0_est_w757, p0_est_w800, p0_est_w850);
% Optical normalization
fprintf(' With optical normaliation...\n');
[s_est_on_w757_w800, c_thb_est_on_w757_w800] = ... % 757, 800 nm
LinearUnmixing2([eps(1, :); eps(2, :)], mu_a_est_w757, mu_a_est_w800);
[s_est_on_w757_w850, c_thb_est_on_w757_w850] = ... % 757, 850 nm
LinearUnmixing2([eps(1, :); eps(3, :)], mu_a_est_w757, mu_a_est_w850);
[s_est_on_w800_w850, c_thb_est_on_w800_w850] = ... % 800, 850 nm
LinearUnmixing2([eps(2, :); eps(3, :)], mu_a_est_w800, mu_a_est_w850);
[s_est_on_w757_w800_w850, c_thb_est_on_w757_w800_w850] = ... % 757, 800, 850 nm
LinearUnmixing3(eps, mu_a_est_w757, mu_a_est_w800, mu_a_est_w850);
%% Multiscale vessel enhancement filtering
fprintf('Applying multiscale vessel filtering...\n');
options.FrangiScaleRange = [1, 5];
options.FrangiScaleRatio = 1;
options.BlackWhite = false;
% No optical normalization
fprintf(' With no optical normaliation...\n');
[filter_non_w757_w800, ~, ~, ~, ~] = ...
FrangiFilter3D(c_thb_est_non_w757_w800, options); % 757, 800 nm
[filter_non_w757_w850, ~, ~, ~, ~] = ...
FrangiFilter3D(c_thb_est_non_w757_w850, options); % 757, 850 nm
[filter_non_w800_w850, ~, ~, ~, ~] = ...
FrangiFilter3D(c_thb_est_non_w800_w850, options); % 800, 850 nm
[filter_non_w757_w800_w850, ~, ~, ~, ~] = ...
FrangiFilter3D(c_thb_est_non_w757_w800_w850, options); % 757, 800, 850 nm
% Optical normalization
fprintf(' With optical normaliation...\n');
[filter_on_w757_w800, ~, ~, ~, ~] = ...
FrangiFilter3D(c_thb_est_on_w757_w800, options); % 757, 800 nm
[filter_on_w757_w850, ~, ~, ~, ~] = ...
FrangiFilter3D(c_thb_est_on_w757_w850, options); % 757, 850 nm
[filter_on_w800_w850, ~, ~, ~, ~] = ...
FrangiFilter3D(c_thb_est_on_w800_w850, options); % 800, 850 nm
[filter_on_w757_w800_w850, ~, ~, ~, ~] = ...
FrangiFilter3D(c_thb_est_on_w757_w800_w850, options); % 757, 800, 850 nm
%% Otsu thresholding
fprintf('Applying Otsu thresholding...\n');
% No optical normalization
fprintf(' With no optical normaliation...\n');
mask_non_w757_w800 = imbinarize( ...
filter_non_w757_w800./max(filter_non_w757_w800(:)));
mask_non_w757_w850 = imbinarize( ...
filter_non_w757_w850./max(filter_non_w757_w850(:)));
mask_non_w800_w850 = imbinarize( ...
filter_non_w800_w850./max(filter_non_w800_w850(:)));
mask_non_w757_w800_w850 = imbinarize(...
filter_non_w757_w800_w850./max(filter_non_w757_w800_w850(:)));
% Optical normalization
fprintf(' With optical normaliation...\n');
mask_on_w757_w800 = imbinarize( ...
filter_on_w757_w800./max(filter_on_w757_w800(:)));
mask_on_w757_w850 = imbinarize( ...
filter_on_w757_w850./max(filter_on_w757_w850(:)));
mask_on_w800_w850 = imbinarize( ...
filter_on_w800_w850./max(filter_on_w757_w850(:)));
mask_on_w757_w800_w850 = imbinarize( ...
filter_on_w757_w800_w850./max(filter_on_w757_w800_w850(:)));
% Save vessel enhancement filtering result and vessel mask
fprintf('Saving vessel enhancement filtering result and vessel mask...\n');
% No optical normalization
fprintf(' With no optical normaliation...\n');
save(filename_vessel_filter_non_w757_w800, ...
'filter_non_w757_w800', 'mask_non_w757_w800');
save(filename_vessel_filter_non_w757_w850, ...
'filter_non_w757_w850', 'mask_non_w757_w850');
save(filename_vessel_filter_non_w800_w850, ...
'filter_non_w800_w850', 'mask_non_w800_w850');
save(filename_vessel_filter_non_w757_w800_w850, ...
'filter_non_w757_w800_w850', 'mask_non_w757_w800_w850');
% Optical normalization
fprintf(' With optical normaliation...\n');
save(filename_vessel_filter_on_w757_w800, ...
'filter_on_w757_w800', 'mask_on_w757_w800');
save(filename_vessel_filter_on_w757_w850, ...
'filter_on_w757_w850', 'mask_on_w757_w850');
save(filename_vessel_filter_on_w800_w850, ...
'filter_on_w800_w850', 'mask_on_w800_w850');
save(filename_vessel_filter_on_w757_w800_w850, ...
'filter_on_w757_w800_w850', 'mask_on_w757_w800_w850');
if flag_fig == 1
% Plot detected blooe vessels
% No optical fluence normalization
figure; % 757, 800 nm
subplot(1, 3, 1); imagesc(squeeze(max(mask_non_w757_w800,[],1)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2); imagesc(squeeze(max(mask_non_w757_w800,[],2)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3); imagesc(squeeze(max(mask_non_w757_w800,[],3)));
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Detected blood vessels, No optical fluence normalization', ...
'757 nm and 800 nm'}, 'Interpreter', 'latex');
figure; % 757, 850 nm
subplot(1, 3, 1); imagesc(squeeze(max(mask_non_w757_w850,[],1)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2); imagesc(squeeze(max(mask_non_w757_w850,[],2)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3); imagesc(squeeze(max(mask_non_w757_w850,[],3)));
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Detected blood vessels, No optical fluence normalization', ...
'757 nm and 850 nm'}, 'Interpreter', 'latex');
figure; % 800, 850 nm
subplot(1, 3, 1); imagesc(squeeze(max(mask_non_w800_w850,[],1)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2); imagesc(squeeze(max(mask_non_w800_w850,[],2)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3); imagesc(squeeze(max(mask_non_w800_w850,[],3)));
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Detected blood vessels, No optical fluence normalization', ...
'800 nm and 850 nm'}, 'Interpreter', 'latex');
figure; % 757, 800, 850 nm
subplot(1, 3, 1); imagesc(squeeze(max(mask_non_w757_w800_w850,[],1)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2); imagesc(squeeze(max(mask_non_w757_w800_w850,[],2)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3); imagesc(squeeze(max(mask_non_w757_w800_w850,[],3)));
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Detected blood vessels, No optical fluence normalization', ...
'757 nm, 800 nm, and 850 nm'}, 'Interpreter', 'latex');
% Optical fluence normalization
figure; % 757, 800 nm
subplot(1, 3, 1); imagesc(squeeze(max(mask_on_w757_w800,[],1)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2); imagesc(squeeze(max(mask_on_w757_w800,[],2)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3); imagesc(squeeze(max(mask_on_w757_w800,[],3)));
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Detected blood vessels, Optical fluence normalization', ...
'757 nm and 800 nm'}, 'Interpreter', 'latex');
figure; % 757, 850 nm
subplot(1, 3, 1); imagesc(squeeze(max(mask_on_w757_w850,[],1)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2); imagesc(squeeze(max(mask_on_w757_w850,[],2)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3); imagesc(squeeze(max(mask_on_w757_w850,[],3)));
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Detected blood vessels, Optical fluence normalization', ...
'757 nm and 850 nm'}, 'Interpreter', 'latex');
figure; % 800, 850 nm
subplot(1, 3, 1); imagesc(squeeze(max(mask_on_w800_w850,[],1)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2); imagesc(squeeze(max(mask_on_w800_w850,[],2)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3); imagesc(squeeze(max(mask_on_w800_w850,[],3)));
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Detected blood vessels, Optical fluence normalization', ...
'800 nm and 850 nm'}, 'Interpreter', 'latex');
figure; % 757, 800, 850 nm
subplot(1, 3, 1); imagesc(squeeze(max(mask_on_w757_w800_w850,[],1)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2); imagesc(squeeze(max(mask_on_w757_w800_w850,[],2)));
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3); imagesc(squeeze(max(mask_on_w757_w800_w850,[],3)));
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap hot; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Detected blood vessels, Optical fluence normalization', ...
'757 nm, 800 nm, and 850 nm'}, 'Interpreter', 'latex');
end
% Classify arteries and veins
fprintf('Classifying arteries and veins...\n');
% No optical normalization
fprintf(' With no optical normaliation...\n');
% 757, 800 nm
s_est_non_w757_w800_av = s_est_non_w757_w800;
s_est_non_w757_w800_av(s_est_non_w757_w800 > threshold) = s_artery;
s_est_non_w757_w800_av(s_est_non_w757_w800 <= threshold) = s_vein;
s_est_non_w757_w800_av = s_est_non_w757_w800_av.*mask_non_w757_w800;
% 757, 850 nm
s_est_non_w757_w850_av = s_est_non_w757_w850;
s_est_non_w757_w850_av(s_est_non_w757_w850 > threshold) = s_artery;
s_est_non_w757_w850_av(s_est_non_w757_w850 <= threshold) = s_vein;
s_est_non_w757_w850_av = s_est_non_w757_w850_av.*mask_non_w757_w850;
% 800, 850 nm
s_est_non_w800_w850_av = s_est_non_w800_w850;
s_est_non_w800_w850_av(s_est_non_w800_w850 > threshold) = s_artery;
s_est_non_w800_w850_av(s_est_non_w800_w850 <= threshold) = s_vein;
s_est_non_w800_w850_av = s_est_non_w800_w850_av.*mask_non_w800_w850;
% 757, 800, 850 nm
s_est_non_w757_w800_w850_av = s_est_non_w757_w800_w850;
s_est_non_w757_w800_w850_av(s_est_non_w757_w800_w850 > threshold) = s_artery;
s_est_non_w757_w800_w850_av(s_est_non_w757_w800_w850 <= threshold) = s_vein;
s_est_non_w757_w800_w850_av = s_est_non_w757_w800_w850_av.*mask_non_w757_w800_w850;
% Optical normalization
fprintf(' With optical normaliation...\n');
% 757, 800 nm
s_est_on_w757_w800_av = s_est_on_w757_w800;
s_est_on_w757_w800_av(s_est_on_w757_w800 > threshold) = s_artery;
s_est_on_w757_w800_av(s_est_on_w757_w800 <= threshold) = s_vein;
s_est_on_w757_w800_av = s_est_on_w757_w800_av.*mask_on_w757_w800;
% 757, 850 nm
s_est_on_w757_w850_av = s_est_on_w757_w850;
s_est_on_w757_w850_av(s_est_on_w757_w850 > threshold) = s_artery;
s_est_on_w757_w850_av(s_est_on_w757_w850 <= threshold) = s_vein;
s_est_on_w757_w850_av = s_est_on_w757_w850_av.*mask_on_w757_w850;
% 800, 850 nm
s_est_on_w800_w850_av = s_est_on_w800_w850;
s_est_on_w800_w850_av(s_est_on_w800_w850 > threshold) = s_artery;
s_est_on_w800_w850_av(s_est_on_w800_w850 <= threshold) = s_vein;
s_est_on_w800_w850_av = s_est_on_w800_w850_av.*mask_on_w800_w850;
% 757, 800, 850 nm
s_est_on_w757_w800_w850_av = s_est_on_w757_w800_w850;
s_est_on_w757_w800_w850_av(s_est_on_w757_w800_w850 > threshold) = s_artery;
s_est_on_w757_w800_w850_av(s_est_on_w757_w800_w850 <= threshold) = s_vein;
s_est_on_w757_w800_w850_av = s_est_on_w757_w800_w850_av.*mask_on_w757_w800_w850;
if flag_fig == 1
% Plot classified arteries and veins
% No optical fluence normalization
figure;
subplot(1, 3, 1);
imagesc(squeeze(max(s_est_non_w757_w800_av,[],1)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2);
imagesc(squeeze(max(s_est_non_w757_w800_av,[],2)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3);
imagesc(squeeze(max(s_est_non_w757_w800_av,[],3)), [0.5, 1]);
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Classified arteries and veins, No optical fluence normalization', ...
'757 nm and 800 nm'}, 'Interpreter', 'latex');
figure;
subplot(1, 3, 1);
imagesc(squeeze(max(s_est_non_w757_w850_av,[],1)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2);
imagesc(squeeze(max(s_est_non_w757_w850_av,[],2)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3);
imagesc(squeeze(max(s_est_non_w757_w850_av,[],3)), [0.5, 1]);
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Classified arteries and veins, No optical fluence normalization', ...
'757 nm and 850 nm'}, 'Interpreter', 'latex');
figure;
subplot(1, 3, 1);
imagesc(squeeze(max(s_est_non_w800_w850_av,[],1)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2);
imagesc(squeeze(max(s_est_non_w800_w850_av,[],2)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3);
imagesc(squeeze(max(s_est_non_w800_w850_av,[],3)), [0.5, 1]);
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Classified arteries and veins, No optical fluence normalization', ...
'800 nm and 850 nm'}, 'Interpreter', 'latex');
figure;
subplot(1, 3, 1);
imagesc(squeeze(max(s_est_non_w757_w800_w850_av,[],1)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2);
imagesc(squeeze(max(s_est_non_w757_w800_w850_av,[],2)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3);
imagesc(squeeze(max(s_est_non_w757_w800_w850_av,[],3)), [0.5, 1]);
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Classified arteries and veins, No optical fluence normalization', ...
'757 nm, 800 nm, and 850 nm'}, 'Interpreter', 'latex');
% Optical fluence normalization
figure;
subplot(1, 3, 1);
imagesc(squeeze(max(s_est_on_w757_w800_av,[],1)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2);
imagesc(squeeze(max(s_est_on_w757_w800_av,[],2)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3);
imagesc(squeeze(max(s_est_on_w757_w800_av,[],3)), [0.5, 1]);
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Classified arteries and veins, Optical fluence normalization', ...
'757 nm and 800 nm'}, 'Interpreter', 'latex');
figure;
subplot(1, 3, 1);
imagesc(squeeze(max(s_est_on_w757_w850_av,[],1)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2);
imagesc(squeeze(max(s_est_on_w757_w850_av,[],2)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3);
imagesc(squeeze(max(s_est_on_w757_w850_av,[],3)), [0.5, 1]);
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Classified arteries and veins, Optical fluence normalization', ...
'757 nm and 850 nm'}, 'Interpreter', 'latex');
figure;
subplot(1, 3, 1);
imagesc(squeeze(max(s_est_on_w800_w850_av,[],1)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2);
imagesc(squeeze(max(s_est_on_w800_w850_av,[],2)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3);
imagesc(squeeze(max(s_est_on_w800_w850_av,[],3)), [0.5, 1]);
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Classified arteries and veins, Optical fluence normalization', ...
'800 nm and 850 nm'}, 'Interpreter', 'latex');
figure;
subplot(1, 3, 1);
imagesc(squeeze(max(s_est_on_w757_w800_w850_av,[],1)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$y$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 2);
imagesc(squeeze(max(s_est_on_w757_w800_w850_av,[],2)), [0.5, 1]);
xlabel('$z$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
subplot(1, 3, 3);
imagesc(squeeze(max(s_est_on_w757_w800_w850_av,[],3)), [0.5, 1]);
xlabel('$y$ [voxel]', 'Interpreter', 'latex');
ylabel('$x$ [voxel]', 'Interpreter', 'latex');
colorbar('TickLabelInterpreter', 'latex'); colormap jet; colorbar; axis image;
set(gca, 'FontSize', 14, 'FontName', 'Times', ...
'TickLabelInterpreter', 'latex');
sgtitle({'Classified arteries and veins, Optical fluence normalization', ...
'757 nm, 800 nm, and 850 nm'}, 'Interpreter', 'latex');
end