added codes

matlab_code/unwrap.m

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+%%PHASE UNWRAP
+%unwraps given data with three different unwrapping methods
+%compares quantitatively to OMME results
+%%
+clear
+clc
+
+%these are from the repository for the Loecher 2014 paper
+addpath('4dflow-lapunwrap/utils');
+addpath('4dflow-lapunwrap/unwrap');
+%%
+struct = load('path_to_data_file');
+wrapped = struct.pca_p;
+mask_struct = load('path_to_mask_file');
+mask = mask_struct.labels;
+si = size(wrapped);
+si(3) = 15;
+phi = zeros(si(1), si(2), 1, si(3));
+noise_std_percent = 0.15;
+noise_std = noise_std_percent *pi;
+rng('default')
+rng(100 + file{1}(2))
+noise = noise_std.*randn(si);
+phi(:, :, 1, 1:si(3)) = (wrapped(:, :, 1:si(3)) + noise).*mask(:, :, 1:si(3));
+phi_wn  = zeros(si(1), si(2), 1, si(3));
+phi_wn(:, :, 1, 1:si(3)) = (wrapped(:, :, 1:si(3))).*mask(:, :, 1:si(3));
+phi = phi - 2*pi*(phi > pi);
+phi = phi + 2*pi*(phi < -pi);
+masked = zeros(si(1), si(2), si(3));
+masked(:, :, :) = phi(:, :, 1, :);
+
+%%
+%laplacian unwrap
+tic
+n_u4 = unwrap_4D(phi);
+toc
+lap4d_phi = phi + double(n_u4).*2*pi;
+n_u3 = zeros(size(n_u4), 'int8');
+tic
+for i=1:si(3)
+    n_u3(:, :, :, i) = unwrap_3D(phi(:, :, :, i));
+end
+lap3d_phi = phi + double(n_u3).*2*pi;
+toc
+
+%%
+%temporal unwrap
+t_ref = 15;
+tic
+temp_phi = temporal(phi, t_ref);
+toc
+
+%%
+%probability unwrap
+w_s = 1.0;
+w_t = 2.5;
+t_low = 0.32;
+t_high = 0.75;
+tic
+prob_phi = probability(phi, t_low, t_high, w_s, w_t);
+toc
+
+%%
+%omme
+struct = load('path_to_higher_venc_file');
+high_data = struct.pca_p;
+high_venc = zeros(size(phi));
+high_venc(:, :, 1, :) = (high_data(:, :, 1:si(3))).*mask(:, :, 1:si(3));
+highv = 150;
+lowv = 75;
+high_venc = high_venc.*(highv/pi);
+low_venc = phi.*(lowv/pi);
+tic
+[omme_v, dyn, conf, std] = omme([high_venc(:), low_venc(:)], [highv, lowv]);
+omme_v = reshape(omme_v, [si(1), si(2), 1, si(3)]);
+toc
+
+%%
+%evaluate!
+temp_v = temp_phi.*lowv/pi;
+lap3d_v = lap3d_phi.*lowv/pi;
+lap4d_v = lap4d_phi.*lowv/pi;
+prob_v = prob_phi.*lowv/pi;
+v = phi.*lowv/pi;
+
+t = 1:si(3);
+base_error = eval_error(v(:, :, 1, t), omme_v(:, :, 1, t))
+t_error = eval_error(temp_v(:, :, 1, t), omme_v(:, :, 1, t))
+l4_error = eval_error(lap4d_v(:, :, 1, t), omme_v(:, :, 1, t))
+l3_error = eval_error(lap3d_v(:, :, 1, t), omme_v(:, :, 1, t))
+prob_error = eval_error(prob_v(:, :, 1, t), omme_v(:, :, 1, t))
+
+%%
+%display!
+t = 4;
+slice = 1;
+h = 145:180;
+w = 35:80;
+im0 = v(h, w, slice, t);
+im1 = temp_v(h, w, slice, t);
+im2 = lap4d_v(h, w, slice, t);
+im4 = prob_v(h, w, slice, t);
+im3 = omme_v(h, w, slice, t);
+im5 = lap3d_v(h, w, slice, t);
+figure(); 
+
+imshow([[im0 im3 im1], [im5, im2 im4]], [], 'border', 'tight', 'InitialMagnification', 300)
+axis off
+colormap("jet")
+a = colorbar
+ylabel(a,'velocity (cm/s)')
+caxis([-160, 220])
+axis off
+