%%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