% two-dimensional segmenter  combined with Deep Learning

clear all   

close all

clc

addpath('functions')

%% load the image 

disp('Load MRI images');

load matFiles/validation_data; 

%%

slice_num=23;

I=t_I(:,:,slice_num);

figure(1)

maxplots=4;

subplot(1,maxplots,1)

imagesc(I);

colormap(gray)

title(['slice number=',num2str(slice_num)]);

% maximum iteration

max_its = 50;

intEweight=.5;

DLweight=0.2;

Dynamic_Window=1;

% region of interest size

Mroi=100;

%--- run DL to find ROI: LV location detection

% load parameters of Deep Learning for ROI

%load DL_ROI_params.mat;

%yROI=DLN(I,stackedAEOptTheta,inputSize,hiddenSizeL1,hiddenSizeL2,outputSize,netconfig);

%subplot(1,maxplots,2)

%magesc(yROI);

%subplot(1,maxplots,2);hold on; plot(m_cnt(1),m_cnt(2),'r+')

% cut ROI from the image

%[subI,m_cnt]=mask2subImage(I,yROI,Mroi);

subI=t_Iroi(:,:,slice_num);

m_cnt=t_centers{slice_num};

subplot(1,maxplots,3)

imagesc(subI);colormap(gray);hold on; plot(50,50,'r+')

% run DL-LV segmentation to get phi_0

load DLconfigure/DL_LV_params.mat;

mask_LV=DLN(subI,stackedAEOptTheta,inputSize,hiddenSizeL1,hiddenSizeL2,outputSize,netconfig);

mask_LV=clean_segs(mask_LV);

init_mask = remap_mask(mask_LV,m_cnt,I);

% run segmentation

figure(2)

[LV_seg,phi,m_cnt] = region_segLargePhi(I,subI,m_cnt,init_mask,max_its,intEweight,DLweight,Dynamic_Window,1);

hold on

%imshow(subI,'initialmagnification',200,'displayrange',[0 255]); hold on;

contour(init_mask, [0 0], 'y','LineWidth',2);

Ct=t_contours{slice_num};

plot(Ct(:,1),Ct(:,2),'r','LineWidth',2)

legend('auto','auto','initial','mamual');