clear;
close all;


% Lecture de l'image
% I=imread('Stablized 0.tif','tif','index',1);
% I=rgb2gray(I);

%lecture nd2
I=uint16(imreadBF('example.nd2',1, 1, 1));
% figure;imshow(I,[]) ;title('ND2');

%figure;imshow(I,[]);title('Source Image');

sk=uint16(imreadBF('example.nd2',1,1,2));



[grayMorph,grayMorphSk] = MorphSegmentation(I);

%figure;imshow(grayMorph,[]);title('Denoising MorphoMath Gray Image');

% Squelette
squ=Skel(sk,4);

figure;imshow(squ,[]);title('Skeleton Image');

% Filtre Sobel
hy = fspecial('sobel');
hx = hy';
Iy = imfilter(double(grayMorph), hy, 'replicate','same');
Ix = imfilter(double(grayMorph), hx, 'replicate','same');

% Calcul du gradient
gradMag = sqrt(Ix.^2 + Iy.^2);

%figure;imshow(gradMag,[]);title('Gradient Magnitude Image');

% Extraction de frontiéres 
g = gradMag - min(gradMag(:));
%figure;imshow(g,[]);title('G');
% Normalisation.
g = g / max(g(:));
%figure;imshow(g,[]);title('Gn');
% Enlever les maximas locaux
a = imhmax(g,graythresh(g));
b = imhmin(g,graythresh(g));
%a= a|b;
%figure;imshow(a,[]);title('A');

% Binairisation
b=im2bw(a,graythresh(a));

% Elements Structurants
elfd=strel('disk',5,4);

% Fermeture
binMorph = imclose(b,elfd);
elfd1=strel('line',3,0);
elfd2=strel('line',3,45);

for i=1:1  
binMorph = imclose(binMorph,elfd1);

binMorph = imclose(binMorph,elfd2);
end
%figure;imshow(binMorph,[]);title('MorphoMath Binary Image');

% Marqueur Background
D = bwdist(1-binMorph);
DL = watershed(D);
%figure;imshow(DL,[]);title('DL');
bgm = DL == 0;


% Watershed 
gradMag2 = imimposemin(gradMag, 1-bgm,8 );

%figure;imshow(1-bgm,[]);title('1-bgm');
%figure;imshow(gradMag2,[]);title('Mag 2');
L = watershed(gradMag2);
%figure;imshow(1-L,[]);title('1-L');

%figure;imshow(L,[]);title('Watershed Image');

% Labelisation
Lrgb = label2rgb(L,'jet',[.5 .5 .5]);

%figure;imshow(Lrgb,[]);title('RGB Watershed Image');

figure;imshow(I);hold on; title('Labels & Source Image With Selected Skeleton');
himage = imshow(Lrgb);
set(himage, 'AlphaData', 0.3);

[xclik,yclik]=ginput(2);% 2 point start and end of run

[Ls,CCs] = Fillsk2(I,squ,L,xclik,yclik);
pixlist = regionprops(Ls,I,'PixelList');
pixlist2 = regionprops(Ls,sk,'PixelList');
area = regionprops(Ls,I,'Area');
moy = regionprops(Ls,I,'MeanIntensity');
moy1 = regionprops(Ls,sk,'MeanIntensity');
max = regionprops(Ls,I,'MaxIntensity');
min = regionprops(Ls,I,'MinIntensity');
perimeter = regionprops(Ls,I,'Perimeter');
pxValue = regionprops(Ls,I,'PixelValues');
StatMat=zeros(CCs.NumObjects,5);
StatMat(:,1)=cell2mat(struct2cell(moy));
StatMat(:,2)=cell2mat(struct2cell(min));
StatMat(:,3)=cell2mat(struct2cell(max));
StatMat(:,4)=cell2mat(struct2cell(perimeter));
StatMat(:,5)=cell2mat(struct2cell(area));