Iso surface from image

isosurfacespots.m

close all 
clear all

fname ='C:\Users\Administrator\Documents\Leslie\Uppsala\registered161101\crops\b1-2-0001-1757-1887-White Top Hat.tif';

info = imfinfo(fname);
num_images = numel(info);
w =info.Width;
h= info.Height;

allg = zeros(h,w,'uint16');
for k = 1:num_images
    A = imread(fname, k, 'Info', info);
    allg(:,:,k)=A;
end

fname ='C:\Users\Administrator\Documents\Leslie\Uppsala\registered161101\crops\b1-3-0001-1757-1887-White Top Hat.tif';

info = imfinfo(fname);
num_images = numel(info);
w =info.Width;
h= info.Height;

all1 = zeros(h,w,'uint16');
for k = 1:num_images
    A = imread(fname, k, 'Info', info);
    all1(:,:,k)=A;
end

fname ='C:\Users\Administrator\Documents\Leslie\Uppsala\registered161101\crops\b1-4-0001-1757-1887-White Top Hat.tif';

info = imfinfo(fname);
num_images = numel(info);
w =info.Width;
h= info.Height;

all2 = zeros(h,w,'uint16');
for k = 1:num_images
    A = imread(fname, k, 'Info', info);
    all2(:,:,k)=A;
end


fname ='C:\Users\Administrator\Documents\Leslie\Uppsala\registered161101\crops\b1-5-0001-1757-1887-White Top Hat.tif';

info = imfinfo(fname);
num_images = numel(info);
w =info.Width;
h= info.Height;

all3 = zeros(h,w,'uint16');
for k = 1:num_images
    A = imread(fname, k, 'Info', info);
    all3(:,:,k)=A;
end


fname ='C:\Users\Administrator\Documents\Leslie\Uppsala\registered161101\crops\b1-6-0001-1757-1887-White Top Hat.tif';

info = imfinfo(fname);
num_images = numel(info);
w =info.Width;
h= info.Height;

all4 = zeros(h,w,'uint16');
for k = 1:num_images
    A = imread(fname, k, 'Info', info);
    all4(:,:,k)=A;
end

% green T ,magenta G ,orange C ,cyan A

all1=permute(all1,[3,2,1]);
all2=permute(all2,[3,2,1]);
all3=permute(all3,[3,2,1]);
all4=permute(all4,[3,2,1]);
allg=permute(allg,[3,2,1]);
% p = patch(isosurface(allg,750));
% isonormals(allg,p);
% p.FaceColor = 'cyan';
% p.EdgeColor = 'none';
% p.SpecularStrength=0.5;
% daspect([1,1,1])
% % view(90,0); 
% view(225,45); 
axis([0 63 0 7 0 66])
set(gca,'Ytick',0:1:7);
% l1=light('color',[1,1,0.25],'Position',[0 0 1]);
% l2=light('color','blue','Position',[0 -1 0]);
% lighting gouraud
box on
grid on
% 
% hold on




hold on

p = patch(isosurface(all1,450));
isonormals(all1,p);
p.FaceColor = 'green';
p.EdgeColor = 'green';
daspect([1,1,0.7])
% set(gca,'Ztick',0:1:7);
camlight 
lighting gouraud

hold on

p = patch(isosurface(all2,300));
isonormals(all2,p);
p.FaceColor = 'magenta';
p.EdgeColor = 'magenta';
daspect([1,1,0.7])
% set(gca,'Ztick',0:1:7);
camlight 
lighting gouraud

hold on

p = patch(isosurface(all3,400));
isonormals(all3,p);
p.FaceColor  = [1,0.5,0.1];
p.EdgeColor= [1,0.5,0.1];
% 'blue';
daspect([1,1,1])
% set(gca,'Ztick',0:1:7);
camlight 
lighting gouraud

hold on

p = patch(isosurface(all4,400));
isonormals(all4,p);
p.FaceColor = 'cyan';
p.EdgeColor = 'cyan';
daspect([1,0.7,1])
axis([0 63 0 7 0 66])
view(225,30); 
% set(gca,'Ytick',0:1:7);
camlight 
lighting gouraud