/
at_cavity.m
executable file
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at_cavity.m
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function [x y theta ROI outgrid] = at_cavity(frame,varargin)
global segmentation
% align cavity to model defined by at_grid
% parse arguments
display = getOption(varargin, 'display');
range = getOptionValue(varargin, 'range'); % mandatory arg
npoints = getOptionValue(varargin, 'npoints'); % mandatory arg
rotation = getOptionValue(varargin, 'rotation');
init = getOptionValue(varargin, 'init');
scale = getOptionValue(varargin, 'scale');
grid = getOptionValue(varargin, 'grid');
%s trategy :
%1 - coarse mode with large screening in rotation - use coarse grid
%2 - tighter screening to refine rotation - use fine grid
%3 - tight screening without rotation
if numel(grid)==0
x0=[0 0 1 8 9 9 mean([9 16]) 16];
y0=[0 -20 -37 -37 -20 0 1 0 ];% works great
else
x0=grid(1,:);
y0=grid(2,:);
end
[xout, yout, xc, yc, w, h, orient]=at_grid(x0,y0);
% if initial guess
if numel(init)==0
init=[0 0 0];
end
if numel(scale)==0
sca=0.2;
else
sca=scale;
end
if numel(rotation)==0
rotation=0;
end
imag1=phy_loadTimeLapseImage(segmentation.position,frame,1,'non');
imagstore=imag1;
%sca=0.5;
%imag1=imresize(imag1,sca);
%x=[]; y=[]; theta=[]; ROI=[]; outgrid=[];
if npoints~=1
[imag1 ang]=detectLines(imag1);
end
%if numel(init)==0
% init=[0 0 ang];
%end
%return;
if display
figure, imshow(imag1,[]); hold on; line(xout,yout,'Color','g','LineWidth',2);
end
imag1=imresize(imag1,sca);
%return;
%imag1=edge(imag1,'prewitt');
xout2=sca*xout;
yout2=sca*yout;
% xy translation
amp=range;
res=2*amp/(npoints-1);
val=sca*(-amp:res:amp);
if npoints==1
val=0;
end
% rotation
amp=rotation;
res=2*amp/(npoints-1);
valt=-amp:res:amp;
if rotation==0
valt=0;
end
maxe=1e12;
%figure
cci=1;
ccj=1;
for i=val
ccj=1;
for j=val
for k=valt
[xt, yt]=rorateLine(xout2,yout2,k+init(3),sca);
xt=xt+i+sca*init(1);
yt=yt+j+sca*init(2);
%figure, imshow(imag1,[]); hold on; line(xt,yt,'Color','r');
%c=improfile(imag1,xt,yt);
c=impixel(imag1,xt,yt);
c=c(~isnan(c));
score = sum(double(c));
%title([ num2str(i) ' - ' num2str(j) ' - ' num2str(score)]);
% pause
% close
if score<maxe(1)
maxe(1)=score; %score
maxe(3)=i+sca*init(1); % xshift
maxe(2)=j+sca*init(2); % y shift
maxe(4)=k+init(3); % same orientation
end
end
p(cci,ccj)=score;
ccj=ccj+1;
end
cci=cci+1;
end
maxe(2:3)=(maxe(2:3))/sca;
[xt, yt]=rorateLine(xout,yout,maxe(4),1);
xt=xt+maxe(3);
yt=yt+maxe(2);
if display % display grid as was used to fit align on the image
%line(xout,yout,'LineWidth',1,'Color','b');
line(xt,yt,'LineWidth',2,'Color','r');
end
% new grid used to create the mask
moy=(x0(3)+x0(4))/2;
x0=[0 0 1 5.5 6.5 6.5 mean([6.5 16]) 16];
y0=[0 -20 -35 -35 -20 0 2.5 0 ];% works great
moy2=(x0(3)+x0(4))/2;
[xout, yout, xc, yc, w, h, orient]=at_grid(x0,y0);
[xt, yt]=rorateLine(xout,yout,maxe(4),1);
shift= 0.985*(moy-moy2)/0.10833; % shift is due to differences in size of cavities
xt=xt+maxe(3)+shift;
yt=yt+maxe(2);
BW=poly2mask(xt,yt,size(imagstore,1),size(imagstore,2));
im=mat2gray(imagstore);
BW=imerode(BW, strel('Disk',15)); %3
outgrid=[xt; yt];
if display
figure, imshow(im + BW, []); hold on;
end
[xt, yt]=rorateLine(xc,yc,maxe(4),1);
xt=xt+maxe(3)+shift;
yt=yt+maxe(2);
cc=1;
ROI=[];
ROI=struct('box',[],'BW',[]);
for l=1:length(xt)
if round(xt(l)-w/2) >= 1 && round(xt(l)+w/2)<size(BW,2)-1 % remove cavitites that are too close to the edges
ROItemp=[round(xt(l)-w/2) round(yt(l)-h/2) round(w) round(h)];
ROI(cc).box=ROItemp;
%ROI(cc).BW=BW(round(yt(l)-h/2):round(yt(l)-h/2)+round(h)-1,round(xt(l)-w/2):round(xt(l)-w/2)+round(w)-1);
ROI(cc).orient=orient(l);
ROI(cc).n=cc; % id of the cavity
cc=cc+1;
if display
if orient(l)==1
line([xt(l)-w/2 xt(l)-w/2 xt(l)+w/2 xt(l)+w/2 xt(l)-w/2],[yt(l)-h/2 yt(l)+h/2 yt(l)+h/2 yt(l)-h/2 yt(l)-h/2],'Color','r');
else
line([xt(l)-w/2 xt(l)-w/2 xt(l)+w/2 xt(l)+w/2 xt(l)-w/2],[yt(l)-h/2 yt(l)+h/2 yt(l)+h/2 yt(l)-h/2 yt(l)-h/2],'Color','b');
end
end
end
end
if display && rotation==0
if npoints>1
figure, pcolor(p);
end
end
x=maxe(3);
y=maxe(2);
theta=maxe(4);
function [BW ang]=detectLines(imag1)
level=graythresh(imag1);
BW=im2bw(imag1,level);
%figure, imshow(BW,[]);
BW=imclose(BW,strel('disk',20));
BW=bwareaopen(BW,100);
%figure, imshow(BW,[]);
L=bwlabel(~BW);
%figure, imshow(L,[0 5]);
stats=regionprops(L,'Area','Perimeter','Extent','Orientation');
a=[stats.Orientation];
bins=0:1:1000;
hi=hist(L(size(L,1)/2:size(L,1)/2,1:size(L,1)),bins);
% [pix ix]=max(hi);
%
% BW=~(L==ix-1);
%
% ang=a(ix-1);
[pix ix]=max(hi(2:end));
BW=~(L==ix);
ang=a(ix);
% BW=edge(BW,'canny');
%
% figure, imshow(BW,[]);
%
% [H,T,R] = hough(BW);
% %figure, imshow(H,[],'XData',T,'YData',R,...
% % 'InitialMagnification','fit');
% %xlabel('\theta'), ylabel('\rho');
% %axis on, axis normal, hold on;
%
% P = houghpeaks(H,200,'threshold',ceil(0.01*max(H(:))));
% x = T(P(:,2)); y = R(P(:,1));
% %plot(x,y,'s','color','white');
%
% % Find lines and plot them
% lines = houghlines(BW,T,R,P,'FillGap',20,'MinLength',50);
% figure, imshow(imag1,[]), hold on
% max_len = 0;
%
% Pmean=0; cc=0; h=[];
%
% for k = 1:length(lines)
% xy = [lines(k).point1; lines(k).point2];
% plot(xy(:,1),xy(:,2),'LineWidth',2,'Color','green');
%
% % Plot beginnings and ends of lines
% plot(xy(1,1),xy(1,2),'x','LineWidth',2,'Color','yellow');
% plot(xy(2,1),xy(2,2),'x','LineWidth',2,'Color','red');
%
% % Determine the endpoints of the longest line segment
% len = norm(lines(k).point1 - lines(k).point2);
% if ( len > max_len)
% max_len = len;
% xy_long = xy;
% end
%
% len=sqrt((xy(2,2)-xy(1,2))^2+(xy(2,1)-xy(1,1))^2);
%
% %if len>200
% P = atan2(xy(2,2)-xy(1,2),xy(2,1)-xy(1,1));
% cc=cc+1;
% Pmean = Pmean+ 180*P/pi;
% h=[h P*180/pi];
% %end
% end
%
% Pmean=Pmean/cc
%
% figure, hist(h,20);
% highlight the longest line segment
%plot(xy_long(:,1),xy_long(:,2),'LineWidth',2,'Color','blue');
function [xout, yout]=rorateLine(x,y,ang,sca)
theta=-ang*pi/180;
R=[cos(theta) -sin(theta); sin(theta) cos(theta)];
xo=1000*sca;
yo=1000*sca;
xc=(x-xo);
yc=(y-yo);
Vr= R*[xc ; yc];
xout=Vr(1,:)+xo;
yout=Vr(2,:)+yo;
function value = getOption(map, key)
value = 0;
for i = 1:1:numel(map)
if strcmp(map{i}, key)
value = 1;
return
end
end
function value = getOptionValue(map, key)
value = [];
for i = 1:1:numel(map)
if strcmp(map{i}, key)
value = map{i+1};
return
end
end