Hello, I have the following code and couldn't figure out what I am doing wrong. I am getting the following error,

%%Matrix dimensions must agree.

%Error in crop4 (line 86) ZTerm=Z.*ROI';

J=imread('3.bmp');
imshow(J)
set(gcf,'position',[1 1 600 600]);

% %binary img
% J=I(:,:,1)>160;
% imshow(J)
% set(gcf,'position',[1 1 600 600]);

%%Thining
% Ridge thining is to eliminate the redundant pixels of ridges till the 
% ridges are just one pixel wide.  
K=bwmorph(~J,'thin','inf');
imshow(~K)
set(gcf,'position',[1 1 600 600]);

%%Minutiae
% We filter the thinned ridge map by the filter "minutie". "minutie"
% compute the number of one-value of each 3x3 window:
% * if the central is 1 and has only 1 one-value neighbor, then the central 
% pixel is a termination.  
% * if the central is 1 and has 3 one-value neighbor, then the central 
% pixel is a bifurcation. 
% * if the central is 1 and has 2 one-value neighbor, then the central 
% pixel is a usual pixel. 
fun=@minutie;
L = nlfilter(K,[3 3],fun);

%%Termination
LTerm=(L==1);
imshow(LTerm)
LTermLab=bwlabel(LTerm);
propTerm=regionprops(LTermLab,'Centroid');
CentroidTerm=round(cat(1,propTerm(:).Centroid));
imshow(~K)
set(gcf,'position',[1 1 600 600]);
hold on
plot(CentroidTerm(:,1),CentroidTerm(:,2),'ro')

%%Bifurcation
LBif=(L==3);
LBifLab=bwlabel(LBif);
propBif=regionprops(LBifLab,'Centroid','Image');
CentroidBif=round(cat(1,propBif(:).Centroid));
plot(CentroidBif(:,1),CentroidBif(:,2),'go')

D=6;

%Process 1
Distance=DistEuclidian(CentroidBif,CentroidTerm);
SpuriousMinutae=Distance<D;
[i,j]=find(SpuriousMinutae);
CentroidBif(i,:)=[];
CentroidTerm(j,:)=[];

%Process 2
Distance=DistEuclidian(CentroidBif);
SpuriousMinutae=Distance<D;
[i,j]=find(SpuriousMinutae);
CentroidBif(i,:)=[];

%Process 3
Distance=DistEuclidian(CentroidTerm);
SpuriousMinutae=Distance<D;
[i,j]=find(SpuriousMinutae);
CentroidTerm(i,:)=[];

hold off
imshow(~K)
hold on
plot(CentroidTerm(:,1),CentroidTerm(:,2),'ro')
plot(CentroidBif(:,1),CentroidBif(:,2),'go')
hold off

%Suppress extrema minutiae
%Once we defined the ROI, we can suppress minutiae external to this ROI.

[m,n]=size(I(:,:,1));
indTerm=sub2ind([m,n],CentroidTerm(:,1),CentroidTerm(:,2));
Z=zeros(m,n);
Z(indTerm)=1;
ZTerm=Z.*ROI';
[CentroidTermX,CentroidTermY]=find(ZTerm);

indBif=sub2ind([m,n],CentroidBif(:,1),CentroidBif(:,2));
Z=zeros(m,n);
Z(indBif)=1;
ZBif=Z.*ROI';
[CentroidBifX,CentroidBifY]=find(ZBif);

imshow(I)
hold on
plot(CentroidTermX,CentroidTermY,'ro','linewidth',2)
plot(CentroidBifX,CentroidBifY,'go','linewidth',2)
Kopen=imclose(K,strel('square',7));

KopenClean= imfill(Kopen,'holes');
KopenClean=bwareaopen(KopenClean,5);
imshow(KopenClean)
KopenClean([1 end],:)=0;
KopenClean(:,[1 end])=0;
ROI=imerode(KopenClean,strel('disk',10));
imshow(ROI)

imshow(I)
hold on
imshow(ROI)
alpha(0.5)

hold on
plot(CentroidTerm(:,1),CentroidTerm(:,2),'ro')
plot(CentroidBif(:,1),CentroidBif(:,2),'go')
hold off

%orientation

Table=[3*pi/4 2*pi/3 pi/2 pi/3 pi/4
       5*pi/6 0 0 0 pi/6
       pi 0 0 0 0
      -5*pi/6 0 0 0 -pi/6
      -3*pi/4 -2*pi/3 -pi/2 -pi/3 -pi/4];

for ind=1:length(CentroidTermX)
    Klocal=K(CentroidTermY(ind)-2:CentroidTermY(ind)+2,CentroidTermX(ind)-2:CentroidTermX(ind)+2);
    Klocal(2:end-1,2:end-1)=0;
    [i,j]=find(Klocal);
    OrientationTerm(ind,1)=Table(i,j);
end
dxTerm=sin(OrientationTerm)*5;
dyTerm=cos(OrientationTerm)*5;
figure
imshow(K)
set(gcf,'position',[1 1 600 600]);
hold on
plot(CentroidTermX,CentroidTermY,'ro','linewidth',2)
plot([CentroidTermX CentroidTermX+dyTerm]',...
    [CentroidTermY CentroidTermY-dxTerm]','r','linewidth',2)

%%Bifurcation Orientation
% For each bifurcation, we have three lines. So we operate the same process than in termination case three times.
for ind=1:length(CentroidBifX)
    Klocal=K(CentroidBifY(ind)-2:CentroidBifY(ind)+2,CentroidBifX(ind)-2:CentroidBifX(ind)+2);
    Klocal(2:end-1,2:end-1)=0;
    [i,j]=find(Klocal);
    if length(i)~=3
        CentroidBifY(ind)=NaN;
        CentroidBifX(ind)=NaN;
        OrientationBif(ind)=NaN;
    else
        for k=1:3
            OrientationBif(ind,k)=Table(i(k),j(k));
            dxBif(ind,k)=sin(OrientationBif(ind,k))*5;
            dyBif(ind,k)=cos(OrientationBif(ind,k))*5;

          end
      end
  end

plot(CentroidBifX,CentroidBifY,'go','linewidth',2)
OrientationLinesX=[CentroidBifX CentroidBifX+dyBif(:,1);CentroidBifX CentroidBifX+dyBif(:,2);CentroidBifX CentroidBifX+dyBif(:,3)]';
OrientationLinesY=[CentroidBifY CentroidBifY-dxBif(:,1);CentroidBifY CentroidBifY-dxBif(:,2);CentroidBifY CentroidBifY-dxBif(:,3)]';
plot(OrientationLinesX,OrientationLinesY,'g','linewidth',2)

%Validation 
MinutiaTerm=[CentroidTermX,CentroidTermY,OrientationTerm];
MinutiaBif=[CentroidBifX,CentroidBifY,OrientationBif];
saveMinutia('John Doe',MinutiaTerm,MinutiaBif);

Answer 1

[Walter Roberson]

It is not possible to reach that line of code.

You have

[m,n]=size(I(:,:,1));
indTerm=sub2ind([m,n],CentroidTerm(:,1),CentroidTerm(:,2));
Z=zeros(m,n);
Z(indTerm)=1;
ZTerm=Z.*ROI';

but I is undefined, so it is not possible to reach the ZTerm line.

ROI is also undefined, so it would not be possible to execute the ZTerm line if you could get there.

[Balaji M. Sontakke]

Sir, I make some changes, now I got this error in following code:

%%Matrix dimensions must agree.
%Error in crop4 (line 86) ZTerm=Z.*ROI';

J=imread('3.bmp');
imshow(J)
set(gcf,'position',[1 1 600 600]);

% %binary img
% J=I(:,:,1)>160;
% imshow(J)
% set(gcf,'position',[1 1 600 600]);

%%Thining
% Ridge thining is to eliminate the redundant pixels of ridges till the 
% ridges are just one pixel wide.  
K=bwmorph(~J,'thin','inf');
imshow(~K)
set(gcf,'position',[1 1 600 600]);

%%Minutiae
% We filter the thinned ridge map by the filter "minutie". "minutie"
% compute the number of one-value of each 3x3 window:
% * if the central is 1 and has only 1 one-value neighbor, then the central 
% pixel is a termination.  
% * if the central is 1 and has 3 one-value neighbor, then the central 
% pixel is a bifurcation. 
% * if the central is 1 and has 2 one-value neighbor, then the central 
% pixel is a usual pixel. 
fun=@minutie;
L = nlfilter(K,[3 3],fun);

%%Termination
LTerm=(L==1);
imshow(LTerm)
LTermLab=bwlabel(LTerm);
propTerm=regionprops(LTermLab,'Centroid');
CentroidTerm=round(cat(1,propTerm(:).Centroid));
imshow(~K)
set(gcf,'position',[1 1 600 600]);
hold on
plot(CentroidTerm(:,1),CentroidTerm(:,2),'ro')

%%Bifurcation
LBif=(L==3);
LBifLab=bwlabel(LBif);
propBif=regionprops(LBifLab,'Centroid','Image');
CentroidBif=round(cat(1,propBif(:).Centroid));
plot(CentroidBif(:,1),CentroidBif(:,2),'go')

D=6;

%Process 1
Distance=DistEuclidian(CentroidBif,CentroidTerm);
SpuriousMinutae=Distance<D;
[i,j]=find(SpuriousMinutae);
CentroidBif(i,:)=[];
CentroidTerm(j,:)=[];

%Process 2
Distance=DistEuclidian(CentroidBif);
SpuriousMinutae=Distance<D;
[i,j]=find(SpuriousMinutae);
CentroidBif(i,:)=[];

%Process 3
Distance=DistEuclidian(CentroidTerm);
SpuriousMinutae=Distance<D;
[i,j]=find(SpuriousMinutae);
CentroidTerm(i,:)=[];

Kopen=imclose(K,strel('square',7));

KopenClean= imfill(Kopen,'holes');
KopenClean=bwareaopen(KopenClean,5);
imshow(KopenClean)
KopenClean([1 end],:)=0;
KopenClean(:,[1 end])=0;
ROI=imerode(KopenClean,strel('disk',10));
imshow(ROI)

imshow(J)
hold on
imshow(ROI)
alpha(0.5)

hold on
plot(CentroidTerm(:,1),CentroidTerm(:,2),'ro')
plot(CentroidBif(:,1),CentroidBif(:,2),'go')
hold off

%%Suppress extrema minutiae

%Once we defined the ROI, we can suppress minutiae external to this ROI.

[m,n]=size(J(:,:,1));
indTerm=sub2ind([m,n],CentroidTerm(:,1),CentroidTerm(:,2));
Z=zeros(m,n);
Z(indTerm)=1;
ZTerm=Z.*ROI';
[CentroidTermX,CentroidTermY]=find(ZTerm);

indBif=sub2ind([m,n],CentroidBif(:,1),CentroidBif(:,2));
Z=zeros(m,n);
Z(indBif)=1;
ZBif=Z.*ROI';
[CentroidBifX,CentroidBifY]=find(ZBif);

imshow(I)
hold on
plot(CentroidTermX,CentroidTermY,'ro','linewidth',2)
plot(CentroidBifX,CentroidBifY,'go','linewidth',2)

%Orientation

%Once we determined the differents minutiae, we have to find the orientation of each one
Table=[3*pi/4 2*pi/3 pi/2 pi/3 pi/4
       5*pi/6 0 0 0 pi/6
       pi 0 0 0 0
      -5*pi/6 0 0 0 -pi/6
      -3*pi/4 -2*pi/3 -pi/2 -pi/3 -pi/4];

%Termination Orientation
%We have to find the orientation of the termination. 
%For finding that, we analyze the position of the pixel on the boundary of a 5 x 5 bounding box of the termination. 
%We compare this position to the Table variable. The Table variable gives the angle in radian. 

for ind=1:length(CentroidTermX)
    Klocal=K(CentroidTermY(ind)-2:CentroidTermY(ind)+2,CentroidTermX(ind)-2:CentroidTermX(ind)+2);
    Klocal(2:end-1,2:end-1)=0;
    [i,j]=find(Klocal);
    OrientationTerm(ind,1)=Table(i,j);
end
dxTerm=sin(OrientationTerm)*5;
dyTerm=cos(OrientationTerm)*5;
figure
imshow(K)
set(gcf,'position',[1 1 600 600]);
hold on
plot(CentroidTermX,CentroidTermY,'ro','linewidth',2)
plot([CentroidTermX CentroidTermX+dyTerm]',...
    [CentroidTermY CentroidTermY-dxTerm]','r','linewidth',2)

%Bifurcation Orientation
%For each bifurcation, we have three lines. So we operate the same
% process than in termination case three times.
for ind=1:length(CentroidBifX)
    Klocal=K(CentroidBifY(ind)-2:CentroidBifY(ind)+2,CentroidBifX(ind)-2:CentroidBifX(ind)+2);
    Klocal(2:end-1,2:end-1)=0;
    [i,j]=find(Klocal);
    if length(i)~=3
        CentroidBifY(ind)=NaN;
        CentroidBifX(ind)=NaN;
        OrientationBif(ind)=NaN;
    else
        for k=1:3
            OrientationBif(ind,k)=Table(i(k),j(k));
            dxBif(ind,k)=sin(OrientationBif(ind,k))*5;
            dyBif(ind,k)=cos(OrientationBif(ind,k))*5;

          end
      end
  end

plot(CentroidBifX,CentroidBifY,'go','linewidth',2)
OrientationLinesX=[CentroidBifX CentroidBifX+dyBif(:,1);CentroidBifX CentroidBifX+dyBif(:,2);CentroidBifX CentroidBifX+dyBif(:,3)]';
OrientationLinesY=[CentroidBifY CentroidBifY-dxBif(:,1);CentroidBifY CentroidBifY-dxBif(:,2);CentroidBifY CentroidBifY-dxBif(:,3)]';
plot(OrientationLinesX,OrientationLinesY,'g','linewidth',2)

% Save in a text file

%In this step, we are going to save the minutia in a file

MinutiaTerm=[CentroidTermX,CentroidTermY,OrientationTerm];
MinutiaBif=[CentroidBifX,CentroidBifY,OrientationBif];
saveMinutia('John Doe',MinutiaTerm,MinutiaBif);

[Walter Roberson]

ROI is constructed from K which is in turn constructed as the same size as the original image, J.

Z is constructed the same size as J(:,:,1) . If your .bmp was grayscale, that would be the same size as K.

If we suppose the grayscale case, then

ZTerm=Z.*ROI';

is multiplying something the size of J by something the size of J transposed . That can only work if the image happened to be square.

If you had coded

ZTerm = Z * ROI';

then that would be (m x n) * (n x m) and that would be valid, giving an m x m result. It is not clear to me that would be meaningful mathematically though.

I think you should be using

ZTerm = Z .* ROI;

with no conjugate transpose.

[Balaji M. Sontakke]

It works, thanks. But at orientation there is a following error

Index exceeds matrix dimensions.

Error in crop4 (line 173)
OrientationLinesX=[CentroidBifX CentroidBifX+dyBif(:,1);CentroidBifX CentroidBifX+dyBif(:,2);CentroidBifX CentroidBifX+dyBif(:,3)]'

[Balaji M. Sontakke]

What happen sir? there is no soluation for this error, please respond me

[Walter Roberson]

You do not construct ROI until after you use it twice.

You attempt to take size(I(:,:,1)) but you have no variable I at that point.

You have the ROI' size problem twice and you did not show how you decided to fix it.

You use functions minutae and DistEuclidean without bothering to mention that you obtained them from https://www.mathworks.com/matlabcentral/fileexchange/16728-fingerprint-application

[Balaji M. Sontakke]

Really It works, Thank you so much Sir...