combine 2 image results of segmentation, into one of axes

Asked by erick saputra on 29 Sep 2015

Latest activity Edited by Yuki Zue on 18 Feb 2017

11 views (last 30 days)

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I want to ask, I hope you see this can help me, thanks I've done segmentation on that image and has 9 parts segmentation, I just want to take segmentation to figures 5 and 6, but I can only take segmentation in figure 5.

I want to ask how to combine figure 5 and figure 6 on the one axes as the final result of segmentation ..

note: I only use one image only, "Lat1.bmp" and I want to know how to combine the two figures on the one axes as the final result of segmentation

1 Comment

Yuki Zue on 18 Feb 2017

Dear sir,
help me!
I can not access database from another code via GUI .Could you please help me?Thanks.
    if true
      % function pushbutton2_Callback(hObject, eventdata, handles)
  if isfield(handles,'image')
       % do stuff
       Image=handles.image;
  I=Image;
  k=1;p=1;
  dim=ndims(I);    
  if dim==2
      I=I;
  else if dim==3
          I=rgb2gray(I);
      else fprintf('Nothing \n');
      end
  end
  %imtool(I);
  I=uint8(I);
  I2=imopen(I,strel('disk',3));%before 3
  %figure,imshow(I);
  M=medfilt2(I2,[3 3]);
  %imtool(M);
  G=imgaussfilt(M,1);
  %imtool(G);
%image=imsharpen(G);
AdjImg=imadjust(G);
%imtool(AdjImg);
initialT=mean2(AdjImg);
T=initialT;
Image=AdjImg;
[row,col]=size(Image);
newT=0;
while T-newT~=0
for i=1:row
    for j=1:col
        if Image(i,j)>=T;
            Image(i,j)=Image(i,j);
        else Image(i,j)=0;
        end
        j=j+1;
    end
    i=i+1;
end
%figure,imshow(Image);
m1=mean2(Image);
%m2=mean2(image);
newT=(m1)/2;
formerT=T;
T=newT;
newT=formerT;
end
%figure,imshow(Image);
%imtool(image);
[R,C]=size(Image);
for i=1:R
    for j=1:C
        if Image(i,j)==0
        Image(i,j)=0;
        else Image(i,j)=255;
        end
    end
    j=j+1;
end
i=i+1;
Final=Image;
%imtool(Final);
openImg1=imopen(Final,strel('disk',4));% for 273.jpg //ealier 6 & 8
%imtool(openImg);
EdgeImg=edge(openImg1,'canny');
%figure,imshow(EdgeImg);
ThinnedImg=bwmorph(EdgeImg,'thin');
%figure,imshow(ThinnedImg);
Td=uint8(ThinnedImg);
Constructed=Td|openImg1;
%figure,imshow(Constructed);
OPENimg=double(Constructed);
%figure,imshow(OPENimg);
[ROW,COL]=size(OPENimg);
cropped = openImg1(1:ROW,1:COL); %%Crop region of interest 
%imtool(cropped);
thresholded = cropped==0;%%Threshold to isolate lungs
%figure,imshow(thresholded);
%imtool(thresholded);
clearThresh = imclearborder(thresholded); %%Remove border artifacts in image  
%figure,imshow(clearThresh);
ClosedClear=imclose(clearThresh,strel('disk',5));
%imtool(clearThresh);
Liver = bwareaopen(ClosedClear,100); %Remove objects less than 100 pixels
%figure,imshow(Liver);
Liver1 = imfill(Liver,'hole'); % fill in the vessels inside the lungs
%figure,imshow(Liver1);
Liver1=uint8(Liver1);
nodule=Liver1.*cropped;
%imtool(nodule);
nodule1=imopen(nodule,strel('disk',5));% 6 ,7and 8 before
%imtool(nodule1);
nodule1a=imclose(nodule1,strel('disk',1));
nodule1a=logical(nodule1a);
nodule2=bwareafilt(nodule1a,[1 4500]);%extract objects whose values are in these range
%imtool(nodule2);
nodule2a=bwareaopen(nodule2,150); % ealier 150,changed for 322.jpg
%imtool(nodule2a);
Nodule=nodule2a;
figure,imshow(Nodule);
[label, Nnodule]=bwlabel(Nodule,8);%label is labeled matrix that includes labeled objects
if Nnodule==1
  I=double(I);
Nodule= Nodule.* I;
     NoduleDatabase{k,p}=Nodule;
      dlmwrite('NoduleData.dat',NoduleDatabase);
  else if Nnodule>1
          if Nnodule==2
  [Row1, Col1]=find(label==1);
  [Row2, Col2]=find(label==2);
  NoduleOne=bwselect(label,Col1,Row1,8);
  NoduleTwo=bwselect(label,Col2,Row2,8);
  I=double(I);
  NoduleOne= NoduleOne.* I;
  NoduleTwo=NoduleTwo.*I;
NoduleDatabase{k,p}=NoduleOne;
NoduleDatabase{k,p+1}=NoduleTwo;
dlmwrite('NoduleData.dat',NoduleDatabase);
        end
        if Nnodule==3
[Row1, Col1]=find(label==1);
[Row2, Col2]=find(label==2);
[Row3, Col3]=find(label==3);
NoduleOne=bwselect(label,Col1,Row1,8);
NoduleTwo=bwselect(label,Col2,Row2,8);
Nodule3=bwselect(label,Col3,Row3,8);
I=double(I);
NoduleOne= NoduleOne.* I;
NoduleTwo=NoduleTwo.*I;
Nodule3= Nodule3.* I;
NoduleDatabase{k,p}=NoduleOne;
NoduleDatabase{k,p+1}=NoduleTwo;
NoduleDatabase{k,p+2}=Nodule3;
dlmwrite('NoduleData.dat',NoduleDatabase);
          end
          if Nnodule>3
  [Row1, Col1]=find(label==1);
  [Row2, Col2]=find(label==2);
  [Row3, Col3]=find(label==3);
  [Row4, Col4]=find(label==4);
  NoduleOne=bwselect(label,Col1,Row1,8);
  NoduleTwo=bwselect(label,Col2,Row2,8);
  Nodule3=bwselect(label,Col3,Row3,8);
  Nodule4=bwselect(label,Col4,Row4,8);
  I=double(I);
  NoduleOne= NoduleOne.* I;
  NoduleTwo=NoduleTwo.*I;
  Nodule3= Nodule3.* I;
  Nodule4=Nodule4.*I;
NoduleDatabase{k,p}=NoduleOne;
NoduleDatabase{k,p+1}=NoduleTwo;
NoduleDatabase{k,p+2}=Nodule3;
NoduleDatabase{k,p+3}=Nodule4;
dlmwrite('NoduleData.dat',NoduleDatabase);
        end
%imtool(Nodule);imtool(NoduleOne);imtool(NoduleTwo);
      else % second TRY for different images
         I2=imopen(I,strel('disk',3));%before 3
         %figure,imshow(I2);
         M=medfilt2(I2,[9 9]);
         G=imgaussfilt(M,1);
         I3=imadjust(G);
         %imtool(I3);
         T=100;
         [r,c]=size(I3);
         for i=1:r
             for j=1:c
                 if I3(i,j)<T
                     I3(i,j)=0;
                 else if I3(i,j)>=T
                         I3(i,j)=255;
                     else fprintf('No');
                     end
                 end
             end
             j=j+1;
         end
         i=i+1;
         %imtool(I3);
         openImg=imclose(I3,strel('disk',5));%before 3
         %imtool(openImg);
EdgeImg=edge(openImg,'canny');
%figure,imshow(EdgeImg);
ThinnedImg=bwmorph(EdgeImg,'thin');
%figure,imshow(ThinnedImg);
Td=uint8(ThinnedImg);
Constructed=Td|openImg;
%figure,imshow(Constructed);
OPENimg=double(Constructed);
%figure,imshow(OPENimg);
[ROW,COL]=size(OPENimg);
cropped = openImg(1:ROW,1:COL); 
%imtool(cropped);
thresholded = cropped==0;
%imtool(thresholded);
clearThresh = imclearborder(thresholded); 
%figure,imshow(clearThresh);
ClosedClear=imclose(clearThresh,strel('disk',5));
%imtool(clearThresh);
Liver = bwareaopen(ClosedClear,100); 
%figure,imshow(Liver);
Liver1 = imfill(Liver,'hole'); 
%figure,imshow(Liver1);
Liver1=uint8(Liver1);
nodule=Liver1.*cropped;
%imtool(nodule);
nodule1=imopen(nodule,strel('disk',5));
%imtool(nodule1);
nodule1a=imclose(nodule1,strel('disk',1));
nodule1a=logical(nodule1a);
nodule2=bwareafilt(nodule1a,[1 4500]);
%imtool(nodule2);
nodule2a=bwareafilt(nodule2,1); 
Nodule=nodule2a;
figure,imshow(Nodule);
[label, Nnodule]=bwlabel(Nodule,8);
if Nnodule==1
    I=double(I);
Nodule= Nodule.* I;
      NoduleDatabase{k,p}=Nodule;
      dlmwrite('NoduleData.dat',NoduleDatabase);
else if Nnodule>1
if Nnodule==2
[Row1, Col1]=find(label==1);
[Row2, Col2]=find(label==2);
NoduleOne=bwselect(label,Col1,Row1,8);
NoduleTwo=bwselect(label,Col2,Row2,8);
I=double(I);
NoduleOne= NoduleOne.* I;
NoduleTwo=NoduleTwo.*I;
NoduleDatabase{k,p}=NoduleOne;
NoduleDatabase{k,p+1}=NoduleTwo;
dlmwrite('NoduleData.dat',NoduleDatabase);
        end
        if Nnodule==3
[Row1, Col1]=find(label==1);
[Row2, Col2]=find(label==2);
[Row3, Col3]=find(label==3);
NoduleOne=bwselect(label,Col1,Row1,8);
NoduleTwo=bwselect(label,Col2,Row2,8);
Nodule3=bwselect(label,Col3,Row3,8);
I=double(I);
NoduleOne= NoduleOne.* I;
NoduleTwo=NoduleTwo.*I;
Nodule3= Nodule3.* I;
NoduleDatabase{k,p}=NoduleOne;
NoduleDatabase{k,p+1}=NoduleTwo;
NoduleDatabase{k,p+2}=Nodule3;
dlmwrite('NoduleData.dat',NoduleDatabase);
        end
        if Nnodule>3
[Row1, Col1]=find(label==1);
[Row2, Col2]=find(label==2);
[Row3, Col3]=find(label==3);
[Row4, Col4]=find(label==4);
NoduleOne=bwselect(label,Col1,Row1,8);
NoduleTwo=bwselect(label,Col2,Row2,8);
Nodule3=bwselect(label,Col3,Row3,8);
Nodule4=bwselect(label,Col4,Row4,8);
dlmwrite('NoduleData.dat',NoduleDatabase);
I=double(I);
NoduleOne= NoduleOne.* I;
NoduleTwo=NoduleTwo.*I;
Nodule3= Nodule3.* I;
Nodule4=Nodule4.*I;
NoduleDatabase{k,p}=NoduleOne;
NoduleDatabase{k,p+1}=NoduleTwo;
NoduleDatabase{k,p+2}=Nodule3;
NoduleDatabase{k,p+3}=Nodule4;
dlmwrite('NoduleData.dat',NoduleDatabase);
          end
      else % Third TRY 
         M=medfilt2(I,[9 9]);
         G=imgaussfilt(M,1);
         I3=imadjust(G);
         T=17;
         [r,c]=size(I3);
         for i=1:r
             for j=1:c
                 if I3(i,j)<T
                     I3(r,c)=0;
                 else if I3(i,j)>=T
                         I3(i,j)=255;
                     else fprintf('No');
                     end
                 end
             end
             j=j+1;
         end
         i=i+1;
         %imtool(I3);
         openImg=imclose(I3,strel('disk',5));
         %imtool(openImg);
  EdgeImg=edge(openImg,'canny');
  %figure,imshow(EdgeImg);
  ThinnedImg=bwmorph(EdgeImg,'thin');
  %figure,imshow(ThinnedImg);
  Td=uint8(ThinnedImg);
  Constructed=Td|openImg;
  %figure,imshow(Constructed);
OPENimg=double(Constructed);
%figure,imshow(OPENimg);
[ROW,COL]=size(OPENimg);
cropped = openImg(1:ROW,1:COL); 
%imtool(cropped);
thresholded = cropped==0;
%imtool(thresholded);
clearThresh = imclearborder(thresholded); 
%figure,imshow(clearThresh);
ClosedClear=imclose(clearThresh,strel('disk',5));
%imtool(clearThresh);
Liver = bwareaopen(ClosedClear,100); 
%figure,imshow(Liver);
Liver1 = imfill(Liver,'hole'); 
%figure,imshow(Liver1);
Liver1=uint8(Liver1);
nodule=Liver1.*cropped;
%imtool(nodule);
nodule1=imopen(nodule,strel('disk',5));
%imtool(nodule1);
nodule1a=imclose(nodule1,strel('disk',1));
nodule1a=logical(nodule1a);
nodule2=bwareafilt(nodule1a,[1 4500]);
%imtool(nodule2);
nodule2a=bwareafilt(nodule2,1); 
%imtool(nodule2a);
Nodule=nodule2a;
figure,imshow(Nodule);
[label, Nnodule]=bwlabel(Nodule,8);
if Nnodule==1
    I=double(I);
Nodule = Nodule .* I;
      NoduleDatabase{k,p}=Nodule;
      dlmwrite('NoduleData.dat',NoduleDatabase);
else if Nnodule>1
if Nnodule==2
[Row1, Col1]=find(label==1);
[Row2, Col2]=find(label==2);
NoduleOne=bwselect(label,Col1,Row1,8);
NoduleTwo=bwselect(label,Col2,Row2,8);
I=double(I);
NoduleOne= NoduleOne.* I;
NoduleTwo=NoduleTwo.*I;
NoduleDatabase{k,p}=NoduleOne;
NoduleDatabase{k,p+1}=NoduleTwo;
dlmwrite('NoduleData.dat',NoduleDatabase);
        end
        if Nnodule==3
[Row1, Col1]=find(label==1);
[Row2, Col2]=find(label==2);
[Row3, Col3]=find(label==3);
NoduleOne=bwselect(label,Col1,Row1,8);
NoduleTwo=bwselect(label,Col2,Row2,8);
Nodule3=bwselect(label,Col3,Row3,8);
I=double(I);
NoduleOne= NoduleOne.* I;
NoduleTwo=NoduleTwo.*I;
Nodule3= Nodule3.* I;
NoduleDatabase{k,p}=NoduleOne;
NoduleDatabase{k,p+1}=NoduleTwo;
NoduleDatabase{k,p+2}=Nodule3;
dlmwrite('NoduleData.dat',NoduleDatabase);
          end
          if Nnodule>3
  [Row1, Col1]=find(label==1);
  [Row2, Col2]=find(label==2);
  [Row3, Col3]=find(label==3);
  [Row4, Col4]=find(label==4);
  NoduleOne=bwselect(label,Col1,Row1,8);
  NoduleTwo=bwselect(label,Col2,Row2,8);
  Nodule3=bwselect(label,Col3,Row3,8);
  Nodule4=bwselect(label,Col4,Row4,8);
I=double(I);
NoduleOne= NoduleOne.* I;
NoduleTwo=NoduleTwo.*I;
Nodule3= Nodule3.* I;
Nodule4=Nodule4.*I;
NoduleDatabase{k,p}=NoduleOne;
NoduleDatabase{k,p+1}=NoduleTwo;
NoduleDatabase{k,p+2}=Nodule3;
NoduleDatabase{k,p+3}=Nodule4;
dlmwrite('NoduleData.dat',NoduleDatabase);
        end
    else
openImg1=imclose(openImg1,strel('disk',4));%before 5 
%imtool(openImg1);
openImg1=logical(openImg1);
RemoveBack=bwareafilt(openImg1,[1 4500]);% remove BACKGROUND
%imtool(RemoveBack);
r1=170;%160
c1=512;
for i=1:r1
    for j=1:c1
        RemoveBack(i,j)=0;
    end
    j=j+1;
end
RemoveBack=bwareafilt(RemoveBack,[1 4500]);
RemovedBack1=RemoveBack;
%imtool(RemovedBack1);
r2=512;
c2=512;
for i=370:r2%360 but Changed for 272.jpg
    for j=1:c2
        RemovedBack1(i,j)=0;
    end
    j=j+1;
end
RemovedBack2=RemovedBack1;
%imtool(RemovedBack2);
r3=512;
c3=512;
for i=1:r3
    for j=425:c3%410
        RemovedBack2(i,j)=0;
    end
    j=j+1;
end
RemovedBack3=RemovedBack2;
r4=512;
c4=85;%60
for i=1:r4
    for j=1:c4
        RemovedBack3(i,j)=0;
    end
    j=j+1;
end
RemovedBack4=RemovedBack3;
Nodule=bwareafilt(RemovedBack4,1);% retain the LARGEST NODULE 
Nodule=imfill(Nodule,'holes');
imtool(Nodule);
[label, Nnodule]=bwlabel(Nodule,8);
if Nnodule==1
    I=double(I);
Nodule= Nodule.* I;
      NoduleDatabase{k,p}=Nodule;
      dlmwrite('NoduleData.dat',NoduleDatabase);
  else if Nnodule>1
  [Row1, Col1]=find(label==1);
  [Row2, Col2]=find(label==2);
  NoduleOne=bwselect(label,Col1,Row1,8);
  NoduleTwo=bwselect(label,Col2,Row2,8);
  %imtool(Nodule);imtool(NoduleOne);imtool(NoduleTwo);
  I=double(I);
  NoduleOne= NoduleOne.* I;
  NoduleTwo=NoduleTwo.*I;
NoduleDatabase{1,p}=NoduleOne;
NoduleDatabase{1,p+1}=NoduleTwo;
dlmwrite('NoduleData.dat',NoduleDatabase);
    end
end
    end
end
    end
end
    end
end
B=NoduleDatabase';
idx=~cellfun(@isempty,B);
DatabaseNodules=B(idx);
end
  end

GUI does not know NoduleDatabase.

2 Answers

Link

Answer by Jon on 29 Sep 2015

Edited by Jon on 29 Sep 2015

Accepted Answer

I may not understand the question, but why not just use segmented portions 5 and 6 as a mask on the original BW image? I guess the workflow would be something like

- extract the segments

- make an image of "falses" the same size as the original called BWsegs

- set the indices of segment 5 as "true" in BWsegs

- set the indices of segment 6 as "true" in BWsegs

The BWsegs is what you're looking for. You can use regionprops to get the bounding box for cropping if you'd like.

2 Comments

erick saputra on 29 Sep 2015

you can see image "hasil akhir segmentasi" ? it is the final result of segmentation. I want to combine the figures 5 and 6, and displays it on "hasil akhir segmentasi". But I do not know how to combine figure 5 and 6 into a single figure

Jon on 29 Sep 2015

It looks to me like Figure 5 = "hasil akhir segmentasi". So you know how to extract Figure 5. It also looks like you know how to extract Figure 6. So just extract them (without cropping them) and use

single_fig = Fig5 | Fig6;

Then you can crop that if you want.

Link

Answer by erick saputra on 29 Sep 2015

please help me... I want to combine the figures 5 and 6, and displays it on "hasil akhir segmentasi". But I do not know how to combine figure 5 and 6 into a single figure

2 Comments

Image Analyst on 29 Sep 2015

Did you solve this since you posted this? It's marked as Accepted so many people are ignoring it.

To combine 5 and 6, don't crop and just OR them together.

Khaing Zin Htwe on 18 Feb 2017

please help me sir, I want to show the segmented image in GUI but it does not show complete image, why? Thanks all.

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erick saputra (view profile)