Issue in plotting binary image boundaries with real axis values

Hi,

I have extracted the image boundaries from binary image and mm). I am able to diplay the binary image with real axis values i.e. x1, y1, (which is in mm), However, while plotting the extracted boundaries, the axes values are displayed in the pixels. (as shown in the attachment of binary image boundary.bmp).. Have anyone encountered simiar problem before ??

A = imgaussfilt(grayImage,5);
A1 = imbinarize (A,1900); %% binary image conversion 
ax = gca;
A2 = imagesc (x1, y1,A1); %% Display binary image
set(gca, 'YDir','normal')
[b,~] = bwboundaries(A1, 8); b1 = b{1}; %% boundary extraction from binary image
b2 = smoothdata (b1(:,2),'sgolay',25);
b3 = smoothdata(b1(:,1),'sgolay',25);
plot(b2,b3,'b'); axis equal %% Plot the extrcated boundary

Answer 1

[Steve Eddins]

The function bwboundaries returns boundary values in pixel coordinates. You'll need to scale those to world coordinates yourself. For this purpose, imref2d and intrinsicToWorld might be useful to you.

R = imref2d(imageSize,xWorldLimits,yWorldLimits)
[xWorld, yWorld] = intrinsicToWorld(R,xIntrinsic,yIntrinsic)

[Turbulence Analysis]

Hi Steeve,

Thanks, I am able to convert the pixel to mm values with the scale factor. But the issue is, As you see from the attachments position of the ''zero '' is not correct on the x axis between two images..

Actually, my whole idea is to supeimpose the extracted boundary from the binary image on to the another image. Due to the mismatch in the zero position, I couldn't able to superimpose. This is my real concern with bwboundaries (); could you please advice on this ??

[Steve Eddins]

Look at the input to bwboundaries: it is just a MATLAB matrix. It does not have any information embedded in it about how matrix subscripts relate to some real-world coordinate system. Therefore, bwboundaries knows nothing about the world coordinate system and must return the output in what we call intrinsic coordinates. The syntax you used for imagesc suggests that, in your case, the intrinsic coordinates are related to the world coordinates by some combination of a multiplicative scale factor and an additive offset, or shift. You'll need to do this computation yourself on the output of bwboundaries. The other functions that I mentioned, imref2d and intrinsicToWorld, are capable of performing this computation for you if you wish.

[Turbulence Analysis]

Hi,

I treid as follows, now I can able to shift the psoition of zero and convert the pixel to mm with the scale factor.. !

b2 = smoothdata ((b1(:,2)/10)-40,'sgolay',35);
b3 = smoothdata((b1(:,1)/10),'sgolay',35);
ax = gca;
plot(b2 ,b3 ,'r'); 
axis equal

Answer 2

[Joseph Cheng]

so you'll need to find the conversion between pixel to linear xy (mm). sort of the mm/px scale factor + offset to 0;

from the looks of it half of the image (row or column) is 0,

xscale = (max(x1)-min(x1))/size(A,2); %mm/pixel
newb2 = (b2-size(A,2)/2)*xscale;

[Turbulence Analysis]

Hi,

Thanks, I am able to convert the pixel to values with the scale factor. But the issue is, position of the ''zero '' is not correct..

[Turbulence Analysis]

sorry, *** position of the ''zero '' in x axis is not correct..