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Hi all,

I want to process a series of images similar to the attached one in order to measure their porosities: V_pores / V_total. For my case, in a 2D context, V_total is the surface of circle containing all pores. It is important to know that the radius and center of the circle changes, and also many circular shapes can be identified in between, however, I am only interested, at this moment, in measuring the general surface of the circle (Vt).

Alernatively, I would be interested in applying a mask to the image. But it seems to be more difficult.

Any help would be appreciated. Many thanks.

KSSV
on 27 Mar 2020

I = imread("SampleXRmorph.PNG");

[y,x] = find(I) ;

% Get center of cricle

C = [mean(x) mean(y)] ;

% GEt raidus

d = sqrt((C(1)-x).^2+(C(2)-y).^2) ;

R = max(d) ;

% plot circle

th = linspace(0,2*pi) ;

xc = C(1)+R*cos(th) ;

yc = C(2)+R*sin(th) ;

%

imshow(I)

hold on

plot(xc,yc,'r')

Image Analyst
on 29 Mar 2020

Edited: Image Analyst
on 29 Mar 2020

Sorry I didn't see this earlier, but anyway...

How I'd solve it is

- Use bwconvhull() to get a convex hull of all the blobs.
- Uuse imerode() to shrink that a certain amount to get a smaller circular blob.
- Use the eroded image to erase every blob in the interior so you have only the outer blobs.
- If you need a perfect circle, call regionprops(mask, 'Centroid') to get a list of (x,y) coordinates.
- Use the FAQ to fit a circle through the centroids.

% Initialization steps.

clc; % Clear the command window.

fprintf('Beginning to run %s.m ...\n', mfilename);

close all; % Close all figures (except those of imtool.)

clear; % Erase all existing variables. Or clearvars if you want.

workspace; % Make sure the workspace panel is showing.

format short g;

format compact;

fontSize = 15;

mask = imread('morequestion.png');

imshow(mask);

if ndims(mask) > 2

mask = mask(:, :, 1); % Take red channel

end

mask2 = bwconvhull(mask, 'union');

se = strel('disk', 20, 0);

smallMask = imerode(mask2, se);

mask3 = mask & ~smallMask;

props = regionprops(mask3, 'Centroid');

xy = vertcat(props.Centroid);

x = xy(:, 1);

y = xy(:, 2);

[xc,yc,R,a] = circfit(x,y);

viscircles([xc, yc], R);

fprintf('Done running %s.m ...\n', mfilename);

function [xc,yc,R,a] = circfit(x,y)

%CIRCFIT Fits a circle in x,y plane

%

% [XC, YC, R, A] = CIRCFIT(X,Y)

% Result is center point (yc,xc) and radius R. A is an optional

% output describing the circle's equation:

%

% x^2+y^2+a(1)*x+a(2)*y+a(3)=0

% by Bucher izhak 25/oct/1991

n=length(x); xx=x.*x; yy=y.*y; xy=x.*y;

A=[sum(x) sum(y) n;sum(xy) sum(yy) sum(y);sum(xx) sum(xy) sum(x)];

B=[-sum(xx+yy) ; -sum(xx.*y+yy.*y) ; -sum(xx.*x+xy.*y)];

a=A\B;

xc = -.5*a(1);

yc = -.5*a(2);

R = sqrt((a(1)^2+a(2)^2)/4-a(3));

end

Adapt as needed.

Image Analyst
on 31 Mar 2020

To get the area of the white in the mask, I'd do

numWhitePixels = nnz(mask)

% Now to get the area of the holes

holesImage = imclearborder(~mask);

imshow(holesImage);

numHolePixels = nnz(holesImage)

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