MATLAB: Pixel to Area conversion accruacy issue with Matlab and im2bw function

Question

I am reformatting and reposting this question to hopefully make it easier for more people to help.

I am writing a short Matlab script to use im2bw to calculate the area of objects in the image. I am trying to validate that the areas are being calculated correctly, but on the reference image I am using the last square's area is 2% off and I cannot figure out why.

myFolder = 'Your Directory';
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, '*.png'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
for k = 1 : length(theFiles)
    baseFileName = theFiles(k).name;
    fullFileName = fullfile(theFiles(k).folder, baseFileName);
    
    J = imread(fullFileName);
    %J = imcrop(I,[500,200,4400,3500]);
    BW = im2bw(J,0.3);
    BW2 = imcomplement(BW);
    BW3 = imfill(BW2,4,'holes');
    
    %figure(1)
    %imshowpair(I,BW3,'montage')
    stats = regionprops(BW3,'area','PixelList','majoraxislength','minoraxislength');
    area = zeros(size(stats));
    for i = 1:size(stats,1)
        area(i) = stats(i).Area;
    end
    scale = 1e-6;
    %scale = 3.134755344e-8;
    cutoff = 0;
    area = area*scale;
    stats(area<cutoff)=[];
    area(area<cutoff)=[];
    
    writematrix(area,'Your Directory','WriteMode','append')
end
    figure(1)
    imshowpair(J,BW3,'montage')

The image is 1000×1000 with 20×20, 100×100, 100×200, and 200×200 squares that I use as a reference.

I assumed the reference image in reality was 1mx1m and scaled accordingly, but the 200×200 square seems to not come out exactly right. The result is 0.0392 when it should be 0.04.

Additionally I have some issues overall with the accuracy of the im2bw function when trying to calculate area using other images, where I get 10-20% error. Any insights into this issue would be awesome as well.

Answer 1

As you can see from this corrected code:

clc;    % Clear the command window.
fprintf('Beginning to run %s.m ...\n', mfilename);
close all;  % Close all figures (except those of imtool.)
imtool close all;  % Close all imtool figures.
clear;  % Erase all existing variables.
workspace;  % Make sure the workspace panel is showing.
fontSize = 22;
myFolder = pwd; % 'Your Directory';
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, 'ar*.png'); % Change to whatever pattern you need.
theFiles = dir(filePattern)
for k = 1 : length(theFiles)
	baseFileName = theFiles(k).name;
	fullFileName = fullfile(theFiles(k).folder, baseFileName);
	
	rgbImage = imread(fullFileName);
	%J = imcrop(I,[500,200,4400,3500]);
	BW = im2bw(rgbImage,0.3);
	BW2 = imcomplement(BW);
	BW3 = imfill(BW2,4,'holes');
	
	stats = regionprops(BW3,'area','PixelList','BoundingBox');
	areaInPixels = [stats.Area]
	bb = vertcat(stats.BoundingBox);
	allWidthsInPixels = bb(:, 3)
	allHeightInPixels = bb(:, 4)
	
	scale = 1e-6;
	areaInMm = areaInPixels * scale
	
% 	%scale = 3.134755344e-8;
% 	cutoff = 0;
% 	stats(areaInMm<cutoff)=[];
% 	areaInMm(areaInMm<cutoff)=[];
% 	
% 	writematrix(areaInMm,'Your Directory','WriteMode','append')
end
% figure(1)
% imshowpair(rgbImage,BW3,'montage')
fprintf('Done running %s.m ...\n', mfilename);

The areas, widths, and heights are

areaInPixels =

400 10000 20000 39204

allWidthsInPixels =

20

100

200

198

allHeightInPixels =

20

100

100

198

areaInMm =

0.0004 0.01 0.02 0.039204

so your last rectangle is not 200x200, it's 198x198.

It is probably because your large rectangle is ringed with a value of 127, unlike the other rectangles, and that 127 is below the threshold so it's not considered part of the blob. Why does only that one blob have a one pixel wide layer of 127 surrounding it?

Try a manual threshold instead.

	BW = rgbImage(:, :, 1) < 255;
	imshow(BW);
% 	BW2 = imcomplement(BW);
% 	BW3 = imfill(BW2,4,'holes');
	BW3 = imfill(BW,4,'holes');

That will work.