How to isolate and display the largest connected component
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Hello all,
I am looking to isolate the largest connected component in an image, and then display it by itself. Right now, the code I am using deletes the largest connected component and keeps everything else. I want everything else in the image to be deleted, and the largest component to remain. My code for the isolation is as follows:
CC = bwconncomp(B);
numOfPixels = cellfun(@numel,CC.PixelIdxList);
[unused,indexOfMax] = max(numOfPixels);
B(CC.PixelIdxList{indexOfMax}) = 0;
imshow(B);
2 Comments
Jeremy Jernigen
on 27 Jun 2017
CC = bwconncomp(B);
numOfPixels = cellfun(@numel,CC.PixelIdxList);
[unused,indexOfMax] = max(numOfPixels);
biggest = zeros(size(B));
biggest(CC.PixelIdxList{indexOfMax}) = 1;
imshow(biggest);
Image Analyst
on 27 Jun 2017
With recent versions of MATLAB, you simply do
biggest = bwareafilt(B);
instead of the 6 lines of code you showed.
Accepted Answer
Image Analyst
on 14 May 2013
See my demo:
function ExtractBiggestBlob()
clc; % Clear the command window.
close all; % Close all figures (except those of imtool.)
imtool close all; % Close all imtool figures if you have the Image Processing Toolbox.
clear; % Erase all existing variables. Or clearvars if you want.
workspace; % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;
% Read in a standard MATLAB gray scale demo image.
folder = fullfile(matlabroot, '\toolbox\images\imdemos');
baseFileName = 'coins.png';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~exist(fullFileName, 'file')
% File doesn't exist -- didn't find it there. Check the search path for it.
fullFileName = baseFileName; % No path this time.
if ~exist(fullFileName, 'file')
% Still didn't find it. Alert user.
errorMessage = sprintf('Error: %s does not exist in the search path folders.', fullFileName);
uiwait(warndlg(errorMessage));
return;
end
end
grayImage = imread(fullFileName);
% Get the dimensions of the image.
% numberOfColorBands should be = 1.
[rows, columns, numberOfColorBands] = size(grayImage);
% Display the original gray scale image.
subplot(2, 2, 1);
imshow(grayImage, []);
title('Original Grayscale Image', 'FontSize', fontSize);
% Enlarge figure to full screen.
set(gcf, 'units','normalized','outerposition',[0 0 1 1]);
% Give a name to the title bar.
set(gcf,'name','Demo by ImageAnalyst','numbertitle','off')
% Let's compute and display the histogram.
[pixelCount, grayLevels] = imhist(grayImage);
subplot(2, 2, 2);
bar(pixelCount);
grid on;
title('Histogram of original image', 'FontSize', fontSize);
xlim([0 grayLevels(end)]); % Scale x axis manually.
% Threshold the image to binarize it.
binaryImage = grayImage > 100;
% Fill holes
binaryImage = imfill(binaryImage, 'holes');
% Display the image.
subplot(2, 2, 3);
imshow(binaryImage, []);
title('Binary Image', 'FontSize', fontSize);
% Get all the blob properties. Can only pass in originalImage in version R2008a and later.
[labeledImage, numberOfBlobs] = bwlabel(binaryImage);
blobMeasurements = regionprops(labeledImage, 'area', 'Centroid');
% Get all the areas
allAreas = [blobMeasurements.Area] % No semicolon so it will print to the command window.
menuOptions{1} = '0'; % Add option to extract no blobs.
% Display areas on image
for k = 1 : numberOfBlobs % Loop through all blobs.
thisCentroid = [blobMeasurements(k).Centroid(1), blobMeasurements(k).Centroid(2)];
message = sprintf('Area = %d', allAreas(k));
text(thisCentroid(1), thisCentroid(2), message, 'Color', 'r');
menuOptions{k+1} = sprintf('%d', k);
end
% Ask user how many blobs to extract.
numberToExtract = menu('How many do you want to extract', menuOptions) - 1;
% Ask user if they want the smallest or largest blobs.
promptMessage = sprintf('Do you want the %d largest, or %d smallest, blobs?',...
numberToExtract, numberToExtract);
titleBarCaption = 'Largest or Smallest?';
sizeOption = questdlg(promptMessage, titleBarCaption, 'Largest', 'Smallest', 'Cancel', 'Largest');
if strcmpi(sizeOption, 'Cancel')
return;
elseif strcmpi(sizeOption, 'Smallest')
% If they want the smallest, make the number negative.
numberToExtract = -numberToExtract;
end
%---------------------------------------------------------------------------
% Extract the largest area using our custom function ExtractNLargestBlobs().
% This is the meat of the demo!
biggestBlob = ExtractNLargestBlobs(binaryImage, numberToExtract);
%---------------------------------------------------------------------------
% Display the image.
subplot(2, 2, 4);
imshow(biggestBlob, []);
% Make the number positive again. We don't need it negative for smallest extraction anymore.
numberToExtract = abs(numberToExtract);
if numberToExtract == 1
caption = sprintf('Extracted %s Blob', sizeOption);
elseif numberToExtract > 1
caption = sprintf('Extracted %d %s Blobs', numberToExtract, sizeOption);
else % It's zero
caption = sprintf('Extracted 0 Blobs.');
end
title(caption, 'FontSize', fontSize);
msgbox('Done with demo!');
% Function to return the specified number of largest or smallest blobs in a binary image.
% If numberToExtract > 0 it returns the numberToExtract largest blobs.
% If numberToExtract < 0 it returns the numberToExtract smallest blobs.
% Example: return a binary image with only the largest blob:
% binaryImage = ExtractNLargestBlobs(binaryImage, 1)
% Example: return a binary image with the 3 smallest blobs:
% binaryImage = ExtractNLargestBlobs(binaryImage, -3)
function binaryImage = ExtractNLargestBlobs(binaryImage, numberToExtract)
try
% Get all the blob properties. Can only pass in originalImage in version R2008a and later.
[labeledImage, numberOfBlobs] = bwlabel(binaryImage);
blobMeasurements = regionprops(labeledImage, 'area');
% Get all the areas
allAreas = [blobMeasurements.Area];
if numberToExtract > 0
% For positive numbers, sort in order of largest to smallest.
% Sort them.
[sortedAreas, sortIndexes] = sort(allAreas, 'descend');
elseif numberToExtract < 0
% For negative numbers, sort in order of smallest to largest.
% Sort them.
[sortedAreas, sortIndexes] = sort(allAreas, 'ascend');
% Need to negate numberToExtract so we can use it in sortIndexes later.
numberToExtract = -numberToExtract;
else
% numberToExtract = 0. Shouldn't happen. Return no blobs.
binaryImage = false(size(binaryImage));
return;
end
% Extract the "numberToExtract" largest blob(a)s using ismember().
biggestBlob = ismember(labeledImage, sortIndexes(1:numberToExtract));
% Convert from integer labeled image into binary (logical) image.
binaryImage = biggestBlob > 0;
catch ME
errorMessage = sprintf('Error in function ExtractNLargestBlobs().\n\nError Message:\n%s', ME.message);
fprintf(1, '%s\n', errorMessage);
uiwait(warndlg(errorMessage));
end
5 Comments
Image Analyst
on 16 May 2013
The first function is the demo code. The main function that does all the work is the second function. As you know, you cannot have a script followed by a function in the same file. You can either have a script and a function in two separate files, OR you can put them both in the same file but you have to make your script into a function. It is this latter method that I used. So save the code into ExtractBiggestBlob.m. ExtractBiggestBlob() will run and do some setup stuff to create the binary image, but then call the main function that you want, which is ExtractNLargestBlobs()
More Answers (3)
Fazal Hassan
on 20 Mar 2014
Sir i have used above code on CT scan of heart in png format .but it give me wrong largest blog area when i change threshod it give an other blob with largest area...in image it should give me AROTA as largest blob but it give me some thing else Need your help plz...why this code is behaving like that Thanks in advance. Engr fazalhassan
2 Comments
Neeru
on 8 May 2014
Is it possible to use a similar code on a 3D mesh, to find the largest connected component of the mesh? I have two CT scans of the skull before and after a piece of the bone has been removed. I have subtracted them and meshed the result, and I want to extract only the largest component. Thanks, Neeru.
Sultan
on 12 Jul 2017
Hello all,
I am looking to mark the largest connected component in an image with special color say 'red', and then color the other components in black while the empty space I wanted to be colored in white. cheers
1 Comment
Image Analyst
on 12 Jul 2017
Use regionprops to find the largest blob. Then setup a colormap where the row with the largest blob number is red, row 1 is white, and all the other rows are black, then use labeled2rgb() to apply that colormap and produce an RGB image.
[labeledImage, numBlobs] = bwlabel(binaryImage);
props = regionprops(labeledImage, 'Area');
[maxArea, largestIndex] = max([props.Area])
cmap = zeros(numBlobs+1, 3);
cmap(largestIndex, :) = [1, 0, 0];
cmap(1, :) = 0;
rgbImage = labeled2rgb(labeledImage, cmap);
Start your own question and upload your binary image if you can't figure it out.
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