MATLAB Answers

finding the distance between points of boundaries

147 views (last 30 days)
Babu Sankhi
Babu Sankhi on 24 Jul 2020 at 16:16
Commented: Babu Sankhi about 7 hours ago
Hi all,
I need help to find the distance between boundaries . I have attached my original microscopy image and the code I wrote to get the more clear boudaries of desired regions of that image . After that my problem is to find the distance between right most points of innner(green) and outer(Red) boundaries . Actually, I have to find the the distance between A and B points indicated in the resulting png.
It would be great if you share some ideas about writing codes for this measurement.
Thank you

  0 Comments

Sign in to comment.

Accepted Answer

Image Analyst
Image Analyst on 26 Jul 2020 at 23:34
Babu, to process many images, see the code samples in the FAQ:
To find the distance on the right between the two circles, try this.
clc; % Clear the command window.
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 long g;
format compact;
fontSize = 22;
%--------------------------------------------------------------------------------------------------------
% READ IN IMAGE
folder = pwd;
baseFileName = 'originalimage.png';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~exist(fullFileName, 'file')
% The file doesn't exist -- didn't find it there in that folder.
% Check the entire search path (other folders) for the file by stripping off the folder.
fullFileNameOnSearchPath = baseFileName; % No path this time.
if ~exist(fullFileNameOnSearchPath, '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.
% numberOfColorChannels should be = 1 for a gray scale image, and 3 for an RGB color image.
[rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
% It's not really gray scale like we expected - it's color.
% Use weighted sum of ALL channels to create a gray scale image.
grayImage = rgb2gray(grayImage);
% ALTERNATE METHOD: Convert it to gray scale by taking only the green channel,
% which in a typical snapshot will be the least noisy channel.
% grayImage = grayImage(:, :, 2); % Take green channel.
end
% Display the image.
subplot(2, 2, 1);
imshow(grayImage, []);
title('Original Grayscale Image', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
hFig = gcf;
hFig.WindowState = 'maximized'; % May not work in earlier versions of MATLAB.
drawnow;
% Display histogram
subplot(2, 2, 2);
imhist(grayImage);
grid on;
title('Histogram of gray image', 'FontSize', fontSize);
%--------------------------------------------------------------------------------------------------------
% SEGMENTATION OF IMAGE
% Get a binary image
brightMask = imbinarize(grayImage);
% Take the 2 biggest blobs
brightMask = bwareafilt(brightMask, 1, 4);
% Get rid of the small dots in the star by doing a hole fill.
% binaryImage = imfill(binaryImage, 'holes');
subplot(2, 2, 3);
imshow(brightMask, []);
impixelinfo;
title('Initial Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
% Need to get rid of little black specks in blob.
props = regionprops(brightMask, 'Area');
brightArea = props.Area
minAllowableArea = brightArea * 0.9
brightMask = ~bwareafilt(~brightMask, 2);
% Blur it a bit to smooth it out.
windowSize = 17;
kernel = ones(windowSize, windowSize) / windowSize ^ 2;
brightMask = imfilter(brightMask, kernel) > 0.5;
subplot(2, 2, 4);
imshow(brightMask, []);
impixelinfo;
title('Final Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
% Get boundaries and plot them, just for fun.
boundaries = bwboundaries(brightMask);
subplot(2, 2, 1);
hold on;
for k = 1 : length(boundaries)
thisBoundary = boundaries{k};
x = thisBoundary(:, 2);
y = thisBoundary(:, 1);
plot(x, y, 'r-', 'LineWidth', 2);
end
%--------------------------------------------------------------------------------------------------------
% FIND DISTANCE BETWEEN CIRCLES ON THE RIGHT HAND SIDE.
% Find the right-most point.
[r, c] = find(brightMask);
[lastColumn, outerIndex] = max(c)
xRight = c(outerIndex)
yRight = r(outerIndex)
innerBoundary = boundaries{2};
x = innerBoundary(:, 2);
y = innerBoundary(:, 1);
% Find the closest point on the inner boundary to that point.
distances = sqrt((x - xRight).^2 + (y - yRight).^2);
[minDistance, innerIndex] = min(distances)
xInner = innerBoundary(innerIndex, 2);
yInner = innerBoundary(innerIndex, 1);
% Draw a line between them
line([xInner, xRight], [yInner, yRight], 'Color', 'r', 'LineWidth', 2);
subplot(2, 2, 4);
line([xInner, xRight], [yInner, yRight], 'Color', 'r', 'LineWidth', 2);
caption = sprintf('Final Mask. Distance = %.1f', minDistance);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');

  25 Comments

Babu Sankhi
Babu Sankhi about 11 hours ago
oh sorry, I have R2019aor b not R2020a.
Yes I tried several ways. I think I set the path by assigning the folder and figures are supposed be saved there. But it still gives the same error. Can you please help me more?
Thank you
For i=1:100
My code is here for everything to get the figures
pngFileName = sprintf('plot_subject_%d.png', i);
fullFileNam = fullfile('F:\2020\microscope\setup\figur', pngFileName);
% Then save it
export_fig(fullFileNam);
%addpath('F:\2020\microscope\setup\figur', '-end')
end
Image Analyst
Image Analyst about 13 hours ago
What does this say if you put it right before that call to export_fig
which -all export_fig
Babu Sankhi
Babu Sankhi about 7 hours ago
It gives the error;
'export_fig(fullFileNam)' not found. when I use this;
For i=1:100
My code is here for everything to get the figures
pngFileName = sprintf('plot_subject_%d.png', i);
fullFileNam = fullfile('F:\2020\microscope\setup\figur', pngFileName);
% Then save it
which -all export_fig(fullFileNam);
%addpath('F:\2020\microscope\setup\figur', '-end')
end
But
I don't get any error when I use this. However no figures are saved. Can you please help me more?
all export_fig(fullFileNam);

Sign in to comment.

More Answers (1)

Matt J
Matt J on 26 Jul 2020 at 17:13
If you have the Statistics Toolbox, you can pdist2
D = pdist2(Red,Green)

  7 Comments

Show 4 older comments
Babu Sankhi
Babu Sankhi on 26 Jul 2020 at 19:50
Thank you Matt
But I have thousands of images to do that so using tool box for each is quiet time consuming/and allmost impossible. So I am looking for the code that will help me to get these coordinates and their difference along right direction/edge only.
How can I define red and green for using this?
Bruno Luong
Bruno Luong on 26 Jul 2020 at 20:12
xred = boundary1(:,2);
xgreen = boundary2(:,2);
distance = max(xred) - max(xgreen);
Matt J
Matt J on 26 Jul 2020 at 21:57
But I have thousands of images to do that so using tool box for each is quiet time consuming/and allmost impossible.
The boundarycalculation.m routine that you attached takes about 0.02 sec on my machine once you remove all of the plotting commands. That should allow you to do thousands of images in about a minute or so - doesn't seem so bad to me.
Using the alternative version below, I was able to cut the time by about half. The imclose operations that I commented out may or may not be helpful in removing noise, and in any case don't add much overhead:
tic;
BW=bwareafilt(imbinarize (II),1);
%BW=imclose(BW,ones(3));
BWhole=bwareafilt(imfill(BW,'holes')-BW>0,1);
%BWhole=imclose(BWhole,ones(3));
[~,J]=find(BW);
[~,Jhole]=find(BW);
distance=max(J)-max(Jhole);
toc
%Elapsed time is 0.009772 seconds.

Sign in to comment.