The axes for subplot(2, 3, 6) is not even showing up in the figure, meaning it never got to that part of your code. Are you sure it did? Set a breakpoint there and you'll see it didn't because you were sloppy in your naming and usage of image variable names. Here is a correction, however your segmentation algorithm of taking the local standard deviation and thresholding it at 5 totally doesn't work for this image -- just look at your binary image!
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 = 20;
mypath = '/home/motmot/Documents/test/';
dinfo = dir(fullfile(mypath,'*.jp*'));
filenames = fullfile({dinfo.folder}, {dinfo.name});
nfiles = length(filenames)
for K = 1 : nfiles
thisfile = filenames{K};
[folder, basename, ext] = fileparts(thisfile);
outfile = fullfile(folder, basename + "_crop" + ext);
rgbImage = imread(thisfile);
% Get the dimensions of the image. numberOfColorChannels should be = 3.
[rows, columns, numberOfColorChannels] = size(rgbImage);
% Display the original color image.
subplot(2, 3, 1);
imshow(rgbImage);
axis on;
hp = impixelinfo(); % Show x,y and RGB as you mouse around.
title('Original Color Image', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
drawnow;
% Take the red channel.
grayImage = rgbImage(:, :, 1);
% Erase the first 110 columns to get rid of the holes.
verticalProfile = mean(grayImage, 2);
for col = 1 : 110
grayImage(:, col) = verticalProfile;
end
% Run a texture filter on it.
stdImage = stdfilt(grayImage);
% Display the image.
subplot(2, 3, 2);
imshow(stdImage, []);
impixelinfo;
axis on;
title('StDev-Filtered Image', 'FontSize', fontSize, 'Interpreter', 'None');
% Enlarge figure
set(gcf, 'Units', 'Normalized', 'Outerposition', [0.05, 0.1, .9, .80]);
drawnow;
% Let's compute and display the histogram.
subplot(2, 3, 3);
histogram(stdImage, 500); % 500 bins.
grid on;
title('Histogram of StDev-Filtered image', 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Gray Level', 'FontSize', fontSize);
ylabel('Pixel Count', 'FontSize', fontSize);
drawnow;
% Threshold the image.
binaryImage = stdImage > 5;
% Display the image.
subplot(2, 3, 4);
imshow(binaryImage);
axis on;
title('Binary Image where SD > 5', 'FontSize', fontSize, 'Interpreter', 'None');
% % Get areas of blobs
% labeledImage = bwlabel(binaryImage);
% props = regionprops(labeledImage, 'Area');
% allAreas = sort([props.Area])
% subplot(2, 3, 5);
% histogram(allAreas); % Show histogram of blob areas.
% title('Blob Areas', 'FontSize', fontSize, 'Interpreter', 'None');
% Get rid of small blobs.
binaryImage = bwareafilt(binaryImage, [70, inf]); % Keep only if 70 pixels or larger.
% Display the image.
subplot(2, 3, 5);
imshow(binaryImage);
axis on;
title('Cleaned Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
% Find the bounding box.
[blobRows, blobColumns] = find(binaryImage);
row1 = min(blobRows)
row2 = max(blobRows)
col1 = min(blobColumns)
col2 = max(blobColumns)
% Crop it.
croppedImage = rgbImage(row1:row2, col1:col2, :);
% Display the cropped, enhanced color image.
subplot(2, 3, 6);
imshow(croppedImage);
axis on;
title('Cropped Color Image', 'FontSize', fontSize, 'Interpreter', 'None');
imwrite(croppedImage, outfile)
end
