I've fixed up the code so try this:
% Initialization Steps.
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 = 18;
markerSize = 40;
fprintf('Beginning to run %s.m ...\n', mfilename);
%-----------------------------------------------------------------------------------------------------------------------------------
% Read in image.
folder = [];
baseFileName = 'color.jpg';
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~isfile(fullFileName)
% 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
fullFileName = fullFileNameOnSearchPath;
end
rgbImage = imread(fullFileName);
[rows, columns, numberOfColorChannels] = size(rgbImage)
numberOfPixels = rows*columns;
% Display the image.
subplot(2, 3, 1);
imshow(rgbImage, []);
axis('on', 'image');
caption = sprintf('RGB Image : "%s"', baseFileName);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
hp = impixelinfo(); % Set up status line to see values when you mouse over the image.
% Set up figure properties:
% Enlarge figure to full screen.
hFig1 = gcf;
hFig1.Units = 'Normalized';
hFig1.WindowState = 'maximized';
% Get rid of tool bar and pulldown menus that are along top of figure.
% set(gcf, 'Toolbar', 'none', 'Menu', 'none');
%-----------------------------------------------------------------------------------------------------------------------------------
% Segment (mask) the image.
[mask, maskedRGBImage] = createMask(rgbImage);
% Take largest blob only.
mask = bwareafilt(mask, 1);
% Fill any possible holes.
mask = imfill(mask, 'holes');
% Get masked image again with new mask
% Mask image by multiplying each channel by the mask.
maskedRgbImage = rgbImage .* cast(mask, 'like', rgbImage);
subplot(2, 3, 2);
imshow(mask, []);
axis('on', 'image');
title('Skin Lesion Mask', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
subplot(2, 3, 3);
imshow(maskedRgbImage, []);
axis('on', 'image');
title('Masked Image', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
% Get the boundary of the mask
lesionBoundary = bwboundaries(mask);
%-----------------------------------------------------------------------------------------------------------------------------------
% CONVERT IMAGE TO CIE LAB USING "BOOK FORMULAS" (UNCALIBRATED!).
lab_Image = rgb2lab(rgbImage);
% Extract out the color bands from the original image
% into 3 separate 2D arrays, one for each color component.
[lImage, aImage, bImage] = imsplit(lab_Image);
% Display the lab images.
subplot(2, 3, 4);
imshow(lImage, []);
impixelinfo;
hold on;
visboundaries(lesionBoundary);
hold off;
title('L Channel', 'FontSize', fontSize);
subplot(2, 3, 5);
imshow(aImage, []);
impixelinfo;
hold on;
visboundaries(lesionBoundary);
hold off;
title('a Channel', 'FontSize', fontSize);
subplot(2, 3, 6);
imshow(bImage, []);
impixelinfo;
hold on;
visboundaries(lesionBoundary);
hold off;
title('b Channel', 'FontSize', fontSize);
% Get the average lab color value.
[LMean, aMean, bMean] = GetMeanLABValues(lImage, aImage, bImage, mask);
%-----------------------------------------------------------------------------------------------------------------------------------
% DEFINE REFERENCE COLORS.
% VERY VERY IMPORTANT: NEED TO BE EITHER UINT8 IF IN THE RANGE 0-255 OR
% NEED TO BE IN THE RANGE 0-1 IF THE TYPE IS DOUBLE.
bluegray = uint8([0 134 139]);
white= uint8([255 255 255]);
black = uint8([0 0 0]);
red = uint8([255 0 0]);
darkbrown = uint8([101 67 33]);
lightbrown = uint8([205 133 63]);
% Convert reference colors from RGB colorspace to lab color space.
refLab_bg = rgb2lab(bluegray)
refLab_wh = rgb2lab(white)
refLab_bl = rgb2lab(black)
refLab_red = rgb2lab(red)
refLab_db = rgb2lab(darkbrown)
refLab_lbr = rgb2lab(lightbrown)
%-----------------------------------------------------------------------------------------------------------------------------------
% Make new figure to hold original images and delta E images.
hFigDE = figure;
subplot(3, 3, 1);
imshow(rgbImage, []);
impixelinfo
title('Original Image', 'FontSize',fontSize)
drawnow;
%-----------------------------------------------------------------------------------------------------------------------------------
% Create the Delta E image for blue gray.
% This is an image that represents the color difference.
deImage_bg = GetDeltaEImage(lImage, aImage, bImage, refLab_bg);
subplot(3, 3, 2);
imshow(deImage_bg, []);
impixelinfo;
hold on;
visboundaries(lesionBoundary);
hold off;
title('Delta E Blue Gray', 'FontSize',fontSize)
drawnow;
%-----------------------------------------------------------------------------------------------------------------------------------
% Compute the Delta E image for white color.
deImage_wh = GetDeltaEImage(lImage, aImage, bImage, refLab_wh);
subplot(3, 3, 3);
imshow(deImage_wh, []);
impixelinfo;
hold on;
visboundaries(lesionBoundary);
hold off;
title('Delta E White', 'FontSize',fontSize)
drawnow;
%-----------------------------------------------------------------------------------------------------------------------------------
% Create the Delta E image for blue gray.
% This is an image that represents the color difference.
deImage_bl = GetDeltaEImage(lImage, aImage, bImage, refLab_bl);
subplot(3, 3, 4);
imshow(deImage_bl, []);
impixelinfo;
hold on;
visboundaries(lesionBoundary);
hold off;
title('Delta E Black', 'FontSize',fontSize)
%-----------------------------------------------------------------------------------------------------------------------------------
% Create the Delta E image for red.
% This is an image that represents the color difference.
deImage_red = GetDeltaEImage(lImage, aImage, bImage, refLab_red);
subplot(3, 3, 5);
imshow(deImage_red, []);
impixelinfo;
hold on;
visboundaries(lesionBoundary);
hold off;
title('Delta E Red', 'FontSize',fontSize)
drawnow;
%-----------------------------------------------------------------------------------------------------------------------------------
% Create the Delta E image for dark brown.
% This is an image that represents the color difference.
deImage_db = GetDeltaEImage(lImage, aImage, bImage, refLab_db);
subplot(3, 3, 6);
imshow(deImage_db, []);
impixelinfo;
hold on;
visboundaries(lesionBoundary);
hold off;
title('Delta E Dark Brown', 'FontSize',fontSize)
drawnow;
%-----------------------------------------------------------------------------------------------------------------------------------
% Create the Delta E image for light brown.
% This is an image that represents the color difference.
deImage_lbr = GetDeltaEImage(lImage, aImage, bImage, refLab_lbr);
subplot(3, 3, 7);
imshow(deImage_lbr, []);
impixelinfo;
hold on;
visboundaries(lesionBoundary);
hold off;
title('Delta E Light Brown', 'FontSize',fontSize)
drawnow;
hFigDE.WindowState = "maximized";
%-----------------------------------------------------------------------------------------------------------------------------------
% Get mean Delta E color difference just within the mask area ONLY:
meanDE_bg = mean(deImage_bg(mask))
meanDE_wh = mean(deImage_wh(mask))
meanDE_bl = mean(deImage_bl(mask))
meanDE_rd = mean(deImage_red(mask))
meanDE_db = mean(deImage_db(mask))
meanDE_lbr = mean(deImage_lbr(mask))
%==============================================================================================================================
function deImage = GetDeltaEImage(lImage, aImage, bImage, refLAB)
try
deImage = sqrt((lImage - refLAB(1)).^2 + (aImage - refLAB(2)).^2 + (bImage - refLAB(3)).^2);
catch ME
errorMessage = sprintf('Error running GetDeltaEImage:\n\n\nThe error message is:\n%s', ...
ME.message);
WarnUser(errorMessage);
end
end
%==============================================================================================================================
% Get the average lab within the mask region.
function [LMean, aMean, bMean] = GetMeanLABValues(LChannel, aChannel, bChannel, mask)
try
LVector = LChannel(mask); % 1D vector of only the pixels within the masked area.
LMean = mean(LVector);
aVector = aChannel(mask); % 1D vector of only the pixels within the masked area.
aMean = mean(aVector);
bVector = bChannel(mask); % 1D vector of only the pixels within the masked area.
bMean = mean(bVector);
catch ME
errorMessage = sprintf('Error running GetMeanLABValues:\n\n\nThe error message is:\n%s', ...
ME.message);
WarnUser(errorMessage);
end
return; % from GetMeanLABValues
end
%==============================================================================================================================
function WarnUser(message)
fprintf('%s\n', message)
uiwait(warndlg(message))
end
%==============================================================================================================================
% Get mask of melanoma.
function [BW,maskedRGBImage] = createMask(RGB)
%createMask Threshold RGB image using auto-generated code from colorThresholder app.
% [BW,MASKEDRGBIMAGE] = createMask(RGB) thresholds image RGB using
% auto-generated code from the colorThresholder app. The colorspace and
% range for each channel of the colorspace were set within the app. The
% segmentation mask is returned in BW, and a composite of the mask and
% original RGB images is returned in maskedRGBImage.
% Auto-generated by colorThresholder app on 22-Sep-2022
%------------------------------------------------------
% Convert RGB image to chosen color space
I = rgb2hsv(RGB);
% Define thresholds for channel 1 based on histogram settings
channel1Min = 0.000;
channel1Max = 1.000;
% Define thresholds for channel 2 based on histogram settings
channel2Min = 0.000;
channel2Max = 1.000;
% Define thresholds for channel 3 based on histogram settings
channel3Min = 0.000;
channel3Max = 0.544;
% Create mask based on chosen histogram thresholds
sliderBW = (I(:,:,1) >= channel1Min ) & (I(:,:,1) <= channel1Max) & ...
(I(:,:,2) >= channel2Min ) & (I(:,:,2) <= channel2Max) & ...
(I(:,:,3) >= channel3Min ) & (I(:,:,3) <= channel3Max);
BW = sliderBW;
% Initialize output masked image based on input image.
maskedRGBImage = RGB;
% Set background pixels where BW is false to zero.
maskedRGBImage(repmat(~BW,[1 1 3])) = 0;
end
