Thermography Camera Image Color Scale cropping

Hello, I am currently doing a project using Thermography Camera Images. I managed to find a code by @Image Analyst which would allow for me to use these images. I am relatively new to the use of Matlab/Mathworks and am not sure how to properly crop to reach the color bar. Is there a basic code/program I can use that would allow auto-cropping of the photo that would allow me to properly crop the colorbar. I attached the code to the description.Thanks for any assistance

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 = 15;

%===============================================================================
% Get the name of the image the user wants to use.
baseFileName = 'Trial1.png'; % Assign the one on the button that they clicked on.
% Get the full filename, with path prepended.
folder = pwd
fullFileName = fullfile(folder, baseFileName);

%===============================================================================
% Read in a demo image.
originalRGBImage = imread(fullFileName);
% Display the image.
subplot(2, 3, 1);
imshow(originalRGBImage, []);
axis on;
caption = sprintf('Original Pseudocolor Image, %s', baseFileName);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Column', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Row', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

grayImage = min(originalRGBImage, [], 3); % Useful for finding image and color map regions of image.
% Get the dimensions of the image.  numberOfColorChannels should be = 3.
[rows, columns, numberOfColorChannels] = size(originalRGBImage);

% Crop off the surrounding clutter to get the colorbar.
colorBarImage = imcrop(originalRGBImage, [1, 20, 17, rows]);
b = colorBarImage(:,:,3);

% Crop off the surrounding clutter to get the RGB image.
rgbImage = imcrop(originalRGBImage, [81, 1, columns-20, rows]);

% Get the dimensions of the image.  
% numberOfColorBands should be = 3.
[rows, columns, numberOfColorChannels] = size(rgbImage);
% Display the image.
subplot(2, 3, 2);
imshow(rgbImage, []);
axis on;
caption = sprintf('Cropped Pseudocolor Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Column', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Row', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
hp = impixelinfo();

% Display the colorbar image.
subplot(2, 3, 3);
imshow(colorBarImage, []);
axis on;
caption = sprintf('Cropped Colorbar Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Column', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Row', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0.05 1 0.95]);
% Get rid of tool bar and pulldown menus that are along top of figure.
% set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst', 'NumberTitle', 'Off') 

% Get the color map.
storedColorMap = colorBarImage(:,1,:);
% Need to call squeeze to get it from a 3D matrix to a 2-D matrix.
% Also need to divide by 255 since colormap values must be between 0 and 1.
storedColorMap = double(squeeze(storedColorMap)) / 255
% Need to flip up/down because the low rows are the high temperatures, not the low temperatures.
storedColorMap = flipud(storedColorMap);

% Convert from an RGB image to a grayscale, indexed, thermal image.
indexedImage = rgb2ind(rgbImage, storedColorMap);
% Display the thermal image.
subplot(2, 3, 4);
imshow(indexedImage, []);
axis on;
caption = sprintf('Indexed Image (Gray Scale Image)');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

% Define the temperature at the top end of the scale
% This will probably be the high temperature.
highTemp = 28.9;
% Define the temperature at the dark end of the scale
% This will probably be the low temperature.
lowTemp = 0.9;

% Scale the image so that it's actual temperatures
thermalImage = lowTemp + (highTemp - lowTemp) * mat2gray(indexedImage);
subplot(2, 3, 5);
imshow(thermalImage, []);
axis on;
colorbar;
title('Floating Point Thermal (Temperature) Image', 'FontSize', fontSize, 'Interpreter', 'None');
hp = impixelinfo(); % Let user mouse around and see temperatures.
hp.Units = 'normalized';
hp.Position = [0.45, 0.03, 0.25, 0.05];

% Get the histogram of the indexed image
subplot(2, 3, 6);
histogram(thermalImage, 'Normalization', 'probability');
axis on;
grid on;
caption = sprintf('Histogram of Thermal Temperature Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Temperature', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Frequency', 'FontSize', fontSize, 'Interpreter', 'None');

[Jacob Kalmanovich]

@Image A@Image Analyst

[DGM]

That was an example tailored for a specific image. It serves as an example for that image. All the positional information used by imcrop() refers to it. The upper and lower limits refer to it.

In order to adjust it for a different image, one needs to actually see the new image.

[Jacob Kalmanovich]

My apologies, I have attached the image here. The code was originally for a different image. All I did was change the name because, whener I tried to chang the positional information I failed and reverted it back to its original before changes. Any help with this image would be greatly appreciated.

[Jacob Kalmanovich]

@DGM

Answer 1

[Image Analyst]

If you want you can ask the user to specify the colorbar and image by dragging out a box around them. You can use imcrop or drawrectangle.

See attached drawrectangle demo here in my other answer: https://www.mathworks.com/matlabcentral/answers/1706650-isolate-low-contrast-rectangle-of-known-size-from-image#answer_952410

[Jacob Kalmanovich]

Thank you Image Analyst for that answer. Would it be possible to isolate the colorbar from this image using the imcrop method already in your code. The reason I ask is because in all other images the colorbar is in the same position. If I can probably get the coordinates for imcrop it would allow me to analyze all the photos. Would you by chance be able to help with with proper cropping through code? I would greatly appreciate.

[Jacob Kalmanovich]

Would it be possible to incorporate the drawrectangle option directly into the code or would just using imcrop by easier?

[Jacob Kalmanovich]

Apologies for all the questions. When I tried to incorporate it into the code, the greyscale thermal image isnt created and the table is also not created

[Image Analyst]

You forgot to attach your code.

[Jacob Kalmanovich]

My apologies. I attached it to this section. Both the greyscale and the table are needed for my analysis. Thanks again for the assistance.

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 = 15;

%===============================================================================
% Get the name of the image the user wants to use.
baseFileName = 'Trial1.png'; % Assign the one on the button that they clicked on.
% Get the full filename, with path prepended.
folder = pwd
fullFileName = fullfile(folder, baseFileName);

%===============================================================================
% Read in a demo image.
originalRGBImage = imread(fullFileName);
% Display the image.
subplot(2, 3, 1);
imshow(originalRGBImage, []);
axis on;
caption = sprintf('Original Pseudocolor Image, %s', baseFileName);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Column', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Row', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

grayImage = min(originalRGBImage, [], 3); % Useful for finding image and color map regions of image.
% Get the dimensions of the image.  numberOfColorChannels should be = 3.
[rows, columns, numberOfColorChannels] = size(originalRGBImage);

% Crop off the surrounding clutter to get the colorbar.
colorBarImage = rgbImage = imread('Trial1.PNG');
hFig = figure;
imshow(rgbImage);
hFig.WindowState = 'maximized';
% Ask user to draw rectangle.
button = 'Redraw';
while contains(button, 'Redraw', 'IgnoreCase',true)
	uiwait(helpdlg('Draw a box'));
	% User draws a box.  It exits as soon as they lift the mouse.
	hBox = drawrectangle('Color', 'r');
	
	% Get the coordinates in the form [xLeft, yTop, width, height].
	roiPosition = hBox.Position;
	% Delete the ROI object.
	delete(hBox);
	% and replace it with a rectangle in the graphical overlay.
	hold on;
	hRect = rectangle('Position', roiPosition, 'EdgeColor', 'r', 'LineWidth', 2);

	% Ask user if the rectangle is acceptable.
	message = sprintf('Is this good?');
	button = questdlg(message, message, 'Accept', 'Redraw', 'Reject and Quit', 'Accept');
	if contains(button, 'Quit','IgnoreCase',true)
		delete(hRect);
		roiPosition = [];
		break;
	elseif contains(button, 'Accept','IgnoreCase',true)
		break;
	end
end
% Close down figure.
close(hFig);
b = colorBarImage(:,:,3);

% Crop off the surrounding clutter to get the RGB image.
rgbImage = imcrop(originalRGBImage, [81, 1, columns-20, rows]);

% Get the dimensions of the image.  
% numberOfColorBands should be = 3.
[rows, columns, numberOfColorChannels] = size(rgbImage);
% Display the image.
subplot(2, 3, 2);
imshow(rgbImage, []);
axis on;
caption = sprintf('Cropped Pseudocolor Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Column', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Row', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
hp = impixelinfo();

% Display the colorbar image.
subplot(2, 3, 3);
imshow(colorBarImage, []);
axis on;
caption = sprintf('Cropped Colorbar Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Column', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Row', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0.05 1 0.95]);
% Get rid of tool bar and pulldown menus that are along top of figure.
% set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst', 'NumberTitle', 'Off') 

% Get the color map.
storedColorMap = colorBarImage(:,1,:);
% Need to call squeeze to get it from a 3D matrix to a 2-D matrix.
% Also need to divide by 255 since colormap values must be between 0 and 1.
storedColorMap = double(squeeze(storedColorMap)) / 255
% Need to flip up/down because the low rows are the high temperatures, not the low temperatures.
storedColorMap = flipud(storedColorMap);

% Convert from an RGB image to a grayscale, indexed, thermal image.
indexedImage = rgb2ind(rgbImage, storedColorMap);
% Display the thermal image.
subplot(2, 3, 4);
imshow(indexedImage, []);
axis on;
caption = sprintf('Indexed Image (Gray Scale Image)');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

% Define the temperature at the top end of the scale
% This will probably be the high temperature.
highTemp = 28.9;
% Define the temperature at the dark end of the scale
% This will probably be the low temperature.
lowTemp = 0.9;

% Scale the image so that it's actual temperatures
thermalImage = lowTemp + (highTemp - lowTemp) * mat2gray(indexedImage);
subplot(2, 3, 5);
imshow(thermalImage, []);
axis on;
colorbar;
title('Floating Point Thermal (Temperature) Image', 'FontSize', fontSize, 'Interpreter', 'None');
hp = impixelinfo(); % Let user mouse around and see temperatures.
hp.Units = 'normalized';
hp.Position = [0.45, 0.03, 0.25, 0.05];

% Get the histogram of the indexed image
subplot(2, 3, 6);
histogram(thermalImage, 'Normalization', 'probability');
axis on;
grid on;
caption = sprintf('Histogram of Thermal Temperature Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Temperature', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Frequency', 'FontSize', fontSize, 'Interpreter', 'None');

[Image Analyst]

Why do you still have this in there???

% Crop off the surrounding clutter to get the RGB image.
rgbImage = imcrop(originalRGBImage, [81, 1, columns-20, rows]);

That totally ignores the box you just drew! You need to extract the image using the drawn rectangle box. You can use imcrop with the proper arguments or use indexing.

Fix that and repost. I'm heading out for a few hours and will check back later.

[Jacob Kalmanovich]

Understood. My apologies for that mistake. My expertise with Matlab as you can tell is very minimal and am quite confused. Would this work?

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 = 15;

%===============================================================================
% Get the name of the image the user wants to use.
baseFileName = 'Trial1.png'; % Assign the one on the button that they clicked on.
% Get the full filename, with path prepended.
folder = pwd;
fullFileName = fullfile(folder, baseFileName);

%===============================================================================
% Read in a demo image.
originalRGBImage = imread(fullFileName);
% Display the image.
subplot(2, 3, 1);
imshow(originalRGBImage, []);
axis on;
caption = sprintf('Original Pseudocolor Image, %s', baseFileName);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Column', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Row', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

grayImage = min(originalRGBImage, [], 3); % Useful for finding image and color map regions of image.
% Get the dimensions of the image.  numberOfColorChannels should be = 3.
[rows, columns, numberOfColorChannels] = size(originalRGBImage);

% Crop off the surrounding clutter to get the colorbar.
rgbImage = imread('Trial1.PNG');
hFig = figure;
imshow(rgbImage);
hFig.WindowState = 'maximized';
% Ask user to draw rectangle.
button = 'Redraw';
while contains(button, 'Redraw', 'IgnoreCase',true)
	uiwait(helpdlg('Draw a box'));
	% User draws a box.  It exits as soon as they lift the mouse.
	hBox = drawrectangle('Color', 'r');
	
	% Get the coordinates in the form [xLeft, yTop, width, height].
	roiPosition = hBox.Position;
	% Delete the ROI object.
	delete(hBox);
	% and replace it with a rectangle in the graphical overlay.
	hold on;
	hRect = rectangle('Position', roiPosition, 'EdgeColor', 'r', 'LineWidth', 2);

	% Ask user if the rectangle is acceptable.
	message = sprintf('Is this good?');
	button = questdlg(message, message, 'Accept', 'Redraw', 'Reject and Quit', 'Accept');
	if contains(button, 'Quit','IgnoreCase',true)
		delete(hRect);
		roiPosition = [];
		break;
	elseif contains(button, 'Accept','IgnoreCase',true)
		break;
	end
end
% Close down figure.
close(hFig);
b = colorBarImage(:,:,3);

% Crop off the surrounding clutter to get the RGB image.
binaryImage = poly2mask(x, y);
measurements = regionprops(binaryImage, 'BoundingBox');
rgbImage = imcrop(originalImage, measurements.BoundingBox);

% Get the dimensions of the image.  
% numberOfColorBands should be = 3.
[rows, columns, numberOfColorChannels] = size(rgbImage);
% Display the image.
subplot(2, 3, 2);
imshow(rgbImage, []);
axis on;
caption = sprintf('Cropped Pseudocolor Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Column', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Row', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
hp = impixelinfo();

% Display the colorbar image.
subplot(2, 3, 3);
imshow(colorBarImage, []);
axis on;
caption = sprintf('Cropped Colorbar Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Column', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Row', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0.05 1 0.95]);
% Get rid of tool bar and pulldown menus that are along top of figure.
% set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst', 'NumberTitle', 'Off') 

% Get the color map.
storedColorMap = colorBarImage(:,1,:);
% Need to call squeeze to get it from a 3D matrix to a 2-D matrix.
% Also need to divide by 255 since colormap values must be between 0 and 1.
storedColorMap = double(squeeze(storedColorMap)) / 255;
% Need to flip up/down because the low rows are the high temperatures, not the low temperatures.
storedColorMap = flipud(storedColorMap);

% Convert from an RGB image to a grayscale, indexed, thermal image.
indexedImage = rgb2ind(rgbImage, storedColorMap);
% Display the thermal image.
subplot(2, 3, 4);
imshow(indexedImage, []);
axis on;
caption = sprintf('Indexed Image (Gray Scale Image)');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

% Define the temperature at the top end of the scale
% This will probably be the high temperature.
highTemp = 28.9;
% Define the temperature at the dark end of the scale
% This will probably be the low temperature.
lowTemp = 0.9;

% Scale the image so that it's actual temperatures
thermalImage = lowTemp + (highTemp - lowTemp) * mat2gray(indexedImage);
subplot(2, 3, 5);
imshow(thermalImage, []);
axis on;
colorbar;
title('Floating Point Thermal (Temperature) Image', 'FontSize', fontSize, 'Interpreter', 'None');
hp = impixelinfo(); % Let user mouse around and see temperatures.
hp.Units = 'normalized';
hp.Position = [0.45, 0.03, 0.25, 0.05];

% Get the histogram of the indexed image
subplot(2, 3, 6);
histogram(thermalImage, 'Normalization', 'probability');
axis on;
grid on;
caption = sprintf('Histogram of Thermal Temperature Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
xlabel('Temperature', 'FontSize', fontSize, 'Interpreter', 'None');
ylabel('Frequency', 'FontSize', fontSize, 'Interpreter', 'None');

[Jacob Kalmanovich]

I seem to still be having issues. I havent been able to properly index/ imcrop the rectangle

[Jacob Kalmanovich]

@Image Analyst Which arguments for imcrop are best to use?

[Jacob Kalmanovich]

Or would indexing be make it easier to isolate and pullout the colorbar to allow for analysis of the image

[Image Analyst]

Try this new one. It lets you drag out a box over the image and colorbar.

[Jacob Kalmanovich]

Thank you so much! It gets the colorbar out perfectly, and while not 100% accurate it will do the job amazingly. Thanks again

[Image Analyst]

I've posted a newer, better version in my File Exchange:

https://www.mathworks.com/matlabcentral/fileexchange/113995-thermal-image-color-to-temperature?s_tid=srchtitle

[Jacob Kalmanovich]

Thank you for the assistance Image Analyst. I do have one follow-up question. Is it possible to add code that would allow the program to also find the average and variance of the pixel associated temperatures?

[Image Analyst]

Yes. Use mean() and std() on the region of interest, or the whole image.