How to sum pixels of a certain area and put a point to stop

Hi

I want to sum all pixels of a certain area of the image and the summation will go on (vertically) until it finds the first red pixel where it should stop and move to the next column. Please help

clc;
s = imread('A2.jpg')

for i = 136:548
    for j = 123:length(s)
        s(i,j)=sum(s)
        if s(i,j)== 100
            break
        end
        s = s+1;
        end
        end
        

I use this code but I get the error "Assignment has more non-singleton rhs dimensions than non-singleton subscripts" at line s(i,j)=sum(s) .

[Image Analyst]

Isn't this a duplicate question? I remember answering where I masked out the area within red, and a second question where I summed the masked area vertically. Why are you asking the same question again? Like I said, just do

horizontalSums = sum(maskedImage, 1);

to get the sum of columns as you go horizontally across the image.

[Stelios Fanourakis]

I'm grateful to your answers sir Analyst, but I am still struggle how to fix the region from specific pixel point (136,123) to point (548,125) and vertically down until it reaches the first red pixel. So the mask includes what is inside the red contour. I don't want this now. What I want is for the user to be able to determine the start and end point of the sum scan. Those points might are outside the upper red boundary area but definitely, when scanning goes down to be able to stop where the bottom red boundary line is.

Do I explain it clearly?

[Image Analyst]

Not really. First, is (136,123) (x,y) or (row, column)?

Let's say it's row, column. So you could just do

subImage = grayImage(136:548, 123:125);
theSums = sum(subImage, 1);

[Stelios Fanourakis]

It gives me 0 0 0 results. I want to count all pixels for the whole column from those points down until the first red pixel where it should stop counting and move forward to the next column.

[Stelios Fanourakis]

But I get results when I use

theSums = sum(subImage, 2);

Is there an option to have the number of pixels for every column?

E.g.

Column 1:

0 0 74 74 255 255 65 66

Column 2:

1 1 0 0 74 74 255 255 23

Column 3:

0 0 67 67 67 88 88 112 113

etc...

Answer 1

[Image Analyst]

If you want to start at some row, and go down to some other row where the red line is for that column (which varies from column to column), use code like this:

% Column 1:
c1 = [0 0 74 74 255 255 65 66 0]'
% Column 2:
c2 = [1 1 0 0 74 74 255 255 23]'
% Column 3:
c3 = [0 0 67 67 67 88 88 112 113]'
% Make image
grayImage = [c1,c2,c3]
% Let's say the red line is at these 3 rows:
redLines = [7, 8, 6];
% Sum from 2 to the red line
[rows, columns] = size(grayImage)
theSums = zeros(1, columns);
theCounts = zeros(1, columns);
startingRow = 2;
for col = 1 : columns
	theSums(col) = sum(grayImage(startingRow : redLines(col), col));
	theCounts(col) = redLines(col) - startingRow + 1;
end

[Stelios Fanourakis]

I think your previous comment was closer to my need.

row1 = 123; % Whatever...
s = zeros(1, columns); % Initialize sums for every column.
for col = 1 : columns
    row2 = find(mask(:, col), 1, 'last'); % Get bottom row of mask
    if ~isempty(row2)
        % Get the sum from row1 to row2
        s(col)  = sum(grayImage(row1:row2, col));
    end
end

The row1 = 123 is correct but at the same time I need to define the column1 = 136, and also, I need to define that the scanning will go on vertically until the first pixel of the mask and then again it moves to the adjacent column starting from row 123 and down, etc, until it reaches the 548 column

[Stelios Fanourakis]

Would it be like this?

row1 = 123; % Whatever...
s = zeros(1, columns); % Initialize sums for every column.
for col = 136 : 548
    row2 = find(mask(:, col), 1, 'last'); % Get bottom row of mask
    if ~isempty(row2)
        % Get the sum from row1 to row2
        s(col)  = sum(grayImage(row1:row2, col));
    end
end

Still I dont get the plot

[Stelios Fanourakis]

Image Analyst, although I use this code, still I don't get a plot graph. Might you know why?

row1 = 123; % Whatever...
s = zeros(1, columns); % Initialize sums for every column.
for col = 136 : 548
    row2 = find(mask(:, col), 1, 'last'); % Get bottom row of mask
    if ~isempty(row2)
        % Get the sum from row1 to row2
        s(col)  = sum(rgbImage(row1:row2, col));
    end
end
    

horizontalProfile = s(col); % Sum vertically.
plot(horizontalProfile, 'b-', 'LineWidth', 2);
xlabel('Column', 'FontSize', 20);
ylabel('Sum of gray levels in column', 'FontSize', 20);

[Stelios Fanourakis]

Moreover, I get the lines of

Columns 10553 through 10556
                       138                       138                       138                       138
                       130                       129                       128                       127
  Columns 10557 through 10560
                       138                       138                       138                       138
                       126                       125                       124                       123
>> 

The image is 640 X 640 pixels. Why I get columns of 10553 - 10556??

[Image Analyst]

Attach ALL of the code, especially how mask was calculated, and the original image.

Also rgbImage should take 3 indexes, not just two like you have.

[Stelios Fanourakis]

It's actually a code you gave me earlier

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 16;
%===============================================================================
% Get the name of the image the user wants to use.
baseFileName = 'A2.jpg';
folder = pwd;
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
%=======================================================================================
% Read in demo image.
rgbImage = imread(fullFileName);
% Get the dimensions of the image.
[rows, columns, numberOfColorChannels] = size(rgbImage)
% Display image.
subplot(2, 2, 1);
imshow(rgbImage, []);
impixelinfo;
axis on;
caption = sprintf('Original Color Image\n%s', baseFileName);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
hp = impixelinfo(); % Set up status line to see values when you mouse over the image.
% 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')
drawnow;
% Extract the individual red, green, and blue color channels.
redChannel = rgbImage(:, :, 1);
greenChannel = rgbImage(:, :, 2);
blueChannel = rgbImage(:, :, 3);
% get a mask for the red line.
mask = redChannel > greenChannel;
% Display the image.
subplot(2, 2, 2);
imshow(mask);
caption = sprintf('Color Segmentation Mask Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
axis('on', 'image');
drawnow;
% fill holes.
mask = imfill(mask, 'holes');
% Take the largest blob only.
mask = bwareafilt(mask, 1);
% Shrink two layers of pixels to come inside the red lines.
mask = imerode(mask, true(5));
% Display the image.
subplot(2, 2, 3);
imshow(mask);
title('Final Mask', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
axis('on', 'image');
% Get a masked image.
% Mask the image using bsxfun() function to multiply the mask by each channel individually.
maskedRgbImage = bsxfun(@times, rgbImage, cast(mask, 'like', rgbImage));
% Display the image.
subplot(2, 2, 4);
imshow(maskedRgbImage);
title('Masked RGB Image', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
axis('on', 'image');
figure
A=contour(mask,'b')
set(gca,'ydir','reverse')

conversion=0.9183; % in mm/pixel
addMM=@(x) sprintf('%.3fmm',x*conversion);
xticklabels(cellfun(addMM,num2cell(xticks'),'UniformOutput',false));
yticklabels(cellfun(addMM,num2cell(yticks'),'UniformOutput',false));
    
   
row1 = 123; % Whatever...
s = zeros(1, columns); % Initialize sums for every column.
for col = 136 : 548
    row2 = find(mask(:, col), 1, 'last'); % Get bottom row of mask
    if ~isempty(row2)
        % Get the sum from row1 to row2
        s(col)  = sum(rgbImage(row1:row2, col));
    end
end
    

horizontalProfile = s(136:548); % Sum vertically.
plot(horizontalProfile, 'b-', 'LineWidth', 2);
xlabel('Column', 'FontSize', 20);
ylabel('Sum of gray levels in column', 'FontSize', 20);


% Tell user the answer.
message = sprintf('Done!');
uiwait(helpdlg(message));

At the horizontalProfile when I have it = s(col) I don't get anything, but when I put s(136:548) I get something but am not sure if it's right (see attached image).

How can I turn the data units to pixels or real world units (mm)?

[Stelios Fanourakis]

I made a small adjustment and I got this plot. I still cannot be sure whether is correct or not. The height is ok but the width is not. I was expecting to see around 70 mm and I see around 5 mm.

[Stelios Fanourakis]

If I am about to plot 2 images and I need to find the difference between them, related to their columns pixel values. So I will eventually plot the difference among the two plots.

[Stelios Fanourakis]

I finally got it right Image Analyst. Thank you so much.

[Stelios Fanourakis]

Image Analyst, can you please give me an explanation of why the plot of the sum area is so jaggy? If you notice at the A2.jpg image I used for it, the bottom red line is smooth. Not jaggy at all.

[Image Analyst]

Because the image is noisy. It looks like that's the sum of gray levels you plotted. I also gave you code for the height of the mask, and, of course, that will be smoother.

[Stelios Fanourakis]

Can you please indicate me which code was it? I used this one.

row1 = 123; % Whatever...
s = zeros(1, columns); % Initialize sums for every column.
for col = 1 : columns
    row2 = find(mask(:, col), 1, 'last'); % Get bottom row of mask
    if ~isempty(row2)
        % Get the sum from row1 to row2
        s(col)  = sum(grayImage(row1:row2, col));
    end
end

I don't want to restrict myself only to the mask area. The rows and columns scans can also exceed the boundaries of the mask but the bottom line should be the area of the mask. Actually, the first red pixel.

Let me explain it further. The red segment area is done manually but an operator. As for the algorithm that I am trying to develop is that we don't care the upper or the side parts of the red contour, only the bottom red line area. So, I need a way for the user to define the rows,columns starting points with no respect to the red mask but we need to end where the red countour lies at the bottom. Am I clear sir Analyst?

If I don't draw the whole area, is it more understood? (See attached image)

[Image Analyst]

Did you want the counts? If so, why did you remove this line

theCounts(col) = redLines(col) - startingRow + 1;

[Stelios Fanourakis]

Yes but how can I define the rows for every red pixel? There should be a way for Matlab to detect whether it is red color and stop, proceeding to the next column starting from the same top row but next column

At your previous code part you say

% Let's say the red line is at these 3 rows:
redLines = [7, 8, 6];

It is impossible to know for every different image the exact rows where the red pixels are. There must be a way to auto trace them

[Stelios Fanourakis]

This line should work

row2 = find(mask(:, col), 1, 'last'); % Get bottom row of mask

But it doesn't, and I don't know the reason why

[Stelios Fanourakis]

If I use this

row2 = find(redChannel(:, col), 1, 'last'); % Get bottom row of mask

I get different and better results (see image) but again not the smooth curve I am looking for

[Image Analyst]

1. OK, are the red lines already in the image somehow, and you're stuck with them? They're not pure red - they're sort of red - but that could be because you're using JPG format, which is lossy, instead of PNG or some other lossless format.
2. OR, is there no read but you want to ask the user to draw the interface manually, and the only reason it's red is because you then plotted a red curve there in the overlay after the user drew it.

So, which scenario is it?

I already gave you code for case #1 in a different post.

[Stelios Fanourakis]

1. It is a jpg image. The contour was drew by the user, using a vector software with red colour.
2. As I have explained earlier, I only care for the bottom red line, that is already in the image. So, I have to track the red pixels. The user will draw the red line and then the algorithm will sum the pixels until the line the user drew.

Can you please remind me the code you gave me for? As far, it is working satisfactory but I need to find why it gets so jaggy, where it should match the contour red line which is smooth. So, something goes wrong

[Image Analyst]

I think this does what you want.

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 16;

%===============================================================================
% Get the name of the image the user wants to use.
baseFileName = 'A2.jpg';
folder = pwd;
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

%=======================================================================================
% Read in demo image.
rgbImage = imread(fullFileName);
% Get the dimensions of the image.
[rows, columns, numberOfColorChannels] = size(rgbImage)
% Display image.
subplot(2, 3, 1);
imshow(rgbImage, []);
impixelinfo;
axis on;
caption = sprintf('Original Color Image\n%s', baseFileName);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
hp = impixelinfo(); % Set up status line to see values when you mouse over the image.
% 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')
drawnow;

%===================================================================================
% FIND THE RED MASK
% Extract the individual red, green, and blue color channels.
redChannel = rgbImage(:, :, 1);
greenChannel = rgbImage(:, :, 2);
blueChannel = rgbImage(:, :, 3);
% get a mask for the red line.
mask = redChannel > greenChannel;
% Display the image.
subplot(2, 3, 2);
imshow(mask);
caption = sprintf('Color Segmentation Mask Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
axis('on', 'image');
drawnow;
% fill holes.
mask = imfill(mask, 'holes');
% Take the largest blob only.
mask = bwareafilt(mask, 1);
% Shrink two layers of pixels to come inside the red lines.
mask = imerode(mask, true(5));
% Display the image.
subplot(2, 3, 3);
imshow(mask);
title('Final Mask', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
axis('on', 'image');
% Get a masked image.
% Mask the image using bsxfun() function to multiply the mask by each channel individually.
maskedRgbImage = bsxfun(@times, rgbImage, cast(mask, 'like', rgbImage));
% Display the image.
subplot(2, 3, 4);
imshow(maskedRgbImage);
title('Masked RGB Image', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
axis('on', 'image');

% A = contour(mask,'b');
set(gca,'ydir','reverse')
conversion = 0.9183; % in mm/pixel
addMM = @(x) sprintf('%.3fmm', x * conversion);
xticklabels(cellfun(addMM, num2cell(xticks'), 'UniformOutput', false));
yticklabels(cellfun(addMM, num2cell(yticks'), 'UniformOutput', false));
    
%===================================================================================
% FIND THE HEIGHT OF THE MASK, AND SUM OF GRAY LEVELS FROM ROW 1 TO RED ROW.
topRow = 1; % Whatever you want.
grayLevelSum = zeros(1, columns); % Initialize sums for every column.
heights = zeros(1, columns); % Initialize heights for every column.
% Find the left and right column of the mask so we know where to sum over.
[rows, columns] = find(mask);
col1 = min(columns);
col2 = max(columns);
for col = col1 : col2
    row2 = find(mask(:, col), 1, 'last'); % Get bottom row of mask
    if ~isempty(row2)
        % Get the sum in the GREEN channel, from row1 to row2.
        grayLevelSum(col)  = sum(greenChannel(topRow:row2, col));
		% Compute the height of the mask at every column.
		heights(col) = sum(mask(topRow:row2, col));
    end
end
    
% Plot integrated gray level.
subplot(2, 3, 5);
plot(grayLevelSum, 'b-', 'LineWidth', 2);
xlabel('Column', 'FontSize', 20);
ylabel('Sum of gray levels in column', 'FontSize', 20);
title('Sum of gray levels in column', 'FontSize', 20);
grid on;
% Plot heights
subplot(2, 3, 6);
plot(heights, 'b-', 'LineWidth', 2);
xlabel('Column', 'FontSize', 20);
ylabel('Height of mask in column', 'FontSize', 20);
title('Mask Height vs. Column', 'FontSize', 20);
grid on;

% Tell user the answer.
message = sprintf('Done!');
uiwait(helpdlg(message));