To calculate mean of ROI drawn using freehand tool

Is there any way to find the mean of the region of interest drawn using 'imfreehand' tool. I could get the mean if I use imcrop tool using 'mean2' syntax, but not when I use freehand tool. Your ideas are welcome.

Answer 1

[Walter Roberson]

Approximately

mean(YourImage(poly2mask(YourRoiPolygon)))

Answer 2

[Image Analyst]

Well you're in luck. Since this is a frequently asked question I have a full-blown demo all ready to go for you. Essentially it does the same as Walter's code - you'll find the line

meanGL = mean(blackMaskedImage(binaryImage));

buried in there amongst all the tutorial stuff.

% Demo to have the user freehand draw an irregular shape over
% a gray scale image, have it extract only that part to a new image,
% and to calculate the mean intensity value of the image within that shape.
% By ImageAnalyst

% Change the current folder to the folder of this m-file.
if(~isdeployed)
  cd(fileparts(which(mfilename)));
end
clc;  % Clear command window.
clear;  % Delete all variables.
close all;  % Close all figure windows except those created by imtool.
imtool close all;  % Close all figure windows created by imtool.
workspace;  % Make sure the workspace panel is showing.
fontSize = 16;

% Read in standard MATLAB gray scale demo image.
grayImage = imread('cameraman.tif');
subplot(2, 3, 1);
imshow(grayImage, []);
title('Original Grayscale Image', 'FontSize', fontSize);
set(gcf, 'Position', get(0,'Screensize')); % Maximize figure.
message = sprintf('Left click and hold to begin drawing.\nSimply lift the mouse button to finish');
uiwait(msgbox(message));
hFH = imfreehand();

% Create a binary image ("mask") from the ROI object.
binaryImage = hFH.createMask();
% Display the freehand mask.
subplot(2, 3, 2);
imshow(binaryImage);
title('Binary mask of the region', 'FontSize', fontSize);

% Calculate the area, in pixels, that they drew.
numberOfPixels1 = sum(binaryImage(:))
% Another way to calculate it that takes fractional pixels into account.
numberOfPixels2 = bwarea(binaryImage)

% Get coordinates of the boundary of the freehand drawn region.
structBoundaries = bwboundaries(binaryImage);
xy=structBoundaries{1}; % Get n by 2 array of x,y coordinates.
x = xy(:, 2); % Columns.
y = xy(:, 1); % Rows.
subplot(2, 3, 1); % Plot over original image.
hold on; % Don't blow away the image.
plot(x, y, 'LineWidth', 2);

% Burn line into image by setting it to 255 wherever the mask is true.
burnedImage = grayImage;
burnedImage(binaryImage) = 255;
% Display the image with the mask "burned in."
subplot(2, 3, 3);
imshow(burnedImage);
caption = sprintf('New image with\nmask burned into image');
title(caption, 'FontSize', fontSize);
% Mask the image and display it.
% Will keep only the part of the image that's inside the mask, zero outside mask.
blackMaskedImage = grayImage;
blackMaskedImage(~binaryImage) = 0;
subplot(2, 3, 4);
imshow(blackMaskedImage);
title('Masked Outside Region', 'FontSize', fontSize);
% Calculate the mean
meanGL = mean(blackMaskedImage(binaryImage));
% Report results.
message = sprintf('Mean value within drawn area = %.3f\nNumber of pixels = %d\nArea in pixels = %.2f', ...
meanGL, numberOfPixels1, numberOfPixels2);
msgbox(message);

% Now do the same but blacken inside the region.
insideMasked = grayImage;
insideMasked(binaryImage) = 0;
subplot(2, 3, 5);
imshow(insideMasked);
title('Masked Inside Region', 'FontSize', fontSize);

% Now crop the image.
topLine = min(x);
bottomLine = max(x);
leftColumn = min(y);
rightColumn = max(y);
width = bottomLine - topLine + 1;
height = rightColumn - leftColumn + 1;
croppedImage = imcrop(blackMaskedImage, [topLine, leftColumn, width, height]);
% Display cropped image.
subplot(2, 3, 6);
imshow(croppedImage);
title('Cropped Image', 'FontSize', fontSize);

[Justin]

Is there a simple change to make this work for a rgb MxNx3 .tif image?

I tried this:

rgb = imread('rgb.tif'); %rgb is a MxNx3 tif file

imshow(rgb);

hFH = imfreehand();

binaryImage = hFH.createMask();

meanGL = mean(rgb(binaryImage))

rect=imcrop;

avg=mean2(rect)

If I try to crop the same region as my free hand, or even an are that I know has similar intensities, avg and meanGL are not the same

[Image Analyst]

Extract each color channel one and do it one at a time on each color channel:

% Extract the individual red, green, and blue color channels.

redChannel = rgbImage(:, :, 1);

greenChannel = rgbImage(:, :, 2);

blueChannel = rgbImage(:, :, 3);

[Image Analyst]

My code will not give a green background. Justin's might but his is totally wrong. You must have done something wrong, but I can't see what it is since you didn't post any code. Start a new thread and post your code.