Crop a image using 'imfreehand' and move the cropped region to the center of black background
I've cropped an ROI with imfreehand() and plotted the center of it using mean (position of cropped region). Then I've plotted the center of completely black image. For the resulting image to have the cropped image at center of black background, is it OK to map the marked centers of both images, or get positions for moving the region manually? I want to do this for multiple images, so is it possible to apply any formula or function? Also I've attached example images and sample output. Kindly help me in this. I've tried also tried using circular shift, circshift(), for moving the cropped portion to the center of black background, but it is not working. Applying a circular shift made the ROI to move like half portion up an remaining down the center of black image. Why did it appear so? Original Image: ROI with centroid marked: Center of black image: Desired output image: Thank you and have a Good Day.
Prashant Kumar answered .
2025-11-20
It's not obvious, but you can use imwarp() instead of circshift. See this demo:
% Shifts / translates an image to the right by 500 pixels and down by 200 pixels.
% Area shifted in is black.
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;
grayImage = imread('concordorthophoto.webp');
[rows, columns, numberOfColorChannels] = size(grayImage);
subplot(1, 2, 1);
imshow(grayImage);
axis on;
title('Original Image', 'fontSize', fontSize);
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
deltaX = 500; % Shift x by 500 pixels.
deltaY = 200; % Shift y by 200 pixels.
D = zeros(rows, columns, 2);
D(:,:,1) = -deltaX; % Shift x by 500 pixels.
D(:,:,2) = -deltaY; % Shift x by 200 pixels.
warpedImage = imwarp(grayImage, D);
subplot(1, 2, 2);
imshow(warpedImage);
axis on;
title('Shifted Image', 'fontSize', fontSize);
So just mask the image in place (see demo script freehand_masking_demo.m), then do the shifting with imwarp().
% Demo to have the user freehand draw an irregular shape over a gray scale image.
% Then it creates new images:
% (1) where the drawn region is all white inside the region and untouched outside the region,
% (2) where the drawn region is all black inside the region and untouched outside the region,
% (3) where the drawn region is untouched inside the region and all black outside the region.
% It also (4) calculates the mean intensity value and standard deviation of the image within that shape,
% (5) calculates the perimeter, centroid, and center of mass (weighted centroid), and
% (6) crops the drawn region to a new, smaller separate image.
% 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 a standard MATLAB gray scale demo image.
folder = fullfile(matlabroot, '\toolbox\images\imdemos');
baseFileName = 'cameraman.tif';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~exist(fullFileName, 'file')
% File doesn't exist -- didn't find it there. Check the search path for it.
fullFileName = baseFileName; % No path this time.
if ~exist(fullFileName, '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
grayImage = imread(fullFileName);
imshow(grayImage, []);
axis on;
title('Original Grayscale Image', 'FontSize', fontSize);
set(gcf, 'Position', get(0,'Screensize')); % Maximize figure.
% Ask user to draw freehand mask.
message = sprintf('Left click and hold to begin drawing.\nSimply lift the mouse button to finish');
uiwait(msgbox(message));
hFH = imfreehand(); % Actual line of code to do the drawing.
% Create a binary image ("mask") from the ROI object.
binaryImage = hFH.createMask();
xy = hFH.getPosition;
% Now make it smaller so we can show more images.
subplot(2, 4, 1);
imshow(grayImage, []);
axis on;
drawnow;
title('Original gray scale image', 'FontSize', fontSize);
% Display the freehand mask.
subplot(2, 4, 2);
imshow(binaryImage);
axis on;
title('Binary mask of the region', 'FontSize', fontSize);
% Label the binary image and computer the centroid and center of mass.
labeledImage = bwlabel(binaryImage);
measurements = regionprops(binaryImage, grayImage, ...
'area', 'Centroid', 'WeightedCentroid', 'Perimeter');
area = measurements.Area
centroid = measurements.Centroid
centerOfMass = measurements.WeightedCentroid
perimeter = measurements.Perimeter
% 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, 4, 1); % Plot over original image.
hold on; % Don't blow away the image.
plot(x, y, 'LineWidth', 2);
drawnow; % Force it to draw immediately.
% Burn region as white 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, 4, 3);
imshow(burnedImage);
axis on;
caption = sprintf('Masked white inside region');
title(caption, 'FontSize', fontSize);
% Burn region as black into image by setting it to 255 wherever the mask is true.
burnedImage = grayImage;
burnedImage(binaryImage) = 0;
% Display the image with the mask "burned in."
subplot(2, 4, 4);
imshow(burnedImage);
axis on;
caption = sprintf('Masked black inside region');
title(caption, 'FontSize', fontSize);
% Mask the image white outside the mask, and display it.
% Will keep only the part of the image that's inside the mask, white outside mask.
whiteMaskedImage = grayImage;
whiteMaskedImage(~binaryImage) = 255;
subplot(2, 4, 5);
imshow(whiteMaskedImage);
axis on;
title('Masked white outside region', 'FontSize', fontSize);
% Mask the image outside the mask, 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, 4, 6);
imshow(blackMaskedImage);
axis on;
title('Masked black outside region', 'FontSize', fontSize);
% Calculate the mean
meanGL = mean(blackMaskedImage(binaryImage));
sdGL = std(double(blackMaskedImage(binaryImage)));
% Put up crosses at the centriod and center of mass
hold on;
plot(centroid(1), centroid(2), 'r+', 'MarkerSize', 30, 'LineWidth', 2);
plot(centerOfMass(1), centerOfMass(2), 'g+', 'MarkerSize', 20, 'LineWidth', 2);
% Now crop the image.
leftColumn = min(x);
rightColumn = max(x);
topLine = min(y);
bottomLine = max(y);
width = rightColumn - leftColumn + 1;
height = bottomLine - topLine + 1;
croppedImage = imcrop(blackMaskedImage, [leftColumn, topLine, width, height]);
% Display cropped image.
subplot(2, 4, 7:8);
imshow(croppedImage);
axis on;
title('Cropped image', 'FontSize', fontSize);
% Put up crosses at the centriod and center of mass
hold on;
plot(centroid(1)-leftColumn, centroid(2)-topLine, 'r+', 'MarkerSize', 30, 'LineWidth', 2);
plot(centerOfMass(1)-leftColumn, centerOfMass(2)-topLine, 'g+', 'MarkerSize', 20, 'LineWidth', 2);
% Report results.
message = sprintf('Mean value within drawn area = %.3f\nStandard deviation within drawn area = %.3f\nNumber of pixels = %d\nArea in pixels = %.2f\nperimeter = %.2f\nCentroid at (x,y) = (%.1f, %.1f)\nCenter of Mass at (x,y) = (%.1f, %.1f)\nRed crosshairs at centroid.\nGreen crosshairs at center of mass.', ...
meanGL, sdGL, numberOfPixels1, numberOfPixels2, perimeter, ...
centroid(1), centroid(2), centerOfMass(1), centerOfMass(2));
msgbox(message);