How do I create a sub image of a larger image?

I have two vectors which define the x and y coordinates of the vertices of a convex polygon. For example:

L = linspace(0,2.*pi,6); xv = cos(L)';yv = sin(L)';
xv = [xv ; xv(1)]; yv = [yv ; yv(1)];

Given an image, I want to display only the part of the image that is inside this polygon. What is the way to do it?

Answer 1

[Image Analyst]

I have a masking demo if you want to see it. It blackens outside the ROI. Do you want that, or you want the bounding box cropped out?

[Charles]

That is probably what I am looking for. I want to study the inside of the polygon. Where do I find the masking demo please?

[Image Analyst]

Actually, my demo does it both ways:

% 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.
% Also calculates the perimeter, centroid, and center of mass (weighted centroid).

% 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.
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();
xy = hFH.getPosition;

% Now make it smaller so we can show more images.
subplot(2, 3, 1);
imshow(grayImage, []);
axis on;
drawnow;
title('Original Grayscale Image', 'FontSize', fontSize);

% Display the freehand mask.
subplot(2, 3, 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, 3, 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 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);
axis on;
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);
axis on;
title('Masked Outside Region', 'FontSize', fontSize);
% Calculate the mean
meanGL = mean(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 do the same but blacken inside the region.
insideMasked = grayImage;
insideMasked(binaryImage) = 0;
subplot(2, 3, 5);
imshow(insideMasked);
axis on;
title('Masked Inside Region', 'FontSize', fontSize);

% 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, 3, 6);
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\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, numberOfPixels1, numberOfPixels2, perimeter, ...
centroid(1), centroid(2), centerOfMass(1), centerOfMass(2));
msgbox(message);

[Image Analyst]

This did not answer your question. Put comments as "Comments", not as "Answers".

[Charles]

This is so helpful. Thank you very much!

[Image Analyst]

You're welcome. Again, this should have been a comment added under my code, not a standalone answer. Please mark my answer as Accepted to close it out.

[Amani]

I got this error when I tried your demo

Error using getimage Too many output arguments.

Error in imroi/getPixelPosition (line 60) [xdata,ydata,a] = getimage(h_im);

Error in imroi/createMask (line 259) [roix,roiy,m,n] = obj.getPixelPosition(h_im);

Error in demo (line 40) binaryImage = hFH.createMask();

what should I do ?

[Image Analyst]

This has now been added to the FAQ

[Aravind Prabhu Gopala Krishnan]

Hi Image Analyst, I need help in creating subimages of my original image. Like I have an image of size 256x256 and i want to create subimage of size 25x25 with moving window left to right 1 pixel and top to bottom 1 pixel i.e stride=1. I used mat2cell and mattiles its giving me only 11^2=121 images. Its not possible to add strides to it. Is there any way to do it?

[Image Analyst]

@Aravind Prabhu Gopala Krishnan, what do you want to do with the image once you have it? You can use conv2() or nlfilter() to move over by one pixel. Sounds like you were using blockproc(). blockproc can also move over by one pixel as I show in the attached demo. All these functions get the subimage and do something with it and return a value or subimage. In the custom function, or the main function, you can save the subimage to disk if you want. Be aware that for a 256x256 image moving over by one pixel each time you'd have 255x255 = 65025 images to save. And for what purpose? Why not just process them as you get them and discard them? Why save them?

[Aravind Prabhu Gopala Krishnan]

I have 10,000 images i cant process that much images in neural network using matlab i dont have gpu, so i have to use google colab to train the images in neural network using python.

Answer 2

[Alex Taylor]

In addition to this demo, you might also take a look at roipoly. You can use the logical image returned by roipoly as a mask.

http://www.mathworks.com/help/images/ref/roipoly.html