I want to draw structures of interest in MRI to implement a variant of the GrowCut algorithm. What's the simple way to do this in Matlab?
MATLAB: How to draw on an image and use what I draw as segmentation seeds
image processingImage Processing Toolbox
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You can use imfreehand. Then mask your image before or after your operations with a binary image defined by imfreehand. Here is a demo if you need one:
% 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)));endclc; % 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; endendgrayImage = 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.Areacentroid = measurements.CentroidcenterOfMass = measurements.WeightedCentroidperimeter = 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 masshold 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);Try this:
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 = 22;%--------------------------------------------------------------------------------------------------------
% READ IN IMAGE
folder = pwd;baseFileName = 'image.png';% Get the full filename, with path prepended.
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; endendgrayImage = imread(fullFileName);% Get the dimensions of the image.
% numberOfColorChannels should be = 1 for a gray scale image, and 3 for an RGB color image.
[rows, columns, numberOfColorChannels] = size(grayImage);if numberOfColorChannels > 1 % It's not really gray scale like we expected - it's color.
% Use weighted sum of ALL channels to create a gray scale image.
grayImage = rgb2gray(grayImage); % ALTERNATE METHOD: Convert it to gray scale by taking only the green channel,
% which in a typical snapshot will be the least noisy channel.
% grayImage = grayImage(:, :, 2); % Take green channel.
end% Display the image.
subplot(2, 2, 1);imshow(grayImage, []);title('Original Grayscale Image', 'FontSize', fontSize, 'Interpreter', 'None');impixelinfo;hFig = gcf;hFig.WindowState = 'maximized'; % May not work in earlier versions of MATLAB.
drawnow;%--------------------------------------------------------------------------------------------------------% SEGMENTATION OF IMAGE
% Get a binary image of just the blob and not including the black background or the white surround.
mask = grayImage > 0 & grayImage < 255; %imbinarize(grayImage);
subplot(2, 2, 2);imshow(mask, []);impixelinfo;title('Initial Mask Image', 'FontSize', fontSize, 'Interpreter', 'None');impixelinfo;% Display histogram of image but only the image within the mask
subplot(2, 3, 4);histogram(grayImage(mask), 0:255);grid on;title('Histogram of gray image', 'FontSize', fontSize);% Now get the threshold
thresh = 255 * graythresh(grayImage(mask))% Put a red line there at the threshold
xline(thresh, 'Color', 'r', 'LineWidth', 2);% Get a binary image of the bright stuff
brightStuff = grayImage >= thresh & mask;subplot(2, 3, 5);imshow(brightStuff, []);impixelinfo;title('Bright Pixels in Region', 'FontSize', fontSize, 'Interpreter', 'None');impixelinfo;subplot(2, 3, 6);darkStuff = ~brightStuff & mask;imshow(darkStuff, []);impixelinfo;title('Dark Pixels in Region', 'FontSize', fontSize, 'Interpreter', 'None');impixelinfo;
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