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how to find volume in the region of interst made by imfreehand

Asked by Muhammad on 28 Aug 2013
Dearc All
Hope you are keeping good. i can made a region of interst (ROI) by imfreehand. can anybody help me to suggest that how can i find the volume of that region made by imfreehand???? i am giving a code here too
if true
% % --- Executes just before JP is made visible.
function JP_OpeningFcn(hObject, eventdata, handles, varargin)
handles.output = hObject;
handles.files=dir(fullfile('C:', 'Users','khanm', 'Desktop','image files\*.jpg'));
for i = 1 : length(handles.files)
handles.X{i}= imread(fullfile('C:', 'Users','khanm', 'Desktop','image files',handles.files(i).name));
end
imshow(handles.X{1},[]);
handles.index = 1;
Cek(hObject, eventdata, handles);
guidata(hObject, handles);
% UIWAIT makes JP wait for user response (see UIRESUME) % uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line. function varargout = JP_OutputFcn(hObject, eventdata, handles) % varargout cell array for returning output args (see VARARGOUT); % hObject handle to figure % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure varargout{1} = handles.output;
% --- Executes on button press in pushbutton1. function pushbutton1_Callback(hObject, eventdata, handles) handles.output = hObject; handles.index = handles.index - 1; Cek(hObject, eventdata, handles); imshow(handles.X{handles.index},[]); guidata(hObject, handles);
% --- Executes on button press in pushbutton2. function pushbutton2_Callback(hObject, eventdata, handles) handles.output = hObject; handles.index = handles.index + 1; Cek(hObject, eventdata, handles); imshow(handles.X{handles.index},[]); imfreehand
function Cek(hObject, eventdata, handles) handles.output = hObject; n = length(handles.files); if handles.index > 1, set(handles.pushbutton1,'enable','on'); else set(handles.pushbutton1,'enable','off'); end if handles.index < n, set(handles.pushbutton2,'enable','on'); else set(handles.pushbutton2,'enable','off'); end guidata(hObject, handles);
end
any appriciation is regarded in advnace.
Muhammad isa

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1 Answer

Answer by Image Analyst
on 28 Aug 2013
 Accepted Answer

See my demo:
% 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.
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));
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 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\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);

  19 Comments

Actually i am new in MATLAB. so, i took time to understand. Sorry for that. one more question please. i have 55 images. i want to show those all one by one in Axis of GUI using slider or using 2 pushbuttons (forward and backward) and want to use this part (given below) of code to calculate just area (which i contour with freehand tool).i made the GUI prog with 2 pushbuttons which i told in my first mail.How can i change in that prog (which i sent in my first mail)to get the results i stated using this part given below.
if true
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('C:\Users\khanm\Desktop\image files');
baseFileName = '004.jpg';
% 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); GrayImage=rgb2gray(grayImage); measurements = regionprops(binaryImage, GrayImage, ... 'area'); area = measurements.Area
end
ya i done that i said in my last post. can we calculate the cpprdinate values of area? means its x nad y values?
The coordinates are in the xy array.

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