how to find volume in the region of interst made by imfreehand
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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
Accepted Answer
Image Analyst
on 28 Aug 2013
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
Image Analyst
on 29 Aug 2013
Area by the slice THICKNESS not slice NUMBER.
Image Analyst
on 30 Aug 2013
There's not really much to go on but I'd guess that the size of binaryImage does not match the size of grayImage. How many rows and columns does each have?
Muhammad
on 30 Aug 2013
Image Analyst
on 30 Aug 2013
Maybe grayImage is really color. What does this say:
size(grayImage)
size(binaryImage) % Don't use semicolons so it will print to window.
Image Analyst
on 30 Aug 2013
What did the size() functions report to you in the command window???????
Muhammad
on 30 Aug 2013
Image Analyst
on 30 Aug 2013
I know you need my help - that's why I offered it but you're confusing me when I tell you to do something - twice! - and you don't do it. Why didn't you put the size commands in there like I told you to (twice)????? In other words, why did you not have this code in your program:
size(grayImage)
size(binaryImage) % Don't use semicolons so it will print to window.
measurements = regionprops(binaryImage, grayImage, 'Centroid', 'Perimeter', 'Area', 'WeightedCentroid');
Please tell me why you are refusing to put that code in there like I instructed, when you know that I need that information to help you. Don't just tell me the error again. I've already seen it three times and don't need to see it a fourth time.
Muhammad
on 31 Aug 2013
Image Analyst
on 31 Aug 2013
Aha! See, what you call "grayImage" is not really gray. It's color, because the third number, the number of color channels, is 3. You need to decide what to do about that, such as take the green channel, or call rgb2gray() or whatever.
Image Analyst
on 3 Sep 2013
Tiff is the format on disk and has nothing to do with what you have in your program. Once it's in the program, it's a 3D array of numbers. You have to use rgb2gray after that, which you're not doing yet.
Muhammad
on 4 Sep 2013
Image Analyst
on 4 Sep 2013
The coordinates are in the xy array.
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