How to make the ROI show on top of the image after drawing ROI with roipoly?

Hi, Guys,

I draw an ROI with roipoly(). After drawing, the blue ROI will disappear. How can I display this ROI on top of the image after drawing it? Please see the following example.

im = imread('cameraman.tif');
figure(1)
imagesc(im);
axis image off; colormap gray;
title('Please Draw ROI');
% This is the image

% Draw ROI
roi=roipoly;
% During drawing ROI

% After drawing ROI (by double clicking the first point), the blue ROI disappears

My question is : How to make the ROI still display on top of the image after drawing? Many thanks!

Answer 1

[Image Analyst]

Try this:

im = imread('cameraman.tif');
imagesc(im);
axis image off; 
colormap gray;
title('Please Draw ROI');
% Draw ROI
[binaryMask, x, y] = roipoly;
hold on;
plot(x, y, 'r.-', 'MarkerSize', 15);

[YZ]

Thank you. It works.

[Michael Liu]

Hi Image Analyst,

I have a follow up question regarding this. I am using a DICOM Viewer that I found on MATLAB's File Exchange. I'm doing exactly what Yue Zhang is doing with the ROI of interest and to make the ROI stay. But as I scroll through the DICOM viewer the ROI that was previously there disappears. How do I get it to stay on the specific slice?

Thanks

[Image Analyst]

I have no idea. I have not used that utility. You'd have to contact the author or figure it out yourself. I don't even have any dicom files myself.

[Louis-Philippe Guinard]

Ieep I'll try for an extra follow-up if you'll allow me!

I have pretty much the same problem, I.E. I want to be able to display the ROI outline on the image after defining the ROI itself. The one problem I get is that my ROI-making code is in a while loop (thus allowing an arbitrary number of ROIs to be taken), and the ROI itself is multi-dimensional. Something like:

figure(1)

imshow(imaDisplay,[])

while cond == true

NbROI = NbROI+1;

ROI(:,:,1,NbROI) = roipoly; % size(ROI) should be 256x256x1xNbROI

choice = menu('Do you want to define and analyze more ROIs?','Yes','No');

if choice == 2 || choice == 0

break

end

end

I've tried putting something like [ROI(:,:,1,NbROI), xROI(:,NbROI) , yROI(:,NbROI)] = ... which works on the only condition that ALL ROIs have the same number of vertices. I do not want this to be a limitation, of course, but understand that doing so will mess up the array's shapes. How can I manage?

Thanks in advance!

[Image Analyst]

@Louis-Philippe Guinard, see my answer below. You can take the coordinates that were clicked on if you accept the 2nd and 3rd output arguments of roipoly(). Then store them for later.

% Read in gray scale image.
grayImage = imread('cameraman.tif');
% Display it.
imshow(grayImage);
axis('image', 'on');
colormap gray;
g = gcf;
g.WindowState = 'maximized';
drawnow;
% Give user instructions for how to draw the ROI:
caption = sprintf('When you see the crosshairs, left click the vertices.  Double-click the last one.\nThen adjust points if needed.  Double-click inside when all done');
title(caption);
message = sprintf('When you see the crosshairs, left click the vertices.\nDouble-click the last one.\nThen adjust points if needed.\nDouble-click inside when all done');
uiwait(helpdlg(message));
buttonText = 'OK';
promptMessage = sprintf('Do you want to draw another ROI?');
titleBarCaption = 'Continue?';
numberOfROIsDrawn = 0;
while contains(buttonText, 'OK', 'ignoreCase', true)
	% Draw ROI.  Be sure to accept the  2nd and 3rd output arguments, which are the coordinates you clicked on.
	[thisBinaryImage, xPerimeter, yPerimeter] = roipoly;
	numberOfROIsDrawn = numberOfROIsDrawn + 1;
	% Include this ROI in the overall mask.
	if numberOfROIsDrawn == 1
		binaryImage = thisBinaryImage;
	else
		binaryImage = binaryImage | thisBinaryImage;
	end
	% Save these coordinates into an array of all of them.
	x{numberOfROIsDrawn} = xPerimeter;
	y{numberOfROIsDrawn} = yPerimeter;
	% The ROI disappeared, so draw perimeter onto original image using xPerimeter and yPerimeter.
	hold on
	plot(xPerimeter, yPerimeter, 'b.-', 'LineWidth', 2, 'MarkerSize', 15);
	buttonText = questdlg(promptMessage, titleBarCaption, 'OK', 'Quit', 'OK');
	if contains(buttonText, 'Quit', 'IgnoreCase', true)
		break;
	end
end
% Show them in the command window
celldisp(x);
celldisp(y);
% Show the binary image.
figure;
imshow(binaryImage);
fprintf('Done running %s.m\n', mfilename);

[Louis-Philippe Guinard]

As far as delimiting and displaying the ROIs go, your code works wonders. However, for what I need, it might not work as well.

Going back to the line where I define ROIs, I wrote:

ROI(:,:,1,NbROI) = roipoly;

This was meant to have a variety of ROIs that I could calculate stuff upon, and later come back to display the images with said ROIs outlined. Your code seems to overwrite them at every next ROI I define. That said, I could theoretically fit the rest of my code in-between, but this would make for a very awkward way of making my code work. Ideally I'd like this to be a function that serves the only purpose of defining the ROIs, applying the ROI mask on my image and save the outlines for later display.

That said, here is my full function as was written before, if it might help you understand where I'm going:

function [imaROI,imaROItot] = GenerateROImasks(NbROI,cond,imaDisplay,imaCorrected)

% Function from part 5. Generates the ROI masks to be analyzed separately.

figure(1)

imshow(imaDisplay,[])

while cond == true

NbROI = NbROI+1;

ROI(:,:,1,NbROI) = roipoly;

choice = menu('Do you want to define and analyze more ROIs?','Yes','No');

if choice == 2 || choice == 0

break

end

end

imaROItot = zeros(size(ROI));

for ROIiter = 1:size(ROI,4)

imaROI(:,:,:,ROIiter) = ROI(:,:,1,ROIiter).*imaCorrected;

imaROItot = sum(imaROI,3);

end

end

...from there onwards I do calculations using the output of my function, in which each ROI is to be analyzed separately. At the end, I display various graphs for each ROI, but I'd want to be included in these subplots the starting image with the ROI corresponding to these graphs. I would then add the xPerimeter and yPerimeter to my outputs.

Sorry if my initial question wasn't precise enough! Also, thanks for your patience :)

[Image Analyst]

Not sure exactly what you're asking. The ROI coordinates are saved at each iteration. They're not overwritten. I don't store all the binary images individually, but if you want to store those too, you can simply do

masks{numberOfROIsDrawn} = thisBinaryImage;

Feel free to modify my code to get it to do exactly what you want.

Answer 2

[Image Analyst]

Try this:

% Read in gray scale image.
grayImage = imread('cameraman.tif');
% Display it.
imshow(grayImage);
axis('image', 'on'); 
colormap gray;
g = gcf;
g.WindowState = 'maximized';
drawnow;
% Give user instructions for how to draw the ROI:
caption = sprintf('When you see the crosshairs, left click the vertices.  Double-click the last one.\nThen adjust points if needed.  Double-click inside when all done');
title(caption);
message = sprintf('When you see the crosshairs, left click the vertices.\nDouble-click the last one.\nThen adjust points if needed.\nDouble-click inside when all done');
uiwait(helpdlg(message));
% Draw ROI.  Be sure to accept the  2nd and 3rd output arguments, which are the coordinates you clicked on.
[binaryImage, xPerimeter, yPerimeter] = roipoly;
% The ROI disappeared, so draw perimeter onto original image using xPerimeter and yPerimeter.
hold on
plot(xPerimeter, yPerimeter, 'b.-', 'LineWidth', 2, 'MarkerSize', 15); 

fprintf('Done running %s.m\n', mfilename);

[byungchan]

dude, you really should earn some money from the Matlab..

All the tips you gave us is truly helpful