Creating masks of open lines with imfreehand and impoly ROI tools

With both the imfreehand and impoly tools one can set the 'Closed' line property to false which allows for the creation of open non straight lines. Surprisingly, masks created with these tools using createMask are always closed even when the 'Closed' property is set to false. This appears to be a bug?

I would like to create masks of non straight lines which precludes using the imline tool. Any suggestions on how to achieve this given the stated issues with the imfreehand and impoly tools? Thanks for any assistance.

Answer 1

[Teja Muppirala]

If I understand you correclty, you want to create an image of the line, without closing the curve. That's certainly doable.

I = imread('peppers.png');
imshow(I);
M = imfreehand(gca,'Closed',0);
F = false(size(M.createMask));
P0 = M.getPosition;

D = round([0; cumsum(sum(abs(diff(P0)),2))]); % Need the distance between points...
P = interp1(D,P0,D(1):.5:D(end)); % ...to close the gaps
P = unique(round(P),'rows');
S = sub2ind(size(I),P(:,2),P(:,1));
F(S) = true;
figure;
imshow(F);

[Neil]

Works beautifully! Filling in the gaps thru interpolation is clever. Would never have thought of that myself. I learned about a few new useful Matlab functions from your code. Thanks Teja.

[Image Analyst]

So are you still going to put in your change request to the Mathworks for how you want the .createMask() method to work? Or is this workaround fine?

[Neil]

I actually tried to put one in yesterday but couldn't. I think that createMask should logically respect the prior properties set with imfreehand and impoly so I will submit a change request for a future update.

[Neil]

When I use Teja's code on a small image (56x59 pixels) I get the following message:

_|Error using griddedInterpolant. The point coordinates are not sequenced in strict monotonic order.

Error in interp1>Interp1D (line 335) F = griddedInterpolant(X,V(:,1),method); | _

I think this has to do with the fact the small image is automatically zoomed for display and therefore interpolated. This appears to trip the call to interp1 in Teja's code. I think making the onscreen axis pixel size the same size as the image might take care of the problem but then I wouldn't really be able to see the image. Any help on how to use | interp1| on zoomed images?

Answer 2

[Image Analyst]

A mask is an area. If you want lines as a mask, like just a one pixel wide path, then you'd have to set those pixels from the x,y coordinates that those functions return. If you want non-straight "lines" then use imfreehand to draw curves of arbitrary shape. Why do you want a "mask" of just a single pixel wide path anyway? You have the coordinates so why do you now need a binary image of those coordinates?

[Neil]

I have images where I can not easily separate some binary objects using techniques such as watershed etc. So I am resorting to just drawing lines between objects I want to split. Generating a binary of the lines using existing tools would be easiest (I'm new to Matlab and not an expert at writing code). One issue is that the x,y positions returned by imfreehand are not in the ordinal units used for image coordinates. If I round the x,y coordinates provided by imfreehand I end up with a line/curve which has significant gaps and is not identical to that generated initially by imfreehand. Using impoly might be a little better since this essentially just puts together a series of small lines to generate a curve/line. But this still requires code to get the end result whereas if the createMask function worked as it should on open impoly or imfreehand lines then my issues would be taken care of without any additional coding on my part.

[Image Analyst]

Neil, see my demo below. Pay particular attention to the imline parts where I create a mask and burn it into the image.

% Demo to write an ellipse and a line into the overlay of an image,
% and then to burn those overlays into the image.

%----- Initializing steps -----
% Clean up
clc;
clear all;
close all;
workspace; % Display the workspace panel.

hasIPT = license('test', 'image_toolbox');
if ~hasIPT
  % User does not have the toolbox installed.
  message = sprintf('Sorry, but you do not seem to have the Image Processing Toolbox.\nDo you want to try to continue anyway?');
  reply = questdlg(message, 'Toolbox missing', 'Yes', 'No', 'Yes');
  if strcmpi(reply, 'No')
    % User said No, so exit.
    return;
  end
end

% Display images to prepare for the demo.
monochromeImage = imread('pout.tif');
subplot(2, 4, 1);
imshow(monochromeImage);
title('Original Image');
subplot(2, 4, 2);
imshow(monochromeImage);
title('Original Image with ellipse in overlay');
subplot(2, 4, 5);
imshow(monochromeImage);
title('Original Image');
subplot(2, 4, 6);
imshow(monochromeImage);
title('Original Image with line in overlay');
set(gcf, 'units','normalized','outerposition',[0 0 1 1]); % Maximize figure.
set(gcf,'name','Demo by ImageAnalyst','numbertitle','off') 

%----- Burn ellipse into image -----
% Create elliptical mask, h, as an ROI object over the second image.
subplot(2, 4, 2);
hEllipse = imellipse(gca,[10 10 50 150]); % Second argument defines ellipse shape and position.
% Create a binary image ("mask") from the ROI object.
binaryImage = hEllipse.createMask();
% Display the ellipse mask.
subplot(2, 4, 3);
imshow(binaryImage);
title('Binary mask of the ellipse');
% Let's try to add some text.  (Doesn't work)
% hText = text(50, 100, 'Line of Text');
% textMask = hText.createMask();
% binaryImage = binaryImage & textMask;
% imshow(binaryImage);
% Burn ellipse into image by setting it to 255 wherever the mask is true.
monochromeImage(binaryImage) = 255;
% Display the image with the "burned in" ellipse.
subplot(2, 4, 4);
imshow(monochromeImage);
title('New image with ellipse burned into image');

%----- Burn line into image -----
burnedImage = imread('pout.tif');
% Create line mask, h, as an ROI object over the second image in the bottom row.
subplot(2, 4, 6);
hLine = imline(gca,[10 100],[10 100]); % Second argument defines line endpoints.
% Create a binary image ("mask") from the ROI object.
binaryImage2 = hLine.createMask();
% Display the line mask.
subplot(2, 4, 7);
imshow(binaryImage2);
title('Binary mask of the line');
% Burn line into image by setting it to 255 wherever the mask is true.
burnedImage(binaryImage2) = 255;
% Display the image with the "burned in" line.
subplot(2, 4, 8);
imshow(burnedImage);
title('New image with line burned into image');

[Neil]

Image Analyst, thanks for your response. Your code describes the process I have been trying to achieve, however, it does not address my initial question. If I do exactly what you have written in your code with the imfreehand tool or the roipoly tool with the 'Closed' parameter set to false, in order to force a line and not a closed shape, I still end up with a mask where the createMask function does not respect the 'Closed' parameter setting. I get a mask not of the open line that I initially created but a closed mask which is no longer a line. I want to achieve something akin to imfreehand.createMask('Closed',false).

I do not wish to use the imline tool to create the mask since I will be computing object shape parameters from my binary and using straight lines for splitting objects will in some cases introduce too much shape distortions to objects.

So, my initial problem remains unsolved.

[Image Analyst]

My very first responses addressed your initial questions. I said basically, that's not how they work. Then I gave you two workarounds (imline, with demo code, and imfreehand) to do what you want to do. So you can either do one of the workarounds and move on, or put in a feature request with the Mathworks and wait for some version in the future that may do it the way you think it should work.

You can try this imfreehand code below, but be aware that imfreehand doesn't give adjacent coordinates, particularly if you draw fast, so in that case you might have to us imline anyway (in between the coordinates that imfreehand gives you) to make sure there are no gaps in the drawn curve.

% Demo to have the user freehand draw an irregular shape over
% a gray scale image, and burn the curve points into the image.

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 = int32(hFH.getPosition);

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

% Display the freehand mask just for fun - we won't use binaryImage.
binaryImage = false(size(grayImage));
linearIndexes = sub2ind(size(grayImage), xy(:, 2), xy(:, 1));
binaryImage(linearIndexes) = true;
subplot(2, 2, 2);
imshow(binaryImage);
axis on;
title('Binary mask of the region', 'FontSize', fontSize);

% Display it.
subplot(2, 2, 3);
grayImage(linearIndexes) = 255;
imshow(grayImage);
axis on;
title('Grayscale Image with freehand curve burned in', 'FontSize', fontSize);

[Neil]

Thanks again for your response Image Analyst. I had tried, almost identically, the various solutions you proposed prior to posting my question. These solutions did not satisfy the specific needs I outlined. I was hoping that there might be another simple solution so I'll just move on.

If anyone else has other ideas as to how I could achieve my specific objectives I'd be glad to hear it.