Several readers commented on my recent roipoly and poly2mask posts, and I wanted to follow up on a couple of issues they raised. The first issue is a common point of confusion about the selection of rectangular regions, and the second is how to access and modify pixels contained within a region of interest.
Contents
Rectangular regions
Users sometimes wonder why poly2mask and roipoly don't return some of the boundary pixels of a rectangular region as part of the mask. Here's an example.
x = [2 4 4 2 2]; y = [2 2 4 4 2]; mask = poly2mask(x, y, 5, 5)
mask =
0 0 0 0 0
0 0 0 0 0
0 0 1 1 0
0 0 1 1 0
0 0 0 0 0
Some users expect rows 2 through 4 and columns 2 through 4 to be included in the mask. One reader commented that he uses a different function instead of roipoly because of this behavior.
As I have illustrated in my previous posts, roipoly and poly2mask treat a pixel not as a point, but as a unit square area. The upper-left corner of the (2,2) pixel is (1.5,1.5), and the lower-right corner is (2.5,2.5). So the polygon defined by the x-y vertices in the example above covers only one-fourth of the (2,2) pixel.
I suggest that you get used to defining rectangles that cover complete pixel areas. Such rectangles go along pixel edges, not through pixel centers. Here's a second example to demonstrate:
xp = [1.5 4.5 4.5 1.5 1.5]; yp = [1.5 1.5 4.5 4.5 1.5]; maskp = poly2mask(xp, yp, 5, 5)
maskp =
0 0 0 0 0
0 1 1 1 0
0 1 1 1 0
0 1 1 1 0
0 0 0 0 0
Now the "mystery" is completely removed about which border rows and columns are in the mask. There's no need to use some other function.
Logical indexing
Another reader asked how to get and modify pixels inside a region of interest. One nice way to do that in MATLAB is to use logical indexing. The expression A(B), if B is logical and the same size as A, selects all the elements in A corresponding to the true elements of B.
I'll demonstrate using an example mask from the roipoly documentation.
clear
I = imread('eight.tif');
imshow(I)
c = [222 272 300 270 221 194]; r = [21 21 75 121 121 75]; mask = roipoly(I,c,r); imshow(mask)
If you use whos or look in the workspace browser, you can see that mask is a logical matrix.
whos
Name Size Bytes Class Attributes I 242x308 74536 uint8 c 1x6 48 double mask 242x308 74536 logical r 1x6 48 double
The expression I(mask) is a column vector containing all the elements of I corresponding to the true values of mask. Here, for example, is how you would compute the mean of the pixels inside the region of interest:
mean(I(mask))
ans = 156.0468
You can use logical indexing on the left-hand side of an assignment as well.
I2 = I;
I2(mask) = 255 - I(mask); % Or imcomplement(I(mask)).
imshow(I2)
Here's a documentation link for logical indexing. Or you might be interested in this MATLAB Digest article that Loren and I wrote about MATLAB indexing.
Get
the MATLAB code
Published with MATLAB® 7.3
Thank you. :)
thank you som uch. it is very informative and useful.
Thank you! But how to decompose the mask to make it work with the decomposed image??
Andy—What’s a decomposed image?
I want to create a mask which contains a ROI.Just like things in JPEG2000,how to create a mask with a given region of interest.the mask should contain all the coefficents in every subband in the wavelet domain.
thank u!
Andy—A mask is just a binary image. The set of nonzero pixels in the mask defines the region of interest. You can create the mask however you like.
Respected Sir
I have gone through above said matlab based commend line. I thiunk its based on only two dimentional image. But how can I made the things for medical (3-D) images.Please give your suggestion.
With warm regards from
SYED ABDAHEER
Syed—For a logical indexing expression A(D), D has to match the size of A. If you have a 2-D logical mask and are working with 3-D data, then you either have to replicate the mask along the third dimension, or you have to work with the data one plane at a time.
Nice explanation, thank you.
if the ROI is a rectangle (axis not verticle), and if we wish to see it in a verticle rectanglular box by using imshow, how to proceed?
how to assign this extracted rectangular ROI to another vertical rectangle? since the indices of mask follow lower to higher column values, not according to the directions of the polygon to be extracted.
Subama—I don’t understand your question.
Hi, Steve,
I am very thankful for your nice explanation. I would like to ask you a question. when we use roipoly and then figure pops up. After that we have option to select region of interest by selecting vertices on figure by mouse. The question is what I should to to save the part of image which I select by mouse.
Thank you so much for your time and consideration.
I am sorry. I mean how I can exract and save the part of image which I select by mouse.
Ilyas—The post you commented on explains how to use the mask returned by roipoly to extract the image pixel values that are inside the polygon. If you have a truecolor (M-by-N-by-3) image, though, you’ll need to use separate logical indexing expressions for each color component, like this: