Hi Kenlo, Thanks for your email.
`np.nan` is only defined for floating point images, but GLCM only works for non-negative integer images, since the intensity values need to serve as indices to a matrix. Therefore, in order to ignore NULL values, you just need to create an array with an arbitrary value as NULL. This is actually not too hard. If you start with a uint8 image, make a uint16 image with a mask where values to be ignored are set to 256. Then, use greycomatrix with levels=257. Finally, from the documentation: > The grey-level co-occurrence histogram. The value > `P[i,j,d,theta]` is the number of times that grey-level `j` > occurs at a distance `d` and at an angle `theta` from > grey-level `i`. Thus you can get your odd-shaped GLCM, ignoring values outside your mask, with: out = greycomatrix(image, […], levels=257) result = out[:256, :256] I hope this helps! If you have suggestions for making this process easier, please let us know! Juan. On 7 Sep 2017, 11:23 AM +1000, NASAHARA Kenlo <24dake...@gmail.com>, wrote: > Dear scikit-image community: > > I am trying GLCM functions in scikit-image. > http://scikit-image.org/docs/dev/auto_examples/features_detection/plot_glcm.html > > I wonder whether they can treat images with irregular > shapes, such as a circle, an oval, or some more complex > forms (not only rectagle). > > In the "greycomatrix", function: > > def greycomatrix(image, distances, angles, levels=None, symmetric=False, > normed=False): > > image : array_like > Integer typed input image. Only positive valued images are supported. > If type is other than uint8, the argument `levels` needs to be set. > > the "image" seems to be required to be a rectangle. > > If NAN or NULL values are allowed in the "image", and the function skips > treating those "no-data" pixels assigned with NAN or NULL, then we > may be able to treat any shapes of image, by filling the pixels outside the > boudary with NAN or NULL. > > However, in the source code of "_glcm_loop" function > (https://searchcode.com/codesearch/view/83509141/), all the pixels > within the rectangular image are scanned, without permitting "no-data". > > My questions: > 1. Do you know how to treat GLCM in non-rectangular image with > scikit-image? > 2. If not, do you know any other ways to do that instead of scikit-image? > 3. Do you think it is a reasonable idea to change GLCM functions in > scikit-image so that they can treat no-data (allowing NAN or NULL)? > > -- > Kenlo Nishida Nasahara > Faculty of Life and Environmental Sciences > University of Tsukuba, Japan 305-8572 > 24dake...@gmail.com > _______________________________________________ > scikit-image mailing list > scikit-image@python.org > https://mail.python.org/mailman/listinfo/scikit-image
_______________________________________________ scikit-image mailing list scikit-image@python.org https://mail.python.org/mailman/listinfo/scikit-image
