I am trying to classify MRI images of brain tumors into benign and malignant using C++ and OpenCV. I am planning on using bag-of-words (BoW) method after clustering SIFT des
Here is the link to the actual paper, http://www.csd.uwo.ca/~olga/Courses/Fall2014/CS9840/Papers/lazebnikcvpr06b.pdf
MATLAB code is provided here http://web.engr.illinois.edu/~slazebni/research/SpatialPyramid.zip
Co-ordinate histogram (mentioned in your post) is just a sub-region in the image in which you compute the histogram. These slides explain it visually, http://web.engr.illinois.edu/~slazebni/slides/ima_poster.pdf.
You have multiple histograms here, one for each different region in the image. The probability (or the number of items would depend on the sift points in that sub-region).
I think you need to define your pyramid kernel as mentioned in the slides.
A Convolutional Neural Network may be better suited for your task if you have enough training samples. You can probably have a look at Torch or Caffe.