How to ensure consistency in SIFT features?

I am working with a classification algorithm that requires the size of the feature vector of all samples in training and testing to be the same.

I am also to use the SIFT feature extractor. This is causing problems as the feature vector of every image is coming up as a different sized matrix. I know that SIFT detects variable keypoints in each image, but is there a way to ensure that the size of the SIFT features is consistent so that I do not get a dimension mismatch error.

I have tried rootSIFT as a workaround:

[~, features] = vl_sift(single(images{i}));
        double_features = double(features);
        root_it = sqrt( double_features/sum(double_features) ); %root-sift
        feats{i} = root_it;

This gives me a consistent 128 x 1 vector for every image, but it is not working for me as the size of each vector is now very small and I am getting a lot of NaN in my classification result.

Is there any way to solve this?

Using SIFT there are 2 steps you need to perform in general.

1. Extract SIFT features. These points (first output argument of size NPx2 (x,y) of your function) are scale invariant, and should in theory be present in each different image of the same object. This is not completely true. Often points are unique to each frame (image). These points are described by 128 descriptors each (second argument of your function).
2. Match points. Each time you compute features of a different image the amount of points computed is different! Lots of them should be the same point as in the previous image, but lots of them WON'T. You will have new points and old points may not be present any more. This is why you should perform a feature matching step, to link those points in different images. usually this is made by knn matching or RANSAC. You can Google how to perform this task and you'll have tons of examples.

After the second step, you should have a fixed amount of points for the whole set of images (considering they are images of the same object). The amount of points will be significantly smaller than in each single image (sometimes 30~ times less amount of points). Then do whatever you want with them!

Hint for matching: http://www.vlfeat.org/matlab/vl_ubcmatch.html

UPDATE:

You seem to be trying to train some kind of OCR. You would need to probably match SIFT features independently for each character.

How to use vl_ubcmatch:

[~, features1] = vl_sift(I1);
[~, features2] = vl_sift(I2);

matches=vl_ubcmatch(features1,features2)