[Insight-users] PCAShapeModelEstimator -- seems way too slow?

[Zachary Pincus]

Hello,

Recently, I've been doing some PCA work, and I noticed that itk's 
ImagePCAShapeModelEstimator seems to be surprisingly slow.

I have, for example, 1100 images of size 20x15 -- a pretty modest data 
set to do PCA on. Matlab (running on a 450 MHz ultrasparc-II) can 
compute the principal components on such a dataset in a few seconds, 
even when I intentionally do things in a particularly slow way.

Using the ITK PCA estimator, this same operation takes 15+ minutes on 
my personal machine (867 mhz g4). It's not a RAM or VM issue since the 
process never seems to grab more than 100 megs of RAM, and doesn't hit 
the disk at all.

This seems especially strange given the effort in the PCA class's 
implementation toward efficiency. (Though I do realize that a dataset 
such as mine with more images than pixels per image does defeat some of 
the optimizations rolled in...)

What could I possibly be doing wrong? I profiled the itk PCA code, and 
nothing looks overtly wrong -- it just seems to take way too long!

Zach Pincus

Department of Biochemistry and Program in Biomedical Informatics
Stanford University School of Medicine