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

[Zachary Pincus]

> Out of curiosity - could you post info about the compiler and compile 
> flags
> that you used on your G4?

I compiled both ITK and my project with GCC 3.3 (using c++, not g++).
Here's the "c++ -v" info: gcc version 3.3 20030304 (Apple Computer, 
Inc. build 1495)

The cmake flags I set for ITK were to compile as shared libs, and the 
build style was RelWithDebInfo. I didn't mess with the default flags 
for this.
Additionally, I compiled my project with both Debug and RelWithDebInfo 
settings, which didn't seem to make much difference.

Do you think I have drastically hindered the ITK/VNL performance with 
these compiler settings? Or might my problems lie elsewhere?

Thanks so much,
Zach


>
>> -----Original Message-----
>> From: Zachary Pincus [mailto:zpincus@stanford.edu]
>> Sent: Friday, May 14, 2004 12:20 AM
>> To: ITK
>> Subject: [Insight-users] PCAShapeModelEstimator -- seems way too slow?
>>
>> 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
>>
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