[Insight-users] Performance regression ImageSeriesReader? (with test)

Tue Mar 23 07:10:49 EDT 2010

I did more tests using a MR perfusion data. I chose this study because the
header of each file is big ( there are a lot of private tags).

I show you the 3 tests using the same data but with some differences. In the
first test the codification is Little Endian Implicit, in the second one the
codification is Little Endian Explicit and the last one the codification
is Little Endian Explicit too but I anonymized it by Osirix in order to
reduce the size of the headers since Osirix anonymization removes all
private tags.

Mr Perfusion data test
======================

http://dl.dropbox.com/u/3613789/perfusion_implicit_anonymized.zip
(The test crashs when the v2.8 is used. I did the test without anonymize it)

TransferSyntax: Little Endian Implicit
41,9MB
1080 Files

           Reading directory   UpdateOutputInformation
UpdateLargestPossibleRegion
Itk 2.8                 4070                         9
   4997
Itk 3.16                4096                     13096
  13655

_____________________________________________

http://dl.dropbox.com/u/3613789/perfusion_explicit_anonymized.zip

TransferSyntax: Little Endian Explicit
41,9MB
1080 Files

           Reading directory   UpdateOutputInformation
UpdateLargestPossibleRegion
Itk 2.8                15439                        32
  17106
Itk 3.16               15510                     16049
  16770

_______________________________________________

http://dl.dropbox.com/u/3613789/perfusion_anonymized_osirix.zip
Anonimized by Osirix. All private tags were removed.

TransferSyntax: Little Endian Explicit
36,9MB
1080 Files

           Reading directory   UpdateOutputInformation
UpdateLargestPossibleRegion
Itk 2.8                 3823                         8
   4590
Itk 3.16                3850                      4901
   5332

Roger

On Tue, Mar 23, 2010 at 4:20 AM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

> Brad,
>
> It looks like the meta data array is populated in both the
> GenerateOutputInformation and GenerateData. Also all slices are
> processed in GenerateOutputInformation. In 2.8, only 2 slices were
> processed.
>
> Why were these changes made? We are also seeing bad dicom performance
> in Slicer3.
>
> Bill
>
> On Mon, Mar 22, 2010 at 6:24 AM, Bradley Lowekamp
> <blowekamp at mail.nih.gov> wrote:
> > Hello,
> > Can you please tell us a little more about your test data and computer.
> What
> > kind of file system is the data on ( locale or network)? How much memory
> > does the computer have? What is the size of the data? What is the native
> > pixel type of the data? What are the actual timings? Does the execution
> seem
> > to be CPU or IO bound?
> > One of the changes that was made to the class was to populate the
> > MetaDataArray in the UpdataOutputInformation phase of the instead of the
> > UpdateOutputData part. This should be just reading the headers of the
> files
> > in the series. There were several reasons this change was made. To help
> > determine the cause of your slowness, lets break up the timing a little
> > further.
> > Could you please call:
> > start timer
> > reader->UpdateOutputInformation();
> > lap timer
> > reader->UpdateLargestPossibleRegion();
> > stop timer
> > And post the timing results.
> >
> > Thanks,
> > Brad
> > On Mar 21, 2010, at 2:52 PM, Roger Bramon Feixas wrote:
> >
> > This week we updated our ITK version from 2.8 to 3.16  and we noticed the
> > medical models are loading 2x slower using the 3.16 ITK version. We use
> > itk::ImageSeriesReader and the problem is focused in its Update() method.
> > I attached a simple test program which reproduces the problem and where
> we
> > can see that the Update() method is 2 times slower using ITK 3.16 vs. ITK
> > 2.8.
> > We compiled both versions using Visual Studio 2008 on Windows XP 32bits
> and
> >  we don't known if this problem also occurs in other platforms.
> > I wonder if other itk users have this same performance problem and if
> there
> > is anybody can help us in order to solve it.
> > Thanks!
> >
> > Roger
> > <test.zip><ATT00001..txt>
> >
> > ========================================================
> >
> > Bradley Lowekamp
> >
> > Lockheed Martin Contractor for
> >
> > Office of High Performance Computing and Communications
> >
> > National Library of Medicine
> >
> > blowekamp at mail.nih.gov
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.html
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://www.itk.org/mailman/listinfo/insight-users
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20100323/f68921f1/attachment-0001.htm>