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

Tue Mar 23 17:57:19 EDT 2010

Bill,

Now I'm at home. You will have the results of the experiment tomorrow
morning.

Thanks,

Roger

On Tue, Mar 23, 2010 at 8:44 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

> Sounds good. So you are saying that in the
> ImageSeriesReader<TOutputImage>
> ::GenerateOutputInformation
>
> that the number of files that are processed will be only 2.
>
> Bill
>
> On Tue, Mar 23, 2010 at 12:39 PM, Bradley Lowekamp
> <blowekamp at mail.nih.gov> wrote:
> > Bill:
> > My proposed solution is to use the old behavior but use a time stamp to
> > avoid the extra updates of the MDDA when streaming.
> > The requested region is set after UpdateOutputInformation is executed, so
> it
> > can't be toggled during the this phase of execution.
> >
> > On Mar 23, 2010, at 3:28 PM, Bill Lorensen wrote:
> >
> > Can we check if streaming is on and revert to the old behavior if it is
> off?
> >
> > This is a huge performance penalty to support streaming which is
> > important but no the usual use case.
> >
> >
> > On Tue, Mar 23, 2010 at 12:12 PM, Bradley Lowekamp
> > <blowekamp at mail.nih.gov> wrote:
> >
> > Bill,
> >
> > Going back would have horrible effects for streaming. It would make slice
> by
> >
> > slice streaming an n^2 algorithm, which is far worse then the current
> order
> >
> > of N hindrance for normals Updates. We must make some improvements from
> 2.8.
> >
> > If we declare the the MetaDataDictionary is suppose to be updated in the
> >
> > update data phase. ( the ImageFileReader does it in the
> >
> > UpdateOutputInformation phase ) Then the prior stated point 1 design
> >
> > requirement is gone. And the following solution come to mind:
> >
> > 1) Modify the GetMMDA methods to produce a warning if the update output
> data
> >
> > has not been called. This is to be nice if some users now expect
> >
> > UpdateOutputInformation to produce the MDDA.
> >
> > 2) Add a time stamp for the MMDA, so that when streaming the MMDA is only
> >
> > updated once and not every time a region is requested.
> >
> > Additionally I believe that we need better DICOM test data which include
> >
> > more tags similar to real world data.
> >
> > Brad
> >
> > On Mar 23, 2010, at 2:54 PM, Bill Lorensen wrote:
> >
> > The UpdateInformation is supposed to update origin, spacing,
> >
> > direction, pixel type, etc. I don't think it is supposed to completely
> >
> > populate the meta data dictionary. At least until itk 2.8 it did not.
> >
> > Why not revert back to the old behavior as a sort term fix.
> >
> > I think this performance hit needs to be repaired before we release
> >
> > 3.16. This has been causing major pain for Slicer3 users who
> >
> > frequently use dicom. Fortunately for us, Roger brought it to light.
> >
> > We missed it because our performance testing is weak.
> >
> > There are other issues for sure.
> >
> > Bill
> >
> > On Tue, Mar 23, 2010 at 11:45 AM, Bradley Lowekamp
> >
> > <blowekamp at mail.nih.gov> wrote:
> >
> > Bill,
> >
> > After my tests I agree that reading the headers in DICOM files is a
> >
> > surprisingly expensive operation as such it should be minimized. The
> coping
> >
> > of the MDAs is insignificant performance wise.  I believe that the best
> >
> > solution would be to have a dedicated DICOM series readers, which also
> >
> > removes the extra header reads needed for the name generation as well as
> the
> >
> > extra one in the UpdateOutputInformation.
> >
> > If we assume that the usually way to utilize the reader is to just
> Update,
> >
> > or stream Update, then the additional read of the headers appears
> >
> > unnecessary.
> >
> > I believe a solution would be to make the GetMDDA method smarter, and by
> >
> > default update this MDDA in the UpdateData. A time stamp would need to be
> >
> > used for the MDDA to check when it needs to be updated in the UpdateData
> >
> > methods. For streaming, the first time through would require reading all
> of
> >
> > the headers for the MDDA, this should bring the time stamp up to date.
> The
> >
> > GetMDDA methods could also check this timestamp and perform the reading
> of
> >
> > the headers if it's out of date. This is my best current idea on how to
> >
> > maintain the 1) and 2) I previously mentioned.
> >
> > Brad
> >
> > On Mar 23, 2010, at 12:33 PM, Bill Lorensen wrote:
> >
> > Brad,
> >
> > I have an itk 2.8 checkout. The difference is due to the processing of
> >
> > all files in the GenerateOutputInformation method. In the past, only
> >
> > two files were processed. If I restrict the number of files to 2
> >
> > rather that number of files, I get pretty reasonable speeds.
> >
> > Roger,
> >
> > As an experiment (and definitely not a fix!), can you in the method
> >
> > void ImageSeriesReader<TOutputImage>
> >
> > ::GenerateOutputInformation(void)
> >
> > change the line:
> >
> > for ( int i = 0; i != numberOfFiles; ++i )
> >
> > to
> >
> > for ( int i = 0; i != 2; ++i )
> >
> > and rerun your tests.
> >
> > Bill
> >
> >
> > On Tue, Mar 23, 2010 at 8:59 AM, Bradley Lowekamp
> >
> > <blowekamp at mail.nih.gov> wrote:
> >
> > Bill,
> >
> > That is only the half of it. Every time an ImageFileReader is used 3 MDDs
> >
> > (meta data dictionaries) are created, one in the ImageIO, one in the
> >
> > ImageFileReader, and one in the output Image. This is in addition to the
> two
> >
> > copies, you pointed out in ImageSeriesReader. Clearly reading with an
> >
> > ImageFileReader the MDD scales very poorly as the it's size increases. I
> >
> > still have the remaining performance questions:
> >
> > How much time is spent coping the MDD vs reading? (leaning towards
> reading
> >
> > as very expensive)
> >
> > As pointed out in Roger's most recent performance tests, there appears to
> be
> >
> > some additional performance problems in the UpdateData, part. This is
> >
> > independent of the additional MDD read in the UpdateOutputInformation.
> This
> >
> > is definitely another problem, perhaps inside the DICOM library.
> >
> > The change of moving (apparently duplicating) the copying to MDDs to the
> MDD
> >
> > array was added over a year ago, when streaming support was added. If I
> >
> > recall correctly the two motivating factors were 1) the MDD array is
> output
> >
> > information and logically should be updating during the
> >
> > UpdateOutputInformation part of the pipeline 2) when streaming each file
> >
> > should not need to be read to create the MMD array. I don't recall where
> >
> > this discussion took place right now.
> >
> > I will run some performance test to try to figure out where the time is
> >
> > being spent. Without changing 1 from above, I am not sure how much could
> be
> >
> > gained.
> >
> > Looking at the performance numbers of the Read Directory part, I would
> guess
> >
> > that the meta data is also read there. I believe that an idea solution
> would
> >
> > only read this information once. But that is beyond this scope.
> >
> > Brad
> >
> > On Mar 22, 2010, at 11:20 PM, Bill Lorensen 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
> >
> >
> > ========================================================
> >
> > Bradley Lowekamp
> >
> > Lockheed Martin Contractor for
> >
> > Office of High Performance Computing and Communications
> >
> > National Library of Medicine
> >
> > blowekamp at mail.nih.gov
> >
> >
> >
> > ========================================================
> >
> > Bradley Lowekamp
> >
> > Lockheed Martin Contractor for
> >
> > Office of High Performance Computing and Communications
> >
> > National Library of Medicine
> >
> > blowekamp at mail.nih.gov
> >
> >
>
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