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

[Bill Lorensen]

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
>
>