[Insight-users] Performance regression in ITK + gdcm 2.0 reading DICOM JPEG files
Roger Bramon Feixas
rogerbramon at gmail.com
Wed Jun 2 08:29:36 EDT 2010
Hi,
I attach the test results on Windows. We can observe that trunk version is
about 2x faster compared to gdcm2.0.14, however gdcm1.2 is still 2x faster
than trunk version.
I'm looking forward your answers and let's me know if you need some help.
Thanks,
Roger
On Tue, Jun 1, 2010 at 9:40 PM, Roger Bramon Feixas
<rogerbramon at gmail.com>wrote:
> Hi Mathieu,
>
> Thanks for you time! I just tested it on Mac OS X (I will also test it on
> Windows soon) and there is a really nice performance improvement, about 2x.
>
> However, I have two code comments: First, there is an abort() at line 350
> of gdcmBitmap.cxx which causes a crash, I commented it to be able to test
> it. The other problem is related to the use of gdcm::PixelFormat::UINT8 at
> line 342 of gdcmBitmap.cxx. If you're working with JPEG files and its pixel
> format is more than 8 bits, a downscale has to be done. Perhaps, it could be
> replaced for GetPixelFormat().
>
> On the other hand, we want to include this commit in our GDCM compilation
> but I would like to know which is the best way:
> - Using GDCM 2.0.14 patched. It's the last stable version but I don't
> know if patch it is a good idea because some changes have been done.
> - Using the trunk version even though it isn't stable, or
> - waiting for GDCM 2.1 if it will be released soon.
>
> I will try to test it on Windows tomorrow and send you the time results.
>
> Many thanks!
>
> Roger
>
>
> On Mon, May 31, 2010 at 11:21 PM, Mathieu Malaterre <
> mathieu.malaterre at gmail.com> wrote:
>
>> Hi Roger,
>>
>> Yes ! I finally found some time, Snakes on a Plane gave this opportunity
>> ;)
>>
>> I think I made some progress with the JPEG DICOM file. JPEG 2000
>> files will be slightly more difficult. See log at:
>>
>> http://sourceforge.net/tracker/index.php?func=detail&aid=3009661&group_id=137895&atid=739587
>>
>> For reference, this issue entered GDCM 2.x, when handling the
>> lossy/lossless duality of J2K and JPEG-LS in DICOM. I am required to
>> know after ExecuteInformation whether the encapsulated JPEG fragment
>> was compressed with lossy algorithm (this is not indicated in the
>> DICOM dataset).
>>
>> Could you please confirm this on your side (again JPEG 2000 will
>> take me some more time) ?
>>
>> Thanks again for your report
>>
>> On Fri, May 28, 2010 at 12:00 AM, Roger Bramon Feixas
>> <rogerbramon at gmail.com> wrote:
>> > Hi,
>> > Have you had time to think about the causes of the performance
>> regression
>> > problem? I can work on it, but I would like to have, if you have it,
>> some
>> > information which helps me to know where I need to focus the effort.
>> >
>> > Thanks,
>> > Roger
>> >
>> > On Tue, May 18, 2010 at 9:14 AM, Roger Bramon Feixas <
>> rogerbramon at gmail.com>
>> > wrote:
>> >>
>> >> Hi Mathieu,
>> >> Perhaps, the answer of question 3 wasn't so clear:
>> >> ITK versions:
>> >> - CMAKE_BUILD_TYPE:RelWithDebInfo
>> >> - BUILD_SHARED_LIBS: OFF
>> >> GDCM: Release from http://gdcm.sourceforge.net
>> >> Test program: Release.
>> >> Compiling the test program in Debug mode, it takes more time but we
>> also
>> >> have large differences between GDCM 1.2.x and GDCM 2.0.
>> >>
>> >> Roger
>> >> On Mon, May 17, 2010 at 11:50 PM, Roger Bramon Feixas
>> >> <rogerbramon at gmail.com> wrote:
>> >>>
>> >>> Hi Mathieu,
>> >>> Thanks for your attention. I answer your questions:
>> >>> 1. What is your platform ?
>> >>> I used a Windows XP 32bits to do the test. However, this behaviour
>> also
>> >>> occurs in Mac OS X platform.
>> >>> 2. What is your compiler ?
>> >>> All ITK versions were compiled with Visual Studio 2008 and we
>> downloaded
>> >>> GDCM 2.0.14 binary from http://gdcm.sourceforge.net
>> >>> 3. What are your compiler option (eg. I hope you do not run bench
>> >>> without CMAKE_BUILD_TYPE:Release) ?
>> >>> RelWithDebInfo
>> >>> 4. Where is the dataset used ?
>> >>> Dataset 5 is from OSIRIX:
>> http://pubimage.hcuge.ch:8080/DATA/CALIX.zip
>> >>> -> CALIX/CT1 abdomen/D30MN BILISCOPIN
>> >>> We are really interested to improve the time needed to load jpeg
>> lossless
>> >>> datasets. The jpeg lossless datasets used are non-anonymized datasets,
>> I
>> >>> will try to anonymize them if you want them.
>> >>> 5. Where is the source code used ?
>> >>> I attach it in this mail.
>> >>>
>> >>> Thanks!
>> >>> Roger
>> >>> On Mon, May 17, 2010 at 10:44 PM, Mathieu Malaterre
>> >>> <mathieu.malaterre at gmail.com> wrote:
>> >>>>
>> >>>> Hi Roger,
>> >>>>
>> >>>> This is a very interesting post !
>> >>>>
>> >>>> On Thu, May 13, 2010 at 11:00 PM, Roger Bramon Feixas
>> >>>> <rogerbramon at gmail.com> wrote:
>> >>>> > Hi,
>> >>>> > Recently we updated our ITK version from ITK 3.16 to ITK 3.18 and
>> we
>> >>>> > decided
>> >>>> > to relink ITK with system GDCM 2.0. After some tests, we concluded
>> ITK
>> >>>> > 3.18+GDCM 2.0 is faster than ITK 3.18 reading DICOM Little Endian
>> >>>> > files,
>> >>>> > however ITK 3.18+GDCM 2.0 is rather slower reading DICOM JPEG
>> files. I
>> >>>> > attach a PDF file which is a time comparison of ITK 2.8, 3.16, 3.18
>> >>>> > and
>> >>>> > 3.18+GDCM2.0 versions.
>> >>>> > I don't know if it's just a GDCM problem or if it depends on how
>> ITK
>> >>>> > uses
>> >>>> > GDCM.
>> >>>>
>> >>>> GDCM Reading
>> >>>> UpdateOutput- UpdateLargest-
>> >>>> Data ITK version version directory Information
>> >>>> PossibleRegion
>> >>>>
>> >>>>
>> >>>> 5 2,8 1,2 642
>> >>>> 6 20153
>> >>>> 3,16 1,2 547
>> >>>> 0 25121
>> >>>> 3,18 1,2 547
>> >>>> 0 25124
>> >>>> 3,18 2 25297
>> >>>> 187 71437
>> >>>>
>> >>>>
>> >>>>
>> >>>> Data Transfer syntax Modality Files
>> >>>> Size (MB)
>> >>>>
>> >>>> 5 JPEG 2000 CT
>> >>>> 243 23
>> >>>>
>> >>>>
>> >>>>
>> >>>> Could you please post a little bit more on :
>> >>>> 1. What is your platform ?
>> >>>> 2. What is your compiler ?
>> >>>> 3. What are your compiler option (eg. I hope you do not run bench
>> >>>> without CMAKE_BUILD_TYPE:Release) ?
>> >>>> 4. Where is the dataset used ?
>> >>>> 5. Where is the source code used ?
>> >>>>
>> >>>> Thanks a bunch !
>> >>>> --
>> >>>> Mathieu
>> >>>
>> >>
>> >
>> >
>>
>>
>>
>> --
>> Mathieu
>>
>
>
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