[Insight-users] Performance regression in ITK + gdcm 2.0 reading DICOM JPEG files

[Mathieu Malaterre]

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