[Insight-developers] TIFF and LSM images failing in sanchome.megason-lab.hms : release
Kishore Mosaliganti
kishoreraom at gmail.com
Tue Jul 29 09:41:18 EDT 2008
Hi Bill/ Luis,
The tests on my machine have passed.
http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=134062
I disabled the TIFF optimization and set ITK_USE_SYSTEM_TIFF flag in CMake.
Kishore
On Tue, Jul 29, 2008 at 9:01 AM, Bill Lorensen <bill.lorensen at gmail.com>wrote:
> I tried disabling optimization for the TIFFImageIO, but tests still fail.
> http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=133716
>
> I'll back out the changes.
>
> Bill
>
> On Mon, Jul 28, 2008 at 11:27 AM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
> > Kishore,
> >
> > Can you add the following to Code/IO/CMakeLists.txt
> >
> >
> > IF(CMAKE_COMPILER_IS_GNUCXX)
> > SET_SOURCE_FILES_PROPERTIES(
> > itkTIFFImageIO.cxx
> > PROPERTIES COMPILE_FLAGS -O0
> > )
> > ENDIF(CMAKE_COMPILER_IS_GNUCXX)
> >
> > Bill
> >
> > On Sun, Jul 27, 2008 at 6:51 PM, Kishore Mosaliganti
> > <kishoreraom at gmail.com> wrote:
> >> Hi Luis,
> >>
> >> The reasons you mentioned 1 and 2 are posing problems. I installed the
> >> latest TIFF libraries for the Fedora 9 linux distribution and set the
> >> ITK_USE_SYSTEM_TIFF as ON.
> >>
> >> The tests have consistently failed once again. I submitted the ctest -D
> >> results as well as the experimental build to the dashboard.
> >>
> >>
> >> Kishore
> >>
> >>
> >>
> >> On Sun, Jul 27, 2008 at 9:58 AM, Luis Ibanez <luis.ibanez at kitware.com>
> >> wrote:
> >>>
> >>> Hi Kishore,
> >>>
> >>> Thanks a lot for running the tests.
> >>>
> >>> Yes, the new tests show that the TIFF reading is failing for
> >>> the Fax formats. Note that this doesn't discard the possibility
> >>> that the writing may be failing as well, (we need to add the
> >>> complementary tests).
> >>>
> >>> The next step is to figure out what is the layer in which
> >>> this is failing.
> >>>
> >>>
> >>> Some of the suspects are:
> >>>
> >>>
> >>> 1) itkTIFFImageIO
> >>> 2) itkTIFFImageIOBase
> >>> 3) libtiff (3.5.2) distributed in Insight/Utilities
> >>>
> >>>
> >>>
> >>> Let's start by checking numeral (3),
> >>> the TIFF library itself.
> >>>
> >>>
> >>> Could you please try the following:
> >>>
> >>>
> >>> A) Install the most recent TIFF library in
> >>> your Linux distribution.
> >>>
> >>> B) Reconfigure ITK with CMake, go to the advanced
> >>> mode enable the flag:
> >>>
> >>> ITK_USE_SYSTEM_TIFF
> >>>
> >>> C) Build ITK, and submit an experimental build to
> >>> the Dashboard
> >>>
> >>> in Linux this is as simple as going to the Binary
> >>> directory where you are building ITK, and typing:
> >>>
> >>>
> >>> make Experimental
> >>>
> >>>
> >>> This will build ITK, run all the tests, package
> >>> the results and submit them to the ITK Dashboard.
> >>>
> >>>
> >>>
> >>> If this makes the test pass, then we will know that the
> >>> problem is that we need to update the libtiff library.
> >>>
> >>>
> >>> If the tests still fail, then we should probably explore
> >>> options (1) and (2).
> >>>
> >>>
> >>>
> >>> Of course, any other suggestions are welcome,
> >>>
> >>>
> >>> Thanks
> >>>
> >>>
> >>> Luis
> >>>
> >>>
> >>>
> >>> ---------------------------
> >>> Kishore Mosaliganti wrote:
> >>>>
> >>>> Hi Luis,
> >>>>
> >>>> The additional two tests have failed as well. It seems there is
> something
> >>>> wrong with the read of images.
> >>>>
> >>>> http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=132319
> >>>> <http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=132319>
> >>>>
> >>>> Kishore
> >>>>
> >>>>
> >>>>
> >>>> On Sat, Jul 26, 2008 at 9:56 AM, Luis Ibanez <luis.ibanez at kitware.com
> >>>> <mailto:luis.ibanez at kitware.com>> wrote:
> >>>>
> >>>>
> >>>> Hi Kishore,
> >>>>
> >>>> Thanks a lot for the report.
> >>>>
> >>>> Now that we know this is reproducible, it is worth to track it
> >>>> before the release of ITK 3.8
> >>>>
> >>>>
> >>>> It is really unfortunate that this
> >>>> only fails when compiling in release mode... :-/
> >>>>
> >>>>
> >>>>
> >>>> Looking at the list of TIFF tests, only some of them fail.
> >>>>
> >>>> itkTIFFImageIOMultiPagesTest Ok
> >>>> itkTIFFImageIOTest Ok
> >>>> itkTIFFImageIOTest1 Ok
> >>>> itkTIFFImageIOTest2 Failed
> >>>> itkTIFFImageIOTest3 Failed
> >>>> itkTIFFImageIOTest4 Ok
> >>>> itkTIFFImageIOTest5 Failed
> >>>> itkTIFFImageIOTest6 Failed
> >>>> itkTIFFImageIOTest7 Ok
> >>>> itkTIFFImageIOTest8 Ok
> >>>> itkTIFFImageIOTest9 Ok
> >>>> itkTIFFImageIOTest10 Failed
> >>>> itkTIFFImageIOTest11 Ok
> >>>> itkTIFFImageIOTest12 Ok
> >>>>
> >>>>
> >>>> One way to start is to identify what is special about the five
> >>>> tests that are failing.
> >>>>
> >>>> Interestingly, all of them use the same executable, so the
> >>>> differences are in the type of TIFF images that are feed
> >>>> as input.
> >>>>
> >>>>
> >>>> For example
> >>>>
> >>>> itkTIFFImageIOTest2 reads RGBTestImageCCITTFax3.tif
> >>>> itkTIFFImageIOTest3 reads RGBTestImageCCITTFax4.tif
> >>>>
> >>>> So, the two Fax format fail...
> >>>>
> >>>> then
> >>>>
> >>>> itkTIFFImageIOTest5 reads RGBTestImageHuffmanRLE.tif
> >>>> itkTIFFImageIOTest6 reads RGBTestImageJPEG.tif
> >>>> itkTIFFImageIOTest10 reads RGBTestImageZIP.tif
> >>>>
> >>>>
> >>>> Looking at the output images, all of them have grid-like artifacts,
> >>>> which leads to suspects that the compression/decompression part of
> >>>> process is the one failing.
> >>>>
> >>>> Due to the way in which the test is setup, we don't know
> >>>> if what is failing is the reading or the writing.
> >>>>
> >>>> These test read an input TIFF image, save it again as TIFF,
> >>>> and then compare the saved image to a TIFF baseline.
> >>>>
> >>>> We are therefore adding duplicates of tests
> >>>>
> >>>> itkTIFFImageIOTest2
> >>>> itkTIFFImageIOTest3
> >>>>
> >>>> numbered now as
> >>>>
> >>>> itkTIFFImageIOTest13
> >>>> itkTIFFImageIOTest14
> >>>>
> >>>> They will read TIFF and Write MetaImage.
> >>>>
> >>>> This will help us discriminate whether the problem is on
> >>>> reading or during the writing of the images.
> >>>>
> >>>>
> >>>> If you have a chance, please submit an experimental build
> >>>> from your Fedora machine, or at least report your observations
> >>>> of the output of these tests back to the mailing list.
> >>>>
> >>>>
> >>>> Thanks a lot for your help,
> >>>>
> >>>>
> >>>> Luis
> >>>>
> >>>>
> >>>> --------------------------
> >>>> Kishore Mosaliganti wrote:
> >>>>
> >>>> Hi Luis,
> >>>>
> >>>> The tests you mention are failing in my machine as well:
> >>>>
> http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=131560
> >>>>
> >>>> <http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=131560>
> >>>> <
> http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=131560
> >>>>
> >>>> <http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=131560>>
> >>>>
> >>>>
> >>>> The configuration of my machine is:
> >>>> Linux Fedora Core 9, gcc-4.3.x86_64, compiled in Release mode.
> >>>>
> >>>> We face the same trouble on 3 PCs with similar configuration.
> >>>>
> >>>>
> >>>> Kishore
> >>>>
> >>>>
> >>>> Date: Wed, 23 Jul 2008 10:54:05 -0400
> >>>> From: Luis Ibanez <luis.ibanez at kitware.com
> >>>> <mailto:luis.ibanez at kitware.com> <mailto:
> luis.ibanez at kitware.com
> >>>> <mailto:luis.ibanez at kitware.com>>>
> >>>>
> >>>> Subject: [Insight-developers] TIFF and LSM images failing in
> >>>> sanchome.megason-lab.hms : release
> >>>> To: 'Alexandre Gouaillard' <
> Alexandre_Gouaillard at hms.harvard.edu
> >>>> <mailto:Alexandre_Gouaillard at hms.harvard.edu>
> >>>> <mailto:Alexandre_Gouaillard at hms.harvard.edu
> >>>> <mailto:Alexandre_Gouaillard at hms.harvard.edu>>>,
> >>>> Insight Developers <Insight-developers at itk.org
> >>>> <mailto:Insight-developers at itk.org>
> >>>> <mailto:Insight-developers at itk.org
> >>>> <mailto:Insight-developers at itk.org>>>
> >>>> Message-ID: <4887460D.70606 at kitware.com
> >>>> <mailto:4887460D.70606 at kitware.com>
> >>>> <mailto:4887460D.70606 at kitware.com
> >>>> <mailto:4887460D.70606 at kitware.com>>>
> >>>>
> >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >>>>
> >>>>
> >>>> Hi Alex,
> >>>>
> >>>> The release submission from
> >>>>
> >>>>
> >>>> sanchome.megason-lab.hms
> >>>>
> >>>>
> >>>> has failing tests for TIFF and LSM images.
> >>>>
> >>>> This happend in the release build and not in the debug build.
> >>>>
> >>>>
> >>>> Do you have any hints on why these tests are failing in this
> >>>> platform ?
> >>>>
> >>>> We have submissions from other Linux 64 bits that seem to be
> >>>> working fine.
> >>>>
> >>>> Can we suspect of a configuration problem in this machine ?
> >>>>
> >>>>
> >>>>
> >>>> Thanks for any help,
> >>>>
> >>>>
> >>>> Luis
> >>>>
> >>>>
> >>
> >>
> >> _______________________________________________
> >> Insight-developers mailing list
> >> Insight-developers at itk.org
> >> http://www.itk.org/mailman/listinfo/insight-developers
> >>
> >>
> >
>
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