[Insight-developers] TIFF and LSM images failing in sanchome.megason-lab.hms : release
Luis Ibanez
luis.ibanez at kitware.com
Sun Jul 27 19:00:43 EDT 2008
Hi Kishore,
Thanks for trying the TIFF system library.
Yeap, this raises the suspicion that the problem might
be in the TIFFImageIO or the ImageIOBase classes.
Thanks
Luis
----------------------------
Kishore Mosaliganti 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
> <mailto: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>
> <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>
> <mailto: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>>
>
> <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>>
> <mailto: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>>
> <mailto: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>>
> <mailto: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>>
> <mailto: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
>
>
>
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