[Insight-developers] TIFF and LSM images failing in sanchome.megason-lab.hms : release

[Kishore Mosaliganti]

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
>>
>>
>>
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