[Insight-developers] TIFF and LSM images failing in sanchome.megason-lab.hms : release
Bill Lorensen
bill.lorensen at gmail.com
Mon Jul 28 11:14:23 EDT 2008
Luis,
I'd like to try disabling optimization for TIFFImageIO. At least it
will narrow down the problem to one file.
Bill
On Sun, Jul 27, 2008 at 7:00 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
> 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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