[Insight-developers] TIFF and LSM images failing in sanchome.megason-lab.hms : release
Bill Lorensen
bill.lorensen at gmail.com
Tue Jul 29 09:01:42 EDT 2008
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
>>>>
>>>>
>>
>>
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>
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