[Insight-developers] TIFF and LSM images failing in sanchome.megason-lab.hms : release
Bill Lorensen
bill.lorensen at gmail.com
Mon Jul 28 11:27:25 EDT 2008
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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