[Insight-developers] How to run the tests: itkGDCMImageIOTest3

Luis Ibanez luis.ibanez at kitware.com
Mon Mar 7 18:13:25 EST 2011 

Hi Mark

On Mon, Mar 7, 2011 at 5:54 PM, Mark Roden <mmroden at gmail.com> wrote:
> Hi Luis,
>
> I can see the failing test, now that I'm in the right place.
>
> How did you get the stack trace there?


1) Type

    gdb     /home/ibanez/bin/ITK/Release/bin/IOCxxTests


(of course, with your own path to   IOCxxTests...)

2)  Once you get the gdb prompt,  type


run  "itkGDCMImageIOTest"
"/home/ibanez/src/ITK/Testing/Data/Input/012345.002.050"
"/home/ibanez/bin/ITK/Release/Testing/Temporary/itkGDCMImageIOTest3.dcm"
"/home/ibanez/bin/ITK/Release/Testing/Temporary/itkGDCMImageIOTest3.png"
"/home/ibanez/bin/ITK/Release/Testing/Temporary/itkGDCMRescaleImageIOTest3.dcm"

(again, with your own paths...)

You will find the correct paths by doing

    ctest -R itkGDCMImageIOTest3   -V   -N



> I'm used to using IDEs, I
> haven't really done command line debugging for a long while.  XCode
> doesn't play nice with CTest, in that I can't figure out how to run
> the test via XCode, which is how I'd normall debug this.
>


I would think that is possible to run GDB from XCode,...
but I don't use IDEs since they just slow down development.    :-)


> As far as I know, it's building in the default for CMake (debug,
> right?).  Debug is set to just have the switch -g, as well as all of
> Bradley's compiler warning switches.
>


In order to Debug, you need to select

                 CMAKE_BUILD_TYPE = Debug

when you configure ITK with CMake.


> Right now, the test output looks like:
>
> Mark-Rodens-MacBook-Pro:itk-build-unix mmroden$ ctest -R
> itkGDCMImageIOTest3 -V -n
> UpdateCTestConfiguration  from
> :/Users/mmroden/Documents/src/itk/itk-build-unix/DartConfiguration.tcl
> Parse Config file:/Users/mmroden/Documents/src/itk/itk-build-unix/DartConfiguration.tcl
>  Add coverage exclude regular expressions.
>  Add coverage exclude: /CMakeFiles/CMakeTmp/
>  Add coverage exclude: .*/Testing/.*
>  Add coverage exclude: .*/Wrapping/.*
>  Add coverage glob: Source/.*/*.h
>  Add coverage glob: Source/.*/*.txx
>  Add coverage glob: Source/.*/*.cxx
> UpdateCTestConfiguration  from
> :/Users/mmroden/Documents/src/itk/itk-build-unix/DartConfiguration.tcl
> Parse Config file:/Users/mmroden/Documents/src/itk/itk-build-unix/DartConfiguration.tcl
> Test project /Users/mmroden/Documents/src/itk/itk-build-unix
> Constructing a list of tests
> Done constructing a list of tests
> Checking test dependency graph...
> test 1212
>    Start 1212: itkGDCMImageIOTest3
>
> 1212: Test command:
> /Users/mmroden/Documents/src/itk/itk-build-unix/bin/IOCxxTests
> "itkGDCMImageIOTest"
> "/Users/mmroden/Documents/src/itk/itk/Testing/Data/Input/012345.002.050"
> "/Users/mmroden/Documents/src/itk/itk-build-unix/Testing/Temporary/itkGDCMImageIOTest3.dcm"
> "/Users/mmroden/Documents/src/itk/itk-build-unix/Testing/Temporary/itkGDCMImageIOTest3.png"
> "/Users/mmroden/Documents/src/itk/itk-build-unix/Testing/Temporary/itkGDCMRescaleImageIOTest3.dcm"
> 1212: Test timeout computed to be: 1500
> 1/1 Test #1212: itkGDCMImageIOTest3 ..............***Exception:
> SegFault  0.23 sec
>
> 0% tests passed, 1 tests failed out of 1
>
> Total Test time (real) =   0.52 sec
>
> The following tests FAILED:
>        1212 - itkGDCMImageIOTest3 (SEGFAULT)
> Errors while running CTest
>


Yeap,once you run it in GDB, you will find that
in your patch, there is a recursive call to the
same method, that saturates the stack.

There is a polymorphism flaw in the way those
methods are dispatched, (which is somehow,
the risk that the warnings where bringing up in
the first place).


       Luis


--------------------------------------
>
> Thanks,
> Mark
>
> On Mon, Mar 7, 2011 at 2:44 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>> Hi Mark,
>>
>>
>> When you downloaded ITK...
>> did you follow the instruction in:
>>
>>   http://www.itk.org/Wiki/ITK/Git/Develop    ?
>>
>>
>>
>> In particular, did you run the script:
>>
>>     ./Utilities/SetupForDevelopment.sh
>>
>> as described in the instructions ?
>>
>>
>> --
>>
>> If you go to the source tree of ITK,
>> do you have a directory:
>>
>>            ITK/Testing/Data     ?
>>
>> Is there anything inside that directory ?
>>
>> If not, it means that you didn't run that
>> script, or that something went wrong
>> when you ran it.
>>
>>
>>
>>      Luis
>>
>>
>> ----------------------------------------------
>> On Mon, Mar 7, 2011 at 5:33 PM, Mark Roden <mmroden at gmail.com> wrote:
>>> Hi Luis,
>>>
>>> 0) Good, I thought so.
>>>
>>> 1) When I do that, after building 'testing', I get the following:
>>> Mark-Rodens-MacBook-Pro:bin mmroden$ ctest -R itkGDCMImageIOTest3
>>> Test project /Users/mmroden/Documents/src/itk/itk-build-unix/bin
>>> No tests were found!!!
>>>
>>> That's what's causing me some consternation.  Is there something else
>>> I need to do to bring those tests out?  Because when I run the IOTests
>>> under xcode, which brings up a testing app, that test isn't listed
>>> either.  I do see it in the cmakelists, I just don't know how to get
>>> there from here.
>>>
>>> Thanks,
>>> Mark
>>>
>>> On Mon, Mar 7, 2011 at 2:30 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>>> Hi Mark,
>>>>
>>>> 0) You don't need GDCM data to run this test.
>>>>
>>>>   The input file that is uses is in:
>>>>
>>>>       ITK/Testing/Data/Input/012345.002.050
>>>>
>>>>    For details please look at lines 1057-1061 of
>>>>    the file  ITK/Testing/Code/IO/CMakeLists.txt:
>>>>
>>>> add_test(itkGDCMImageIOTest3 ${TestDriver} itkGDCMImageIOTest
>>>>        ${ITK_DATA_ROOT}/Input/012345.002.050
>>>>        ${ITK_TEST_OUTPUT_DIR}/itkGDCMImageIOTest3.dcm
>>>>        ${ITK_TEST_OUTPUT_DIR}/itkGDCMImageIOTest3.png
>>>>        ${ITK_TEST_OUTPUT_DIR}/itkGDCMRescaleImageIOTest3.dcm)
>>>>
>>>>
>>>> 1) To run this single test you can "cd" into
>>>>     the ITK binary directory and type:
>>>>
>>>>            ctest   -R      itkGDCMImageIOTest3
>>>>
>>>> 2) If you want the actual command line that
>>>>     directly executes this test, type:
>>>>
>>>>       ctest -R itkGDCMImageIOTest3 -V -N
>>>>
>>>> you will get something like:
>>>>
>>>> ITK_BINARY_DIR/bin/IOCxxTests "itkGDCMImageIOTest"
>>>> "/home/ibanez/src/ITK/Testing/Data/Input/012345.002.050"
>>>> "/home/ibanez/bin/ITK/Release/Testing/Temporary/itkGDCMImageIOTest3.dcm"
>>>> "/home/ibanez/bin/ITK/Release/Testing/Temporary/itkGDCMImageIOTest3.png"
>>>> "/home/ibanez/bin/ITK/Release/Testing/Temporary/itkGDCMRescaleImageIOTest3.dcm"
>>>>
>>>> 4) Here is the link to the same tests as it is executed
>>>>     in the Dashboard machines:
>>>>
>>>> http://www.cdash.org/CDash/testSummary.php?project=2&name=itkGDCMImageIOTest3&date=2011-03-07
>>>>
>>>>
>>>>       Luis
>>>>
>>>>
>>>> -------------------------------------------
>>>> On Sat, Mar 5, 2011 at 7:50 PM, Mark Roden <mmroden at gmail.com> wrote:
>>>>> Hi Luis,
>>>>>
>>>>> OK, now I've spent quite a bit of time trying to fix this patch and
>>>>> this failing test with no luck. There has to be a better way.
>>>>>
>>>>> How can I find just this test to run it from the command line?  I've
>>>>> cmade everything using unix makefiles on my mac using Bradley
>>>>> Lowecamp's switches to expose warnings:
>>>>>
>>>>> Cxx : -Wall -Wextra -Wunused -Wpointer-arith -Winvalid-pch
>>>>> -Wcast-align -Woverloaded-virtual -Wshadow -Wwrite-strings
>>>>> -Wstrict-null-sentinel
>>>>> C: -Wall -Wextra -Wunused -Wpointer-arith -Winvalid-pch -Wcast-align
>>>>> -Wno-deprecated-declarations -Wno-uninitialized
>>>>>
>>>>> I then run make with default options on, as well as testing and
>>>>> examples.  Everything builds, no tests are produced (or are they in
>>>>> some directory that I don't know about).
>>>>>
>>>>> In what may not be a related error, if I turn on anything in gdcm (ie,
>>>>> gdcm testing), I'll get these cmake errors:
>>>>>
>>>>> CMake Error at Utilities/gdcm/CMakeLists.txt:510 (SUBDIRS):
>>>>>  subdirs Incorrect SUBDIRS command.  Directory: Testing does not exists.
>>>>>
>>>>>
>>>>> If you want to build the test suite, you must set GDCM_DATA_ROOT
>>>>> (advanced option) to the full path name of the gdcmData directory; if
>>>>> you don't want, disable GDCM_BUILD_TESTING.
>>>>> What is gdcmData? Please read:
>>>>> http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=General_questions#What_is_gdcmData_.3F
>>>>> CMake Error at Utilities/gdcm/Utilities/CMakeLists.txt:54 (SUBDIRS):
>>>>>  subdirs Incorrect SUBDIRS command.  Directory: gdcmmd5 does not exists.
>>>>>
>>>>>
>>>>> Configuring incomplete, errors occurred!
>>>>>
>>>>> The second error makes sense, since I haven't put the gdcm testing
>>>>> data in their yet (do I need that for the failing test for this
>>>>> patch?).  But what's the deal with that first error?  The 'Testing'
>>>>> directory does 'exists' (sic) in the cmake target directory.
>>>>>
>>>>> If I set the testing directory to be the directory from the gdcm root,
>>>>> CMake now reports:
>>>>> CMake Error at Utilities/gdcm/CMakeLists.txt:510 (SUBDIRS):
>>>>>  subdirs Incorrect SUBDIRS command.  Directory: Testing does not exists.
>>>>>
>>>>>
>>>>> CMake Error at Utilities/gdcm/Utilities/CMakeLists.txt:54 (SUBDIRS):
>>>>>  subdirs Incorrect SUBDIRS command.  Directory: gdcmmd5 does not exists.
>>>>>
>>>>>
>>>>> Configuring incomplete, errors occurred!
>>>>>
>>>>> If this is related to the failing test, then I'll need to fix it in
>>>>> order to fix the test, right?
>>>>>
>>>>> I'd like to just run  directly so that I can fix that particular test
>>>>> (and perhaps develop further tests that check codecs other than jpeg).
>>>>>
>>>>> Thanks,
>>>>> Mark
>>>>>
>>>>>
>>>>> On Fri, Mar 4, 2011 at 9:58 AM, Code Review <review at kitware.com> wrote:
>>>>>> From Mathieu Malaterre <mathieu.malaterre at gmail.com>:
>>>>>>
>>>>>> Mathieu Malaterre has posted comments on this change.
>>>>>>
>>>>>> Change subject: COMP: attempts to fix gdcm function hiding warnings
>>>>>> ......................................................................
>>>>>>
>>>>>>
>>>>>> Patch Set 1: Fails; I would prefer that you didn't submit this
>>>>>>
>>>>>> --
>>>>>> To view, visit http://review.source.kitware.com/1120
>>>>>> To unsubscribe, visit http://review.source.kitware.com/settings
>>>>>>
>>>>>> Gerrit-MessageType: comment
>>>>>> Gerrit-Change-Id: I413102b25d1c9eee60eace2585c2f857ad564a67
>>>>>> Gerrit-PatchSet: 1
>>>>>> Gerrit-Project: ITK
>>>>>> Gerrit-Branch: master
>>>>>> Gerrit-Owner: Mark Roden <mmroden at gmail.com>
>>>>>> Gerrit-Reviewer: Hans J. Johnson <hans-johnson at uiowa.edu>
>>>>>> Gerrit-Reviewer: Luis Ibanez <luis.ibanez at kitware.com>
>>>>>> Gerrit-Reviewer: Mathieu Malaterre <mathieu.malaterre at gmail.com>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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