[Ctk-developers] DCMTK_DIR is found incorrectly

Mon Nov 4 15:01:54 UTC 2013

Hi Csaba, Jc -

London calling (always wanted to say that).  We talked over the issue a bit
and didn't see any obvious issues but there was a request from some folks
for a further discussion of the underlying issue so we put it on the agenda
for a Tuesday afternoon (15:00 London time) hangout.  Does that work for
you two?

Most of the work here this week so far is on CLI, XNAT/REST API, and DICOM.

http://www.commontk.org/index.php/CTK-Hackfest-Nov-2013

-Steve

On Mon, Nov 4, 2013 at 9:34 AM, Csaba Pinter <csaba.pinter at queensu.ca>wrote:

>  Hi JC,
>
>
>
> Yes, it seems to have solved our CTK build problem. The reason I was
> asking about opinions is that I don't know what repercussions it may have
> on other platforms.
>
> If it seems OK the I'd appreciate propagating it to the CTK core or ITK. I
> can create a CTK topic branch containing the change if it makes the process
> easier.
>
>
>
> Thanks,
>
> csaba
>
>
>
>
>
> *From:* Jean-Christophe Fillion-Robin [mailto:jchris.fillionr at kitware.com]
>
> *Sent:* November 4, 2013 09:30
> *To:* Csaba Pinter
> *Cc:* pieper at bwh.harvard.edu; CTK mailing list
>
> *Subject:* Re: [Ctk-developers] DCMTK_DIR is found incorrectly
>
>
>
> Based on your entry in the CTK tracker. I am assuming it is good to go ?
> See https://github.com/commontk/CTK/issues/382
>
>
>
> On Mon, Nov 4, 2013 at 9:28 AM, Jean-Christophe Fillion-Robin <
> jchris.fillionr at kitware.com> wrote:
>
> Hi Csaba,
>
> After you confirm that adding NO_DEFAULT_PATH to [1] works. I will
> coordinate with ITK folks so that they also update their FindDCMTK.cmake
> file.
>
> Thanks
>
> Jc
>
>
> [1]
> https://github.com/commontk/CTK/blob/f64b68acd717dab060db41e8bee3f0f30df1a58f/Utilities/CMake/FindDCMTK.cmake#L42
>
>
>
> On Thu, Oct 31, 2013 at 4:46 PM, Csaba Pinter <csaba.pinter at queensu.ca>
> wrote:
>
> Hi Steve,
>
>
>
> I was going to do just that, thanks for the reminder!
>
> I created issue https://github.com/commontk/CTK/issues/382.
>
> The main reason I haven't created a topic branch yet is that I would like
> to hear some opinions about it first, as I don't know what consequences it
> has on Linux and Mac.
>
>
>
> FYI my agenda for next week besides this small change is to try our
> display tables and DICOM roles enhancement for the DICOM browser (that
> Andras and I implemented during the last hackfest) against the latest
> listview-based browser and integrate it if it turns out to be working fine.
>
>
>
> Thanks,
>
> csaba
>
>
>
>
>
> *From:* Steve Pieper [mailto:pieper at ibility.net]
> *Sent:* October 31, 2013 16:37
>
>
> *To:* Csaba Pinter
> *Cc:* CTK mailing list
> *Subject:* Re: [Ctk-developers] DCMTK_DIR is found incorrectly
>
>
>
> Hi Csaba -
>
>
>
> We'll be discussing open issues next week in London - can you make sure
> there's a ctk issue that points to your assembla report?
>
>
>
> http://www.commontk.org/index.php/CTK-Hackfest-Nov-2013#Monday
>
>
>
> Thanks,
>
> Steve
>
>
>
> On Thu, Oct 17, 2013 at 11:02 AM, Csaba Pinter <csaba.pinter at queensu.ca>
> wrote:
>
> Hi there,
>
>
>
> Any thoughts about the FindDCMTK changes proposed below?
>
> I'd appreciate any feedback.
>
>
>
> Thanks,
>
> csaba
>
>
>
>
>
> *From:* ctk-developers-bounces at commontk.org [mailto:
> ctk-developers-bounces at commontk.org] *On Behalf Of *Csaba Pinter
> *Sent:* October 10, 2013 15:14
> *To:* CTK mailing list
>
>
> *Subject:* Re: [Ctk-developers] DCMTK_DIR is found incorrectly
>
>
>
> Hello,
>
>
>
> I tried the NO_DEFAULT_PATH idea Jc was suggesting (see below), and now I
> could successfully build CTK with DCMTK.
>
>
>
> As we have the same issue from time to time with CTK in Slicer (but
> finally we could reproduce it, see [1]), I propose adding this flag to
> FindDCMTK.cmake in the CTK master, at least until the DCMTKConfig.cmake
> change is not integrated to DCMTK.
>
> As my CMake knowledge is limited, I don't know if this change causes any
> problem on other operating systems though.
>
>
>
> I'd appreciate to hear your opinions about this.
>
>
>
> Thank you,
>
> csaba
>
>
>
> [1] https://www.assembla.com/spaces/slicerrt/tickets/325#/activity/ticket
>
>
>
>
>
> *From:* Jean-Christophe Fillion-Robin [mailto:jchris.fillionr at kitware.com<jchris.fillionr at kitware.com>]
>
> *Sent:* October 4, 2013 18:34
> *To:* Csaba Pinter
> *Cc:* Andras Lasso; CTK mailing list
> *Subject:* Re: [Ctk-developers] DCMTK_DIR is found incorrectly
>
>
>
> Hi Csaba,
>
>
>
> As illustrated in the enclosed screenshot, build tree can be exported into
> the CMake package registry. As some point, the DCMTK build tree has
> probably been exported [1][2][3].
>
> Since when building CTK, it is expected that there are no
> DCMTKConfig.cmake available, the first should be failing. In your case, it
> seems not to be failing because it resolves to that previous build added to
> the registery.
>
> I would suggest to try adding the parameter "NO_DEFAULT_PATH" to the
> FindDCMTK.cmake module available in CTK. See [4]
>
>
>
> Hth
>
> Jc
>
>
>
> [1] http://www.cmake.org/cmake/help/v2.8.11/cmake.html#command:export
> [2]
> http://slicer-devel.65872.n3.nabble.com/Packaging-seems-to-work-again-tp4028121p4028134.html
>
> [3]
> https://www.assembla.com/spaces/slicerrt/tickets/244-dcmtk_dir-vs--dcmtkconfig-cmake?comment=267984263#comment:267984263
>
> [4]
> https://github.com/commontk/CTK/blob/f64b68acd717dab060db41e8bee3f0f30df1a58f/Utilities/CMake/FindDCMTK.cmake#L42
>
>
>
> On Fri, Oct 4, 2013 at 5:39 PM, Csaba Pinter <csaba.pinter at queensu.ca>
> wrote:
>
> Hi Jc,
>
>
>
> I tried building CTK in many ways, but the result is always the same, so
> the problem is completely reproducible, at least on my computer (I haven't
> tried it elsewhere yet, but I plan to). As we have been struggling with
> this issue for quite a while, but haven't been able to consistently
> reproduce it, this is a great opportunity to fix it once and for all.
>
>
>
> I did some digging and this is what I found:
>
> -          FindDCMTK.cmake finds DCMTKConfig.cmake, but it is in the
> incorrect directory that is used later (in one of my slicer builds)
>
> -          The reason why the DCMTK downloaded by the superbuild is not
> found is most probably that it is a version that doesn't have
> DCMTKConfig.cmake (as you described earlier)
>
> -          The same thing (finding the wrong DCMTK) happens if I add
> NO_CMAKE_BUILDS_PATH to the find_package call in FindDCMTK.cmake
>
>
>
> Now I don't have any idea how to get the superbuild to use its own DCMTK.
>
> Also even if I can do a workaround and have a good build of CTK on my
> machine, this is an issue that other people who want to build CTK on
> Windows while already having a Slicer build have to face.
>
>
>
> Cheers,
>
> csaba
>
>
>
>
>
> *From:* Jean-Christophe Fillion-Robin [mailto:jchris.fillionr at kitware.com]
>
> *Sent:* October 4, 2013 12:07
> *To:* Andras Lasso
> *Cc:* Csaba Pinter; CTK mailing list
>
>
> *Subject:* Re: [Ctk-developers] DCMTK_DIR is found incorrectly
>
>
>
> Hi Csaba, Andras,
>
> Within the file FindDCMTK.cmake [1] provided by CTK, where would you
> suggest to add the NO_CMAKE_BUILDS_PATH ?
>
> Let's also note that the FindDCMTK.cmake provided by ITK would have to
> patched also ...
>
> If you can reproduce the problem, with a combination of clearing cache +
> adding some "message()" statement, you should be able to find out or
> confirm what is the source of the problem.
>
>
>
> Jc
>
>
> [1]
> https://github.com/commontk/CTK/blob/master/Utilities/CMake/FindDCMTK.cmake
>
>
>
> On Wed, Oct 2, 2013 at 1:42 PM, Andras Lasso <lasso at queensu.ca> wrote:
>
> I have this annoying issue during Slicer builds as well: my nightly slicer
> builds usually break after a few days because after I configure other
> projects in CMake CTK finds DCMTK of another project instead of its own.
>
>
>
> It may be due to the find_package path finding rule 5: “Search project
> build trees recently configured in a CMake GUI. This can be skipped if
> NO_CMAKE_BUILDS_PATH is passed. It is intended for the case when a user is
> building multiple dependent projects one after another.“ (
> http://www.cmake.org/cmake/help/v2.8.10/ctest.html). Probably CTK should
> rely on rules 1-4 or disable rule 5 – or it may be possible that something
> else goes wrong and that’s why the rule 5 kicks in.
>
>
>
> Andras
>
>
>
>
>
> *From:* ctk-developers-bounces at commontk.org [mailto:
> ctk-developers-bounces at commontk.org] *On Behalf Of *Jean-Christophe
> Fillion-Robin
> *Sent:* Wednesday, October 02, 2013 11:39 AM
>
>
> *To:* Csaba Pinter
> *Cc:* CTK mailing list
> *Subject:* Re: [Ctk-developers] DCMTK_DIR is found incorrectly
>
>
>
> Hi Csaba,
>
> In CTKConfig, the variable "CMAKE_MODULE_PATH" is a CMake global variable
> that is empty by default. On the other hand "CTK_CMAKE_UTILITIES_DIR"
> should not be empty as illustrated below:
>
> $ cat ../CTKConfig.cmake | ack -i "set\(CTK_CMAKE_UTILITIES_DIR"
> SET(CTK_CMAKE_UTILITIES_DIR "/home/jchris/Projects/CTK/Utilities/CMake")
>
>
>
>
>
> Otherwise, you will find below the result of my experiment. When
> configured, CTK found the expected DCMTK.
>
>
> On Ubuntu 13.04 using CMake 2.8.11.2, after installing the package
> "python2.7-dev" doing so the following works.
>
> Note that I didn't enable CTK_ENABLE_ALL since I didn't the build system
> to build VTK or ITK components. Instead, I passed the following options:
>   -DCTK_ENABLE_Python_Wrapping:BOOL=ON
>   -DCTK_ENABLE_DICOM:BOOL=ON
>   -DCTK_BUILD_EXAMPLES
>
>
>
> $ git clone git at github.com:commontk/CTK
>
> $ mkdir CTK-Debug
>
> $ cd CTK-Debug
>
> $ cmake
> -DQT_QMAKE_EXECUTABLE:FILEPATH=/home/jchris/Support/QtSDK-1.2.1/Desktop/Qt/4.8.1/gcc/bin/qmake
> -DCTK_ENABLE_Python_Wrapping:BOOL=ON -DCTK_ENABLE_DICOM:BOOL=ON
> -DCTK_BUILD_EXAMPLES:BOOL=ON ../CTK
> [...]
> -- Enabling [CTK_LIB_DICOM/Core] because of [ CTK_ENABLE_DICOM:1 OR (
> CTK_ENABLE_DICOMApplicationHosting:0 AND CTK_BUILD_EXAMPLES:1 )] evaluates
> to True
> -- Enabling [CTK_APP_ctkDICOM] because of [ CTK_ENABLE_DICOM:1 AND
> CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Enabling [CTK_APP_ctkDICOM2] because of [ CTK_ENABLE_DICOM:1 AND
> CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Enabling [CTK_APP_ctkDICOMIndexer] because of [ CTK_ENABLE_DICOM:1 AND
> CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Enabling [CTK_APP_ctkDICOMDemoSCU] because of [ CTK_ENABLE_DICOM:1 AND
> CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Enabling [CTK_APP_ctkDICOMQuery] because of [ CTK_ENABLE_DICOM:1 AND
> CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Enabling [CTK_APP_ctkDICOMRetrieve] because of [ CTK_ENABLE_DICOM:1 AND
> CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Enabling [CTK_APP_ctkDICOMQueryRetrieve] because of [
> CTK_ENABLE_DICOM:1 AND CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Enabling [CTK_APP_ctkCommandLineModuleExplorer] because of [
> CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Enabling [CTK_APP_ctkDICOMObjectViewer] because of [ CTK_ENABLE_DICOM:1
> AND CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Enabling [CTK_APP_ctkSimplePythonShell] because of [
> CTK_ENABLE_Python_Wrapping:1 AND CTK_BUILD_EXAMPLES:1] evaluates to True
> -- Generated: /home/jchris/Projects/CTK-Debug/DGraphInput-alldep.txt
> -- Generated:
> /home/jchris/Projects/CTK-Debug/DGraphInput-alldep-withext.txt
> -- Enabling option [CTK_LIB_DICOM/Widgets] required by [ctkDICOM]
> -- Enabling option [CTK_LIB_Widgets] required by [ctkDICOM]
> -- Enabling option [CTK_LIB_CommandLineModules/Frontend/QtGui] required by
> [ctkCommandLineModuleExplorer]
> -- Enabling option [CTK_LIB_CommandLineModules/Frontend/QtWebKit] required
> by [ctkCommandLineModuleExplorer]
> -- Enabling option [CTK_LIB_CommandLineModules/Backend/LocalProcess]
> required by [ctkCommandLineModuleExplorer]
> -- Enabling option [CTK_LIB_CommandLineModules/Backend/FunctionPointer]
> required by [ctkCommandLineModuleExplorer]
> -- Enabling option [CTK_LIB_CommandLineModules/Core] required by
> [ctkCommandLineModuleExplorer]
> -- Enabling option [CTK_LIB_Scripting/Python/Widgets] required by
> [ctkSimplePythonShell]
> -- Enabling option [CTK_LIB_Scripting/Python/Core] required by
> [ctkSimplePythonShell]
> -- Found PythonInterp: /usr/bin/python (found version "2.7.4")
> -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found
> version "2.7.4")
> -- Generated: /home/jchris/Projects/CTK-Debug/DGraphInput.txt
> -- Generated: /home/jchris/Projects/CTK-Debug/Project.xml
> -- Found Git: /usr/bin/git (found version "1.8.1.2")
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/jchris/Projects/CTK-Debug
>
> $ make -j6
> [...]
> [ 90%] Performing configure step for 'CTK-Configure'
> [...]
> -- Found PythonInterp: /usr/bin/python (found version "2.7.4")
> -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found
> version "2.7.4")
> -- Generated: /home/jchris/Projects/CTK-Debug/CTK-build/DGraphInput.txt
> -- Generated: /home/jchris/Projects/CTK-Debug/CTK-build/Project.xml
> -- Trying to find DCMTK expecting DCMTKConfig.cmake
> -- Trying to find DCMTK expecting DCMTKConfig.cmake - failed
> -- Trying to find DCMTK relying on FindDCMTK.cmake
> -- Looking for include file pthread.h
> -- Looking fothe r include file pthread.h - found
> -- Looking for pthread_create
> -- Looking for pthread_create - not found
> -- Looking for pthread_create in pthreads
> -- Looking for pthread_create in pthreads - not found
> -- Looking for pthread_create in pthread
> -- Looking for pthread_create in pthread - found
> -- Found Threads: TRUE
> -- Found DCMTK:
> /home/jchris/Projects/CTK-Debug/CMakeExternals/Install/include/dcmtk/config
>
> -- Trying to find DCMTK relying on FindDCMTK.cmake - ok
> -- CTKCore: BFD support disabled
> -- Configuring done
> -- Generating done
> [...]
> -- Build files have been written to:
> /home/jchris/Projects/CTK-Debug/CTK-build
>
> [...]
> [100%] Built target CTKWidgetsCppTests
> [100%] Built target CTK-build
>
>
>
> $ cd CTK-build
> $ $ cat CMakeCache.txt | ack DCMTK_DIR\:PATH
> DCMTK_DIR:PATH=/home/jchris/Projects/CTK-Debug/CMakeExternals/Install
>
> Let's note that DCMTK couldn't be found using DCMTKConfig.cmake, this is
> explained by the fact the official DCMTK didn't integrate yet our latest
> and greatest contribution [1]
>
> Hth
>
> Jc
>
>
> [1]
> https://github.com/commontk/DCMTK/commit/f461865d1759854db56e4c840991c81c77e45bb9
>
>
>
>
>
>
>
> On Wed, Oct 2, 2013 at 10:18 AM, Csaba Pinter <csaba.pinter at queensu.ca>
> wrote:
>
> Hi all,
>
>
>
> I'm trying to build CTK separately, but I have problems with linking DCMTK.
>
>
>
> The way I build CTK:
>
> -          Turn on CTK_BUILD_ALL
>
> -          Turn on CTK_ENABLE_DICOM (I need this as I want to merge and
> test my changes in the CTK/Core/DICOM project)
>
> -          Set the qmake executable
>
> -          Configure
>
> -          CMake complains about python paths, I set those manually
>
> -          Configure, Generate
>
> -          Build superbuild
>
>
>
> Then DCMTK is downloaded and built by the superbuild, but later on, CTK
> projects find a completely different DCMTK directory (in my Slicer nightly
> build directory). I tried to manually add the DCMTK directory to CMake, but
> this variable does not exist in the superbuild (it is also not passed
> down), and setting it to the inner CTK project doesn't work.
>
>
>
> Basically no matter what I do, the DCMTK path is set to whatever
> find_project finds. This is what I found in CTKConfig.cmake:
>
> # Update CMake module path so that calling "find_package(DCMTK)" works as
> expected
>
> # after calling "find_package(CTK)"
>
> # Ideally projects like DCMTK or PythonQt should provide both "Config" and
> "Use" files.
>
> set(CMAKE_MODULE_PATH
>
>   ${CTK_CMAKE_UTILITIES_DIR}
>
>   ${CMAKE_MODULE_PATH}
>
>   )
>
>
>
> Now the problem with this is that ${CMAKE_MODULE_PATH} is empty, so there
> is no chance DCMTK is found correctly.
>
>
>
> Can someone please help with this?
>
>
>
> Thanks a lot,
>
> csaba
>
>
>
> ________________________________
>
> Csaba Pinter
>
> Medical Software Systems Engineer
>
> Laboratory for Percutanous Surgery
>
> School of Computing
>
> Queen’s University
>
> Kingston, ON, Canada
>
> Email: csaba.pinter at queensu.ca
>
> Web: http://perk.cs.queensu.ca
>
>
> _______________________________________________
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>
>
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