[Insight-users] Problems with ITK and Linux

[Matt McCormick]

Hi Gabriel,

I do not have much experience with Eclipse.  Could you please try the
Unix Makefiles first to see if that works?

Thanks,
Matt

On Wed, Sep 26, 2012 at 1:29 PM, Gabriel Santiago
<santiago.eletrica at gmail.com> wrote:
> I don't know if it is important, but in "Includes" folder in Eclipse, the
> path "/usrlocal//include/ITK-4.2" is not there.
>
> On 26 September 2012 14:12, Gabriel Santiago <santiago.eletrica at gmail.com>
> wrote:
>>
>> Well, I did use "Eclipse CDT 4" option, but still not working.
>>
>> Actually, I am using Eclipse Indigo. Could this be a problem?
>>
>>
>> On 26 September 2012 14:03, Matt McCormick <matt.mccormick at kitware.com>
>> wrote:
>>>
>>> PS.  Please reply-to-all so the messages are archived on the mailing
>>> list.
>>>
>>> On Wed, Sep 26, 2012 at 12:59 PM, Matt McCormick
>>> <matt.mccormick at kitware.com> wrote:
>>> > Hi Gabriel,
>>> >
>>> > You must use CMake to generate the Makefiles/Project Files.  Then, use
>>> > your build system of choice to run the Makefiles/Project Files.  The
>>> > CMake default "generator" on Linux is "Unix Makefiles".  If you use
>>> > this, then run the "make" command in the CMake binary directory.  If
>>> > you want to use Eclipse, you must specify the "Eclipse CDT4 - Unix
>>> > Makefiles" generator.  This will create Eclipse CDT 4.9 projects
>>> > files.  You need to use these when you try to build, so Eclipse will
>>> > not
>>> > know where to look for the header files, libraries.
>>> >
>>> > HTH,
>>> > Matt
>>> >
>>> > On Wed, Sep 26, 2012 at 12:43 PM, Gabriel Santiago
>>> > <santiago.eletrica at gmail.com> wrote:
>>> >> Ok, I just run the example and got the same error:
>>> >>
>>> >> fatal error: vcl_config_manual.h: No such file or directory
>>> >> ComputeGradientMagnitudeOfGrayscaleImage        line 242, external
>>> >> location:
>>> >> /usr/local/include/ITK-4.2/vcl_compiler.h    C/C++ Problem
>>> >>
>>> >>
>>> >>
>>> >> On 26 September 2012 13:31, Gabriel Santiago
>>> >> <santiago.eletrica at gmail.com>
>>> >> wrote:
>>> >>>
>>> >>> In fact, when I import those files to Eclipse, it shows that every
>>> >>> single
>>> >>> line of the code has some kind of error and I can not build it.
>>> >>>
>>> >>>
>>> >>> On 26 September 2012 13:28, Gabriel Santiago
>>> >>> <santiago.eletrica at gmail.com>
>>> >>> wrote:
>>> >>>>
>>> >>>> Yes, that's correct. That's the the ITK_DIR:
>>> >>>> /usr/local/lib/cmake/ITK-4.2/
>>> >>>> I am trying to run the example you told me. But no success up to
>>> >>>> now...
>>> >>>> What should I do?
>>> >>>>
>>> >>>> thx!
>>> >>>>
>>> >>>>
>>> >>>> On 26 September 2012 13:24, Matt McCormick
>>> >>>> <matt.mccormick at kitware.com>
>>> >>>> wrote:
>>> >>>>>
>>> >>>>> Hi Gabriel,
>>> >>>>>
>>> >>>>> On Wed, Sep 26, 2012 at 12:02 PM, Gabriel Santiago
>>> >>>>> <santiago.eletrica at gmail.com> wrote:
>>> >>>>> > Thank you, Matt. But can you please, tell step by step exactly
>>> >>>>> > what
>>> >>>>> > should I
>>> >>>>> > do? I am a beginner to this CMake thing. What should be the
>>> >>>>> > ITK_DIR
>>> >>>>> > correct
>>> >>>>> > configuration?
>>> >>>>>
>>> >>>>> ITK_DIR should be the directory containing the file
>>> >>>>> ITKConfig.cmake.
>>> >>>>> If ITK is not install, it is the location of the binary build
>>> >>>>> directory.  If ITK is installed, I believe in your case it would be
>>> >>>>> /usr/local/lib/cmake/ITK-4.2/
>>> >>>>>
>>> >>>>> HTH,
>>> >>>>> Matt
>>> >>>>>
>>> >>>>>
>>> >>>>> >
>>> >>>>> > Thanks again,
>>> >>>>> >
>>> >>>>> >
>>> >>>>> > On 26 September 2012 12:35, Matt McCormick
>>> >>>>> > <matt.mccormick at kitware.com>
>>> >>>>> > wrote:
>>> >>>>> >>
>>> >>>>> >> On Wed, Sep 26, 2012 at 10:37 AM, Gabriel Santiago
>>> >>>>> >> <santiago.eletrica at gmail.com> wrote:
>>> >>>>> >> > Hi Matt,
>>> >>>>> >> >
>>> >>>>> >> > Thanks for your reply.
>>> >>>>> >> >
>>> >>>>> >> > Here it is:
>>> >>>>> >> > //- File name: myProject.cpp in myProject folder.
>>> >>>>> >> > // -- Code:
>>> >>>>> >> >
>>> >>>>> >> > #include "/usr/local/include/ITK-4.2/itkImage.h"
>>> >>>>> >> > #include "/usr/local/include/ITK-4.2/itkImageFileReader.h"
>>> >>>>> >> > #include
>>> >>>>> >> > "/usr/local/include/ITK-4.2/itkGradientMagnitudeImageFilter.h"
>>> >>>>> >> >
>>> >>>>> >> > int main(int arcg, char** argv)
>>> >>>>> >> > {
>>> >>>>> >> >     typedef itk::Image<unsigned short, 2> ImageType;
>>> >>>>> >> >     typedef itk::ImageFileReader<ImageType> ReaderType;
>>> >>>>> >> >     typedef itk::GradientMagnitudeImageFilter<ImageType,
>>> >>>>> >> > ImageType>
>>> >>>>> >> > FilterType;
>>> >>>>> >> >
>>> >>>>> >> >     ReaderType::Pointer reader = ReaderType::New();
>>> >>>>> >> >     FilterType::Pointer filter = FilterType::New();
>>> >>>>> >> >
>>> >>>>> >> >     reader->SetFileName(argv[1]);
>>> >>>>> >> >     filter->SetInput(reader->GetOutput());
>>> >>>>> >> >     filter->Update();
>>> >>>>> >> >
>>> >>>>> >> >     return 0;
>>> >>>>> >> >
>>> >>>>> >> > }
>>> >>>>> >> >
>>> >>>>> >> > // -- CMakeLists.txt in myProject folder.
>>> >>>>> >> >
>>> >>>>> >> > PROJECT( myProject )
>>> >>>>> >> > FIND_PACKAGE ( ITK REQUIRED )
>>> >>>>> >> > IF ( ITK_FOUND )
>>> >>>>> >> > INCLUDE( ${ITK_USE_FILE} )
>>> >>>>> >> > ENDIF( ITK_FOUND )
>>> >>>>> >> > ADD_EXECUTABLE( myProject myProject.cpp )
>>> >>>>> >> > TARGET_LINK_LIBRARIES ( myProject ITKCommon ITKIO)
>>> >>>>> >> >
>>> >>>>> >> >
>>> >>>>> >> > Ow! And I forgot to mention that in order to make things work,
>>> >>>>> >> > I
>>> >>>>> >> > had to
>>> >>>>> >> > include the whole path to itk libraries.
>>> >>>>> >>
>>> >>>>> >> Yes, that should not be necessary.  It should be '#include
>>> >>>>> >> "itkImage.h"', etc.   The "INCLUDE" statement of your
>>> >>>>> >> CMakeLists.txt
>>> >>>>> >> should be calling the CMake "include_directories" statement,
>>> >>>>> >> which
>>> >>>>> >> sets up the right include "-I" flags when building.
>>> >>>>> >>
>>> >>>>> >> Some sanity checks:
>>> >>>>> >>
>>> >>>>> >> *  Make sure ITK_DIR is set correctly in the CMake
>>> >>>>> >> configuration.
>>> >>>>> >> *  build with "make VERBOSE=1" and make use there is a
>>> >>>>> >> "-I/usr/local/include/ITK-4.2"
>>> >>>>> >>
>>> >>>>> >> Try this example (code downloadable in the sidebar on the left):
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> http://itk.org/ITKExamples/Examples/Filtering/ImageGradient/ComputeGradientMagnitudeOfGrayscaleImage/ComputeGradientMagnitudeOfGrayscaleImage.html
>>> >>>>> >>
>>> >>>>> >> Hope this helps,
>>> >>>>> >> Matt
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> >
>>> >>>>> >> >
>>> >>>>> >> > On 26 September 2012 11:34, Matt McCormick
>>> >>>>> >> > <matt.mccormick at kitware.com>
>>> >>>>> >> > wrote:
>>> >>>>> >> >>
>>> >>>>> >> >> Hi Gabriel,
>>> >>>>> >> >>
>>> >>>>> >> >> Could you please share the source code you are using for the
>>> >>>>> >> >> project.
>>> >>>>> >> >>
>>> >>>>> >> >> Thanks,
>>> >>>>> >> >> Matt
>>> >>>>> >> >>
>>> >>>>> >> >> On Wed, Sep 26, 2012 at 10:12 AM, Gabriel Santiago
>>> >>>>> >> >> <santiago.eletrica at gmail.com> wrote:
>>> >>>>> >> >> > Hi guys,
>>> >>>>> >> >> >
>>> >>>>> >> >> > I am trying to run ITK on my Ubuntu 12.04.1. I did exactly
>>> >>>>> >> >> > what
>>> >>>>> >> >> > the
>>> >>>>> >> >> > tutorial
>>> >>>>> >> >> > says, except that my Cmake and ITK are the most recent
>>> >>>>> >> >> > versions.
>>> >>>>> >> >> > I also installed the CMake gui interface, which does
>>> >>>>> >> >> > exactly
>>> >>>>> >> >> > what the
>>> >>>>> >> >> > ccmake
>>> >>>>> >> >> > does and has the same interface that the Windows version.
>>> >>>>> >> >> >
>>> >>>>> >> >> > After I installed ITK on my linux, I tried myProject
>>> >>>>> >> >> > example, as
>>> >>>>> >> >> > described
>>> >>>>> >> >> > in the tutorial. After I made the .cpp (or .cxx) file and
>>> >>>>> >> >> > the
>>> >>>>> >> >> > CMakeLists.txt
>>> >>>>> >> >> > with the same code found in "Getting Started I", I used
>>> >>>>> >> >> > CMake,
>>> >>>>> >> >> > choosing
>>> >>>>> >> >> > my
>>> >>>>> >> >> > /workspace/myProject as source folder and
>>> >>>>> >> >> > /workspace/myProject/bin as
>>> >>>>> >> >> > binary
>>> >>>>> >> >> > directory. Everything seems to work fine, until I try to
>>> >>>>> >> >> > build
>>> >>>>> >> >> > it.
>>> >>>>> >> >> >
>>> >>>>> >> >> > I get the following error message:
>>> >>>>> >> >> >
>>> >>>>> >> >> > fatal error: vcl_config_manual.h: No such file or directory
>>> >>>>> >> >> > myProject
>>> >>>>> >> >> > line 242, external location:
>>> >>>>> >> >> > /usr/local/include/ITK-4.2/vcl_compiler.h
>>> >>>>> >> >> > C/C++ Problem
>>> >>>>> >> >> >
>>> >>>>> >> >> > Can anyone, please, help me?
>>> >>>>> >> >> >
>>> >>>>> >> >> > Thanks in advance,
>>> >>>>> >> >> >
>>> >>>>> >> >> > --
>>> >>>>> >> >> > Gabriel Santiago
>>> >>>>> >> >> >
>>> >>>>> >> >
>>> >>>>> >> >
>>> >>>>> >> >
>>> >>>>> >> >
>>> >>>>> >
>>> >>>>> >
>>> >>>>> >
>>> >>>>> >
>>> >>>>> > --
>>>
>>>
>>
>