Try modifying the CMakeList.txt line

TARGET_LINK_LIBRARIES(ImageReadWrite  ITKIO)

to 

TARGET_LINK_LIBRARIES(ImageReadWrite  ITKIO  ITKIOMINC2)

reconfigure and make and you should be fine

Leila

On Tue, 2009-04-21 at 13:20 -0400, Geoff Topping wrote:
> Hi all.
> 
> I've enabled the MINC2 IO review code and rebuilt ITK.  Now I'd like
> to actually test this functionality, but am having trouble setting up
> the code and CMakeLists.txt necessary to do so.
> 
> I started with the basic ImageReadWrite example code, and modified it
> based on the results of various web searches.  A seemingly helpful
> example is here:
> 
> http://en.wikibooks.org/wiki/MINC/Tutorials/part2
> 
> The result is this code:
> 
> My current code:
> 
> *****************************************************
> 
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "itkImage.h"
> 
> #include "itkImageIOFactory.h"
> #include "itkMINC2ImageIOFactory.h"
> #include "itkMINC2ImageIO.h"
> 
> 
> namespace {
>     typedef float                               PixelType;
>     const   unsigned int                        Dimension = 3;
>     typedef itk::Image<PixelType, Dimension>    ImageType;
> 
>     typedef itk::ImageFileReader<ImageType>     ReaderType;
>     typedef itk::ImageFileWriter<ImageType>     WriterType;
> 
>     typedef itk::MINC2ImageIO                   ImageIOType;
> }
> 
> int main(int argc, char ** argv) {
>     // Verify the number of parameters in the command line
>     if ( argc < 3 ) {
>         std::cerr << "Usage: " << std::endl;
>         std::cerr << argv[0] << " inputImageFile outputImageFile " <<
> std::endl;
>         return EXIT_FAILURE;
>     }
> 
>     ReaderType::Pointer reader = ReaderType::New();
>     ImageIOType::Pointer minc2ImageIO = ImageIOType::New();
>     reader->SetImageIO( minc2ImageIO );
>     const char* inputFilename  = argv[1];
>     reader->SetFileName(inputFilename);
> 
> 
>     WriterType::Pointer writer = WriterType::New();
>     const char* outputFilename = argv[2];
>     writer->SetFileName(outputFilename);
> 
> 
>     writer->SetInput(reader->GetOutput());
> 
> 
>     try { 
>         writer->Update(); 
>     } catch(itk::ExceptionObject & err) { 
>         std::cerr << "ExceptionObject caught !" << std::endl; 
>         std::cerr << err << std::endl; 
>         return EXIT_FAILURE;
>     } 
> 
>     return EXIT_SUCCESS;
> }
> 
> ******************************************************
> 
> I tried building this using my existing CMakeLists.txt that works for
> the same code without the minc-related parts...
> 
> ******************************************************
> 
> # This is the root ITK CMakeLists file.
> CMAKE_MINIMUM_REQUIRED(VERSION 2.4)
> IF(COMMAND CMAKE_POLICY)
>   CMAKE_POLICY(SET CMP0003 NEW)
> ENDIF(COMMAND CMAKE_POLICY)
> 
> 
> # This project is designed to be built outside the Insight source
> tree.
> PROJECT(IOExamples)
> 
> # Find ITK.
> FIND_PACKAGE(ITK REQUIRED)
> INCLUDE(${ITK_USE_FILE})
> 
> ADD_EXECUTABLE(ImageReadWrite ImageReadWrite.cxx )
> TARGET_LINK_LIBRARIES(ImageReadWrite  ITKIO)
> 
> *******************************************************
> 
> After re-running ccmake and running make, I got errors about missing
> headers:
> 
> *******************************************************
> 
> /work/geoff/itk/iotest > make
> [100%] Building CXX object
> CMakeFiles/ImageReadWrite.dir/ImageReadWrite.o
> In file included from /work/geoff/itk/iotest/ImageReadWrite.cxx:8:
> /work/geoff/InsightToolkit-3.12.0/Code/Review/itkMINC2ImageIO.h:37:19:
> minc2.h: No such file or directory
> In file included from /work/geoff/itk/iotest/ImageReadWrite.cxx:8:
> /work/geoff/InsightToolkit-3.12.0/Code/Review/itkMINC2ImageIO.h:100:
> error: `midimhandle_t' has not been declared
> /work/geoff/InsightToolkit-3.12.0/Code/Review/itkMINC2ImageIO.h:100:
> error: ISO C++ forbids declaration of `hdims' with no type
> /work/geoff/InsightToolkit-3.12.0/Code/Review/itkMINC2ImageIO.h:145:
> error: `mihandle_t' has not been declared
> /work/geoff/InsightToolkit-3.12.0/Code/Review/itkMINC2ImageIO.h:145:
> error: ISO C++ forbids declaration of `volume' with no type
> /work/geoff/InsightToolkit-3.12.0/Code/Review/itkMINC2ImageIO.h:149:
> error: `mihandle_t' has not been declared
> /work/geoff/InsightToolkit-3.12.0/Code/Review/itkMINC2ImageIO.h:149:
> error: ISO C++ forbids declaration of `volume' with no type
> make[2]: *** [CMakeFiles/ImageReadWrite.dir/ImageReadWrite.o] Error 1
> make[1]: *** [CMakeFiles/ImageReadWrite.dir/all] Error 2
> make: *** [all] Error 2
> /work/geoff/itk/iotest > ccmake .
> 
> ****************************************************
> 
> So I hit net searched a bit more, and found some promising looking
> alterations to the previous CMakeLists.txt, starting after the
> INCLUDE(${ITK_USE_FILE}) line:
> 
> ****************************************************
> 
> FIND_PACKAGE(MINC2)
> INCLUDE_DIRECTORIES(${MINC2_INCLUDE_PATH} ${HDF5_INCLUDE_PATH}
> ${NETCDF_INCLUDE_PATH})
> 
> ADD_EXECUTABLE(ImageReadWrite ImageReadWrite.cxx )
> TARGET_LINK_LIBRARIES(ImageReadWrite ITKIO ITKIOMINC2 ${MINC2_LIB}
> ${HDF5_LIB} ${NETCDF_LIB})
> 
> *****************************************************
> 
> After doing this, when I run ccmake, I have an extra line where I need
> to enter the location of MINC2_DIR.  I give it the same directory as I
> used to build ITK after turning on MINC and related options, but after
> pressing c to configure, I get an error message:
> 
> CMake Error: MINC2_DIR is set to "/opt/minc2", which is not a
> directory containing MINC2Config.cmake
> 
> I've searched for a file by that name in my ITK binary or code
> directories.
> 
> I also tried without the FIND_PACKAGE(MINC2) line, but just got the
> same missing headers error during compiling.
> 
> I don't know how else to point ccmake to the location of the minc2
> headers.  Can someone suggest what modifications need to be made to
> CMakeLists.txt so the compiler can find the necessary headers to build
> a program using the MINC ITK IO classes, or whatever else I need to be
> doing?  Is this documented somewhere I haven't found?
> 
> Thanks,
> Geoff Topping
> 
> 
> 
> 
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