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I have successfully compiled GDCM 2.4.4 and VTK 5.10.1 on Ubuntu server 14.04. But now I have to use JPEG2000 images and my program, that uses GDCM and VTK, is very slow. So i have decided to recompile GDCM with OPENJPEG 1.5 library (alredy compiled), but for some reason it doesn't finished .

And then ask me for three folders:

OPENJPEG_INCLUDE_DIR = /opt/ipv/3d/utils/openjpeg-1.5.2-Linux-i386/include/openjpeg-1.5
OPENJPEG_LIBRARY = /opt/ipv/3d/utils/openjpeg-1.5.2-Linux-i386/lib/libopenjpeg.so
OpenJPEG_DIR = /opt/ipv/3d/utils/openjpeg-1.5.2-Linux-i386/lib/openjpeg-1.5

I give him the right folders and then I have this error after execute "make" for the GDCM:

.....
  [ 56%] building gdcm.jar
[ 56%] Built target GDCMJavaJar
Linking CXX shared library ../../bin/libgdcmDSED.so
[ 56%] Built target gdcmDSED
Scanning dependencies of target gdcmIOD
[ 57%] [ 57%] [ 57%] [ 57%] [ 57%] Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmMacro.cxx.o
Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmMacros.cxx.o                                                          
Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmModule.cxx.o                                                          
Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmModules.cxx.o                                                         
[ 58%] Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmNestedModuleEntries.cxx.o                                      
[ 58%] Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmIODEntry.cxx.o                                                 
Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmTableReader.cxx.o                                                     
[ 58%] Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmTable.cxx.o                                                    
[ 58%] [ 58%] [ 58%] Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmSeries.cxx.o                                     
Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmDefs.cxx.o                                                            
Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmDefinedTerms.cxx.o                                                    
[ 59%] [ 59%] Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmEnumeratedValues.cxx.o                                  
Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmStudy.cxx.o                                                           
[ 59%] [ 59%] Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmPatient.cxx.o                                           
Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmType.cxx.o                                                            
[ 59%] Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmUsage.cxx.o                                                    
[ 60%] Building CXX object Source/InformationObjectDefinition/CMakeFiles/gdcmIOD.dir/gdcmIOD.cxx.o                                                      
Linking CXX shared library ../../bin/libgdcmIOD.so
[ 60%] Built target gdcmIOD
Scanning dependencies of target gdcmDICT
[ 60%] [ 61%] [ 61%] Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmDictEntry.cxx.o
[ 61%] [ 61%] Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmDicts.cxx.o                                                         
[ 61%] [ 62%] [ 62%] Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmDefaultDicts.cxx.o                                           
Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmPrivateDefaultDicts.cxx.o                                                         
Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmGlobal.cxx.o                                                                      
Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmGroupDict.cxx.o                                                                   
Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmDefaultGroupNames.cxx.o                                                           
Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmUIDs.cxx.o                                                                        
[ 62%] Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmSOPClassUIDToIOD.cxx.o                                                     
[ 62%] Building CXX object Source/DataDictionary/CMakeFiles/gdcmDICT.dir/gdcmCSAHeaderDefaultDicts.cxx.o                                                
Linking CXX shared library ../../bin/libgdcmDICT.so
[ 62%] Built target gdcmDICT
Scanning dependencies of target gdcmMSFF
[ 63%] [ 63%] [ 63%] [ 63%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmFileStreamer.cxx.o
[ 63%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmJSON.cxx.o                                                      
[ 64%] [ 64%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmAnonymizer.cxx.o                                         
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmFileChangeTransferSyntax.cxx.o                                         
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmFileAnonymizer.cxx.o                                                   
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmIconImageFilter.cxx.o                                                  
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmIconImageGenerator.cxx.o                                               
[ 64%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmDICOMDIRGenerator.cxx.o                                         
[ 64%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSpacing.cxx.o                                                   
[ 64%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmFileExplicitFilter.cxx.o                                        
[ 64%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmFileDerivation.cxx.o                                            
[ 65%] [ 65%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageFragmentSplitter.cxx.o                              
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmTagPath.cxx.o                                                          
[ 65%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSimpleSubjectWatcher.cxx.o                                      
[ 65%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmAnonymizeEvent.cxx.o                                            
[ 65%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPixmap.cxx.o                                                    
[ 66%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmBitmap.cxx.o                                                    
[ 66%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmRescaler.cxx.o                                                  
[ 66%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageToImageFilter.cxx.o                                        
[ 66%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmBitmapToBitmapFilter.cxx.o                                      
[ 66%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPixmapToPixmapFilter.cxx.o                                      
[ 67%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageChangeTransferSyntax.cxx.o                                 
[ 67%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageApplyLookupTable.cxx.o                                     
[ 67%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmOrientation.cxx.o                                               
[ 67%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmDataSetHelper.cxx.o                                             
[ 67%] [ 67%] [ 68%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageChangePlanarConfiguration.cxx.o              
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageChangePhotometricInterpretation.cxx.o                             
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmDirectionCosines.cxx.o                                                 
[ 68%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSorter.cxx.o                                                    
[ 68%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSerieHelper.cxx.o                                               
[ 68%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmIPPSorter.cxx.o                                                 
[ 68%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmApplicationEntity.cxx.o                                         
[ 69%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmDICOMDIR.cxx.o                                                  
[ 69%] [ 69%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSpectroscopy.cxx.o                                       
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmEncapsulatedDocument.cxx.o                                             
[ 69%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSplitMosaicFilter.cxx.o                                         
[ 69%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmFiducials.cxx.o                                                 
[ 70%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmWaveform.cxx.o                                                  
[ 70%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPersonName.cxx.o                                                
[ 70%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmIconImage.cxx.o                                                 
[ 70%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmUIDGenerator.cxx.o                                              
[ 70%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmUUIDGenerator.cxx.o                                             
[ 71%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPrinter.cxx.o                                                   
[ 71%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmDictPrinter.cxx.o                                               
[ 71%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmXMLPrinter.cxx.o                                                
[ 71%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmScanner.cxx.o                                                   
[ 71%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPixmapReader.cxx.o                                              
[ 72%] [ 72%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageReader.cxx.o                                        
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPixmapWriter.cxx.o                                                     
[ 72%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageWriter.cxx.o                                               
[ 72%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmStringFilter.cxx.o                                              
[ 72%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageHelper.cxx.o                                               
[ 72%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmValidate.cxx.o                                                  
[ 73%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmDumper.cxx.o                                                    
[ 73%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImage.cxx.o                                                     
[ 73%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageConverter.cxx.o                                            
[ 73%] [ 73%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageCodec.cxx.o                                         
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmJPEG12Codec.cxx.o                                                      
[ 74%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmRLECodec.cxx.o                                                  
[ 74%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPDFCodec.cxx.o                                                  
[ 74%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmAudioCodec.cxx.o                                                
[ 74%] [ 74%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmJPEG16Codec.cxx.o                                        
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmJPEGLSCodec.cxx.o                                                      
[ 75%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmJPEG8Codec.cxx.o                                                
[ 75%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmJPEGCodec.cxx.o                                                 
[ 75%] [ 75%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPVRGCodec.cxx.o                                          
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmKAKADUCodec.cxx.o                                                      
[ 75%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPNMCodec.cxx.o                                                  
[ 76%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPGXCodec.cxx.o                                                  
[ 76%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmRAWCodec.cxx.o                                                  
[ 76%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmLookupTable.cxx.o                                               
[ 76%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmOverlay.cxx.o                                                   
[ 76%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmCurve.cxx.o                                                     
[ 77%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPhotometricInterpretation.cxx.o                                 
[ 77%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmPixelFormat.cxx.o                                               
[ 77%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSegmentedPaletteColorLookupTable.cxx.o                          
[ 77%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmStreamImageReader.cxx.o                                         
[ 77%] [ 78%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmImageRegionReader.cxx.o                                  
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmDirectoryHelper.cxx.o
[ 78%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSegment.cxx.o
[ 78%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSurface.cxx.o
[ 78%] [ 78%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmMeshPrimitive.cxx.o
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSegmentWriter.cxx.o
[ 78%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSurfaceWriter.cxx.o
[ 79%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSegmentReader.cxx.o
[ 79%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSurfaceReader.cxx.o
[ 79%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSurfaceHelper.cxx.o
[ 79%] [ 79%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmSegmentHelper.cxx.o
Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/gdcmJPEG2000Codec.cxx.o
[ 80%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/__/__/Utilities/gdcmrle/rle.cxx.o
[ 80%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/__/__/Utilities/gdcmrle/info.cxx.o
[ 80%] Building CXX object Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/__/__/Utilities/gdcmrle/io.cxx.o
Linking CXX shared library ../../bin/libgdcmMSFF.so
/opt/ipv/3d/utils/openjpeg-1.5.2-Linux-i386/lib/libopenjpeg.so.1.5.2: error adding symbols: File in wrong format
collect2: error: ld returned 1 exit status
make[2]: *** [bin/libgdcmMSFF.so.2.4.4] Error 1
make[1]: *** [Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/all] Error 2
make: *** [all] Error 2
cp: cannot stat ‘/opt/ipv/3d/utils/gdcm-build/bin/vtkgdcm.jar’: No such file or directory
enrico@ubuntu-sever:/opt/ipv/3d/utils$

What can I do? Should I use onother library to open quickly JPEG2000?

user4970092
  • 21
  • 3

2 Answers2

1

Ok, i solved using the automatic installation for openjpeg:

cmake .
make
sudo make install

But the program still take a lot of time as before to open JPEG2000 images..

user4970092
  • 21
  • 3
0

When you turn on: GDCM_USE_SYSTEM_OPENJPEG (this is a setting for advanced user). CMake will inspect your system and will look for OpenJPEG*.cmake config files. In my case (default debian jessie installation) they are located here:

/usr/lib/x86_64-linux-gnu/openjpeg-1.5/OpenJPEGTargets-none.cmake
/usr/lib/x86_64-linux-gnu/openjpeg-1.5/OpenJPEGTargets.cmake
/usr/lib/x86_64-linux-gnu/openjpeg-1.5/OpenJPEGConfig.cmake

Which means that when configuring GDCM with cmake, the file are automatically found and the value for OpenJPEG_DIR is set automatically to: /usr/lib/x86_64-linux-gnu/openjpeg-1.5

I fail to understand why FindOpenJPEG.cmake would be looking for OPENJPEG_LIBRARY, but that should point to a library instead of a directory. Eg: OPENJPEG_LIBRARY should /usr/lib/x86_64-linux-gnu/libopenjpeg.so

malat
  • 12,152
  • 13
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