ITK/Examples/IO/VolumeFromSlices

Thanks to Dora Szasz whose original example inspired this one.

This examples creates a 3D volume from a series of 2D images. The image filenames are generated from a user supplied pattern. The pattern uses printf format. For example, to select the following files for the volume:

c:/itkguru/File001.jpg
c:/itkguru/File002.jpg
c:/itkguru/File003.jpg
...
c:/itkguru/File010.jpg

run:

VolumeFromSlices c:/itkguru/File%03d.jpg 1 10 out.mhd

VolumeFromSlices.cxx

<source lang=cpp>

1. include "itkImage.h"
2. include "itkImageSeriesReader.h"
3. include "itkImageFileWriter.h"
4. include "itkNumericSeriesFileNames.h"

int main( int argc, char * argv[] ) {

 // Verify the number of parameters in the command line
 if( argc < 5 )
   {
   std::cerr << "Usage: " << std::endl;
   std::cerr << argv[0] 
             << " pattern firstSliceValue lastSliceValue outputImageFile"
             << std::endl;
   return EXIT_FAILURE;
   }

 typedef unsigned char   PixelType;
 const unsigned int Dimension = 3;

 typedef itk::Image< PixelType, Dimension >  ImageType;
 typedef itk::ImageSeriesReader< ImageType > ReaderType;
 typedef itk::ImageFileWriter<   ImageType > WriterType;

 ReaderType::Pointer reader = ReaderType::New();
 WriterType::Pointer writer = WriterType::New();

 const unsigned int first = atoi( argv[2] );
 const unsigned int last  = atoi( argv[3] );

 const char * outputFilename = argv[4];

 typedef itk::NumericSeriesFileNames    NameGeneratorType;

 NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();

 nameGenerator->SetSeriesFormat( argv[1] );

 nameGenerator->SetStartIndex( first );
 nameGenerator->SetEndIndex( last );
 nameGenerator->SetIncrementIndex( 1 );
 std::vector<std::string> names = nameGenerator->GetFileNames();

 // List the files
 //
 std::vector<std::string>::iterator nit;
 for (nit = names.begin();
      nit != names.end();
      nit++)
   {
   std::cout << "File: " << (*nit).c_str() << std::endl;
   }
 
 reader->SetFileNames( names  );

 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;
}

</source>

CMakeLists.txt

<syntaxhighlight lang="cmake"> cmake_minimum_required(VERSION 3.9.5)

project(VolumeFromSlices)

find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED)

 find_package(VTK REQUIRED)
 include(${VTK_USE_FILE})

endif()

add_executable(VolumeFromSlices MACOSX_BUNDLE VolumeFromSlices.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(VolumeFromSlices ITKReview ${ITK_LIBRARIES})

else( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(VolumeFromSlices ${ITK_LIBRARIES})

endif( "${ITK_VERSION_MAJOR}" LESS 4 )

</syntaxhighlight>

Download and Build VolumeFromSlices

Click here to download VolumeFromSlices and its CMakeLists.txt file. Once the tarball VolumeFromSlices.tar has been downloaded and extracted,

cd VolumeFromSlices/build

• If ITK is installed:

cmake ..

• If ITK is not installed but compiled on your system, you will need to specify the path to your ITK build:

cmake -DITK_DIR:PATH=/home/me/itk_build ..

Build the project:

make

and run it:

./VolumeFromSlices

WINDOWS USERS PLEASE NOTE: Be sure to add the ITK bin directory to your path. This will resolve the ITK dll's at run time.

Building All of the Examples

Many of the examples in the ITK Wiki Examples Collection require VTK. You can build all of the the examples by following these instructions. If you are a new VTK user, you may want to try the Superbuild which will build a proper ITK and VTK.

ItkVtkGlue

ITK >= 4

For examples that use QuickView (which depends on VTK), you must have built ITK with Module_ITKVtkGlue=ON.

ITK < 4

Some of the ITK Examples require VTK to display the images. If you download the entire ITK Wiki Examples Collection, the ItkVtkGlue directory will be included and configured. If you wish to just build a few examples, then you will need to download ItkVtkGlue and build it. When you run cmake it will ask you to specify the location of the ItkVtkGlue binary directory.