[Insight-users] how to modify InsightApplications

[John Drescher]

On Wed, Jan 27, 2010 at 8:29 AM, URI <zallen at wheelinghospital.com> wrote:
>
> Can somebody give me just a quick answer?  I'm not looking for specific
> information on this particular program, I'm just asking what the proper
> method is in general for modifying open-source code like this.  Do I modify
> the raw source code files and then run CMake, or do I first run CMake on the
> original source code files and then modify the resulting Visual Studio
> solution?

I take the ITK example code to my folder and create a new project for
that that is independent from ITK. I put it in my own cvs/svn server
so that I can have it anywhere I program. I have a small collection of
such examples for itk, cmake, and vtk.

Here is one from ITK:

CMakeLists.txt

PROJECT(DicomSeriesMetaDictionary)

IF(WIN32)
    CMAKE_MINIMUM_REQUIRED(VERSION 2.5 FATAL_ERROR)
    SET(CMAKE_CXX_FLAGS "/WL /GR /EHsc" )
    ADD_DEFINITIONS(-D_CRT_SECURE_NO_WARNINGS)
ENDIF(WIN32)

IF(COMMAND cmake_policy)
  cmake_policy(SET CMP0003 NEW)
endif(COMMAND cmake_policy)

SET (LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE INTERNAL
"Single output directory for building all libraries.")
SET (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE INTERNAL
"Single output directory for building all executables.")

FIND_PACKAGE( ITK REQUIRED )

INCLUDE( ${ITK_USE_FILE} )

SET( DICOM_SERIES_META_SRCS
	./src/main.cxx
)

LINK_LIBRARIES ( DicomSeriesMetaDictionary ITKCommon ITKBasicFilters ITKIO )

ADD_EXECUTABLE( DicomSeriesMetaDictionary ${DICOM_SERIES_META_SRCS} )



now src/main.cxx
#define USE_GDCM

#include "itkImage.h"
#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"

#ifdef USE_GDCM
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#else
#include "itkDICOMImageIO2.h"
#include "itkDICOMSeriesFileNames.h"
#endif //def USE_GDCM

#include <iostream>


int main(int argc, char *argv[])
{
	if (argc > 2) {
		typedef signed short    PixelType;
		const unsigned int      Dimension = 3;
		typedef itk::Image< PixelType, Dimension >      ImageType;
		typedef itk::ImageSeriesReader< ImageType >     ReaderType;
		typedef itk::ImageFileReader< ImageType >       ReaderMHDType;

#ifdef USE_GDCM
		typedef itk::GDCMImageIO                        ImageIOType;
		typedef itk::GDCMSeriesFileNames                NamesGeneratorType;
#else
		typedef itk::DICOMImageIO2                        ImageIOType;

		typedef  itk::DICOMSeriesFileNames				SeriesFileNamesType;
		typedef  SeriesFileNamesType					NamesGeneratorType;
#endif //def USE_GDCM
		

		ImageIOType::Pointer gdcmIO = ImageIOType::New();
		NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();

#ifdef USE_GDCM
		namesGenerator->SetInputDirectory( argv[1] );

		const ReaderType::FileNamesContainer & filenames =
			namesGenerator->GetInputFileNames();

		namesGenerator->SetInputDirectory( argv[1] );

#else

		namesGenerator->SetDirectory( argv[1] );

		const ReaderType::FileNamesContainer & filenames =
			namesGenerator->GetFileNames();

#endif //def USE_GDCM

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

		reader->SetImageIO( gdcmIO );
		reader->SetFileNames( filenames );

		reader->Update();
		reader->GenerateOutputInformation();

		// BEGIN IMPORTANT CODE*

		unsigned int nbSlices = filenames.size();

		ReaderType::DictionaryRawPointer dictionary;
		ReaderType::DictionaryArrayType outputArray;

		for (unsigned int i = 0; i < nbSlices; i++)
		{
			dictionary = (*(reader->GetMetaDataDictionaryArray()))[i];

			std::string entryId("0008|103e");
			std::string value("MARTIN IS THE BEST"); // it was just a test ;-)*
				itk::EncapsulateMetaData<std::string>( *dictionary, entryId, value
				);
			outputArray.push_back(dictionary);
		}

		// END*


		typedef signed short    OutputPixelType;
		const unsigned int      OutputDimension = 2;

		typedef itk::Image< OutputPixelType, OutputDimension >    Image2DType;

		typedef itk::ImageSeriesWriter< ImageType, Image2DType >
			SeriesWriterType;

		SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();

		seriesWriter->SetInput( reader->GetOutput() );
		seriesWriter->SetImageIO( gdcmIO );

#ifdef USE_GDCM
		namesGenerator->SetOutputDirectory( argv[2] );

		seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );
#else
		namesGenerator->SetDirectory( argv[2] );

		seriesWriter->SetFileNames( namesGenerator->GetFileNames() );
#endif //def USE_CDCM

		// BEGIN IMPORTANT CODE*
			seriesWriter->SetMetaDataDictionaryArray( &outputArray );
			// instead of :
			// seriesWriter->SetMetaDataDictionaryArray(
			// reader->GetMetaDataDictionaryArray());
		// END*

			seriesWriter->Update();

	}
	else
	{
		std::cout << "Usage: "<< argv[0] << " <input folder> <output folder>
" << std::endl;
	}
	
}


John