GDCM 2.2.1

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csa2img.cxx
/*=========================================================================
Program: GDCM (Grassroots DICOM). A DICOM library
Copyright (c) 2006-2011 Mathieu Malaterre
All rights reserved.
See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notice for more information.
=========================================================================*/
/*
* I do not know what the format is, just guessing from info found on the net:
*
* http://atonal.ucdavis.edu/matlab/fmri/spm5/spm_dicom_convert.m
*
* This example is an attempt at understanding the format used by SIEMENS
* their "SIEMENS CSA NON-IMAGE" DICOM file (1.3.12.2.1107.5.9.1)
*
* Everything done in this code is for the sole purpose of writing interoperable
* software under Sect. 1201 (f) Reverse Engineering exception of the DMCA.
* If you believe anything in this code violates any law or any of your rights,
* please contact us (gdcm-developers@lists.sourceforge.net) so that we can
* find a solution.
*
*/
#include "gdcmReader.h"
#include "gdcmImageReader.h"
#include "gdcmImageWriter.h"
#include "gdcmCSAHeader.h"
#include "gdcmAttribute.h"
#include "gdcmPrivateTag.h"
#include <math.h>
int main(int argc, char *argv [])
{
if( argc < 2 ) return 1;
// gdcmDataExtra/gdcmNonImageData/exCSA_Non-Image_Storage.dcm
// PHANTOM.MR.CARDIO_COEUR_S_QUENCE_DE_REP_RAGE.9.257.2008.03.20.14.53.25.578125.43151705.IMA
const char *filename = argv[1];
gdcm::Reader reader; // Do not use ImageReader
reader.SetFileName( filename );
if( !reader.Read() )
{
std::cerr << "Failed to read: " << filename << std::endl;
return 1;
}
gdcm::CSAHeader csa;
const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
const gdcm::PrivateTag &t1 = csa.GetCSAImageHeaderInfoTag();
//std::cout << t1 << std::endl;
//const gdcm::PrivateTag &t2 = csa.GetCSASeriesHeaderInfoTag();
if( ds.FindDataElement( t1 ) )
{
csa.LoadFromDataElement( ds.GetDataElement( t1 ) );
csa.Print( std::cout );
}
int dims[2] = {};
if( csa.FindCSAElementByName( "Columns" ) )
{
const gdcm::CSAElement &csael = csa.GetCSAElementByName( "Columns" );
std::cout << csael << std::endl;
//const gdcm::ByteValue *bv = csael.GetByteValue();
gdcm::Element<gdcm::VR::IS, gdcm::VM::VM1> el;
el.Set( csael.GetValue() );
dims[0] = el.GetValue();
std::cout << "Columns:" << el.GetValue() << std::endl;
}
if( csa.FindCSAElementByName( "Rows" ) )
{
const gdcm::CSAElement &csael2 = csa.GetCSAElementByName( "Rows" );
std::cout << csael2 << std::endl;
gdcm::Element<gdcm::VR::IS, gdcm::VM::VM1> el2;
el2.Set( csael2.GetValue() );
dims[1] = el2.GetValue();
std::cout << "Rows:" << el2.GetValue() << std::endl;
}
double spacing[2] = { 1. , 1. };
bool spacingfound = false;
if( csa.FindCSAElementByName( "PixelSpacing" ) )
{
const gdcm::CSAElement &csael3 = csa.GetCSAElementByName( "PixelSpacing" );
if( !csael3.IsEmpty() )
{
std::cout << csael3 << std::endl;
gdcm::Element<gdcm::VR::DS, gdcm::VM::VM2> el3;
el3.Set( csael3.GetValue() );
spacing[0] = el3.GetValue(0);
spacing[1] = el3.GetValue(1);
std::cout << "PixelSpacing:" << el3.GetValue() << "," << el3.GetValue(1) << std::endl;
spacingfound = true;
}
}
if( !spacingfound )
{
std::cerr << "Problem with PixelSpacing" << std::endl;
//return 1;
}
if( !dims[0] || !dims[1] )
{
std::cerr << "Problem with dims" << std::endl;
return 1;
}
gdcm::ImageWriter writer;
gdcm::Image &image = writer.GetImage();
image.SetNumberOfDimensions( 2 ); // good default
image.SetDimension(0, dims[0] );
image.SetDimension(1, dims[1] );
image.SetSpacing(0, spacing[0] );
image.SetSpacing(1, spacing[1] );
gdcm::PixelFormat pixeltype = gdcm::PixelFormat::INT16; // bytepix = spm_type('int16','bits')/8;
//unsigned long l = image.GetBufferLength();
//const int p = l / (dims[0] * dims[1]);
//image.SetNumberOfDimensions( 3 );
//image.SetDimension(2, p / pixeltype.GetPixelSize() );
gdcm::PhotometricInterpretation pi;
pi = gdcm::PhotometricInterpretation::MONOCHROME2;
//pixeltype.SetSamplesPerPixel( );
image.SetPhotometricInterpretation( pi );
image.SetPixelFormat( pixeltype );
//image.SetIntercept( inputimage.GetIntercept() );
//image.SetSlope( inputimage.GetSlope() );
//gdcm::DataElement pixeldata( gdcm::Tag(0x7fe1,0x1010) );
//pixeldata.SetByteValue( &outbuf[0], outbuf.size() );
gdcm::PrivateTag csanonimaget(0x7fe1,0x10,"SIEMENS CSA NON-IMAGE");
const gdcm::DataElement &pixeldata = ds.GetDataElement( csanonimaget );
image.SetDataElement( pixeldata );
std::string outfilename = "outcsa.dcm";
//writer.SetFile( reader.GetFile() );
writer.SetFileName( outfilename.c_str() );
if( !writer.Write() )
{
std::cerr << "could not write: " << outfilename << std::endl;
return 1;
}
return 0;
}