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/*=========================================================================
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.
=========================================================================*/
#include "gdcmSplitMosaicFilter.h"
#include "gdcmCSAHeader.h"
#include "gdcmAttribute.h"
#include "gdcmImageHelper.h"
#include <math.h>
namespace gdcm
{
SplitMosaicFilter::SplitMosaicFilter():F(new File),I(new Image) {}
SplitMosaicFilter::~SplitMosaicFilter() {}
namespace details {
/*
* gdcmDataExtra/gdcmSampleData/images_of_interest/MR-sonata-3D-as-Tile.dcm
*/
static bool reorganize_mosaic(const unsigned short *input, const unsigned int *inputdims,
unsigned int square, const unsigned int *outputdims, unsigned short *output )
{
for(unsigned int x = 0; x < outputdims[0]; ++x)
{
for(unsigned int y = 0; y < outputdims[1]; ++y)
{
for(unsigned int z = 0; z < outputdims[2]; ++z)
{
const size_t outputidx = x + y*outputdims[0] + z*outputdims[0]*outputdims[1];
const size_t inputidx = (x + (z%square)*outputdims[0]) +
(y + (z/square)*outputdims[1])*inputdims[0];
output[ outputidx ] = input[ inputidx ];
}
}
}
return true;
}
}
void SplitMosaicFilter::SetImage(const Image& image)
{
I = image;
}
bool SplitMosaicFilter::ComputeMOSAICDimensions( unsigned int dims[3] )
{
CSAHeader csa;
DataSet& ds = GetFile().GetDataSet();
const PrivateTag &t1 = csa.GetCSAImageHeaderInfoTag();
int numberOfImagesInMosaic = 0;
if( csa.LoadFromDataElement( ds.GetDataElement( t1 ) ) )
{
// SliceThickness ??
if( csa.FindCSAElementByName( "NumberOfImagesInMosaic" ) )
{
const CSAElement &csael4 = csa.GetCSAElementByName( "NumberOfImagesInMosaic" );
if( !csael4.IsEmpty() )
{
Element<VR::IS, VM::VM1> el4 = {{ 0 }};
el4.Set( csael4.GetValue() );
numberOfImagesInMosaic = el4.GetValue();
}
}
}
else
{
// Some weird anonymizer remove the private creator but leave the actual element.
// oh well, let try harder:
// (0019,100a) US 72 # 2,1 NumberOfImagesInMosaic
PrivateTag t2 (0x0019,0x0a, "SIEMENS MR HEADER");
const DataElement &de = ds.GetDataElement( t2 );
const ByteValue * bv = de.GetByteValue();
if( bv )
{
Element<VR::US, VM::VM1> el1 = {{0}};
std::istringstream is;
is.str( std::string( bv->GetPointer(), bv->GetLength() ) );
el1.Read( is );
numberOfImagesInMosaic = el1.GetValue();
}
}
if( !numberOfImagesInMosaic )
{
gdcmErrorMacro( "Could not find NumberOfImagesInMosaic" );
return false;
}
std::vector<unsigned int> colrow =
ImageHelper::GetDimensionsValue( GetFile() );
dims[0] = colrow[0];
dims[1] = colrow[1];
const unsigned int div = (unsigned int )ceil(sqrt( (double)numberOfImagesInMosaic ) );
dims[0] /= div;
dims[1] /= div;
dims[2] = numberOfImagesInMosaic;
return true;
}
bool SplitMosaicFilter::Split()
{
bool success = true;
DataSet& ds = GetFile().GetDataSet();
unsigned int dims[3] = {0,0,0};
if( ! ComputeMOSAICDimensions( dims ) )
{
return false;
}
unsigned int div = (unsigned int )ceil(sqrt( (double)dims[2]) );
const Image &inputimage = GetImage();
if( inputimage.GetPixelFormat() != PixelFormat::UINT16 )
{
gdcmDebugMacro( "Expecting UINT16 PixelFormat" );
return false;
}
unsigned long l = inputimage.GetBufferLength();
std::vector<char> buf;
buf.resize(l);
inputimage.GetBuffer( &buf[0] );
DataElement pixeldata( Tag(0x7fe0,0x0010) );
std::vector<char> outbuf;
outbuf.resize(l);
bool b = details::reorganize_mosaic(
(unsigned short*)&buf[0], inputimage.GetDimensions(), div, dims,
(unsigned short*)&outbuf[0] );
if( !b ) return false;
VL::Type outbufSize = (VL::Type)outbuf.size();
pixeldata.SetByteValue( &outbuf[0], outbufSize );
Image &image = GetImage();
image.SetNumberOfDimensions( 3 );
image.SetDimension(0, dims[0] );
image.SetDimension(1, dims[1] );
image.SetDimension(2, dims[2] );
PhotometricInterpretation pi;
pi = PhotometricInterpretation::MONOCHROME2;
image.SetDataElement( pixeldata );
// Second part need to fix the Media Storage, now that this is not a single slice anymore
MediaStorage ms = MediaStorage::SecondaryCaptureImageStorage;
ms.SetFromFile( GetFile() );
if( ms == MediaStorage::MRImageStorage )
{
// Ok make it a MediaStorage::EnhancedMRImageStorage
// ms = MediaStorage::EnhancedMRImageStorage;
//
// // Remove old MRImageStorage attribute then:
// ds.Remove( Tag(0x0020,0x0032) ); // Image Position (Patient)
// ds.Remove( Tag(0x0020,0x0037) ); // Image Orientation (Patient)
// ds.Remove( Tag(0x0028,0x1052) ); // Rescale Intercept
// ds.Remove( Tag(0x0028,0x1053) ); // Rescale Slope
// ds.Remove( Tag(0x0028,0x1054) ); // Rescale Type
}
else
{
gdcmDebugMacro( "Expecting MRImageStorage" );
return false;
}
DataElement de( Tag(0x0008, 0x0016) );
const char* msstr = MediaStorage::GetMSString(ms);
VL::Type strlenMsstr = (VL::Type)strlen(msstr);
de.SetByteValue( msstr, strlenMsstr );
de.SetVR( Attribute<0x0008, 0x0016>::GetVR() );
ds.Replace( de );
return success;
}
} // end namespace gdcm
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