rle2img.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.
=========================================================================*/
/*
* This example shows how to rewrite a ELSCINT1/PMSCT_RLE1 compressed
* image so that it is readable by most 3rd party software (DICOM does
* not specify this particular encoding).
* This is required for the sake of interoperability with any standard
* conforming DICOM system.
*
* 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.
*
* Everything you do with this code is at your own risk, since decompression
* algorithm was not written from specification documents.
*
* Special thanks to:
* Mauro Maiorca for bringing to our attention on this new ELSCINT1
* compression algorithm : PMSCT_RLE1 (different from the 'LOSSLESS RICE')
* See post at:
* http://groups.google.com/group/comp.protocols.dicom/msg/f2b99bf706a7f8ca
*
* Thanks to Jesus Spinola, for more datasets,
* http://www.itk.org/pipermail/insight-users/2008-April/025571.html
*
* And last but not least, a very big thank to Ivo van Poorten, without
* whom we would still be looking at this compressed byte stream as if
* it was RLE compressed.
*/
#include "gdcmReader.h"
#include "gdcmPrivateTag.h"
#include "gdcmAttribute.h"
#include "gdcmImageWriter.h"
/* FIXME: Why is PhilipsLosslessRice.dcm a 512x512 image ... */
void delta_decode(const char *inbuffer, size_t length, std::vector<unsigned short> &output)
{
// RLE pass
std::vector<char> temp;
for(size_t i = 0; i < length; ++i)
{
if( inbuffer[i] == (char)0xa5 )
{
//unsigned char repeat = (unsigned char)inbuffer[i+1] + 1;
//assert( (unsigned char)inbuffer[i+1] != 255 );
int repeat = (unsigned char)inbuffer[i+1] + 1;
char value = inbuffer[i+2];
while(repeat)
{
temp.push_back( value );
--repeat;
}
i+=2;
}
else
{
temp.push_back( inbuffer[i] );
}
}
// Delta encoding pass
unsigned short delta = 0;
for(size_t i = 0; i < temp.size(); ++i)
{
if( temp[i] == 0x5a )
{
unsigned char v1 = (unsigned char)temp[i+1];
unsigned char v2 = (unsigned char)temp[i+2];
unsigned short value = (unsigned short)(v2 * 256 + v1);
output.push_back( value );
delta = value;
i+=2;
}
else
{
unsigned short value = (unsigned short)(temp[i] + delta);
output.push_back( value );
delta = value;
}
//assert( output[output.size()-1] == ref[output.size()-1] );
}
if ( output.size() % 2 )
{
output.resize( output.size() - 1 );
}
std::cout << length << " -> " << output.size() * 2 << std::endl;
}
int main(int argc, char *argv [])
{
if( argc < 2 )
{
std::cerr << argv[0] << "input.dcm [output.dcm]" << std::endl;
std::cerr << "will default to 'outrle.dcm' unless output.dcm is specified."
<< std::endl;
return 1;
}
const char *filename = argv[1];
gdcm::Reader reader;
reader.SetFileName( filename );
if( !reader.Read() )
{
std::cerr << "Failed to read: " << filename << std::endl;
return 1;
}
const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
// (07a1,1011) CS [PMSCT_RLE1] # 10,1 Tamar Compression Type
const gdcm::PrivateTag tcompressiontype(0x07a1,0x0011,"ELSCINT1");
if( !ds.FindDataElement( tcompressiontype ) ) return 1;
const gdcm::DataElement& compressiontype = ds.GetDataElement( tcompressiontype );
if ( compressiontype.IsEmpty() ) return 1;
const gdcm::ByteValue * bv = compressiontype.GetByteValue();
std::string comprle = "PMSCT_RLE1";
std::string comprgb = "PMSCT_RGB1";
bool isrle = false;
bool isrgb = false;
if( strncmp( bv->GetPointer(), comprle.c_str(), comprle.size() ) == 0 )
{
isrle = true;
}
if( strncmp( bv->GetPointer(), comprgb.c_str(), comprgb.size() ) == 0 )
{
isrgb = true;
std::cerr << "See: pmsct_rgb1.cxx instead" << std::endl;
return 1;
}
if( !isrgb && !isrle ) return 1;
// check if compressed pixel data reside in private or standard tag
const gdcm::PrivateTag tprivatepixeldata(0x07a1,0x100a,"ELSCINT1");
const gdcm::Tag tstandardpixeldata(0x7fe0, 0x0010);
gdcm::Tag tpixeldata;
if(ds.FindDataElement(tprivatepixeldata)) tpixeldata = tprivatepixeldata;
else if(ds.FindDataElement(tstandardpixeldata)) tpixeldata = tstandardpixeldata;
if(!ds.FindDataElement(tpixeldata)) return 1;
const gdcm::DataElement& compressionpixeldata = ds.GetDataElement( tpixeldata);
if ( compressionpixeldata.IsEmpty() ) return 1;
const gdcm::ByteValue * bv2 = compressionpixeldata.GetByteValue();
gdcm::Attribute<0x0028,0x0010> at1;
at1.SetFromDataSet( ds );
gdcm::Attribute<0x0028,0x0011> at2;
at2.SetFromDataSet( ds );
gdcm::DataElement pixeldata;
// if standard voxel data element does not exist, create it
if( !reader.GetFile().GetDataSet().FindDataElement( tpixeldata ) )
{
pixeldata = gdcm::DataElement( tpixeldata, 0, gdcm::VR::OW );
}
else{
pixeldata = reader.GetFile().GetDataSet().GetDataElement( tpixeldata );
}
pixeldata.SetVR( gdcm::VR::OW );
gdcm::VL bv2l = bv2->GetLength();
gdcm::VL at1l = at1.GetValue() * at2.GetValue() * 2; /* sizeof(unsigned short) == 2 */
// Handle special case that is not compressed:
if( bv2l == at1l )
{
pixeldata.SetByteValue( bv2->GetPointer(), bv2->GetLength() );
}
else
{
std::vector<unsigned short> buffer;
delta_decode(bv2->GetPointer(), bv2->GetLength(), buffer);
pixeldata.SetByteValue( (char*)buffer.data(), (uint32_t)(buffer.size() * sizeof( unsigned short )) );
}
// TODO we should check that decompress byte buffer match the expected size (row*col*...)
// Add the pixel data element
if( reader.GetFile().GetDataSet().FindDataElement( tpixeldata ) )
{
reader.GetFile().GetDataSet().Replace( pixeldata );
}
else
{
reader.GetFile().GetDataSet().ReplaceEmpty( pixeldata );
}
reader.GetFile().GetHeader().SetDataSetTransferSyntax(
gdcm::TransferSyntax::ExplicitVRLittleEndian);
gdcm::Writer writer;
writer.SetFile( reader.GetFile() );
// Cleanup stuff:
// This makes the code equivalent to Philips workstation IntelliSpace Portal
if( writer.GetFile().GetDataSet().FindDataElement( tcompressiontype ) )
{
writer.GetFile().GetDataSet().Remove( gdcm::Tag(0x07a1,0x1011) );
}
if( writer.GetFile().GetDataSet().FindDataElement( tprivatepixeldata ) )
{
writer.GetFile().GetDataSet().Remove( gdcm::Tag(0x07a1,0x100a) );
}
std::string outfilename;
if (argc > 2)
outfilename = argv[2];
else
outfilename = "outrle.dcm";
writer.SetFileName( outfilename.c_str() );
if( !writer.Write() )
{
std::cerr << "Failed to write" << std::endl;
return 1;
}
std::cout << "success !" << std::endl;
return 0;
}
gdcm::Attribute
Attribute class This class use template metaprograming tricks to let the user know when the template ...
Definition gdcmAttribute.h:86
gdcm::Attribute::GetValue
ArrayType & GetValue(unsigned int idx=0)
Definition gdcmAttribute.h:154
gdcm::Attribute::SetFromDataSet
void SetFromDataSet(DataSet const &ds)
Definition gdcmAttribute.h:229
gdcm::ByteValue
Class to represent binary value (array of bytes).
Definition gdcmByteValue.h:35
gdcm::ByteValue::GetPointer
const char * GetPointer() const
Definition gdcmByteValue.h:110
gdcm::ByteValue::GetLength
VL GetLength() const override
Definition gdcmByteValue.h:77
gdcm::DataElement
Class to represent a Data Element either Implicit or Explicit.
Definition gdcmDataElement.h:59
gdcm::DataElement::GetByteValue
const ByteValue * GetByteValue() const
Definition gdcmDataElement.h:133
gdcm::DataElement::IsEmpty
bool IsEmpty() const
Check if Data Element is empty.
Definition gdcmDataElement.h:106
gdcm::DataElement::SetByteValue
void SetByteValue(const char *array, VL length)
Definition gdcmDataElement.h:126
gdcm::DataElement::SetVR
void SetVR(VR const &vr)
Definition gdcmDataElement.h:88
gdcm::DataSet
Class to represent a Data Set (which contains Data Elements).
Definition gdcmDataSet.h:56
gdcm::DataSet::GetDataElement
const DataElement & GetDataElement(const Tag &t) const
Definition gdcmDataSet.h:188
gdcm::DataSet::ReplaceEmpty
void ReplaceEmpty(const DataElement &de)
Only replace a DICOM attribute when it is missing or empty.
Definition gdcmDataSet.h:161
gdcm::DataSet::FindDataElement
bool FindDataElement(const PrivateTag &t) const
Look up if private tag 't' is present in the dataset:
gdcm::DataSet::Remove
SizeType Remove(const Tag &tag)
Completely remove a dataelement from the dataset.
Definition gdcmDataSet.h:172
gdcm::DataSet::Replace
void Replace(const DataElement &de)
Replace a dataelement with another one.
Definition gdcmDataSet.h:150
gdcm::FileMetaInformation::SetDataSetTransferSyntax
void SetDataSetTransferSyntax(const TransferSyntax &ts)
gdcm::File::GetDataSet
const DataSet & GetDataSet() const
Get Data Set.
Definition gdcmFile.h:57
gdcm::File::GetHeader
const FileMetaInformation & GetHeader() const
Get File Meta Information.
Definition gdcmFile.h:48
gdcm::PrivateTag
Class to represent a Private DICOM Data Element (Attribute) Tag (Group, Element, Owner).
Definition gdcmPrivateTag.h:39
gdcm::Reader
Reader ala DOM (Document Object Model).
Definition gdcmReader.h:54
gdcm::Reader::GetFile
const File & GetFile() const
Set/Get File.
Definition gdcmReader.h:72
gdcm::Reader::Read
virtual bool Read()
Main function to read a file.
gdcm::Reader::SetFileName
void SetFileName(const char *filename_native)
gdcm::Tag
Class to represent a DICOM Data Element (Attribute) Tag (Group, Element).
Definition gdcmTag.h:39
gdcm::TransferSyntax::ExplicitVRLittleEndian
@ ExplicitVRLittleEndian
Definition gdcmTransferSyntax.h:64
gdcm::VL
Value Length.
Definition gdcmVL.h:30
gdcm::VR::OW
@ OW
Definition gdcmVR.h:77
gdcm::Writer
Writer ala DOM (Document Object Model).
Definition gdcmWriter.h:49
gdcm::Writer::GetFile
File & GetFile()
Definition gdcmWriter.h:67
gdcm::Writer::Write
virtual bool Write()
Main function to tell the writer to write.
gdcm::Writer::SetFile
void SetFile(const File &f)
Set/Get the DICOM file (DataSet + Header).
Definition gdcmWriter.h:66
gdcm::Writer::SetFileName
void SetFileName(const char *filename_native)
Set the filename of DICOM file to write:
gdcmAttribute.h
gdcmImageWriter.h
gdcmPrivateTag.h
gdcmReader.h