pmsct_rgb1.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_RGB1 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:
* Jean-Pierre Roux for providing the sample datasets
*/
#include "gdcmReader.h"
#include "gdcmPrivateTag.h"
#include "gdcmAttribute.h"
#include "gdcmImageWriter.h"
void delta_decode(const unsigned char *data_in, size_t data_size,
std::vector<unsigned char> &new_stream, unsigned short pc, size_t w, size_t h)
{
const size_t plane_size = h * w;
const size_t outputlen = 3 * plane_size;
new_stream.resize( outputlen );
assert( data_size != outputlen );
if( data_size == outputlen )
{
return;
}
typedef unsigned char byte;
enum {
COLORMODE = 0x81,
ESCMODE = 0x82,
REPEATMODE = 0x83
};
const byte* src = (const byte*)data_in;
byte* dest = (byte*)new_stream.data();
union { byte gray; byte rgb[3]; } pixel;
pixel.rgb[0] = pixel.rgb[1] = pixel.rgb[2] = 0;
// always start in grayscale mode
bool graymode = true;
size_t dx = 1;
size_t dy = 3;
// algorithm works with both planar configuration
// It does produce surprising greenish background color for planar
// configuration is 0, while the nested Icon SQ display a nice black
// background
if (pc)
{
dx = plane_size;
dy = 1;
}
size_t ps = plane_size;
// The following is highly unoptimized as we have nested if statement in a while loop
// we need to switch from one algorithm to the other (RGB <-> GRAY)
while (ps)
{
// next byte:
byte b = *src++;
assert( src < data_in + data_size );
// mode selection:
switch ( b )
{
case ESCMODE:
// Used to treat a byte 81/82/83 as a normal byte
if (graymode)
{
pixel.gray += *src++;
dest[0*dx] = pixel.gray;
dest[1*dx] = pixel.gray;
dest[2*dx] = pixel.gray;
}
else
{
pixel.rgb[0] += *src++;
pixel.rgb[1] += *src++;
pixel.rgb[2] += *src++;
dest[0*dx] = pixel.rgb[0];
dest[1*dx] = pixel.rgb[1];
dest[2*dx] = pixel.rgb[2];
}
dest += dy;
ps--;
break;
case REPEATMODE:
// repeat mode (RLE)
b = *src++;
ps -= b;
if (graymode)
{
while (b-- > 0)
{
dest[0*dx] = pixel.gray;
dest[1*dx] = pixel.gray;
dest[2*dx] = pixel.gray;
dest += dy;
}
}
else
{
while (b-- > 0)
{
dest[0*dx] = pixel.rgb[0];
dest[1*dx] = pixel.rgb[1];
dest[2*dx] = pixel.rgb[2];
dest += dy;
}
}
break;
case COLORMODE:
// We are switching from one mode to the other. The stream contains an intermixed
// compression of RGB codec and GRAY codec. Each one not knowing of the other
// reset old value to 0.
if (graymode)
{
graymode = false;
pixel.rgb[0] = pixel.rgb[1] = pixel.rgb[2] = 0;
}
else
{
graymode = true;
pixel.gray = 0;
}
break;
default:
// This is identical to ESCMODE, it would be nicer to use fall-through
if (graymode)
{
pixel.gray += b;
dest[0*dx] = pixel.gray;
dest[1*dx] = pixel.gray;
dest[2*dx] = pixel.gray;
}
else
{
pixel.rgb[0] += b;
pixel.rgb[1] += *src++;
pixel.rgb[2] += *src++;
dest[0*dx] = pixel.rgb[0];
dest[1*dx] = pixel.rgb[1];
dest[2*dx] = pixel.rgb[2];
}
dest += dy;
ps--;
break;
} // end switch
} // end while
}
int main(int argc, char *argv [])
{
if( argc < 2 ) 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_RGB1] # 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;
return 1;
}
if( strncmp( bv->GetPointer(), comprgb.c_str(), comprgb.size() ) == 0 )
{
isrgb = true;
}
if( !isrgb && !isrle ) return 1;
const gdcm::PrivateTag tcompressedpixeldata(0x07a1,0x000a,"ELSCINT1");
if( !ds.FindDataElement( tcompressedpixeldata) ) return 1;
const gdcm::DataElement& compressionpixeldata = ds.GetDataElement( tcompressedpixeldata);
if ( compressionpixeldata.IsEmpty() ) return 1;
const gdcm::ByteValue * bv2 = compressionpixeldata.GetByteValue();
gdcm::Attribute<0x0028,0x0006> at0;
at0.SetFromDataSet( ds );
gdcm::Attribute<0x0028,0x0010> at1;
at1.SetFromDataSet( ds );
gdcm::Attribute<0x0028,0x0011> at2;
at2.SetFromDataSet( ds );
std::vector<unsigned char> buffer;
delta_decode((const unsigned char*)bv2->GetPointer(), bv2->GetLength(), buffer,
at0.GetValue(), at1.GetValue(), at2.GetValue() );
gdcm::DataElement pixeldata( gdcm::Tag(0x7fe0,0x0010) );
pixeldata.SetVR( gdcm::VR::OW );
pixeldata.SetByteValue( (char*)buffer.data(), (uint32_t)buffer.size() );
// TODO we should check that decompress byte buffer match the expected size (row*col*...)
// Add the pixel data element
reader.GetFile().GetDataSet().Replace( pixeldata );
reader.GetFile().GetHeader().SetDataSetTransferSyntax(
gdcm::TransferSyntax::ExplicitVRLittleEndian);
gdcm::Writer writer;
writer.SetFile( reader.GetFile() );
// Cleanup stuff:
// remove the compressed pixel data:
// FIXME: should I remove more private tags ? all of them ?
// oh well this is just an example
// use gdcm::Anonymizer::RemovePrivateTags if needed...
writer.GetFile().GetDataSet().Remove( compressionpixeldata.GetTag() );
std::string outfilename;
if (argc > 2)
outfilename = argv[2];
else
outfilename = "outrgb.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::GetTag
const Tag & GetTag() const
Get Tag.
Definition gdcmDataElement.h:67
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::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::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::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