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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.
=========================================================================*/
#ifndef GDCMSEQUENCEOFFRAGMENTS_H
#define GDCMSEQUENCEOFFRAGMENTS_H
#include "gdcmValue.h"
#include "gdcmVL.h"
#include "gdcmFragment.h"
#include "gdcmBasicOffsetTable.h"
namespace gdcm_ns
{
// FIXME gdcmSequenceOfItems and gdcmSequenceOfFragments
// should be rethink (duplicate code)
/**
* \brief Class to represent a Sequence Of Fragments
* \todo I do not enforce that Sequence of Fragments ends with a SQ end del
*/
class GDCM_EXPORT SequenceOfFragments : public Value
{
public:
// Typdefs:
typedef std::vector<Fragment> FragmentVector;
typedef FragmentVector::size_type SizeType;
typedef FragmentVector::iterator Iterator;
typedef FragmentVector::const_iterator ConstIterator;
Iterator Begin() { return Fragments.begin(); }
Iterator End() { return Fragments.end(); }
ConstIterator Begin() const { return Fragments.begin(); }
ConstIterator End() const { return Fragments.end(); }
/// \brief constructor (UndefinedLength by default)
SequenceOfFragments():Table(),SequenceLengthField(0xFFFFFFFF) { }
/// \brief Returns the SQ length, as read from disk
VL GetLength() const override {
return SequenceLengthField;
}
/// \brief Sets the actual SQ length
void SetLength(VL length) override {
SequenceLengthField = length;
}
/// \brief Clear
void Clear() override;
/// \brief Appends a Fragment to the already added ones
void AddFragment(Fragment const &item);
// Compute the length of all fragments (and framents only!).
// Basically the size of the PixelData as stored (in bytes).
unsigned long ComputeByteLength() const;
// Compute the length of fragments (in bytes)+ length of tag...
// to be used for computation of Group Length
VL ComputeLength() const;
// Get the buffer
bool GetBuffer(char *buffer, unsigned long length) const;
bool GetFragBuffer(unsigned int fragNb, char *buffer, unsigned long &length) const;
SizeType GetNumberOfFragments() const;
const Fragment& GetFragment(SizeType num) const;
// Write the buffer of each fragment (call WriteBuffer on all Fragments, which are
// ByteValue). No Table information is written.
bool WriteBuffer(std::ostream &os) const;
const BasicOffsetTable &GetTable() const { return Table; }
BasicOffsetTable &GetTable() { return Table; }
template <typename TSwap>
std::istream& Read(std::istream &is, bool readvalues = true)
{
assert( SequenceLengthField.IsUndefined() );
ReadPreValue<TSwap>(is);
return ReadValue<TSwap>(is, readvalues);
}
template <typename TSwap>
std::istream& ReadPreValue(std::istream &is)
{
// First item is the basic offset table:
#if 0
try
{
Table.Read<TSwap>(is);
gdcmDebugMacro( "Table: " << Table );
}
catch(...)
{
// throw "SIEMENS Icon thingy";
// Bug_Siemens_PrivateIconNoItem.dcm
// First thing first let's rewind
is.seekg(-4, std::ios::cur);
// FF D8 <=> Start of Image (SOI) marker
// FF E0 <=> APP0 Reserved for Application Use
if ( Table.GetTag() == Tag(0xd8ff,0xe0ff) )
{
Table = BasicOffsetTable(); // clear up stuff
//Table.SetByteValue( "", 0 );
Fragment frag;
if( FillFragmentWithJPEG( frag, is ) )
{
Fragments.push_back( frag );
}
return is;
}
else
{
throw "Catch me if you can";
//assert(0);
}
}
#else
Table.Read<TSwap>(is);
gdcmDebugMacro( "Table: " << Table );
#endif
return is;
}
template <typename TSwap>
std::istream& ReadValue(std::istream &is, bool /*readvalues*/)
{
const Tag seqDelItem(0xfffe,0xe0dd);
// not used for now...
Fragment frag;
try
{
while( frag.Read<TSwap>(is) && frag.GetTag() != seqDelItem )
{
//gdcmDebugMacro( "Frag: " << frag );
Fragments.push_back( frag );
}
assert( frag.GetTag() == seqDelItem && frag.GetVL() == 0 );
}
catch(Exception &ex)
{
(void)ex;
#ifdef GDCM_SUPPORT_BROKEN_IMPLEMENTATION
// that's ok ! In all cases the whole file was read, because
// Fragment::Read only fail on eof() reached 1.
// SIEMENS-JPEG-CorruptFrag.dcm is more difficult to deal with, we have a
// partial fragment, read we decide to add it anyway to the stack of
// fragments (eof was reached so we need to clear error bit)
if( frag.GetTag() == Tag(0xfffe,0xe000) )
{
gdcmWarningMacro( "Pixel Data Fragment could be corrupted. Use file at own risk" );
Fragments.push_back( frag );
is.clear(); // clear the error bit
}
// 2. GENESIS_SIGNA-JPEG-CorruptFrag.dcm
else if ( frag.GetTag() == Tag(0xddff,0x00e0) )
{
assert( Fragments.size() == 1 );
const ByteValue *bv = Fragments[0].GetByteValue();
assert( (unsigned char)bv->GetPointer()[ bv->GetLength() - 1 ] == 0xfe );
// Yes this is an extra copy, this is a bug anyway, go fix YOUR code
Fragments[0].SetByteValue( bv->GetPointer(), bv->GetLength() - 1 );
gdcmWarningMacro( "JPEG Fragment length was declared with an extra byte"
" at the end: stripped !" );
is.clear(); // clear the error bit
}
// 3. LEICA/WSI
else if ( (frag.GetTag().GetGroup() == 0x00ff)
&& ((frag.GetTag().GetElement() & 0x00ff) == 0xe0) )
{
// Looks like there is a mess with offset and odd byte array
// We are going first to backtrack one byte back, and then use a
// ReadBacktrack function which in turn may backtrack up to 10 bytes
// backward. This appears to be working on a set of DICOM/WSI files from
// LEICA
gdcmWarningMacro( "Trying to fix the even-but-odd value length bug #1" );
assert( Fragments.size() );
const size_t lastf = Fragments.size() - 1;
const ByteValue *bv = Fragments[ lastf ].GetByteValue();
const char *a = bv->GetPointer();
gdcmAssertAlwaysMacro( (unsigned char)a[ bv->GetLength() - 1 ] == 0xfe );
Fragments[ lastf ].SetByteValue( bv->GetPointer(), bv->GetLength() - 1 );
is.seekg( -9, std::ios::cur );
assert( is.good() );
while( frag.ReadBacktrack<TSwap>(is) && frag.GetTag() != seqDelItem )
{
gdcmDebugMacro( "Frag: " << frag );
Fragments.push_back( frag );
}
assert( frag.GetTag() == seqDelItem && frag.GetVL() == 0 );
}
// 4. LEICA/WSI (bis)
else if ( frag.GetTag().GetGroup() == 0xe000 )
{
// Looks like there is a mess with offset and odd byte array
// We are going first to backtrack one byte back, and then use a
// ReadBacktrack function which in turn may backtrack up to 10 bytes
// backward. This appears to be working on a set of DICOM/WSI files from
// LEICA
gdcmWarningMacro( "Trying to fix the even-but-odd value length bug #2" );
assert( Fragments.size() );
const size_t lastf = Fragments.size() - 1;
const ByteValue *bv = Fragments[ lastf ].GetByteValue();
const char *a = bv->GetPointer();
gdcmAssertAlwaysMacro( (unsigned char)a[ bv->GetLength() - 2 ] == 0xfe );
Fragments[ lastf ].SetByteValue( bv->GetPointer(), bv->GetLength() - 2 );
is.seekg( -10, std::ios::cur );
assert( is.good() );
while( frag.ReadBacktrack<TSwap>(is) && frag.GetTag() != seqDelItem )
{
gdcmDebugMacro( "Frag: " << frag );
Fragments.push_back( frag );
}
assert( frag.GetTag() == seqDelItem && frag.GetVL() == 0 );
}
// 5. LEICA/WSI (ter)
else if ( (frag.GetTag().GetGroup() & 0x00ff) == 0x00e0
&& (frag.GetTag().GetElement() & 0xff00) == 0x0000 )
{
// Looks like there is a mess with offset and odd byte array
// We are going first to backtrack one byte back, and then use a
// ReadBacktrack function which in turn may backtrack up to 10 bytes
// backward. This appears to be working on a set of DICOM/WSI files from
// LEICA
gdcmWarningMacro( "Trying to fix the even-but-odd value length bug #3" );
assert( Fragments.size() );
const size_t lastf = Fragments.size() - 1;
const ByteValue *bv = Fragments[ lastf ].GetByteValue();
const char *a = bv->GetPointer();
gdcmAssertAlwaysMacro( (unsigned char)a[ bv->GetLength() - 3 ] == 0xfe );
Fragments[ lastf ].SetByteValue( bv->GetPointer(), bv->GetLength() - 3 );
is.seekg( -11, std::ios::cur );
assert( is.good() );
while( frag.ReadBacktrack<TSwap>(is) && frag.GetTag() != seqDelItem )
{
gdcmDebugMacro( "Frag: " << frag );
Fragments.push_back( frag );
}
assert( frag.GetTag() == seqDelItem && frag.GetVL() == 0 );
}
else
{
// 3. gdcm-JPEG-LossLess3a.dcm: easy case, an extra tag was found
// instead of terminator (eof is the next char)
gdcmWarningMacro( "Reading failed at Tag:" << frag.GetTag() << " Index #"
<< Fragments.size() << " Offset " << is.tellg() << ". Use file at own risk."
<< ex.what() );
}
#endif /* GDCM_SUPPORT_BROKEN_IMPLEMENTATION */
}
return is;
}
template <typename TSwap>
std::ostream const &Write(std::ostream &os) const
{
if( !Table.Write<TSwap>(os) )
{
assert(0 && "Should not happen");
return os;
}
for(ConstIterator it = Begin();it != End(); ++it)
{
it->Write<TSwap>(os);
}
// seq del item is not stored, write it !
const Tag seqDelItem(0xfffe,0xe0dd);
seqDelItem.Write<TSwap>(os);
VL zero = 0;
zero.Write<TSwap>(os);
return os;
}
//#if defined(SWIGPYTHON) || defined(SWIGCSHARP) || defined(SWIGJAVA)
// For now leave it there, this does not make sense in the C++ layer
// Create a new object
static SmartPointer<SequenceOfFragments> New()
{
return new SequenceOfFragments();
}
//#endif
protected:
public:
void Print(std::ostream &os) const override {
os << "SQ L= " << SequenceLengthField << "\n";
os << "Table:" << Table << "\n";
for(ConstIterator it = Begin();it != End(); ++it)
{
os << " " << *it << "\n";
}
assert( SequenceLengthField.IsUndefined() );
{
const Tag seqDelItem(0xfffe,0xe0dd);
VL zero = 0;
os << seqDelItem;
os << "\t" << zero;
}
}
bool operator==(const Value &val) const override
{
const SequenceOfFragments &sqf = dynamic_cast<const SequenceOfFragments&>(val);
return Table == sqf.Table &&
SequenceLengthField == sqf.SequenceLengthField &&
Fragments == sqf.Fragments;
}
private:
BasicOffsetTable Table;
VL SequenceLengthField;
/// \brief Vector of Sequence Fragments
FragmentVector Fragments;
private:
bool FillFragmentWithJPEG( Fragment & frag, std::istream & is );
};
/**
* \example DecompressJPEGFile.cs
* This is a C# example on how to use gdcm::SequenceOfFragments
*/
} // end namespace gdcm_ns
#endif //GDCMSEQUENCEOFFRAGMENTS_H
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