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| Current File : //proc/thread-self/root/usr/include/gdcm-3.0/gdcmDataSet.txx |
/*=========================================================================
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 GDCMDATASET_TXX
#define GDCMDATASET_TXX
#include "gdcmByteValue.h"
#include "gdcmPrivateTag.h"
#include "gdcmParseException.h"
#include <cstring>
namespace gdcm_ns
{
template <typename TDE, typename TSwap>
std::istream &DataSet::ReadNested(std::istream &is) {
DataElement de;
const Tag itemDelItem(0xfffe,0xe00d);
assert( de.GetTag() != itemDelItem ); // precondition before while loop
try
{
while( de.Read<TDE,TSwap>(is) && de.GetTag() != itemDelItem ) // Keep that order please !
{
//std::cerr << "DEBUG Nested: " << de << std::endl;
InsertDataElement( de );
}
}
catch(ParseException &pe)
{
if( pe.GetLastElement().GetTag() == Tag(0xfffe,0xe0dd) )
{
// BogusItemStartItemEnd.dcm
gdcmWarningMacro( "SQ End found but no Item end found" );
de.SetTag( itemDelItem );
is.seekg( -4, std::ios::cur );
}
else
{
// MR_Philips_Intera_PrivateSequenceExplicitVR_in_SQ_2001_e05f_item_wrong_lgt_use_NOSHADOWSEQ.dcm
// Need to rethrow the exception...sigh
throw pe;
}
}
assert( de.GetTag() == itemDelItem );
return is;
}
template <typename TDE, typename TSwap>
std::istream &DataSet::Read(std::istream &is) {
DataElement de;
while( !is.eof() && de.Read<TDE,TSwap>(is) )
{
//std::cerr << "DEBUG:" << de << std::endl;
InsertDataElement( de );
}
return is;
}
template <typename TDE, typename TSwap>
std::istream &DataSet::ReadUpToTag(std::istream &is, const Tag &t, const std::set<Tag> & skiptags) {
DataElement de;
while( !is.eof() && de.template ReadPreValue<TDE,TSwap>(is, skiptags) )
{
// If tag read was in skiptags then we should NOT add it:
if( skiptags.count( de.GetTag() ) == 0 )
{
de.template ReadValue<TDE,TSwap>(is, skiptags);
InsertDataElement( de );
}
else
{
assert( is.good() );
if( de.GetTag() != t )
is.seekg( de.GetVL(), std::ios::cur );
}
// tag was found, we can exit the loop:
if ( t <= de.GetTag() )
{
assert( is.good() );
break;
}
}
return is;
}
template <typename TDE, typename TSwap>
std::istream &DataSet::ReadUpToTagWithLength(std::istream &is, const Tag &t, std::set<Tag> const & skiptags, VL & length) {
DataElement de;
while( !is.eof() && de.template ReadPreValue<TDE,TSwap>(is, skiptags) )
{
// If tag read was in skiptags then we should NOT add it:
if( skiptags.count( de.GetTag() ) == 0 )
{
de.template ReadValueWithLength<TDE,TSwap>(is, length, skiptags);
InsertDataElement( de );
}
else
{
assert( is.good() );
if( de.GetTag() != t )
is.seekg( de.GetVL(), std::ios::cur );
}
// tag was found, we can exit the loop:
if ( t <= de.GetTag() )
{
assert( is.good() );
break;
}
}
return is;
}
template <typename TDE, typename TSwap>
std::istream &DataSet::ReadSelectedTags(std::istream &inputStream, const std::set<Tag> & selectedTags, bool readvalues ) {
if ( ! (selectedTags.empty() || inputStream.fail()) )
{
const Tag maxTag = *(selectedTags.rbegin());
std::set<Tag> tags = selectedTags;
DataElement dataElem;
while( !inputStream.eof() )
{
static_cast<TDE&>(dataElem).template ReadPreValue<TSwap>(inputStream);
const Tag& tag = dataElem.GetTag();
if ( inputStream.fail() || maxTag < tag )
{
if( inputStream.good() )
{
const int l = dataElem.GetVR().GetLength();
inputStream.seekg( - 4 - 2 * l, std::ios::cur );
}
else
{
inputStream.clear();
inputStream.seekg( 0, std::ios::end );
}
// Failed to read the tag, or the read tag exceeds the maximum.
// As we assume ascending tag ordering, we can exit the loop.
break;
}
static_cast<TDE&>(dataElem).template ReadValue<TSwap>(inputStream, readvalues);
const std::set<Tag>::iterator found = tags.find(tag);
if ( found != tags.end() )
{
InsertDataElement( dataElem );
tags.erase(found);
if ( tags.empty() )
{
// All selected tags were found, we can exit the loop:
break;
}
}
if ( ! (tag < maxTag ) )
{
// The maximum tag was encountered, and as we assume
// ascending tag ordering, we can exit the loop:
break;
}
}
}
assert( inputStream.good() );
return inputStream;
}
template <typename TDE, typename TSwap>
std::istream &DataSet::ReadSelectedPrivateTags(std::istream &inputStream, const std::set<PrivateTag> & selectedPTags, bool readvalues) {
if ( ! (selectedPTags.empty() || inputStream.fail()) )
{
assert( selectedPTags.size() == 1 );
const PrivateTag refPTag = *(selectedPTags.rbegin());
PrivateTag nextPTag = refPTag;
nextPTag.SetElement( (uint16_t)(nextPTag.GetElement() + 0x1) );
assert( nextPTag.GetElement() & 0x00ff ); // no wrap please
Tag maxTag;
maxTag.SetPrivateCreator( nextPTag );
DataElement dataElem;
while( !inputStream.eof() )
{
static_cast<TDE&>(dataElem).template ReadPreValue<TSwap>(inputStream);
const Tag& tag = dataElem.GetTag();
if ( inputStream.fail() || maxTag < tag )
{
if( inputStream.good() )
{
const int l = dataElem.GetVR().GetLength();
inputStream.seekg( - 4 - 2 * l, std::ios::cur );
}
else
{
inputStream.clear();
inputStream.seekg( 0, std::ios::end );
}
// Failed to read the tag, or the read tag exceeds the maximum.
// As we assume ascending tag ordering, we can exit the loop.
break;
}
static_cast<TDE&>(dataElem).template ReadValue<TSwap>(inputStream, readvalues);
if ( inputStream.fail() )
{
// Failed to read the value.
break;
}
if( tag.GetPrivateCreator() == refPTag )
{
DES.insert( dataElem );
}
if ( ! (tag < maxTag ) )
{
// The maximum group was encountered, and as we assume
// ascending tag ordering, we can exit the loop:
break;
}
}
}
return inputStream;
}
template <typename TDE, typename TSwap>
std::istream &DataSet::ReadSelectedTagsWithLength(std::istream &inputStream, const std::set<Tag> & selectedTags, VL & length, bool readvalues )
{
(void)length;
if ( ! selectedTags.empty() )
{
const Tag maxTag = *(selectedTags.rbegin());
std::set<Tag> tags = selectedTags;
DataElement dataElem;
while( !inputStream.eof() )
{
static_cast<TDE&>(dataElem).template ReadPreValue<TSwap>(inputStream);
const Tag tag = dataElem.GetTag();
if ( inputStream.fail() || maxTag < tag )
{
if( inputStream.good() )
{
const int l = dataElem.GetVR().GetLength();
inputStream.seekg( - 4 - 2 * l, std::ios::cur );
}
else
{
inputStream.clear();
inputStream.seekg( 0, std::ios::end );
}
// Failed to read the tag, or the read tag exceeds the maximum.
// As we assume ascending tag ordering, we can exit the loop.
break;
}
static_cast<TDE&>(dataElem).template ReadValue<TSwap>(inputStream, readvalues);
if ( inputStream.fail() )
{
// Failed to read the value.
break;
}
const std::set<Tag>::iterator found = tags.find(tag);
if ( found != tags.end() )
{
InsertDataElement( dataElem );
tags.erase(found);
if ( tags.empty() )
{
// All selected tags were found, we can exit the loop:
break;
}
}
if ( ! (tag < maxTag ) )
{
// The maximum tag was encountered, and as we assume
// ascending tag ordering, we can exit the loop:
break;
}
}
}
return inputStream;
}
template <typename TDE, typename TSwap>
std::istream &DataSet::ReadSelectedPrivateTagsWithLength(std::istream &inputStream, const std::set<PrivateTag> & selectedPTags, VL & length, bool readvalues ) {
(void)length;
if ( ! (selectedPTags.empty() || inputStream.fail()) )
{
assert( selectedPTags.size() == 1 );
const PrivateTag refPTag = *(selectedPTags.rbegin());
PrivateTag nextPTag = refPTag;
nextPTag.SetElement( (uint16_t)(nextPTag.GetElement() + 0x1) );
assert( nextPTag.GetElement() ); // no wrap please
Tag maxTag;
maxTag.SetPrivateCreator( nextPTag );
DataElement dataElem;
while( !inputStream.eof() )
{
static_cast<TDE&>(dataElem).template ReadPreValue<TSwap>(inputStream);
const Tag& tag = dataElem.GetTag();
if ( inputStream.fail() || maxTag < tag )
{
if( inputStream.good() )
{
const int l = dataElem.GetVR().GetLength();
inputStream.seekg( - 4 - 2 * l, std::ios::cur );
}
else
{
inputStream.clear();
inputStream.seekg( 0, std::ios::end );
}
// Failed to read the tag, or the read tag exceeds the maximum.
// As we assume ascending tag ordering, we can exit the loop.
break;
}
static_cast<TDE&>(dataElem).template ReadValue<TSwap>(inputStream, readvalues);
if ( inputStream.fail() )
{
// Failed to read the value.
break;
}
//const std::set<uint16_t>::iterator found = selectedPTags.find(tag.GetGroup());
//if ( found != groups.end() )
if( tag.GetPrivateCreator() == refPTag )
{
InsertDataElement( dataElem );
}
if ( ! (tag < maxTag ) )
{
// The maximum group was encountered, and as we assume
// ascending tag ordering, we can exit the loop:
break;
}
}
}
return inputStream;
}
template <typename TDE, typename TSwap>
std::istream &DataSet::ReadWithLength(std::istream &is, VL &length) {
DataElement de;
VL l = 0;
//std::cout << "ReadWithLength Length: " << length << std::endl;
VL locallength = length;
const std::streampos startpos = is.tellg();
try
{
while( l != locallength && de.ReadWithLength<TDE,TSwap>(is, locallength))
{
//std::cout << "Nested: " << de << std::endl;
#ifndef GDCM_SUPPORT_BROKEN_IMPLEMENTATION
assert( de.GetTag() != Tag(0xfffe,0xe000) ); // We should not be reading the next item...
#endif
InsertDataElement( de );
const VL oflen = de.GetLength<TDE>();
l += oflen;
const std::streampos curpos = is.tellg();
//assert( (curpos - startpos) == l || (curpos - startpos) + 1 == l );
//std::cout << "l:" << l << std::endl;
//assert( !de.GetVL().IsUndefined() );
//std::cerr << "DEBUG: " << de.GetTag() << " "<< de.GetLength() <<
// "," << de.GetVL() << "," << l << std::endl;
// Bug_Philips_ItemTag_3F3F
// (0x2005, 0x1080): for some reason computation of length fails...
if( l == 70 && locallength == 63 )
{
gdcmWarningMacro( "PMS: Super bad hack. Changing length" );
length = locallength = 140;
}
if( (curpos - startpos) + 1 == l )
{
gdcmDebugMacro( "Papyrus odd padding detected" );
throw Exception( "Papyrus odd padding" );
}
if( l > locallength )
{
if( (curpos - startpos) == locallength )
{
// this means that something went wrong somewhere, and upon recomputing the length
// we found a discrepandy with own vendor made its layout.
// update the length directly
locallength = length = l;
throw Exception( "Changed Length" );
}
else
{
gdcmDebugMacro( "Out of Range SQ detected: " << l << " while max: " << locallength );
throw Exception( "Out of Range" );
}
}
}
}
catch(ParseException &pe)
{
if( pe.GetLastElement().GetTag() == Tag(0xfffe,0xe000) )
{
// gdcm-MR-PHILIPS-16-Multi-Seq.dcm
// Long story short, I think Philips engineer inserted 0xfffe,0x0000 instead of an item start element
// assert( FindDataElement( Tag(0xfffe,0x0000) ) == false );
is.seekg(-6, std::ios::cur );
length = locallength = l;
}
else if( /*pe.GetLastElement().GetTag() == Tag(0xffd8,0xffe0) &&*/ de.GetTag() == Tag(0x7fe0,0x0010) && de.IsUndefinedLength() )
{
// PET-GE-dicomwrite-PixelDataSQUN.dcm
// some bozo crafted an undefined length Pixel Data but is actually
// defined length. Since inside SQ/Item it should be possible to
// compute the proper length
is.seekg(-16, std::ios::cur );
TDE pd;
pd.template ReadPreValue<TSwap>(is);
gdcmAssertAlwaysMacro( pd.GetTag() == Tag(0x7fe0,0x0010) );
gdcmAssertAlwaysMacro( pd.GetVR() == VR::OB );
gdcmAssertAlwaysMacro( pd.IsUndefinedLength() );
const VL pdlen = locallength - l - 12;
pd.SetVL( pdlen );
pd.template ReadValue<TSwap>(is, true);
InsertDataElement( pd );
length = locallength = l;
}
else
{
// Could be the famous :
// gdcmDataExtra/gdcmBreakers/BuggedDicomWorksImage_Hopeless.dcm
// let's just give up:
gdcmErrorMacro( "Last Tag is : " << pe.GetLastElement().GetTag() );
throw Exception( "Unhandled" );
}
}
catch(Exception &pe)
{
if( strcmp( pe.GetDescription(), "Out of Range" ) == 0 )
{
// BogugsItemAndSequenceLength.dcm
// This is most likely the "Out of Range" one
// Cautiously read until we find the next item starter and then stop.
//std::cout << "Length read was:" << l << " should be at most:" << locallength ;
while( de.Read<TDE,TSwap>(is) && de.GetTag() != Tag(0xfffe,0xe000) && de.GetTag().GetElement() != 0x0 )
{
//std::cout << "Nested2: " << de << std::endl;
InsertDataElement( de );
l += de.GetLength<TDE>();
//std::cout << l << std::endl;
}
// seek back since we read the next item starter:
int iteml = de.GetLength<TDE>();
//assert( de.GetTag().GetElement() );
if( !de.GetTag().GetElement() )
{
assert( iteml == 12 ); (void)iteml;
is.seekg( -12, std::ios::cur );
}
else
{
//assert( de.GetTag() == Tag(0xfffe,0xe000) );
is.seekg( -4, std::ios::cur );
}
// let's fix the length now:
length = locallength = l;
gdcmWarningMacro( "Item length is wrong" );
throw Exception( "Changed Length" );
}
else if( strcmp( pe.GetDescription(), "Papyrus odd padding" ) == 0 )
{
is.get();
throw Exception( "Changed Length" );
}
else
{
// re throw
throw pe;
}
}
// technically we could only do this assert if the dataset did not contains
// duplicate data elements so only do a <= instead:
//assert( l == locallength );
assert( l <= locallength );
return is;
}
template <typename TDE, typename TSwap>
std::ostream const &DataSet::Write(std::ostream &os) const {
typename DataSet::ConstIterator it = DES.begin();
for( ; it != DES.end(); ++it)
{
const DataElement & de = *it;
//if( de.GetTag().GetGroup() >= 0x0008 || de.GetTag().GetGroup() == 0x0002 )
{
de.Write<TDE,TSwap>(os);
}
}
return os;
}
} // end namespace gdcm_ns
#endif // GDCMDATASET_TXX