Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2004/11/24 16:39:18 $
- Version: $Revision: 1.137 $
+ Date: $Date: 2004/12/07 13:39:33 $
+ Version: $Revision: 1.149 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
+#include "gdcmTS.h"
+#include "gdcmException.h"
+#include "gdcmDictSet.h"
+#include "gdcmRLEFramesInfo.h"
+#include "gdcmJPEGFragmentsInfo.h"
+#include "gdcmDocEntrySet.h"
+#include "gdcmSQItem.h"
#include <vector>
#include <iomanip>
namespace gdcm
{
+//-----------------------------------------------------------------------------
static const char *TransferSyntaxStrings[] = {
// Implicit VR Little Endian
"1.2.840.10008.1.2",
// Unknown
"Unknown Transfer Syntax"
};
-
+
//-----------------------------------------------------------------------------
// Refer to Document::CheckSwap()
-const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
+//const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
// Refer to Document::SetMaxSizeLoadEntry()
const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
dbg.Verbose(0, "Document::Document: starting parsing of file: ",
Filename.c_str());
- Fp->seekg( 0, std::ios_base::beg);
+ Fp->seekg( 0, std::ios::beg);
- Fp->seekg(0, std::ios_base::end);
+ Fp->seekg(0, std::ios::end);
long lgt = Fp->tellg();
- Fp->seekg( 0, std::ios_base::beg);
+ Fp->seekg( 0, std::ios::beg);
CheckSwap();
long beg = Fp->tellg();
lgt -= beg;
ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
- Fp->seekg( 0, std::ios_base::beg);
+ Fp->seekg( 0, std::ios::beg);
// Load 'non string' values
*/
std::ifstream* Document::OpenFile()
{
- if (Filename.length() == 0) return 0;
+ if (Filename.length() == 0)
+ {
+ return 0;
+ }
+
if(Fp)
{
dbg.Verbose( 0,
}
Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
-
- if(!Fp)
+ if( ! *Fp )
{
dbg.Verbose( 0,
"Document::OpenFile cannot open file: ",
Filename.c_str());
+ delete Fp;
+ Fp = 0;
return 0;
}
uint16_t zero;
- Fp->read((char*)&zero, (size_t)2 );
+ Fp->read((char*)&zero, (size_t)2);
+ if( Fp->eof() )
+ {
+ CloseFile();
+ return 0;
+ }
//ACR -- or DICOM with no Preamble; may start with a Shadow Group --
if(
}
//DICOM
- Fp->seekg(126L, std::ios_base::cur);
+ Fp->seekg(126L, std::ios::cur);
char dicm[4];
Fp->read(dicm, (size_t)4);
+ if( Fp->eof() )
+ {
+ CloseFile();
+ return 0;
+ }
if( memcmp(dicm, "DICM", 4) == 0 )
{
return Fp;
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* \return Always true.
*/
-void Document::Write(std::ofstream* fp, FileType filetype)
+void Document::WriteContent(std::ofstream* fp, FileType filetype)
{
/// \todo move the following lines (and a lot of others, to be written)
/// to a future function CheckAndCorrectHeader
fp->write("DICM", 4);
}
- if (filetype == ImplicitVR)
- {
- std::string ts =
- Util::DicomString( TransferSyntaxStrings[ImplicitVRLittleEndian] );
- ReplaceOrCreateByNumber(ts, 0x0002, 0x0010);
-
- /// \todo Refer to standards on page 21, chapter 6.2
- /// "Value representation": values with a VR of UI shall be
- /// padded with a single trailing null
- /// in the following case we have to padd manually with a 0
-
- SetEntryLengthByNumber(18, 0x0002, 0x0010);
- }
-
- if (filetype == ExplicitVR)
- {
- std::string ts =
- Util::DicomString( TransferSyntaxStrings[ExplicitVRLittleEndian] );
- ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); //LEAK
-
- /// \todo Refer to standards on page 21, chapter 6.2
- /// "Value representation": values with a VR of UI shall be
- /// padded with a single trailing null
- /// Dans le cas suivant on doit pader manuellement avec un 0
-
- SetEntryLengthByNumber(20, 0x0002, 0x0010);
- }
-
/**
* \todo rewrite later, if really usefull
* - 'Group Length' element is optional in DICOM
* UpdateGroupLength(true,ACR);
*/
- ElementSet::Write(fp, filetype); // This one is recursive
-
+ ElementSet::WriteContent(fp, filetype); // This one is recursive
}
/**
dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
" failed allthough this is a creation.");
}
+ delete currentEntry;
}
else
{
return true;
}
+std::string Document::GetTransferSyntaxValue(TransferSyntaxType type)
+{
+ return TransferSyntaxStrings[type];
+}
+
//-----------------------------------------------------------------------------
// Protected
std::string Document::GetEntryByNumber(uint16_t group, uint16_t element)
{
TagKey key = DictEntry::TranslateToKey(group, element);
- /// \todo use map methods, instead of multimap JPR
if ( !TagHT.count(key))
{
return GDCM_UNFOUND;
bool Document::SetEntryByNumber(std::string const& content,
uint16_t group, uint16_t element)
{
- int c;
- int l;
-
ValEntry* valEntry = GetValEntryByNumber(group, element);
if (!valEntry )
{
return false;
}
// Non even content must be padded with a space (020H)...
- std::string finalContent = Util::DicomString( content.c_str() );
- assert( !(finalContent.size() % 2) );
- valEntry->SetValue(finalContent);
-
- // Integers have a special treatement for their length:
-
- l = finalContent.length();
- if ( l != 0) // To avoid to be cheated by 'zero length' integers
- {
- VRKey vr = valEntry->GetVR();
- if( vr == "US" || vr == "SS" )
- {
- // for multivaluated items
- c = Util::CountSubstring(content, "\\") + 1;
- l = c*2;
- }
- else if( vr == "UL" || vr == "SL" )
- {
- // for multivaluated items
- c = Util::CountSubstring(content, "\\") + 1;
- l = c*4;;
- }
- }
- valEntry->SetLength(l);
+ valEntry->SetValue(content);
return true;
}
return true;
}
-/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * in the PubDocEntrySet of this instance
- * through it's (group, element) and modifies it's length with
- * the given value.
- * \warning Use with extreme caution.
- * @param l new length to substitute with
- * @param group group number of the Entry to modify
- * @param element element number of the Entry to modify
- * @return true on success, false otherwise.
- */
-bool Document::SetEntryLengthByNumber(uint32_t l,
- uint16_t group, uint16_t element)
-{
- /// \todo use map methods, instead of multimap JPR
- TagKey key = DictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key) )
- {
- return false;
- }
- if ( l % 2 )
- {
- l++; // length must be even
- }
- ( ((TagHT.equal_range(key)).first)->second )->SetLength(l);
-
- return true ;
-}
-
-/**
- * \brief Gets (from Header) the offset of a 'non string' element value
- * (LoadElementValues has already be executed)
- * @param group group number of the Entry
- * @param elem element number of the Entry
- * @return File Offset of the Element Value
- */
-size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem)
-{
- DocEntry* entry = GetDocEntryByNumber(group, elem);
- if (!entry)
- {
- dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present.");
- return 0;
- }
- return entry->GetOffset();
-}
-
/**
* \brief Gets (from Header) a 'non string' element value
* (LoadElementValues has already be executed)
return;
LoadEntryBinArea(binElement);
-/* size_t o =(size_t)docElement->GetOffset();
- Fp->seekg( o, std::ios_base::beg);
- size_t l = docElement->GetLength();
- uint8_t* a = new uint8_t[l];
- if(!a)
- {
- dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a");
- return;
- }
-
- // Read the value
- Fp->read((char*)a, l);
- if( Fp->fail() || Fp->eof() )//Fp->gcount() == 1
- {
- delete[] a;
- return;
- }
-
- // Set the value to the DocEntry
- if( !SetEntryBinAreaByNumber( a, group, elem ) )
- {
- delete[] a;
- dbg.Verbose(0, "Document::LoadEntryBinArea setting failed.");
- }*/
}
/**
OpenFile();
size_t o =(size_t)element->GetOffset();
- Fp->seekg(o, std::ios_base::beg);
+ Fp->seekg(o, std::ios::beg);
size_t l = element->GetLength();
uint8_t* a = new uint8_t[l];
* @param element Element number of the searched Dicom Element
* @return
*/
-bool Document::SetEntryBinAreaByNumber(uint8_t* area,
+/*bool Document::SetEntryBinAreaByNumber(uint8_t* area,
uint16_t group, uint16_t element)
{
DocEntry* currentEntry = GetDocEntryByNumber(group, element);
}
return false;
-}
+}*/
/**
* \brief Update the entries with the shadow dictionary.
*/
void Document::LoadDocEntrySafe(DocEntry * entry)
{
- long PositionOnEntry = Fp->tellg();
- LoadDocEntry(entry);
- Fp->seekg(PositionOnEntry, std::ios_base::beg);
+ if(Fp)
+ {
+ long PositionOnEntry = Fp->tellg();
+ LoadDocEntry(entry);
+ Fp->seekg(PositionOnEntry, std::ios::beg);
+ }
}
/**
}
//////////////////// BinEntry or UNKOWN VR:
-/* BinEntry* newBinEntry =
- new BinEntry( newDocEntry->GetDictEntry() ); //LEAK
- newBinEntry->Copy( newDocEntry );*/
BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK
// When "this" is a Document the Key is simply of the
if ( ts == RLELossless )
{
long PositionOnEntry = Fp->tellg();
- Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg );
+ Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
ComputeRLEInfo();
- Fp->seekg( PositionOnEntry, std::ios_base::beg );
+ Fp->seekg( PositionOnEntry, std::ios::beg );
}
else if ( IsJPEG() )
{
long PositionOnEntry = Fp->tellg();
- Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg );
+ Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
ComputeJPEGFragmentInfo();
- Fp->seekg( PositionOnEntry, std::ios_base::beg );
+ Fp->seekg( PositionOnEntry, std::ios::beg );
}
}
std::string vr = entry->GetVR();
uint32_t length = entry->GetLength();
- Fp->seekg((long)entry->GetOffset(), std::ios_base::beg);
+ Fp->seekg((long)entry->GetOffset(), std::ios::beg);
// A SeQuence "contains" a set of Elements.
// (fffe e000) tells us an Element is beginning
// to be sure we are at the end of the value ...
Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
- std::ios_base::beg);
+ std::ios::beg);
return;
}
// The following reserved two bytes (see PS 3.5-2003, section
// "7.1.2 Data element structure with explicit vr", p 27) must be
// skipped before proceeding on reading the length on 4 bytes.
- Fp->seekg( 2L, std::ios_base::cur);
+ Fp->seekg( 2L, std::ios::cur);
uint32_t length32 = ReadInt32();
if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
// until the end of the file. Hence we artificially fix the
// the length and proceed.
long currentPosition = Fp->tellg();
- Fp->seekg(0L,std::ios_base::end);
+ Fp->seekg(0L,std::ios::end);
long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
- Fp->seekg(currentPosition, std::ios_base::beg);
+ Fp->seekg(currentPosition, std::ios::beg);
entry->SetLength(lengthUntilEOF);
return;
}
// within an explicit VR file. Hence we make sure the present tag
// is in explicit VR and try to fix things if it happens not to be
// the case.
-
Fp->read (vr, (size_t)2);
vr[2] = 0;
if( !CheckDocEntryVR(entry, vr) )
{
- Fp->seekg(positionOnEntry, std::ios_base::beg);
+ Fp->seekg(positionOnEntry, std::ios::beg);
// When this element is known in the dictionary we shall use, e.g. for
// the semantics (see the usage of IsAnInteger), the VR proposed by the
// dictionary entry. Still we have to flag the element as implicit since
*/
void Document::SkipToNextDocEntry(DocEntry *entry)
{
- Fp->seekg((long)(entry->GetOffset()), std::ios_base::beg);
- Fp->seekg( (long)(entry->GetReadLength()), std::ios_base::cur);
+ Fp->seekg((long)(entry->GetOffset()), std::ios::beg);
+ Fp->seekg( (long)(entry->GetReadLength()), std::ios::cur);
}
/**
{
dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item "
"tag nor a Sequence delimiter tag.");
- Fp->seekg(positionOnEntry, std::ios_base::beg);
+ Fp->seekg(positionOnEntry, std::ios::beg);
throw FormatUnexpected("Document::FindDocEntryLengthOB()",
"Neither an Item tag nor a Sequence "
"delimiter tag.");
break;
}
}
- Fp->seekg( positionOnEntry, std::ios_base::beg);
+ Fp->seekg( positionOnEntry, std::ios::beg);
return totalLength;
}
void Document::SkipBytes(uint32_t nBytes)
{
//FIXME don't dump the returned value
- Fp->seekg((long)nBytes, std::ios_base::cur);
+ Fp->seekg((long)nBytes, std::ios::cur);
}
/**
RefShaDict = NULL;
RLEInfo = new RLEFramesInfo;
JPEGInfo = new JPEGFragmentsInfo;
+ Filetype = Unknown;
}
/**
uint32_t s32;
uint16_t s16;
- char deb[256]; //HEADER_LENGTH_TO_READ];
+ char deb[256];
// First, compare HostByteOrder and NetworkByteOrder in order to
// determine if we shall need to swap bytes (i.e. the Endian type).
// The easiest case is the one of a DICOM header, since it possesses a
// file preamble where it suffice to look for the string "DICM".
- Fp->read(deb, HEADER_LENGTH_TO_READ);
+ Fp->read(deb, 256);
char *entCur = deb + 128;
if( memcmp(entCur, "DICM", (size_t)4) == 0 )
// Position the file position indicator at first tag (i.e.
// after the file preamble and the "DICM" string).
- Fp->seekg(0, std::ios_base::beg);
- Fp->seekg ( 132L, std::ios_base::beg);
+ Fp->seekg(0, std::ios::beg);
+ Fp->seekg ( 132L, std::ios::beg);
return true;
} // End of DicomV3
// preamble. We can reset the file position indicator to where the data
// is (i.e. the beginning of the file).
dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file");
- Fp->seekg(0, std::ios_base::beg);
+ Fp->seekg(0, std::ios::beg);
// Our next best chance would be to be considering a 'clean' ACR/NEMA file.
// By clean we mean that the length of the first tag is written down.
// representation of a 32 bits integer. Hence the following dirty
// trick :
s32 = *((uint32_t *)(entCur));
-
+
switch( s32 )
{
case 0x00040000 :
s << " at address: " << (unsigned)currentPosition << std::endl;
dbg.Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:");
dbg.Verbose(0, s.str().c_str());
- Fp->seekg(positionOnEntry, std::ios_base::beg);
+ Fp->seekg(positionOnEntry, std::ios::beg);
return false;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff