Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2004/10/06 22:31:31 $
- Version: $Revision: 1.96 $
+ Date: $Date: 2005/01/11 23:06:35 $
+ Version: $Revision: 1.180 $
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>
// For nthos:
-#ifdef _MSC_VER
+#if defined(_MSC_VER) || defined(__BORLANDC__)
#include <winsock.h>
#else
#include <netinet/in.h>
#endif
-# include <iomanip>
-
-// Implicit VR Little Endian
-#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2"
-// Explicit VR Little Endian
-#define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1"
-// Deflated Explicit VR Little Endian
-#define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99"
-// Explicit VR Big Endian
-#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2"
-// JPEG Baseline (Process 1)
-#define UI1_2_840_10008_1_2_4_50 "1.2.840.10008.1.2.4.50"
-// JPEG Extended (Process 2 & 4)
-#define UI1_2_840_10008_1_2_4_51 "1.2.840.10008.1.2.4.51"
-// JPEG Extended (Process 3 & 5)
-#define UI1_2_840_10008_1_2_4_52 "1.2.840.10008.1.2.4.52"
-// JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8)
-#define UI1_2_840_10008_1_2_4_53 "1.2.840.10008.1.2.4.53"
-// JPEG Full Progression, Non-Hierarchical (Process 10 & 12)
-#define UI1_2_840_10008_1_2_4_55 "1.2.840.10008.1.2.4.55"
-// JPEG Lossless, Non-Hierarchical (Process 14)
-#define UI1_2_840_10008_1_2_4_57 "1.2.840.10008.1.2.4.57"
-// JPEG Lossless, Hierarchical, First-Order Prediction (Process 14,
-// [Selection Value 1])
-#define UI1_2_840_10008_1_2_4_70 "1.2.840.10008.1.2.4.70"
-// JPEG 2000 Lossless
-#define UI1_2_840_10008_1_2_4_90 "1.2.840.10008.1.2.4.90"
-// JPEG 2000
-#define UI1_2_840_10008_1_2_4_91 "1.2.840.10008.1.2.4.91"
-// RLE Lossless
-#define UI1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5"
-// UI1_1_2_840_10008_1_2_5
-#define str2num(str, typeNum) *((typeNum *)(str))
+namespace gdcm
+{
//-----------------------------------------------------------------------------
-// Refer to gdcmDocument::CheckSwap()
-const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256;
+// Refer to Document::CheckSwap()
+//const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
-// Refer to gdcmDocument::SetMaxSizeLoadEntry()
-const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
-const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff;
+// Refer to Document::SetMaxSizeLoadEntry()
+const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
+const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff;
//-----------------------------------------------------------------------------
// Constructor / Destructor
* \brief constructor
* @param filename file to be opened for parsing
*/
-gdcmDocument::gdcmDocument( std::string const & filename )
- : gdcmElementSet(-1)
+Document::Document( std::string const &filename ) : ElementSet(-1)
{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Filename = filename;
Initialise();
+ Fp = 0;
if ( !OpenFile() )
{
return;
}
- dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ",
- Filename.c_str());
- rewind(Fp);
+ Group0002Parsed = false;
+
+ gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str());
+ // Fp->seekg( 0, std::ios::beg);
- fseek(Fp,0L,SEEK_END);
- long lgt = ftell(Fp);
+ Fp->seekg(0, std::ios::end);
+ long lgt = Fp->tellg();
- rewind(Fp);
+ Fp->seekg( 0, std::ios::beg);
CheckSwap();
- long beg = ftell(Fp);
+ long beg = Fp->tellg();
lgt -= beg;
ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
- rewind(Fp);
+ Fp->seekg( 0, std::ios::beg);
// Load 'non string' values
- std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
+ std::string PhotometricInterpretation = GetEntry(0x0028,0x0004);
if( PhotometricInterpretation == "PALETTE COLOR " )
{
LoadEntryBinArea(0x0028,0x1200); // gray LUT
/// defined as having an US Value Representation in the public
/// dictionnary. BUT the semantics implied by the three following
/// lines state that the corresponding tag contents are in fact
- /// the ones of a gdcmBinEntry.
+ /// the ones of a BinEntry.
/// In order to fix things "Quick and Dirty" the dictionnary was
/// altered on PURPOUS but now contains a WRONG value.
/// In order to fix things and restore the dictionary to its
/// correct value, one needs to decided of the semantics by deciding
/// wether the following tags are either:
- /// - multivaluated US, and hence loaded as gdcmValEntry, but afterwards
- /// also used as gdcmBinEntry, which requires the proper conversion,
- /// - OW, and hence loaded as gdcmBinEntry, but afterwards also used
- /// as gdcmValEntry, which requires the proper conversion.
+ /// - multivaluated US, and hence loaded as ValEntry, but afterwards
+ /// also used as BinEntry, which requires the proper conversion,
+ /// - OW, and hence loaded as BinEntry, but afterwards also used
+ /// as ValEntry, which requires the proper conversion.
LoadEntryBinArea(0x0028,0x1201); // R LUT
LoadEntryBinArea(0x0028,0x1202); // G LUT
LoadEntryBinArea(0x0028,0x1203); // B LUT
// we switch lineNumber and columnNumber
//
std::string RecCode;
- RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code
+ RecCode = GetEntry(0x0008, 0x0010); // recognition code
if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
// with "little-endian strings"
{
- Filetype = gdcmACR_LIBIDO;
- std::string rows = GetEntryByNumber(0x0028, 0x0010);
- std::string columns = GetEntryByNumber(0x0028, 0x0011);
- SetEntryByNumber(columns, 0x0028, 0x0010);
- SetEntryByNumber(rows , 0x0028, 0x0011);
+ Filetype = ACR_LIBIDO;
+ std::string rows = GetEntry(0x0028, 0x0010);
+ std::string columns = GetEntry(0x0028, 0x0011);
+ SetEntry(columns, 0x0028, 0x0010);
+ SetEntry(rows , 0x0028, 0x0011);
}
// ----------------- End of ACR-LibIDO kludge ------------------
-
- PrintLevel = 1; // 'Medium' print level by default
}
/**
* \brief This default constructor doesn't parse the file. You should
- * then invoke \ref gdcmDocument::SetFileName and then the parsing.
+ * then invoke \ref Document::SetFileName and then the parsing.
*/
-gdcmDocument::gdcmDocument()
- :gdcmElementSet(-1)
+Document::Document() : ElementSet(-1)
{
+ Fp = 0;
+
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Initialise();
- PrintLevel = 1; // 'Medium' print level by default
+ SwapCode = 1234;
+ Filetype = ExplicitVR;
+ Group0002Parsed = false;
}
/**
* \brief Canonical destructor.
*/
-gdcmDocument::~gdcmDocument ()
+Document::~Document ()
{
RefPubDict = NULL;
RefShaDict = NULL;
- // Recursive clean up of sequences
- for (TagDocEntryHT::const_iterator it = TagHT.begin();
- it != TagHT.end(); ++it )
- {
- //delete it->second; //temp remove
- }
- TagHT.clear();
+ delete RLEInfo;
+ delete JPEGInfo;
}
//-----------------------------------------------------------------------------
* \brief Prints The Dict Entries of THE public Dicom Dictionary
* @return
*/
-void gdcmDocument::PrintPubDict(std::ostream & os)
+void Document::PrintPubDict(std::ostream &os)
{
+ RefPubDict->SetPrintLevel(PrintLevel);
RefPubDict->Print(os);
}
* \brief Prints The Dict Entries of THE shadow Dicom Dictionary
* @return
*/
-void gdcmDocument::PrintShaDict(std::ostream & os)
+void Document::PrintShaDict(std::ostream &os)
{
+ RefShaDict->SetPrintLevel(PrintLevel);
RefShaDict->Print(os);
}
/**
* \brief Get the public dictionary used
*/
-gdcmDict* gdcmDocument::GetPubDict()
+Dict *Document::GetPubDict()
{
return RefPubDict;
}
/**
* \brief Get the shadow dictionary used
*/
-gdcmDict* gdcmDocument::GetShaDict()
+Dict *Document::GetShaDict()
{
return RefShaDict;
}
/**
* \brief Set the shadow dictionary used
- * \param dict dictionary to use in shadow
+ * @param dict dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(gdcmDict *dict)
+bool Document::SetShaDict(Dict *dict)
{
RefShaDict = dict;
return !RefShaDict;
/**
* \brief Set the shadow dictionary used
- * \param dictName name of the dictionary to use in shadow
+ * @param dictName name of the dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(DictKey const & dictName)
+bool Document::SetShaDict(DictKey const &dictName)
{
- RefShaDict = gdcmGlobal::GetDicts()->GetDict(dictName);
+ RefShaDict = Global::GetDicts()->GetDict(dictName);
return !RefShaDict;
}
/**
* \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current gdcmDocument was properly parsed
+ * decides whether or not the current Document was properly parsed
* and contains the mandatory information for being considered as
* a well formed and usable Dicom/Acr File.
- * @return true when gdcmDocument is the one of a reasonable Dicom/Acr file,
+ * @return true when Document is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmDocument::IsReadable()
+bool Document::IsReadable()
{
- if( Filetype == gdcmUnknown)
+ if( Filetype == Unknown)
{
- dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype");
+ gdcmVerboseMacro( "Wrong filetype");
return false;
}
if( TagHT.empty() )
{
- dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal"
- " hash table.");
+ gdcmVerboseMacro( "No tags in internal hash table.");
return false;
}
return true;
}
-
/**
- * \brief Internal function that checks whether the Transfer Syntax given
- * as argument is the one present in the current document.
- * @param syntaxToCheck The transfert syntax we need to check against.
- * @return True when SyntaxToCheck corresponds to the Transfer Syntax of
- * the current document. False either when the document contains
- * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match.
+ * \brief Accessor to the Transfer Syntax (when present) of the
+ * current document (it internally handles reading the
+ * value from disk when only parsing occured).
+ * @return The encountered Transfer Syntax of the current document.
*/
-bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck)
+std::string Document::GetTransferSyntax()
{
- gdcmDocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010);
+ DocEntry *entry = GetDocEntry(0x0002, 0x0010);
if ( !entry )
{
- return false;
+ return GDCM_UNKNOWN;
}
// The entry might be present but not loaded (parsing and loading
// happen at different stages): try loading and proceed with check...
LoadDocEntrySafe(entry);
- if (gdcmValEntry* valEntry = dynamic_cast< gdcmValEntry* >(entry) )
+ if (ValEntry *valEntry = dynamic_cast< ValEntry* >(entry) )
{
std::string transfer = valEntry->GetValue();
// The actual transfer (as read from disk) might be padded. We
// first need to remove the potential padding. We can make the
// weak assumption that padding was not executed with digits...
- if ( transfer.length() == 0 ) { // for brain damaged headers
- return false;
- }
- while ( ! isdigit(transfer[transfer.length()-1]) )
+ if ( transfer.length() == 0 )
{
- transfer.erase(transfer.length()-1, 1);
+ // for brain damaged headers
+ return GDCM_UNKNOWN;
}
- if ( transfer == syntaxToCheck )
+ while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
{
- return true;
+ transfer.erase(transfer.length()-1, 1);
}
+ return transfer;
}
- return false;
-}
-
-/**
- * \brief Determines if the Transfer Syntax of the present document
- * corresponds to a Implicit Value Representation of
- * Little Endian.
- * \sa \ref gdcmDocument::IsGivenTransferSyntax.
- * @return True when ImplicitVRLittleEndian found. False in all other cases.
- */
-bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax()
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2);
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a ExplicitVRLittleEndian one.
- * @return True when ExplicitVRLittleEndian found. False in all other cases.
- */
-bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax()
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1);
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a DeflatedExplicitVRLittleEndian one.
- * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
- */
-bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax()
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99);
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a Explicit VR Big Endian one.
- * @return True when big endian found. False in all other cases.
- */
-bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax()
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2);
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGBaseLineProcess1 one.
- * @return True when JPEGBaseLineProcess1found. False in all other cases.
- */
-bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax()
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50);
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGExtendedProcess2-4 one.
- * @return True when JPEGExtendedProcess2-4 found. False in all other cases.
- */
-bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax()
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51);
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGExtendeProcess3-5 one.
- * @return True when JPEGExtendedProcess3-5 found. False in all other cases.
- */
-bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax()
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52);
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one.
- * @return True when JPEGSpectralSelectionProcess6-8 found. False in all
- * other cases.
- */
-bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax()
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53);
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a RLE Lossless one.
- * @return True when RLE Lossless found. False in all
- * other cases.
- */
-bool gdcmDocument::IsRLELossLessTransferSyntax()
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5);
-}
-
-/**
- * \brief Determines if Transfer Syntax was already encountered
- * and if it corresponds to a JPEG Lossless one.
- * @return True when RLE Lossless found. False in all
- * other cases.
- */
-
-bool gdcmDocument::IsJPEGLossless()
-{
- return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55)
- || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57)
- || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70) );
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEG2000 one
- * @return True when JPEG2000 (Lossly or LossLess) found. False in all
- * other cases.
- */
-bool gdcmDocument::IsJPEG2000()
-{
- return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90)
- || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) );
-}
-
-/**
- * \brief Determines if the Transfer Syntax corresponds to encapsulated
- * of encoded Pixel Data (as opposed to native).
- * @return True when encapsulated. False when native.
- */
-bool gdcmDocument::IsEncapsulateTransferSyntax()
-{
- return ( IsJPEGBaseLineProcess1TransferSyntax()
- || IsJPEGExtendedProcess2_4TransferSyntax()
- || IsJPEGExtendedProcess3_5TransferSyntax()
- || IsJPEGSpectralSelectionProcess6_8TransferSyntax()
- || IsRLELossLessTransferSyntax()
- || IsJPEGLossless()
- || IsJPEG2000() );
+ return GDCM_UNKNOWN;
}
/**
* \brief Predicate for dicom version 3 file.
* @return True when the file is a dicom version 3.
*/
-bool gdcmDocument::IsDicomV3()
+bool Document::IsDicomV3()
{
- // Checking if Transfert Syntax exists is enough
+ // Checking if Transfer Syntax exists is enough
// Anyway, it's to late check if the 'Preamble' was found ...
// And ... would it be a rich idea to check ?
// (some 'no Preamble' DICOM images exist !)
- return GetDocEntryByNumber(0x0002, 0x0010) != NULL;
+ return GetDocEntry(0x0002, 0x0010) != NULL;
}
/**
* (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
* @return the FileType code
*/
-FileType gdcmDocument::GetFileType()
+FileType Document::GetFileType()
{
return Filetype;
}
/**
- * \brief Tries to open the file \ref gdcmDocument::Filename and
+ * \brief Tries to open the file \ref Document::Filename and
* checks the preamble when existing.
* @return The FILE pointer on success.
*/
-FILE* gdcmDocument::OpenFile()
+std::ifstream *Document::OpenFile()
{
- Fp = fopen(Filename.c_str(),"rb");
- if(!Fp)
+ HasDCMPreamble = false;
+ if (Filename.length() == 0)
+ {
+ return 0;
+ }
+
+ if(Fp)
{
- dbg.Verbose( 0,
- "gdcmDocument::OpenFile cannot open file: ",
- Filename.c_str());
+ gdcmVerboseMacro( "File already open: " << Filename.c_str());
+ }
+
+ Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
+ if( ! *Fp )
+ {
+ gdcmVerboseMacro( "Cannot open file: " << Filename.c_str());
+ delete Fp;
+ Fp = 0;
return 0;
}
uint16_t zero;
- fread(&zero, (size_t)2, (size_t)1, Fp);
-
- //ACR -- or DICOM with no Preamble --
- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 )
+ 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(
+ zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 ||
+ zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 ||
+ zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 ||
+ zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 )
+ {
+ std::string msg
+ = Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero);
+ gdcmVerboseMacro( msg.c_str() );
return Fp;
}
//DICOM
- fseek(Fp, 126L, SEEK_CUR);
+ Fp->seekg(126L, std::ios::cur);
char dicm[4];
- fread(dicm, (size_t)4, (size_t)1, Fp);
+ Fp->read(dicm, (size_t)4);
+ if( Fp->eof() )
+ {
+ CloseFile();
+ return 0;
+ }
if( memcmp(dicm, "DICM", 4) == 0 )
{
+ HasDCMPreamble = true;
return Fp;
}
- fclose(Fp);
- dbg.Verbose( 0,
- "gdcmDocument::OpenFile not DICOM/ACR (missing preamble)",
- Filename.c_str());
+ CloseFile();
+ gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
return 0;
}
* \brief closes the file
* @return TRUE if the close was successfull
*/
-bool gdcmDocument::CloseFile()
+bool Document::CloseFile()
{
- int closed = fclose(Fp);
- Fp = 0;
+ if( Fp )
+ {
+ Fp->close();
+ delete Fp;
+ Fp = 0;
+ }
- return closed;
+ return true; //FIXME how do we detect a non-close ifstream ?
}
/**
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* \return Always true.
*/
-void gdcmDocument::Write(FILE* 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
/// (necessary if user wants to write a DICOM V3 file
- /// starting from an ACR-NEMA (V2) gdcmHeader
-
- if (filetype == gdcmImplicitVR)
- {
- std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2;
- ReplaceOrCreateByNumber(implicitVRTransfertSyntax,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);
- }
+ /// starting from an ACR-NEMA (V2) Header
- if (filetype == gdcmExplicitVR)
+ if ( filetype == ImplicitVR || filetype == ExplicitVR )
{
- std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1;
- ReplaceOrCreateByNumber(explicitVRTransfertSyntax,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
- /// Dans le cas suivant on doit pader manuellement avec un 0
-
- SetEntryLengthByNumber(20, 0x0002, 0x0010);
+ // writing Dicom File Preamble
+ char filePreamble[128];
+ memset(filePreamble, 0, 128);
+ fp->write(filePreamble, 128);
+ fp->write("DICM", 4);
}
-
+
/**
* \todo rewrite later, if really usefull
* - 'Group Length' element is optional in DICOM
* UpdateGroupLength(true,ACR);
*/
- gdcmElementSet::Write(fp, filetype); // This one is recursive
-
+ ElementSet::WriteContent(fp, filetype); // This one is recursive
}
/**
- * \brief Modifies the value of a given Header Entry (Dicom Element)
+ * \brief Modifies the value of a given Doc Entry (Dicom Element)
* when it exists. Create it with the given value when unexistant.
* @param value (string) Value to be set
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * @param VR V(alue) R(epresentation) of the Entry -if private Entry-
+ * @param vr V(alue) R(epresentation) of the Entry -if private Entry-
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-gdcmValEntry* gdcmDocument::ReplaceOrCreateByNumber(
- std::string const & value,
- uint16_t group,
- uint16_t elem,
- std::string const & VR )
-{
- gdcmValEntry* valEntry = 0;
- gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
+ValEntry *Document::ReplaceOrCreate(std::string const &value,
+ uint16_t group,
+ uint16_t elem,
+ TagName const &vr )
+{
+ ValEntry *valEntry = 0;
+ DocEntry *currentEntry = GetDocEntry( group, elem);
- if (!currentEntry)
+ if (currentEntry)
{
- // check if (group,element) DictEntry exists
- // if it doesn't, create an entry in gdcmDictSet::VirtualEntry
- // and use it
+ valEntry = dynamic_cast< ValEntry* >(currentEntry);
- // Find out if the tag we received is in the dictionaries:
- gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
- gdcmDictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem);
- if (!dictEntry)
- {
- currentEntry = NewDocEntryByNumber(group, elem,VR);
- }
- else
- {
- currentEntry = NewDocEntryByNumber(group, elem);
- }
+ // Verify the VR
+ if( valEntry )
+ if( valEntry->GetVR()!=vr )
+ valEntry=NULL;
- if (!currentEntry)
+ // if currentEntry doesn't correspond to the requested valEntry
+ if( !valEntry)
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
- " NewDocEntryByNumber failed.");
- return NULL;
- }
- valEntry = new gdcmValEntry(currentEntry);
- if ( !AddEntry(valEntry))
- {
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry"
- " failed allthough this is a creation.");
- }
- }
- else
- {
- valEntry = dynamic_cast< gdcmValEntry* >(currentEntry);
- if ( !valEntry ) // Euuuuh? It wasn't a ValEntry
- // then we change it to a ValEntry ?
- // Shouldn't it be considered as an error ?
- {
- // We need to promote the gdcmDocEntry to a gdcmValEntry:
- valEntry = new gdcmValEntry(currentEntry);
if (!RemoveEntry(currentEntry))
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
- " of previous DocEntry failed.");
- return NULL;
- }
- if ( !AddEntry(valEntry))
- {
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
- " promoted ValEntry failed.");
+ gdcmVerboseMacro( "Removal of previous DocEntry failed.");
+
return NULL;
}
}
}
- SetEntryByNumber(value, group, elem);
+ // Create a new valEntry if necessary
+ if (!valEntry)
+ {
+ valEntry = NewValEntry(group, elem, vr);
+
+ if ( !AddEntry(valEntry))
+ {
+ gdcmVerboseMacro("AddEntry failed although this is a creation.");
+
+ delete valEntry;
+ return NULL;
+ }
+ }
+ // Set the binEntry value
+ SetEntry(value, valEntry);
return valEntry;
}
/*
* \brief Modifies the value of a given Header Entry (Dicom Element)
* when it exists. Create it with the given value when unexistant.
+ * A copy of the binArea is made to be kept in the Document.
* @param binArea (binary) value to be set
* @param Group Group number of the Entry
* @param Elem Element number of the Entry
+ * @param vr V(alue) R(epresentation) of the Entry -if private Entry-
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-gdcmBinEntry* gdcmDocument::ReplaceOrCreateByNumber(
- uint8_t* binArea,
- int lgth,
- uint16_t group,
- uint16_t elem,
- std::string const& VR )
+BinEntry *Document::ReplaceOrCreate(uint8_t *binArea,
+ int lgth,
+ uint16_t group,
+ uint16_t elem,
+ TagName const &vr )
{
- gdcmBinEntry* binEntry = 0;
- gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
- if (!currentEntry)
- {
+ BinEntry *binEntry = 0;
+ DocEntry *currentEntry = GetDocEntry( group, elem);
- // check if (group,element) DictEntry exists
- // if it doesn't, create an entry in gdcmDictSet::VirtualEntry
- // and use it
+ // Verify the currentEntry
+ if (currentEntry)
+ {
+ binEntry = dynamic_cast< BinEntry* >(currentEntry);
- // Find out if the tag we received is in the dictionaries:
- gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
- gdcmDictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem);
+ // Verify the VR
+ if( binEntry )
+ if( binEntry->GetVR()!=vr )
+ binEntry=NULL;
- if (!dictEntry)
- {
- currentEntry = NewDocEntryByNumber(group, elem, VR);
- }
- else
+ // if currentEntry doesn't correspond to the requested valEntry
+ if( !binEntry)
{
- currentEntry = NewDocEntryByNumber(group, elem);
- }
- if (!currentEntry)
- {
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
- " NewDocEntryByNumber failed.");
- return NULL;
+ if (!RemoveEntry(currentEntry))
+ {
+ gdcmVerboseMacro( "Removal of previous DocEntry failed.");
+
+ return NULL;
+ }
}
- binEntry = new gdcmBinEntry(currentEntry);
+ }
+
+ // Create a new binEntry if necessary
+ if (!binEntry)
+ {
+ binEntry = NewBinEntry(group, elem, vr);
+
if ( !AddEntry(binEntry))
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry"
- " failed allthough this is a creation.");
+ gdcmVerboseMacro( "AddEntry failed allthough this is a creation.");
+
+ delete binEntry;
+ return NULL;
}
}
+
+ // Set the binEntry value
+ uint8_t *tmpArea;
+ if (lgth>0 && binArea)
+ {
+ tmpArea = new uint8_t[lgth];
+ memcpy(tmpArea,binArea,lgth);
+ }
else
{
- binEntry = dynamic_cast< gdcmBinEntry* >(currentEntry);
- if ( !binEntry ) // Euuuuh? It wasn't a BinEntry
- // then we change it to a BinEntry ?
- // Shouldn't it be considered as an error ?
+ tmpArea = 0;
+ }
+ if (!SetEntry(tmpArea,lgth,binEntry))
+ {
+ if (tmpArea)
{
- // We need to promote the gdcmDocEntry to a gdcmBinEntry:
- binEntry = new gdcmBinEntry(currentEntry);
- if (!RemoveEntry(currentEntry))
- {
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
- " of previous DocEntry failed.");
- return NULL;
- }
- if ( !AddEntry(binEntry))
- {
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
- " promoted BinEntry failed.");
- return NULL;
- }
+ delete[] tmpArea;
}
}
- SetEntryByNumber(binArea, lgth, group, elem);
-
return binEntry;
}
-
/*
* \brief Modifies the value of a given Header Entry (Dicom Element)
* when it exists. Create it when unexistant.
* \return pointer to the modified/created SeqEntry (NULL when creation
* failed).
*/
-gdcmSeqEntry* gdcmDocument::ReplaceOrCreateByNumber(
- uint16_t group,
- uint16_t elem)
+SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem)
{
- gdcmSeqEntry* b = 0;
- gdcmDocEntry* a = GetDocEntryByNumber( group, elem);
- if (!a)
+ SeqEntry *seqEntry = 0;
+ DocEntry *currentEntry = GetDocEntry( group, elem);
+
+ // Verify the currentEntry
+ if (currentEntry)
{
- a = NewSeqEntryByNumber(group, elem);
- if (!a)
+ seqEntry = dynamic_cast< SeqEntry* >(currentEntry);
+
+ // Verify the VR
+ if( seqEntry )
+ if( seqEntry->GetVR()!="SQ" )
+ seqEntry=NULL;
+
+ // if currentEntry doesn't correspond to the requested valEntry
+ if( !seqEntry)
{
- return 0;
+ if (!RemoveEntry(currentEntry))
+ {
+ gdcmVerboseMacro( "Removal of previous DocEntry failed.");
+
+ return NULL;
+ }
}
+ }
- b = new gdcmSeqEntry(a, 1); // FIXME : 1 (Depth)
- AddEntry(b);
- }
- return b;
+ // Create a new seqEntry if necessary
+ if (!seqEntry)
+ {
+ seqEntry = NewSeqEntry(group, elem);
+
+ if ( !AddEntry(seqEntry))
+ {
+ gdcmVerboseMacro( "AddEntry failed allthough this is a creation.");
+
+ delete seqEntry;
+ return NULL;
+ }
+ }
+
+ return seqEntry;
}
/**
* @param elem element number of the Entry
* \return boolean
*/
-bool gdcmDocument::ReplaceIfExistByNumber(std::string const & value,
- uint16_t group, uint16_t elem )
+bool Document::ReplaceIfExist(std::string const &value,
+ uint16_t group, uint16_t elem )
{
- SetEntryByNumber(value, group, elem);
+ SetEntry(value, group, elem);
return true;
}
* @param element Element number of the searched Dicom Element
* @return true is found
*/
-bool gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
+bool Document::CheckIfEntryExist(uint16_t group, uint16_t element )
{
- const std::string &key = gdcmDictEntry::TranslateToKey(group, element );
- return TagHT.count(key);
+ const std::string &key = DictEntry::TranslateToKey(group, element );
+ return TagHT.count(key) != 0;
}
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value of a given tag.
- * \warning Don't use any longer : use GetPubEntryByName
- * @param tagName name of the searched element.
- * @return Corresponding element value when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmDocument::GetEntryByName(TagName const& tagName)
-{
- gdcmDictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( !dictEntry )
- {
- return GDCM_UNFOUND;
- }
-
- return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement());
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param tagName name of the searched element.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmDocument::GetEntryVRByName(TagName const& tagName)
-{
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- {
- return GDCM_UNFOUND;
- }
-
- gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
- return elem->GetVR();
-}
/**
* \brief Searches within Header Entries (Dicom Elements) parsed with
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryByNumber(uint16_t group, uint16_t element)
+std::string Document::GetEntry(uint16_t group, uint16_t element)
{
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
- /// \todo use map methods, instead of multimap JPR
+ TagKey key = DictEntry::TranslateToKey(group, element);
if ( !TagHT.count(key))
{
return GDCM_UNFOUND;
}
- return ((gdcmValEntry *)TagHT.find(key)->second)->GetValue();
+ return ((ValEntry *)TagHT.find(key)->second)->GetValue();
}
/**
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryVRByNumber(uint16_t group, uint16_t element)
+std::string Document::GetEntryVR(uint16_t group, uint16_t element)
{
- gdcmDocEntry* elem = GetDocEntryByNumber(group, element);
+ DocEntry *elem = GetDocEntry(group, element);
if ( !elem )
{
return GDCM_UNFOUND;
* @param element Element number of the searched tag.
* @return Corresponding element length; -2 if not found
*/
-int gdcmDocument::GetEntryLengthByNumber(uint16_t group, uint16_t element)
+int Document::GetEntryLength(uint16_t group, uint16_t element)
{
- gdcmDocEntry* elem = GetDocEntryByNumber(group, element);
+ DocEntry *elem = GetDocEntry(group, element);
if ( !elem )
{
return -2; //magic number
}
return elem->GetLength();
}
-/**
- * \brief Sets the value (string) of the Header Entry (Dicom Element)
- * @param content string value of the Dicom Element
- * @param tagName name of the searched Dicom Element.
- * @return true when found
- */
-bool gdcmDocument::SetEntryByName(std::string const & content,std::string const & tagName)
-{
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( !dictEntry )
- {
- return false;
- }
-
- return SetEntryByNumber(content,dictEntry->GetGroup(),
- dictEntry->GetElement());
-}
/**
- * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
* @param content new value (string) to substitute with
* @param group group number of the Dicom Element to modify
* @param element element number of the Dicom Element to modify
*/
-bool gdcmDocument::SetEntryByNumber(std::string const& content,
- uint16_t group,
- uint16_t element)
+bool Document::SetEntry(std::string const& content,
+ uint16_t group, uint16_t element)
{
- int c;
- int l;
-
- gdcmValEntry* valEntry = GetValEntryByNumber(group, element);
- if (!valEntry )
+ ValEntry *entry = GetValEntry(group, element);
+ if (!entry )
{
- dbg.Verbose(0, "gdcmDocument::SetEntryByNumber: no corresponding",
- " ValEntry (try promotion first).");
+ gdcmVerboseMacro( "No corresponding ValEntry (try promotion first).");
return false;
}
- // Non even content must be padded with a space (020H)...
- std::string finalContent = content;
- if( finalContent.length() % 2 )
- {
- finalContent += '\0'; // ... therefore we padd with (000H) .!?!
- }
- 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
- {
- gdcmVRKey vr = valEntry->GetVR();
- if( vr == "US" || vr == "SS" )
- {
- c = CountSubstring(content, "\\") + 1; // for multivaluated items
- l = c*2;
- }
- else if( vr == "UL" || vr == "SL" )
- {
- c = CountSubstring(content, "\\") + 1; // for multivaluated items
- l = c*4;;
- }
- }
- valEntry->SetLength(l);
- return true;
+ return SetEntry(content,entry);
}
/**
- * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
* @param content new value (void* -> uint8_t*) to substitute with
* @param group group number of the Dicom Element to modify
* @param element element number of the Dicom Element to modify
*/
-bool gdcmDocument::SetEntryByNumber(uint8_t*content,
- int lgth,
- uint16_t group,
- uint16_t element)
+bool Document::SetEntry(uint8_t*content, int lgth,
+ uint16_t group, uint16_t element)
{
- (void)lgth; //not used
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key))
+ BinEntry *entry = GetBinEntry(group, element);
+ if (!entry )
{
+ gdcmVerboseMacro( "No corresponding ValEntry (try promotion first).");
return false;
}
-/* Hope Binary field length is *never* wrong
- if(lgth%2) // Non even length are padded with a space (020H).
- {
- lgth++;
- //content = content + '\0'; // fing a trick to enlarge a binary field?
- }
-*/
- gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key];
- a->SetBinArea(content);
- a->SetLength(lgth);
- a->SetValue(GDCM_BINLOADED);
-
- return true;
+ return SetEntry(content,lgth,entry);
}
/**
- * \brief Accesses an existing gdcmDocEntry (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.
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
+ * and modifies it's content with the given value.
+ * @param content new value (string) to substitute with
+ * @param entry Entry to be modified
*/
-bool gdcmDocument::SetEntryLengthByNumber(uint32_t l,
- uint16_t group,
- uint16_t element)
+bool Document::SetEntry(std::string const &content,ValEntry *entry)
{
- /// \todo use map methods, instead of multimap JPR
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key) )
+ if(entry)
{
- return false;
- }
- if ( l % 2 )
- {
- l++; // length must be even
+ entry->SetValue(content);
+ return true;
}
- ( ((TagHT.equal_range(key)).first)->second )->SetLength(l);
-
- return true ;
+ return false;
}
/**
- * \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
+ * \brief Accesses an existing BinEntry (i.e. a Dicom Element)
+ * and modifies it's content with the given value.
+ * @param content new value (void* -> uint8_t*) to substitute with
+ * @param entry Entry to be modified
+ * @param lgth new value length
*/
-size_t gdcmDocument::GetEntryOffsetByNumber(uint16_t group, uint16_t elem)
+bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry)
{
- gdcmDocEntry* entry = GetDocEntryByNumber(group, elem);
- if (!entry)
+ if(entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry present.");
- return 0;
+ // Hope Binary field length is *never* wrong
+ /*if(lgth%2) // Non even length are padded with a space (020H).
+ {
+ lgth++;
+ //content = content + '\0'; // fing a trick to enlarge a binary field?
+ }*/
+
+ entry->SetBinArea(content);
+ entry->SetLength(lgth);
+ entry->SetValue(GDCM_BINLOADED);
+ return true;
}
- return entry->GetOffset();
+ return false;
}
/**
* @param elem element number of the Entry
* @return Pointer to the 'non string' area
*/
-void* gdcmDocument::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem)
+void *Document::GetEntryBinArea(uint16_t group, uint16_t elem)
{
- gdcmDocEntry* entry = GetDocEntryByNumber(group, elem);
+ DocEntry *entry = GetDocEntry(group, elem);
if (!entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry");
+ gdcmVerboseMacro( "No entry");
return 0;
}
- return ((gdcmBinEntry *)entry)->GetBinArea();
+ if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(entry) )
+ {
+ return binEntry->GetBinArea();
+ }
+
+ return 0;
}
/**
* @param group group number of the Entry
* @param elem element number of the Entry
*/
-void* gdcmDocument::LoadEntryBinArea(uint16_t group, uint16_t elem)
+void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
- gdcmDocEntry *docElement = GetDocEntryByNumber(group, elem);
+ // Search the corresponding DocEntry
+ DocEntry *docElement = GetDocEntry(group, elem);
if ( !docElement )
- {
- return NULL;
- }
- size_t o =(size_t)docElement->GetOffset();
- fseek(Fp, o, SEEK_SET);
- size_t l = docElement->GetLength();
- uint8_t* a = new uint8_t[l];
- if(!a)
- {
- dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea cannot allocate a");
- return NULL;
- }
- size_t l2 = fread(a, 1, l , Fp);
- if( l != l2 )
- {
- delete[] a;
- return NULL;
- }
- /// \todo Drop any already existing void area! JPR
- if( !SetEntryBinAreaByNumber( a, group, elem ) );
- {
- dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea setting failed.");
- }
- return a;
+ return;
+
+ BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
+ if( !binElement )
+ return;
+
+ LoadEntryBinArea(binElement);
}
+
/**
* \brief Loads (from disk) the element content
* when a string is not suitable
* @param element Entry whose binArea is going to be loaded
*/
-void* gdcmDocument::LoadEntryBinArea(gdcmBinEntry* element)
+void Document::LoadEntryBinArea(BinEntry *element)
{
+ if(element->GetBinArea())
+ return;
+
+ bool openFile = !Fp;
+ if(openFile)
+ OpenFile();
+
size_t o =(size_t)element->GetOffset();
- fseek(Fp, o, SEEK_SET);
+ Fp->seekg(o, std::ios::beg);
+
size_t l = element->GetLength();
- uint8_t* a = new uint8_t[l];
+ uint8_t *a = new uint8_t[l];
if( !a )
{
- dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea cannot allocate a");
- return NULL;
+ gdcmVerboseMacro( "Cannot allocate a");
+ return;
}
- element->SetBinArea((uint8_t*)a);
+
/// \todo check the result
- size_t l2 = fread(a, 1, l , Fp);
- if( l != l2 )
+ Fp->read((char*)a, l);
+ if( Fp->fail() || Fp->eof())
{
delete[] a;
- return NULL;
+ return;
}
- return a;
+ element->SetBinArea(a);
+
+ if(openFile)
+ CloseFile();
}
/**
* @param element Element number of the searched Dicom Element
* @return
*/
-bool gdcmDocument::SetEntryBinAreaByNumber(uint8_t* area,
- uint16_t group,
- uint16_t element)
+/*bool Document::SetEntryBinArea(uint8_t *area,
+ uint16_t group, uint16_t element)
{
- gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ DocEntry *currentEntry = GetDocEntry(group, element);
if ( !currentEntry )
{
return false;
}
- if ( gdcmBinEntry* binEntry = dynamic_cast<gdcmBinEntry*>(currentEntry) )
+
+ if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(currentEntry) )
{
binEntry->SetBinArea( area );
return true;
}
- return true;
-}
-
-/**
- * \brief Update the entries with the shadow dictionary.
- * Only non even entries are analyzed
- */
-void gdcmDocument::UpdateShaEntries()
-{
- //gdcmDictEntry *entry;
- std::string vr;
-
- /// \todo TODO : still any use to explore recursively the whole structure?
-/*
- for(ListTag::iterator it=listEntries.begin();
- it!=listEntries.end();
- ++it)
- {
- // Odd group => from public dictionary
- if((*it)->GetGroup()%2==0)
- continue;
-
- // Peer group => search the corresponding dict entry
- if(RefShaDict)
- entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement());
- else
- entry=NULL;
-
- if((*it)->IsImplicitVR())
- vr="Implicit";
- else
- vr=(*it)->GetVR();
-
- (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling
- if(entry){
- // Set the new entry and the new value
- (*it)->SetDictEntry(entry);
- CheckDocEntryVR(*it,vr);
-
- (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling
-
- }
- else
- {
- // Remove precedent value transformation
- (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr));
- }
- }
-*/
-}
-/**
- * \brief Searches within the Header Entries for a Dicom Element of
- * a given tag.
- * @param tagName name of the searched Dicom Element.
- * @return Corresponding Dicom Element when it exists, and NULL
- * otherwise.
- */
-gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string const & tagName)
-{
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( !dictEntry )
- {
- return NULL;
- }
-
- return GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement());
-}
+ return false;
+}*/
/**
* \brief retrieves a Dicom Element (the first one) using (group, element)
* @param element Element number of the searched Dicom Element
* @return
*/
-gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(uint16_t group,
- uint16_t element)
+DocEntry *Document::GetDocEntry(uint16_t group, uint16_t element)
{
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ TagKey key = DictEntry::TranslateToKey(group, element);
if ( !TagHT.count(key))
{
return NULL;
}
/**
- * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only
+ * \brief Same as \ref Document::GetDocEntry except it only
* returns a result when the corresponding entry is of type
* ValEntry.
* @return When present, the corresponding ValEntry.
*/
-gdcmValEntry* gdcmDocument::GetValEntryByNumber(uint16_t group,
- uint16_t element)
+ValEntry *Document::GetValEntry(uint16_t group, uint16_t element)
+{
+ DocEntry *currentEntry = GetDocEntry(group, element);
+ if ( !currentEntry )
+ {
+ return 0;
+ }
+ if ( ValEntry *entry = dynamic_cast<ValEntry*>(currentEntry) )
+ {
+ return entry;
+ }
+ gdcmVerboseMacro( "Unfound ValEntry.");
+
+ return 0;
+}
+
+/**
+ * \brief Same as \ref Document::GetDocEntry except it only
+ * returns a result when the corresponding entry is of type
+ * BinEntry.
+ * @return When present, the corresponding BinEntry.
+ */
+BinEntry *Document::GetBinEntry(uint16_t group, uint16_t element)
{
- gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ DocEntry *currentEntry = GetDocEntry(group, element);
if ( !currentEntry )
{
return 0;
}
- if ( gdcmValEntry* valEntry = dynamic_cast<gdcmValEntry*>(currentEntry) )
+ if ( BinEntry *entry = dynamic_cast<BinEntry*>(currentEntry) )
{
- return valEntry;
+ return entry;
}
- dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry.");
+ gdcmVerboseMacro( "Unfound BinEntry.");
return 0;
}
/**
* \brief Loads the element while preserving the current
- * underlying file position indicator as opposed to
+ * underlying file position indicator as opposed to
* to LoadDocEntry that modifies it.
* @param entry Header Entry whose value shall be loaded.
* @return
*/
-void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry)
+void Document::LoadDocEntrySafe(DocEntry *entry)
{
- long PositionOnEntry = ftell(Fp);
- LoadDocEntry(entry);
- fseek(Fp, PositionOnEntry, SEEK_SET);
+ if(Fp)
+ {
+ long PositionOnEntry = Fp->tellg();
+ LoadDocEntry(entry);
+ Fp->seekg(PositionOnEntry, std::ios::beg);
+ }
}
/**
* processor order.
* @return The properly swaped 32 bits integer.
*/
-uint32_t gdcmDocument::SwapLong(uint32_t a)
+uint32_t Document::SwapLong(uint32_t a)
{
switch (SwapCode)
{
- case 0 :
+ case 1234 :
break;
case 4321 :
a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
break;
default :
- //std::cout << "swapCode= " << SwapCode << std::endl;
- dbg.Error(" gdcmDocument::SwapLong : unset swap code");
+ gdcmErrorMacro( "Unset swap code:" << SwapCode );
a = 0;
}
return a;
* processor order.
* @return The properly unswaped 32 bits integer.
*/
-uint32_t gdcmDocument::UnswapLong(uint32_t a)
+uint32_t Document::UnswapLong(uint32_t a)
{
return SwapLong(a);
}
* \brief Swaps the bytes so they agree with the processor order
* @return The properly swaped 16 bits integer.
*/
-uint16_t gdcmDocument::SwapShort(uint16_t a)
+uint16_t Document::SwapShort(uint16_t a)
{
if ( SwapCode == 4321 || SwapCode == 2143 )
{
* \brief Unswaps the bytes so they agree with the processor order
* @return The properly unswaped 16 bits integer.
*/
-uint16_t gdcmDocument::UnswapShort(uint16_t a)
+uint16_t Document::UnswapShort(uint16_t a)
{
return SwapShort(a);
}
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
* @return length of the parsed set.
*/
-void gdcmDocument::ParseDES(gdcmDocEntrySet *set,
- long offset,
- long l_max,
- bool delim_mode)
+void Document::ParseDES(DocEntrySet *set, long offset,
+ long l_max, bool delim_mode)
{
- gdcmDocEntry *newDocEntry = 0;
-
+ DocEntry *newDocEntry = 0;
+ ValEntry *newValEntry;
+ BinEntry *newBinEntry;
+ SeqEntry *newSeqEntry;
+ VRKey vr;
+ bool used=false;
+
while (true)
- {
- if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ {
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
break;
}
+
+ used=true;
newDocEntry = ReadNextDocEntry( );
if ( !newDocEntry )
{
break;
}
- gdcmVRKey vr = newDocEntry->GetVR();
- if ( vr != "SQ" )
- {
-
- if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) )
+ vr = newDocEntry->GetVR();
+ newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
+ newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
+ newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
+
+ if ( newValEntry || newBinEntry )
+ {
+ if ( newBinEntry )
+ {
+ if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) )
+ {
+ ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
+ gdcmVerboseMacro( "Neither Valentry, nor BinEntry."
+ "Probably unknown VR.");
+ }
+
+ //////////////////// BinEntry or UNKOWN VR:
+ // When "this" is a Document the Key is simply of the
+ // form ( group, elem )...
+ if (Document *dummy = dynamic_cast< Document* > ( set ) )
+ {
+ (void)dummy;
+ newBinEntry->SetKey( newBinEntry->GetKey() );
+ }
+ // but when "this" is a SQItem, we are inserting this new
+ // valEntry in a sequence item, and the kay has the
+ // generalized form (refer to \ref BaseTagKey):
+ if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ {
+ newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newBinEntry->GetKey() );
+ }
+
+ LoadDocEntry( newBinEntry );
+ if( !set->AddEntry( newBinEntry ) )
+ {
+ //Expect big troubles if here
+ //delete newBinEntry;
+ used=false;
+ }
+ }
+ else
{
/////////////////////// ValEntry
- gdcmValEntry* newValEntry =
- new gdcmValEntry( newDocEntry->GetDictEntry() );
- newValEntry->Copy( newDocEntry );
-
- // When "set" is a gdcmDocument, then we are at the top of the
+ // When "set" is a Document, then we are at the top of the
// hierarchy and the Key is simply of the form ( group, elem )...
- if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ if (Document *dummy = dynamic_cast< Document* > ( set ) )
{
(void)dummy;
newValEntry->SetKey( newValEntry->GetKey() );
}
- // ...but when "set" is a gdcmSQItem, we are inserting this new
+ // ...but when "set" is a SQItem, we are inserting this new
// valEntry in a sequence item. Hence the key has the
- // generalized form (refer to \ref gdcmBaseTagKey):
- if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ // generalized form (refer to \ref BaseTagKey):
+ if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newValEntry->SetKey( parentSQItem->GetBaseTagKey()
+ newValEntry->GetKey() );
}
- set->AddEntry( newValEntry );
LoadDocEntry( newValEntry );
- if (newValEntry->IsItemDelimitor())
- {
- break;
- }
- if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ bool delimitor=newValEntry->IsItemDelimitor();
+ if( !set->AddEntry( newValEntry ) )
{
- break;
- }
- }
- else
- {
- if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
- {
- ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, "
- "nor BinEntry. Probably unknown VR.");
+ // If here expect big troubles
+ //delete newValEntry; //otherwise mem leak
+ used=false;
}
- //////////////////// BinEntry or UNKOWN VR:
- gdcmBinEntry* newBinEntry =
- new gdcmBinEntry( newDocEntry->GetDictEntry() );
- newBinEntry->Copy( newDocEntry );
-
- // When "this" is a gdcmDocument the Key is simply of the
- // form ( group, elem )...
- if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ if (delimitor)
{
- newBinEntry->SetKey( newBinEntry->GetKey() );
+ if(!used)
+ delete newDocEntry;
+ break;
}
- // but when "this" is a SQItem, we are inserting this new
- // valEntry in a sequence item, and the kay has the
- // generalized form (refer to \ref gdcmBaseTagKey):
- if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
- + newBinEntry->GetKey() );
+ if(!used)
+ delete newDocEntry;
+ break;
}
-
- set->AddEntry( newBinEntry );
- LoadDocEntry( newBinEntry );
}
- if (newDocEntry->GetGroup() == 0x7fe0 &&
- newDocEntry->GetElement() == 0x0010 )
+ if ( ( newDocEntry->GetGroup() == 0x7fe0 )
+ && ( newDocEntry->GetElement() == 0x0010 ) )
{
- if ( IsRLELossLessTransferSyntax() )
+ std::string ts = GetTransferSyntax();
+ if ( Global::GetTS()->IsRLELossless(ts) )
{
- long PositionOnEntry = ftell(Fp);
- fseek(Fp, newDocEntry->GetOffset(), SEEK_SET);
+ long positionOnEntry = Fp->tellg();
+ Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
ComputeRLEInfo();
- fseek(Fp, PositionOnEntry, SEEK_SET);
+ Fp->seekg( positionOnEntry, std::ios::beg );
}
- else
+ else if ( Global::GetTS()->IsJPEG(ts) )
{
- SkipToNextDocEntry(newDocEntry);
+ long positionOnEntry = Fp->tellg();
+ Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
+ ComputeJPEGFragmentInfo();
+ Fp->seekg( positionOnEntry, std::ios::beg );
}
}
- else
- {
- // to be sure we are at the beginning
- SkipToNextDocEntry(newDocEntry);
- }
+
+ // Just to make sure we are at the beginning of next entry.
+ SkipToNextDocEntry(newDocEntry);
}
else
{
}
}
// no other way to create it ...
- gdcmSeqEntry* newSeqEntry =
- new gdcmSeqEntry( newDocEntry->GetDictEntry() );
- newSeqEntry->Copy( newDocEntry );
newSeqEntry->SetDelimitorMode( delim_mode );
- // At the top of the hierarchy, stands a gdcmDocument. When "set"
- // is a gdcmDocument, then we are building the first depth level.
- // Hence the gdcmSeqEntry we are building simply has a depth
+ // At the top of the hierarchy, stands a Document. When "set"
+ // is a Document, then we are building the first depth level.
+ // Hence the SeqEntry we are building simply has a depth
// level of one:
- if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ if (Document *dummy = dynamic_cast< Document* > ( set ) )
{
(void)dummy;
newSeqEntry->SetDepthLevel( 1 );
newSeqEntry->SetKey( newSeqEntry->GetKey() );
}
// But when "set" is allready a SQItem, we are building a nested
- // sequence, and hence the depth level of the new gdcmSeqEntry
+ // sequence, and hence the depth level of the new SeqEntry
// we are building, is one level deeper:
- if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
l, delim_mode);
}
set->AddEntry( newSeqEntry );
- if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
break;
}
}
- delete newDocEntry;
+
+ if(!used)
+ delete newDocEntry;
}
}
* \brief Parses a Sequence ( SeqEntry after SeqEntry)
* @return parsed length for this level
*/
-void gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry,
- long offset, long l_max, bool delim_mode)
+void Document::ParseSQ( SeqEntry *seqEntry,
+ long offset, long l_max, bool delim_mode)
{
int SQItemNumber = 0;
bool dlm_mod;
while (true)
{
- gdcmDocEntry* newDocEntry = ReadNextDocEntry();
+ DocEntry *newDocEntry = ReadNextDocEntry();
if ( !newDocEntry )
{
// FIXME Should warn user
{
if ( newDocEntry->IsSequenceDelimitor() )
{
- seqEntry->SetSequenceDelimitationItem( newDocEntry );
+ seqEntry->SetSequenceDelimitationItem( newDocEntry );
break;
}
}
- if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- break;
+ delete newDocEntry;
+ break;
}
- gdcmSQItem *itemSQ = new gdcmSQItem( seqEntry->GetDepthLevel() );
+ SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
std::ostringstream newBase;
newBase << seqEntry->GetKey()
<< "/"
}
ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+ delete newDocEntry;
seqEntry->AddEntry( itemSQ, SQItemNumber );
SQItemNumber++;
- if ( !delim_mode && ( ftell(Fp) - offset ) >= l_max )
+ if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
{
break;
}
/**
* \brief Loads the element content if its length doesn't exceed
- * the value specified with gdcmDocument::SetMaxSizeLoadEntry()
+ * the value specified with Document::SetMaxSizeLoadEntry()
* @param entry Header Entry (Dicom Element) to be dealt with
*/
-void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry)
+void Document::LoadDocEntry(DocEntry *entry)
{
- size_t item_read;
uint16_t group = entry->GetGroup();
std::string vr = entry->GetVR();
uint32_t length = entry->GetLength();
- fseek(Fp, (long)entry->GetOffset(), SEEK_SET);
+ Fp->seekg((long)entry->GetOffset(), std::ios::beg);
// A SeQuence "contains" a set of Elements.
// (fffe e000) tells us an Element is beginning
// When the length is zero things are easy:
if ( length == 0 )
{
- ((gdcmValEntry *)entry)->SetValue("");
+ ((ValEntry *)entry)->SetValue("");
return;
}
std::ostringstream s;
if (length > MaxSizeLoadEntry)
{
- if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) )
+ if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
{
//s << "gdcm::NotLoaded (BinEntry)";
s << GDCM_NOTLOADED;
s << " x(" << std::hex << entry->GetLength() << ")";
binEntryPtr->SetValue(s.str());
}
- // Be carefull : a BinEntry IS_A ValEntry ...
- else if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) )
+ // Be carefull : a BinEntry IS_A ValEntry ...
+ else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) )
{
// s << "gdcm::NotLoaded. (ValEntry)";
s << GDCM_NOTLOADED;
else
{
// fusible
- std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry "
- << "nor a ValEntry ?! Should never print that !" << std::endl;
+ gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry "
+ << "nor a ValEntry ?! Should never print that !" );
}
// to be sure we are at the end of the value ...
- fseek(Fp,(long)entry->GetOffset()+(long)entry->GetLength(),SEEK_SET);
+ Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
+ std::ios::beg);
return;
}
// When we find a BinEntry not very much can be done :
- if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) )
+ if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
{
s << GDCM_BINLOADED;
binEntryPtr->SetValue(s.str());
LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
return;
}
-
+
/// \todo Any compacter code suggested (?)
if ( IsDocEntryAnInteger(entry) )
{
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
- ((gdcmValEntry *)entry)->SetValue(s.str());
+ ((ValEntry *)entry)->SetValue(s.str());
return;
}
- // We need an additional byte for storing \0 that is not on disk
- //std::string newValue(length,0);
- //item_read = fread(&(newValue[0]), (size_t)length, (size_t)1, Fp);
- //rah !! I can't believe it could work, normally this is a const char* !!!
+ // FIXME: We need an additional byte for storing \0 that is not on disk
char *str = new char[length+1];
- item_read = fread(str, (size_t)length, (size_t)1, Fp);
- str[length] = '\0';
- std::string newValue = str;
+ Fp->read(str, (size_t)length);
+ str[length] = '\0'; //this is only useful when length is odd
+ // Special DicomString call to properly handle \0 and even length
+ std::string newValue;
+ if( length % 2 )
+ {
+ newValue = Util::DicomString(str, length+1);
+ gdcmVerboseMacro("Warning: bad length: " << length <<
+ ",For string :" << newValue.c_str());
+ // Since we change the length of string update it length
+ //entry->SetReadLength(length+1);
+ }
+ else
+ {
+ newValue = Util::DicomString(str, length);
+ }
delete[] str;
- if ( gdcmValEntry* valEntry = dynamic_cast<gdcmValEntry* >(entry) )
- {
- if ( item_read != 1 )
+
+ if ( ValEntry *valEntry = dynamic_cast<ValEntry* >(entry) )
+ {
+ if ( Fp->fail() || Fp->eof())
{
- dbg.Verbose(1, "gdcmDocument::LoadDocEntry",
- "unread element value");
+ gdcmVerboseMacro("Unread element value");
valEntry->SetValue(GDCM_UNREAD);
return;
}
}
else
{
- dbg.Error(true, "gdcmDocument::LoadDocEntry"
- "Should have a ValEntry, here !");
+ gdcmErrorMacro( "Should have a ValEntry, here !");
}
}
* \brief Find the value Length of the passed Header Entry
* @param entry Header Entry whose length of the value shall be loaded.
*/
-void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry )
- throw ( gdcmFormatError )
+void Document::FindDocEntryLength( DocEntry *entry )
+ throw ( FormatError )
{
uint16_t element = entry->GetElement();
std::string vr = entry->GetVR();
uint16_t length16;
- if ( Filetype == gdcmExplicitVR && !entry->IsImplicitVR() )
+ if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" )
{
- // The following reserved two bytes (see PS 3.5-2001, section
- // 7.1.2 Data element structure with explicit vr p27) must be
+ // 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.
- fseek(Fp, 2L, SEEK_CUR);
+ Fp->seekg( 2L, std::ios::cur);
uint32_t length32 = ReadInt32();
if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
uint32_t lengthOB;
try
{
- /// \todo rename that to FindDocEntryLengthOBOrOW since
- /// the above test is on both OB and OW...
- lengthOB = FindDocEntryLengthOB();
+ lengthOB = FindDocEntryLengthOBOrOW();
}
- catch ( gdcmFormatUnexpected )
+ catch ( FormatUnexpected )
{
// Computing the length failed (this happens with broken
// files like gdcm-JPEG-LossLess3a.dcm). We still have a
// chance to get the pixels by deciding the element goes
// until the end of the file. Hence we artificially fix the
// the length and proceed.
- long currentPosition = ftell(Fp);
- fseek(Fp,0L,SEEK_END);
- long lengthUntilEOF = ftell(Fp) - currentPosition;
- fseek(Fp, currentPosition, SEEK_SET);
+ long currentPosition = Fp->tellg();
+ Fp->seekg(0L,std::ios::end);
+
+ long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
+ Fp->seekg(currentPosition, std::ios::beg);
+
+ entry->SetReadLength(lengthUntilEOF);
entry->SetLength(lengthUntilEOF);
return;
}
+ entry->SetReadLength(lengthOB);
entry->SetLength(lengthOB);
return;
}
// big endian and proceed...
if ( element == 0x0000 && length16 == 0x0400 )
{
- if ( !IsExplicitVRBigEndianTransferSyntax() )
+ std::string ts = GetTransferSyntax();
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts)
+ != TS::ExplicitVRBigEndian )
{
- throw gdcmFormatError( "gdcmDocument::FindDocEntryLength()",
- " not explicit VR." );
+ throw FormatError( "Document::FindDocEntryLength()",
+ " not explicit VR." );
return;
}
length16 = 4;
- SwitchSwapToBigEndian();
+ SwitchByteSwapCode();
+
// Restore the unproperly loaded values i.e. the group, the element
// and the dictionary entry depending on them.
uint16_t correctGroup = SwapShort( entry->GetGroup() );
uint16_t correctElem = SwapShort( entry->GetElement() );
- gdcmDictEntry* newTag = GetDictEntryByNumber( correctGroup,
- correctElem );
+ DictEntry *newTag = GetDictEntry( correctGroup, correctElem );
if ( !newTag )
{
// This correct tag is not in the dictionary. Create a new one.
/**
* \brief Find the Value Representation of the current Dicom Element.
- * @param entry
+ * @return Value Representation of the current Entry
*/
-void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry )
+std::string Document::FindDocEntryVR()
{
- if ( Filetype != gdcmExplicitVR )
- {
- return;
- }
-
- char vr[3];
+ if ( Filetype != ExplicitVR )
+ return GDCM_UNKNOWN;
- long positionOnEntry = ftell(Fp);
+ long positionOnEntry = Fp->tellg();
// Warning: we believe this is explicit VR (Value Representation) because
// we used a heuristic that found "UL" in the first tag. Alas this
// doesn't guarantee that all the tags will be in explicit VR. In some
// 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.
-
- fread (vr, (size_t)2,(size_t)1, Fp);
+
+ char vr[3];
+ Fp->read (vr, (size_t)2);
vr[2] = 0;
- if( !CheckDocEntryVR(entry, vr) )
+ if( !CheckDocEntryVR(vr) )
{
- fseek(Fp, positionOnEntry, SEEK_SET);
- // 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
- // we know now our assumption on expliciteness is not furfilled.
- // avoid .
- if ( entry->IsVRUnknown() )
- {
- entry->SetVR("Implicit");
- }
- entry->SetImplicitVR();
+ Fp->seekg(positionOnEntry, std::ios::beg);
+ return GDCM_UNKNOWN;
}
+ return vr;
}
/**
* \brief Check the correspondance between the VR of the header entry
* and the taken VR. If they are different, the header entry is
* updated with the new VR.
- * @param entry Header Entry to check
* @param vr Dicom Value Representation
* @return false if the VR is incorrect of if the VR isn't referenced
* otherwise, it returns true
*/
-bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr)
+bool Document::CheckDocEntryVR(VRKey vr)
{
- char msg[100]; // for sprintf
- bool realExplicit = true;
-
- // Assume we are reading a falsely explicit VR file i.e. we reached
- // a tag where we expect reading a VR but are in fact we read the
- // first to bytes of the length. Then we will interogate (through find)
- // the dicom_vr dictionary with oddities like "\004\0" which crashes
- // both GCC and VC++ implementations of the STL map. Hence when the
- // expected VR read happens to be non-ascii characters we consider
- // we hit falsely explicit VR tag.
-
- if ( !isalpha(vr[0]) && !isalpha(vr[1]) )
- {
- realExplicit = false;
- }
-
// CLEANME searching the dicom_vr at each occurence is expensive.
// PostPone this test in an optional integrity check at the end
// of parsing or only in debug mode.
- if ( realExplicit && !gdcmGlobal::GetVR()->Count(vr) )
- {
- realExplicit = false;
- }
-
- if ( !realExplicit )
- {
- // We thought this was explicit VR, but we end up with an
- // implicit VR tag. Let's backtrack.
- sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
- entry->GetGroup(), entry->GetElement());
- dbg.Verbose(1, "gdcmDocument::FindVR: ",msg);
-
- if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000)
- {
- // Group length is UL !
- gdcmDictEntry* newEntry = NewVirtualDictEntry(
- entry->GetGroup(), entry->GetElement(),
- "UL", "FIXME", "Group Length");
- entry->SetDictEntry( newEntry );
- }
+ if ( !Global::GetVR()->IsValidVR(vr) )
return false;
- }
-
- if ( entry->IsVRUnknown() )
- {
- // When not a dictionary entry, we can safely overwrite the VR.
- if( entry->GetElement() == 0x0000 )
- {
- // Group length is UL !
- entry->SetVR("UL");
- }
- else
- {
- entry->SetVR(vr);
- }
- }
- else if ( entry->GetVR() != vr )
- {
- // The VR present in the file and the dictionary disagree. We assume
- // the file writer knew best and use the VR of the file. Since it would
- // be unwise to overwrite the VR of a dictionary (since it would
- // compromise it's next user), we need to clone the actual DictEntry
- // and change the VR for the read one.
- gdcmDictEntry* newEntry = NewVirtualDictEntry(
- entry->GetGroup(), entry->GetElement(),
- vr, "FIXME", entry->GetName());
- entry->SetDictEntry(newEntry);
- }
return true;
}
* @param entry entry to tranform
* @return Transformed entry value
*/
-std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *entry)
+std::string Document::GetDocEntryValue(DocEntry *entry)
{
if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
- std::string val = ((gdcmValEntry *)entry)->GetValue();
+ std::string val = ((ValEntry *)entry)->GetValue();
std::string vr = entry->GetVR();
uint32_t length = entry->GetLength();
std::ostringstream s;
return s.str();
}
- return ((gdcmValEntry *)entry)->GetValue();
+ return ((ValEntry *)entry)->GetValue();
}
/**
* @param entry Entry to reverse transform
* @return Reverse transformed entry value
*/
-std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* entry)
+std::string Document::GetDocEntryUnvalue(DocEntry *entry)
{
if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
uint16_t newInt16;
tokens.erase( tokens.begin(), tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)entry)->GetValue(), tokens, "\\");
+ Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size(); i++)
{
newInt16 = atoi(tokens[i].c_str());
uint32_t newInt32;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)entry)->GetValue(), tokens, "\\");
+ Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
newInt32 = atoi(tokens[i].c_str());
return s.str();
}
- return ((gdcmValEntry *)entry)->GetValue();
+ return ((ValEntry *)entry)->GetValue();
}
/**
* \warning NOT end user intended method !
* @param entry entry to skip
*/
-void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry)
+void Document::SkipDocEntry(DocEntry *entry)
{
SkipBytes(entry->GetLength());
}
/**
* \brief Skips to the begining of the next Header Entry
* \warning NOT end user intended method !
- * @param entry entry to skip
+ * @param currentDocEntry entry to skip
*/
-void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry)
+void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
{
- fseek(Fp, (long)(entry->GetOffset()), SEEK_SET);
- fseek(Fp, (long)(entry->GetReadLength()), SEEK_CUR);
+ Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
+ Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur);
}
/**
* the parser went Jabberwocky) one can hope improving things by
* applying some heuristics.
* @param entry entry to check
- * @param foundLength fist assumption about length
+ * @param foundLength first assumption about length
*/
-void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry,
- uint32_t foundLength)
+void Document::FixDocEntryFoundLength(DocEntry *entry,
+ uint32_t foundLength)
{
entry->SetReadLength( foundLength ); // will be updated only if a bug is found
if ( foundLength == 0xffffffff)
foundLength = 0;
}
- uint16_t gr = entry->GetGroup();
- uint16_t el = entry->GetElement();
+ uint16_t gr = entry->GetGroup();
+ uint16_t elem = entry->GetElement();
if ( foundLength % 2)
{
- std::ostringstream s;
- s << "Warning : Tag with uneven length "
- << foundLength
- << " in x(" << std::hex << gr << "," << el <<")" << std::dec;
- dbg.Verbose(0, s.str().c_str());
+ gdcmVerboseMacro( "Warning : Tag with uneven length " << foundLength
+ << " in x(" << std::hex << gr << "," << elem <<")");
}
//////// Fix for some naughty General Electric images.
// Allthough not recent many such GE corrupted images are still present
// on Creatis hard disks. Hence this fix shall remain when such images
- // are no longer in user (we are talking a few years, here)...
+ // are no longer in use (we are talking a few years, here)...
// Note: XMedCom probably uses such a trick since it is able to read
// those pesky GE images ...
if ( foundLength == 13)
{
// Only happens for this length !
- if ( entry->GetGroup() != 0x0008
- || ( entry->GetElement() != 0x0070
- && entry->GetElement() != 0x0080 ) )
+ if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) )
{
foundLength = 10;
entry->SetReadLength(10); /// \todo a bug is to be fixed !?
// Occurence of such images is quite low (unless one leaves close to a
// 'Leonardo' source. Hence, one might consider commenting out the
// following fix on efficiency reasons.
- else if ( entry->GetGroup() == 0x0009
- && ( entry->GetElement() == 0x1113
- || entry->GetElement() == 0x1114 ) )
+ else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
{
foundLength = 4;
entry->SetReadLength(4); /// \todo a bug is to be fixed !?
//////// We encountered a 'delimiter' element i.e. a tag of the form
// "fffe|xxxx" which is just a marker. Delimiters length should not be
// taken into account.
- else if( entry->GetGroup() == 0xfffe )
+ else if( gr == 0xfffe )
{
// According to the norm, fffe|0000 shouldn't exist. BUT the Philips
// image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to
}
}
- entry->SetUsableLength(foundLength);
+ entry->SetLength(foundLength);
}
/**
* @param entry The element value on which to apply the predicate.
* @return The result of the heuristical predicate.
*/
-bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *entry)
+bool Document::IsDocEntryAnInteger(DocEntry *entry)
{
- uint16_t element = entry->GetElement();
+ uint16_t elem = entry->GetElement();
uint16_t group = entry->GetGroup();
- std::string vr = entry->GetVR();
+ const std::string &vr = entry->GetVR();
uint32_t length = entry->GetLength();
// When we have some semantics on the element we just read, and if we
// a priori know we are dealing with an integer, then we shall be
// able to swap it's element value properly.
- if ( element == 0 ) // This is the group length of the group
+ if ( elem == 0 ) // This is the group length of the group
{
if ( length == 4 )
{
// test is useless (and might even look a bit paranoid), when we
// encounter such an ill-formed image, we simply display a warning
// message and proceed on parsing (while crossing fingers).
- std::ostringstream s;
- int filePosition = ftell(Fp);
- s << "Erroneous Group Length element length on : (" \
- << std::hex << group << " , " << element
+ long filePosition = Fp->tellg();
+ gdcmVerboseMacro( "Erroneous Group Length element length on : ("
+ << std::hex << group << " , " << elem
<< ") -before- position x(" << filePosition << ")"
- << "lgt : " << length;
- dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() );
+ << "lgt : " << length );
}
}
if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" )
{
return true;
- }
-
+ }
return false;
}
* @return
*/
-uint32_t gdcmDocument::FindDocEntryLengthOB()
- throw( gdcmFormatUnexpected )
+uint32_t Document::FindDocEntryLengthOBOrOW()
+ throw( FormatUnexpected )
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
- long positionOnEntry = ftell(Fp);
+ long positionOnEntry = Fp->tellg();
bool foundSequenceDelimiter = false;
uint32_t totalLength = 0;
group = ReadInt16();
elem = ReadInt16();
}
- catch ( gdcmFormatError )
+ catch ( FormatError )
{
- throw gdcmFormatError("gdcmDocument::FindDocEntryLengthOB()",
- " group or element not present.");
+ throw FormatError("Unexpected end of file encountered during ",
+ "Document::FindDocEntryLengthOBOrOW()");
}
// We have to decount the group and element we just read
if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- dbg.Verbose(1, "gdcmDocument::FindDocEntryLengthOB: neither an Item "
- "tag nor a Sequence delimiter tag.");
- fseek(Fp, positionOnEntry, SEEK_SET);
- throw gdcmFormatUnexpected("gdcmDocument::FindDocEntryLengthOB()",
- "Neither an Item tag nor a Sequence "
- "delimiter tag.");
+ long filePosition = Fp->tellg();
+ gdcmVerboseMacro( "Neither an Item tag nor a Sequence delimiter tag on :"
+ << std::hex << group << " , " << elem
+ << ") -before- position x(" << filePosition << ")" );
+
+ Fp->seekg(positionOnEntry, std::ios::beg);
+ throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag.");
}
if ( elem == 0xe0dd )
break;
}
}
- fseek(Fp, positionOnEntry, SEEK_SET);
+ Fp->seekg( positionOnEntry, std::ios::beg);
return totalLength;
}
* (swaps it depending on processor endianity)
* @return read value
*/
-uint16_t gdcmDocument::ReadInt16()
- throw( gdcmFormatError )
+uint16_t Document::ReadInt16()
+ throw( FormatError )
{
uint16_t g;
- size_t item_read = fread (&g, (size_t)2,(size_t)1, Fp);
- if ( item_read != 1 )
+ Fp->read ((char*)&g, (size_t)2);
+ if ( Fp->fail() )
{
- if( ferror(Fp) )
- {
- throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
- }
- throw gdcmFormatError( "gdcmDocument::ReadInt16()", "EOF." );
+ throw FormatError( "Document::ReadInt16()", " file error." );
+ }
+ if( Fp->eof() )
+ {
+ throw FormatError( "Document::ReadInt16()", "EOF." );
}
g = SwapShort(g);
return g;
* (swaps it depending on processor endianity)
* @return read value
*/
-uint32_t gdcmDocument::ReadInt32()
- throw( gdcmFormatError )
+uint32_t Document::ReadInt32()
+ throw( FormatError )
{
uint32_t g;
- size_t item_read = fread (&g, (size_t)4,(size_t)1, Fp);
- if ( item_read != 1 )
+ Fp->read ((char*)&g, (size_t)4);
+ if ( Fp->fail() )
{
- if( ferror(Fp) )
- {
- throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
- }
- throw gdcmFormatError( "gdcmDocument::ReadInt32()", "EOF." );
+ throw FormatError( "Document::ReadInt32()", " file error." );
+ }
+ if( Fp->eof() )
+ {
+ throw FormatError( "Document::ReadInt32()", "EOF." );
}
g = SwapLong(g);
return g;
* \warning NOT end user intended method !
* @return
*/
-void gdcmDocument::SkipBytes(uint32_t nBytes)
+void Document::SkipBytes(uint32_t nBytes)
{
//FIXME don't dump the returned value
- (void)fseek(Fp, (long)nBytes, SEEK_CUR);
+ Fp->seekg((long)nBytes, std::ios::cur);
}
/**
* \brief Loads all the needed Dictionaries
* \warning NOT end user intended method !
*/
-void gdcmDocument::Initialise()
+void Document::Initialise()
{
- RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
+ RefPubDict = Global::GetDicts()->GetDefaultPubDict();
RefShaDict = NULL;
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
+ Filetype = Unknown;
}
/**
* it's neither ACR-NEMA nor DICOM
* true when we hope ours assuptions are OK
*/
-bool gdcmDocument::CheckSwap()
+bool Document::CheckSwap()
{
// The only guaranted way of finding the swap code is to find a
// group tag since we know it's length has to be of four bytes i.e.
uint32_t s32;
uint16_t s16;
- char deb[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".
- int lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, Fp);
- (void)lgrLue; //FIXME not used
+ Fp->read(deb, 256);
char *entCur = deb + 128;
if( memcmp(entCur, "DICM", (size_t)4) == 0 )
{
- dbg.Verbose(1, "gdcmDocument::CheckSwap:", "looks like DICOM Version3");
+ gdcmVerboseMacro( "Looks like DICOM Version3" );
// Next, determine the value representation (VR). Let's skip to the
// first element (0002, 0000) and check there if we find "UL"
// FIXME : FIXME:
// Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR,
- // but elem 0002,0010 (Transfert Syntax) tells us the file is
+ // but elem 0002,0010 (Transfer Syntax) tells us the file is
// *Implicit* VR. -and it is !-
if( memcmp(entCur, "UL", (size_t)2) == 0 ||
memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later
// when Write DCM *adds*
// FIXME
- // Use gdcmDocument::dicom_vr to test all the possibilities
+ // Use Document::dicom_vr to test all the possibilities
// instead of just checking for UL, OB and UI !? group 0000
{
- Filetype = gdcmExplicitVR;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
- "explicit Value Representation");
+ Filetype = ExplicitVR;
+ gdcmVerboseMacro( "Explicit Value Representation");
}
else
{
- Filetype = gdcmImplicitVR;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
- "not an explicit Value Representation");
+ Filetype = ImplicitVR;
+ gdcmVerboseMacro( "Not an explicit Value Representation");
}
if ( net2host )
{
SwapCode = 4321;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
- "HostByteOrder != NetworkByteOrder");
+ gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder");
}
else
{
- SwapCode = 0;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
- "HostByteOrder = NetworkByteOrder");
+ SwapCode = 1234;
+ gdcmVerboseMacro( "HostByteOrder = NetworkByteOrder");
}
// Position the file position indicator at first tag (i.e.
// after the file preamble and the "DICM" string).
- rewind(Fp);
- fseek (Fp, 132L, SEEK_SET);
+ Fp->seekg(0, std::ios::beg);
+ Fp->seekg ( 132L, std::ios::beg);
return true;
} // End of DicomV3
// Alas, this is not a DicomV3 file and whatever happens there is no file
// preamble. We can reset the file position indicator to where the data
// is (i.e. the beginning of the file).
- dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not a DICOM Version3 file");
- rewind(Fp);
+ gdcmVerboseMacro( "Not a DICOM Version3 file");
+ 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 :
SwapCode = 3412;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
case 0x04000000 :
SwapCode = 4321;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
case 0x00000400 :
SwapCode = 2143;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
case 0x00000004 :
- SwapCode = 0;
- Filetype = gdcmACR;
+ SwapCode = 1234;
+ Filetype = ACR;
return true;
default :
// We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
// So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA,
// i.e. the 'group length' element is not present :
- // check the supposed to be 'group number'
- // 0x0002 or 0x0004 or 0x0008
+ // check the supposed-to-be 'group number'
+ // in ( 0x0001 .. 0x0008 )
// to determine ' SwapCode' value .
// Only 0 or 4321 will be possible
// (no oportunity to check for the formerly well known
// ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
- // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -4, 8-)
+ // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -3, 4, ..., 8-)
// the file IS NOT ACR-NEMA nor DICOM V3
// Find a trick to tell it the caller...
switch ( s16 )
{
+ case 0x0001 :
case 0x0002 :
+ case 0x0003 :
case 0x0004 :
- case 0x0008 :
- SwapCode = 0;
- Filetype = gdcmACR;
+ case 0x0005 :
+ case 0x0006 :
+ case 0x0007 :
+ case 0x0008 :
+ SwapCode = 1234;
+ Filetype = ACR;
return true;
+ case 0x0100 :
case 0x0200 :
+ case 0x0300 :
case 0x0400 :
- case 0x0800 :
+ case 0x0500 :
+ case 0x0600 :
+ case 0x0700 :
+ case 0x0800 :
SwapCode = 4321;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
default :
- dbg.Verbose(0, "gdcmDocument::CheckSwap:",
- "ACR/NEMA unfound swap info (Really hopeless !)");
- Filetype = gdcmUnknown;
+ gdcmVerboseMacro( "ACR/NEMA unfound swap info (Really hopeless !)");
+ Filetype = Unknown;
return false;
}
// Then the only info we have is the net2host one.
//if (! net2host )
- // SwapCode = 0;
+ // SwapCode = 1234;
//else
// SwapCode = 4321;
//return;
}
}
+
+
/**
- * \brief Restore the unproperly loaded values i.e. the group, the element
- * and the dictionary entry depending on them.
+ * \brief Change the Byte Swap code.
*/
-void gdcmDocument::SwitchSwapToBigEndian()
+void Document::SwitchByteSwapCode()
{
- dbg.Verbose(1, "gdcmDocument::SwitchSwapToBigEndian",
- "Switching to BigEndian mode.");
- if ( SwapCode == 0 )
+ gdcmVerboseMacro( "Switching Byte Swap code.");
+ if ( SwapCode == 1234 )
{
SwapCode = 4321;
}
else if ( SwapCode == 4321 )
{
- SwapCode = 0;
+ SwapCode = 1234;
}
else if ( SwapCode == 3412 )
{
* \brief during parsing, Header Elements too long are not loaded in memory
* @param newSize
*/
-void gdcmDocument::SetMaxSizeLoadEntry(long newSize)
+void Document::SetMaxSizeLoadEntry(long newSize)
{
if ( newSize < 0 )
{
/**
* \brief Header Elements too long will not be printed
- * \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE
+ * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE
* @param newSize
*/
-void gdcmDocument::SetMaxSizePrintEntry(long newSize)
+void Document::SetMaxSizePrintEntry(long newSize)
{
//DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME
if ( newSize < 0 )
+/**
+ * \brief Handle broken private tag from Philips NTSCAN
+ * where the endianess is being switch to BigEndian for no
+ * apparent reason
+ * @return no return
+ */
+void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
+{
+ // Endian reversion. Some files contain groups of tags with reversed endianess.
+ static int reversedEndian = 0;
+ // try to fix endian switching in the middle of headers
+ if ((group == 0xfeff) && (elem == 0x00e0))
+ {
+ // start endian swap mark for group found
+ reversedEndian++;
+ SwitchByteSwapCode();
+ // fix the tag
+ group = 0xfffe;
+ elem = 0xe000;
+ }
+ else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
+ {
+ // end of reversed endian group
+ reversedEndian--;
+ SwitchByteSwapCode();
+ }
+}
+
+/**
+ * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS
+ * else 1.
+ * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
+ */
+std::string Document::GetTransferSyntaxName()
+{
+ // use the TS (TS : Transfer Syntax)
+ std::string transferSyntax = GetEntry(0x0002,0x0010);
+
+ if ( transferSyntax == GDCM_NOTLOADED )
+ {
+ gdcmVerboseMacro( "Transfer Syntax not loaded. " << std::endl
+ << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" );
+ return "Uncompressed ACR-NEMA";
+ }
+ if ( transferSyntax == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Transfer Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
+ }
+
+ while ( ! isdigit((unsigned char)transferSyntax[transferSyntax.length()-1]) )
+ {
+ transferSyntax.erase(transferSyntax.length()-1, 1);
+ }
+ // we do it only when we need it
+ TS* ts = Global::GetTS();
+ std::string tsName = ts->GetValue( transferSyntax );
+
+ // Global::GetTS() is a global static you shall never try to delete it!
+ return tsName;
+}
+
+/**
+ * \brief Group 0002 is always coded Little Endian
+ * whatever Transfer Syntax is
+ * @return no return
+ */
+void Document::HandleOutOfGroup0002(uint16_t group)
+{
+ // Endian reversion. Some files contain groups of tags with reversed endianess.
+ if ( !Group0002Parsed && group != 0x0002)
+ {
+ Group0002Parsed = true;
+ // we just came out of group 0002
+ // if Transfer syntax is Big Endian we have to change CheckSwap
+
+ std::string ts = GetTransferSyntaxName();
+ if ( !Global::GetTS()->IsTransferSyntax(ts) )
+ {
+ gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
+ return;
+ }
+
+ // FIXME Strangely, this works with
+ //'Implicit VR Transfer Syntax (GE Private)
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
+ {
+ gdcmVerboseMacro("Tansfer Syntax = Explicit VR - Big Endian");
+ SwitchByteSwapCode();
+ }
+ }
+}
+
/**
* \brief Read the next tag but WITHOUT loading it's value
* (read the 'Group Number', the 'Element Number',
- * gets the Dict Entry
+ * gets the Dict Entry
* gets the VR, gets the length, gets the offset value)
* @return On succes the newly created DocEntry, NULL on failure.
*/
-gdcmDocEntry* gdcmDocument::ReadNextDocEntry()
+DocEntry *Document::ReadNextDocEntry()
{
uint16_t group;
uint16_t elem;
group = ReadInt16();
elem = ReadInt16();
}
- catch ( gdcmFormatError e )
+ catch ( FormatError e )
{
// We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
return 0;
}
- gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem);
- FindDocEntryVR(newEntry);
+ // Sometimes file contains groups of tags with reversed endianess.
+ HandleBrokenEndian(group, elem);
+
+// In 'true DICOM' files Group 0002 is allways little endian
+ if ( HasDCMPreamble )
+ HandleOutOfGroup0002(group);
+
+ std::string vr = FindDocEntryVR();
+ std::string realVR = vr;
+
+ if( vr == GDCM_UNKNOWN)
+ {
+ DictEntry *dictEntry = GetDictEntry(group,elem);
+ if( dictEntry )
+ realVR = dictEntry->GetVR();
+ }
+
+ DocEntry *newEntry;
+ if( Global::GetVR()->IsVROfSequence(realVR) )
+ newEntry = NewSeqEntry(group, elem);
+ else if( Global::GetVR()->IsVROfStringRepresentable(realVR) )
+ newEntry = NewValEntry(group, elem,vr);
+ else
+ newEntry = NewBinEntry(group, elem,vr);
+
+ if( vr == GDCM_UNKNOWN )
+ {
+ if( Filetype == ExplicitVR )
+ {
+ // We thought this was explicit VR, but we end up with an
+ // implicit VR tag. Let's backtrack.
+ std::string msg;
+ msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n",
+ newEntry->GetGroup(), newEntry->GetElement());
+ gdcmVerboseMacro( msg.c_str() );
+ }
+ newEntry->SetImplicitVR();
+ }
try
{
FindDocEntryLength(newEntry);
}
- catch ( gdcmFormatError e )
+ catch ( FormatError e )
{
// Call it quits
//std::cout << e;
return 0;
}
- newEntry->SetOffset(ftell(Fp));
+ newEntry->SetOffset(Fp->tellg());
return newEntry;
}
/**
- * \brief Generate a free gdcmTagKey i.e. a gdcmTagKey that is not present
+ * \brief Generate a free TagKey i.e. a TagKey that is not present
* in the TagHt dictionary.
* @param group The generated tag must belong to this group.
* @return The element of tag with given group which is fee.
*/
-uint32_t gdcmDocument::GenerateFreeTagKeyInGroup(uint16_t group)
+uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group)
{
for (uint32_t elem = 0; elem < UINT32_MAX; elem++)
{
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, elem);
+ TagKey key = DictEntry::TranslateToKey(group, elem);
if (TagHT.count(key) == 0)
{
return elem;
}
/**
- * \brief Assuming the internal file pointer \ref gdcmDocument::Fp
+ * \brief Assuming the internal file pointer \ref Document::Fp
* is placed at the beginning of a tag check whether this
* tag is (TestGroup, TestElement).
- * \warning On success the internal file pointer \ref gdcmDocument::Fp
+ * \warning On success the internal file pointer \ref Document::Fp
* is modified to point after the tag.
* On failure (i.e. when the tag wasn't the expected tag
* (TestGroup, TestElement) the internal file pointer
- * \ref gdcmDocument::Fp is restored to it's original position.
+ * \ref Document::Fp is restored to it's original position.
* @param testGroup The expected group of the tag.
* @param testElement The expected Element of the tag.
* @return True on success, false otherwise.
*/
-bool gdcmDocument::ReadTag(uint16_t testGroup, uint16_t testElement)
+bool Document::ReadTag(uint16_t testGroup, uint16_t testElement)
{
- long positionOnEntry = ftell(Fp);
- long currentPosition = ftell(Fp); // On debugging purposes
+ long positionOnEntry = Fp->tellg();
+ long currentPosition = Fp->tellg(); // On debugging purposes
//// Read the Item Tag group and element, and make
// sure they are what we expected:
- uint16_t itemTagGroup = ReadInt16();
- uint16_t itemTagElement = ReadInt16();
+ uint16_t itemTagGroup;
+ uint16_t itemTagElement;
+ try
+ {
+ itemTagGroup = ReadInt16();
+ itemTagElement = ReadInt16();
+ }
+ catch ( FormatError e )
+ {
+ //std::cerr << e << std::endl;
+ return false;
+ }
if ( itemTagGroup != testGroup || itemTagElement != testElement )
{
- std::ostringstream s;
- s << " We should have found tag (";
- s << std::hex << testGroup << "," << testElement << ")" << std::endl;
- s << " but instead we encountered tag (";
- s << std::hex << itemTagGroup << "," << itemTagElement << ")"
- << std::endl;
- s << " at address: " << (unsigned)currentPosition << std::endl;
- dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:");
- dbg.Verbose(0, s.str().c_str());
- fseek(Fp, positionOnEntry, SEEK_SET);
+ gdcmVerboseMacro( "Wrong Item Tag found:"
+ << " We should have found tag ("
+ << std::hex << testGroup << "," << testElement << ")" << std::endl
+ << " but instead we encountered tag ("
+ << std::hex << itemTagGroup << "," << itemTagElement << ")"
+ << " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
+ ) ;
+ Fp->seekg(positionOnEntry, std::ios::beg);
return false;
}
}
/**
- * \brief Assuming the internal file pointer \ref gdcmDocument::Fp
+ * \brief Assuming the internal file pointer \ref Document::Fp
* is placed at the beginning of a tag (TestGroup, TestElement),
* read the length associated to the Tag.
- * \warning On success the internal file pointer \ref gdcmDocument::Fp
+ * \warning On success the internal file pointer \ref Document::Fp
* is modified to point after the tag and it's length.
* On failure (i.e. when the tag wasn't the expected tag
* (TestGroup, TestElement) the internal file pointer
- * \ref gdcmDocument::Fp is restored to it's original position.
+ * \ref Document::Fp is restored to it's original position.
* @param testGroup The expected group of the tag.
* @param testElement The expected Element of the tag.
* @return On success returns the length associated to the tag. On failure
* returns 0.
*/
-uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement)
+uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement)
{
- long positionOnEntry = ftell(Fp);
+ long positionOnEntry = Fp->tellg();
(void)positionOnEntry;
if ( !ReadTag(testGroup, testElement) )
}
//// Then read the associated Item Length
- long currentPosition = ftell(Fp);
+ long currentPosition = Fp->tellg();
uint32_t itemLength = ReadInt32();
{
- std::ostringstream s;
- s << "Basic Item Length is: "
- << itemLength << std::endl;
- s << " at address: " << (unsigned)currentPosition << std::endl;
- dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: ", s.str().c_str());
+ gdcmVerboseMacro( "Basic Item Length is: "
+ << itemLength << std::endl
+ << " at address: " << std::hex << (unsigned int)currentPosition);
}
return itemLength;
}
/**
- * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
- * Compute the RLE extra information and store it in \ref RLEInfo
- * for later pixel retrieval usage.
+ * \brief When parsing the Pixel Data of an encapsulated file, read
+ * the basic offset table (when present, and BTW dump it).
*/
-void gdcmDocument::ComputeRLEInfo()
+void Document::ReadAndSkipEncapsulatedBasicOffsetTable()
{
- if ( ! IsRLELossLessTransferSyntax() )
- {
- return;
- }
- // Encoded pixel data: for the time being we are only concerned with
- // Jpeg or RLE Pixel data encodings.
- // As stated in ps-3.3, 8.2:
- // "If sent in Encapsulated Format (i.e. other than the Native Format) the
- // value representation OB is used".
- // Hence we expect an OB value representation. Concerning OB VR,
- // the section PS3.3, A.4.c (p58 and p59), states:
- // "For the Value Representations OB and OW, the encoding shall meet the
- // following specifications depending on the Data element tag:"
- // [...snip...]
- // - the first item in the sequence of items before the encoded pixel
- // data stream shall be basic offset table item. The basic offset table
- // item value, however, is not required to be present"
-
//// Read the Basic Offset Table Item Tag length...
uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
// lengths, but we won't bother with such fuses for the time being.
if ( itemLength != 0 )
{
- char* basicOffsetTableItemValue = new char[itemLength + 1];
- fread(basicOffsetTableItemValue, itemLength, 1, Fp);
+ char *basicOffsetTableItemValue = new char[itemLength + 1];
+ Fp->read(basicOffsetTableItemValue, itemLength);
+#ifdef GDCM_DEBUG
for (unsigned int i=0; i < itemLength; i += 4 )
{
uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
uint32_t);
- std::ostringstream s;
- s << " Read one length: ";
- s << std::hex << individualLength << std::endl;
- dbg.Verbose(0, "gdcmDocument::ComputeRLEInfo: ", s.str().c_str());
+ gdcmVerboseMacro( "Read one length: " <<
+ std::hex << individualLength );
}
+#endif //GDCM_DEBUG
+
delete[] basicOffsetTableItemValue;
}
+}
- // Encapsulated RLE Compressed Images (see PS-3.3, Annex G).
- // Loop on the frame[s] and store the parsed information in a
- // gdcmRLEFramesInfo.
- long frameLength;
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
+ * Compute the RLE extra information and store it in \ref RLEInfo
+ * for later pixel retrieval usage.
+ */
+void Document::ComputeRLEInfo()
+{
+ std::string ts = GetTransferSyntax();
+ if ( !Global::GetTS()->IsRLELossless(ts) )
+ {
+ return;
+ }
+
+ // Encoded pixel data: for the time being we are only concerned with
+ // Jpeg or RLE Pixel data encodings.
+ // As stated in PS 3.5-2003, section 8.2 p44:
+ // "If sent in Encapsulated Format (i.e. other than the Native Format) the
+ // value representation OB is used".
+ // Hence we expect an OB value representation. Concerning OB VR,
+ // the section PS 3.5-2003, section A.4.c p 58-59, states:
+ // "For the Value Representations OB and OW, the encoding shall meet the
+ // following specifications depending on the Data element tag:"
+ // [...snip...]
+ // - the first item in the sequence of items before the encoded pixel
+ // data stream shall be basic offset table item. The basic offset table
+ // item value, however, is not required to be present"
+
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+ // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
// Loop on the individual frame[s] and store the information
- // on the RLE fragments in a gdcmRLEFramesInfo.
+ // on the RLE fragments in a RLEFramesInfo.
// Note: - when only a single frame is present, this is a
// classical image.
// - when more than one frame are present, then we are in
// the case of a multi-frame image.
+ long frameLength;
while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
{
// Parse the RLE Header and store the corresponding RLE Segment
// Offset Table information on fragments of this current Frame.
// Note that the fragment pixels themselves are not loaded
// (but just skipped).
- long frameOffset = ftell(Fp);
+ long frameOffset = Fp->tellg();
uint32_t nbRleSegments = ReadInt32();
+ if ( nbRleSegments > 16 )
+ {
+ // There should be at most 15 segments (refer to RLEFrame class)
+ gdcmVerboseMacro( "Too many segments.");
+ }
- uint32_t rleSegmentOffsetTable[15];
+ uint32_t rleSegmentOffsetTable[16];
for( int k = 1; k <= 15; k++ )
{
rleSegmentOffsetTable[k] = ReadInt32();
// Deduce from both the RLE Header and the frameLength the
// fragment length, and again store this info in a
- // gdcmRLEFramesInfo.
+ // RLEFramesInfo.
long rleSegmentLength[15];
// skipping (not reading) RLE Segments
if ( nbRleSegments > 1)
SkipBytes(rleSegmentLength[nbRleSegments]);
// Store the collected info
- gdcmRLEFrame* newFrameInfo = new gdcmRLEFrame;
+ RLEFrame *newFrameInfo = new RLEFrame;
newFrameInfo->NumberFragments = nbRleSegments;
- for( unsigned int k = 1; k <= nbRleSegments; k++ )
+ for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
{
- newFrameInfo->Offset[k] = frameOffset + rleSegmentOffsetTable[k];
- newFrameInfo->Length[k] = rleSegmentLength[k];
+ newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk];
+ newFrameInfo->Length[uk] = rleSegmentLength[uk];
}
- RLEInfo.Frames.push_back( newFrameInfo );
+ RLEInfo->Frames.push_back( newFrameInfo );
+ }
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence");
+ }
+}
+
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
+ * Compute the jpeg extra information (fragment[s] offset[s] and
+ * length) and store it[them] in \ref JPEGInfo for later pixel
+ * retrieval usage.
+ */
+void Document::ComputeJPEGFragmentInfo()
+{
+ // If you need to, look for comments of ComputeRLEInfo().
+ std::string ts = GetTransferSyntax();
+ if ( ! Global::GetTS()->IsJPEG(ts) )
+ {
+ return;
+ }
+
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Loop on the fragments[s] and store the parsed information in a
+ // JPEGInfo.
+ long fragmentLength;
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ long fragmentOffset = Fp->tellg();
+
+ // Store the collected info
+ JPEGFragment *newFragment = new JPEGFragment;
+ newFragment->Offset = fragmentOffset;
+ newFragment->Length = fragmentLength;
+ JPEGInfo->Fragments.push_back( newFragment );
+
+ SkipBytes( fragmentLength );
}
// Make sure that at the end of the item we encounter a 'Sequence
// Delimiter Item':
if ( !ReadTag(0xfffe, 0xe0dd) )
{
- dbg.Verbose(0, "gdcmDocument::ComputeRLEInfo: no sequence delimiter ");
- dbg.Verbose(0, " item at end of RLE item sequence");
+ gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence");
}
}
/**
- * \brief Walk recursively the given \ref gdcmDocEntrySet, and feed
+ * \brief Walk recursively the given \ref DocEntrySet, and feed
* the given hash table (\ref TagDocEntryHT) with all the
- * \ref gdcmDocEntry (Dicom entries) encountered.
+ * \ref DocEntry (Dicom entries) encountered.
* This method does the job for \ref BuildFlatHashTable.
- * @param builtHT Where to collect all the \ref gdcmDocEntry encountered
+ * @param builtHT Where to collect all the \ref DocEntry encountered
* when recursively walking the given set.
* @param set The structure to be traversed (recursively).
*/
-void gdcmDocument::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT,
- gdcmDocEntrySet* set )
+void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT,
+ DocEntrySet *set )
{
- if (gdcmElementSet* elementSet = dynamic_cast< gdcmElementSet* > ( set ) )
+ if (ElementSet *elementSet = dynamic_cast< ElementSet* > ( set ) )
{
- TagDocEntryHT* currentHT = elementSet->GetTagHT();
- for( TagDocEntryHT::const_iterator i = currentHT->begin();
- i != currentHT->end();
+ TagDocEntryHT const ¤tHT = elementSet->GetTagHT();
+ for( TagDocEntryHT::const_iterator i = currentHT.begin();
+ i != currentHT.end();
++i)
{
- gdcmDocEntry* entry = i->second;
- if ( gdcmSeqEntry* seqEntry = dynamic_cast<gdcmSeqEntry*>(entry) )
+ DocEntry *entry = i->second;
+ if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
{
- ListSQItem& items = seqEntry->GetSQItems();
+ const ListSQItem& items = seqEntry->GetSQItems();
for( ListSQItem::const_iterator item = items.begin();
item != items.end();
++item)
return;
}
- if (gdcmSQItem* SQItemSet = dynamic_cast< gdcmSQItem* > ( set ) )
+ if (SQItem *SQItemSet = dynamic_cast< SQItem* > ( set ) )
{
- ListDocEntry& currentList = SQItemSet->GetDocEntries();
- for (ListDocEntry::iterator i = currentList.begin();
- i != currentList.end();
- ++i)
+ const ListDocEntry& currentList = SQItemSet->GetDocEntries();
+ for (ListDocEntry::const_iterator i = currentList.begin();
+ i != currentList.end();
+ ++i)
{
- gdcmDocEntry* entry = *i;
- if ( gdcmSeqEntry* seqEntry = dynamic_cast<gdcmSeqEntry*>(entry) )
+ DocEntry *entry = *i;
+ if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
{
- ListSQItem& items = seqEntry->GetSQItems();
+ const ListSQItem& items = seqEntry->GetSQItems();
for( ListSQItem::const_iterator item = items.begin();
item != items.end();
++item)
/**
* \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current
- * gdcmDocument.
+ * Document.
*
- * The structure used by a gdcmDocument (through \ref gdcmElementSet),
- * in order to old the parsed entries of a Dicom header, is a recursive
+ * The structure used by a Document (through \ref ElementSet),
+ * in order to hold the parsed entries of a Dicom header, is a recursive
* one. This is due to the fact that the sequences (when present)
* can be nested. Additionaly, the sequence items (represented in
- * gdcm as \ref gdcmSQItem) add an extra complexity to the data
+ * gdcm as \ref SQItem) add an extra complexity to the data
* structure. Hence, a gdcm user whishing to visit all the entries of
* a Dicom header will need to dig in the gdcm internals (which
* implies exposing all the internal data structures to the API).
* Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a
* std::map<>).
* \warning Of course there is NO integrity constrain between the
- * returned \ref TagDocEntryHT and the \ref gdcmElementSet used
- * to build it. Hence if the underlying \ref gdcmElementSet is
+ * returned \ref TagDocEntryHT and the \ref ElementSet used
+ * to build it. Hence if the underlying \ref ElementSet is
* altered, then it is the caller responsability to invoke
* \ref BuildFlatHashTable again...
* @return The flat std::map<> we juste build.
*/
-TagDocEntryHT* gdcmDocument::BuildFlatHashTable()
+TagDocEntryHT *Document::BuildFlatHashTable()
{
- TagDocEntryHT* FlatHT = new TagDocEntryHT;
+ TagDocEntryHT *FlatHT = new TagDocEntryHT;
BuildFlatHashTableRecurse( *FlatHT, this );
return FlatHT;
}
/**
- * \brief Compares two documents, according to \ref gdcmDicomDir rules
+ * \brief Compares two documents, according to \ref DicomDir rules
* \warning Does NOT work with ACR-NEMA files
* \todo Find a trick to solve the pb (use RET fields ?)
* @param document
* @return true if 'smaller'
*/
-bool gdcmDocument::operator<(gdcmDocument &document)
+bool Document::operator<(Document &document)
{
// Patient Name
- std::string s1 = GetEntryByNumber(0x0010,0x0010);
- std::string s2 = document.GetEntryByNumber(0x0010,0x0010);
+ std::string s1 = GetEntry(0x0010,0x0010);
+ std::string s2 = document.GetEntry(0x0010,0x0010);
if(s1 < s2)
{
return true;
else
{
// Patient ID
- s1 = GetEntryByNumber(0x0010,0x0020);
- s2 = document.GetEntryByNumber(0x0010,0x0020);
+ s1 = GetEntry(0x0010,0x0020);
+ s2 = document.GetEntry(0x0010,0x0020);
if ( s1 < s2 )
{
return true;
else
{
// Study Instance UID
- s1 = GetEntryByNumber(0x0020,0x000d);
- s2 = document.GetEntryByNumber(0x0020,0x000d);
+ s1 = GetEntry(0x0020,0x000d);
+ s2 = document.GetEntry(0x0020,0x000d);
if ( s1 < s2 )
{
return true;
else
{
// Serie Instance UID
- s1 = GetEntryByNumber(0x0020,0x000e);
- s2 = document.GetEntryByNumber(0x0020,0x000e);
+ s1 = GetEntry(0x0020,0x000e);
+ s2 = document.GetEntry(0x0020,0x000e);
if ( s1 < s2 )
{
return true;
}
+/**
+ * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
+ * @param filetype Type of the File to be written
+ */
+int Document::ComputeGroup0002Length( FileType filetype )
+{
+ uint16_t gr, el;
+ std::string vr;
+
+ int groupLength = 0;
+ bool found0002 = false;
+
+ // for each zero-level Tag in the DCM Header
+ DocEntry *entry;
+
+ Initialize();
+ entry = GetNextEntry();
+ while(entry)
+ {
+ gr = entry->GetGroup();
+
+ if (gr == 0x0002)
+ {
+ found0002 = true;
+
+ el = entry->GetElement();
+ vr = entry->GetVR();
+
+ if (filetype == ExplicitVR)
+ {
+ if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
+ {
+ groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes
+ }
+ }
+ groupLength += 2 + 2 + 4 + entry->GetLength();
+ }
+ else if (found0002 )
+ break;
+
+ entry = GetNextEntry();
+ }
+ return groupLength;
+}
+
+} // end namespace gdcm
+
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff