Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2004/10/20 14:30:40 $
- Version: $Revision: 1.106 $
+ Date: $Date: 2005/01/23 10:12:33 $
+ Version: $Revision: 1.204 $
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__) || defined(__MINGW32__)
#include <winsock.h>
-#else
- #include <netinet/in.h>
#endif
-#include <iomanip>
+#ifdef CMAKE_HAVE_NETINET_IN_H
+ #include <netinet/in.h>
+#endif
namespace gdcm
{
-// 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))
-
//-----------------------------------------------------------------------------
// Refer to Document::CheckSwap()
-const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
+//const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
// Refer to Document::SetMaxSizeLoadEntry()
const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
/**
* \brief constructor
- * @param filename file to be opened for parsing
+ * @param filename 'Document' (File or DicomDir) to be opened for parsing
*/
-Document::Document( std::string const & filename )
- : ElementSet(-1)
+Document::Document( std::string const &filename ) : ElementSet(-1)
{
+ RLEInfo = NULL;
+ JPEGInfo = NULL;
+
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Filename = filename;
- Initialise();
+ Initialize();
+ Fp = 0;
if ( !OpenFile() )
{
return;
}
- dbg.Verbose(0, "Document::Document: 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
+ ParseDES( this, beg, lgt, false); // Loading is done during parsing
- 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
/// FIXME FIXME FIXME
/// The tags refered by the three following lines used to be CORRECTLY
/// defined as having an US Value Representation in the public
- /// dictionnary. BUT the semantics implied by the three following
+ /// dictionary. BUT the semantics implied by the three following
/// lines state that the corresponding tag contents are in fact
/// 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 "Quick and Dirty" the dictionary was
+ /// altered on PURPOSE 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:
+ /// whether the following tags are either:
/// - 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
// we switch lineNumber and columnNumber
//
std::string RecCode;
- RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code
+ RecCode = GetEntry(0x0008, 0x0010); // recognition code (RET)
if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
// with "little-endian strings"
{
Filetype = ACR_LIBIDO;
- std::string rows = GetEntryByNumber(0x0028, 0x0010);
- std::string columns = GetEntryByNumber(0x0028, 0x0011);
- SetEntryByNumber(columns, 0x0028, 0x0010);
- SetEntryByNumber(rows , 0x0028, 0x0011);
+ 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 Document::SetFileName and then the parsing.
*/
-Document::Document()
- :ElementSet(-1)
+Document::Document() : ElementSet(-1)
{
+ RLEInfo = NULL;
+ JPEGInfo = NULL;
+
+ Fp = 0;
+
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialise();
- PrintLevel = 1; // 'Medium' print level by default
+ Initialize();
+ SwapCode = 1234;
+ Filetype = ExplicitVR;
+ Group0002Parsed = false;
}
/**
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();
+ if( RLEInfo )
+ delete RLEInfo;
+ if( JPEGInfo )
+ delete JPEGInfo;
}
//-----------------------------------------------------------------------------
* \brief Prints The Dict Entries of THE public Dicom Dictionary
* @return
*/
-void Document::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 Document::PrintShaDict(std::ostream & os)
+void Document::PrintShaDict(std::ostream &os)
{
+ RefShaDict->SetPrintLevel(PrintLevel);
RefShaDict->Print(os);
}
/**
* \brief Get the public dictionary used
*/
-Dict* Document::GetPubDict()
+Dict *Document::GetPubDict()
{
return RefPubDict;
}
/**
* \brief Get the shadow dictionary used
*/
-Dict* Document::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 Document::SetShaDict(Dict *dict)
{
/**
* \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 Document::SetShaDict(DictKey const & dictName)
+bool Document::SetShaDict(DictKey const &dictName)
{
RefShaDict = Global::GetDicts()->GetDict(dictName);
return !RefShaDict;
{
if( Filetype == Unknown)
{
- dbg.Verbose(0, "Document::IsReadable: wrong filetype");
+ gdcmVerboseMacro( "Wrong filetype");
return false;
}
- if( TagHT.empty() )
- {
- dbg.Verbose(0, "Document::IsReadable: no tags in internal"
- " hash table.");
+ //if( TagHT.empty() )
+ if ( IsEmpty() )
+ {
+ gdcmVerboseMacro( "No tag 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 Document::IsGivenTransferSyntax(std::string const & syntaxToCheck)
+std::string Document::GetTransferSyntax()
{
- DocEntry *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 (ValEntry* valEntry = dynamic_cast< ValEntry* >(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 Document::IsGivenTransferSyntax.
- * @return True when ImplicitVRLittleEndian found. False in all other cases.
- */
-bool Document::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 Document::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 Document::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 Document::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 Document::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 Document::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 Document::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 Document::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 Document::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 Document::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 Document::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 any form
- * of Jpeg encoded Pixel data.
- * @return True when any form of JPEG found. False otherwise.
- */
-bool Document::IsJPEGTransferSyntax()
-{
- return ( IsJPEGBaseLineProcess1TransferSyntax()
- || IsJPEGExtendedProcess2_4TransferSyntax()
- || IsJPEGExtendedProcess3_5TransferSyntax()
- || IsJPEGSpectralSelectionProcess6_8TransferSyntax()
- || IsJPEGLossless()
- || IsJPEG2000() );
-}
-
-
-/**
- * \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 Document::IsEncapsulateTransferSyntax()
-{
- return ( IsJPEGTransferSyntax()
- || IsRLELossLessTransferSyntax() );
+ return GDCM_UNKNOWN;
}
/**
*/
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;
+}
+
+/**
+ * \brief Predicate for Papyrus file
+ * Dedicated to whomsoever it may concern
+ * @return True when the file is a Papyrus file.
+ */
+bool Document::IsPapyrus()
+{
+ // check for Papyrus private Sequence
+ DocEntry *e = GetDocEntry(0x0041, 0x1050);
+ if ( !e )
+ return false;
+ // check if it's actually a Sequence
+ if ( !dynamic_cast<SeqEntry*>(e) )
+ return false;
+ return true;
}
/**
* checks the preamble when existing.
* @return The FILE pointer on success.
*/
-FILE* Document::OpenFile()
+std::ifstream *Document::OpenFile()
{
- Fp = fopen(Filename.c_str(),"rb");
- if(!Fp)
+ HasDCMPreamble = false;
+ if (Filename.length() == 0)
+ {
+ return 0;
+ }
+
+ if(Fp)
+ {
+ gdcmVerboseMacro( "File already open: " << Filename.c_str());
+ }
+
+ Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
+ if( ! *Fp )
{
- dbg.Verbose( 0,
- "Document::OpenFile cannot open file: ",
- Filename.c_str());
+ gdcmDebugMacro( "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,
- "Document::OpenFile not DICOM/ACR (missing preamble)",
- Filename.c_str());
+ CloseFile();
+ gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
return 0;
}
*/
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-closed ifstream ?
}
/**
* \brief Writes in a file all the Header Entries (Dicom Elements)
- * @param fp file pointer on an already open file
+ * @param fp file pointer on an already open file (actually: Output File Stream)
* @param filetype Type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* \return Always true.
*/
-void Document::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) Header
- if (filetype == ImplicitVR)
+ if ( filetype == ImplicitVR || filetype == ExplicitVR )
{
- 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);
- }
-
- if (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);
*/
- ElementSet::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).
*/
-ValEntry* Document::ReplaceOrCreateByNumber(
- std::string const & value,
- uint16_t group,
- uint16_t elem,
- std::string const & VR )
-{
- ValEntry* valEntry = 0;
- DocEntry* 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 DictSet::VirtualEntry
- // and use it
+ valEntry = dynamic_cast< ValEntry* >(currentEntry);
- // Find out if the tag we received is in the dictionaries:
- Dict *pubDict = Global::GetDicts()->GetDefaultPubDict();
- DictEntry* 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)
- {
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to"
- " NewDocEntryByNumber failed.");
- return NULL;
- }
- valEntry = new ValEntry(currentEntry);
- if ( !AddEntry(valEntry))
- {
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
- " failed allthough this is a creation.");
- }
- }
- else
- {
- valEntry = dynamic_cast< ValEntry* >(currentEntry);
- if ( !valEntry ) // Euuuuh? It wasn't a ValEntry
- // then we change it to a ValEntry ?
- // Shouldn't it be considered as an error ?
+ // if currentEntry doesn't correspond to the requested valEntry
+ if( !valEntry)
{
- // We need to promote the DocEntry to a ValEntry:
- valEntry = new ValEntry(currentEntry);
if (!RemoveEntry(currentEntry))
{
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
- " of previous DocEntry failed.");
- return NULL;
- }
- if ( !AddEntry(valEntry))
- {
- dbg.Verbose(0, "Document::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 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).
*/
-BinEntry* Document::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 )
{
- BinEntry* binEntry = 0;
- DocEntry* 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 DictSet::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:
- Dict *pubDict = Global::GetDicts()->GetDefaultPubDict();
- DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem);
+ // Verify the VR
+ if( binEntry )
+ if( binEntry->GetVR()!=vr )
+ binEntry=NULL;
- if (!dictEntry)
- {
- currentEntry = NewDocEntryByNumber(group, elem, VR);
- }
- else
- {
- currentEntry = NewDocEntryByNumber(group, elem);
- }
- if (!currentEntry)
+ // if currentEntry doesn't correspond to the requested valEntry
+ if( !binEntry)
{
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to"
- " NewDocEntryByNumber failed.");
- return NULL;
+ if (!RemoveEntry(currentEntry))
+ {
+ gdcmVerboseMacro( "Removal of previous DocEntry failed.");
+
+ return NULL;
+ }
}
- binEntry = new BinEntry(currentEntry);
+ }
+
+ // Create a new binEntry if necessary
+ if (!binEntry)
+ {
+ binEntry = NewBinEntry(group, elem, vr);
+
if ( !AddEntry(binEntry))
{
- dbg.Verbose(0, "Document::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< BinEntry* >(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 DocEntry to a BinEntry:
- binEntry = new BinEntry(currentEntry);
- if (!RemoveEntry(currentEntry))
- {
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
- " of previous DocEntry failed.");
- return NULL;
- }
- if ( !AddEntry(binEntry))
- {
- dbg.Verbose(0, "Document::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.
- * @param Group Group number of the Entry
- * @param Elem Element number of the Entry
+ * @param group Group number of the Entry
+ * @param elem Element number of the Entry
* \return pointer to the modified/created SeqEntry (NULL when creation
* failed).
*/
-SeqEntry* Document::ReplaceOrCreateByNumber(
- uint16_t group,
- uint16_t elem)
+SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem)
{
- SeqEntry* b = 0;
- DocEntry* 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;
+ }
}
+ }
+ // Create a new seqEntry if necessary
+ if (!seqEntry)
+ {
+ seqEntry = NewSeqEntry(group, elem);
- b = new SeqEntry(a, 1); // FIXME : 1 (Depth)
- AddEntry(b);
- }
- return b;
+ 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 Document::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;
}
//-----------------------------------------------------------------------------
// Protected
-/**
- * \brief Checks if a given Dicom Element exists within the H table
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return true is found
- */
-bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
-{
- const std::string &key = DictEntry::TranslateToKey(group, element );
- return TagHT.count(key);
-}
-
-/**
- * \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 Document::GetEntryByName(TagName const& tagName)
-{
- DictEntry* 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 Document::GetEntryVRByName(TagName const& tagName)
-{
- DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- {
- return GDCM_UNFOUND;
- }
-
- DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
- return elem->GetVR();
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- * @param group Group number of the searched tag.
- * @param element Element number of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string Document::GetEntryByNumber(uint16_t group, uint16_t element)
-{
- TagKey key = DictEntry::TranslateToKey(group, element);
- /// \todo use map methods, instead of multimap JPR
- if ( !TagHT.count(key))
- {
- return GDCM_UNFOUND;
- }
-
- return ((ValEntry *)TagHT.find(key)->second)->GetValue();
-}
-
/**
* \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 group Group number of the searched tag.
- * @param element Element number of the searched tag.
+ * @param group Group number of the searched tag.
+ * @param elem Element number of the searched tag.
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element)
+std::string Document::GetEntryVR(uint16_t group, uint16_t elem)
{
- DocEntry* elem = GetDocEntryByNumber(group, element);
- if ( !elem )
+ DocEntry *element = GetDocEntry(group, elem);
+ if ( !element )
{
return GDCM_UNFOUND;
}
- return elem->GetVR();
+ return element->GetVR();
}
/**
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the value length of a given tag..
- * @param group Group number of the searched tag.
- * @param element Element number of the searched tag.
+ * @param group Group number of the searched tag.
+ * @param elem Element number of the searched tag.
* @return Corresponding element length; -2 if not found
*/
-int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element)
+int Document::GetEntryLength(uint16_t group, uint16_t elem)
{
- DocEntry* elem = GetDocEntryByNumber(group, element);
- if ( !elem )
+ DocEntry *element = GetDocEntry(group, elem);
+ if ( !element )
{
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 Document::SetEntryByName(std::string const & content,std::string const & tagName)
-{
- DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( !dictEntry )
- {
- return false;
- }
-
- return SetEntryByNumber(content,dictEntry->GetGroup(),
- dictEntry->GetElement());
+ return element->GetLength();
}
/**
* 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
+ * @param group group number of the Dicom Element to modify
+ * @param elem element number of the Dicom Element to modify
*/
-bool Document::SetEntryByNumber(std::string const& content,
- uint16_t group,
- uint16_t element)
+bool Document::SetEntry(std::string const& content,
+ uint16_t group, uint16_t elem)
{
- int c;
- int l;
-
- ValEntry* valEntry = GetValEntryByNumber(group, element);
- if (!valEntry )
+ ValEntry *entry = GetValEntry(group, elem);
+ if (!entry )
{
- dbg.Verbose(0, "Document::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
- {
- VRKey vr = valEntry->GetVR();
- if( vr == "US" || vr == "SS" )
- {
- // for multivaluated items
- c = Util::CountSubstring(content, "\\") + 1;
- l = c*2;
- }
- else if( vr == "UL" || vr == "SL" )
- {
- // for multivaluated items
- c = Util::CountSubstring(content, "\\") + 1;
- l = c*4;;
- }
- }
- valEntry->SetLength(l);
- return true;
+ return SetEntry(content,entry);
}
/**
* the given value.
* @param content new value (void* -> uint8_t*) to substitute with
* @param lgth new value length
- * @param group group number of the Dicom Element to modify
- * @param element element number of the Dicom Element to modify
+ * @param group group number of the Dicom Element to modify
+ * @param elem element number of the Dicom Element to modify
*/
-bool Document::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 elem)
{
- (void)lgth; //not used
- TagKey key = DictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key))
+ BinEntry *entry = GetBinEntry(group, elem);
+ 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?
- }
-*/
- BinEntry* a = (BinEntry *)TagHT[key];
- a->SetBinArea(content);
- a->SetLength(lgth);
- a->SetValue(GDCM_BINLOADED);
-
- return true;
+ return SetEntry(content,lgth,entry);
}
/**
* \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * in the PubDocEntrySet of this instance
- * through it's (group, element) and modifies it's length with
- * the given value.
- * \warning Use with extreme caution.
- * @param l new length to substitute with
- * @param group group number of the Entry to modify
- * @param element element number of the Entry to modify
- * @return true on success, false otherwise.
+ * and modifies it's content with the given value.
+ * @param content new value (string) to substitute with
+ * @param entry Entry to be modified
*/
-bool Document::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
- TagKey key = DictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key) )
- {
- return false;
- }
- if ( l % 2 )
+ if(entry)
{
- 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 Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem)
+bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry)
{
- DocEntry* entry = GetDocEntryByNumber(group, elem);
- if (!entry)
+ if(entry)
{
- dbg.Verbose(1, "Document::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* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem)
+void *Document::GetEntryBinArea(uint16_t group, uint16_t elem)
{
- DocEntry* entry = GetDocEntryByNumber(group, elem);
+ DocEntry *entry = GetDocEntry(group, elem);
if (!entry)
{
- dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry");
+ gdcmVerboseMacro( "No entry");
return 0;
}
- if ( BinEntry* binEntry = dynamic_cast<BinEntry*>(entry) )
+ if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(entry) )
{
return binEntry->GetBinArea();
}
}
/**
- * \brief Loads (from disk) the element content
- * when a string is not suitable
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
* @param group group number of the Entry
* @param elem element number of the Entry
*/
-void* Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
+void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
- DocEntry *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, "Document::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, "Document::LoadEntryBinArea setting failed.");
- }
- return a;
-}
-/**
- * \brief Loads (from disk) the element content
- * when a string is not suitable
- * @param element Entry whose binArea is going to be loaded
- */
-void* Document::LoadEntryBinArea(BinEntry* element)
-{
- size_t o =(size_t)element->GetOffset();
- fseek(Fp, o, SEEK_SET);
- size_t l = element->GetLength();
- uint8_t* a = new uint8_t[l];
- if( !a )
- {
- dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a");
- return NULL;
- }
- element->SetBinArea((uint8_t*)a);
- /// \todo check the result
- size_t l2 = fread(a, 1, l , Fp);
- if( l != l2 )
- {
- delete[] a;
- return NULL;
- }
+ return;
- return a;
-}
+ BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
+ if( !binElement )
+ return;
-/**
- * \brief Sets a 'non string' value to a given Dicom Element
- * @param area area containing the 'non string' value
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return
- */
-bool Document::SetEntryBinAreaByNumber(uint8_t* area,
- uint16_t group,
- uint16_t element)
-{
- DocEntry* currentEntry = GetDocEntryByNumber(group, element);
- if ( !currentEntry )
- {
- return false;
- }
- if ( BinEntry* binEntry = dynamic_cast<BinEntry*>(currentEntry) )
- {
- binEntry->SetBinArea( area );
- return true;
- }
- return true;
+ LoadEntryBinArea(binElement);
}
/**
- * \brief Update the entries with the shadow dictionary.
- * Only non even entries are analyzed
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
+ * @param elem Entry whose binArea is going to be loaded
*/
-void Document::UpdateShaEntries()
+void Document::LoadEntryBinArea(BinEntry *elem)
{
- //DictEntry *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(elem->GetBinArea())
+ return;
- if((*it)->IsImplicitVR())
- vr="Implicit";
- else
- vr=(*it)->GetVR();
+ bool openFile = !Fp;
+ if(openFile)
+ OpenFile();
- (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling
- if(entry){
- // Set the new entry and the new value
- (*it)->SetDictEntry(entry);
- CheckDocEntryVR(*it,vr);
+ size_t o =(size_t)elem->GetOffset();
+ Fp->seekg(o, std::ios::beg);
- (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling
-
- }
- else
- {
- // Remove precedent value transformation
- (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr));
- }
+ size_t l = elem->GetLength();
+ uint8_t *a = new uint8_t[l];
+ if( !a )
+ {
+ gdcmVerboseMacro( "Cannot allocate BinEntry content");
+ return;
}
-*/
-}
-/**
- * \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.
- */
-DocEntry* Document::GetDocEntryByName(std::string const & tagName)
-{
- DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( !dictEntry )
+ /// \todo check the result
+ Fp->read((char*)a, l);
+ if( Fp->fail() || Fp->eof())
{
- return NULL;
+ delete[] a;
+ return;
}
- return GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement());
-}
+ elem->SetBinArea(a);
-/**
- * \brief retrieves a Dicom Element (the first one) using (group, element)
- * \warning (group, element) IS NOT an identifier inside the Dicom Header
- * if you think it's NOT UNIQUE, check the count number
- * and use iterators to retrieve ALL the Dicoms Elements within
- * a given couple (group, element)
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return
- */
-DocEntry* Document::GetDocEntryByNumber(uint16_t group,
- uint16_t element)
-{
- TagKey key = DictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key))
- {
- return NULL;
- }
- return TagHT.find(key)->second;
+ if(openFile)
+ CloseFile();
}
/**
- * \brief Same as \ref Document::GetDocEntryByNumber except it only
- * returns a result when the corresponding entry is of type
- * ValEntry.
- * @return When present, the corresponding ValEntry.
+ * \brief Sets a 'non string' value to a given Dicom Element
+ * @param area area containing the 'non string' value
+ * @param group Group number of the searched Dicom Element
+ * @param elem Element number of the searched Dicom Element
+ * @return
*/
-ValEntry* Document::GetValEntryByNumber(uint16_t group,
- uint16_t element)
+/*bool Document::SetEntryBinArea(uint8_t *area,
+ uint16_t group, uint16_t elem)
{
- DocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ DocEntry *currentEntry = GetDocEntry(group, elem);
if ( !currentEntry )
{
- return 0;
+ return false;
}
- if ( ValEntry* valEntry = dynamic_cast<ValEntry*>(currentEntry) )
+
+ if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(currentEntry) )
{
- return valEntry;
+ binEntry->SetBinArea( area );
+ return true;
}
- dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry.");
- return 0;
-}
+ return false;
+}*/
+
/**
- * \brief Loads the element while preserving the current
- * underlying file position indicator as opposed to
- * to LoadDocEntry that modifies it.
- * @param entry Header Entry whose value shall be loaded.
+ * \brief Loads the element while preserving the current
+ * underlying file position indicator as opposed to
+ * LoadDocEntry that modifies it.
+ * @param entry Header Entry whose value will be loaded.
* @return
*/
-void Document::LoadDocEntrySafe(DocEntry * 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);
+ }
}
/**
{
switch (SwapCode)
{
- case 0 :
+ case 1234 :
break;
case 4321 :
a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
- break;
-
+ break;
case 3412 :
a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
- break;
-
+ break;
case 2143 :
a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
- break;
+ break;
default :
- //std::cout << "swapCode= " << SwapCode << std::endl;
- dbg.Error(" Document::SwapLong : unset swap code");
+ gdcmErrorMacro( "Unset swap code:" << SwapCode );
a = 0;
}
return a;
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
* @return length of the parsed set.
*/
-void Document::ParseDES(DocEntrySet *set,
- long offset,
- long l_max,
- bool delim_mode)
+void Document::ParseDES(DocEntrySet *set, long offset,
+ long l_max, bool delim_mode)
{
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;
}
- VRKey vr = newDocEntry->GetVR();
- if ( vr != "SQ" )
+ vr = newDocEntry->GetVR();
+ newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
+ newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
+ newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
+
+ if ( newValEntry || newBinEntry )
{
-
- if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) )
+ if ( newBinEntry )
+ {
+ if ( Filetype == ExplicitVR && ! Global::GetVR()->IsVROfBinaryRepresentable(vr) )
+ {
+ ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
+ gdcmVerboseMacro( std::hex << newDocEntry->GetGroup()
+ << "|" << newDocEntry->GetElement()
+ << " : 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 ( dynamic_cast< Document* > ( set ) )
+ {
+ newBinEntry->SetKey( newBinEntry->GetKey() );
+ }
+ // but when "this" is a SQItem, we are inserting this new
+ // valEntry in a sequence item, and the key 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
- ValEntry* newValEntry =
- new ValEntry( newDocEntry->GetDictEntry() );
- newValEntry->Copy( newDocEntry );
-
// 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 (Document* dummy = dynamic_cast< Document* > ( set ) )
+ if ( dynamic_cast< Document* > ( set ) )
{
- (void)dummy;
newValEntry->SetKey( newValEntry->GetKey() );
}
// ...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 BaseTagKey):
- if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ 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 ( ! Global::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
- {
- ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- dbg.Verbose(0, "Document::ParseDES: neither Valentry, "
- "nor BinEntry. Probably unknown VR.");
+ // If here expect big troubles
+ //delete newValEntry; //otherwise mem leak
+ used=false;
}
- //////////////////// BinEntry or UNKOWN VR:
- BinEntry* newBinEntry =
- new BinEntry( newDocEntry->GetDictEntry() );
- newBinEntry->Copy( newDocEntry );
-
- // When "this" is a Document the Key is simply of the
- // form ( group, elem )...
- if (Document* dummy = dynamic_cast< Document* > ( set ) )
+ if (delimitor)
{
- (void)dummy;
- 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 BaseTagKey):
- if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( 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 ( 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
- if ( IsJPEGTransferSyntax() )
+ else if ( Global::GetTS()->IsJPEG(ts) )
{
- long PositionOnEntry = ftell(Fp);
- fseek( Fp, newDocEntry->GetOffset(), SEEK_SET );
+ long positionOnEntry = Fp->tellg();
+ Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
ComputeJPEGFragmentInfo();
- fseek( Fp, PositionOnEntry, SEEK_SET );
+ Fp->seekg( positionOnEntry, std::ios::beg );
}
}
-
+
// Just to make sure we are at the beginning of next entry.
SkipToNextDocEntry(newDocEntry);
}
}
}
// no other way to create it ...
- SeqEntry* newSeqEntry =
- new SeqEntry( newDocEntry->GetDictEntry() );
- newSeqEntry->Copy( newDocEntry );
newSeqEntry->SetDelimitorMode( delim_mode );
// 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 (Document* dummy = dynamic_cast< Document* > ( set ) )
+ if (/*Document *dummy =*/ dynamic_cast< Document* > ( set ) )
{
- (void)dummy;
+ //(void)dummy;
newSeqEntry->SetDepthLevel( 1 );
newSeqEntry->SetKey( newSeqEntry->GetKey() );
}
- // But when "set" is allready a SQItem, we are building a nested
+ // But when "set" is already a SQItem, we are building a nested
// sequence, and hence the depth level of the new SeqEntry
// we are building, is one level deeper:
- if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( 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 Document::ParseSQ( SeqEntry* 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;
+ long offsetStartCurrentSQItem = offset;
while (true)
{
- DocEntry* newDocEntry = ReadNextDocEntry();
+ // the first time, we read the fff0,e000 of the first SQItem
+ DocEntry *newDocEntry = ReadNextDocEntry();
+
if ( !newDocEntry )
{
// FIXME Should warn user
{
if ( newDocEntry->IsSequenceDelimitor() )
{
- seqEntry->SetSequenceDelimitationItem( newDocEntry );
+ seqEntry->SetDelimitationItem( newDocEntry );
break;
}
}
- if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- break;
+ delete newDocEntry;
+ break;
}
-
+ // create the current SQItem
SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
std::ostringstream newBase;
newBase << seqEntry->GetKey()
{
dlm_mod = false;
}
-
- ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
-
- seqEntry->AddEntry( itemSQ, SQItemNumber );
+ // FIXME, TODO
+ // when we're here, element fffe,e000 is already passed.
+ // it's lost for the SQItem we're going to process !!
+
+ //ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+ //delete newDocEntry; // FIXME well ... it's too late to use it !
+
+ // Let's try :------------
+ // remove fff0,e000, created out of the SQItem
+ delete newDocEntry;
+ Fp->seekg(offsetStartCurrentSQItem, std::ios::beg);
+ // fill up the current SQItem, starting at the beginning of fff0,e000
+ ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod);
+ offsetStartCurrentSQItem = Fp->tellg();
+ // end try -----------------
+
+ seqEntry->AddSQItem( itemSQ, SQItemNumber );
SQItemNumber++;
- if ( !delim_mode && ( ftell(Fp) - offset ) >= l_max )
+ if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
{
break;
}
* the value specified with Document::SetMaxSizeLoadEntry()
* @param entry Header Entry (Dicom Element) to be dealt with
*/
-void Document::LoadDocEntry(DocEntry* 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
std::ostringstream s;
if (length > MaxSizeLoadEntry)
{
- if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(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 (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(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 (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(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) )
{
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 ( ValEntry* valEntry = dynamic_cast<ValEntry* >(entry) )
- {
- if ( item_read != 1 )
+
+ if ( ValEntry *valEntry = dynamic_cast<ValEntry* >(entry) )
+ {
+ if ( Fp->fail() || Fp->eof())
{
- dbg.Verbose(1, "Document::LoadDocEntry",
- "unread element value");
+ gdcmVerboseMacro("Unread element value");
valEntry->SetValue(GDCM_UNREAD);
return;
}
}
else
{
- dbg.Error(true, "Document::LoadDocEntry"
- "Should have a ValEntry, here !");
+ gdcmErrorMacro( "Should have a ValEntry, here !");
}
}
void Document::FindDocEntryLength( DocEntry *entry )
throw ( FormatError )
{
- uint16_t element = entry->GetElement();
std::string vr = entry->GetVR();
uint16_t length16;
// 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 ( FormatUnexpected )
{
// 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;
}
// Length is encoded on 2 bytes.
length16 = ReadInt16();
+
+ // FIXME : This heuristic supposes that the first group following
+ // group 0002 *has* and element 0000.
+ // BUT ... Element 0000 is optionnal :-(
+
+
+ // Fixed using : HandleOutOfGroup0002()
+ // (first hereafter strategy ...)
// We can tell the current file is encoded in big endian (like
// Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag
// ones with zero as element number) has to be of 4 (0x0004). When we
// encounter 1024 (0x0400) chances are the encoding changed and we
// found a group with big endian encoding.
+ //---> Unfortunately, element 0000 is optional.
+ //---> This will not work when missing!
// We shall use this second strategy. In order to make sure that we
// can interpret the presence of an apparently big endian encoded
// length of a "Group Length" without committing a big mistake, we
// endian encoding". When this is the case, chances are we have got our
// hands on a big endian encoded file: we switch the swap code to
// big endian and proceed...
- if ( element == 0x0000 && length16 == 0x0400 )
- {
- if ( !IsExplicitVRBigEndianTransferSyntax() )
- {
- throw FormatError( "Document::FindDocEntryLength()",
- " not explicit VR." );
- return;
- }
- length16 = 4;
- SwitchSwapToBigEndian();
- // 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() );
- DictEntry* newTag = GetDictEntryByNumber( correctGroup,
- correctElem );
- if ( !newTag )
- {
- // This correct tag is not in the dictionary. Create a new one.
- newTag = NewVirtualDictEntry(correctGroup, correctElem);
- }
- // FIXME this can create a memory leaks on the old entry that be
- // left unreferenced.
- entry->SetDictEntry( newTag );
- }
-
- // Heuristic: well, some files are really ill-formed.
+
+// if ( element == 0x0000 && length16 == 0x0400 )
+// {
+// std::string ts = GetTransferSyntax();
+// if ( Global::GetTS()->GetSpecialTransferSyntax(ts)
+// != TS::ExplicitVRBigEndian )
+// {
+// throw FormatError( "Document::FindDocEntryLength()",
+// " not explicit VR." );
+// return;
+// }
+// length16 = 4;
+// 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() );
+// DictEntry *newTag = GetDictEntry( correctGroup, correctElem );
+// if ( !newTag )
+// {
+// // This correct tag is not in the dictionary. Create a new one.
+// newTag = NewVirtualDictEntry(correctGroup, correctElem);
+// }
+// // FIXME this can create a memory leaks on the old entry that be
+// // left unreferenced.
+// entry->SetDictEntry( newTag );
+// }
+
+ // 0xffff means that we deal with 'No Length' Sequence
+ // or 'No Length' SQItem
if ( length16 == 0xffff)
- {
- // 0xffff means that we deal with 'Unknown Length' Sequence
+ {
length16 = 0;
}
FixDocEntryFoundLength( entry, (uint32_t)length16 );
// on Data elements "Implicit and Explicit VR Data Elements shall
// not coexist in a Data Set and Data Sets nested within it".]
// Length is on 4 bytes.
+
+ // Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
+ // even if Transfer Syntax is 'Implicit VR ...'
FixDocEntryFoundLength( entry, ReadInt32() );
return;
/**
* \brief Find the Value Representation of the current Dicom Element.
- * @param entry
+ * @return Value Representation of the current Entry
*/
-void Document::FindDocEntryVR( DocEntry *entry )
+std::string Document::FindDocEntryVR()
{
if ( Filetype != ExplicitVR )
- {
- return;
- }
-
- char vr[3];
+ 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 Document::CheckDocEntryVR(DocEntry *entry, VRKey vr)
+bool Document::CheckDocEntryVR(VRKey vr)
{
- std::string msg;
- 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 && !Global::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.
- msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n",
- entry->GetGroup(), entry->GetElement());
- dbg.Verbose(1, "Document::FindVR: ", msg.c_str());
-
- if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000)
- {
- // Group length is UL !
- DictEntry* 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.
- DictEntry* newEntry = NewVirtualDictEntry(
- entry->GetGroup(), entry->GetElement(),
- vr, "FIXME", entry->GetName());
- entry->SetDictEntry(newEntry);
- }
return true;
}
* @param entry Entry to reverse transform
* @return Reverse transformed entry value
*/
-std::string Document::GetDocEntryUnvalue(DocEntry* entry)
+std::string Document::GetDocEntryUnvalue(DocEntry *entry)
{
if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
/**
* \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 Document::SkipToNextDocEntry(DocEntry *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);
+ if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb
+ 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 Document::FixDocEntryFoundLength(DocEntry *entry,
- uint32_t foundLength)
+ 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);
}
/**
*/
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;
- long 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, "Document::IsDocEntryAnInteger", s.str().c_str() );
+ << "lgt : " << length );
}
}
if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" )
{
return true;
- }
-
+ }
return false;
}
* @return
*/
-uint32_t Document::FindDocEntryLengthOB()
+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;
}
catch ( FormatError )
{
- throw FormatError("Document::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, "Document::FindDocEntryLengthOB: neither an Item "
- "tag nor a Sequence delimiter tag.");
- fseek(Fp, positionOnEntry, SEEK_SET);
- throw FormatUnexpected("Document::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;
}
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() )
+ {
+ throw FormatError( "Document::ReadInt16()", " file error." );
+ }
+ if( Fp->eof() )
{
- if( ferror(Fp) )
- {
- throw FormatError( "Document::ReadInt16()", " file error." );
- }
throw FormatError( "Document::ReadInt16()", "EOF." );
}
g = SwapShort(g);
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() )
+ {
+ throw FormatError( "Document::ReadInt32()", " file error." );
+ }
+ if( Fp->eof() )
{
- if( ferror(Fp) )
- {
- throw FormatError( "Document::ReadInt16()", " file error." );
- }
throw FormatError( "Document::ReadInt32()", "EOF." );
}
g = SwapLong(g);
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 Document::Initialise()
+void Document::Initialize()
{
RefPubDict = Global::GetDicts()->GetDefaultPubDict();
RefShaDict = NULL;
RLEInfo = new RLEFramesInfo;
JPEGInfo = new JPEGFragmentsInfo;
+ Filetype = Unknown;
}
/**
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).
net2host = false;
}
- // 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
+ // The easiest case is the one of a 'true' DICOM header, we just have
+ // to look for the string "DICM" inside the file preamble.
+ Fp->read(deb, 256);
char *entCur = deb + 128;
if( memcmp(entCur, "DICM", (size_t)4) == 0 )
{
- dbg.Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3");
+ gdcmVerboseMacro( "Looks like DICOM Version3 (preamble + DCM)" );
- // Next, determine the value representation (VR). Let's skip to the
- // first element (0002, 0000) and check there if we find "UL"
- // - or "OB" if the 1st one is (0002,0001) -,
+ // Group 0002 should always be VR, and the first element 0000
+ // Let's be carefull (so many wrong headers ...)
+ // and determine the value representation (VR) :
+ // Let's skip to the first element (0002,0000) and check there if we find
+ // "UL" - or "OB" if the 1st one is (0002,0001) -,
// in which case we (almost) know it is explicit VR.
// WARNING: if it happens to be implicit VR then what we will read
// is the length of the group. If this ascii representation of this
// length happens to be "UL" then we shall believe it is explicit VR.
- // FIXME: in order to fix the above warning, we could read the next
- // element value (or a couple of elements values) in order to make
- // sure we are not commiting a big mistake.
// We need to skip :
// * the 128 bytes of File Preamble (often padded with zeroes),
// * the 4 bytes of "DICM" string,
// i.e. a total of 136 bytes.
entCur = deb + 136;
- // FIXME : FIXME:
- // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR,
- // but elem 0002,0010 (Transfert Syntax) tells us the file is
- // *Implicit* VR. -and it is !-
+ // group 0x0002 *is always* Explicit VR Sometimes ,
+ // even if elem 0002,0010 (Transfer Syntax) tells us the file is
+ // *Implicit* VR (see former 'gdcmData/icone.dcm')
if( memcmp(entCur, "UL", (size_t)2) == 0 ||
memcmp(entCur, "OB", (size_t)2) == 0 ||
memcmp(entCur, "UI", (size_t)2) == 0 ||
memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later
- // when Write DCM *adds*
+ // when Write DCM *adds*
// FIXME
// Use Document::dicom_vr to test all the possibilities
// instead of just checking for UL, OB and UI !? group 0000
{
Filetype = ExplicitVR;
- dbg.Verbose(1, "Document::CheckSwap:",
- "explicit Value Representation");
+ gdcmVerboseMacro( "Group 0002 : Explicit Value Representation");
}
else
{
Filetype = ImplicitVR;
- dbg.Verbose(1, "Document::CheckSwap:",
- "not an explicit Value Representation");
+ gdcmVerboseMacro( "Group 0002 :Not an explicit Value Representation;"
+ << "Looks like a bugged Header!");
}
if ( net2host )
{
SwapCode = 4321;
- dbg.Verbose(1, "Document::CheckSwap:",
- "HostByteOrder != NetworkByteOrder");
+ gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder");
}
else
{
- SwapCode = 0;
- dbg.Verbose(1, "Document::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);
+ // Position the file position indicator at first tag
+ // (i.e. after the file preamble and the "DICM" string).
+ 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, "Document::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 :
Filetype = ACR;
return true;
case 0x00000004 :
- SwapCode = 0;
+ SwapCode = 1234;
Filetype = ACR;
return true;
default :
// 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;
+ 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 = ACR;
return true;
default :
- dbg.Verbose(0, "Document::CheckSwap:",
- "ACR/NEMA unfound swap info (Really hopeless !)");
- Filetype = Unknown;
+ 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;
- //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 Document::SwitchSwapToBigEndian()
+void Document::SwitchByteSwapCode()
{
- dbg.Verbose(1, "Document::SwitchSwapToBigEndian",
- "Switching to BigEndian mode.");
- if ( SwapCode == 0 )
+ gdcmVerboseMacro( "Switching Byte Swap code from "<< SwapCode);
+ if ( SwapCode == 1234 )
{
SwapCode = 4321;
}
else if ( SwapCode == 4321 )
{
- SwapCode = 0;
+ SwapCode = 1234;
}
else if ( SwapCode == 3412 )
{
*/
void Document::SetMaxSizePrintEntry(long newSize)
{
- //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME
if ( newSize < 0 )
{
return;
+/**
+ * \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
+ * @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.find(GDCM_NOTLOADED) < transferSyntax.length()) )
+ {
+ gdcmErrorMacro( "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";
+ }
+
+ // we do it only when we need it
+ const TSKey &tsName = Global::GetTS()->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, uint16_t &elem)
+{
+ // 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 = GetTransferSyntax();
+ if ( !Global::GetTS()->IsTransferSyntax(ts) )
+ {
+ gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
+ return;
+ }
+
+ // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..."
+
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian )
+ {
+ Filetype = ImplicitVR;
+ }
+
+ // FIXME Strangely, this works with
+ //'Implicit VR Transfer Syntax (GE Private)
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
+ {
+ gdcmVerboseMacro("Transfer Syntax Name = ["
+ << GetTransferSyntaxName() << "]" );
+ SwitchByteSwapCode();
+ group = SwapShort(group);
+ elem = SwapShort(elem);
+ }
+ }
+}
+
/**
* \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.
*/
-DocEntry* Document::ReadNextDocEntry()
+DocEntry *Document::ReadNextDocEntry()
{
uint16_t group;
uint16_t elem;
return 0;
}
- DocEntry *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 always little endian
+ if ( HasDCMPreamble )
+ HandleOutOfGroup0002(group, elem);
+
+ 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.
+ if ( newEntry->GetGroup() != 0xfffe )
+ {
+ std::string msg;
+ msg = Util::Format("Entry (%04x,%04x) should be Explicit VR\n",
+ newEntry->GetGroup(), newEntry->GetElement());
+ gdcmVerboseMacro( msg.c_str() );
+ }
+ }
+ newEntry->SetImplicitVR();
+ }
try
{
return 0;
}
- newEntry->SetOffset(ftell(Fp));
+ newEntry->SetOffset(Fp->tellg());
return newEntry;
}
-
+//GenerateFreeTagKeyInGroup? What was it designed for ?!?
/**
* \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 Document::GenerateFreeTagKeyInGroup(uint16_t group)
-{
- for (uint32_t elem = 0; elem < UINT32_MAX; elem++)
- {
- TagKey key = DictEntry::TranslateToKey(group, elem);
- if (TagHT.count(key) == 0)
- {
- return elem;
- }
- }
- return UINT32_MAX;
-}
+//uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group)
+//{
+// for (uint32_t elem = 0; elem < UINT32_MAX; elem++)
+// {
+// TagKey key = DictEntry::TranslateToKey(group, elem);
+// if (TagHT.count(key) == 0)
+// {
+// return elem;
+// }
+// }
+// return UINT32_MAX;
+//}
/**
* \brief Assuming the internal file pointer \ref Document::Fp
*/
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, "Document::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;
}
*/
uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement)
{
- long positionOnEntry = ftell(Fp);
- (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, "Document::ReadItemTagLength: ", s.str().c_str());
+ gdcmVerboseMacro( "Basic Item Length is: "
+ << itemLength << std::endl
+ << " at address: " << std::hex << (unsigned int)currentPosition);
}
return itemLength;
}
// 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,
- "Document::ReadAndSkipEncapsulatedBasicOffsetTable: ",
- s.str().c_str());
+ gdcmVerboseMacro( "Read one length: " <<
+ std::hex << individualLength );
}
#endif //GDCM_DEBUG
*/
void Document::ComputeRLEInfo()
{
- if ( ! IsRLELossLessTransferSyntax() )
+ std::string ts = GetTransferSyntax();
+ if ( !Global::GetTS()->IsRLELossless(ts) )
{
return;
}
// 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();
SkipBytes(rleSegmentLength[nbRleSegments]);
// Store the collected info
- RLEFrame* newFrameInfo = new RLEFrame;
+ RLEFrame *newFrameInfo = new RLEFrame;
newFrameInfo->NumberFragments = nbRleSegments;
for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
{
// Delimiter Item':
if ( !ReadTag(0xfffe, 0xe0dd) )
{
- dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
- dbg.Verbose(0, " item at end of RLE item sequence");
+ gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence");
}
}
void Document::ComputeJPEGFragmentInfo()
{
// If you need to, look for comments of ComputeRLEInfo().
- if ( ! IsJPEGTransferSyntax() )
+ std::string ts = GetTransferSyntax();
+ if ( ! Global::GetTS()->IsJPEG(ts) )
{
return;
}
long fragmentLength;
while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
{
- long fragmentOffset = ftell(Fp);
+ long fragmentOffset = Fp->tellg();
// Store the collected info
- JPEGFragment* newFragment = new JPEGFragment;
+ JPEGFragment *newFragment = new JPEGFragment;
newFragment->Offset = fragmentOffset;
newFragment->Length = fragmentLength;
JPEGInfo->Fragments.push_back( newFragment );
// Delimiter Item':
if ( !ReadTag(0xfffe, 0xe0dd) )
{
- dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
- dbg.Verbose(0, " item at end of JPEG item sequence");
+ gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence");
}
}
-/**
+/*
* \brief Walk recursively the given \ref DocEntrySet, and feed
* the given hash table (\ref TagDocEntryHT) with all the
* \ref DocEntry (Dicom entries) encountered.
* when recursively walking the given set.
* @param set The structure to be traversed (recursively).
*/
-void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT,
- DocEntrySet* set )
+/*void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT,
+ DocEntrySet *set )
{
- if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( 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)
{
- DocEntry* entry = i->second;
- if ( SeqEntry* seqEntry = dynamic_cast<SeqEntry*>(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 (SQItem* SQItemSet = dynamic_cast< SQItem* > ( 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)
{
- DocEntry* entry = *i;
- if ( SeqEntry* seqEntry = dynamic_cast<SeqEntry*>(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
* Document.
*
* The structure used by a Document (through \ref ElementSet),
- * in order to old the parsed entries of a Dicom header, is a recursive
+ * 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 SQItem) add an extra complexity to the data
* \ref BuildFlatHashTable again...
* @return The flat std::map<> we juste build.
*/
-TagDocEntryHT* Document::BuildFlatHashTable()
+/*TagDocEntryHT *Document::BuildFlatHashTable()
{
- TagDocEntryHT* FlatHT = new TagDocEntryHT;
+ TagDocEntryHT *FlatHT = new TagDocEntryHT;
BuildFlatHashTableRecurse( *FlatHT, this );
return FlatHT;
-}
+}*/
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;
return false;
}
+
+/**
+ * \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 = GetFirstEntry();
+ 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