-// gdcmDocument.cxx
-//-----------------------------------------------------------------------------
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmDocument.cxx,v $
+ Language: C++
+ Date: $Date: 2004/10/20 14:30:40 $
+ Version: $Revision: 1.106 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
#include "gdcmDocument.h"
#include "gdcmValEntry.h"
#include "gdcmBinEntry.h"
#include "gdcmSeqEntry.h"
-
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
-#include <errno.h>
#include <vector>
// For nthos:
#include <netinet/in.h>
#endif
-# include <iomanip>
+#include <iomanip>
+
+namespace gdcm
+{
// Implicit VR Little Endian
#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2"
#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 gdcmDocument::CheckSwap()
-const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256;
-
-// Refer to gdcmDocument::SetMaxSizeLoadEntry()
-const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
+// Refer to Document::CheckSwap()
+const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
-const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64;
+// Refer to Document::SetMaxSizeLoadEntry()
+const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
+const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff;
//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
* \brief constructor
- * @param inFilename file to be opened for parsing
- * @param exception_on_error whether we throw an exception or not
- * @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences,
- * when they have an actual length
- * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
- * @param ignore_shadow to allow skipping the shadow elements,
- * to save memory space.
- * \warning The TRUE value for this param has to be used
- * with a FALSE value for the 'enable_sequence' param.
- * ('public elements' may be embedded in 'shadow Sequences')
- */
-gdcmDocument::gdcmDocument(const char *inFilename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow)
- : gdcmElementSet(-1) {
- enableSequences=enable_sequences;
- ignoreShadow =ignore_shadow;
-
+ * @param filename file to be opened for parsing
+ */
+Document::Document( std::string const & filename )
+ : ElementSet(-1)
+{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- filename = inFilename;
+ Filename = filename;
Initialise();
- if ( !OpenFile(exception_on_error))
+ if ( !OpenFile() )
+ {
return;
+ }
+
+ dbg.Verbose(0, "Document::Document: starting parsing of file: ",
+ Filename.c_str());
+ rewind(Fp);
- rewind(fp);
- //if (!CheckSwap())
- // return false; // to go on compiling
-
- fseek(fp,0L,SEEK_END);
- long lgt = ftell(fp);
+ fseek(Fp,0L,SEEK_END);
+ long lgt = ftell(Fp);
- rewind(fp);
+ rewind(Fp);
CheckSwap();
- long beg = ftell(fp);
+ long beg = ftell(Fp);
lgt -= beg;
- SQDepthLevel=0;
+ ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
+
+ rewind(Fp);
- long l=ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
+ // Load 'non string' values
+
+ std::string PhotometricInterpretation = GetEntryByNumber(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
+ /// 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 and restore the dictionary to its
+ /// correct value, one needs to decided of the semantics by deciding
+ /// wether the following tags are either:
+ /// - multivaluated US, and hence loaded as ValEntry, but afterwards
+ /// also used as BinEntry, which requires the proper conversion,
+ /// - OW, and hence loaded as BinEntry, but afterwards also used
+ /// as ValEntry, which requires the proper conversion.
+ LoadEntryBinArea(0x0028,0x1201); // R LUT
+ LoadEntryBinArea(0x0028,0x1202); // G LUT
+ LoadEntryBinArea(0x0028,0x1203); // B LUT
+
+ // Segmented Red Palette Color LUT Data
+ LoadEntryBinArea(0x0028,0x1221);
+ // Segmented Green Palette Color LUT Data
+ LoadEntryBinArea(0x0028,0x1222);
+ // Segmented Blue Palette Color LUT Data
+ LoadEntryBinArea(0x0028,0x1223);
+ }
+ //FIXME later : how to use it?
+ LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent)
+
CloseFile();
// --------------------------------------------------------------
- // Special Patch to allow gdcm to read ACR-LibIDO formated images
+ // Specific code to allow gdcm to read ACR-LibIDO formated images
+ // Note: ACR-LibIDO is an extension of the ACR standard that was
+ // used at CREATIS. For the time being (say a couple years)
+ // we keep this kludge to allow a smooth move to gdcm for
+ // CREATIS developpers (sorry folks).
//
// if recognition code tells us we deal with a LibIDO image
// we switch lineNumber and columnNumber
RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
// with "little-endian strings"
{
- filetype = gdcmACR_LIBIDO;
+ Filetype = ACR_LIBIDO;
std::string rows = GetEntryByNumber(0x0028, 0x0010);
std::string columns = GetEntryByNumber(0x0028, 0x0011);
SetEntryByNumber(columns, 0x0028, 0x0010);
SetEntryByNumber(rows , 0x0028, 0x0011);
}
- // ----------------- End of Special Patch ----------------
+ // ----------------- End of ACR-LibIDO kludge ------------------
- printLevel = 1; // 'Medium' print level by default
+ PrintLevel = 1; // 'Medium' print level by default
}
/**
- * \brief constructor
- * @param exception_on_error
+ * \brief This default constructor doesn't parse the file. You should
+ * then invoke \ref Document::SetFileName and then the parsing.
*/
-gdcmDocument::gdcmDocument(bool exception_on_error)
- :gdcmElementSet(-1) {
- (void)exception_on_error;
- enableSequences=0;
-
+Document::Document()
+ :ElementSet(-1)
+{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Initialise();
-
- printLevel = 1; // 'Medium' print level by default
+ PrintLevel = 1; // 'Medium' print level by default
}
/**
* \brief Canonical destructor.
*/
-gdcmDocument::~gdcmDocument (void) {
+Document::~Document ()
+{
RefPubDict = NULL;
RefShaDict = NULL;
+
+ // Recursive clean up of sequences
+ for (TagDocEntryHT::const_iterator it = TagHT.begin();
+ it != TagHT.end(); ++it )
+ {
+ //delete it->second; //temp remove
+ }
+ TagHT.clear();
}
//-----------------------------------------------------------------------------
// Print
-/**
-
/**
* \brief Prints The Dict Entries of THE public Dicom Dictionary
* @return
*/
-void gdcmDocument::PrintPubDict(std::ostream & os) {
+void Document::PrintPubDict(std::ostream & os)
+{
RefPubDict->Print(os);
}
* \brief Prints The Dict Entries of THE shadow Dicom Dictionary
* @return
*/
-void gdcmDocument::PrintShaDict(std::ostream & os) {
+void Document::PrintShaDict(std::ostream & os)
+{
RefShaDict->Print(os);
}
/**
* \brief Get the public dictionary used
*/
-gdcmDict *gdcmDocument::GetPubDict(void) {
- return(RefPubDict);
+Dict* Document::GetPubDict()
+{
+ return RefPubDict;
}
/**
* \brief Get the shadow dictionary used
*/
-gdcmDict *gdcmDocument::GetShaDict(void) {
- return(RefShaDict);
+Dict* Document::GetShaDict()
+{
+ return RefShaDict;
}
/**
* \brief Set the shadow dictionary used
* \param dict dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(gdcmDict *dict){
- RefShaDict=dict;
- return(!RefShaDict);
+bool Document::SetShaDict(Dict *dict)
+{
+ RefShaDict = dict;
+ return !RefShaDict;
}
/**
* \brief Set the shadow dictionary used
* \param dictName name of the dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(DictKey dictName){
- RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName);
- return(!RefShaDict);
+bool Document::SetShaDict(DictKey const & dictName)
+{
+ RefShaDict = Global::GetDicts()->GetDict(dictName);
+ return !RefShaDict;
}
/**
* \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current gdcmDocument was properly parsed
+ * decides whether or not the current Document was properly parsed
* and contains the mandatory information for being considered as
* a well formed and usable Dicom/Acr File.
- * @return true when gdcmDocument is the one of a reasonable Dicom/Acr file,
+ * @return true when Document is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmDocument::IsReadable(void) {
- if(filetype==gdcmUnknown) {
- dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype");
- return(false);
+bool Document::IsReadable()
+{
+ if( Filetype == Unknown)
+ {
+ dbg.Verbose(0, "Document::IsReadable: wrong filetype");
+ return false;
}
- if(!tagHT.empty()<=0) {
- std::cout << "gdcmDocument::IsReadable: wrong tagHT size : "
- << tagHT.size()
- <<std::endl;
- return(false);
+
+ if( TagHT.empty() )
+ {
+ dbg.Verbose(0, "Document::IsReadable: no tags in internal"
+ " hash table.");
+ return false;
}
- return(true);
+ 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.
+ * @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 don't match.
+ * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match.
*/
-bool gdcmDocument::IsGivenTransferSyntax(const std::string & SyntaxToCheck)
+bool Document::IsGivenTransferSyntax(std::string const & syntaxToCheck)
{
- gdcmDocEntry *Entry = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Entry )
+ DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010);
+ if ( !entry )
+ {
return false;
+ }
// The entry might be present but not loaded (parsing and loading
- // happen at differente stages): try loading and proceed with check...
- LoadDocEntrySafe(Entry);
- if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(Entry) )
+ // happen at different stages): try loading and proceed with check...
+ LoadDocEntrySafe(entry);
+ if (ValEntry* valEntry = dynamic_cast< ValEntry* >(entry) )
{
- std::string Transfer = ValEntry->GetValue();
+ 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...
- while ( ! isdigit(Transfer[Transfer.length()-1]) )
+ if ( transfer.length() == 0 ) { // for brain damaged headers
+ return false;
+ }
+ while ( ! isdigit(transfer[transfer.length()-1]) )
{
- Transfer.erase(Transfer.length()-1, 1);
+ transfer.erase(transfer.length()-1, 1);
}
- if ( Transfer == SyntaxToCheck )
+ if ( transfer == syntaxToCheck )
+ {
return true;
+ }
}
return false;
}
* \brief Determines if the Transfer Syntax of the present document
* corresponds to a Implicit Value Representation of
* Little Endian.
- * \sa \ref gdcmDocument::IsGivenTransferSyntax.
+ * \sa \ref Document::IsGivenTransferSyntax.
* @return True when ImplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void)
+bool Document::IsImplicitVRLittleEndianTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2);
}
* and if it corresponds to a ExplicitVRLittleEndian one.
* @return True when ExplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void)
+bool Document::IsExplicitVRLittleEndianTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1);
}
* and if it corresponds to a DeflatedExplicitVRLittleEndian one.
* @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void)
+bool Document::IsDeflatedExplicitVRLittleEndianTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99);
}
* and if it corresponds to a Explicit VR Big Endian one.
* @return True when big endian found. False in all other cases.
*/
-bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void)
+bool Document::IsExplicitVRBigEndianTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2);
}
* and if it corresponds to a JPEGBaseLineProcess1 one.
* @return True when JPEGBaseLineProcess1found. False in all other cases.
*/
-bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax(void)
+bool Document::IsJPEGBaseLineProcess1TransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50);
}
* and if it corresponds to a JPEGExtendedProcess2-4 one.
* @return True when JPEGExtendedProcess2-4 found. False in all other cases.
*/
-bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax(void)
+bool Document::IsJPEGExtendedProcess2_4TransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51);
}
* and if it corresponds to a JPEGExtendeProcess3-5 one.
* @return True when JPEGExtendedProcess3-5 found. False in all other cases.
*/
-bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax(void)
+bool Document::IsJPEGExtendedProcess3_5TransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52);
}
* @return True when JPEGSpectralSelectionProcess6-8 found. False in all
* other cases.
*/
-bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void)
+bool Document::IsJPEGSpectralSelectionProcess6_8TransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53);
}
* @return True when RLE Lossless found. False in all
* other cases.
*/
-bool gdcmDocument::IsRLELossLessTransferSyntax(void)
+bool Document::IsRLELossLessTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5);
}
* @return True when RLE Lossless found. False in all
* other cases.
*/
-bool gdcmDocument::IsJPEGLossless(void)
+
+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_90) );
+ || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70) );
}
/**
* @return True when JPEG2000 (Lossly or LossLess) found. False in all
* other cases.
*/
-bool gdcmDocument::IsJPEG2000(void)
+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 ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70)
- || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) );
+ return ( IsJPEGTransferSyntax()
+ || IsRLELossLessTransferSyntax() );
}
/**
* \brief Predicate for dicom version 3 file.
* @return True when the file is a dicom version 3.
*/
-bool gdcmDocument::IsDicomV3(void) {
+bool Document::IsDicomV3()
+{
// Checking if Transfert 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 GetDocEntryByNumber(0x0002, 0x0010) != NULL;
}
/**
* (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
* @return the FileType code
*/
-FileType gdcmDocument::GetFileType(void) {
- return(filetype);
+FileType Document::GetFileType()
+{
+ return Filetype;
}
/**
- * \brief opens the file
- * @param exception_on_error
- * @return
+ * \brief Tries to open the file \ref Document::Filename and
+ * checks the preamble when existing.
+ * @return The FILE pointer on success.
*/
-FILE *gdcmDocument::OpenFile(bool exception_on_error)
- throw(gdcmFileError)
+FILE* Document::OpenFile()
{
- fp=fopen(filename.c_str(),"rb");
-
- if(!fp)
- {
- if(exception_on_error)
- throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)");
- else
- {
- std::cout <<"gdcmDocument::OpenFile cannot open file: "
- << filename.c_str() << std::endl;
- dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ",
- filename.c_str());
- return (NULL);
- }
- }
-
- if ( fp )
- {
- guint16 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)
- return(fp);
+ Fp = fopen(Filename.c_str(),"rb");
- //DICOM
- fseek(fp, 126L, SEEK_CUR);
- char dicm[4];
- fread(dicm, (size_t)4, (size_t)1, fp);
- if( memcmp(dicm, "DICM", 4) == 0 )
- return(fp);
-
- fclose(fp);
- dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", filename.c_str());
- }
- else {
- dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", filename.c_str());
- }
- return(NULL);
+ if(!Fp)
+ {
+ dbg.Verbose( 0,
+ "Document::OpenFile cannot open file: ",
+ Filename.c_str());
+ 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 )
+ {
+ return Fp;
+ }
+
+ //DICOM
+ fseek(Fp, 126L, SEEK_CUR);
+ char dicm[4];
+ fread(dicm, (size_t)4, (size_t)1, Fp);
+ if( memcmp(dicm, "DICM", 4) == 0 )
+ {
+ return Fp;
+ }
+
+ fclose(Fp);
+ dbg.Verbose( 0,
+ "Document::OpenFile not DICOM/ACR (missing preamble)",
+ Filename.c_str());
+
+ return 0;
}
/**
* \brief closes the file
* @return TRUE if the close was successfull
*/
-bool gdcmDocument::CloseFile(void) {
- int closed = fclose(fp);
- fp = (FILE *)0;
- if (! closed)
- return false;
- return true;
+bool Document::CloseFile()
+{
+ int closed = fclose(Fp);
+ Fp = 0;
+
+ return closed;
}
/**
* \brief Writes in a file all the Header Entries (Dicom Elements)
- * of the Chained List
* @param fp file pointer on an already open file
- * @param type Type of the File to be written
+ * @param filetype Type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* \return Always true.
*/
-bool gdcmDocument::Write(FILE *fp, FileType type) {
-/// \todo
-/// ==============
-/// The stuff will have to be rewritten using the SeQuence based
-/// tree-like stucture instead of the chained list .
-/// (so we shall remove the Group*HT from the gdcmDocument)
-/// To be checked
-/// =============
-
+void Document::Write(FILE* fp,FileType filetype)
+{
/// \todo move the following lines (and a lot of others, to be written)
- /// to a future function CheckAndCorrectHeader
-
- /// \todo
- /// Question :
- /// Comment pourrait-on savoir si le DcmHeader vient d'un fichier
- /// DicomV3 ou non (FileType est un champ de gdcmDocument ...)
- /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA
- /// no way
- /// a moins de se livrer a un tres complique ajout des champs manquants.
- /// faire un CheckAndCorrectHeader (?)
+ /// to a future function CheckAndCorrectHeader
+ /// (necessary if user wants to write a DICOM V3 file
+ /// starting from an ACR-NEMA (V2) Header
- if (type == gdcmImplicitVR)
+ if (filetype == ImplicitVR)
{
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
- /// Dans le cas suivant on doit pader manuellement avec un 0
+ /// in the following case we have to padd manually with a 0
SetEntryLengthByNumber(18, 0x0002, 0x0010);
}
- if (type == gdcmExplicitVR)
+ if (filetype == ExplicitVR)
{
std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1;
ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
SetEntryLengthByNumber(20, 0x0002, 0x0010);
}
-
+
/**
* \todo rewrite later, if really usefull
+ * - 'Group Length' element is optional in DICOM
+ * - but un-updated odd groups lengthes can causes pb
+ * (xmedcon breaker)
*
- * --> Warning : un-updated odd groups lengths can causes pb
- * --> (xmedcon breaks)
- * --> to be re- written with future org.
- *
- * if ( (type == ImplicitVR) || (type == ExplicitVR) )
- * UpdateGroupLength(false,type);
- * if ( type == ACR)
+ * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) )
+ * UpdateGroupLength(false,filetype);
+ * if ( filetype == ACR)
* UpdateGroupLength(true,ACR);
*/
+
+ ElementSet::Write(fp, filetype); // This one is recursive
- WriteEntries(fp,type);
- return(true);
}
/**
* \brief Modifies the value of a given Header 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 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-
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
- */
-
-gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
- std::string Value,
- guint16 Group,
- guint16 Elem ){
- gdcmDocEntry* a;
- gdcmValEntry* b;
- a = GetDocEntryByNumber( Group, Elem);
- if (a == NULL) {
- a =NewDocEntryByNumber(Group, Elem);
- if (a == NULL)
+ */
+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);
+
+ if (!currentEntry)
+ {
+ // check if (group,element) DictEntry exists
+ // if it doesn't, create an entry in DictSet::VirtualEntry
+ // and use it
+
+ // 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);
+ }
+
+ if (!currentEntry)
+ {
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to"
+ " NewDocEntryByNumber failed.");
return NULL;
- b = new gdcmValEntry(a);
- AddEntry(b);
- }
- SetEntryByNumber(Value, Group, Elem);
- b->SetValue(Value);
- return (gdcmValEntry*)b;
-}
+ }
+ 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 ?
+ {
+ // 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.");
+ return NULL;
+ }
+ }
+ }
+ SetEntryByNumber(value, group, elem);
+
+ return valEntry;
+}
/*
* \brief Modifies the value of a given Header Entry (Dicom Element)
* when it exists. Create it with the given value when unexistant.
- * @param voidArea (binary) value to be set
+ * @param binArea (binary) value to be set
* @param Group Group number of the Entry
* @param Elem Element number of the Entry
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-
-
-gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber(
- void *voidArea,
+BinEntry* Document::ReplaceOrCreateByNumber(
+ uint8_t* binArea,
int lgth,
- guint16 Group,
- guint16 Elem ){
- gdcmDocEntry* a;
- gdcmBinEntry* b;
- a = GetDocEntryByNumber( Group, Elem);
- if (a == NULL) {
- a =NewBinEntryByNumber(Group, Elem);
- if (a == NULL)
+ uint16_t group,
+ uint16_t elem,
+ std::string const& VR )
+{
+ BinEntry* binEntry = 0;
+ DocEntry* currentEntry = GetDocEntryByNumber( group, elem);
+ if (!currentEntry)
+ {
+
+ // check if (group,element) DictEntry exists
+ // if it doesn't, create an entry in DictSet::VirtualEntry
+ // and use it
+
+ // 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);
+ }
+ if (!currentEntry)
+ {
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to"
+ " NewDocEntryByNumber failed.");
return NULL;
- b = new gdcmBinEntry(a);
- AddEntry(b);
- }
- SetEntryByNumber(voidArea, lgth, Group, Elem);
- b->SetVoidArea(voidArea);
- return (gdcmBinEntry*)b;
+ }
+ binEntry = new BinEntry(currentEntry);
+ if ( !AddEntry(binEntry))
+ {
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
+ " failed allthough this is a creation.");
+ }
+ }
+ 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 ?
+ {
+ // 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;
+ }
+ }
+ }
+
+ 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
+ * \return pointer to the modified/created SeqEntry (NULL when creation
+ * failed).
+ */
+SeqEntry* Document::ReplaceOrCreateByNumber(
+ uint16_t group,
+ uint16_t elem)
+{
+ SeqEntry* b = 0;
+ DocEntry* a = GetDocEntryByNumber( group, elem);
+ if (!a)
+ {
+ a = NewSeqEntryByNumber(group, elem);
+ if (!a)
+ {
+ return 0;
+ }
+ b = new SeqEntry(a, 1); // FIXME : 1 (Depth)
+ AddEntry(b);
+ }
+ return b;
+}
+
/**
* \brief Set a new value if the invoked element exists
* Seems to be useless !!!
- * @param Value new element value
- * @param Group group number of the Entry
- * @param Elem element number of the Entry
+ * @param value new element value
+ * @param group group number of the Entry
+ * @param elem element number of the Entry
* \return boolean
*/
-bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem )
+bool Document::ReplaceIfExistByNumber(std::string const & value,
+ uint16_t group, uint16_t elem )
{
- std::string v = Value;
- SetEntryByNumber(v, Group, Elem);
+ SetEntryByNumber(value, group, elem);
+
return true;
}
* \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 number of occurences
+ * @return true is found
*/
-int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) {
- std::string key = gdcmDictEntry::TranslateToKey(group, element );
- return (tagHT.count(key));
+bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
+{
+ const std::string &key = DictEntry::TranslateToKey(group, element );
+ return TagHT.count(key);
}
/**
* @return Corresponding element value when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
+std::string Document::GetEntryByName(TagName const& tagName)
+{
+ DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName);
+ if( !dictEntry )
+ {
return GDCM_UNFOUND;
+ }
- return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
+ return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement());
}
/**
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryVRByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
+std::string Document::GetEntryVRByName(TagName const& tagName)
+{
+ DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
+ {
return GDCM_UNFOUND;
+ }
- gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
+ DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
+ dictEntry->GetElement());
return elem->GetVR();
}
-
/**
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+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 ((gdcmValEntry *)tagHT.find(key)->second)->GetValue();
+ }
+
+ return ((ValEntry *)TagHT.find(key)->second)->GetValue();
}
/**
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) {
- gdcmDocEntry* elem = GetDocEntryByNumber(group, element);
+std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element)
+{
+ DocEntry* elem = GetDocEntryByNumber(group, element);
if ( !elem )
+ {
return GDCM_UNFOUND;
+ }
return elem->GetVR();
}
* @param element Element number of the searched tag.
* @return Corresponding element length; -2 if not found
*/
-int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) {
- gdcmDocEntry* elem = GetDocEntryByNumber(group, element);
+int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element)
+{
+ DocEntry* elem = GetDocEntryByNumber(group, element);
if ( !elem )
- return -2;
+ {
+ return -2; //magic number
+ }
return elem->GetLength();
}
/**
* @param tagName name of the searched Dicom Element.
* @return true when found
*/
-bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return false;
+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 SetEntryByNumber(content,dictEntry->GetGroup(),
+ dictEntry->GetElement());
}
/**
- * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
* @param content new value (string) to substitute with
* @param group group number of the Dicom Element to modify
* @param element element number of the Dicom Element to modify
*/
-bool gdcmDocument::SetEntryByNumber(std::string content,
- guint16 group,
- guint16 element)
+bool Document::SetEntryByNumber(std::string const& content,
+ uint16_t group,
+ uint16_t element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+ int c;
+ int l;
+
+ ValEntry* valEntry = GetValEntryByNumber(group, element);
+ if (!valEntry )
+ {
+ dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding",
+ " ValEntry (try promotion first).");
return false;
- int l = content.length();
- if(l%2) // Non even length are padded with a space (020H).
- {
- l++;
- content = content + '\0';
}
-
- gdcmValEntry * a;
- a = (gdcmValEntry *)tagHT[key];
-
- a->SetValue(content);
-
- VRKey vr = a->GetVR();
+ // 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);
- guint32 lgr;
- if( (vr == "US") || (vr == "SS") )
- lgr = 2;
- else if( (vr == "UL") || (vr == "SL") )
- lgr = 4;
- else
- lgr = l;
+ // Integers have a special treatement for their length:
- a->SetLength(lgr);
+ 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;
}
/**
- * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
- * @param content new value (void *) to substitute with
+ * @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
*/
-bool gdcmDocument::SetEntryByNumber(void *content,
- int lgth,
- guint16 group,
- guint16 element)
+bool Document::SetEntryByNumber(uint8_t*content,
+ int lgth,
+ uint16_t group,
+ uint16_t element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+ (void)lgth; //not used
+ TagKey key = DictEntry::TranslateToKey(group, element);
+ if ( !TagHT.count(key))
+ {
return false;
-
-/* Hope Binray field length is never wrong
+ }
+
+/* Hope Binary field length is *never* wrong
if(lgth%2) // Non even length are padded with a space (020H).
{
lgth++;
//content = content + '\0'; // fing a trick to enlarge a binary field?
}
*/
- gdcmBinEntry * a;
- a = (gdcmBinEntry *)tagHT[key];
- a->SetVoidArea(content);
- //a->SetLength(lgth); // ???
+ BinEntry* a = (BinEntry *)TagHT[key];
+ a->SetBinArea(content);
+ a->SetLength(lgth);
+ a->SetValue(GDCM_BINLOADED);
+
return true;
}
/**
- * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * \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.
* @param element element number of the Entry to modify
* @return true on success, false otherwise.
*/
-bool gdcmDocument::SetEntryLengthByNumber(guint32 l,
- guint16 group,
- guint16 element)
+bool Document::SetEntryLengthByNumber(uint32_t l,
+ uint16_t group,
+ uint16_t element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+ /// \todo use map methods, instead of multimap JPR
+ TagKey key = DictEntry::TranslateToKey(group, element);
+ if ( !TagHT.count(key) )
+ {
return false;
- if (l%2) l++; // length must be even
- ( ((tagHT.equal_range(key)).first)->second )->SetLength(l);
+ }
+ if ( l % 2 )
+ {
+ l++; // length must be even
+ }
+ ( ((TagHT.equal_range(key)).first)->second )->SetLength(l);
return true ;
}
/**
* \brief Gets (from Header) the offset of a 'non string' element value
* (LoadElementValues has already be executed)
- * @param Group group number of the Entry
- * @param Elem element number of the Entry
+ * @param group group number of the Entry
+ * @param elem element number of the Entry
* @return File Offset of the Element Value
*/
-size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem)
+size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem)
{
- gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
- if (!Entry)
+ DocEntry* entry = GetDocEntryByNumber(group, elem);
+ if (!entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber",
- "failed to Locate gdcmDocEntry");
- return (size_t)0;
+ dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present.");
+ return 0;
}
- return Entry->GetOffset();
+ return entry->GetOffset();
}
/**
* \brief Gets (from Header) a 'non string' element value
* (LoadElementValues has already be executed)
- * @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 'non string' area
*/
-void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem)
+void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem)
{
- gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
- if (!Entry)
+ DocEntry* entry = GetDocEntryByNumber(group, elem);
+ if (!entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber",
- "failed to Locate gdcmDocEntry");
- return (NULL);
+ dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry");
+ return 0;
+ }
+ if ( BinEntry* binEntry = dynamic_cast<BinEntry*>(entry) )
+ {
+ return binEntry->GetBinArea();
}
- return ((gdcmBinEntry *)Entry)->GetVoidArea();
+
+ return 0;
}
/**
* \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
+ * @param group group number of the Entry
+ * @param elem element number of the Entry
*/
-void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem)
+void* Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
- gdcmDocEntry * Element= GetDocEntryByNumber(Group, Elem);
- if ( !Element )
+ DocEntry *docElement = GetDocEntryByNumber(group, elem);
+ if ( !docElement )
+ {
return NULL;
- size_t o =(size_t)Element->GetOffset();
- fseek(fp, o, SEEK_SET);
- size_t l=Element->GetLength();
- char* a = new char[l];
- if(!a)
+ }
+ 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;
-
- SetEntryVoidAreaByNumber(a, Group, Elem);
+ }
+ 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)
+ size_t l2 = fread(a, 1, l , Fp);
+ if( l != l2 )
{
delete[] a;
return NULL;
}
- return a;
+ return a;
}
/**
* \brief Sets a 'non string' value to a given Dicom Element
- * @param area
+ * @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 gdcmDocument::SetEntryVoidAreaByNumber(void * area,
- guint16 group,
- guint16 element)
+bool Document::SetEntryBinAreaByNumber(uint8_t* area,
+ uint16_t group,
+ uint16_t element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+ DocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ if ( !currentEntry )
+ {
return false;
- // This was for multimap ?
- (( gdcmBinEntry *)( ((tagHT.equal_range(key)).first)->second ))->SetVoidArea(area);
-
+ }
+ if ( BinEntry* binEntry = dynamic_cast<BinEntry*>(currentEntry) )
+ {
+ binEntry->SetBinArea( area );
+ return true;
+ }
return true;
}
* \brief Update the entries with the shadow dictionary.
* Only non even entries are analyzed
*/
-void gdcmDocument::UpdateShaEntries(void) {
- gdcmDictEntry *entry;
+void Document::UpdateShaEntries()
+{
+ //DictEntry *entry;
std::string vr;
/// \todo TODO : still any use to explore recursively the whole structure?
* @return Corresponding Dicom Element when it exists, and NULL
* otherwise.
*/
- gdcmDocEntry *gdcmDocument::GetDocEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
+DocEntry* Document::GetDocEntryByName(std::string const & tagName)
+{
+ DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
+ if( !dictEntry )
+ {
return NULL;
+ }
- return(GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
+ return GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement());
}
/**
* @param element Element number of the searched Dicom Element
* @return
*/
-gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element)
+DocEntry* Document::GetDocEntryByNumber(uint16_t group,
+ uint16_t element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+ TagKey key = DictEntry::TranslateToKey(group, element);
+ if ( !TagHT.count(key))
+ {
return NULL;
- return tagHT.find(key)->second;
-}
-
-/**
- * \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.
- * @return
- */
-void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) {
- long PositionOnEntry = ftell(fp);
- LoadDocEntry(entry);
- fseek(fp, PositionOnEntry, SEEK_SET);
-}
-
-
-/**
- * \brief Writes in a file (according to the requested format)
- * the group, the element, the value representation and the length
- * of a single gdcmDocEntry passed as argument.
- * @param tag pointer on the gdcmDocEntry to be written
- * @param _fp already open file pointer
- * @param type type of the File to be written
- */
-void gdcmDocument::WriteEntryTagVRLength(gdcmDocEntry *tag,
- FILE *_fp,
- FileType type)
-{
- guint16 group = tag->GetGroup();
- VRKey vr = tag->GetVR();
- guint16 el = tag->GetElement();
- guint32 lgr = tag->GetReadLength();
-
- if ( (group == 0xfffe) && (el == 0x0000) )
- // Fix in order to make some MR PHILIPS images e-film readable
- // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm:
- // we just *always* ignore spurious fffe|0000 tag !
- return;
-
- fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group
- fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
-
- if ( type == gdcmExplicitVR ) {
-
- // Special case of delimiters:
- if (group == 0xfffe) {
- // Delimiters have NO Value Representation and have NO length.
- // Hence we skip writing the VR and length and we pad by writing
- // 0xffffffff
-
- int ff=0xffffffff;
- fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp);
- return;
- }
-
- guint16 z=0;
- guint16 shortLgr = lgr;
- if (vr == "unkn") { // Unknown was 'written'
- // deal with Little Endian
- fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
- fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
- } else {
- fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp);
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
- {
- fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
- fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
- } else {
- fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
- }
- }
- }
- else // IMPLICIT VR
- {
- fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
- }
-}
-
-/**
- * \brief Writes in a file (according to the requested format)
- * the value of a single gdcmDocEntry passed as argument.
- * @param tag Pointer on the gdcmDocEntry to be written
- * @param _fp Already open file pointer
- * @param type type of the File to be written
- */
-
-// \todo TODO : to be re -written recursively !
-void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type)
-{
- (void)type;
- guint16 group = tag->GetGroup();
- VRKey vr = tag->GetVR();
- guint32 lgr = tag->GetReadLength();
-
- if (vr == "SQ")
- // SeQuences have no value:
- return;
- if (group == 0xfffe)
- // Delimiters have no associated value:
- return;
-
- //--------------------------------
- //
- // FIXME :right now, both value and voidArea belong to gdcmValue
- //
- // -------------------------------
-
-// if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) ) {
- void *voidArea;
- gdcmBinEntry *BinEntry= (gdcmBinEntry *)tag;;
- voidArea = BinEntry->GetVoidArea();
- if (voidArea != NULL)
- { // there is a 'non string' LUT, overlay, etc
- fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
- return;
- }
-// }
-
- if (vr == "US" || vr == "SS")
- {
- // some 'Short integer' fields may be mulivaluated
- // each single value is separated from the next one by '\'
- // we split the string and write each value as a short int
- std::vector<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- guint16 val_uint16 = atoi(tokens[i].c_str());
- void *ptr = &val_uint16;
- fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- return;
}
- if (vr == "UL" || vr == "SL")
- {
- // Some 'Integer' fields may be multivaluated (multiple instances
- // of integers). But each single integer value is separated from the
- // next one by '\' (backslash character). Hence we split the string
- // along the '\' and write each value as an int:
- std::vector<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- guint32 val_uint32 = atoi(tokens[i].c_str());
- void *ptr = &val_uint32;
- fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- return;
- }
- fwrite (((gdcmValEntry *)tag)->GetValue().c_str(),
- (size_t)lgr ,(size_t)1, _fp); // Elem value
+ return TagHT.find(key)->second;
}
/**
- * \brief Writes in a file (according to the requested format)
- * a single gdcmDocEntry passed as argument.
- * \sa WriteEntryValue, WriteEntryTagVRLength.
- * @param tag Pointer on the gdcmDocEntry to be written
- * @param _fp Already open file pointer
- * @param type type of the File to be written
+ * \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.
*/
-
-bool gdcmDocument::WriteEntry(gdcmDocEntry *tag, FILE *_fp,FileType type)
+ValEntry* Document::GetValEntryByNumber(uint16_t group,
+ uint16_t element)
{
- guint32 length = tag->GetLength();
-
- if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(tag) )
+ DocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ if ( !currentEntry )
{
- // The value of a tag MUST (see the DICOM norm) be an odd number of
- // bytes. When this is not the case, pad with an additional byte:
- if(length%2==1) {
- ValEntry->SetValue(ValEntry->GetValue()+"\0");
- ValEntry->SetLength(ValEntry->GetReadLength()+1);
- }
- WriteEntryTagVRLength(ValEntry, _fp, type);
- WriteEntryValue(ValEntry, _fp, type);
- return true;
+ return 0;
}
-
- if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) )
+ if ( ValEntry* valEntry = dynamic_cast<ValEntry*>(currentEntry) )
{
- /// \todo FIXME : when voidArea belong to gdcmBinEntry only, fix
- /// voidArea length
- //
- // The value of a tag MUST (see the DICOM norm) be an odd number of
- // bytes. When this is not the case, pad with an additional byte:
-/*
- if(length%2==1) {
- tag->SetValue(tag->GetValue()+"\0");
- tag->SetLength(tag->GetReadLength()+1);
- }
-*/
- WriteEntryTagVRLength(tag, _fp, type);
- WriteEntryValue(tag, _fp, type);
- return true;
+ return valEntry;
}
+ dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry.");
+
+ return 0;
}
/**
- * \brief writes on disc according to the requested format
- * (ACR-NEMA, ExplicitVR, ImplicitVR) the image
- * using the Chained List
- * \warning does NOT add the missing elements in the header :
- * it's up to the user doing it !
- * (function CheckHeaderCoherence to be written)
- * \warning DON'T try, right now, to write a DICOM image
- * from an ACR Header (meta elements will be missing!)
- * @param type type of the File to be written
- * (ACR-NEMA, ExplicitVR, ImplicitVR)
- * @param _fp already open file pointer
+ * \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.
+ * @return
*/
-
-bool gdcmDocument::WriteEntries(FILE *_fp,FileType type)
-{
- /// \todo FIXME : explore recursively the whole structure...
- /// \todo (?) check write failures (after *each* fwrite)
-
- dbg.Verbose(0, "gdcmDocument::WriteEntries: entering.");
- for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it )
- {
- gdcmDocEntry * entry = it->second;
- entry->Print();
-
- if ( type == gdcmACR ){
- if (entry->GetGroup() < 0x0008)
- // Ignore pure DICOM V3 groups
- continue;
- if (entry->GetGroup() %2)
- // Ignore the "shadow" groups
- continue;
- if (entry->GetVR() == "SQ" ) // ignore Sequences
- continue;
- }
- if (! WriteEntry(entry, _fp, type) ) {
- dbg.Verbose(0, "gdcmDocument::WriteEntries: write failure.");
- return false;
- }
- }
- return true;
-}
-
+void Document::LoadDocEntrySafe(DocEntry * entry)
+{
+ long PositionOnEntry = ftell(Fp);
+ LoadDocEntry(entry);
+ fseek(Fp, PositionOnEntry, SEEK_SET);
+}
/**
* \brief Swaps back the bytes of 4-byte long integer accordingly to
* processor order.
* @return The properly swaped 32 bits integer.
*/
-guint32 gdcmDocument::SwapLong(guint32 a) {
- switch (sw) {
+uint32_t Document::SwapLong(uint32_t a)
+{
+ switch (SwapCode)
+ {
case 0 :
break;
case 4321 :
break;
case 2143 :
- a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
+ a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
break;
default :
- std::cout << "swapCode= " << sw << std::endl;
- dbg.Error(" gdcmDocument::SwapLong : unset swap code");
- a=0;
+ //std::cout << "swapCode= " << SwapCode << std::endl;
+ dbg.Error(" Document::SwapLong : unset swap code");
+ a = 0;
}
- return(a);
-}
+ return a;
+}
/**
* \brief Unswaps back the bytes of 4-byte long integer accordingly to
* processor order.
* @return The properly unswaped 32 bits integer.
*/
-guint32 gdcmDocument::UnswapLong(guint32 a) {
- return (SwapLong(a));
+uint32_t Document::UnswapLong(uint32_t a)
+{
+ return SwapLong(a);
}
/**
* \brief Swaps the bytes so they agree with the processor order
* @return The properly swaped 16 bits integer.
*/
-guint16 gdcmDocument::SwapShort(guint16 a) {
- if ( (sw==4321) || (sw==2143) )
- a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
- return (a);
+uint16_t Document::SwapShort(uint16_t a)
+{
+ if ( SwapCode == 4321 || SwapCode == 2143 )
+ {
+ a = ((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) );
+ }
+ return a;
}
/**
* \brief Unswaps the bytes so they agree with the processor order
* @return The properly unswaped 16 bits integer.
*/
-guint16 gdcmDocument::UnswapShort(guint16 a) {
- return (SwapShort(a));
+uint16_t Document::UnswapShort(uint16_t a)
+{
+ return SwapShort(a);
}
//-----------------------------------------------------------------------------
/**
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
- * @return false if file is not ACR-NEMA / PAPYRUS / DICOM
+ * @return length of the parsed set.
*/
-
-long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
-
- gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
- gdcmValEntry *vl;
- gdcmBinEntry *bn;
- gdcmSeqEntry *sq;
- VRKey vr;
- long l;
- int depth;
-
- depth = set->GetDepthLevel();
- while (true) {
+void Document::ParseDES(DocEntrySet *set,
+ long offset,
+ long l_max,
+ bool delim_mode)
+{
+ DocEntry *newDocEntry = 0;
- if ( !delim_mode && ftell(fp)-offset >= l_max) {
- break;
+ while (true)
+ {
+ if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ {
+ break;
}
- NewDocEntry = ReadNextDocEntry( );
- if (!NewDocEntry)
+ newDocEntry = ReadNextDocEntry( );
+ if ( !newDocEntry )
+ {
break;
+ }
- vr = NewDocEntry->GetVR();
- if (vr!="SQ") {
+ VRKey vr = newDocEntry->GetVR();
+ if ( vr != "SQ" )
+ {
- if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) )
+ if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) )
{
- /////// ValEntry
- vl= new gdcmValEntry(NewDocEntry->GetDictEntry());
- vl->Copy(NewDocEntry);
- vl->SetDepthLevel(depth);
- set->AddEntry(vl);
- LoadDocEntry(vl);
- if (/*!delim_mode && */vl->isItemDelimitor())
+ /////////////////////// 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 ) )
+ {
+ (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 ) )
+ {
+ newValEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newValEntry->GetKey() );
+ }
+
+ set->AddEntry( newValEntry );
+ LoadDocEntry( newValEntry );
+ if (newValEntry->IsItemDelimitor())
+ {
break;
- if ( !delim_mode && ftell(fp)-offset >= l_max)
+ }
+ if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
{
break;
}
}
else
{
- if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
+ if ( ! Global::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
{
////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, "
+ dbg.Verbose(0, "Document::ParseDES: neither Valentry, "
"nor BinEntry. Probably unknown VR.");
}
- ////// BinEntry or UNKOWN VR:
- bn = new gdcmBinEntry(NewDocEntry->GetDictEntry());
- bn->Copy(NewDocEntry);
- set->AddEntry(bn);
- LoadDocEntry(bn);
+ //////////////////// 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 ) )
+ {
+ (void)dummy;
+ newBinEntry->SetKey( newBinEntry->GetKey() );
+ }
+ // but when "this" is a SQItem, we are inserting this new
+ // valEntry in a sequence item, and the kay has the
+ // generalized form (refer to \ref BaseTagKey):
+ if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ {
+ newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newBinEntry->GetKey() );
+ }
+
+ set->AddEntry( newBinEntry );
+ LoadDocEntry( newBinEntry );
}
- if (NewDocEntry->GetGroup() == 0x7fe0 &&
- NewDocEntry->GetElement() == 0x0010 )
+ if ( ( newDocEntry->GetGroup() == 0x7fe0 )
+ && ( newDocEntry->GetElement() == 0x0010 ) )
{
- if (NewDocEntry->GetLength()==0xffffffff)
- // Broken US.3405.1.dcm
- Parse7FE0(); // to skip the pixels
- // (multipart JPEG/RLE are trouble makers)
+ if ( IsRLELossLessTransferSyntax() )
+ {
+ long PositionOnEntry = ftell(Fp);
+ fseek( Fp, newDocEntry->GetOffset(), SEEK_SET );
+ ComputeRLEInfo();
+ fseek( Fp, PositionOnEntry, SEEK_SET );
+ }
+ else
+ if ( IsJPEGTransferSyntax() )
+ {
+ long PositionOnEntry = ftell(Fp);
+ fseek( Fp, newDocEntry->GetOffset(), SEEK_SET );
+ ComputeJPEGFragmentInfo();
+ fseek( Fp, PositionOnEntry, SEEK_SET );
+ }
}
- else
+
+ // Just to make sure we are at the beginning of next entry.
+ SkipToNextDocEntry(newDocEntry);
+ }
+ else
+ {
+ // VR = "SQ"
+ unsigned long l = newDocEntry->GetReadLength();
+ if ( l != 0 ) // don't mess the delim_mode for zero-length sequence
{
- // to be sure we are at the beginning
- SkipToNextDocEntry(NewDocEntry);
- l = NewDocEntry->GetFullLength();
- }
- } else { // VR = "SQ"
-
- l=NewDocEntry->GetReadLength();
- if (l != 0) // don't mess the delim_mode for zero-length sequence
- if (l == 0xffffffff)
+ if ( l == 0xffffffff )
+ {
delim_mode = true;
+ }
else
+ {
delim_mode = false;
+ }
+ }
// no other way to create it ...
- sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry(),
- set->GetDepthLevel());
- sq->Copy(NewDocEntry);
- sq->SetDelimitorMode(delim_mode);
- sq->SetDepthLevel(depth);
+ 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 ) )
+ {
+ (void)dummy;
+ newSeqEntry->SetDepthLevel( 1 );
+ newSeqEntry->SetKey( newSeqEntry->GetKey() );
+ }
+ // But when "set" is allready a SQItem, we are building a nested
+ // sequence, and hence the depth level of the new SeqEntry
+ // we are building, is one level deeper:
+ if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ {
+ newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
+ newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newSeqEntry->GetKey() );
+ }
- if (l != 0)
+ if ( l != 0 )
{ // Don't try to parse zero-length sequences
- long lgt = ParseSQ( sq,
- NewDocEntry->GetOffset(),
- l, delim_mode);
+ ParseSQ( newSeqEntry,
+ newDocEntry->GetOffset(),
+ l, delim_mode);
}
- // FIXME : on en fait quoi, de lgt ?
- set->AddEntry(sq);
- if ( !delim_mode && ftell(fp)-offset >= l_max)
+ set->AddEntry( newSeqEntry );
+ if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
{
break;
}
}
+ delete newDocEntry;
}
- delete NewDocEntry;
- return l; // ??
}
/**
* \brief Parses a Sequence ( SeqEntry after SeqEntry)
* @return parsed length for this level
*/
-long gdcmDocument::ParseSQ(gdcmSeqEntry *set,
- long offset, long l_max, bool delim_mode)
+void Document::ParseSQ( SeqEntry* seqEntry,
+ long offset, long l_max, bool delim_mode)
{
int SQItemNumber = 0;
-
- gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
- gdcmSQItem *itemSQ;
bool dlm_mod;
- int lgr, l, lgth;
- int depth = set->GetDepthLevel();
-
- while (true) {
- NewDocEntry = ReadNextDocEntry();
- if(delim_mode) {
- if (NewDocEntry->isSequenceDelimitor()) {
- /// \todo add the Sequence Delimitor
- /// \todo find the trick to put it properly !
- set->SetSequenceDelimitationItem(NewDocEntry);
+
+ while (true)
+ {
+ DocEntry* newDocEntry = ReadNextDocEntry();
+ if ( !newDocEntry )
+ {
+ // FIXME Should warn user
+ break;
+ }
+ if( delim_mode )
+ {
+ if ( newDocEntry->IsSequenceDelimitor() )
+ {
+ seqEntry->SetSequenceDelimitationItem( newDocEntry );
break;
- }
+ }
}
- if (!delim_mode && (ftell(fp)-offset) >= l_max) {
+ if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ {
break;
}
- itemSQ = new gdcmSQItem(set->GetDepthLevel());
- itemSQ->AddEntry(NewDocEntry);
- /// \todo no value, no voidArea. Think of it while printing !
- l= NewDocEntry->GetReadLength();
+ SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
+ std::ostringstream newBase;
+ newBase << seqEntry->GetKey()
+ << "/"
+ << SQItemNumber
+ << "#";
+ itemSQ->SetBaseTagKey( newBase.str() );
+ unsigned int l = newDocEntry->GetReadLength();
- if (l == 0xffffffff)
+ if ( l == 0xffffffff )
+ {
dlm_mod = true;
+ }
else
- dlm_mod=false;
+ {
+ dlm_mod = false;
+ }
- lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod);
+ ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
- set->AddEntry(itemSQ,SQItemNumber);
- SQItemNumber ++;
- if (!delim_mode && (ftell(fp)-offset) >= l_max) {
+ seqEntry->AddEntry( itemSQ, SQItemNumber );
+ SQItemNumber++;
+ if ( !delim_mode && ( ftell(Fp) - offset ) >= l_max )
+ {
break;
}
}
- lgth = ftell(fp) - offset;
- return(lgth);
}
/**
* \brief Loads the element content if its length doesn't exceed
- * the value specified with gdcmDocument::SetMaxSizeLoadEntry()
- * @param Entry Header Entry (Dicom Element) to be dealt with
+ * the value specified with Document::SetMaxSizeLoadEntry()
+ * @param entry Header Entry (Dicom Element) to be dealt with
*/
-void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) {
+void Document::LoadDocEntry(DocEntry* entry)
+{
size_t item_read;
- guint16 group = Entry->GetGroup();
- std::string vr= Entry->GetVR();
- guint32 length = Entry->GetLength();
+ uint16_t group = entry->GetGroup();
+ std::string vr = entry->GetVR();
+ uint32_t length = entry->GetLength();
- fseek(fp, (long)Entry->GetOffset(), SEEK_SET);
+ fseek(Fp, (long)entry->GetOffset(), SEEK_SET);
// A SeQuence "contains" a set of Elements.
// (fffe e000) tells us an Element is beginning
// (fffe e00d) tells us an Element just ended
// (fffe e0dd) tells us the current SeQuence just ended
- if( group == 0xfffe ) {
+ if( group == 0xfffe )
+ {
// NO more value field for SQ !
- //Entry->SetValue("gdcm::Skipped");
- // appel recursif de Load Value
- // (meme pb que pour le parsing)
return;
}
// When the length is zero things are easy:
- if ( length == 0 ) {
- ((gdcmValEntry *)Entry)->SetValue("");
+ if ( length == 0 )
+ {
+ ((ValEntry *)entry)->SetValue("");
return;
}
// The elements whose length is bigger than the specified upper bound
// are not loaded. Instead we leave a short notice of the offset of
// the element content and it's length.
- if (length > MaxSizeLoadEntry) {
- if (gdcmValEntry* ValEntryPtr = dynamic_cast< gdcmValEntry* >(Entry) )
+
+ std::ostringstream s;
+ if (length > MaxSizeLoadEntry)
+ {
+ if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) )
+ {
+ //s << "gdcm::NotLoaded (BinEntry)";
+ s << GDCM_NOTLOADED;
+ s << " Address:" << (long)entry->GetOffset();
+ s << " Length:" << entry->GetLength();
+ 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) )
{
- std::ostringstream s;
- s << "gdcm::NotLoaded.";
- s << " Address:" << (long)Entry->GetOffset();
- s << " Length:" << Entry->GetLength();
- s << " x(" << std::hex << Entry->GetLength() << ")";
- ValEntryPtr->SetValue(s.str());
+ // s << "gdcm::NotLoaded. (ValEntry)";
+ s << GDCM_NOTLOADED;
+ s << " Address:" << (long)entry->GetOffset();
+ s << " Length:" << entry->GetLength();
+ s << " x(" << std::hex << entry->GetLength() << ")";
+ valEntryPtr->SetValue(s.str());
+ }
+ else
+ {
+ // fusible
+ std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry "
+ << "nor a ValEntry ?! Should never print that !" << std::endl;
}
+
// to be sure we are at the end of the value ...
- fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET);
-
+ fseek(Fp,(long)entry->GetOffset()+(long)entry->GetLength(),SEEK_SET);
+ return;
+ }
+
+ // When we find a BinEntry not very much can be done :
+ if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) )
+ {
+ s << GDCM_BINLOADED;
+ binEntryPtr->SetValue(s.str());
+ LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
return;
}
- // Any compacter code suggested (?)
- if ( IsDocEntryAnInteger(Entry) ) {
- guint32 NewInt;
- std::ostringstream s;
+ /// \todo Any compacter code suggested (?)
+ if ( IsDocEntryAnInteger(entry) )
+ {
+ uint32_t NewInt;
int nbInt;
- // When short integer(s) are expected, read and convert the following
- // n *two characters properly i.e. as short integers as opposed to strings.
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- if (vr == "US" || vr == "SS") {
+ // When short integer(s) are expected, read and convert the following
+ // n *two characters properly i.e. consider them as short integers as
+ // opposed to strings.
+ // Elements with Value Multiplicity > 1
+ // contain a set of integers (not a single one)
+ if (vr == "US" || vr == "SS")
+ {
nbInt = length / 2;
NewInt = ReadInt16();
s << NewInt;
- if (nbInt > 1){
- for (int i=1; i < nbInt; i++) {
+ if (nbInt > 1)
+ {
+ for (int i=1; i < nbInt; i++)
+ {
s << '\\';
NewInt = ReadInt16();
s << NewInt;
}
}
}
- // When integer(s) are expected, read and convert the following
- // n * four characters properly i.e. as integers as opposed to strings.
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- else if (vr == "UL" || vr == "SL") {
+ // See above comment on multiple integers (mutatis mutandis).
+ else if (vr == "UL" || vr == "SL")
+ {
nbInt = length / 4;
NewInt = ReadInt32();
s << NewInt;
- if (nbInt > 1) {
- for (int i=1; i < nbInt; i++) {
+ if (nbInt > 1)
+ {
+ for (int i=1; i < nbInt; i++)
+ {
s << '\\';
NewInt = ReadInt32();
s << NewInt;
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
- ((gdcmValEntry *)Entry)->SetValue(s.str());
+ ((ValEntry *)entry)->SetValue(s.str());
return;
}
// We need an additional byte for storing \0 that is not on disk
- std::string NewValue(length,0);
- item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp);
- if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmDocument::LoadElementValue","unread element value");
- ((gdcmValEntry *)Entry)->SetValue("gdcm::UnRead");
- return;
- }
+ //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* !!!
+ char *str = new char[length+1];
+ item_read = fread(str, (size_t)length, (size_t)1, Fp);
+ str[length] = '\0';
+ std::string newValue = str;
+ delete[] str;
+ if ( ValEntry* valEntry = dynamic_cast<ValEntry* >(entry) )
+ {
+ if ( item_read != 1 )
+ {
+ dbg.Verbose(1, "Document::LoadDocEntry",
+ "unread element value");
+ valEntry->SetValue(GDCM_UNREAD);
+ return;
+ }
- if( (vr == "UI") ) // Because of correspondance with the VR dic
- ((gdcmValEntry *)Entry)->SetValue(NewValue.c_str());
+ if( vr == "UI" )
+ {
+ // Because of correspondance with the VR dic
+ valEntry->SetValue(newValue);
+ }
+ else
+ {
+ valEntry->SetValue(newValue);
+ }
+ }
else
- ((gdcmValEntry *)Entry)->SetValue(NewValue);
+ {
+ dbg.Error(true, "Document::LoadDocEntry"
+ "Should have a ValEntry, here !");
+ }
}
/**
* \brief Find the value Length of the passed Header Entry
- * @param Entry Header Entry whose length of the value shall be loaded.
+ * @param entry Header Entry whose length of the value shall be loaded.
*/
- void gdcmDocument::FindDocEntryLength (gdcmDocEntry *Entry) {
- guint16 element = Entry->GetElement();
- //guint16 group = Entry->GetGroup(); //FIXME
- std::string vr = Entry->GetVR();
- guint16 length16;
-
+void Document::FindDocEntryLength( DocEntry *entry )
+ throw ( FormatError )
+{
+ uint16_t element = entry->GetElement();
+ std::string vr = entry->GetVR();
+ uint16_t length16;
- if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) )
+ if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
- if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") )
+ if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" )
{
- // The following reserved two bytes (see PS 3.5-2001, section
- // 7.1.2 Data element structure with explicit vr p27) must be
+ // The following reserved two bytes (see PS 3.5-2003, section
+ // "7.1.2 Data element structure with explicit vr", p 27) must be
// skipped before proceeding on reading the length on 4 bytes.
- fseek(fp, 2L, SEEK_CUR);
- guint32 length32 = ReadInt32();
+ fseek(Fp, 2L, SEEK_CUR);
+ uint32_t length32 = ReadInt32();
- if ( (vr == "OB") && (length32 == 0xffffffff) )
+ if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
{
- Entry->SetLength(FindDocEntryLengthOB());
+ uint32_t lengthOB;
+ try
+ {
+ /// \todo rename that to FindDocEntryLengthOBOrOW since
+ /// the above test is on both OB and OW...
+ lengthOB = FindDocEntryLengthOB();
+ }
+ catch ( FormatUnexpected )
+ {
+ // Computing the length failed (this happens with broken
+ // files like gdcm-JPEG-LossLess3a.dcm). We still have a
+ // chance to get the pixels by deciding the element goes
+ // until the end of the file. Hence we artificially fix the
+ // the length and proceed.
+ long currentPosition = ftell(Fp);
+ fseek(Fp,0L,SEEK_END);
+ long lengthUntilEOF = ftell(Fp) - currentPosition;
+ fseek(Fp, currentPosition, SEEK_SET);
+ entry->SetLength(lengthUntilEOF);
+ return;
+ }
+ entry->SetLength(lengthOB);
return;
}
- FixDocEntryFoundLength(Entry, length32);
+ FixDocEntryFoundLength(entry, length32);
return;
}
// 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 ( element == 0x0000 && length16 == 0x0400 )
{
- if ( ! IsExplicitVRBigEndianTransferSyntax() )
+ if ( !IsExplicitVRBigEndianTransferSyntax() )
{
- dbg.Verbose(0, "gdcmDocument::FindLength", "not explicit VR");
- errno = 1;
+ 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.
- guint16 CorrectGroup = SwapShort(Entry->GetGroup());
- guint16 CorrectElem = SwapShort(Entry->GetElement());
- gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup,
- CorrectElem);
- if (!NewTag)
+ 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);
+ newTag = NewVirtualDictEntry(correctGroup, correctElem);
}
// FIXME this can create a memory leaks on the old entry that be
// left unreferenced.
- Entry->SetDictEntry(NewTag);
+ entry->SetDictEntry( newTag );
}
- // Heuristic: well some files are really ill-formed.
+ // Heuristic: well, some files are really ill-formed.
if ( length16 == 0xffff)
{
+ // 0xffff means that we deal with 'Unknown Length' Sequence
length16 = 0;
- //dbg.Verbose(0, "gdcmDocument::FindLength",
- // "Erroneous element length fixed.");
- // Actually, length= 0xffff means that we deal with
- // Unknown Sequence Length
}
- FixDocEntryFoundLength(Entry, (guint32)length16);
+ FixDocEntryFoundLength( entry, (uint32_t)length16 );
return;
}
else
// not coexist in a Data Set and Data Sets nested within it".]
// Length is on 4 bytes.
- FixDocEntryFoundLength(Entry, ReadInt32());
+ FixDocEntryFoundLength( entry, ReadInt32() );
return;
}
}
/**
* \brief Find the Value Representation of the current Dicom Element.
- * @param Entry
+ * @param entry
*/
-void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry)
+void Document::FindDocEntryVR( DocEntry *entry )
{
- if (filetype != gdcmExplicitVR)
+ if ( Filetype != ExplicitVR )
+ {
return;
+ }
- char VR[3];
+ char vr[3];
- long PositionOnEntry = ftell(fp);
+ long positionOnEntry = ftell(Fp);
// 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
// is in explicit VR and try to fix things if it happens not to be
// the case.
- (void)fread (&VR, (size_t)2,(size_t)1, fp);
- VR[2]=0;
- if(!CheckDocEntryVR(Entry,VR))
+ fread (vr, (size_t)2,(size_t)1, Fp);
+ vr[2] = 0;
+
+ if( !CheckDocEntryVR(entry, vr) )
{
- fseek(fp, PositionOnEntry, SEEK_SET);
+ 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();
+ if ( entry->IsVRUnknown() )
+ {
+ entry->SetVR("Implicit");
+ }
+ entry->SetImplicitVR();
}
}
* \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 entry Header Entry to check
* @param vr Dicom Value Representation
* @return false if the VR is incorrect of if the VR isn't referenced
* otherwise, it returns true
*/
-bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, VRKey vr)
+bool Document::CheckDocEntryVR(DocEntry *entry, VRKey vr)
{
- char msg[100]; // for sprintf
- bool RealExplicit = true;
+ 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
// 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;
+ if ( !isalpha(vr[0]) && !isalpha(vr[1]) )
+ {
+ realExplicit = false;
+ }
// CLEANME searching the dicom_vr at each occurence is expensive.
// PostPone this test in an optional integrity check at the end
// of parsing or only in debug mode.
- if ( RealExplicit && !gdcmGlobal::GetVR()->Count(vr) )
- RealExplicit= false;
+ if ( realExplicit && !Global::GetVR()->Count(vr) )
+ {
+ realExplicit = false;
+ }
- if ( !RealExplicit )
+ if ( !realExplicit )
{
// We thought this was explicit VR, but we end up with an
// implicit VR tag. Let's backtrack.
- sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
- Entry->GetGroup(),Entry->GetElement());
- dbg.Verbose(1, "gdcmDocument::FindVR: ",msg);
- if (Entry->GetGroup()%2 && Entry->GetElement() == 0x0000) { // Group length is UL !
- gdcmDictEntry* NewEntry = NewVirtualDictEntry(
- Entry->GetGroup(),Entry->GetElement(),
- "UL","FIXME","Group Length");
- Entry->SetDictEntry(NewEntry);
+ 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 );
}
- return(false);
+ return false;
}
- if ( Entry->IsVRUnknown() )
+ 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);
+ if( entry->GetElement() == 0x0000 )
+ {
+ // Group length is UL !
+ entry->SetVR("UL");
+ }
+ else
+ {
+ entry->SetVR(vr);
}
}
- else if ( Entry->GetVR() != vr )
+ else if ( entry->GetVR() != vr )
{
// The VR present in the file and the dictionary disagree. We assume
// the file writer knew best and use the VR of the file. Since it would
// be unwise to overwrite the VR of a dictionary (since it would
// compromise it's next user), we need to clone the actual DictEntry
// and change the VR for the read one.
- gdcmDictEntry* NewEntry = NewVirtualDictEntry(
- Entry->GetGroup(),Entry->GetElement(),
- vr,"FIXME",Entry->GetName());
- Entry->SetDictEntry(NewEntry);
+ DictEntry* newEntry = NewVirtualDictEntry(
+ entry->GetGroup(), entry->GetElement(),
+ vr, "FIXME", entry->GetName());
+ entry->SetDictEntry(newEntry);
}
- return(true);
+
+ return true;
}
/**
* \brief Get the transformed value of the header entry. The VR value
* is used to define the transformation to operate on the value
* \warning NOT end user intended method !
- * @param Entry
+ * @param entry entry to tranform
* @return Transformed entry value
*/
-std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry)
+std::string Document::GetDocEntryValue(DocEntry *entry)
{
- if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
+ if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
- std::string val=((gdcmValEntry *)Entry)->GetValue();
- std::string vr=Entry->GetVR();
- guint32 length = Entry->GetLength();
+ std::string val = ((ValEntry *)entry)->GetValue();
+ std::string vr = entry->GetVR();
+ uint32_t length = entry->GetLength();
std::ostringstream s;
int nbInt;
- // When short integer(s) are expected, read and convert the following
- // n * 2 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // as usual for standard multivaluated filels
- // Elements with Value Multiplicity > 1
- // contain a set of short integers (not a single one)
+ // When short integer(s) are expected, read and convert the following
+ // n * 2 bytes properly i.e. as a multivaluated strings
+ // (each single value is separated fromthe next one by '\'
+ // as usual for standard multivaluated filels
+ // Elements with Value Multiplicity > 1
+ // contain a set of short integers (not a single one)
- if (vr == "US" || vr == "SS")
+ if( vr == "US" || vr == "SS" )
{
- guint16 NewInt16;
+ uint16_t newInt16;
nbInt = length / 2;
for (int i=0; i < nbInt; i++)
{
- if(i!=0)
+ if( i != 0 )
+ {
s << '\\';
- NewInt16 = (val[2*i+0]&0xFF)+((val[2*i+1]&0xFF)<<8);
- NewInt16 = SwapShort(NewInt16);
- s << NewInt16;
+ }
+ newInt16 = ( val[2*i+0] & 0xFF ) + ( ( val[2*i+1] & 0xFF ) << 8);
+ newInt16 = SwapShort( newInt16 );
+ s << newInt16;
}
}
- // When integer(s) are expected, read and convert the following
- // n * 4 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // as usual for standard multivaluated filels
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- else if (vr == "UL" || vr == "SL")
+ // When integer(s) are expected, read and convert the following
+ // n * 4 bytes properly i.e. as a multivaluated strings
+ // (each single value is separated fromthe next one by '\'
+ // as usual for standard multivaluated filels
+ // Elements with Value Multiplicity > 1
+ // contain a set of integers (not a single one)
+ else if( vr == "UL" || vr == "SL" )
{
- guint32 NewInt32;
+ uint32_t newInt32;
nbInt = length / 4;
for (int i=0; i < nbInt; i++)
{
- if(i!=0)
+ if( i != 0)
+ {
s << '\\';
- NewInt32= (val[4*i+0]&0xFF)+((val[4*i+1]&0xFF)<<8)+
- ((val[4*i+2]&0xFF)<<16)+((val[4*i+3]&0xFF)<<24);
- NewInt32=SwapLong(NewInt32);
- s << NewInt32;
+ }
+ newInt32 = ( val[4*i+0] & 0xFF )
+ + (( val[4*i+1] & 0xFF ) << 8 )
+ + (( val[4*i+2] & 0xFF ) << 16 )
+ + (( val[4*i+3] & 0xFF ) << 24 );
+ newInt32 = SwapLong( newInt32 );
+ s << newInt32;
}
}
#ifdef GDCM_NO_ANSI_STRING_STREAM
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
- return(s.str());
+ return s.str();
}
- return(((gdcmValEntry *)Entry)->GetValue());
+ return ((ValEntry *)entry)->GetValue();
}
/**
* value is used to define the reverse transformation to operate on
* the value
* \warning NOT end user intended method !
- * @param Entry
+ * @param entry Entry to reverse transform
* @return Reverse transformed entry value
*/
-std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry)
+std::string Document::GetDocEntryUnvalue(DocEntry* entry)
{
- if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
+ if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
- std::string vr=Entry->GetVR();
- std::ostringstream s;
+ std::string vr = entry->GetVR();
std::vector<std::string> tokens;
+ std::ostringstream s;
- if (vr == "US" || vr == "SS")
+ if ( vr == "US" || vr == "SS" )
{
- guint16 NewInt16;
+ uint16_t newInt16;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
+ tokens.erase( tokens.begin(), tokens.end()); // clean any previous value
+ Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
+ for (unsigned int i=0; i<tokens.size(); i++)
{
- NewInt16 = atoi(tokens[i].c_str());
- s<<(NewInt16&0xFF)<<((NewInt16>>8)&0xFF);
+ newInt16 = atoi(tokens[i].c_str());
+ s << ( newInt16 & 0xFF )
+ << (( newInt16 >> 8 ) & 0xFF );
}
tokens.clear();
}
- if (vr == "UL" || vr == "SL")
+ if ( vr == "UL" || vr == "SL")
{
- guint32 NewInt32;
+ uint32_t newInt32;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\");
+ Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
- NewInt32 = atoi(tokens[i].c_str());
- s<<(char)(NewInt32&0xFF)<<(char)((NewInt32>>8)&0xFF)
- <<(char)((NewInt32>>16)&0xFF)<<(char)((NewInt32>>24)&0xFF);
+ newInt32 = atoi(tokens[i].c_str());
+ s << (char)( newInt32 & 0xFF )
+ << (char)(( newInt32 >> 8 ) & 0xFF )
+ << (char)(( newInt32 >> 16 ) & 0xFF )
+ << (char)(( newInt32 >> 24 ) & 0xFF );
}
tokens.clear();
}
#ifdef GDCM_NO_ANSI_STRING_STREAM
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
- return(s.str());
+ return s.str();
}
- return(((gdcmValEntry *)Entry)->GetValue());
+ return ((ValEntry *)entry)->GetValue();
}
/**
* \brief Skip a given Header Entry
* \warning NOT end user intended method !
- * @param entry
+ * @param entry entry to skip
*/
-void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry)
+void Document::SkipDocEntry(DocEntry *entry)
{
SkipBytes(entry->GetLength());
}
/**
* \brief Skips to the begining of the next Header Entry
* \warning NOT end user intended method !
- * @param entry
+ * @param entry entry to skip
*/
-void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry)
+void Document::SkipToNextDocEntry(DocEntry *entry)
{
- (void)fseek(fp, (long)(entry->GetOffset()), SEEK_SET);
- (void)fseek(fp, (long)(entry->GetReadLength()), SEEK_CUR);
+ fseek(Fp, (long)(entry->GetOffset()), SEEK_SET);
+ fseek(Fp, (long)(entry->GetReadLength()), SEEK_CUR);
}
-/**
- * \brief Loads the value for a a given VLEntry
- * \warning NOT end user intended method !
- * @param entry
- */
-void gdcmDocument::LoadVLEntry(gdcmDocEntry *entry)
-{
- //SkipBytes(entry->GetLength());
- LoadDocEntry(entry);
-}
/**
* \brief When the length of an element value is obviously wrong (because
* the parser went Jabberwocky) one can hope improving things by
* applying some heuristics.
+ * @param entry entry to check
+ * @param foundLength fist assumption about length
*/
-void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry,
- guint32 FoundLength)
+void Document::FixDocEntryFoundLength(DocEntry *entry,
+ uint32_t foundLength)
{
- Entry->SetReadLength(FoundLength); // will be updated only if a bug is found
- if ( FoundLength == 0xffffffff) {
- FoundLength = 0;
+ entry->SetReadLength( foundLength ); // will be updated only if a bug is found
+ if ( foundLength == 0xffffffff)
+ {
+ foundLength = 0;
}
- guint16 gr =Entry->GetGroup();
- guint16 el =Entry->GetElement();
+ uint16_t gr = entry->GetGroup();
+ uint16_t el = entry->GetElement();
- if (FoundLength%2) {
+ if ( foundLength % 2)
+ {
std::ostringstream s;
s << "Warning : Tag with uneven length "
- << FoundLength
+ << foundLength
<< " in x(" << std::hex << gr << "," << el <<")" << std::dec;
dbg.Verbose(0, s.str().c_str());
}
// are no longer in user (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 ( foundLength == 13)
+ {
+ // Only happens for this length !
+ if ( entry->GetGroup() != 0x0008
+ || ( entry->GetElement() != 0x0070
+ && entry->GetElement() != 0x0080 ) )
{
- FoundLength = 10;
- Entry->SetReadLength(10); /// \todo a bug is to be fixed !?
+ 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 ( entry->GetGroup() == 0x0009
+ && ( entry->GetElement() == 0x1113
+ || entry->GetElement() == 0x1114 ) )
{
- FoundLength = 4;
- Entry->SetReadLength(4); /// \todo a bug is to be fixed !?
+ foundLength = 4;
+ entry->SetReadLength(4); /// \todo a bug is to be fixed !?
}
- //////// Deal with sequences, but only on users request:
- else
- if ( ( Entry->GetVR() == "SQ") && enableSequences)
+ else if ( entry->GetVR() == "SQ" )
{
- FoundLength = 0; // ReadLength is unchanged
+ foundLength = 0; // ReadLength is unchanged
}
//////// 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( entry->GetGroup() == 0xfffe )
{
// According to the norm, fffe|0000 shouldn't exist. BUT the Philips
// image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to
// causes extra troubles...
- if( Entry->GetElement() != 0x0000 )
+ if( entry->GetElement() != 0x0000 )
{
- FoundLength = 0;
+ foundLength = 0;
}
}
- Entry->SetUsableLength(FoundLength);
+ entry->SetUsableLength(foundLength);
}
/**
* \brief Apply some heuristics to predict whether the considered
* element value contains/represents an integer or not.
- * @param Entry The element value on which to apply the predicate.
+ * @param entry The element value on which to apply the predicate.
* @return The result of the heuristical predicate.
*/
-bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) {
- guint16 element = Entry->GetElement();
- guint16 group = Entry->GetGroup();
- std::string vr = Entry->GetVR();
- guint32 length = Entry->GetLength();
+bool Document::IsDocEntryAnInteger(DocEntry *entry)
+{
+ uint16_t element = entry->GetElement();
+ uint16_t group = entry->GetGroup();
+ 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 (length == 4)
+ if ( length == 4 )
+ {
return true;
+ }
else
{
// Allthough this should never happen, still some images have a
// encounter such an ill-formed image, we simply display a warning
// message and proceed on parsing (while crossing fingers).
std::ostringstream s;
- int filePosition = ftell(fp);
+ long filePosition = ftell(Fp);
s << "Erroneous Group Length element length on : (" \
<< std::hex << group << " , " << element
<< ") -before- position x(" << filePosition << ")"
<< "lgt : " << length;
- dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() );
+ dbg.Verbose(0, "Document::IsDocEntryAnInteger", s.str().c_str() );
}
}
- if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
+ if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" )
+ {
return true;
+ }
return false;
}
* @return
*/
- guint32 gdcmDocument::FindDocEntryLengthOB(void) {
+uint32_t Document::FindDocEntryLengthOB()
+ throw( FormatUnexpected )
+{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
- guint16 g;
- guint16 n;
- long PositionOnEntry = ftell(fp);
- bool FoundSequenceDelimiter = false;
- guint32 TotalLength = 0;
- guint32 ItemLength;
-
- while ( ! FoundSequenceDelimiter)
- {
- g = ReadInt16();
- n = ReadInt16();
- if (errno == 1)
- return 0;
- TotalLength += 4; // We even have to decount the group and element
+ long positionOnEntry = ftell(Fp);
+ bool foundSequenceDelimiter = false;
+ uint32_t totalLength = 0;
+
+ while ( !foundSequenceDelimiter )
+ {
+ uint16_t group;
+ uint16_t elem;
+ try
+ {
+ group = ReadInt16();
+ elem = ReadInt16();
+ }
+ catch ( FormatError )
+ {
+ throw FormatError("Document::FindDocEntryLengthOB()",
+ " group or element not present.");
+ }
+
+ // We have to decount the group and element we just read
+ totalLength += 4;
- if ( g != 0xfffe && g!=0xb00c ) //for bogus header
+ if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- char msg[100]; // for sprintf. Sorry
- sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n);
- dbg.Verbose(1, "gdcmDocument::FindLengthOB: ",msg);
- errno = 1;
- return 0;
+ 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.");
}
- if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) // for bogus header
- FoundSequenceDelimiter = true;
- else if ( n != 0xe000 )
+
+ if ( elem == 0xe0dd )
{
- char msg[100]; // for sprintf. Sorry
- sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",
- n, g,n);
- dbg.Verbose(1, "gdcmDocument::FindLengthOB: ",msg);
- errno = 1;
- return 0;
+ foundSequenceDelimiter = true;
+ }
+
+ uint32_t itemLength = ReadInt32();
+ // We add 4 bytes since we just read the ItemLength with ReadInt32
+ totalLength += itemLength + 4;
+ SkipBytes(itemLength);
+
+ if ( foundSequenceDelimiter )
+ {
+ break;
}
- ItemLength = ReadInt32();
- TotalLength += ItemLength + 4; // We add 4 bytes since we just read
- // the ItemLength with ReadInt32
- SkipBytes(ItemLength);
}
- fseek(fp, PositionOnEntry, SEEK_SET);
- return TotalLength;
+ fseek(Fp, positionOnEntry, SEEK_SET);
+ return totalLength;
}
/**
* (swaps it depending on processor endianity)
* @return read value
*/
-guint16 gdcmDocument::ReadInt16(void) {
- guint16 g;
- size_t item_read;
- item_read = fread (&g, (size_t)2,(size_t)1, fp);
- if ( item_read != 1 ) {
- if(ferror(fp))
- dbg.Verbose(0, "gdcmDocument::ReadInt16", " File Error");
- errno = 1;
- return 0;
+uint16_t Document::ReadInt16()
+ throw( FormatError )
+{
+ uint16_t g;
+ size_t item_read = fread (&g, (size_t)2,(size_t)1, Fp);
+ if ( item_read != 1 )
+ {
+ if( ferror(Fp) )
+ {
+ throw FormatError( "Document::ReadInt16()", " file error." );
+ }
+ throw FormatError( "Document::ReadInt16()", "EOF." );
}
- errno = 0;
- g = SwapShort(g);
+ g = SwapShort(g);
return g;
}
* (swaps it depending on processor endianity)
* @return read value
*/
-guint32 gdcmDocument::ReadInt32(void) {
- guint32 g;
- size_t item_read;
- item_read = fread (&g, (size_t)4,(size_t)1, fp);
- if ( item_read != 1 ) {
- if(ferror(fp))
- dbg.Verbose(0, "gdcmDocument::ReadInt32", " File Error");
- errno = 1;
- return 0;
+uint32_t Document::ReadInt32()
+ throw( FormatError )
+{
+ uint32_t g;
+ size_t item_read = fread (&g, (size_t)4,(size_t)1, Fp);
+ if ( item_read != 1 )
+ {
+ if( ferror(Fp) )
+ {
+ throw FormatError( "Document::ReadInt16()", " file error." );
+ }
+ throw FormatError( "Document::ReadInt32()", "EOF." );
}
- errno = 0;
g = SwapLong(g);
return g;
}
* \warning NOT end user intended method !
* @return
*/
-void gdcmDocument::SkipBytes(guint32 NBytes) {
+void Document::SkipBytes(uint32_t nBytes)
+{
//FIXME don't dump the returned value
- (void)fseek(fp, (long)NBytes, SEEK_CUR);
+ (void)fseek(Fp, (long)nBytes, SEEK_CUR);
}
/**
* \brief Loads all the needed Dictionaries
* \warning NOT end user intended method !
*/
-void gdcmDocument::Initialise(void)
+void Document::Initialise()
{
- RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
- RefShaDict = (gdcmDict*)0;
+ RefPubDict = Global::GetDicts()->GetDefaultPubDict();
+ RefShaDict = NULL;
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
}
/**
* it's neither ACR-NEMA nor DICOM
* true when we hope ours assuptions are OK
*/
-bool gdcmDocument::CheckSwap() {
-
+bool Document::CheckSwap()
+{
// The only guaranted way of finding the swap code is to find a
// group tag since we know it's length has to be of four bytes i.e.
// 0x00000004. Finding the swap code in then straigthforward. Trouble
// occurs when we can't find such group...
- guint32 x=4; // x : for ntohs
+ uint32_t x = 4; // x : for ntohs
bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
- guint32 s32;
- guint16 s16;
+ uint32_t s32;
+ uint16_t s16;
- int lgrLue;
- char *entCur;
char deb[HEADER_LENGTH_TO_READ];
// First, compare HostByteOrder and NetworkByteOrder in order to
// determine if we shall need to swap bytes (i.e. the Endian type).
- if (x==ntohs(x))
+ if ( x == ntohs(x) )
+ {
net2host = true;
+ }
else
- net2host = false;
+ {
+ 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".
- lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp);
+ int lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, Fp);
+ (void)lgrLue; //FIXME not used
- entCur = deb + 128;
- if(memcmp(entCur, "DICM", (size_t)4) == 0) {
- dbg.Verbose(1, "gdcmDocument::CheckSwap:", "looks like DICOM Version3");
+ char *entCur = deb + 128;
+ if( memcmp(entCur, "DICM", (size_t)4) == 0 )
+ {
+ dbg.Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3");
// Next, determine the value representation (VR). Let's skip to the
// first element (0002, 0000) and check there if we find "UL"
// but elem 0002,0010 (Transfert Syntax) tells us the file is
// *Implicit* VR. -and it is !-
- 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
+ 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*
// FIXME
- // Use gdcmDocument::dicom_vr to test all the possibilities
+ // Use Document::dicom_vr to test all the possibilities
// instead of just checking for UL, OB and UI !? group 0000
{
- filetype = gdcmExplicitVR;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ Filetype = ExplicitVR;
+ dbg.Verbose(1, "Document::CheckSwap:",
"explicit Value Representation");
}
else
{
- filetype = gdcmImplicitVR;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ Filetype = ImplicitVR;
+ dbg.Verbose(1, "Document::CheckSwap:",
"not an explicit Value Representation");
}
- if (net2host)
+ if ( net2host )
{
- sw = 4321;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ SwapCode = 4321;
+ dbg.Verbose(1, "Document::CheckSwap:",
"HostByteOrder != NetworkByteOrder");
- }
+ }
else
{
- sw = 0;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ SwapCode = 0;
+ dbg.Verbose(1, "Document::CheckSwap:",
"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);
+ rewind(Fp);
+ fseek (Fp, 132L, SEEK_SET);
return true;
} // End of DicomV3
// Alas, this is not a DicomV3 file and whatever happens there is no file
// preamble. We can reset the file position indicator to where the data
// is (i.e. the beginning of the file).
- dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not a DICOM Version3 file");
- rewind(fp);
+ dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file");
+ rewind(Fp);
// 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.
// We assume the array of char we are considering contains the binary
// representation of a 32 bits integer. Hence the following dirty
// trick :
- s32 = *((guint32 *)(entCur));
+ s32 = *((uint32_t *)(entCur));
- switch (s32) {
+ switch( s32 )
+ {
case 0x00040000 :
- sw = 3412;
- filetype = gdcmACR;
+ SwapCode = 3412;
+ Filetype = ACR;
return true;
case 0x04000000 :
- sw = 4321;
- filetype = gdcmACR;
+ SwapCode = 4321;
+ Filetype = ACR;
return true;
case 0x00000400 :
- sw = 2143;
- filetype = gdcmACR;
+ SwapCode = 2143;
+ Filetype = ACR;
return true;
case 0x00000004 :
- sw = 0;
- filetype = gdcmACR;
+ SwapCode = 0;
+ Filetype = ACR;
return true;
default :
-
- // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
- // It is time for despaired wild guesses.
- // 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
- // to determine ' sw' 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-)
- // the file IS NOT ACR-NEMA nor DICOM V3
- // Find a trick to tell it the caller...
+ // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
+ // It is time for despaired wild guesses.
+ // 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
+ // 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-)
+ // the file IS NOT ACR-NEMA nor DICOM V3
+ // Find a trick to tell it the caller...
- s16 = *((guint16 *)(deb));
+ s16 = *((uint16_t *)(deb));
- switch (s16) {
- case 0x0002 :
- case 0x0004 :
- case 0x0008 :
- sw = 0;
- filetype = gdcmACR;
- return true;
- case 0x0200 :
- case 0x0400 :
- case 0x0800 :
- sw = 4321;
- filetype = gdcmACR;
- return true;
- default :
- dbg.Verbose(0, "gdcmDocument::CheckSwap:",
+ switch ( s16 )
+ {
+ case 0x0002 :
+ case 0x0004 :
+ case 0x0008 :
+ SwapCode = 0;
+ Filetype = ACR;
+ return true;
+ case 0x0200 :
+ case 0x0400 :
+ case 0x0800 :
+ SwapCode = 4321;
+ Filetype = ACR;
+ return true;
+ default :
+ dbg.Verbose(0, "Document::CheckSwap:",
"ACR/NEMA unfound swap info (Really hopeless !)");
- filetype = gdcmUnknown;
- return false;
- }
-
- // Then the only info we have is the net2host one.
- //if (! net2host )
- // sw = 0;
+ Filetype = Unknown;
+ return false;
+ }
+ // Then the only info we have is the net2host one.
+ //if (! net2host )
+ // SwapCode = 0;
//else
- // sw = 4321;
+ // SwapCode = 4321;
//return;
}
}
* \brief Restore the unproperly loaded values i.e. the group, the element
* and the dictionary entry depending on them.
*/
-void gdcmDocument::SwitchSwapToBigEndian(void)
+void Document::SwitchSwapToBigEndian()
{
- dbg.Verbose(1, "gdcmDocument::SwitchSwapToBigEndian",
+ dbg.Verbose(1, "Document::SwitchSwapToBigEndian",
"Switching to BigEndian mode.");
- if ( sw == 0 )
+ if ( SwapCode == 0 )
{
- sw = 4321;
- return;
+ SwapCode = 4321;
}
- if ( sw == 4321 )
+ else if ( SwapCode == 4321 )
{
- sw = 0;
- return;
+ SwapCode = 0;
}
- if ( sw == 3412 )
+ else if ( SwapCode == 3412 )
{
- sw = 2143;
- return;
+ SwapCode = 2143;
+ }
+ else if ( SwapCode == 2143 )
+ {
+ SwapCode = 3412;
}
- if ( sw == 2143 )
- sw = 3412;
}
/**
* \brief during parsing, Header Elements too long are not loaded in memory
- * @param NewSize
+ * @param newSize
*/
-void gdcmDocument::SetMaxSizeLoadEntry(long NewSize)
+void Document::SetMaxSizeLoadEntry(long newSize)
{
- if (NewSize < 0)
+ if ( newSize < 0 )
+ {
return;
- if ((guint32)NewSize >= (guint32)0xffffffff)
+ }
+ if ((uint32_t)newSize >= (uint32_t)0xffffffff )
{
MaxSizeLoadEntry = 0xffffffff;
return;
}
- MaxSizeLoadEntry = NewSize;
+ MaxSizeLoadEntry = newSize;
}
/**
* \brief Header Elements too long will not be printed
- * \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE
- * @param NewSize
+ * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE
+ * @param newSize
*/
-void gdcmDocument::SetMaxSizePrintEntry(long NewSize)
+void Document::SetMaxSizePrintEntry(long newSize)
{
- if (NewSize < 0)
+ //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME
+ if ( newSize < 0 )
+ {
return;
- if ((guint32)NewSize >= (guint32)0xffffffff)
+ }
+ if ((uint32_t)newSize >= (uint32_t)0xffffffff )
{
MaxSizePrintEntry = 0xffffffff;
return;
}
- MaxSizePrintEntry = NewSize;
+ MaxSizePrintEntry = newSize;
}
* gets the VR, gets the length, gets the offset value)
* @return On succes the newly created DocEntry, NULL on failure.
*/
-gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) {
- guint16 g,n;
- gdcmDocEntry *NewEntry;
- g = ReadInt16();
- n = ReadInt16();
-
- if (errno == 1)
- // We reached the EOF (or an error occured) therefore
- // header parsing has to be considered as finished.
- return (gdcmDocEntry *)0;
-
-// Pb : how to propagate the element length (used in SkipDocEntry)
-// direct call to SkipBytes ?
-
-// if (ignoreShadow == 1 && g%2 ==1)
- // if user wants to skip shadow groups
- // and current element *is* a shadow element
- // we don't create anything
-// return (gdcmDocEntry *)1; // to tell caller it's NOT finished
-
- NewEntry = NewDocEntryByNumber(g, n);
- FindDocEntryVR(NewEntry);
- FindDocEntryLength(NewEntry);
-
- if (errno == 1) {
- // Call it quits
- delete NewEntry;
- return NULL;
- }
- NewEntry->SetOffset(ftell(fp));
- return NewEntry;
-}
-
-/**
- * \brief Build a new Element Value from all the low level arguments.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Name Name of the underlying DictEntry
- */
-gdcmDocEntry *gdcmDocument::NewDocEntryByName(std::string Name)
+DocEntry* Document::ReadNextDocEntry()
{
- gdcmDictEntry *NewTag = GetDictEntryByName(Name);
- if (!NewTag)
- NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name);
+ uint16_t group;
+ uint16_t elem;
- gdcmDocEntry* NewEntry = new gdcmDocEntry(NewTag);
- if (!NewEntry)
+ try
{
- dbg.Verbose(1, "gdcmDocument::ObtainDocEntryByName",
- "failed to allocate gdcmDocEntry");
- return (gdcmDocEntry *)0;
+ group = ReadInt16();
+ elem = ReadInt16();
}
- return NewEntry;
-}
-
-/**
- * \brief Request a new virtual dict entry to the dict set
- * @param group group number of the underlying DictEntry
- * @param element element number of the underlying DictEntry
- * @param vr VR of the underlying DictEntry
- * @param fourth owner group
- * @param name english name
- */
-gdcmDictEntry *gdcmDocument::NewVirtualDictEntry(guint16 group, guint16 element,
- std::string vr,
- std::string fourth,
- std::string name)
-{
- return gdcmGlobal::GetDicts()->NewVirtualDictEntry(group,element,vr,fourth,name);
-}
-
-/**
- * \brief Build a new Element Value from all the low level arguments.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Group group number of the underlying DictEntry
- * @param Elem element number of the underlying DictEntry
- */
-gdcmDocEntry *gdcmDocument::NewDocEntryByNumber(guint16 Group, guint16 Elem)
-{
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
- if (!DictEntry)
- DictEntry = NewVirtualDictEntry(Group, Elem);
-
- gdcmDocEntry *NewEntry = new gdcmDocEntry(DictEntry);
- if (!NewEntry)
+ catch ( FormatError e )
{
- dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber",
- "failed to allocate gdcmDocEntry");
- return NULL;
+ // We reached the EOF (or an error occured) therefore
+ // header parsing has to be considered as finished.
+ //std::cout << e;
+ return 0;
}
- return NewEntry;
-}
+ DocEntry *newEntry = NewDocEntryByNumber(group, elem);
+ FindDocEntryVR(newEntry);
-/**
- * \brief Build a new Element Value from all the low level arguments.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Group group number of the underlying DictEntry
- * @param Elem element number of the underlying DictEntry
- */
-gdcmValEntry *gdcmDocument::NewValEntryByNumber(guint16 Group, guint16 Elem)
-{
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
- if (!DictEntry)
- DictEntry = NewVirtualDictEntry(Group, Elem);
-
- gdcmValEntry *NewEntry = new gdcmValEntry(DictEntry);
- if (!NewEntry)
+ try
{
- dbg.Verbose(1, "gdcmDocument::NewValEntryByNumber",
- "failed to allocate gdcmValEntry");
- return NULL;
+ FindDocEntryLength(newEntry);
}
- return NewEntry;
-}
-
-
-/**
- * \brief Build a new Element Value from all the low level arguments.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Group group number of the underlying DictEntry
- * @param Elem element number of the underlying DictEntry
- */
-gdcmBinEntry *gdcmDocument::NewBinEntryByNumber(guint16 Group, guint16 Elem)
-{
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
- if (!DictEntry)
- DictEntry = NewVirtualDictEntry(Group, Elem);
-
- gdcmBinEntry *NewEntry = new gdcmBinEntry(DictEntry);
- if (!NewEntry)
+ catch ( FormatError e )
{
- dbg.Verbose(1, "gdcmDocument::NewBinEntryByNumber",
- "failed to allocate gdcmBinEntry");
- return NULL;
+ // Call it quits
+ //std::cout << e;
+ delete newEntry;
+ return 0;
}
- return NewEntry;
+
+ newEntry->SetOffset(ftell(Fp));
+
+ return newEntry;
}
+
/**
* \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.
*/
-guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group)
+uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group)
{
- for (guint32 elem = 0; elem < UINT32_MAX; elem++)
+ for (uint32_t elem = 0; elem < UINT32_MAX; elem++)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, elem);
- if (tagHT.count(key) == 0)
+ TagKey key = DictEntry::TranslateToKey(group, elem);
+ if (TagHT.count(key) == 0)
+ {
return elem;
+ }
}
return UINT32_MAX;
}
-
/**
- * \brief Searches both the public and the shadow dictionary (when they
- * exist) for the presence of the DictEntry with given name.
- * The public dictionary has precedence on the shadow one.
- * @param Name name of the searched DictEntry
- * @return Corresponding DictEntry when it exists, NULL otherwise.
+ * \brief Assuming the internal file pointer \ref Document::Fp
+ * is placed at the beginning of a tag check whether this
+ * tag is (TestGroup, TestElement).
+ * \warning On success the internal file pointer \ref Document::Fp
+ * is modified to point after the tag.
+ * On failure (i.e. when the tag wasn't the expected tag
+ * (TestGroup, TestElement) the internal file pointer
+ * \ref Document::Fp is restored to it's original position.
+ * @param testGroup The expected group of the tag.
+ * @param testElement The expected Element of the tag.
+ * @return True on success, false otherwise.
*/
-gdcmDictEntry *gdcmDocument::GetDictEntryByName(std::string Name)
+bool Document::ReadTag(uint16_t testGroup, uint16_t testElement)
{
- gdcmDictEntry *found = (gdcmDictEntry *)0;
- if (!RefPubDict && !RefShaDict)
- {
- dbg.Verbose(0, "gdcmDocument::GetDictEntry",
- "we SHOULD have a default dictionary");
- }
- if (RefPubDict)
- {
- found = RefPubDict->GetDictEntryByName(Name);
- if (found)
- return found;
- }
- if (RefShaDict)
- {
- found = RefShaDict->GetDictEntryByName(Name);
- if (found)
- return found;
- }
- return found;
-}
+ long positionOnEntry = ftell(Fp);
+ long currentPosition = ftell(Fp); // On debugging purposes
-/**
- * \brief Searches both the public and the shadow dictionary (when they
- * exist) for the presence of the DictEntry with given
- * group and element. The public dictionary has precedence on the
- * shadow one.
- * @param group group number of the searched DictEntry
- * @param element element number of the searched DictEntry
- * @return Corresponding DictEntry when it exists, NULL otherwise.
- */
-gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element)
-{
- gdcmDictEntry *found = (gdcmDictEntry *)0;
- if (!RefPubDict && !RefShaDict)
- {
- dbg.Verbose(0, "gdcmDocument::GetDictEntry",
- "we SHOULD have a default dictionary");
- }
- if (RefPubDict)
- {
- found = RefPubDict->GetDictEntryByNumber(group, element);
- if (found)
- return found;
- }
- if (RefShaDict)
+ //// Read the Item Tag group and element, and make
+ // sure they are what we expected:
+ uint16_t itemTagGroup = ReadInt16();
+ uint16_t itemTagElement = ReadInt16();
+ if ( itemTagGroup != testGroup || itemTagElement != testElement )
{
- found = RefShaDict->GetDictEntryByNumber(group, element);
- if (found)
- return found;
+ 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);
+
+ return false;
}
- return found;
+ return true;
}
/**
- * \brief Assuming the internal file pointer \ref gdcmDocument::fp
+ * \brief Assuming the internal file pointer \ref Document::Fp
* is placed at the beginning of a tag (TestGroup, TestElement),
* read the length associated to the Tag.
- * \warning On success the internal file pointer \ref gdcmDocument::fp
+ * \warning On success the internal file pointer \ref Document::Fp
* is modified to point after the tag and it's length.
* On failure (i.e. when the tag wasn't the expected tag
* (TestGroup, TestElement) the internal file pointer
- * \ref gdcmDocument::fp is restored to it's original position.
- * @param TestGroup The expected group of the tag.
- * @param TestElement The expected Element of the tag.
+ * \ref Document::Fp is restored to it's original position.
+ * @param testGroup The expected group of the tag.
+ * @param testElement The expected Element of the tag.
* @return On success returns the length associated to the tag. On failure
* returns 0.
*/
-guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement)
+uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement)
{
- guint16 ItemTagGroup;
- guint16 ItemTagElement;
- long PositionOnEntry = ftell(fp);
- long CurrentPosition = ftell(fp); // On debugging purposes
+ long positionOnEntry = ftell(Fp);
+ (void)positionOnEntry;
- //// Read the Item Tag group and element, and make
- // sure they are respectively 0xfffe and 0xe000:
- ItemTagGroup = ReadInt16();
- ItemTagElement = ReadInt16();
- if ( (ItemTagGroup != TestGroup) || (ItemTagElement != TestElement ) )
+ if ( !ReadTag(testGroup, testElement) )
{
- std::ostringstream s;
- s << " We should have found tag (";
- s << std::hex << TestGroup << "," << TestElement << ")" << std::endl;
- s << " but instead we encountered tag (";
- s << std::hex << ItemTagGroup << "," << ItemTagElement << ")"
- << std::endl;
- s << " at address: " << (unsigned)CurrentPosition << std::endl;
- dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:");
- dbg.Verbose(0, s.str().c_str());
- fseek(fp, PositionOnEntry, SEEK_SET);
return 0;
}
//// Then read the associated Item Length
- CurrentPosition=ftell(fp);
- guint32 ItemLength;
- ItemLength = ReadInt32();
+ long currentPosition = ftell(Fp);
+ uint32_t itemLength = ReadInt32();
{
std::ostringstream s;
s << "Basic Item Length is: "
- << ItemLength << std::endl;
- s << " at address: " << (unsigned)CurrentPosition << std::endl;
- dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: ", s.str().c_str());
+ << itemLength << std::endl;
+ s << " at address: " << (unsigned)currentPosition << std::endl;
+ dbg.Verbose(0, "Document::ReadItemTagLength: ", s.str().c_str());
}
- return ItemLength;
+ return itemLength;
}
/**
- * \brief Read the length of an exptected Item tag i.e. (0xfffe, 0xe000).
- * \sa \ref gdcmDocument::ReadTagLength
- * \warning See warning of \ref gdcmDocument::ReadTagLength
- * @return On success returns the length associated to the item tag.
- * On failure returns 0.
- */
-guint32 gdcmDocument::ReadItemTagLength(void)
+ * \brief When parsing the Pixel Data of an encapsulated file, read
+ * the basic offset table (when present, and BTW dump it).
+ */
+void Document::ReadAndSkipEncapsulatedBasicOffsetTable()
{
- return ReadTagLength(0xfffe, 0xe000);
+ //// Read the Basic Offset Table Item Tag length...
+ uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
+
+ // When present, read the basic offset table itself.
+ // Notes: - since the presence of this basic offset table is optional
+ // we can't rely on it for the implementation, and we will simply
+ // trash it's content (when present).
+ // - still, when present, we could add some further checks on the
+ // 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);
+
+#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());
+ }
+#endif //GDCM_DEBUG
+
+ delete[] basicOffsetTableItemValue;
+ }
}
/**
- * \brief Read the length of an exptected Sequence Delimiter tag i.e.
- * (0xfffe, 0xe0dd).
- * \sa \ref gdcmDocument::ReadTagLength
- * \warning See warning of \ref gdcmDocument::ReadTagLength
- * @return On success returns the length associated to the Sequence
- * Delimiter tag. On failure returns 0.
+ * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
+ * Compute the RLE extra information and store it in \ref RLEInfo
+ * for later pixel retrieval usage.
*/
-guint32 gdcmDocument::ReadSequenceDelimiterTagLength(void)
+void Document::ComputeRLEInfo()
{
- return ReadTagLength(0xfffe, 0xe0dd);
-}
+ if ( ! IsRLELossLessTransferSyntax() )
+ {
+ return;
+ }
+
+ // Encoded pixel data: for the time being we are only concerned with
+ // Jpeg or RLE Pixel data encodings.
+ // As stated in PS 3.5-2003, section 8.2 p44:
+ // "If sent in Encapsulated Format (i.e. other than the Native Format) the
+ // value representation OB is used".
+ // Hence we expect an OB value representation. Concerning OB VR,
+ // the section PS 3.5-2003, section A.4.c p 58-59, states:
+ // "For the Value Representations OB and OW, the encoding shall meet the
+ // following specifications depending on the Data element tag:"
+ // [...snip...]
+ // - the first item in the sequence of items before the encoded pixel
+ // data stream shall be basic offset table item. The basic offset table
+ // item value, however, is not required to be present"
+
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
+ // Loop on the individual frame[s] and store the information
+ // on the RLE fragments in a RLEFramesInfo.
+ // Note: - when only a single frame is present, this is a
+ // classical image.
+ // - when more than one frame are present, then we are in
+ // the case of a multi-frame image.
+ long frameLength;
+ while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ // Parse the RLE Header and store the corresponding RLE Segment
+ // Offset Table information on fragments of this current Frame.
+ // Note that the fragment pixels themselves are not loaded
+ // (but just skipped).
+ long frameOffset = ftell(Fp);
+ uint32_t nbRleSegments = ReadInt32();
+
+ uint32_t rleSegmentOffsetTable[15];
+ for( int k = 1; k <= 15; k++ )
+ {
+ rleSegmentOffsetTable[k] = ReadInt32();
+ }
+
+ // Deduce from both the RLE Header and the frameLength the
+ // fragment length, and again store this info in a
+ // RLEFramesInfo.
+ long rleSegmentLength[15];
+ // skipping (not reading) RLE Segments
+ if ( nbRleSegments > 1)
+ {
+ for(unsigned int k = 1; k <= nbRleSegments-1; k++)
+ {
+ rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
+ - rleSegmentOffsetTable[k];
+ SkipBytes(rleSegmentLength[k]);
+ }
+ }
+
+ rleSegmentLength[nbRleSegments] = frameLength
+ - rleSegmentOffsetTable[nbRleSegments];
+ SkipBytes(rleSegmentLength[nbRleSegments]);
+
+ // Store the collected info
+ RLEFrame* newFrameInfo = new RLEFrame;
+ newFrameInfo->NumberFragments = nbRleSegments;
+ for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
+ {
+ newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk];
+ newFrameInfo->Length[uk] = rleSegmentLength[uk];
+ }
+ RLEInfo->Frames.push_back( newFrameInfo );
+ }
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
+ dbg.Verbose(0, " item at end of RLE item sequence");
+ }
+}
/**
- * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files
- * No other way so 'skip' the Data
- *
+ * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
+ * Compute the jpeg extra information (fragment[s] offset[s] and
+ * length) and store it[them] in \ref JPEGInfo for later pixel
+ * retrieval usage.
*/
-void gdcmDocument::Parse7FE0 (void)
+void Document::ComputeJPEGFragmentInfo()
{
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return;
-
- if ( IsImplicitVRLittleEndianTransferSyntax()
- || IsExplicitVRLittleEndianTransferSyntax()
- || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier !
- || IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+ // If you need to, look for comments of ComputeRLEInfo().
+ if ( ! IsJPEGTransferSyntax() )
+ {
return;
-
- // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels
+ }
- //// Read the Basic Offset Table Item Tag length...
- guint32 ItemLength = ReadItemTagLength();
-
- //// ... and then read length[s] itself[themselves]. We don't use
- // the values read (BTW what is the purpous of those lengths ?)
- if (ItemLength != 0) {
- // BTW, what is the purpous of those length anyhow !?
- char * BasicOffsetTableItemValue = new char[ItemLength + 1];
- fread(BasicOffsetTableItemValue, ItemLength, 1, fp);
- for (int i=0; i < ItemLength; i += 4){
- guint32 IndividualLength;
- IndividualLength = str2num(&BasicOffsetTableItemValue[i],guint32);
- std::ostringstream s;
- s << " Read one length: ";
- s << std::hex << IndividualLength << std::endl;
- dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str());
- }
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Loop on the fragments[s] and store the parsed information in a
+ // JPEGInfo.
+ long fragmentLength;
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ long fragmentOffset = ftell(Fp);
+
+ // Store the collected info
+ JPEGFragment* newFragment = new JPEGFragment;
+ newFragment->Offset = fragmentOffset;
+ newFragment->Length = fragmentLength;
+ JPEGInfo->Fragments.push_back( newFragment );
+
+ SkipBytes( fragmentLength );
}
- if ( ! IsRLELossLessTransferSyntax() )
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
{
- // JPEG Image
-
- //// We then skip (not reading them) all the fragments of images:
- while ( ItemLength = ReadItemTagLength() )
- {
- SkipBytes(ItemLength);
- }
-
+ dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
+ dbg.Verbose(0, " item at end of JPEG item sequence");
}
- else
+}
+
+/**
+ * \brief Walk recursively the given \ref DocEntrySet, and feed
+ * the given hash table (\ref TagDocEntryHT) with all the
+ * \ref DocEntry (Dicom entries) encountered.
+ * This method does the job for \ref BuildFlatHashTable.
+ * @param builtHT Where to collect all the \ref DocEntry encountered
+ * when recursively walking the given set.
+ * @param set The structure to be traversed (recursively).
+ */
+void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT,
+ DocEntrySet* set )
+{
+ if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) )
{
- // RLE Image
- long ftellRes;
- long RleSegmentLength[15], fragmentLength;
-
- // while 'Sequence Delimiter Item' (fffe,e0dd) not found
- while ( fragmentLength = ReadSequenceDelimiterTagLength() )
- {
- // Parse fragments of the current Fragment (Frame)
- //------------------ scanning (not reading) fragment pixels
- guint32 nbRleSegments = ReadInt32();
- printf(" Nb of RLE Segments : %d\n",nbRleSegments);
-
- //// Reading RLE Segments Offset Table
- guint32 RleSegmentOffsetTable[15];
- for(int k=1; k<=15; k++) {
- ftellRes=ftell(fp);
- RleSegmentOffsetTable[k] = ReadInt32();
- printf(" at : %x Offset Segment %d : %d (%x)\n",
- (unsigned)ftellRes,k,RleSegmentOffsetTable[k],
- RleSegmentOffsetTable[k]);
+ TagDocEntryHT* currentHT = elementSet->GetTagHT();
+ for( TagDocEntryHT::const_iterator i = currentHT->begin();
+ i != currentHT->end();
+ ++i)
+ {
+ DocEntry* entry = i->second;
+ if ( SeqEntry* seqEntry = dynamic_cast<SeqEntry*>(entry) )
+ {
+ ListSQItem& items = seqEntry->GetSQItems();
+ for( ListSQItem::const_iterator item = items.begin();
+ item != items.end();
+ ++item)
+ {
+ BuildFlatHashTableRecurse( builtHT, *item );
+ }
+ continue;
}
+ builtHT[entry->GetKey()] = entry;
+ }
+ return;
+ }
- // skipping (not reading) RLE Segments
- if (nbRleSegments>1) {
- for(unsigned int k=1; k<=nbRleSegments-1; k++) {
- RleSegmentLength[k]= RleSegmentOffsetTable[k+1]
- - RleSegmentOffsetTable[k];
- ftellRes=ftell(fp);
- printf (" Segment %d : Length = %d x(%x) Start at %x\n",
- k,(unsigned)RleSegmentLength[k],
- (unsigned)RleSegmentLength[k], (unsigned)ftellRes);
- SkipBytes(RleSegmentLength[k]);
- }
- }
+ if (SQItem* SQItemSet = dynamic_cast< SQItem* > ( set ) )
+ {
+ ListDocEntry& currentList = SQItemSet->GetDocEntries();
+ for (ListDocEntry::iterator i = currentList.begin();
+ i != currentList.end();
+ ++i)
+ {
+ DocEntry* entry = *i;
+ if ( SeqEntry* seqEntry = dynamic_cast<SeqEntry*>(entry) )
+ {
+ ListSQItem& items = seqEntry->GetSQItems();
+ for( ListSQItem::const_iterator item = items.begin();
+ item != items.end();
+ ++item)
+ {
+ BuildFlatHashTableRecurse( builtHT, *item );
+ }
+ continue;
+ }
+ builtHT[entry->GetKey()] = entry;
+ }
- RleSegmentLength[nbRleSegments]= fragmentLength
- - RleSegmentOffsetTable[nbRleSegments];
- ftellRes=ftell(fp);
- printf (" Segment %d : Length = %d x(%x) Start at %x\n",
- nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments],
- (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes);
- SkipBytes(RleSegmentLength[nbRleSegments]);
- }
}
- return;
}
/**
- * \brief Compares two documents, according to \ref gdcmDicomDir rules
+ * \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
+ * 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
+ * structure. Hence, a gdcm user whishing to visit all the entries of
+ * a Dicom header will need to dig in the gdcm internals (which
+ * implies exposing all the internal data structures to the API).
+ * In order to avoid this burden to the user, \ref BuildFlatHashTable
+ * recursively builds a temporary hash table, which holds all the
+ * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a
+ * std::map<>).
+ * \warning Of course there is NO integrity constrain between the
+ * returned \ref TagDocEntryHT and the \ref ElementSet used
+ * to build it. Hence if the underlying \ref ElementSet is
+ * altered, then it is the caller responsability to invoke
+ * \ref BuildFlatHashTable again...
+ * @return The flat std::map<> we juste build.
+ */
+TagDocEntryHT* Document::BuildFlatHashTable()
+{
+ TagDocEntryHT* FlatHT = new TagDocEntryHT;
+ BuildFlatHashTableRecurse( *FlatHT, this );
+ return FlatHT;
+}
+
+
+
+/**
+ * \brief Compares two documents, according to \ref DicomDir rules
* \warning Does NOT work with ACR-NEMA files
* \todo Find a trick to solve the pb (use RET fields ?)
* @param document
* @return true if 'smaller'
*/
- bool gdcmDocument::operator<(gdcmDocument &document){
- std::string s1,s2;
-
+bool Document::operator<(Document &document)
+{
// Patient Name
- s1=this->GetEntryByNumber(0x0010,0x0010);
- s2=document.GetEntryByNumber(0x0010,0x0010);
+ std::string s1 = GetEntryByNumber(0x0010,0x0010);
+ std::string s2 = document.GetEntryByNumber(0x0010,0x0010);
if(s1 < s2)
- return(true);
- else if(s1 > s2)
- return(false);
+ {
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
else
{
// Patient ID
- s1=this->GetEntryByNumber(0x0010,0x0020);
- s2=document.GetEntryByNumber(0x0010,0x0020);
- if (s1 < s2)
- return(true);
- else if (s1 > s2)
- return(1);
+ s1 = GetEntryByNumber(0x0010,0x0020);
+ s2 = document.GetEntryByNumber(0x0010,0x0020);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if ( s1 > s2 )
+ {
+ return false;
+ }
else
{
// Study Instance UID
- s1=this->GetEntryByNumber(0x0020,0x000d);
- s2=document.GetEntryByNumber(0x0020,0x000d);
- if (s1 < s2)
- return(true);
- else if(s1 > s2)
- return(false);
+ s1 = GetEntryByNumber(0x0020,0x000d);
+ s2 = document.GetEntryByNumber(0x0020,0x000d);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
else
{
// Serie Instance UID
- s1=this->GetEntryByNumber(0x0020,0x000e);
- s2=document.GetEntryByNumber(0x0020,0x000e);
- if (s1 < s2)
- return(true);
- else if(s1 > s2)
- return(false);
+ s1 = GetEntryByNumber(0x0020,0x000e);
+ s2 = document.GetEntryByNumber(0x0020,0x000e);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
}
}
}
- return(false);
+ return false;
}
+} // end namespace gdcm
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff