-// gdcmDocument.cxx
-//-----------------------------------------------------------------------------
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmDocument.cxx,v $
+ Language: C++
+ Date: $Date: 2004/08/02 16:42:14 $
+ Version: $Revision: 1.65 $
+
+ 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.htm 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 "gdcmUtil.h"
#include "gdcmDebug.h"
-#include <errno.h>
#include <vector>
// For nthos:
# include <iomanip>
+// Implicit VR Little Endian
#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2"
+// Explicit VR Little Endian
#define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1"
-#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2"
+// Deflated Explicit VR Little Endian
#define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99"
-#define UI1_1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5"
-
+// Explicit VR Big Endian
+#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2"
+// JPEG Baseline (Process 1)
+#define UI1_2_840_10008_1_2_4_50 "1.2.840.10008.1.2.4.50"
+// JPEG Extended (Process 2 & 4)
+#define UI1_2_840_10008_1_2_4_51 "1.2.840.10008.1.2.4.51"
+// JPEG Extended (Process 3 & 5)
+#define UI1_2_840_10008_1_2_4_52 "1.2.840.10008.1.2.4.52"
+// JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8)
+#define UI1_2_840_10008_1_2_4_53 "1.2.840.10008.1.2.4.53"
+// JPEG Full Progression, Non-Hierarchical (Process 10 & 12)
+#define UI1_2_840_10008_1_2_4_55 "1.2.840.10008.1.2.4.55"
+// JPEG Lossless, Non-Hierarchical (Process 14)
+#define UI1_2_840_10008_1_2_4_57 "1.2.840.10008.1.2.4.57"
+// JPEG Lossless, Hierarchical, First-Order Prediction (Process 14,
+// [Selection Value 1])
+#define UI1_2_840_10008_1_2_4_70 "1.2.840.10008.1.2.4.70"
+// JPEG 2000 Lossless
+#define UI1_2_840_10008_1_2_4_90 "1.2.840.10008.1.2.4.90"
+// JPEG 2000
+#define UI1_2_840_10008_1_2_4_91 "1.2.840.10008.1.2.4.91"
+// RLE Lossless
+#define UI1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5"
+// UI1_1_2_840_10008_1_2_5
#define str2num(str, typeNum) *((typeNum *)(str))
//-----------------------------------------------------------------------------
const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256;
// Refer to gdcmDocument::SetMaxSizeLoadEntry()
-const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
-
-const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64;
+const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
+const unsigned int gdcmDocument::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;
-
+ */
+gdcmDocument::gdcmDocument( std::string const & filename )
+ : gdcmElementSet(-1)
+{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- filename = inFilename;
+ Filename = filename;
Initialise();
- if ( !OpenFile(exception_on_error))
+ if ( !OpenFile() )
+ {
return;
+ }
- rewind(fp);
- //if (!CheckSwap())
- // return false; // to go on compiling
+ dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ",
+ Filename.c_str());
+ rewind(Fp);
- 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;
+ SQDepthLevel = 0;
- long l=ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
+ long l = ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
+ (void)l; //is l used anywhere ?
+
+ rewind(Fp);
+
+ // Load 'non string' values
+
+ std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
+ if( PhotometricInterpretation == "PALETTE COLOR " )
+ {
+ LoadEntryVoidArea(0x0028,0x1200); // gray LUT
+ LoadEntryVoidArea(0x0028,0x1201); // R LUT
+ LoadEntryVoidArea(0x0028,0x1202); // G LUT
+ LoadEntryVoidArea(0x0028,0x1203); // B LUT
+
+ LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data
+ LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data
+ LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data
+ }
+ //FIXME later : how to use it?
+ LoadEntryVoidArea(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 = gdcmACR_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 gdcmDocument::SetFileName and then the parsing.
*/
-gdcmDocument::gdcmDocument(bool exception_on_error)
- :gdcmElementSet(-1) {
- (void)exception_on_error;
- enableSequences=0;
-
+gdcmDocument::gdcmDocument()
+ :gdcmElementSet(-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) {
+gdcmDocument::~gdcmDocument ()
+{
RefPubDict = NULL;
RefShaDict = NULL;
+
+ // Recursive clean up of sequences
+ for (TagDocEntryHT::const_iterator it = TagHT.begin();
+ it != TagHT.end(); ++it )
+ {
+ delete it->second;
+ }
+ TagHT.clear();
}
//-----------------------------------------------------------------------------
// Print
-/**
-
/**
* \brief Prints The Dict Entries of THE public Dicom Dictionary
* @return
*/
-void gdcmDocument::PrintPubDict(std::ostream & os) {
+void gdcmDocument::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 gdcmDocument::PrintShaDict(std::ostream & os)
+{
RefShaDict->Print(os);
}
/**
* \brief Get the public dictionary used
*/
-gdcmDict *gdcmDocument::GetPubDict(void) {
- return(RefPubDict);
+gdcmDict *gdcmDocument::GetPubDict()
+{
+ return RefPubDict;
}
/**
* \brief Get the shadow dictionary used
*/
-gdcmDict *gdcmDocument::GetShaDict(void) {
- return(RefShaDict);
+gdcmDict *gdcmDocument::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 gdcmDocument::SetShaDict(gdcmDict *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 gdcmDocument::SetShaDict(DictKey const & dictName)
+{
+ RefShaDict = gdcmGlobal::GetDicts()->GetDict(dictName);
+ return !RefShaDict;
}
/**
* @return true when gdcmDocument is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmDocument::IsReadable(void) {
- if(filetype==gdcmUnknown) {
- std::cout << "wrong filetype" <<std::endl;
- return(false);
+bool gdcmDocument::IsReadable()
+{
+ if( Filetype == gdcmUnknown)
+ {
+ std::cout << " gdcmDocument::IsReadable: Filetype " << Filetype
+ << " " << "gdcmUnknown " << gdcmUnknown << std::endl; //JPR
+ dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype");
+ return false;
}
- if(!tagHT.empty()<=0) {
- std::cout << "wrong tagHT size "<< tagHT.size() <<std::endl;
- return(false);
+
+ if( TagHT.empty() )
+ {
+ dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal"
+ " hash table.");
+ return false;
}
- return(true);
+ return true;
}
+
/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a ImplicitVRLittleEndian one.
- * @return True when ImplicitVRLittleEndian found. False in all other cases.
+ * \brief Internal function that checks whether the Transfer Syntax given
+ * as argument is the one present in the current document.
+ * @param SyntaxToCheck The transfert syntax we need to check against.
+ * @return True when SyntaxToCheck corresponds to the Transfer Syntax of
+ * the current document. False either when the document contains
+ * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match.
*/
-bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) {
- gdcmDocEntry *Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
+bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck)
+{
+ gdcmDocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010);
+ if ( !entry )
+ {
return false;
- LoadDocEntrySafe(Element);
+ }
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2 )
- return true;
+ // The entry might be present but not loaded (parsing and loading
+ // happen at different stages): try loading and proceed with check...
+ LoadDocEntrySafe(entry);
+ if (gdcmValEntry* valEntry = dynamic_cast< gdcmValEntry* >(entry) )
+ {
+ std::string transfer = valEntry->GetValue();
+ // The actual transfer (as read from disk) might be padded. We
+ // first need to remove the potential padding. We can make the
+ // weak assumption that padding was not executed with digits...
+ if ( transfer.length() == 0 ) { // for brain damaged headers
+ return false;
+ }
+ while ( ! isdigit(transfer[transfer.length()-1]) )
+ {
+ transfer.erase(transfer.length()-1, 1);
+ }
+ 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.
+ * @return True when ImplicitVRLittleEndian found. False in all other cases.
+ */
+bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax()
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2);
+}
+
/**
* \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a ExplicitVRLittleEndian one.
* @return True when ExplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) {
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadDocEntrySafe(Element);
-
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2_1 )
- return true;
- return false;
+bool gdcmDocument::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) {
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadDocEntrySafe(Element);
-
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2_1_99 )
- return true;
- return false;
+bool gdcmDocument::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) {
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadDocEntrySafe(Element);
+bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax()
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2);
+}
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier !
- return true;
- return false;
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGBaseLineProcess1 one.
+ * @return True when JPEGBaseLineProcess1found. False in all other cases.
+ */
+bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax()
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50);
+}
+
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGExtendedProcess2-4 one.
+ * @return True when JPEGExtendedProcess2-4 found. False in all other cases.
+ */
+bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax()
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51);
+}
+
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGExtendeProcess3-5 one.
+ * @return True when JPEGExtendedProcess3-5 found. False in all other cases.
+ */
+bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax()
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52);
}
/**
- * \brief returns the File Type
- * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
- * @return the FileType code
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one.
+ * @return True when JPEGSpectralSelectionProcess6-8 found. False in all
+ * other cases.
*/
-FileType gdcmDocument::GetFileType(void) {
- return(filetype);
+bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax()
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53);
}
/**
- * \brief opens the file
- * @param exception_on_error
- * @return
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a RLE Lossless one.
+ * @return True when RLE Lossless found. False in all
+ * other cases.
*/
-FILE *gdcmDocument::OpenFile(bool exception_on_error)
- throw(gdcmFileError)
+bool gdcmDocument::IsRLELossLessTransferSyntax()
{
- fp=fopen(filename.c_str(),"rb");
- if(exception_on_error)
- {
- if(!fp)
- throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)");
- }
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5);
+}
- if ( fp )
- {
- guint16 zero;
- fread(&zero, (size_t)2, (size_t)1, fp);
+/**
+ * \brief Determines if Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG Lossless one.
+ * @return True when RLE Lossless found. False in all
+ * other cases.
+ */
+
+bool gdcmDocument::IsJPEGLossless()
+{
+ return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55)
+ || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57)
+ || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70) );
+}
+
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG2000 one
+ * @return True when JPEG2000 (Lossly or LossLess) found. False in all
+ * other cases.
+ */
+bool gdcmDocument::IsJPEG2000()
+{
+ return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90)
+ || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) );
+}
+
+/**
+ * \brief Predicate for dicom version 3 file.
+ * @return True when the file is a dicom version 3.
+ */
+bool gdcmDocument::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;
+}
- //ACR -- or DICOM with no Preamble --
- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200)
- return(fp);
+/**
+ * \brief returns the File Type
+ * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
+ * @return the FileType code
+ */
+FileType gdcmDocument::GetFileType()
+{
+ return Filetype;
+}
- //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);
+/**
+ * \brief Tries to open the file \ref gdcmDocument::Filename and
+ * checks the preamble when existing.
+ * @return The FILE pointer on success.
+ */
+FILE* gdcmDocument::OpenFile()
+{
+ Fp = fopen(Filename.c_str(),"rb");
- 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,
+ "gdcmDocument::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,
+ "gdcmDocument::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 gdcmDocument::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 gdcmDocument::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
+ /// no way (check : FileType est un champ de gdcmDocument ...)
/// a moins de se livrer a un tres complique ajout des champs manquants.
- /// faire un CheckAndCorrectHeader (?)
-
- if (type == gdcmImplicitVR)
+ /// faire un CheckAndCorrectHeader (?)
+
+ if (filetype == gdcmImplicitVR)
{
std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2;
ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
/// \todo Refer to standards on page 21, chapter 6.2
/// "Value representation": values with a VR of UI shall be
/// padded with a single trailing null
- /// 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 == gdcmExplicitVR)
{
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);
*/
+
+ gdcmElementSet::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 Value to be set
+ * @param Value (string) 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).
*/
-
-
-gdcmDocEntry * gdcmDocument::ReplaceOrCreateByNumber(
- std::string Value,
- guint16 Group,
- guint16 Elem ){
- gdcmDocEntry* a;
- a = GetDocEntryByNumber( Group, Elem);
- if (a == NULL) {
- a =NewDocEntryByNumber(Group, Elem);
- if (a == NULL)
+
+gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
+ std::string const & value,
+ uint16_t group,
+ uint16_t elem )
+{
+ gdcmValEntry* valEntry = 0;
+
+ gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
+ if (!currentEntry)
+ {
+ // The entry wasn't present and we simply create the required ValEntry:
+ currentEntry = NewDocEntryByNumber(group, elem);
+ if (!currentEntry)
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
+ " NewDocEntryByNumber failed.");
return NULL;
- AddEntry(a);
- }
- SetEntryByNumber(Value, Group, Elem);
- //a->SetValue(Value);
- return(a);
+ }
+ valEntry = new gdcmValEntry(currentEntry);
+ if ( !AddEntry(valEntry))
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry"
+ " failed allthough this is a creation.");
+ }
+ }
+ else
+ {
+ valEntry = dynamic_cast< gdcmValEntry* >(currentEntry);
+ if ( !valEntry )
+ {
+ // We need to promote the gdcmDocEntry to a gdcmValEntry:
+ valEntry = new gdcmValEntry(currentEntry);
+ if (!RemoveEntry(currentEntry))
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
+ " of previous DocEntry failed.");
+ return NULL;
+ }
+ if ( !AddEntry(valEntry))
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
+ " promoted ValEntry failed.");
+ 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 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,
+ int lgth,
+ uint16_t group,
+ uint16_t elem)
+{
+ gdcmBinEntry* b = 0;
+ gdcmDocEntry* a = GetDocEntryByNumber( group, elem);
+ if (!a)
+ {
+ a = NewBinEntryByNumber(group, elem);
+ if (!a)
+ {
+ return 0;
+ }
+
+ b = new gdcmBinEntry(a);
+ AddEntry(b);
+ b->SetVoidArea(voidArea);
+ }
+ SetEntryByNumber(voidArea, lgth, group, elem);
+ //b->SetVoidArea(voidArea); //what if b == 0 !!
+
+ return b;
+}
+
/**
* \brief Set a new value if the invoked element exists
* Seems to be useless !!!
* @param Elem element number of the Entry
* \return boolean
*/
-bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem )
+bool gdcmDocument::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;
}
* @param element Element number of the searched Dicom Element
* @return number of occurences
*/
-int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) {
- std::string key = gdcmDictEntry::TranslateToKey(group, element );
- return (tagHT.count(key));
+int gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
+{
+ const std::string &key = gdcmDictEntry::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) {
+std::string gdcmDocument::GetEntryByName(TagName const & tagName)
+{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
+ 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) {
+std::string gdcmDocument::GetEntryVRByName(TagName const & tagName)
+{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
+ {
return GDCM_UNFOUND;
+ }
- gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
+ gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
+ dictEntry->GetElement());
return elem->GetVR();
}
* @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 gdcmDocument::GetEntryByNumber(uint16_t group, uint16_t element)
+{
+ gdcmTagKey key = gdcmDictEntry::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 ((gdcmValEntry *)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 gdcmDocument::GetEntryVRByNumber(uint16_t group, uint16_t element)
+{
+ gdcmDocEntry* 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) {
+int gdcmDocument::GetEntryLengthByNumber(uint16_t group, uint16_t element)
+{
gdcmDocEntry* 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) {
+bool gdcmDocument::SetEntryByName(std::string const & content,std::string const & tagName)
+{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return false;
+ 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)
* through it's (group, element) and modifies it's content with
* the given value.
- * @param content new value to substitute with
+ * @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 gdcmDocument::SetEntryByNumber(std::string const & content,
+ uint16_t group,
+ uint16_t element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+ gdcmValEntry* valEntry = GetValEntryByNumber(group, element);
+ if (!valEntry )
+ {
+ dbg.Verbose(0, "gdcmDocument::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';
}
-
- gdcmDocEntry * a;
- a = tagHT[key];
-
- ((gdcmValEntry*)a)->SetValue(content);
-
- std::string vr = a->GetVR();
+ // Non even content must be padded with a space (020H)...
+ std::string evenContent = content;
+ if( evenContent.length() % 2 )
+ {
+ evenContent += '\0'; // ... therefore we padd with (000H) .!?!
+ }
+ valEntry->SetValue(evenContent);
- guint32 lgr;
- if( (vr == "US") || (vr == "SS") )
- lgr = 2;
- else if( (vr == "UL") || (vr == "SL") )
- lgr = 4;
+ // Integers have a special treatement for their length:
+ gdcmVRKey vr = valEntry->GetVR();
+ if( vr == "US" || vr == "SS" )
+ {
+ valEntry->SetLength(2);
+ }
+ else if( vr == "UL" || vr == "SL" )
+ {
+ valEntry->SetLength(4);
+ }
else
- lgr = l;
+ {
+ valEntry->SetLength(evenContent.length());
+ }
- a->SetLength(lgr);
return true;
-}
+}
+
+/**
+ * \brief Accesses an existing gdcmDocEntry (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 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,
+ uint16_t group,
+ uint16_t element)
+{
+ (void)lgth; //not used
+ gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ if ( !TagHT.count(key))
+ {
+ return false;
+ }
+
+/* Hope Binary field length is *never* wrong
+ if(lgth%2) // Non even length are padded with a space (020H).
+ {
+ lgth++;
+ //content = content + '\0'; // fing a trick to enlarge a binary field?
+ }
+*/
+ gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key];
+ a->SetVoidArea(content);
+ //a->SetLength(lgth); // ???
+
+ return true;
+}
/**
* \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
* @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 gdcmDocument::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
+ gdcmTagKey key = gdcmDictEntry::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 ;
}
* @param Elem element number of the Entry
* @return File Offset of the Element Value
*/
-size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem)
+size_t gdcmDocument::GetEntryOffsetByNumber(uint16_t group, uint16_t elem)
{
- gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
- if (!Entry)
+ gdcmDocEntry* entry = GetDocEntryByNumber(group, elem);
+ if (!entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber",
- "failed to Locate gdcmDocEntry");
- return (size_t)0;
+ dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry present.");
+ return 0;
}
- return Entry->GetOffset();
+ return entry->GetOffset();
}
/**
* @param Elem element number of the Entry
* @return Pointer to the 'non string' area
*/
-void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem)
+void * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem)
{
- gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
- if (!Entry)
+ gdcmDocEntry* entry = GetDocEntryByNumber(group, elem);
+ if (!entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber",
- "failed to Locate gdcmDocEntry");
- return (NULL);
+ dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry");
+ return 0;
}
- return ((gdcmBinEntry *)Entry)->GetVoidArea();
+ return ((gdcmBinEntry *)entry)->GetVoidArea();
}
/**
* @param Group group number of the Entry
* @param Elem element number of the Entry
*/
-void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem)
+void *gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem)
{
- gdcmDocEntry * Element= GetDocEntryByNumber(Group, Elem);
- if ( !Element )
+ gdcmDocEntry *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();
+ }
+ size_t o =(size_t)docElement->GetOffset();
+ fseek(Fp, o, SEEK_SET);
+ size_t l = docElement->GetLength();
char* a = new char[l];
- if(!a)
+ if(!a)
+ {
+ dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a");
+ return NULL;
+ }
+ size_t l2 = fread(a, 1, l , Fp);
+ if( l != l2 )
+ {
+ delete[] a;
return NULL;
+ }
+ /// \todo Drop any already existing void area! JPR
+ SetEntryVoidAreaByNumber(a, group, elem);
- SetEntryVoidAreaByNumber(a, Group, Elem);
+ return a;
+}
+/**
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
+ * @param Element Entry whose voidArea is going to be loaded
+ */
+void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element)
+{
+ size_t o =(size_t)element->GetOffset();
+ fseek(Fp, o, SEEK_SET);
+ size_t l = element->GetLength();
+ char* a = new char[l];
+ if( !a )
+ {
+ dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a");
+ return NULL;
+ }
+ element->SetVoidArea((void *)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)
+ uint16_t group,
+ uint16_t element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+ gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ if ( !TagHT.count(key))
+ {
return false;
- // This was for multimap ?
- (( gdcmBinEntry *)( ((tagHT.equal_range(key)).first)->second ))->SetVoidArea(area);
+ }
+
+ // This was for multimap ?
+ (( gdcmBinEntry *)( ((TagHT.equal_range(key)).first)->second ))->SetVoidArea(area);
return true;
}
* \brief Update the entries with the shadow dictionary.
* Only non even entries are analyzed
*/
-void gdcmDocument::UpdateShaEntries(void) {
- gdcmDictEntry *entry;
+void gdcmDocument::UpdateShaEntries()
+{
+ //gdcmDictEntry *entry;
std::string vr;
- // TODO : if still any use (?) explore recursively the whole structure
+ /// \todo TODO : still any use to explore recursively the whole structure?
/*
for(ListTag::iterator it=listEntries.begin();
it!=listEntries.end();
CheckDocEntryVR(*it,vr);
(*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling
-
+
}
else
{
* @return Corresponding Dicom Element when it exists, and NULL
* otherwise.
*/
- gdcmDocEntry *gdcmDocument::GetDocEntryByName(std::string tagName) {
+gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string const & tagName)
+{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
+ 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)
+gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(uint16_t group,
+ uint16_t element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+ gdcmTagKey key = gdcmDictEntry::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();
- std::string 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);
}
+ return TagHT.find(key)->second;
}
-
+
/**
- * \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
+ * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only
+ * returns a result when the corresponding entry is of type
+ * ValEntry.
+ * @return When present, the corresponding ValEntry.
*/
-
- // TODO : to be re -written recursively !
-
-void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type)
+gdcmValEntry* gdcmDocument::GetValEntryByNumber(uint16_t group,
+ uint16_t element)
{
- (void)type;
- guint16 group = tag->GetGroup();
- std::string 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
- //
- // -------------------------------
-
-
-/* // to go on compiling
- void *voidArea;
- voidArea = tag->GetVoidArea(); // to go on compiling
- 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")
+ gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ if ( !currentEntry )
{
- // 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;
+ return 0;
}
- // some 'Integer' fields may be mulivaluated
- // each single value is separated from the next one by '\'
- // we split the string and write each value as an int
- if (vr == "UL" || vr == "SL")
+ if ( gdcmValEntry* valEntry = dynamic_cast<gdcmValEntry*>(currentEntry) )
{
- 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
-}
-
-/**
- * \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
- */
-
-bool gdcmDocument::WriteEntry(gdcmDocEntry *tag, FILE *_fp,FileType type)
-{
- guint32 length = tag->GetLength();
- gdcmValEntry * Vtag = (gdcmValEntry *) tag;
-std::cout << "gdcmDocument::WriteEntry Vtag->GetValue() " << Vtag->GetValue() << std::endl;
- // 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)
- {
- Vtag->SetValue(Vtag->GetValue()+"\0");
- Vtag->SetLength(Vtag->GetReadLength()+1);
+ return valEntry;
}
+ dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry.");
- WriteEntryTagVRLength(Vtag, _fp, type);
- std::cout << "after WriteEntryTagVRLength " << std::endl;
- WriteEntryValue(Vtag, _fp, type);
- std::cout << "after WriteEntryValue " << std::endl;
- return true;
+ 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)
-{
-
-// FIXME : explore recursively the whole structure...
-
- /// \todo (?) check write failures (after *each* fwrite)
-
- std::cout << "--------------------- gdcmDocument::WriteEntries " << std::endl;
- for (TagDocEntryHT::iterator tag2=tagHT.begin();
- tag2 != tagHT.end();
- ++tag2)
- {
-
- (*tag2).second->Print();
-
- if ( type == gdcmACR ){
- if ((*tag2).second->GetGroup() < 0x0008)
- // Ignore pure DICOM V3 groups
- continue;
- if ((*tag2).second->GetElement() %2)
- // Ignore the "shadow" groups
- continue;
- if ((*tag2).second->GetVR() == "SQ" ) // ignore Sequences
- continue;
- //if ((*tag2).second->GetDepthLevel() != 0) // Not only ignore the SQ element
- // continue;
- }
- if (! WriteEntry((*tag2).second,_fp,type) ) {
- std::cout << "Write Failure " << std::endl;
- return false;
- } else {
-
- }
- }
- return true;
-}
-
+void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * 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 gdcmDocument::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;
+ std::cout << "swapCode= " << SwapCode << std::endl;
dbg.Error(" gdcmDocument::SwapLong : unset swap code");
- a=0;
+ 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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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;
- std::string vr;
- long l;
- int depth;
-
- depth = set->GetDepthLevel();
- while (true) {
+long gdcmDocument::ParseDES(gdcmDocEntrySet *set,
+ long offset,
+ long l_max,
+ bool delim_mode)
+{
+ gdcmDocEntry *newDocEntry = 0;
+ gdcmValEntry *newValEntry = 0;
+ unsigned long l = 0;
- if ( !delim_mode && ftell(fp)-offset >= l_max) {
- break;
+ int depth = set->GetDepthLevel();
+ 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") {
+ }
+
+ gdcmVRKey vr = newDocEntry->GetVR();
+ if ( vr != "SQ" )
+ {
- if (vr == "AE" || vr == "AS" || vr == "DA" || vr == "PN" ||
- vr == "UI" || vr == "TM" || vr == "SH" || vr == "LO" ||
- vr == "CS" || vr == "IS" || vr == "LO" || vr == "LT" ||
- vr == "SH" || vr == "ST" || vr == "DS" ||
- vr == "SL" || vr == "SS" || vr == "UL" || vr == "US"
- ) {
- // --- ValEntry
- vl= new gdcmValEntry(NewDocEntry->GetDictEntry());
- vl->Copy(NewDocEntry);
- vl->SetDepthLevel(depth),
- set->AddEntry(vl);
- LoadDocEntry(vl);
- if (/*!delim_mode && */vl->isItemDelimitor())
+ if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) )
+ {
+ /////// ValEntry
+ newValEntry = new gdcmValEntry(newDocEntry->GetDictEntry());
+ newValEntry->Copy(newDocEntry);
+ newValEntry->SetDepthLevel(depth);
+ 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 { // BinEntry
-
- // Hope the following VR *do* correspond to a BinEntry
-
- //AT Attribute Tag; // 2 16-bit unsigned short integers
- //FL Floating Point Single; // 32-bit IEEE 754:1985 float
- //FD Floating Point Double; // 64-bit IEEE 754:1985 double
- //UN Unknown; // Any length of bytes
- //UT Unlimited Text; // At most 2^32 -1 chars
- //OB Other Byte String; // String of bytes (VR independant)
- //OW Other Word String; // String of 16-bit words (VR dependant)
-
- bn = new gdcmBinEntry(NewDocEntry->GetDictEntry());
- bn->Copy(NewDocEntry);
- set->AddEntry(bn);
- LoadDocEntry(bn);
- }
- if (NewDocEntry->GetGroup() == 0x7fe0 &&
- NewDocEntry->GetElement() == 0x0010 ) {
- if (NewDocEntry->GetLength()==0xffffffff)
- // Broke US.3405.1.dcm
-
+ }
+ }
+ else
+ {
+ if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
+ {
+ ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
+ dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, "
+ "nor BinEntry. Probably unknown VR.");
+ }
+
+ ////// BinEntry or UNKOWN VR:
+ gdcmBinEntry *bn = new gdcmBinEntry(newDocEntry->GetDictEntry());
+ bn->Copy(newDocEntry);
+ set->AddEntry(bn);
+ LoadDocEntry(bn);
+ }
+
+ if (newDocEntry->GetGroup() == 0x7fe0 &&
+ newDocEntry->GetElement() == 0x0010 )
+ {
+ if (newDocEntry->GetReadLength()==0xffffffff)
+ {
+ // Broken US.3405.1.dcm
Parse7FE0(); // to skip the pixels
- // (multipart JPEG/RLE are trouble makers)
- } else {
- SkipToNextDocEntry(NewDocEntry); // to be sure we are at the beginning
- 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)
+ // (multipart JPEG/RLE are trouble makers)
+ }
+ else
+ {
+ SkipToNextDocEntry(newDocEntry);
+ l = newDocEntry->GetFullLength();
+ }
+ }
+ else
+ {
+ // 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 )
+ {
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);
-
- if (l != 0) { // Don't try to parse zero-length sequences
-
+ }
+ }
+ // no other way to create it ...
+ gdcmSeqEntry *sq = new gdcmSeqEntry(newDocEntry->GetDictEntry(),
+ set->GetDepthLevel());
+ sq->Copy(newDocEntry);
+ sq->SetDelimitorMode(delim_mode);
+ sq->SetDepthLevel(depth);
+
+ if ( l != 0 )
+ { // Don't try to parse zero-length sequences
long lgt = ParseSQ( sq,
- NewDocEntry->GetOffset(),
+ newDocEntry->GetOffset(),
l, delim_mode);
- }
- // FIXME : on en fait quoi, de lgt ?
+ (void)lgt; //not used...
+ }
set->AddEntry(sq);
- if ( !delim_mode && ftell(fp)-offset >= l_max) {
+ if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ {
break;
- }
- }
+ }
+ }
+ delete newDocEntry;
}
- delete NewDocEntry;
- return l; // ??
+
+ return l; // Probably useless
}
/**
* \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) {
+long gdcmDocument::ParseSQ(gdcmSeqEntry *set,
+ 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()) {
- //add the Sequence Delimitor // TODO : find the trick to put it properly !
- set->SetSequenceDelimitationItem(NewDocEntry);
- break;
- }
- }
- if (!delim_mode && (ftell(fp)-offset) >= l_max) {
- break;
+ //int depth = set->GetDepthLevel();
+ //(void)depth; //not used
+
+ while (true)
+ {
+ gdcmDocEntry *newDocEntry = ReadNextDocEntry();
+ if ( !newDocEntry )
+ {
+ // FIXME Should warn user
+ break;
+ }
+ if( delim_mode )
+ {
+ if ( newDocEntry->IsSequenceDelimitor() )
+ {
+ set->SetSequenceDelimitationItem( newDocEntry );
+ break;
+ }
+ }
+ if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ {
+ break;
}
- itemSQ = new gdcmSQItem(set->GetDepthLevel());
- itemSQ->AddEntry(NewDocEntry); // no value, no voidArea. Think of it while printing !
- l= NewDocEntry->GetReadLength();
+
+ gdcmSQItem *itemSQ = new gdcmSQItem(set->GetDepthLevel());
+ itemSQ->AddEntry(newDocEntry);
+ unsigned int l = newDocEntry->GetReadLength();
- if (l ==0xffffffff)
+ if ( l == 0xffffffff )
+ {
dlm_mod = true;
+ }
else
- dlm_mod=false;
-
- lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod);
+ {
+ dlm_mod = false;
+ }
+
+ int lgr = ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+ (void)lgr; //FIXME not used
- set->AddEntry(itemSQ);
- SQItemNumber ++; // a voir
- if (!delim_mode && (ftell(fp)-offset) >= l_max) {
+ set->AddEntry(itemSQ, SQItemNumber);
+ SQItemNumber++;
+ if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ {
break;
- }
+ }
}
- lgth = ftell(fp) - offset;
- return(lgth);
+
+ int lgth = ftell(Fp) - offset;
+ return lgth;
}
/**
* the value specified with gdcmDocument::SetMaxSizeLoadEntry()
* @param Entry Header Entry (Dicom Element) to be dealt with
*/
-void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) {
+void gdcmDocument::LoadDocEntry(gdcmDocEntry* 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 )
+ {
+ ((gdcmValEntry *)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) {
- std::ostringstream s;
- ((gdcmValEntry *)Entry)->SetValue(s.str());
+
+ std::ostringstream s;
+ if (length > MaxSizeLoadEntry)
+ {
+ if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) )
+ {
+ s << "gdcm::NotLoaded (BinEntry)";
+ s << " Address:" << (long)entry->GetOffset();
+ s << " Length:" << entry->GetLength();
+ s << " x(" << std::hex << entry->GetLength() << ")";
+ binEntryPtr->SetValue(s.str());
+ }
// 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);
+ // Following return introduced by JPR on version 1.25. Since the
+ // treatement of a ValEntry is never executed (doh!) this means
+ // we were lucky up to now because we NEVER encountered a ValEntry
+ // whose length was bigger thant MaxSizeLoadEntry !? I can't believe
+ // this could ever work...
+ return; //FIXME FIXME FIXME FIXME JPR ????
+
+ // Be carefull : a BinEntry IS_A ValEntry ...
+ if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) )
+ {
+ s << "gdcm::NotLoaded. (ValEntry)";
+ s << " Address:" << (long)entry->GetOffset();
+ s << " Length:" << entry->GetLength();
+ s << " x(" << std::hex << entry->GetLength() << ")";
+ valEntryPtr->SetValue(s.str());
+ }
+ // to be sure we are at the end of the value ...
+ fseek(Fp,(long)entry->GetOffset()+(long)entry->GetLength(),SEEK_SET);
+
+ return;
+ }
+
+ // When we find a BinEntry not very much can be done :
+ if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) )
+ {
+
+ LoadEntryVoidArea(binEntryPtr);
+ s << "gdcm::Loaded (BinEntry)";
+ binEntryPtr->SetValue(s.str());
return;
}
- // Any compacter code suggested (?)
- if ( IsDocEntryAnInteger(Entry) ) {
- guint32 NewInt;
+ /// \todo Any compacter code suggested (?)
+ if ( IsDocEntryAnInteger(entry) )
+ {
+ uint32_t NewInt;
std::ostringstream s;
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());
+ ((gdcmValEntry *)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 ( gdcmValEntry* valEntry = dynamic_cast<gdcmValEntry* >(entry) )
+ {
+ if ( item_read != 1 )
+ {
+ dbg.Verbose(1, "gdcmDocument::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, "gdcmDocument::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.
*/
- void gdcmDocument::FindDocEntryLength (gdcmDocEntry *Entry) {
- guint16 element = Entry->GetElement();
- //guint16 group = Entry->GetGroup(); //FIXME
- std::string vr = Entry->GetVR();
- guint16 length16;
+void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry )
+ throw ( gdcmFormatError )
+{
+ uint16_t element = entry->GetElement();
+ std::string vr = entry->GetVR();
+ uint16_t length16;
- if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) )
+ if ( Filetype == gdcmExplicitVR && !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
// 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" && length32 == 0xffffffff )
{
- Entry->SetLength(FindDocEntryLengthOB());
+ uint32_t lengthOB;
+ try
+ {
+ lengthOB = FindDocEntryLengthOB();
+ }
+ catch ( gdcmFormatUnexpected )
+ {
+ // 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 gdcmFormatError( "gdcmDocument::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() );
+ gdcmDictEntry* 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
*/
-void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry)
+void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry )
{
- if (filetype != gdcmExplicitVR)
+ if ( Filetype != gdcmExplicitVR )
+ {
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();
}
}
* @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 gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr)
{
char msg[100]; // for sprintf
- bool RealExplicit = true;
+ 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 && !gdcmGlobal::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());
+ entry->GetGroup(), entry->GetElement());
dbg.Verbose(1, "gdcmDocument::FindVR: ",msg);
- if (Entry->GetGroup()%2 && Entry->GetElement() == 0x0000) { // Group length is UL !
- gdcmDictEntry* NewEntry = NewVirtualDictEntry(
- Entry->GetGroup(),Entry->GetElement(),
- "UL","FIXME","Group Length");
- Entry->SetDictEntry(NewEntry);
+
+ if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000)
+ {
+ // Group length is UL !
+ gdcmDictEntry* 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);
+ gdcmDictEntry* newEntry = NewVirtualDictEntry(
+ entry->GetGroup(), entry->GetElement(),
+ vr, "FIXME", entry->GetName());
+ entry->SetDictEntry(newEntry);
}
- return(true);
+
+ return true;
}
/**
* @param Entry
* @return Transformed entry value
*/
-std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry)
+std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *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 = ((gdcmValEntry *)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 ((gdcmValEntry *)entry)->GetValue();
}
/**
* @param Entry
* @return Reverse transformed entry value
*/
-std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry)
+std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* 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
+ Tokenize (((gdcmValEntry *)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, "\\");
+ Tokenize (((gdcmValEntry *)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 ((gdcmValEntry *)entry)->GetValue();
}
/**
*/
void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *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 this heuristic.
+ * applying some heuristics.
*/
-void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, guint32 FoundLength)
+void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *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
- << " in x(" << std::hex << gr << "," << el <<")" << std::dec;
- dbg.Verbose(0,s.str().c_str());
+ s << "Warning : Tag with uneven length "
+ << foundLength
+ << " in x(" << std::hex << gr << "," << el <<")" << std::dec;
+ dbg.Verbose(0, s.str().c_str());
}
- // Sorry for the patch!
- // XMedCom did the trick to read some naughty GE images ...
- if (FoundLength == 13) {
- // The following 'if' will be removed when there is no more
- // images on Creatis HDs with a 13 length for Manufacturer...
- if ( (Entry->GetGroup() != 0x0008) ||
- ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){
- // end of remove area
- FoundLength =10;
- Entry->SetReadLength(10); // a bug is to be fixed
+ //////// Fix for some naughty General Electric images.
+ // Allthough not recent many such GE corrupted images are still present
+ // on Creatis hard disks. Hence this fix shall remain when such images
+ // are no longer in user (we are talking a few years, here)...
+ // 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 ) )
+ {
+ foundLength = 10;
+ entry->SetReadLength(10); /// \todo a bug is to be fixed !?
}
}
- // to fix some garbage 'Leonardo' Siemens images
- // May be commented out to avoid overhead
- else if ( (Entry->GetGroup() == 0x0009) &&
- ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){
- FoundLength =4;
- Entry->SetReadLength(4); // a bug is to be fixed
+ //////// Fix for some brain-dead 'Leonardo' Siemens images.
+ // 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 ) )
+ {
+ foundLength = 4;
+ entry->SetReadLength(4); /// \todo a bug is to be fixed !?
}
- // end of fix
- // to try to 'go inside' SeQuences (with length), and not to skip them
- else if ( Entry->GetVR() == "SQ")
- {
- if (enableSequences) // only if the user does want to !
- FoundLength =0; // ReadLength is unchanged
+ else if ( entry->GetVR() == "SQ" )
+ {
+ foundLength = 0; // ReadLength is unchanged
}
- // we found a 'delimiter' element
- // fffe|xxxx is just a marker, we don't take its length into account
- else if(Entry->GetGroup() == 0xfffe)
+ //////// 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 )
{
- // *normally, fffe|0000 doesn't exist !
- if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm
- // causes extra troubles :-(
- FoundLength =0;
+ // 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 )
+ {
+ foundLength = 0;
+ }
}
- Entry->SetUsableLength(FoundLength);
+ entry->SetUsableLength(foundLength);
}
/**
* @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 gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *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
+ // corrupted group length [e.g. have a glance at offset x(8336) of
+ // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm].
+ // Since for dicom compliant and well behaved headers, the present
+ // test is useless (and might even look a bit paranoid), when we
+ // encounter such an ill-formed image, we simply display a warning
+ // message and proceed on parsing (while crossing fingers).
std::ostringstream s;
- int filePosition = ftell(fp);
+ int filePosition = ftell(Fp);
s << "Erroneous Group Length element length on : (" \
<< std::hex << group << " , " << element
<< ") -before- position x(" << filePosition << ")"
<< "lgt : " << length;
- // These 2 lines commented out : a *very dirty* patch
- // to go on PrintHeader'ing gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
- // have a glance at offset x(8336) ...
- // For *regular* headers, the test is useless..
- // lets's print a warning message and go on,
- // instead of giving up with an error message
-
- //std::cout << s.str().c_str() << std::endl;
- // dbg.Error("gdcmDocument::IsDocEntryAnInteger",
- // s.str().c_str());
+ dbg.Verbose(0, "gdcmDocument::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;
}
+
/**
* \brief Find the Length till the next sequence delimiter
* \warning NOT end user intended method !
* @return
*/
- guint32 gdcmDocument::FindDocEntryLengthOB(void) {
+uint32_t gdcmDocument::FindDocEntryLengthOB()
+ throw( gdcmFormatUnexpected )
+{
// 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 ( gdcmFormatError )
+ {
+ throw gdcmFormatError("gdcmDocument::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, "gdcmDocument::FindDocEntryLengthOB: neither an Item "
+ "tag nor a Sequence delimiter tag.");
+ fseek(Fp, positionOnEntry, SEEK_SET);
+ throw gdcmFormatUnexpected("gdcmDocument::FindDocEntryLengthOB()",
+ "Neither an Item tag nor a Sequence "
+ "delimiter tag.");
+ }
+
+ if ( elem == 0xe0dd )
+ {
+ foundSequenceDelimiter = true;
}
- if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) // for bogus header
- FoundSequenceDelimiter = true;
- else if ( n != 0xe000 )
+
+ uint32_t itemLength = ReadInt32();
+ // We add 4 bytes since we just read the ItemLength with ReadInt32
+ totalLength += itemLength + 4;
+ SkipBytes(itemLength);
+
+ if ( foundSequenceDelimiter )
{
- 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;
+ 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 gdcmDocument::ReadInt16()
+ throw( gdcmFormatError )
+{
+ uint16_t g;
+ size_t item_read = fread (&g, (size_t)2,(size_t)1, Fp);
+ if ( item_read != 1 )
+ {
+ if( ferror(Fp) )
+ {
+ throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
+ }
+ throw gdcmFormatError( "gdcmDocument::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 gdcmDocument::ReadInt32()
+ throw( gdcmFormatError )
+{
+ uint32_t g;
+ size_t item_read = fread (&g, (size_t)4,(size_t)1, Fp);
+ if ( item_read != 1 )
+ {
+ if( ferror(Fp) )
+ {
+ throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
+ }
+ throw gdcmFormatError( "gdcmDocument::ReadInt32()", "EOF." );
}
- errno = 0;
g = SwapLong(g);
return g;
}
* \warning NOT end user intended method !
* @return
*/
-void gdcmDocument::SkipBytes(guint32 NBytes) {
+void gdcmDocument::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 gdcmDocument::Initialise()
{
RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
- RefShaDict = (gdcmDict*)0;
+ RefShaDict = NULL;
}
/**
* it's neither ACR-NEMA nor DICOM
* true when we hope ours assuptions are OK
*/
-bool gdcmDocument::CheckSwap() {
-
+bool gdcmDocument::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) {
+ char *entCur = deb + 128;
+ if( memcmp(entCur, "DICM", (size_t)4) == 0 )
+ {
dbg.Verbose(1, "gdcmDocument::CheckSwap:", "looks like DICOM Version3");
// Next, determine the value representation (VR). Let's skip to the
// 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
// instead of just checking for UL, OB and UI !? group 0000
{
- filetype = gdcmExplicitVR;
+ Filetype = gdcmExplicitVR;
dbg.Verbose(1, "gdcmDocument::CheckSwap:",
"explicit Value Representation");
}
else
{
- filetype = gdcmImplicitVR;
+ Filetype = gdcmImplicitVR;
dbg.Verbose(1, "gdcmDocument::CheckSwap:",
"not an explicit Value Representation");
}
- if (net2host)
+ if ( net2host )
{
- sw = 4321;
+ SwapCode = 4321;
dbg.Verbose(1, "gdcmDocument::CheckSwap:",
"HostByteOrder != NetworkByteOrder");
- }
+ }
else
{
- sw = 0;
+ SwapCode = 0;
dbg.Verbose(1, "gdcmDocument::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
// 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);
+ 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 = gdcmACR;
return true;
case 0x04000000 :
- sw = 4321;
- filetype = gdcmACR;
+ SwapCode = 4321;
+ Filetype = gdcmACR;
return true;
case 0x00000400 :
- sw = 2143;
- filetype = gdcmACR;
+ SwapCode = 2143;
+ Filetype = gdcmACR;
return true;
case 0x00000004 :
- sw = 0;
- filetype = gdcmACR;
+ SwapCode = 0;
+ Filetype = gdcmACR;
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 = gdcmACR;
+ return true;
+ case 0x0200 :
+ case 0x0400 :
+ case 0x0800 :
+ SwapCode = 4321;
+ Filetype = gdcmACR;
+ return true;
+ default :
+ dbg.Verbose(0, "gdcmDocument::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 = gdcmUnknown;
+ 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 gdcmDocument::SwitchSwapToBigEndian()
{
dbg.Verbose(1, "gdcmDocument::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
*/
-void gdcmDocument::SetMaxSizeLoadEntry(long NewSize)
+void gdcmDocument::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;
}
* \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE
* @param NewSize
*/
-void gdcmDocument::SetMaxSizePrintEntry(long NewSize)
+void gdcmDocument::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)
+gdcmDocEntry* gdcmDocument::ReadNextDocEntry()
+{
+ uint16_t group;
+ uint16_t elem;
+
+ try
+ {
+ group = ReadInt16();
+ elem = ReadInt16();
+ }
+ catch ( gdcmFormatError e )
+ {
// 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;
+ std::cout << e;
+ return 0;
}
- 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)
-{
- gdcmDictEntry *NewTag = GetDictEntryByName(Name);
- if (!NewTag)
- NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name);
+ gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem);
+ FindDocEntryVR(newEntry);
- gdcmDocEntry* NewEntry = new gdcmDocEntry(NewTag);
- if (!NewEntry)
+ try
{
- dbg.Verbose(1, "gdcmDocument::ObtainDocEntryByName",
- "failed to allocate gdcmDocEntry");
- return (gdcmDocEntry *)0;
+ FindDocEntryLength(newEntry);
+ }
+ catch ( gdcmFormatError e )
+ {
+ // Call it quits
+ std::cout << e;
+ delete newEntry;
+ return 0;
}
- 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);
+ 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 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)
- {
- dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber",
- "failed to allocate gdcmDocEntry");
- return NULL;
- }
- return NewEntry;
-}
-
-/// \todo Never used; commented out, waiting for removal.
-/**
- * \brief Small utility function that creates a new manually crafted
- * (as opposed as read from the file) gdcmDocEntry with user
- * specified name and adds it to the public tag hash table.
- * \note A fake TagKey is generated so the PubDict can keep it's coherence.
- * @param NewTagName The name to be given to this new tag.
- * @param VR The Value Representation to be given to this new tag.
- * @return The newly hand crafted Element Value.
- */
-//gdcmDocEntry *gdcmDocument::NewManualDocEntryToPubDict(std::string NewTagName,
-// std::string VR)
-//{
-// gdcmDocEntry *NewEntry = NULL;
-// guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
-// guint32 FreeElem = 0;
-// gdcmDictEntry *DictEntry = NULL;
-//
-// FreeElem = GenerateFreeTagKeyInGroup(StuffGroup);
-// if (FreeElem == UINT32_MAX)
-// {
-// dbg.Verbose(1, "gdcmHeader::NewManualDocEntryToPubDict",
-// "Group 0xffff in Public Dict is full");
-// return NULL;
-// }
-//
-// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem,
-// VR, "GDCM", NewTagName);
-// NewEntry = new gdcmDocEntry(DictEntry);
-// AddEntry(NewEntry);
-// return NewEntry;
-//}
-
-/**
- * \brief Generate a free TagKey i.e. a TagKey that is not present
+/**
+ * \brief Generate a free gdcmTagKey i.e. a gdcmTagKey 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 gdcmDocument::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)
+ gdcmTagKey key = gdcmDictEntry::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 gdcmDocument::fp
+ * is placed at the beginning of a tag check whether this
+ * tag is (TestGroup, TestElement).
+ * \warning On success the internal file pointer \ref gdcmDocument::fp
+ * is modified to point after the tag.
+ * On failure (i.e. when the tag wasn't the expected tag
+ * (TestGroup, TestElement) the internal file pointer
+ * \ref gdcmDocument::fp is restored to it's original position.
+ * @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 gdcmDocument::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)
+ long positionOnEntry = ftell(Fp);
+ long currentPosition = ftell(Fp); // On debugging purposes
+
+ //// Read the Item Tag group and element, and make
+ // sure they are what we expected:
+ uint16_t itemTagGroup = ReadInt16();
+ uint16_t itemTagElement = ReadInt16();
+ if ( itemTagGroup != testGroup || itemTagElement != testElement )
{
- found = RefPubDict->GetDictEntryByName(Name);
- if (found)
- return found;
- }
- if (RefShaDict)
- {
- found = RefShaDict->GetDictEntryByName(Name);
- 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, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:");
+ dbg.Verbose(0, s.str().c_str());
+ fseek(Fp, positionOnEntry, SEEK_SET);
+
+ return false;
}
- return found;
+ return true;
}
/**
- * \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 of the searched DictEntry
- * @param element element of the searched DictEntry
- * @return Corresponding DictEntry when it exists, NULL otherwise.
+ * \brief Assuming the internal file pointer \ref gdcmDocument::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
+ * 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.
+ * @return On success returns the length associated to the tag. On failure
+ * returns 0.
*/
-gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element)
+uint32_t gdcmDocument::ReadTagLength(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)
+ long positionOnEntry = ftell(Fp);
+ (void)positionOnEntry;
+
+ if ( !ReadTag(testGroup, testElement) )
{
- found = RefPubDict->GetDictEntryByNumber(group, element);
- if (found)
- return found;
+ return 0;
}
- if (RefShaDict)
+
+ //// Then read the associated Item Length
+ long currentPosition = ftell(Fp);
+ uint32_t itemLength = ReadInt32();
{
- found = RefShaDict->GetDictEntryByNumber(group, element);
- if (found)
- return found;
+ 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());
}
- return found;
+ return itemLength;
}
-
/**
- * \ingroup gdcmDocument
* \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files
- * \ No other way so 'skip' the Data
+ * No other way so 'skip' the Data
*
*/
-void gdcmDocument::Parse7FE0 (void) {
-
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
+void gdcmDocument::Parse7FE0 ()
+{
+ gdcmDocEntry* element = GetDocEntryByNumber(0x0002, 0x0010);
+ if ( !element )
+ {
+ // Should warn user FIXME
return;
+ }
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if (Transfer == UI1_2_840_10008_1_2 )
- return;
- if ( Transfer == UI1_2_840_10008_1_2_1 )
- return;
- if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier !
- return;
- if ( Transfer == UI1_2_840_10008_1_2_1_99 )
+ if ( IsImplicitVRLittleEndianTransferSyntax()
+ || IsExplicitVRLittleEndianTransferSyntax()
+ || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier !
+ || IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+ {
return;
-
- int nb;
- std::string str_nb=GetEntryByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16;
}
-
- guint16 ItemTagGr,ItemTagEl;
- int ln;
- long ftellRes;
- // -------------------- for Parsing : Position on begining of Jpeg/RLE Pixels
+ // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels
- if ( Transfer != UI1_1_2_840_10008_1_2_5 ) { // !RLELossLessTransferSyntax
- // JPEG Image
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr
- fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
- ftellRes=ftell(fp);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Basic Offset Table Item Length
- printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n",
- (unsigned)ftellRes,ln,ln);
- if (ln != 0) {
- // What is it used for ??
- char * BasicOffsetTableItemValue= new char[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
- guint32 a;
- for (int i=0;i<ln;i+=4){
- a=str2num(&BasicOffsetTableItemValue[i],guint32);
- printf(" x(%08x) %d\n",a,a);
- }
- }
-
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
-
- while ( ( ItemTagGr==0xfffe) && (ItemTagEl!=0xe0dd) ) { // Parse fragments
-
- ftellRes=ftell(fp);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // length
- printf(" at %x : fragment length %d x(%08x)\n",
- (unsigned)ftellRes, ln,ln);
-
- // ------------------------
- fseek(fp,ln,SEEK_CUR); // skipping (not reading) fragment pixels
- // ------------------------
-
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
- }
+ //// Read the Basic Offset Table Item Tag length...
+ uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
- } else {
+ //// ... 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);
- // RLE Image
- long RleSegmentLength[15],fragmentLength;
- guint32 nbRleSegments;
- guint32 RleSegmentOffsetTable[15];
- ftellRes=ftell(fp);
- // Basic Offset Table with Item Value
- // Item Tag
- fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr
- fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
- // Item Length
- ftellRes=ftell(fp);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Basic Offset Table Item Length
- printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n",
- (unsigned)ftellRes,ln,ln);
- if (ln != 0) {
- // What is it used for ??
- char * BasicOffsetTableItemValue= new char[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
- guint32 a;
- for (int i=0;i<ln;i+=4){
- a=str2num(&BasicOffsetTableItemValue[i],guint32);
- printf(" x(%08x) %d\n",a,a);
- }
+ for (unsigned int i=0; i < itemLength; i += 4 )
+ {
+ uint32_t individualLength = str2num(&basicOffsetTableItemValue[i],uint32_t);
+ std::ostringstream s;
+ s << " Read one length: ";
+ s << std::hex << individualLength << std::endl;
+ dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str());
}
+ delete[] basicOffsetTableItemValue;
+ }
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
-
- // while 'Sequence Delimiter Item' (fffe,e0dd) not found
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
- // Parse fragments of the current Fragment (Frame)
- ftellRes=ftell(fp);
- fread(&fragmentLength,4,1,fp);
- if(GetSwapCode())
- fragmentLength=SwapLong(fragmentLength); // length
- printf(" at %x : 'fragment' length %d x(%08x)\n",
- (unsigned)ftellRes, (unsigned)fragmentLength,(unsigned)fragmentLength);
-
- //------------------ scanning (not reading) fragment pixels
-
- fread(&nbRleSegments,4,1,fp); // Reading : Number of RLE Segments
- if(GetSwapCode())
- nbRleSegments=SwapLong(nbRleSegments);
- printf(" Nb of RLE Segments : %d\n",nbRleSegments);
+ if ( ! IsRLELossLessTransferSyntax() )
+ {
+ // JPEG Image
+
+ //// We then skip (not reading them) all the fragments of images:
+ while ( (itemLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ SkipBytes(itemLength);
+ }
+ }
+ else
+ {
+ // RLE Image
+ long ftellRes;
+ long rleSegmentLength[15], fragmentLength;
+
+ // While we find some items:
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ // Parse fragments of the current Fragment (Frame)
+ //------------------ scanning (not reading) fragment pixels
+ uint32_t nbRleSegments = ReadInt32();
- for(int k=1; k<=15; k++) { // Reading RLE Segments Offset Table
- ftellRes=ftell(fp);
- fread(&RleSegmentOffsetTable[k],4,1,fp);
- if(GetSwapCode())
- RleSegmentOffsetTable[k]=SwapLong(RleSegmentOffsetTable[k]);
- printf(" at : %x Offset Segment %d : %d (%x)\n",
- (unsigned)ftellRes,k,RleSegmentOffsetTable[k],
- RleSegmentOffsetTable[k]);
+ //// Reading RLE Segments Offset Table
+ uint32_t rleSegmentOffsetTable[15];
+ for(int k=1; k<=15; k++)
+ {
+ ftellRes = ftell(Fp);
+ rleSegmentOffsetTable[k] = ReadInt32();
}
- if (nbRleSegments>1) { // skipping (not reading) RLE Segments
- 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);
- fseek(fp,RleSegmentLength[k],SEEK_CUR);
+ // 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);
+ SkipBytes(rleSegmentLength[k]);
}
}
- 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);
-
- fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR);
-
- // ------------------ end of scanning fragment pixels
-
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
- }
+
+ rleSegmentLength[nbRleSegments] = fragmentLength
+ - rleSegmentOffsetTable[nbRleSegments];
+ ftellRes = ftell(Fp);
+ SkipBytes(rleSegmentLength[nbRleSegments]);
+ }
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item");
+ dbg.Verbose(0, " at end of RLE item sequence");
+ }
}
- return;
}
+/**
+ * \brief Compares two documents, according to \ref gdcmDicomDir 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)
+{
+ // Patient Name
+ std::string s1 = GetEntryByNumber(0x0010,0x0010);
+ std::string s2 = document.GetEntryByNumber(0x0010,0x0010);
+ if(s1 < s2)
+ {
+ return true;
+ }
+ else if(s1 > s2)
+ {
+ return false;
+ }
+ else
+ {
+ // Patient ID
+ s1 = GetEntryByNumber(0x0010,0x0020);
+ s2 = document.GetEntryByNumber(0x0010,0x0020);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if ( s1 > s2 )
+ {
+ return true;
+ }
+ else
+ {
+ // Study Instance UID
+ 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 = GetEntryByNumber(0x0020,0x000e);
+ s2 = document.GetEntryByNumber(0x0020,0x000e);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
+ }
+ }
+ }
+ return false;
+}
+
+
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff