Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2004/06/28 09:51:02 $
- Version: $Revision: 1.37 $
+ Date: $Date: 2005/02/07 09:51:03 $
+ Version: $Revision: 1.225 $
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.
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
#include "gdcmValEntry.h"
#include "gdcmBinEntry.h"
#include "gdcmSeqEntry.h"
-
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
+#include "gdcmTS.h"
+#include "gdcmDictSet.h"
+#include "gdcmDocEntrySet.h"
+#include "gdcmSQItem.h"
-#include <errno.h>
#include <vector>
+#include <iomanip>
+#include <fstream>
// For nthos:
-#ifdef _MSC_VER
+#if defined(_MSC_VER) || defined(__BORLANDC__) || defined(__MINGW32__)
#include <winsock.h>
-#else
- #include <netinet/in.h>
#endif
-# include <iomanip>
-
-// Implicit VR Little Endian
-#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2"
-// Explicit VR Little Endian
-#define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1"
-// Deflated Explicit VR Little Endian
-#define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99"
-// Explicit VR Big Endian
-#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2"
-// JPEG Baseline (Process 1)
-#define UI1_2_840_10008_1_2_4_50 "1.2.840.10008.1.2.4.50"
-// JPEG Extended (Process 2 & 4)
-#define UI1_2_840_10008_1_2_4_51 "1.2.840.10008.1.2.4.51"
-// JPEG Extended (Process 3 & 5)
-#define UI1_2_840_10008_1_2_4_52 "1.2.840.10008.1.2.4.52"
-// JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8)
-#define UI1_2_840_10008_1_2_4_53 "1.2.840.10008.1.2.4.53"
-// JPEG Full Progression, Non-Hierarchical (Process 10 & 12)
-#define UI1_2_840_10008_1_2_4_55 "1.2.840.10008.1.2.4.55"
-// JPEG Lossless, Non-Hierarchical (Process 14)
-#define UI1_2_840_10008_1_2_4_57 "1.2.840.10008.1.2.4.57"
-// JPEG Lossless, Hierarchical, First-Order Prediction (Process 14,
-// [Selection Value 1])
-#define UI1_2_840_10008_1_2_4_70 "1.2.840.10008.1.2.4.70"
-// JPEG 2000 Lossless
-#define UI1_2_840_10008_1_2_4_90 "1.2.840.10008.1.2.4.90"
-// JPEG 2000
-#define UI1_2_840_10008_1_2_4_91 "1.2.840.10008.1.2.4.91"
-// RLE Lossless
-#define UI1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5"
-// UI1_1_2_840_10008_1_2_5
-#define str2num(str, typeNum) *((typeNum *)(str))
+#ifdef CMAKE_HAVE_NETINET_IN_H
+ #include <netinet/in.h>
+#endif
+namespace gdcm
+{
//-----------------------------------------------------------------------------
-// Refer to gdcmDocument::CheckSwap()
-const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256;
+// Refer to Document::CheckSwap()
+//const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
-// Refer to gdcmDocument::SetMaxSizeLoadEntry()
-const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 0x7fffffff;// 4096;//
-const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff;//64;
+// Refer to Document::SetMaxSizeLoadEntry()
+const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
+const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff;
//-----------------------------------------------------------------------------
// Constructor / Destructor
-
+// Constructors and destructors are protected to avoid user to invoke directly
/**
* \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')
+ * @param filename 'Document' (File or DicomDir) to be opened for parsing
*/
-gdcmDocument::gdcmDocument(std::string const & inFilename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow)
- : gdcmElementSet(-1) {
- enableSequences=enable_sequences;
- IgnoreShadow =ignore_shadow;
-
+Document::Document( std::string const &filename )
+ :ElementSet(-1)
+{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Filename = inFilename;
- Initialise();
+ Filename = filename;
+ Initialize();
- if ( !OpenFile(exception_on_error))
+ Fp = 0;
+ if ( !OpenFile() )
+ {
return;
+ }
+
+ Group0002Parsed = false;
+
+ gdcmWarningMacro( "Starting parsing of file: " << Filename.c_str());
+ // Fp->seekg( 0, std::ios::beg);
- dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ",
- Filename.c_str());
- rewind(fp);
-
- fseek(fp,0L,SEEK_END);
- long lgt = ftell(fp);
+ Fp->seekg(0, std::ios::end);
+ long lgt = Fp->tellg();
- rewind(fp);
+ Fp->seekg(0, std::ios::beg);
+
CheckSwap();
- long beg = ftell(fp);
+ long beg = Fp->tellg();
lgt -= beg;
- SQDepthLevel=0;
-
- long l=ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
- (void)l; //is l used anywhere ?
+ ParseDES( this, beg, lgt, false); // Loading is done during parsing
- rewind(fp);
+ Fp->seekg( 0, std::ios::beg);
// Load 'non string' values
- std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
- if( PhotometricInterpretation == "PALETTE COLOR " ) {
- LoadEntryVoidArea(0x0028,0x1200); // gray LUT
- LoadEntryVoidArea(0x0028,0x1201); // R LUT
- LoadEntryVoidArea(0x0028,0x1202); // G LUT
- LoadEntryVoidArea(0x0028,0x1203); // B LUT
+ std::string PhotometricInterpretation = GetEntryValue(0x0028,0x0004);
+ if( PhotometricInterpretation == "PALETTE COLOR " )
+ {
+ LoadEntryBinArea(0x0028,0x1200); // gray LUT
+ /// FIXME FIXME FIXME
+ /// The tags refered by the three following lines used to be CORRECTLY
+ /// defined as having an US Value Representation in the public
+ /// dictionary. BUT the semantics implied by the three following
+ /// lines state that the corresponding tag contents are in fact
+ /// the ones of a BinEntry.
+ /// In order to fix things "Quick and Dirty" the dictionary was
+ /// altered on PURPOSE but now contains a WRONG value.
+ /// In order to fix things and restore the dictionary to its
+ /// correct value, one needs to decided of the semantics by deciding
+ /// whether the following tags are either:
+ /// - multivaluated US, and hence loaded as ValEntry, but afterwards
+ /// also used as BinEntry, which requires the proper conversion,
+ /// - OW, and hence loaded as BinEntry, but afterwards also used
+ /// as ValEntry, which requires the proper conversion.
+ LoadEntryBinArea(0x0028,0x1201); // R LUT
+ LoadEntryBinArea(0x0028,0x1202); // G LUT
+ LoadEntryBinArea(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
+ // Segmented Red Palette Color LUT Data
+ LoadEntryBinArea(0x0028,0x1221);
+ // Segmented Green Palette Color LUT Data
+ LoadEntryBinArea(0x0028,0x1222);
+ // Segmented Blue Palette Color LUT Data
+ LoadEntryBinArea(0x0028,0x1223);
}
//FIXME later : how to use it?
- LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent)
+ LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent)
CloseFile();
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to read ACR-LibIDO formated images
+ // ----------------------------
+ // Specific code to allow gdcm to read ACR-LibIDO formated images
+ // Note: ACR-LibIDO is an extension of the ACR standard that was
+ // used at CREATIS. For the time being (say a couple years)
+ // we keep this kludge to allow a smooth move to gdcm for
+ // CREATIS developpers (sorry folks).
//
// if recognition code tells us we deal with a LibIDO image
// we switch lineNumber and columnNumber
//
std::string RecCode;
- RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code
+ RecCode = GetEntryValue(0x0008, 0x0010); // recognition code (RET)
if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
// with "little-endian strings"
{
- Filetype = gdcmACR_LIBIDO;
- std::string rows = GetEntryByNumber(0x0028, 0x0010);
- std::string columns = GetEntryByNumber(0x0028, 0x0011);
- SetEntryByNumber(columns, 0x0028, 0x0010);
- SetEntryByNumber(rows , 0x0028, 0x0011);
+ Filetype = ACR_LIBIDO;
+ std::string rows = GetEntryValue(0x0028, 0x0010);
+ std::string columns = GetEntryValue(0x0028, 0x0011);
+ SetValEntry(columns, 0x0028, 0x0010);
+ SetValEntry(rows , 0x0028, 0x0011);
}
- // ----------------- End of Special Patch ----------------
-
- printLevel = 1; // 'Medium' print level by default
+ // --- End of ACR-LibIDO kludge ---
}
/**
- * \brief constructor
- * @param exception_on_error
+ * \brief This default constructor doesn't parse the file. You should
+ * then invoke \ref Document::SetFileName and then the parsing.
*/
-gdcmDocument::gdcmDocument(bool exception_on_error)
- :gdcmElementSet(-1) {
- (void)exception_on_error;
- enableSequences=0;
+Document::Document()
+ :ElementSet(-1)
+{
+ Fp = 0;
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialise();
-
- printLevel = 1; // 'Medium' print level by default
+ Initialize();
+ SwapCode = 1234;
+ Filetype = ExplicitVR;
+ Group0002Parsed = false;
}
/**
* \brief Canonical destructor.
*/
-gdcmDocument::~gdcmDocument (void) {
+Document::~Document ()
+{
RefPubDict = NULL;
RefShaDict = NULL;
-
- // Recursive clean up of sequences
- for (TagDocEntryHT::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) {
- RefPubDict->Print(os);
-}
-
-/**
- * \brief Prints The Dict Entries of THE shadow Dicom Dictionary
- * @return
- */
-void gdcmDocument::PrintShaDict(std::ostream & os) {
- RefShaDict->Print(os);
}
//-----------------------------------------------------------------------------
/**
* \brief Get the public dictionary used
*/
-gdcmDict *gdcmDocument::GetPubDict(void) {
+Dict *Document::GetPubDict()
+{
return RefPubDict;
}
/**
* \brief Get the shadow dictionary used
*/
-gdcmDict *gdcmDocument::GetShaDict(void) {
+Dict *Document::GetShaDict()
+{
return RefShaDict;
}
/**
* \brief Set the shadow dictionary used
- * \param dict dictionary to use in shadow
+ * @param dict dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(gdcmDict *dict){
- RefShaDict=dict;
+bool Document::SetShaDict(Dict *dict)
+{
+ RefShaDict = dict;
return !RefShaDict;
}
/**
* \brief Set the shadow dictionary used
- * \param dictName name of the dictionary to use in shadow
+ * @param dictName name of the dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(DictKey dictName){
- RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName);
+bool Document::SetShaDict(DictKey const &dictName)
+{
+ RefShaDict = Global::GetDicts()->GetDict(dictName);
return !RefShaDict;
}
/**
* \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current gdcmDocument was properly parsed
+ * decides whether or not the current Document was properly parsed
* and contains the mandatory information for being considered as
* a well formed and usable Dicom/Acr File.
- * @return true when gdcmDocument is the one of a reasonable Dicom/Acr file,
+ * @return true when Document is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmDocument::IsReadable(void) {
- if(Filetype==gdcmUnknown) {
- //std::cout << " gdcmDocument::IsReadable: Filetype " << Filetype
- // << " " << "gdcmUnknown " << gdcmUnknown << std::endl; //JPR
- dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype");
+bool Document::IsReadable()
+{
+ if( Filetype == Unknown)
+ {
+ gdcmWarningMacro( "Wrong filetype");
return false;
}
- if(tagHT.empty()) {
- dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal"
- " hash table.");
+
+ if ( IsEmpty() )
+ {
+ gdcmWarningMacro( "No tag in internal hash table.");
return false;
}
- return(true);
+ return true;
}
-
/**
- * \brief Internal function that checks whether the Transfer Syntax given
- * as argument is the one present in the current document.
- * @param SyntaxToCheck The transfert syntax we need to check against.
- * @return True when SyntaxToCheck corresponds to the Transfer Syntax of
- * the current document. False either when the document contains
- * no Transfer Syntax, or when the Tranfer Syntaxes don't match.
+ * \brief Predicate for dicom version 3 file.
+ * @return True when the file is a dicom version 3.
*/
-bool gdcmDocument::IsGivenTransferSyntax(const std::string & SyntaxToCheck)
+bool Document::IsDicomV3()
{
- gdcmDocEntry *Entry = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Entry )
- return false;
-
- // The entry might be present but not loaded (parsing and loading
- // happen at differente stages): try loading and proceed with check...
- LoadDocEntrySafe(Entry);
- if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(Entry) )
- {
- std::string Transfer = ValEntry->GetValue();
- // The actual transfer (as read from disk) might be padded. We
- // first need to remove the potential padding. We can make the
- // weak assumption that padding was not executed with digits...
- while ( ! isdigit(Transfer[Transfer.length()-1]) )
- {
- Transfer.erase(Transfer.length()-1, 1);
- }
- if ( Transfer == SyntaxToCheck )
- return true;
- }
- return false;
+ // Checking if Transfer Syntax exists is enough
+ // Anyway, it's to late check if the 'Preamble' was found ...
+ // And ... would it be a rich idea to check ?
+ // (some 'no Preamble' DICOM images exist !)
+ return GetDocEntry(0x0002, 0x0010) != NULL;
}
/**
- * \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.
+ * \brief Predicate for Papyrus file
+ * Dedicated to whomsoever it may concern
+ * @return True when the file is a Papyrus file.
*/
-bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void)
+bool Document::IsPapyrus()
{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2);
+ // check for Papyrus private Sequence
+ DocEntry *e = GetDocEntry(0x0041, 0x1050);
+ if ( !e )
+ return false;
+ // check if it's actually a Sequence
+ if ( !dynamic_cast<SeqEntry*>(e) )
+ return false;
+ return true;
}
/**
- * \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.
+ * \brief returns the File Type
+ * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
+ * @return the FileType code
*/
-bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void)
+FileType Document::GetFileType()
{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1);
+ return Filetype;
}
/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a DeflatedExplicitVRLittleEndian one.
- * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
+ * \brief Accessor to the Transfer Syntax (when present) of the
+ * current document (it internally handles reading the
+ * value from disk when only parsing occured).
+ * @return The encountered Transfer Syntax of the current document.
*/
-bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void)
+std::string Document::GetTransferSyntax()
{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99);
-}
+ DocEntry *entry = GetDocEntry(0x0002, 0x0010);
+ if ( !entry )
+ {
+ return GDCM_UNKNOWN;
+ }
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a Explicit VR Big Endian one.
- * @return True when big endian found. False in all other cases.
- */
-bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void)
-{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2);
+ // The entry might be present but not loaded (parsing and loading
+ // happen at different stages): try loading and proceed with check...
+ LoadDocEntrySafe(entry);
+ if (ValEntry *valEntry = dynamic_cast< ValEntry* >(entry) )
+ {
+ 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 GDCM_UNKNOWN;
+ }
+ while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
+ {
+ transfer.erase(transfer.length()-1, 1);
+ }
+ return transfer;
+ }
+ return GDCM_UNKNOWN;
}
/**
- * \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(void)
-{
- 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.
+ * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS
+ * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
*/
-bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax(void)
+std::string Document::GetTransferSyntaxName()
{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51);
+ // use the TS (TS : Transfer Syntax)
+ std::string transferSyntax = GetEntryValue(0x0002,0x0010);
+
+ if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) )
+ {
+ gdcmErrorMacro( "Transfer Syntax not loaded. " << std::endl
+ << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" );
+ return "Uncompressed ACR-NEMA";
+ }
+ if ( transferSyntax == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Unfound Transfer Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
+ }
+
+ // we do it only when we need it
+ const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax );
+
+ // Global::GetTS() is a global static you shall never try to delete it!
+ return tsName;
}
-
+//
+// --------------- Swap Code ------------------
/**
- * \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.
+ * \brief Swaps the bytes so they agree with the processor order
+ * @return The properly swaped 16 bits integer.
*/
-bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax(void)
+uint16_t Document::SwapShort(uint16_t a)
{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52);
+ if ( SwapCode == 4321 || SwapCode == 2143 )
+ {
+ a = ((( a << 8 ) & 0xff00 ) | (( a >> 8 ) & 0x00ff ) );
+ }
+ return a;
}
/**
- * \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.
+ * \brief Swaps back the bytes of 4-byte long integer accordingly to
+ * processor order.
+ * @return The properly swaped 32 bits integer.
*/
-bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void)
+uint32_t Document::SwapLong(uint32_t a)
{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53);
-}
+ switch (SwapCode)
+ {
+ case 1234 :
+ break;
+ case 4321 :
+ a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
+ ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
+ break;
+ case 3412 :
+ a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
+ break;
+ case 2143 :
+ a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
+ break;
+ default :
+ gdcmErrorMacro( "Unset swap code:" << SwapCode );
+ a = 0;
+ }
+ return a;
+}
+//
+// -----------------File I/O ---------------
/**
- * \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.
+ * \brief Tries to open the file \ref Document::Filename and
+ * checks the preamble when existing.
+ * @return The FILE pointer on success.
*/
-bool gdcmDocument::IsRLELossLessTransferSyntax(void)
+std::ifstream *Document::OpenFile()
{
- return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5);
-}
+ HasDCMPreamble = false;
+ if (Filename.length() == 0)
+ {
+ return 0;
+ }
-/**
- * \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.
- */
+ if(Fp)
+ {
+ gdcmWarningMacro( "File already open: " << Filename.c_str());
+ CloseFile();
+ }
+
+ Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
+ if( ! *Fp )
+ {
+ gdcmDebugMacro( "Cannot open file: " << Filename.c_str());
+ delete Fp;
+ Fp = 0;
+ return 0;
+ }
-bool gdcmDocument::IsJPEGLossless(void)
-{
- 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) );
+ uint16_t zero = 0;
+ Fp->read((char*)&zero, (size_t)2);
+ if( Fp->eof() )
+ {
+ CloseFile();
+ return 0;
+ }
+
+ //ACR -- or DICOM with no Preamble; may start with a Shadow Group --
+ if(
+ zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 ||
+ zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 ||
+ zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 ||
+ zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 )
+ {
+ std::string msg
+ = Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero);
+ gdcmWarningMacro( msg.c_str() );
+ return Fp;
+ }
+
+ //DICOM
+ Fp->seekg(126L, std::ios::cur);
+ char dicm[4] = {' ',' ',' ',' '};
+ Fp->read(dicm, (size_t)4);
+ if( Fp->eof() )
+ {
+ CloseFile();
+ return 0;
+ }
+ if( memcmp(dicm, "DICM", 4) == 0 )
+ {
+ HasDCMPreamble = true;
+ return Fp;
+ }
+
+ CloseFile();
+ gdcmWarningMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
+
+ return 0;
}
-
+
/**
- * \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.
+ * \brief closes the file
+ * @return TRUE if the close was successfull
*/
-bool gdcmDocument::IsJPEG2000(void)
+bool Document::CloseFile()
{
- return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90)
- || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) );
+ if( Fp )
+ {
+ Fp->close();
+ delete Fp;
+ Fp = 0;
+ }
+ return true; //FIXME how do we detect a non-closed ifstream ?
}
/**
- * \brief Predicate for dicom version 3 file.
- * @return True when the file is a dicom version 3.
+ * \brief Writes in a file all the Header Entries (Dicom Elements)
+ * @param fp file pointer on an already open file (actually: Output File Stream)
+ * @param filetype Type of the File to be written
+ * (ACR-NEMA, ExplicitVR, ImplicitVR)
+ * @return Always true.
*/
-bool gdcmDocument::IsDicomV3(void) {
- // 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);
-}
+void Document::WriteContent(std::ofstream *fp, FileType filetype)
+{
+ // \TODO move the following lines (and a lot of others, to be written)
+ // to a future function CheckAndCorrectHeader
-/**
- * \brief returns the File Type
- * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
- * @return the FileType code
- */
-FileType gdcmDocument::GetFileType(void) {
- return Filetype;
+ // (necessary if user wants to write a DICOM V3 file
+ // starting from an ACR-NEMA (V2) Header
+
+ if ( filetype == ImplicitVR || filetype == ExplicitVR )
+ {
+ // writing Dicom File Preamble
+ char filePreamble[128];
+ memset(filePreamble, 0, 128);
+ fp->write(filePreamble, 128);
+ fp->write("DICM", 4);
+ }
+
+ /*
+ * \todo rewrite later, if really usefull
+ * - 'Group Length' element is optional in DICOM
+ * - but un-updated odd groups lengthes can causes pb
+ * (xmedcon breaker)
+ *
+ * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) )
+ * UpdateGroupLength(false,filetype);
+ * if ( filetype == ACR)
+ * UpdateGroupLength(true,ACR);
+ */
+
+ ElementSet::WriteContent(fp, filetype); // This one is recursive
}
+// -----------------------------------------
+// Content entries
/**
- * \brief opens the file
- * @param exception_on_error
- * @return
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
+ * @param group group number of the Entry
+ * @param elem element number of the Entry
*/
-FILE *gdcmDocument::OpenFile(bool exception_on_error)
- throw(gdcmFileError)
+void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
- fp=fopen(Filename.c_str(),"rb");
+ // Search the corresponding DocEntry
+ DocEntry *docElement = GetDocEntry(group, elem);
+ if ( !docElement )
+ return;
- if(!fp)
- {
- if(exception_on_error)
- throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)");
- else
- {
- dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ",
- Filename.c_str());
- return NULL;
- }
- }
-
- if ( fp )
- {
- guint16 zero;
- fread(&zero, (size_t)2, (size_t)1, fp);
-
- //ACR -- or DICOM with no Preamble --
- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200)
- return fp;
-
- //DICOM
- fseek(fp, 126L, SEEK_CUR);
- char dicm[4];
- fread(dicm, (size_t)4, (size_t)1, fp);
- if( memcmp(dicm, "DICM", 4) == 0 )
- return fp;
-
- fclose(fp);
- dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", Filename.c_str());
- }
- else {
- dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", Filename.c_str());
- }
- return NULL;
-}
+ BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
+ if( !binElement )
+ return;
-/**
- * \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;
+ LoadEntryBinArea(binElement);
}
/**
- * \brief Writes in a file all the Header Entries (Dicom Elements)
- * @param fp file pointer on an already open file
- * @param filetype Type of the File to be written
- * (ACR-NEMA, ExplicitVR, ImplicitVR)
- * \return Always true.
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
+ * @param elem Entry whose binArea is going to be loaded
*/
-void gdcmDocument::Write(FILE* fp,FileType filetype) {
+void Document::LoadEntryBinArea(BinEntry *elem)
+{
+ if(elem->GetBinArea())
+ return;
- /// \todo move the following lines (and a lot of others, to be written)
- /// to a future function CheckAndCorrectHeader
-
- /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA
- /// 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 (filetype == gdcmImplicitVR)
+ bool openFile = !Fp;
+ if(openFile)
+ OpenFile();
+
+ size_t o =(size_t)elem->GetOffset();
+ Fp->seekg(o, std::ios::beg);
+
+ size_t l = elem->GetLength();
+ uint8_t *a = new uint8_t[l];
+ if( !a )
{
- std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2;
- ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
-
- /// \todo Refer to standards on page 21, chapter 6.2
- /// "Value representation": values with a VR of UI shall be
- /// padded with a single trailing null
- /// in the following case we have to padd manually with a 0
-
- SetEntryLengthByNumber(18, 0x0002, 0x0010);
- }
+ gdcmWarningMacro( "Cannot allocate BinEntry content");
+ return;
+ }
- if (filetype == gdcmExplicitVR)
+ /// \todo check the result
+ Fp->read((char*)a, l);
+ if( Fp->fail() || Fp->eof())
{
- std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1;
- ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
-
- /// \todo Refer to standards on page 21, chapter 6.2
- /// "Value representation": values with a VR of UI shall be
- /// padded with a single trailing null
- /// Dans le cas suivant on doit pader manuellement avec un 0
-
- SetEntryLengthByNumber(20, 0x0002, 0x0010);
+ delete[] a;
+ return;
}
-
-/**
- * \todo rewrite later, if really usefull
- * - 'Group Length' element is optional in DICOM
- * - but un-updated odd groups lengthes can causes pb
- * (xmedcon breaker)
- *
- * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) )
- * UpdateGroupLength(false,filetype);
- * if ( filetype == ACR)
- * UpdateGroupLength(true,ACR);
- */
-
- gdcmElementSet::Write(fp,filetype); // This one is recursive
+ elem->SetBinArea(a);
+
+ if(openFile)
+ CloseFile();
}
/**
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * @param Value (string) Value to be set
- * @param Group Group number of the Entry
- * @param Elem Element number of the Entry
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
+ * \brief Loads the element while preserving the current
+ * underlying file position indicator as opposed to
+ * LoadDocEntry that modifies it.
+ * @param entry DocEntry whose value will be loaded.
*/
-
-gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
- std::string Value,
- guint16 Group,
- guint16 Elem )
+void Document::LoadDocEntrySafe(DocEntry *entry)
{
- gdcmDocEntry* CurrentEntry;
- gdcmValEntry* ValEntry;
+ if(Fp)
+ {
+ long PositionOnEntry = Fp->tellg();
+ LoadDocEntry(entry);
+ Fp->seekg(PositionOnEntry, std::ios::beg);
+ }
+}
- CurrentEntry = GetDocEntryByNumber( Group, Elem);
- if (!CurrentEntry)
+/**
+ * \brief Compares two documents, according to \ref DicomDir rules
+ * \warning Does NOT work with ACR-NEMA files
+ * \todo Find a trick to solve the pb (use RET fields ?)
+ * @param document to compare with current one
+ * @return true if 'smaller'
+ */
+bool Document::operator<(Document &document)
+{
+ // Patient Name
+ std::string s1 = GetEntryValue(0x0010,0x0010);
+ std::string s2 = document.GetEntryValue(0x0010,0x0010);
+ if(s1 < s2)
+ {
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
+ else
{
- // The entry wasn't present and we simply create the required ValEntry:
- CurrentEntry = NewDocEntryByNumber(Group, Elem);
- if (!CurrentEntry)
+ // Patient ID
+ s1 = GetEntryValue(0x0010,0x0020);
+ s2 = document.GetEntryValue(0x0010,0x0020);
+ if ( s1 < s2 )
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
- " NewDocEntryByNumber failed.");
- return NULL;
+ return true;
}
- ValEntry = new gdcmValEntry(CurrentEntry);
- if ( !AddEntry(ValEntry))
+ else if ( s1 > s2 )
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry"
- " failed allthough this is a creation.");
+ return false;
}
- }
- else
- {
- ValEntry = dynamic_cast< gdcmValEntry* >(CurrentEntry);
- if ( !ValEntry )
+ else
{
- // We need to promote the gdcmDocEntry to a gdcmValEntry:
- ValEntry = new gdcmValEntry(CurrentEntry);
- if (!RemoveEntry(CurrentEntry))
+ // Study Instance UID
+ s1 = GetEntryValue(0x0020,0x000d);
+ s2 = document.GetEntryValue(0x0020,0x000d);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if( s1 > s2 )
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
- " of previous DocEntry failed.");
- return NULL;
+ return false;
}
- if ( !AddEntry(ValEntry))
+ else
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
- " promoted ValEntry failed.");
- return NULL;
+ // Serie Instance UID
+ s1 = GetEntryValue(0x0020,0x000e);
+ s2 = document.GetEntryValue(0x0020,0x000e);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
}
}
}
+ return false;
+}
- 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).
+//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \brief Reads a supposed to be 16 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
*/
-gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber(
- void *voidArea,
- int lgth,
- guint16 Group,
- guint16 Elem)
+uint16_t Document::ReadInt16()
+ throw( FormatError )
{
- gdcmDocEntry* a;
- gdcmBinEntry* b = 0;
- a = GetDocEntryByNumber( Group, Elem);
- if (a == NULL) {
- a =NewBinEntryByNumber(Group, Elem);
- if (a == NULL)
- return NULL;
-
- b = new gdcmBinEntry(a);
- AddEntry(b);
- }
- SetEntryByNumber(voidArea, lgth, Group, Elem);
- b->SetVoidArea(voidArea);
-
- return b;
-}
-
-
-
-/**
- * \brief Set a new value if the invoked element exists
- * Seems to be useless !!!
- * @param Value new element value
- * @param Group group number of the Entry
- * @param Elem element number of the Entry
- * \return boolean
- */
-bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem )
-{
- std::string v = Value;
- SetEntryByNumber(v, Group, Elem);
- return true;
-}
-
-//-----------------------------------------------------------------------------
-// Protected
-
-/**
- * \brief Checks if a given Dicom Element exists within the H table
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return number of occurences
- */
-int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) {
- std::string key = gdcmDictEntry::TranslateToKey(group, element );
- return tagHT.count(key);
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value of a given tag.
- * \warning Don't use any longer : use GetPubEntryByName
- * @param tagName name of the searched element.
- * @return Corresponding element value when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmDocument::GetEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return GDCM_UNFOUND;
-
- return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement());
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param tagName name of the searched element.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmDocument::GetEntryVRByName(TagName tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return GDCM_UNFOUND;
-
- gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
- return elem->GetVR();
-}
-
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- * @param group Group number of the searched tag.
- * @param element Element number of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return GDCM_UNFOUND;
- return ((gdcmValEntry *)tagHT.find(key)->second)->GetValue();
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag..
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param group Group number of the searched tag.
- * @param element Element number of the searched tag.
- * @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);
- if ( !elem )
- return GDCM_UNFOUND;
- return elem->GetVR();
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the value length of a given tag..
- * @param group Group number of the searched tag.
- * @param element Element number of the searched tag.
- * @return Corresponding element length; -2 if not found
- */
-int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) {
- gdcmDocEntry* elem = GetDocEntryByNumber(group, element);
- if ( !elem )
- return -2;
- return elem->GetLength();
-}
-/**
- * \brief Sets the value (string) of the Header Entry (Dicom Element)
- * @param content string value of the Dicom Element
- * @param tagName name of the searched Dicom Element.
- * @return true when found
- */
-bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return false;
-
- 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 (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)
-{
- gdcmValEntry* ValEntry = GetValEntryByNumber(group, element);
- if (!ValEntry)
+ uint16_t g;
+ Fp->read ((char*)&g, (size_t)2);
+ if ( Fp->fail() )
{
- dbg.Verbose(0, "gdcmDocument::SetEntryByNumber: no corresponding",
- " ValEntry (try promotion first).");
- return false;
+ throw FormatError( "Document::ReadInt16()", " file error." );
}
-
- // Non even content must be padded with a space (020H).
- if((content.length())%2)
- content = content + '\0';
-
- ValEntry->SetValue(content);
-
- // Integers have a special treatement for their length:
- VRKey vr = ValEntry->GetVR();
- if( (vr == "US") || (vr == "SS") )
- ValEntry->SetLength(2);
- else if( (vr == "UL") || (vr == "SL") )
- ValEntry->SetLength(4);
- else
- ValEntry->SetLength(content.length());
-
- 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 group group number of the Dicom Element to modify
- * @param element element number of the Dicom Element to modify
- */
-bool gdcmDocument::SetEntryByNumber(void *content,
- int lgth,
- guint16 group,
- guint16 element)
-{
- (void)lgth; //not used
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return false;
-
-/* Hope Binray field length is never wrong
- if(lgth%2) // Non even length are padded with a space (020H).
- {
- lgth++;
- //content = content + '\0'; // fing a trick to enlarge a binary field?
- }
-*/
- gdcmBinEntry * a;
- a = (gdcmBinEntry *)tagHT[key];
- a->SetVoidArea(content);
- //a->SetLength(lgth); // ???
- return true;
-}
-
-/**
- * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
- * in the PubDocEntrySet of this instance
- * through it's (group, element) and modifies it's length with
- * the given value.
- * \warning Use with extreme caution.
- * @param l new length to substitute with
- * @param group group number of the Entry to modify
- * @param element element number of the Entry to modify
- * @return true on success, false otherwise.
- */
-bool gdcmDocument::SetEntryLengthByNumber(guint32 l,
- guint16 group,
- guint16 element)
-{
- TagKey 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);
-
- return true ;
-}
-
-/**
- * \brief Gets (from Header) the offset of a 'non string' element value
- * (LoadElementValues has already be executed)
- * @param Group group number of the Entry
- * @param Elem element number of the Entry
- * @return File Offset of the Element Value
- */
-size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem)
-{
- gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
- if (!Entry)
- {
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry present.");
- return (size_t)0;
- }
- return Entry->GetOffset();
-}
-
-/**
- * \brief Gets (from Header) a 'non string' element value
- * (LoadElementValues has already be executed)
- * @param Group group number of the Entry
- * @param Elem element number of the Entry
- * @return Pointer to the 'non string' area
- */
-void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem)
-{
- gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
- if (!Entry)
+ if( Fp->eof() )
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry");
- return (NULL);
+ throw FormatError( "Document::ReadInt16()", "EOF." );
}
- return ((gdcmBinEntry *)Entry)->GetVoidArea();
+ g = SwapShort(g);
+ return g;
}
/**
- * \brief Loads (from disk) the element content
- * when a string is not suitable
- * @param Group group number of the Entry
- * @param Elem element number of the Entry
+ * \brief Reads a supposed to be 32 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
*/
-void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem)
+uint32_t Document::ReadInt32()
+ throw( FormatError )
{
- gdcmDocEntry * Element= GetDocEntryByNumber(Group, Elem);
- if ( !Element )
- return NULL;
- size_t o =(size_t)Element->GetOffset();
- fseek(fp, o, SEEK_SET);
- size_t l = Element->GetLength();
- char* a = new char[l];
- if(!a) {
- dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a");
- return NULL;
- }
- SetEntryVoidAreaByNumber(a, Group, Elem);
- /// \todo check the result
- size_t l2 = fread(a, 1, l ,fp);
- if(l != l2)
+ uint32_t g;
+ Fp->read ((char*)&g, (size_t)4);
+ if ( Fp->fail() )
{
- delete[] a;
- return NULL;
+ throw FormatError( "Document::ReadInt32()", " file error." );
}
- 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)
+ if( Fp->eof() )
{
- delete[] a;
- return NULL;
+ throw FormatError( "Document::ReadInt32()", "EOF." );
}
- return a;
+ g = SwapLong(g);
+ return g;
}
/**
- * \brief Sets a 'non string' value to a given Dicom Element
- * @param area area containing the 'non string' value
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return
+ * \brief skips bytes inside the source file
+ * \warning NOT end user intended method !
+ * @return
*/
-bool gdcmDocument::SetEntryVoidAreaByNumber(void * area,
- guint16 group,
- guint16 element)
+void Document::SkipBytes(uint32_t nBytes)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return false;
- // This was for multimap ?
- (( gdcmBinEntry *)( ((tagHT.equal_range(key)).first)->second ))->SetVoidArea(area);
-
- return true;
+ //FIXME don't dump the returned value
+ Fp->seekg((long)nBytes, std::ios::cur);
}
/**
- * \brief Update the entries with the shadow dictionary.
- * Only non even entries are analyzed
+ * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
+ * @param filetype Type of the File to be written
*/
-void gdcmDocument::UpdateShaEntries(void) {
- //gdcmDictEntry *entry;
+int Document::ComputeGroup0002Length( FileType filetype )
+{
+ uint16_t gr;
std::string vr;
- /// \todo TODO : still any use to explore recursively the whole structure?
-/*
- for(ListTag::iterator it=listEntries.begin();
- it!=listEntries.end();
- ++it)
- {
- // Odd group => from public dictionary
- if((*it)->GetGroup()%2==0)
- continue;
-
- // Peer group => search the corresponding dict entry
- if(RefShaDict)
- entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement());
- else
- entry=NULL;
-
- if((*it)->IsImplicitVR())
- vr="Implicit";
- else
- vr=(*it)->GetVR();
+ int groupLength = 0;
+ bool found0002 = false;
+
+ // for each zero-level Tag in the DCM Header
+ DocEntry *entry = GetFirstEntry();
+ while( entry )
+ {
+ gr = entry->GetGroup();
- (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling
- if(entry){
- // Set the new entry and the new value
- (*it)->SetDictEntry(entry);
- CheckDocEntryVR(*it,vr);
+ if( gr == 0x0002 )
+ {
+ found0002 = true;
- (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling
+ if( entry->GetElement() != 0x0000 )
+ {
+ vr = entry->GetVR();
+ if( filetype == ExplicitVR )
+ {
+ if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
+ {
+ // explicit VR AND OB, OW, SQ : 4 more bytes
+ groupLength += 4;
+ }
+ }
+ groupLength += 2 + 2 + 4 + entry->GetLength();
+ }
}
- else
- {
- // Remove precedent value transformation
- (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr));
- }
- }
-*/
-}
-
-/**
- * \brief Searches within the Header Entries for a Dicom Element of
- * a given tag.
- * @param tagName name of the searched Dicom Element.
- * @return Corresponding Dicom Element when it exists, and NULL
- * otherwise.
- */
- gdcmDocEntry *gdcmDocument::GetDocEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return NULL;
+ else if (found0002 )
+ break;
- return(GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
+ entry = GetNextEntry();
+ }
+ return groupLength;
}
+//-----------------------------------------------------------------------------
+// Private
/**
- * \brief retrieves a Dicom Element (the first one) using (group, element)
- * \warning (group, element) IS NOT an identifier inside the Dicom Header
- * if you think it's NOT UNIQUE, check the count number
- * and use iterators to retrieve ALL the Dicoms Elements within
- * a given couple (group, element)
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return
+ * \brief Loads all the needed Dictionaries
+ * \warning NOT end user intended method !
*/
-gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element)
+void Document::Initialize()
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return NULL;
- return tagHT.find(key)->second;
+ RefPubDict = Global::GetDicts()->GetDefaultPubDict();
+ RefShaDict = NULL;
+ Filetype = Unknown;
}
/**
- * \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.
- */
-gdcmValEntry* gdcmDocument::GetValEntryByNumber(guint16 group, guint16 element)
+ * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
+ * @return length of the parsed set.
+ */
+void Document::ParseDES(DocEntrySet *set, long offset,
+ long l_max, bool delim_mode)
{
- gdcmDocEntry* CurrentEntry = GetDocEntryByNumber(group, element);
- if (! CurrentEntry)
- return (gdcmValEntry*)0;
- if ( gdcmValEntry* ValEntry = dynamic_cast<gdcmValEntry*>(CurrentEntry) )
- {
- return ValEntry;
- }
- dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry.");
- return (gdcmValEntry*)0;
-}
-
-/**
- * \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);
-}
+ DocEntry *newDocEntry = 0;
+ ValEntry *newValEntry;
+ BinEntry *newBinEntry;
+ SeqEntry *newSeqEntry;
+ VRKey vr;
+ bool used = false;
-/**
- * \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) {
- case 0 :
- break;
- case 4321 :
- a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
- ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
- break;
-
- case 3412 :
- a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
- break;
-
- case 2143 :
- a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
+ while (true)
+ {
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ {
break;
- default :
- std::cout << "swapCode= " << sw << std::endl;
- dbg.Error(" gdcmDocument::SwapLong : unset swap code");
- a=0;
- }
- 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);
-}
-
-/**
- * \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;
-}
-
-/**
- * \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);
-}
+ }
-//-----------------------------------------------------------------------------
-// Private
+ used = true;
+ newDocEntry = ReadNextDocEntry( );
-/**
- * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
- * @return length of the parsed set.
- */
+ if ( !newDocEntry )
+ {
+ break;
+ }
-long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
+ vr = newDocEntry->GetVR();
+ newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
+ newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
+ newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
- gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
- gdcmValEntry *NewValEntry = (gdcmValEntry *)0;
- gdcmBinEntry *bn;
- gdcmSeqEntry *sq;
- VRKey vr;
- unsigned long l = 0;
- int depth;
-
- depth = set->GetDepthLevel();
- while (true) {
-
- if ( !delim_mode && ftell(fp)-offset >= l_max) {
- break;
- }
- NewDocEntry = ReadNextDocEntry( );
- if (!NewDocEntry)
- break;
- // NewDocEntry->Print(); cout << endl; //JPR
- vr = NewDocEntry->GetVR();
- if (vr!="SQ")
+ if ( newValEntry || newBinEntry )
{
-
- if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) )
+ if ( newBinEntry )
{
- /////// 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)
- {
- break;
- }
- }
- else
- {
- if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
+ if ( Filetype == ExplicitVR &&
+ !Global::GetVR()->IsVROfBinaryRepresentable(vr) )
{
////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, "
- "nor BinEntry. Probably unknown VR.");
+ gdcmWarningMacro( std::hex << newDocEntry->GetGroup()
+ << "|" << newDocEntry->GetElement()
+ << " : Neither Valentry, nor BinEntry."
+ "Probably unknown VR.");
}
- ////// BinEntry or UNKOWN VR:
- bn = new gdcmBinEntry(NewDocEntry->GetDictEntry());
- bn->Copy(NewDocEntry);
- set->AddEntry(bn);
- LoadDocEntry(bn);
- }
+ //////////////////// BinEntry or UNKOWN VR:
+ // When "this" is a Document the Key is simply of the
+ // form ( group, elem )...
+ if ( dynamic_cast< Document* > ( set ) )
+ {
+ newBinEntry->SetKey( newBinEntry->GetKey() );
+ }
+ // but when "this" is a SQItem, we are inserting this new
+ // valEntry in a sequence item, and the key has the
+ // generalized form (refer to \ref BaseTagKey):
+ if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ {
+ newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newBinEntry->GetKey() );
+ }
- 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);
- l = NewDocEntry->GetFullLength();
- }
+ LoadDocEntry( newBinEntry );
+ if( !set->AddEntry( newBinEntry ) )
+ {
+ //Expect big troubles if here
+ //delete newBinEntry;
+ used=false;
+ }
}
else
{
- // to be sure we are at the beginning
- SkipToNextDocEntry(NewDocEntry);
- l = NewDocEntry->GetFullLength();
+ /////////////////////// ValEntry
+ // When "set" is a Document, then we are at the top of the
+ // hierarchy and the Key is simply of the form ( group, elem )...
+ if ( dynamic_cast< Document* > ( set ) )
+ {
+ newValEntry->SetKey( newValEntry->GetKey() );
+ }
+ // ...but when "set" is a SQItem, we are inserting this new
+ // valEntry in a sequence item. Hence the key has the
+ // generalized form (refer to \ref BaseTagKey):
+ if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ {
+ newValEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newValEntry->GetKey() );
+ }
+
+ LoadDocEntry( newValEntry );
+ bool delimitor=newValEntry->IsItemDelimitor();
+ if( !set->AddEntry( newValEntry ) )
+ {
+ // If here expect big troubles
+ //delete newValEntry; //otherwise mem leak
+ used=false;
+ }
+
+ if (delimitor)
+ {
+ if(!used)
+ delete newDocEntry;
+ break;
+ }
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ {
+ if(!used)
+ delete newDocEntry;
+ break;
+ }
}
+
+ // Just to make sure we are at the beginning of next entry.
+ SkipToNextDocEntry(newDocEntry);
}
else
- { // VR = "SQ"
-
- l=NewDocEntry->GetReadLength();
- if (l != 0) // don't mess the delim_mode for zero-length sequence
- if (l == 0xffffffff)
+ {
+ // VR = "SQ"
+ unsigned long 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);
+ newSeqEntry->SetDelimitorMode( delim_mode );
- if (l != 0)
+ // At the top of the hierarchy, stands a Document. When "set"
+ // is a Document, then we are building the first depth level.
+ // Hence the SeqEntry we are building simply has a depth
+ // level of one:
+ if (/*Document *dummy =*/ dynamic_cast< Document* > ( set ) )
+ {
+ //(void)dummy;
+ newSeqEntry->SetDepthLevel( 1 );
+ newSeqEntry->SetKey( newSeqEntry->GetKey() );
+ }
+ // But when "set" is already a SQItem, we are building a nested
+ // sequence, and hence the depth level of the new SeqEntry
+ // we are building, is one level deeper:
+ if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ {
+ newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
+ newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newSeqEntry->GetKey() );
+ }
+
+ if ( l != 0 )
{ // Don't try to parse zero-length sequences
- long lgt = ParseSQ( sq,
- NewDocEntry->GetOffset(),
- l, delim_mode);
- (void)lgt; //not used...
+ ParseSQ( newSeqEntry,
+ newDocEntry->GetOffset(),
+ l, delim_mode);
}
- set->AddEntry(sq);
- if ( !delim_mode && ftell(fp)-offset >= l_max)
+ if( !set->AddEntry( newSeqEntry ) )
{
+ used = false;
+ }
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ {
+ if( !used )
+ delete newDocEntry;
break;
}
}
- delete NewDocEntry;
+
+ if( !used )
+ delete newDocEntry;
}
- 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)
+void Document::ParseSQ( SeqEntry *seqEntry,
+ long offset, long l_max, bool delim_mode)
{
int SQItemNumber = 0;
-
- gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
- gdcmSQItem *itemSQ;
bool dlm_mod;
- int lgr, lgth;
- unsigned int l;
- int depth = set->GetDepthLevel();
- (void)depth; //not used
+ long offsetStartCurrentSQItem = offset;
- while (true) {
+ while (true)
+ {
+ // the first time, we read the fff0,e000 of the first SQItem
+ DocEntry *newDocEntry = ReadNextDocEntry();
- NewDocEntry = ReadNextDocEntry();
- if (!NewDocEntry)
+ if ( !newDocEntry )
+ {
+ // FIXME Should warn user
break;
- if(delim_mode) {
- if (NewDocEntry->isSequenceDelimitor()) {
- set->SetSequenceDelimitationItem(NewDocEntry);
+ }
+ if( delim_mode )
+ {
+ if ( newDocEntry->IsSequenceDelimitor() )
+ {
+ seqEntry->SetDelimitationItem( newDocEntry );
break;
- }
+ }
}
- if (!delim_mode && (ftell(fp)-offset) >= l_max) {
- break;
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ {
+ delete newDocEntry;
+ break;
}
-
- itemSQ = new gdcmSQItem(set->GetDepthLevel());
- itemSQ->AddEntry(NewDocEntry);
- l= NewDocEntry->GetReadLength();
+ // create the current SQItem
+ SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
+ std::ostringstream newBase;
+ newBase << seqEntry->GetKey()
+ << "/"
+ << SQItemNumber
+ << "#";
+ itemSQ->SetBaseTagKey( newBase.str() );
+ unsigned int l = newDocEntry->GetReadLength();
- if (l == 0xffffffff)
+ if ( l == 0xffffffff )
+ {
dlm_mod = true;
+ }
else
- dlm_mod=false;
-
- lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod);
-
- set->AddEntry(itemSQ,SQItemNumber);
- SQItemNumber ++;
- if (!delim_mode && (ftell(fp)-offset) >= l_max) {
+ {
+ dlm_mod = false;
+ }
+ // FIXME, TODO
+ // when we're here, element fffe,e000 is already passed.
+ // it's lost for the SQItem we're going to process !!
+
+ //ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+ //delete newDocEntry; // FIXME well ... it's too late to use it !
+
+ // Let's try :------------
+ // remove fff0,e000, created out of the SQItem
+ delete newDocEntry;
+ Fp->seekg(offsetStartCurrentSQItem, std::ios::beg);
+ // fill up the current SQItem, starting at the beginning of fff0,e000
+ ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod);
+ offsetStartCurrentSQItem = Fp->tellg();
+ // end try -----------------
+
+ seqEntry->AddSQItem( itemSQ, SQItemNumber );
+ SQItemNumber++;
+ if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
+ {
break;
}
}
- lgth = ftell(fp) - offset;
- return lgth;
}
/**
- * \brief Loads the element content if its length doesn't exceed
- * the value specified with gdcmDocument::SetMaxSizeLoadEntry()
- * @param Entry Header Entry (Dicom Element) to be dealt with
+ * \brief Loads the element content if its length doesn't exceed
+ * the value specified with Document::SetMaxSizeLoadEntry()
+ * @param entry Header Entry (Dicom Element) to be dealt with
*/
-void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry)
+void Document::LoadDocEntry(DocEntry *entry)
{
- size_t item_read;
- guint16 group = Entry->GetGroup();
- std::string vr= Entry->GetVR();
- guint32 length = Entry->GetLength();
+ uint16_t group = entry->GetGroup();
+ std::string vr = entry->GetVR();
+ uint32_t length = entry->GetLength();
- fseek(fp, (long)Entry->GetOffset(), SEEK_SET);
+ Fp->seekg((long)entry->GetOffset(), std::ios::beg);
// 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 !
return;
}
// When the length is zero things are easy:
- if ( length == 0 ) {
- ((gdcmValEntry *)Entry)->SetValue("");
+ if ( length == 0 )
+ {
+ ((ValEntry *)entry)->SetValue("");
return;
}
// the element content and it's length.
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());
+ if (length > MaxSizeLoadEntry)
+ {
+ if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
+ {
+ //s << "gdcm::NotLoaded (BinEntry)";
+ s << GDCM_NOTLOADED;
+ s << " Address:" << (long)entry->GetOffset();
+ s << " Length:" << entry->GetLength();
+ s << " x(" << std::hex << entry->GetLength() << ")";
+ binEntryPtr->SetValue(s.str());
}
- // to be sure we are at the end of the value ...
- fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET);
- return;
- // Be carefull : a BinEntry IS_A ValEntry ...
- if (gdcmValEntry* ValEntryPtr = dynamic_cast< gdcmValEntry* >(Entry) )
+ // Be carefull : a BinEntry IS_A ValEntry ...
+ else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) )
{
- s << "gdcm::NotLoaded. (ValEntry)";
- s << " Address:" << (long)Entry->GetOffset();
- s << " Length:" << Entry->GetLength();
- s << " x(" << std::hex << Entry->GetLength() << ")";
- ValEntryPtr->SetValue(s.str());
+ // s << "gdcm::NotLoaded. (ValEntry)";
+ s << GDCM_NOTLOADED;
+ s << " Address:" << (long)entry->GetOffset();
+ s << " Length:" << entry->GetLength();
+ s << " x(" << std::hex << entry->GetLength() << ")";
+ valEntryPtr->SetValue(s.str());
}
+ else
+ {
+ // fusible
+ gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry "
+ << "nor a ValEntry ?! Should never print that !" );
+ }
+
// to be sure we are at the end of the value ...
- fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET);
+ Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
+ std::ios::beg);
return;
}
// When we find a BinEntry not very much can be done :
- if (gdcmBinEntry* BinEntryPtr = dynamic_cast< gdcmBinEntry* >(Entry) ) {
-
- LoadEntryVoidArea(BinEntryPtr);
- s << "gdcm::Loaded (BinEntry)";
- BinEntryPtr->SetValue(s.str());
+ if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
+ {
+ s << GDCM_BINLOADED;
+ binEntryPtr->SetValue(s.str());
+ LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
return;
}
-
-
- // Any compacter code suggested (?)
- if ( IsDocEntryAnInteger(Entry) ) {
- guint32 NewInt;
- std::ostringstream s;
+
+ /// \todo Any compacter code suggested (?)
+ if ( IsDocEntryAnInteger(entry) )
+ {
+ uint32_t NewInt;
int nbInt;
- // When short integer(s) are expected, read and convert the following
- // n *two characters properly i.e. as short integers as opposed to strings.
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- if (vr == "US" || vr == "SS") {
+ // When short integer(s) are expected, read and convert the following
+ // n *two characters properly i.e. consider them as short integers as
+ // opposed to strings.
+ // Elements with Value Multiplicity > 1
+ // contain a set of integers (not a single one)
+ if (vr == "US" || vr == "SS")
+ {
nbInt = length / 2;
NewInt = ReadInt16();
s << NewInt;
- if (nbInt > 1){
- for (int i=1; i < nbInt; i++) {
+ if (nbInt > 1)
+ {
+ for (int i=1; i < nbInt; i++)
+ {
s << '\\';
NewInt = ReadInt16();
s << NewInt;
}
}
}
- // When integer(s) are expected, read and convert the following
- // n * four characters properly i.e. as integers as opposed to strings.
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- else if (vr == "UL" || vr == "SL") {
+ // See above comment on multiple integers (mutatis mutandis).
+ else if (vr == "UL" || vr == "SL")
+ {
nbInt = length / 4;
NewInt = ReadInt32();
s << NewInt;
- if (nbInt > 1) {
- for (int i=1; i < nbInt; i++) {
+ if (nbInt > 1)
+ {
+ for (int i=1; i < nbInt; i++)
+ {
s << '\\';
NewInt = ReadInt32();
s << NewInt;
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
- ((gdcmValEntry *)Entry)->SetValue(s.str());
+ ((ValEntry *)entry)->SetValue(s.str());
return;
}
- // We need an additional byte for storing \0 that is not on disk
- std::string NewValue(length,0);
- item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp);
- if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(Entry) ) {
- if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmDocument::LoadElementValue","unread element value");
- ValEntry->SetValue("gdcm::UnRead");
+ // FIXME: We need an additional byte for storing \0 that is not on disk
+ char *str = new char[length+1];
+ Fp->read(str, (size_t)length);
+ str[length] = '\0'; //this is only useful when length is odd
+ // Special DicomString call to properly handle \0 and even length
+ std::string newValue;
+ if( length % 2 )
+ {
+ newValue = Util::DicomString(str, length+1);
+ gdcmWarningMacro("Warning: bad length: " << length <<
+ ",For string :" << newValue.c_str());
+ // Since we change the length of string update it length
+ //entry->SetReadLength(length+1);
+ }
+ else
+ {
+ newValue = Util::DicomString(str, length);
+ }
+ delete[] str;
+
+ if ( ValEntry *valEntry = dynamic_cast<ValEntry* >(entry) )
+ {
+ if ( Fp->fail() || Fp->eof())
+ {
+ gdcmWarningMacro("Unread element value");
+ valEntry->SetValue(GDCM_UNREAD);
return;
}
- if( (vr == "UI") ) // Because of correspondance with the VR dic
- ValEntry->SetValue(NewValue.c_str());
+ if( vr == "UI" )
+ {
+ // Because of correspondance with the VR dic
+ valEntry->SetValue(newValue);
+ }
else
- ValEntry->SetValue(NewValue);
- } else {
- // fusible
- std::cout << "Should have a ValEntry, here !" << std::endl;
+ {
+ valEntry->SetValue(newValue);
+ }
+ }
+ else
+ {
+ gdcmErrorMacro( "Should have a ValEntry, here !");
}
-
}
-
/**
* \brief Find the value Length of the passed Header Entry
- * @param Entry Header Entry whose length of the value shall be loaded.
+ * @param entry Header Entry whose length of the value shall be loaded.
*/
- void gdcmDocument::FindDocEntryLength (gdcmDocEntry *Entry) {
- guint16 element = Entry->GetElement();
- //guint16 group = Entry->GetGroup(); //FIXME
- std::string vr = Entry->GetVR();
- guint16 length16;
-
+void Document::FindDocEntryLength( DocEntry *entry )
+ throw ( FormatError )
+{
+ std::string vr = entry->GetVR();
+ uint16_t length16;
- if ( (Filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) )
+ if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
- if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") )
+ if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" )
{
- // The following reserved two bytes (see PS 3.5-2001, section
- // 7.1.2 Data element structure with explicit vr p27) must be
+ // The following reserved two bytes (see PS 3.5-2003, section
+ // "7.1.2 Data element structure with explicit vr", p 27) must be
// skipped before proceeding on reading the length on 4 bytes.
- fseek(fp, 2L, SEEK_CUR);
- guint32 length32 = ReadInt32();
+ Fp->seekg( 2L, std::ios::cur);
+ uint32_t length32 = ReadInt32();
- if ( (vr == "OB") && (length32 == 0xffffffff) )
+ if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
{
- Entry->SetLength(FindDocEntryLengthOB());
+ uint32_t lengthOB;
+ try
+ {
+ lengthOB = FindDocEntryLengthOBOrOW();
+ }
+ catch ( FormatUnexpected )
+ {
+ // Computing the length failed (this happens with broken
+ // files like gdcm-JPEG-LossLess3a.dcm). We still have a
+ // chance to get the pixels by deciding the element goes
+ // until the end of the file. Hence we artificially fix the
+ // the length and proceed.
+ long currentPosition = Fp->tellg();
+ Fp->seekg(0L,std::ios::end);
+
+ long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
+ Fp->seekg(currentPosition, std::ios::beg);
+
+ entry->SetReadLength(lengthUntilEOF);
+ entry->SetLength(lengthUntilEOF);
+ return;
+ }
+ entry->SetReadLength(lengthOB);
+ entry->SetLength(lengthOB);
return;
}
- FixDocEntryFoundLength(Entry, length32);
+ FixDocEntryFoundLength(entry, length32);
return;
}
// Length is encoded on 2 bytes.
length16 = ReadInt16();
+
+ // FIXME : This heuristic supposes that the first group following
+ // group 0002 *has* and element 0000.
+ // BUT ... Element 0000 is optionnal :-(
+
+
+ // Fixed using : HandleOutOfGroup0002()
+ // (first hereafter strategy ...)
// We can tell the current file is encoded in big endian (like
// Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag
// ones with zero as element number) has to be of 4 (0x0004). When we
// encounter 1024 (0x0400) chances are the encoding changed and we
// found a group with big endian encoding.
+ //---> Unfortunately, element 0000 is optional.
+ //---> This will not work when missing!
// We shall use this second strategy. In order to make sure that we
// can interpret the presence of an apparently big endian encoded
// length of a "Group Length" without committing a big mistake, we
// endian encoding". When this is the case, chances are we have got our
// hands on a big endian encoded file: we switch the swap code to
// big endian and proceed...
- if ( (element == 0x0000) && (length16 == 0x0400) )
- {
- if ( ! IsExplicitVRBigEndianTransferSyntax() )
- {
- dbg.Verbose(0, "gdcmDocument::FindLength", "not explicit VR");
- errno = 1;
- 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)
- {
- // This correct tag is not in the dictionary. Create a new one.
- NewTag = NewVirtualDictEntry(CorrectGroup, CorrectElem);
- }
- // FIXME this can create a memory leaks on the old entry that be
- // left unreferenced.
- Entry->SetDictEntry(NewTag);
- }
-
- // Heuristic: well, some files are really ill-formed.
+
+// if ( element == 0x0000 && length16 == 0x0400 )
+// {
+// std::string ts = GetTransferSyntax();
+// if ( Global::GetTS()->GetSpecialTransferSyntax(ts)
+// != TS::ExplicitVRBigEndian )
+// {
+// throw FormatError( "Document::FindDocEntryLength()",
+// " not explicit VR." );
+// return;
+// }
+// length16 = 4;
+// SwitchByteSwapCode();
+//
+// // Restore the unproperly loaded values i.e. the group, the element
+// // and the dictionary entry depending on them.
+// uint16_t correctGroup = SwapShort( entry->GetGroup() );
+// uint16_t correctElem = SwapShort( entry->GetElement() );
+// DictEntry *newTag = GetDictEntry( correctGroup, correctElem );
+// if ( !newTag )
+// {
+// // This correct tag is not in the dictionary. Create a new one.
+// newTag = NewVirtualDictEntry(correctGroup, correctElem);
+// }
+// // FIXME this can create a memory leaks on the old entry that be
+// // left unreferenced.
+// entry->SetDictEntry( newTag );
+// }
+
+ // 0xffff means that we deal with 'No Length' Sequence
+ // or 'No Length' SQItem
if ( length16 == 0xffff)
- {
+ {
length16 = 0;
- // Length16= 0xffff means that we deal with
- // 'Unknown Length' Sequence
}
- FixDocEntryFoundLength(Entry, (guint32)length16);
+ FixDocEntryFoundLength( entry, (uint32_t)length16 );
return;
}
else
// on Data elements "Implicit and Explicit VR Data Elements shall
// not coexist in a Data Set and Data Sets nested within it".]
// Length is on 4 bytes.
+
+ // Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
+ // even if Transfer Syntax is 'Implicit VR ...'
- FixDocEntryFoundLength(Entry, ReadInt32());
+ FixDocEntryFoundLength( entry, ReadInt32() );
return;
}
}
/**
- * \brief Find the Value Representation of the current Dicom Element.
- * @param Entry
+ * \brief Find the Length till the next sequence delimiter
+ * \warning NOT end user intended method !
+ * @return
*/
-void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry)
+uint32_t Document::FindDocEntryLengthOBOrOW()
+ throw( FormatUnexpected )
{
- if (Filetype != gdcmExplicitVR)
- return;
+ // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
+ long positionOnEntry = Fp->tellg();
+ bool foundSequenceDelimiter = false;
+ uint32_t totalLength = 0;
+
+ while ( !foundSequenceDelimiter )
+ {
+ uint16_t group;
+ uint16_t elem;
+ try
+ {
+ group = ReadInt16();
+ elem = ReadInt16();
+ }
+ catch ( FormatError )
+ {
+ throw FormatError("Unexpected end of file encountered during ",
+ "Document::FindDocEntryLengthOBOrOW()");
+ }
+ // We have to decount the group and element we just read
+ totalLength += 4;
+ if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
+ {
+ long filePosition = Fp->tellg();
+ gdcmWarningMacro( "Neither an Item tag nor a Sequence delimiter tag on :"
+ << std::hex << group << " , " << elem
+ << ") -before- position x(" << filePosition << ")" );
+
+ Fp->seekg(positionOnEntry, std::ios::beg);
+ throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag.");
+ }
+ if ( elem == 0xe0dd )
+ {
+ foundSequenceDelimiter = true;
+ }
+ uint32_t itemLength = ReadInt32();
+ // We add 4 bytes since we just read the ItemLength with ReadInt32
+ totalLength += itemLength + 4;
+ SkipBytes(itemLength);
+
+ if ( foundSequenceDelimiter )
+ {
+ break;
+ }
+ }
+ Fp->seekg( positionOnEntry, std::ios::beg);
+ return totalLength;
+}
- char VR[3];
+/**
+ * \brief Find the Value Representation of the current Dicom Element.
+ * @return Value Representation of the current Entry
+ */
+std::string Document::FindDocEntryVR()
+{
+ if ( Filetype != ExplicitVR )
+ return GDCM_UNKNOWN;
- long PositionOnEntry = ftell(fp);
+ long positionOnEntry = Fp->tellg();
// Warning: we believe this is explicit VR (Value Representation) because
// we used a heuristic that found "UL" in the first tag. Alas this
// doesn't guarantee that all the tags will be in explicit VR. In some
// within an explicit VR file. Hence we make sure the present tag
// is in explicit VR and try to fix things if it happens not to be
// the case.
-
- (void)fread (&VR, (size_t)2,(size_t)1, fp);
- VR[2]=0;
- if(!CheckDocEntryVR(Entry,VR))
- {
- fseek(fp, PositionOnEntry, SEEK_SET);
- // When this element is known in the dictionary we shall use, e.g. for
- // the semantics (see the usage of IsAnInteger), the VR proposed by the
- // dictionary entry. Still we have to flag the element as implicit since
- // we know now our assumption on expliciteness is not furfilled.
- // avoid .
- if ( Entry->IsVRUnknown() )
- Entry->SetVR("Implicit");
- Entry->SetImplicitVR();
+
+ char vr[3];
+ Fp->read (vr, (size_t)2);
+ vr[2] = 0;
+
+ if( !CheckDocEntryVR(vr) )
+ {
+ Fp->seekg(positionOnEntry, std::ios::beg);
+ return GDCM_UNKNOWN;
}
+ return vr;
}
/**
* \brief Check the correspondance between the VR of the header entry
* and the taken VR. If they are different, the header entry is
* updated with the new VR.
- * @param Entry Header Entry to check
* @param vr Dicom Value Representation
* @return false if the VR is incorrect of if the VR isn't referenced
* otherwise, it returns true
*/
-bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, VRKey vr)
+bool Document::CheckDocEntryVR(VRKey vr)
{
- char msg[100]; // for sprintf
- bool RealExplicit = true;
-
- // Assume we are reading a falsely explicit VR file i.e. we reached
- // a tag where we expect reading a VR but are in fact we read the
- // first to bytes of the length. Then we will interogate (through find)
- // the dicom_vr dictionary with oddities like "\004\0" which crashes
- // both GCC and VC++ implementations of the STL map. Hence when the
- // expected VR read happens to be non-ascii characters we consider
- // we hit falsely explicit VR tag.
-
- if ( (!isalpha(vr[0])) && (!isalpha(vr[1])) )
- RealExplicit = false;
-
- // CLEANME searching the dicom_vr at each occurence is expensive.
- // PostPone this test in an optional integrity check at the end
- // of parsing or only in debug mode.
- if ( RealExplicit && !gdcmGlobal::GetVR()->Count(vr) )
- RealExplicit= false;
-
- if ( !RealExplicit )
- {
- // We thought this was explicit VR, but we end up with an
- // implicit VR tag. Let's backtrack.
- sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
- Entry->GetGroup(),Entry->GetElement());
- dbg.Verbose(1, "gdcmDocument::FindVR: ",msg);
- if (Entry->GetGroup()%2 && Entry->GetElement() == 0x0000) { // Group length is UL !
- gdcmDictEntry* NewEntry = NewVirtualDictEntry(
- Entry->GetGroup(),Entry->GetElement(),
- "UL","FIXME","Group Length");
- Entry->SetDictEntry(NewEntry);
- }
+ if ( !Global::GetVR()->IsValidVR(vr) )
return false;
- }
- if ( Entry->IsVRUnknown() )
- {
- // When not a dictionary entry, we can safely overwrite the VR.
- if (Entry->GetElement() == 0x0000) { // Group length is UL !
- Entry->SetVR("UL");
- } else {
- Entry->SetVR(vr);
- }
- }
- else if ( Entry->GetVR() != vr )
- {
- // The VR present in the file and the dictionary disagree. We assume
- // the file writer knew best and use the VR of the file. Since it would
- // be unwise to overwrite the VR of a dictionary (since it would
- // compromise it's next user), we need to clone the actual DictEntry
- // and change the VR for the read one.
- gdcmDictEntry* NewEntry = NewVirtualDictEntry(
- Entry->GetGroup(),Entry->GetElement(),
- vr,"FIXME",Entry->GetName());
- Entry->SetDictEntry(NewEntry);
- }
return true;
}
* \brief Get the transformed value of the header entry. The VR value
* is used to define the transformation to operate on the value
* \warning NOT end user intended method !
- * @param Entry
+ * @param entry entry to tranform
* @return Transformed entry value
*/
-std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry)
+std::string Document::GetDocEntryValue(DocEntry *entry)
{
- if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
+ if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
- std::string val=((gdcmValEntry *)Entry)->GetValue();
- std::string vr=Entry->GetVR();
- guint32 length = Entry->GetLength();
+ std::string val = ((ValEntry *)entry)->GetValue();
+ std::string vr = entry->GetVR();
+ uint32_t length = entry->GetLength();
std::ostringstream s;
int nbInt;
- // When short integer(s) are expected, read and convert the following
- // n * 2 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // as usual for standard multivaluated filels
- // Elements with Value Multiplicity > 1
- // contain a set of short integers (not a single one)
+ // When short integer(s) are expected, read and convert the following
+ // n * 2 bytes properly i.e. as a multivaluated strings
+ // (each single value is separated fromthe next one by '\'
+ // as usual for standard multivaluated filels
+ // Elements with Value Multiplicity > 1
+ // contain a set of short integers (not a single one)
- if (vr == "US" || vr == "SS")
+ if( vr == "US" || vr == "SS" )
{
- guint16 NewInt16;
+ uint16_t newInt16;
nbInt = length / 2;
for (int i=0; i < nbInt; i++)
{
- if(i!=0)
+ if( i != 0 )
+ {
s << '\\';
- NewInt16 = (val[2*i+0]&0xFF)+((val[2*i+1]&0xFF)<<8);
- NewInt16 = SwapShort(NewInt16);
- s << NewInt16;
+ }
+ newInt16 = ( val[2*i+0] & 0xFF ) + ( ( val[2*i+1] & 0xFF ) << 8);
+ newInt16 = SwapShort( newInt16 );
+ s << newInt16;
}
}
- // When integer(s) are expected, read and convert the following
- // n * 4 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // as usual for standard multivaluated filels
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- else if (vr == "UL" || vr == "SL")
+ // When integer(s) are expected, read and convert the following
+ // n * 4 bytes properly i.e. as a multivaluated strings
+ // (each single value is separated fromthe next one by '\'
+ // as usual for standard multivaluated filels
+ // Elements with Value Multiplicity > 1
+ // contain a set of integers (not a single one)
+ else if( vr == "UL" || vr == "SL" )
{
- guint32 NewInt32;
+ uint32_t newInt32;
nbInt = length / 4;
for (int i=0; i < nbInt; i++)
{
- if(i!=0)
+ if( i != 0)
+ {
s << '\\';
- NewInt32= (val[4*i+0]&0xFF)+((val[4*i+1]&0xFF)<<8)+
- ((val[4*i+2]&0xFF)<<16)+((val[4*i+3]&0xFF)<<24);
- NewInt32=SwapLong(NewInt32);
- s << NewInt32;
+ }
+ newInt32 = ( val[4*i+0] & 0xFF )
+ + (( val[4*i+1] & 0xFF ) << 8 )
+ + (( val[4*i+2] & 0xFF ) << 16 )
+ + (( val[4*i+3] & 0xFF ) << 24 );
+ newInt32 = SwapLong( newInt32 );
+ s << newInt32;
}
}
#ifdef GDCM_NO_ANSI_STRING_STREAM
#endif //GDCM_NO_ANSI_STRING_STREAM
return s.str();
}
-
- return ((gdcmValEntry *)Entry)->GetValue();
+ return ((ValEntry *)entry)->GetValue();
}
/**
* value is used to define the reverse transformation to operate on
* the value
* \warning NOT end user intended method !
- * @param Entry
+ * @param entry Entry to reverse transform
* @return Reverse transformed entry value
*/
-std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry)
+std::string Document::GetDocEntryUnvalue(DocEntry *entry)
{
- if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
+ if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
- std::string vr=Entry->GetVR();
- std::ostringstream s;
+ std::string vr = entry->GetVR();
std::vector<std::string> tokens;
+ std::ostringstream s;
- if (vr == "US" || vr == "SS")
+ if ( vr == "US" || vr == "SS" )
{
- guint16 NewInt16;
+ uint16_t newInt16;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
+ tokens.erase( tokens.begin(), tokens.end()); // clean any previous value
+ Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
+ for (unsigned int i=0; i<tokens.size(); i++)
{
- NewInt16 = atoi(tokens[i].c_str());
- s<<(NewInt16&0xFF)<<((NewInt16>>8)&0xFF);
+ newInt16 = atoi(tokens[i].c_str());
+ s << ( newInt16 & 0xFF )
+ << (( newInt16 >> 8 ) & 0xFF );
}
tokens.clear();
}
- if (vr == "UL" || vr == "SL")
+ if ( vr == "UL" || vr == "SL")
{
- guint32 NewInt32;
+ uint32_t newInt32;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\");
+ Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
- NewInt32 = atoi(tokens[i].c_str());
- s<<(char)(NewInt32&0xFF)<<(char)((NewInt32>>8)&0xFF)
- <<(char)((NewInt32>>16)&0xFF)<<(char)((NewInt32>>24)&0xFF);
+ newInt32 = atoi(tokens[i].c_str());
+ s << (char)( newInt32 & 0xFF )
+ << (char)(( newInt32 >> 8 ) & 0xFF )
+ << (char)(( newInt32 >> 16 ) & 0xFF )
+ << (char)(( newInt32 >> 24 ) & 0xFF );
}
tokens.clear();
}
return s.str();
}
- return ((gdcmValEntry *)Entry)->GetValue();
+ return ((ValEntry *)entry)->GetValue();
}
/**
* \brief Skip a given Header Entry
* \warning NOT end user intended method !
- * @param entry
+ * @param entry entry to skip
*/
-void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry)
+void Document::SkipDocEntry(DocEntry *entry)
{
SkipBytes(entry->GetLength());
}
/**
- * \brief Skips to the begining of the next Header Entry
+ * \brief Skips to the beginning of the next Header Entry
* \warning NOT end user intended method !
- * @param entry
+ * @param currentDocEntry entry to skip
*/
-void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry)
+void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
{
- (void)fseek(fp, (long)(entry->GetOffset()), SEEK_SET);
- (void)fseek(fp, (long)(entry->GetReadLength()), SEEK_CUR);
+ Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
+ if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb
+ Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur);
}
/**
* \brief When the length of an element value is obviously wrong (because
* the parser went Jabberwocky) one can hope improving things by
* applying some heuristics.
+ * @param entry entry to check
+ * @param foundLength first assumption about length
*/
-void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry,
- guint32 FoundLength)
+void Document::FixDocEntryFoundLength(DocEntry *entry,
+ uint32_t foundLength)
{
- Entry->SetReadLength(FoundLength); // will be updated only if a bug is found
- if ( FoundLength == 0xffffffff) {
- FoundLength = 0;
+ entry->SetReadLength( foundLength ); // will be updated only if a bug is found
+ if ( foundLength == 0xffffffff)
+ {
+ foundLength = 0;
}
- guint16 gr =Entry->GetGroup();
- guint16 el =Entry->GetElement();
+ uint16_t gr = entry->GetGroup();
+ uint16_t elem = entry->GetElement();
- if (FoundLength%2) {
- std::ostringstream s;
- s << "Warning : Tag with uneven length "
- << FoundLength
- << " in x(" << std::hex << gr << "," << el <<")" << std::dec;
- dbg.Verbose(0, s.str().c_str());
+ if ( foundLength % 2)
+ {
+ gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength
+ << " in x(" << std::hex << gr << "," << elem <<")");
}
//////// Fix for some naughty General Electric images.
// Allthough not recent many such GE corrupted images are still present
// on Creatis hard disks. Hence this fix shall remain when such images
- // are no longer in user (we are talking a few years, here)...
+ // are no longer in use (we are talking a few years, here)...
// Note: XMedCom probably uses such a trick since it is able to read
// those pesky GE images ...
- if (FoundLength == 13) { // Only happens for this length !
- if ( (Entry->GetGroup() != 0x0008)
- || ( (Entry->GetElement() != 0x0070)
- && (Entry->GetElement() != 0x0080) ) )
+ if ( foundLength == 13)
+ {
+ // Only happens for this length !
+ if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) )
{
- FoundLength = 10;
- Entry->SetReadLength(10); /// \todo a bug is to be fixed !?
+ foundLength = 10;
+ entry->SetReadLength(10); /// \todo a bug is to be fixed !?
}
}
// Occurence of such images is quite low (unless one leaves close to a
// 'Leonardo' source. Hence, one might consider commenting out the
// following fix on efficiency reasons.
- else
- if ( (Entry->GetGroup() == 0x0009)
- && ( (Entry->GetElement() == 0x1113)
- || (Entry->GetElement() == 0x1114) ) )
+ else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
{
- FoundLength = 4;
- Entry->SetReadLength(4); /// \todo a bug is to be fixed !?
+ foundLength = 4;
+ entry->SetReadLength(4); /// \todo a bug is to be fixed !?
}
- //////// Deal with sequences, but only on users request:
- else
- if ( ( Entry->GetVR() == "SQ") && enableSequences)
+ else if ( entry->GetVR() == "SQ" )
{
- FoundLength = 0; // ReadLength is unchanged
+ foundLength = 0; // ReadLength is unchanged
}
//////// We encountered a 'delimiter' element i.e. a tag of the form
// "fffe|xxxx" which is just a marker. Delimiters length should not be
// taken into account.
- else
- if(Entry->GetGroup() == 0xfffe)
+ else if( gr == 0xfffe )
{
// According to the norm, fffe|0000 shouldn't exist. BUT the Philips
// image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to
// causes extra troubles...
- if( Entry->GetElement() != 0x0000 )
+ if( entry->GetElement() != 0x0000 )
{
- FoundLength = 0;
+ foundLength = 0;
}
- }
-
- Entry->SetUsableLength(FoundLength);
+ }
+ entry->SetLength(foundLength);
}
/**
* \brief Apply some heuristics to predict whether the considered
* element value contains/represents an integer or not.
- * @param Entry The element value on which to apply the predicate.
+ * @param entry The element value on which to apply the predicate.
* @return The result of the heuristical predicate.
*/
-bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) {
- guint16 element = Entry->GetElement();
- guint16 group = Entry->GetGroup();
- std::string vr = Entry->GetVR();
- guint32 length = Entry->GetLength();
+bool Document::IsDocEntryAnInteger(DocEntry *entry)
+{
+ uint16_t elem = entry->GetElement();
+ uint16_t group = entry->GetGroup();
+ const std::string &vr = entry->GetVR();
+ uint32_t length = entry->GetLength();
// When we have some semantics on the element we just read, and if we
// a priori know we are dealing with an integer, then we shall be
// able to swap it's element value properly.
- if ( element == 0 ) // This is the group length of the group
+ if ( elem == 0 ) // This is the group length of the group
{
- if (length == 4)
+ if ( length == 4 )
+ {
return true;
+ }
else
{
// Allthough this should never happen, still some images have a
// test is useless (and might even look a bit paranoid), when we
// encounter such an ill-formed image, we simply display a warning
// message and proceed on parsing (while crossing fingers).
- std::ostringstream s;
- int filePosition = ftell(fp);
- s << "Erroneous Group Length element length on : (" \
- << std::hex << group << " , " << element
+ long filePosition = Fp->tellg();
+ gdcmWarningMacro( "Erroneous Group Length element length on : ("
+ << std::hex << group << " , " << elem
<< ") -before- position x(" << filePosition << ")"
- << "lgt : " << length;
- dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() );
+ << "lgt : " << length );
}
}
- if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
+ 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) {
- // 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
-
- if ( g != 0xfffe && g!=0xb00c ) //for bogus header
- {
- 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;
- }
- if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) // for bogus header
- FoundSequenceDelimiter = true;
- else if ( n != 0xe000 )
- {
- 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;
- }
- 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;
-}
-
-/**
- * \brief Reads a supposed to be 16 Bits integer
- * (swaps it depending on processor endianity)
- * @return read value
- */
-guint16 gdcmDocument::ReadInt16() {
- 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;
- }
- errno = 0;
- g = SwapShort(g);
- return g;
-}
-
-/**
- * \brief Reads a supposed to be 32 Bits integer
- * (swaps it depending on processor endianity)
- * @return read value
- */
-guint32 gdcmDocument::ReadInt32() {
- 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;
- }
- errno = 0;
- g = SwapLong(g);
- return g;
-}
-
-/**
- * \brief skips bytes inside the source file
- * \warning NOT end user intended method !
- * @return
- */
-void gdcmDocument::SkipBytes(guint32 NBytes) {
- //FIXME don't dump the returned value
- (void)fseek(fp, (long)NBytes, SEEK_CUR);
-}
-
-/**
- * \brief Loads all the needed Dictionaries
- * \warning NOT end user intended method !
- */
-void gdcmDocument::Initialise(void)
-{
- RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
- RefShaDict = NULL;
-}
-
/**
* \brief Discover what the swap code is (among little endian, big endian,
* bad little endian, bad big endian).
* it's neither ACR-NEMA nor DICOM
* true when we hope ours assuptions are OK
*/
-bool gdcmDocument::CheckSwap() {
-
+bool Document::CheckSwap()
+{
// The only guaranted way of finding the swap code is to find a
// group tag since we know it's length has to be of four bytes i.e.
// 0x00000004. Finding the swap code in then straigthforward. Trouble
// occurs when we can't find such group...
- guint32 x=4; // x : for ntohs
+ uint32_t x = 4; // x : for ntohs
bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
- guint32 s32;
- guint16 s16;
+ uint32_t s32;
+ uint16_t s16;
- int lgrLue;
- char *entCur;
- char deb[HEADER_LENGTH_TO_READ];
+ char deb[256];
// 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);
+ // The easiest case is the one of a 'true' DICOM header, we just have
+ // to look for the string "DICM" inside the file preamble.
+ Fp->read(deb, 256);
- entCur = deb + 128;
- if(memcmp(entCur, "DICM", (size_t)4) == 0) {
- dbg.Verbose(1, "gdcmDocument::CheckSwap:", "looks like DICOM Version3");
+ char *entCur = deb + 128;
+ if( memcmp(entCur, "DICM", (size_t)4) == 0 )
+ {
+ gdcmWarningMacro( "Looks like DICOM Version3 (preamble + DCM)" );
- // Next, determine the value representation (VR). Let's skip to the
- // first element (0002, 0000) and check there if we find "UL"
- // - or "OB" if the 1st one is (0002,0001) -,
+ // Group 0002 should always be VR, and the first element 0000
+ // Let's be carefull (so many wrong headers ...)
+ // and determine the value representation (VR) :
+ // Let's skip to the first element (0002,0000) and check there if we find
+ // "UL" - or "OB" if the 1st one is (0002,0001) -,
// in which case we (almost) know it is explicit VR.
// WARNING: if it happens to be implicit VR then what we will read
// is the length of the group. If this ascii representation of this
// length happens to be "UL" then we shall believe it is explicit VR.
- // FIXME: in order to fix the above warning, we could read the next
- // element value (or a couple of elements values) in order to make
- // sure we are not commiting a big mistake.
// We need to skip :
// * the 128 bytes of File Preamble (often padded with zeroes),
// * the 4 bytes of "DICM" string,
// i.e. a total of 136 bytes.
entCur = deb + 136;
- // FIXME : FIXME:
- // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR,
- // but elem 0002,0010 (Transfert Syntax) tells us the file is
- // *Implicit* VR. -and it is !-
+ // group 0x0002 *is always* Explicit VR Sometimes ,
+ // even if elem 0002,0010 (Transfer Syntax) tells us the file is
+ // *Implicit* VR (see former 'gdcmData/icone.dcm')
- if( (memcmp(entCur, "UL", (size_t)2) == 0) ||
- (memcmp(entCur, "OB", (size_t)2) == 0) ||
- (memcmp(entCur, "UI", (size_t)2) == 0) ||
- (memcmp(entCur, "CS", (size_t)2) == 0) ) // CS, to remove later
- // when Write DCM *adds*
+ if( memcmp(entCur, "UL", (size_t)2) == 0 ||
+ memcmp(entCur, "OB", (size_t)2) == 0 ||
+ memcmp(entCur, "UI", (size_t)2) == 0 ||
+ memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later
+ // when Write DCM *adds*
// FIXME
- // Use gdcmDocument::dicom_vr to test all the possibilities
+ // Use Document::dicom_vr to test all the possibilities
// instead of just checking for UL, OB and UI !? group 0000
{
- Filetype = gdcmExplicitVR;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
- "explicit Value Representation");
+ Filetype = ExplicitVR;
+ gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
}
else
{
- Filetype = gdcmImplicitVR;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
- "not an explicit Value Representation");
+ Filetype = ImplicitVR;
+ gdcmWarningMacro( "Group 0002 :Not an explicit Value Representation;"
+ << "Looks like a bugged Header!");
}
- if (net2host)
+ if ( net2host )
{
- sw = 4321;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
- "HostByteOrder != NetworkByteOrder");
- }
+ SwapCode = 4321;
+ gdcmWarningMacro( "HostByteOrder != NetworkByteOrder");
+ }
else
{
- sw = 0;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
- "HostByteOrder = NetworkByteOrder");
+ SwapCode = 1234;
+ gdcmWarningMacro( "HostByteOrder = NetworkByteOrder");
}
- // Position the file position indicator at first tag (i.e.
- // after the file preamble and the "DICM" string).
- rewind(fp);
- fseek (fp, 132L, SEEK_SET);
+ // Position the file position indicator at first tag
+ // (i.e. after the file preamble and the "DICM" string).
+ Fp->seekg(0, std::ios::beg);
+ Fp->seekg ( 132L, std::ios::beg);
return true;
} // End of DicomV3
// Alas, this is not a DicomV3 file and whatever happens there is no file
// preamble. We can reset the file position indicator to where the data
// is (i.e. the beginning of the file).
- dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not a DICOM Version3 file");
- rewind(fp);
+ gdcmWarningMacro( "Not a DICOM Version3 file");
+ Fp->seekg(0, std::ios::beg);
// Our next best chance would be to be considering a 'clean' ACR/NEMA file.
// By clean we mean that the length of the first tag is written down.
// 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));
-
- switch (s32) {
+ s32 = *((uint32_t *)(entCur));
+
+ switch( s32 )
+ {
case 0x00040000 :
- sw = 3412;
- Filetype = gdcmACR;
+ SwapCode = 3412;
+ Filetype = ACR;
return true;
case 0x04000000 :
- sw = 4321;
- Filetype = gdcmACR;
+ SwapCode = 4321;
+ Filetype = ACR;
return true;
case 0x00000400 :
- sw = 2143;
- Filetype = gdcmACR;
+ SwapCode = 2143;
+ Filetype = ACR;
return true;
case 0x00000004 :
- sw = 0;
- Filetype = gdcmACR;
+ SwapCode = 1234;
+ Filetype = ACR;
return true;
default :
-
- // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
- // It is time for despaired wild guesses.
- // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA,
- // i.e. the 'group length' element is not present :
-
- // check the supposed to be 'group number'
- // 0x0002 or 0x0004 or 0x0008
- // to determine ' sw' value .
- // Only 0 or 4321 will be possible
- // (no oportunity to check for the formerly well known
- // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
- // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -4, 8-)
- // the file IS NOT ACR-NEMA nor DICOM V3
- // Find a trick to tell it the caller...
-
- s16 = *((guint16 *)(deb));
+ // 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'
+ // in ( 0x0001 .. 0x0008 )
+ // to determine ' SwapCode' value .
+ // Only 0 or 4321 will be possible
+ // (no oportunity to check for the formerly well known
+ // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
+ // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -3, 4, ..., 8-)
+ // the file IS NOT ACR-NEMA nor DICOM V3
+ // Find a trick to tell it the caller...
- 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:",
- "ACR/NEMA unfound swap info (Really hopeless !)");
- Filetype = gdcmUnknown;
- return false;
- }
+ s16 = *((uint16_t *)(deb));
- // Then the only info we have is the net2host one.
- //if (! net2host )
- // sw = 0;
- //else
- // sw = 4321;
- //return;
+ switch ( s16 )
+ {
+ case 0x0001 :
+ case 0x0002 :
+ case 0x0003 :
+ case 0x0004 :
+ case 0x0005 :
+ case 0x0006 :
+ case 0x0007 :
+ case 0x0008 :
+ SwapCode = 1234;
+ Filetype = ACR;
+ return true;
+ case 0x0100 :
+ case 0x0200 :
+ case 0x0300 :
+ case 0x0400 :
+ case 0x0500 :
+ case 0x0600 :
+ case 0x0700 :
+ case 0x0800 :
+ SwapCode = 4321;
+ Filetype = ACR;
+ return true;
+ default :
+ gdcmWarningMacro( "ACR/NEMA unfound swap info (Really hopeless !)");
+ Filetype = Unknown;
+ return false;
+ }
}
}
/**
- * \brief Restore the unproperly loaded values i.e. the group, the element
- * and the dictionary entry depending on them.
+ * \brief Change the Byte Swap code.
*/
-void gdcmDocument::SwitchSwapToBigEndian(void)
+void Document::SwitchByteSwapCode()
{
- dbg.Verbose(1, "gdcmDocument::SwitchSwapToBigEndian",
- "Switching to BigEndian mode.");
- if ( sw == 0 )
+ gdcmWarningMacro( "Switching Byte Swap code from "<< SwapCode);
+ if ( SwapCode == 1234 )
{
- sw = 4321;
- return;
+ SwapCode = 4321;
}
- if ( sw == 4321 )
+ else if ( SwapCode == 4321 )
{
- sw = 0;
- return;
+ SwapCode = 1234;
}
- if ( sw == 3412 )
+ else if ( SwapCode == 3412 )
{
- sw = 2143;
- return;
+ SwapCode = 2143;
+ }
+ else if ( SwapCode == 2143 )
+ {
+ SwapCode = 3412;
}
- if ( sw == 2143 )
- sw = 3412;
}
/**
* \brief during parsing, Header Elements too long are not loaded in memory
- * @param NewSize
+ * @param newSize
*/
-void gdcmDocument::SetMaxSizeLoadEntry(long NewSize)
+void Document::SetMaxSizeLoadEntry(long newSize)
{
- if (NewSize < 0)
+ if ( newSize < 0 )
+ {
return;
- if ((guint32)NewSize >= (guint32)0xffffffff)
+ }
+ if ((uint32_t)newSize >= (uint32_t)0xffffffff )
{
MaxSizeLoadEntry = 0xffffffff;
return;
}
- MaxSizeLoadEntry = NewSize;
+ MaxSizeLoadEntry = newSize;
}
-
/**
* \brief Header Elements too long will not be printed
- * \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE
- * @param NewSize
+ * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE
+ * @param newSize
*/
-void gdcmDocument::SetMaxSizePrintEntry(long NewSize)
+void Document::SetMaxSizePrintEntry(long newSize)
{
- if (NewSize < 0)
+ if ( newSize < 0 )
+ {
return;
- if ((guint32)NewSize >= (guint32)0xffffffff)
+ }
+ if ((uint32_t)newSize >= (uint32_t)0xffffffff )
{
MaxSizePrintEntry = 0xffffffff;
return;
}
- MaxSizePrintEntry = NewSize;
+ MaxSizePrintEntry = newSize;
}
-
/**
* \brief Read the next tag but WITHOUT loading it's value
* (read the 'Group Number', the 'Element Number',
- * gets the Dict Entry
+ * gets the Dict Entry
* gets the VR, gets the length, gets the offset value)
* @return On succes the newly created DocEntry, NULL on failure.
*/
-gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) {
- guint16 g,n;
- gdcmDocEntry *NewEntry;
- g = ReadInt16();
- n = ReadInt16();
-
- if (errno == 1)
+DocEntry *Document::ReadNextDocEntry()
+{
+ uint16_t group;
+ uint16_t elem;
+
+ try
+ {
+ group = ReadInt16();
+ elem = ReadInt16();
+ }
+ catch ( FormatError e )
+ {
// We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
- return (gdcmDocEntry *)0;
-
- NewEntry = NewDocEntryByNumber(g, n);
- FindDocEntryVR(NewEntry);
- FindDocEntryLength(NewEntry);
-
- if (errno == 1) {
- // Call it quits
- delete NewEntry;
- return NULL;
+ return 0;
}
- NewEntry->SetOffset(ftell(fp));
- return NewEntry;
-}
+ // Sometimes file contains groups of tags with reversed endianess.
+ HandleBrokenEndian(group, elem);
-/**
- * \brief Generate a free TagKey i.e. a TagKey that is not present
- * in the TagHt dictionary.
- * @param group The generated tag must belong to this group.
- * @return The element of tag with given group which is fee.
- */
-guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group)
-{
- for (guint32 elem = 0; elem < UINT32_MAX; elem++)
+ // In 'true DICOM' files Group 0002 is always little endian
+ if ( HasDCMPreamble )
+ HandleOutOfGroup0002(group, elem);
+
+ std::string vr = FindDocEntryVR();
+ std::string realVR = vr;
+
+ if( vr == GDCM_UNKNOWN)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, elem);
- if (tagHT.count(key) == 0)
- return elem;
+ DictEntry *dictEntry = GetDictEntry(group,elem);
+ if( dictEntry )
+ realVR = dictEntry->GetVR();
}
- return UINT32_MAX;
-}
+ DocEntry *newEntry;
+ if( Global::GetVR()->IsVROfSequence(realVR) )
+ newEntry = NewSeqEntry(group, elem);
+ else if( Global::GetVR()->IsVROfStringRepresentable(realVR) )
+ newEntry = NewValEntry(group, elem,vr);
+ else
+ newEntry = NewBinEntry(group, elem,vr);
-/**
- * \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.
- */
-guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement)
-{
- guint16 ItemTagGroup;
- guint16 ItemTagElement;
- long PositionOnEntry = ftell(fp);
- long CurrentPosition = ftell(fp); // On debugging purposes
+ if( vr == GDCM_UNKNOWN )
+ {
+ if( Filetype == ExplicitVR )
+ {
+ // We thought this was explicit VR, but we end up with an
+ // implicit VR tag. Let's backtrack.
+ if ( newEntry->GetGroup() != 0xfffe )
+ {
+ std::string msg;
+ msg = Util::Format("Entry (%04x,%04x) should be Explicit VR\n",
+ newEntry->GetGroup(), newEntry->GetElement());
+ gdcmWarningMacro( msg.c_str() );
+ }
+ }
+ newEntry->SetImplicitVR();
+ }
- //// Read the Item Tag group and element, and make
- // sure they are respectively 0xfffe and 0xe000:
- ItemTagGroup = ReadInt16();
- ItemTagElement = ReadInt16();
- if ( (ItemTagGroup != TestGroup) || (ItemTagElement != TestElement ) )
+ try
{
- std::ostringstream s;
- s << " We should have found tag (";
- s << std::hex << TestGroup << "," << TestElement << ")" << std::endl;
- s << " but instead we encountered tag (";
- s << std::hex << ItemTagGroup << "," << ItemTagElement << ")"
- << std::endl;
- s << " at address: " << (unsigned)CurrentPosition << std::endl;
- dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:");
- dbg.Verbose(0, s.str().c_str());
- fseek(fp, PositionOnEntry, SEEK_SET);
- return 0;
+ FindDocEntryLength(newEntry);
}
-
- //// Then read the associated Item Length
- CurrentPosition=ftell(fp);
- guint32 ItemLength;
- ItemLength = ReadInt32();
+ catch ( FormatError e )
{
- 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());
+ // Call it quits
+ //std::cout << e;
+ delete newEntry;
+ return 0;
}
- return ItemLength;
-}
-/**
- * \brief Read the length of an exptected Item tag i.e. (0xfffe, 0xe000).
- * \sa \ref gdcmDocument::ReadTagLength
- * \warning See warning of \ref gdcmDocument::ReadTagLength
- * @return On success returns the length associated to the item tag.
- * On failure returns 0.
- */
-guint32 gdcmDocument::ReadItemTagLength(void)
-{
- return ReadTagLength(0xfffe, 0xe000);
-}
+ newEntry->SetOffset(Fp->tellg());
-/**
- * \brief Read the length of an expected Sequence Delimiter tag i.e.
- * (0xfffe, 0xe0dd).
- * \sa \ref gdcmDocument::ReadTagLength
- * \warning See warning of \ref gdcmDocument::ReadTagLength
- * @return On success returns the length associated to the Sequence
- * Delimiter tag. On failure returns 0.
- */
-guint32 gdcmDocument::ReadSequenceDelimiterTagLength(void)
-{
- return ReadTagLength(0xfffe, 0xe0dd);
+ return newEntry;
}
-
/**
- * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files
- * No other way so 'skip' the Data
- *
+ * \brief Handle broken private tag from Philips NTSCAN
+ * where the endianess is being switch to BigEndian for no
+ * apparent reason
+ * @return no return
*/
-
-void gdcmDocument::Parse7FE0 (void)
+void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
{
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return;
-
- if ( IsImplicitVRLittleEndianTransferSyntax()
- || IsExplicitVRLittleEndianTransferSyntax()
- || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier !
- || IsDeflatedExplicitVRLittleEndianTransferSyntax() )
- return;
-
- // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels
-
- //// Read the Basic Offset Table Item Tag length...
- guint32 ItemLength = ReadItemTagLength();
-
- //// ... and then read length[s] itself[themselves]. We don't use
- // the values read (BTW what is the purpous of those lengths ?)
- if (ItemLength != 0) {
- // BTW, what is the purpous of those length anyhow !?
- char * BasicOffsetTableItemValue = new char[ItemLength + 1];
- fread(BasicOffsetTableItemValue, ItemLength, 1, fp);
- for (unsigned int i=0; i < ItemLength; i += 4){
- guint32 IndividualLength;
- IndividualLength = str2num(&BasicOffsetTableItemValue[i],guint32);
- std::ostringstream s;
- s << " Read one length: ";
- s << std::hex << IndividualLength << std::endl;
- dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str());
- }
- }
-
- if ( ! IsRLELossLessTransferSyntax() )
- {
- // JPEG Image
-
- //// We then skip (not reading them) all the fragments of images:
- while ( (ItemLength = ReadItemTagLength()) )
- {
- SkipBytes(ItemLength);
- }
-
- }
- else
+ // Endian reversion. Some files contain groups of tags with reversed endianess.
+ static int reversedEndian = 0;
+ // try to fix endian switching in the middle of headers
+ if ((group == 0xfeff) && (elem == 0x00e0))
{
- // RLE Image
- long ftellRes;
- long RleSegmentLength[15], fragmentLength;
-
- // while 'Sequence Delimiter Item' (fffe,e0dd) not found
- while ( (fragmentLength = ReadSequenceDelimiterTagLength()) )
- {
- // Parse fragments of the current Fragment (Frame)
- //------------------ scanning (not reading) fragment pixels
- guint32 nbRleSegments = ReadInt32();
- printf(" Nb of RLE Segments : %d\n",nbRleSegments);
-
- //// Reading RLE Segments Offset Table
- guint32 RleSegmentOffsetTable[15];
- for(int k=1; k<=15; k++) {
- ftellRes=ftell(fp);
- RleSegmentOffsetTable[k] = ReadInt32();
- printf(" at : %x Offset Segment %d : %d (%x)\n",
- (unsigned)ftellRes,k,RleSegmentOffsetTable[k],
- RleSegmentOffsetTable[k]);
- }
-
- // skipping (not reading) RLE Segments
- if (nbRleSegments>1) {
- for(unsigned int k=1; k<=nbRleSegments-1; k++) {
- RleSegmentLength[k]= RleSegmentOffsetTable[k+1]
- - RleSegmentOffsetTable[k];
- ftellRes=ftell(fp);
- printf (" Segment %d : Length = %d x(%x) Start at %x\n",
- k,(unsigned)RleSegmentLength[k],
- (unsigned)RleSegmentLength[k], (unsigned)ftellRes);
- SkipBytes(RleSegmentLength[k]);
- }
- }
-
- RleSegmentLength[nbRleSegments]= fragmentLength
- - RleSegmentOffsetTable[nbRleSegments];
- ftellRes=ftell(fp);
- printf (" Segment %d : Length = %d x(%x) Start at %x\n",
- nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments],
- (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes);
- SkipBytes(RleSegmentLength[nbRleSegments]);
- }
+ // start endian swap mark for group found
+ reversedEndian++;
+ SwitchByteSwapCode();
+ // fix the tag
+ group = 0xfffe;
+ elem = 0xe000;
+ }
+ else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
+ {
+ // end of reversed endian group
+ reversedEndian--;
+ SwitchByteSwapCode();
}
}
-
-
/**
- * \brief 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'
+ * \brief Group 0002 is always coded Little Endian
+ * whatever Transfer Syntax is
+ * @return no return
*/
-bool gdcmDocument::operator<(gdcmDocument &document)
+void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem)
{
- std::string s1,s2;
-
- // Patient Name
- s1=this->GetEntryByNumber(0x0010,0x0010);
- s2=document.GetEntryByNumber(0x0010,0x0010);
- if(s1 < s2)
- return true;
- else if(s1 > s2)
- return false;
- else
+ // Endian reversion. Some files contain groups of tags with reversed endianess.
+ if ( !Group0002Parsed && group != 0x0002)
{
- // Patient ID
- s1=this->GetEntryByNumber(0x0010,0x0020);
- s2=document.GetEntryByNumber(0x0010,0x0020);
- if (s1 < s2)
- return true;
- else if (s1 > s2)
- return true;
- else
+ Group0002Parsed = true;
+ // we just came out of group 0002
+ // if Transfer syntax is Big Endian we have to change CheckSwap
+
+ std::string ts = GetTransferSyntax();
+ if ( !Global::GetTS()->IsTransferSyntax(ts) )
{
- // Study Instance UID
- s1=this->GetEntryByNumber(0x0020,0x000d);
- s2=document.GetEntryByNumber(0x0020,0x000d);
- if (s1 < s2)
- return true;
- else if(s1 > s2)
- return false;
- else
+ gdcmWarningMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
+ return;
+ }
+
+ // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..."
+
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian )
{
- // Serie Instance UID
- s1=this->GetEntryByNumber(0x0020,0x000e);
- s2=document.GetEntryByNumber(0x0020,0x000e);
- if (s1 < s2)
- return true;
- else if(s1 > s2)
- return false;
+ Filetype = ImplicitVR;
}
+
+ // FIXME Strangely, this works with
+ //'Implicit VR Transfer Syntax (GE Private)
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
+ {
+ gdcmWarningMacro("Transfer Syntax Name = ["
+ << GetTransferSyntaxName() << "]" );
+ SwitchByteSwapCode();
+ group = SwapShort(group);
+ elem = SwapShort(elem);
}
}
- return false;
}
+//-----------------------------------------------------------------------------
+// Print
//-----------------------------------------------------------------------------
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff