Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/01/14 11:28:30 $
- Version: $Revision: 1.190 $
+ Date: $Date: 2011/03/29 07:36:00 $
+ Version: $Revision: 1.386 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
#include "gdcmDocument.h"
-#include "gdcmValEntry.h"
-#include "gdcmBinEntry.h"
#include "gdcmSeqEntry.h"
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
#include "gdcmTS.h"
-#include "gdcmException.h"
#include "gdcmDictSet.h"
-#include "gdcmRLEFramesInfo.h"
-#include "gdcmJPEGFragmentsInfo.h"
#include "gdcmDocEntrySet.h"
#include "gdcmSQItem.h"
+#include "gdcmDataEntry.h"
#include <vector>
#include <iomanip>
+#include <fstream>
+#include <ctype.h> // for isdigit
+#include <stdlib.h> // for atoi
-// For nthos:
-#if defined(_MSC_VER) || defined(__BORLANDC__)
- #include <winsock.h>
-#else
- #include <netinet/in.h>
-#endif
+#if defined(__BORLANDC__)
+ #include <mem.h> // for memset
+#endif
-namespace gdcm
+namespace GDCM_NAME_SPACE
{
-
//-----------------------------------------------------------------------------
-// Refer to Document::CheckSwap()
-//const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
// 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 This default constructor neither loads nor parses the file.
+ * You should then invoke Document::Load.
+ *
+ */
+Document::Document()
+ :ElementSet()
+{
+ Fp = 0;
+
+ SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
+ Initialize();
+ SwapCode = 1234;
+ Filetype = ExplicitVR;
+ CurrentOffsetPosition = 0;
+ OffsetOfPreviousParseDES =0;
+ // Load will set it to true if sucessfull
+ Group0002Parsed = false;
+ IsDocumentAlreadyLoaded = false;
+ IsDocumentModified = true;
+ LoadMode = LD_ALL; // default : load everything, later
+
+ SetFileName("");
+ changeFromUN=false;
+ UnexpectedEOF=false;
+}
+
+/**
+ * \brief Canonical destructor.
+ */
+Document::~Document ()
+{
+ CloseFile();
+}
+
+//-----------------------------------------------------------------------------
+// Public
+/**
+ * \brief Loader. use SetLoadMode(), SetFileName() before !
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool Document::Load( )
+{
+ if ( GetFileName() == "" )
+ {
+ gdcmWarningMacro( "Use SetFileName, before !" );
+ return false;
+ }
+ return DoTheLoadingDocumentJob( );
+}
+
+//#ifndef GDCM_LEGACY_REMOVE
/**
- * \brief constructor
- * @param filename file to be opened for parsing
+ * \brief Loader. (DEPRECATED : not to break the API)
+ * @param fileName 'Document' (File or DicomDir) to be open for parsing
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
*/
-Document::Document( std::string const &filename ) : ElementSet(-1)
+ /*
+bool Document::Load( std::string const &fileName )
{
- SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Filename = filename;
- Initialise();
+ Filename = fileName;
+ return DoTheLoadingDocumentJob( );
+}
+*/
+//#endif
+
+/**
+ * \brief Performs the Loading Job (internal use only)
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool Document::DoTheLoadingDocumentJob( )
+{
+ if ( ! IsDocumentModified ) // Nothing to do !
+ return true;
+
+ ClearEntry();
Fp = 0;
if ( !OpenFile() )
{
- return;
+ // warning already performed in OpenFile()
+ Filetype = Unknown;
+ return false;
}
Group0002Parsed = false;
- gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str());
- // Fp->seekg( 0, std::ios::beg);
-
- Fp->seekg(0, std::ios::end);
- long lgt = Fp->tellg();
-
- Fp->seekg( 0, std::ios::beg);
-
- CheckSwap();
- long beg = Fp->tellg();
- lgt -= beg;
-
- ParseDES( this, beg, lgt, false); // Loading is done during parsing
+ gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str());
+
+ // Computes the total length of the file
+ Fp->seekg(0, std::ios::end); // Once per Document !
+ long lgt = Fp->tellg(); // Once per Document !
+ Fp->seekg(0, std::ios::beg); // Once per Document !
+
+ // CheckSwap returns a boolean
+ // (false if no swap info of any kind was found)
+ if (! CheckSwap() )
+ {
+ gdcmWarningMacro( "Neither a DICOM V3 nor an ACR-NEMA file: "
+ << Filename.c_str());
+ CloseFile();
+ return false;
+ }
- Fp->seekg( 0, std::ios::beg);
+ long beg = Fp->tellg(); // just after DICOM preamble (if any)
+
+ lgt -= beg; // remaining length to parse
+
+ // Recursive call.
+ // Loading is done during parsing
+ OffsetOfPreviousParseDES = beg;
+ ParseDES( this, beg, lgt, false); // delim_mode is first defaulted to false
+
+ if ( IsEmpty() )
+ {
+ gdcmErrorMacro( "No tag in internal hash table for: "
+ << Filename.c_str());
+ CloseFile();
+ return false;
+ }
+ IsDocumentAlreadyLoaded = true;
+
+ //Fp->seekg(0, std::ios::beg); // Once per Document!
// Load 'non string' values
- std::string PhotometricInterpretation = GetEntry(0x0028,0x0004);
- if( PhotometricInterpretation == "PALETTE COLOR " )
+ std::string PhotometricInterpretation = GetEntryString(0x0028,0x0004);
+ if ( PhotometricInterpretation == "PALETTE COLOR " )
{
- LoadEntryBinArea(0x0028,0x1200); // gray LUT
- /// FIXME FIXME FIXME
+ // FIXME
+ // Probabely this line should be outside the 'if'
+ // Try to find an image sample holding a 'gray LUT'
+ LoadEntryBinArea(0x0028,0x1200); // gray LUT
+
+ /// FIXME
+ /// --> FIXME : The difference between BinEntry and DataEntry
+ /// --> no longer exists, but the alteration of Dicom Dictionary remains.
+ /// --> Old comment restored on purpose.
+ /// --> New one (replacing both BinEntry and ValEntry by DataEntry)
+ /// --> had absolutely no meaning.
+ /// --> The whole comment will be removed when the stuff is cleaned !
+ /// -->
/// The tags refered by the three following lines used to be CORRECTLY
/// defined as having an US Value Representation in the public
- /// dictionnary. BUT the semantics implied by the three following
+ /// dictionary. BUT the semantics implied by the three following
/// lines state that the corresponding tag contents are in fact
/// the ones of a BinEntry.
- /// In order to fix things "Quick and Dirty" the dictionnary was
+ /// In order to fix things "Quick and Dirty" the dictionary was
/// altered on PURPOSE but now contains a WRONG value.
/// In order to fix things and restore the dictionary to its
- /// correct value, one needs to decided of the semantics by deciding
- /// wether the following tags are either:
+ /// correct value, one needs to decide 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.
+
+ // --> OB (byte aray) or OW (short int aray)
+ // The actual VR has to be deduced from other entries.
+ // Our way of loading them may fail in some cases :
+ // We must or not SwapByte depending on other field values.
+
LoadEntryBinArea(0x0028,0x1201); // R LUT
LoadEntryBinArea(0x0028,0x1202); // G LUT
LoadEntryBinArea(0x0028,0x1203); // B LUT
LoadEntryBinArea(0x0028,0x1222);
// Segmented Blue Palette Color LUT Data
LoadEntryBinArea(0x0028,0x1223);
- }
+ }
+
//FIXME later : how to use it?
- LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent)
+ SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000); // Modality LUT Sequence
+ if ( modLutSeq !=0 )
+ {
+ SQItem *sqi= modLutSeq->GetFirstSQItem();
+ if ( sqi != 0 )
+ {
+ DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006); // LUT Data
+ if ( dataEntry != 0 )
+ {
+ if ( dataEntry->GetLength() != 0 )
+ {
+ // FIXME : CTX dependent means : contexted dependant.
+ // see upper comment.
+ LoadEntryBinArea(dataEntry); //LUT Data (CTX dependent)
+ }
+ }
+ }
+ }
+
+ // Force Loading some more elements if user asked to.
+
+ GDCM_NAME_SPACE::DocEntry *d;
+ for (ListElements::iterator it = UserForceLoadList.begin();
+ it != UserForceLoadList.end();
+ ++it)
+ {
+ gdcmDebugMacro( "Force Load " << std::hex
+ << (*it).Group << "|" <<(*it).Elem );
+
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( d == NULL)
+ {
+ gdcmWarningMacro( "You asked to ForceLoad " << std::hex
+ << (*it).Group <<"|"<< (*it).Elem
+ << " that doesn't exist" );
+ continue;
+ }
+
+ LoadDocEntry(d, true);
+ }
- CloseFile();
+ CloseFile();
- // --------------------------------------------------------------
+ // ----------------------------
// 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).
+ // used at CREATIS. For the time being (say a couple of years)
+ // we keep this kludge to allow CREATIS users
+ // reading their old images.
//
// if recognition code tells us we deal with a LibIDO image
// we switch lineNumber and columnNumber
//
std::string RecCode;
- RecCode = GetEntry(0x0008, 0x0010); // recognition code
- if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
- RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
- // with "little-endian strings"
+ RecCode = GetEntryString(0x0008, 0x0010); // recognition code (RET)
+
+
+ if(RecCode.find("ACRNEMA_LIBIDO") == 0 || // any version
+ RecCode.find("CANRME_AILIBOD") == 0) // for brain-damaged softwares
+ // with "little-endian strings"
{
+
Filetype = ACR_LIBIDO;
- std::string rows = GetEntry(0x0028, 0x0010);
- std::string columns = GetEntry(0x0028, 0x0011);
- SetEntry(columns, 0x0028, 0x0010);
- SetEntry(rows , 0x0028, 0x0011);
+ std::string rows = GetEntryString(0x0028, 0x0010);
+ std::string columns = GetEntryString(0x0028, 0x0011);
+ SetEntryString(columns, 0x0028, 0x0010);
+ SetEntryString(rows , 0x0028, 0x0011);
}
- // ----------------- End of ACR-LibIDO kludge ------------------
+ // --- End of ACR-LibIDO kludge ---
+ return true;
}
-/**
- * \brief This default constructor doesn't parse the file. You should
- * then invoke \ref Document::SetFileName and then the parsing.
- */
-Document::Document() : ElementSet(-1)
-{
- Fp = 0;
-
- SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialise();
- SwapCode = 1234;
- Filetype = ExplicitVR;
- Group0002Parsed = false;
-}
/**
- * \brief Canonical destructor.
+ * \brief Adds a new element we want to load anyway
+ * @param group Group number of the target tag.
+ * @param elem Element number of the target tag.
*/
-Document::~Document ()
-{
- RefPubDict = NULL;
- RefShaDict = NULL;
-
- delete RLEInfo;
- delete JPEGInfo;
-}
-
-//-----------------------------------------------------------------------------
-// Print
-
-/**
- * \brief Prints The Dict Entries of THE public Dicom Dictionary
- * @return
- */
-void Document::PrintPubDict(std::ostream &os)
-{
- RefPubDict->SetPrintLevel(PrintLevel);
- RefPubDict->Print(os);
-}
-
-/**
- * \brief Prints The Dict Entries of THE shadow Dicom Dictionary
- * @return
- */
-void Document::PrintShaDict(std::ostream &os)
-{
- RefShaDict->SetPrintLevel(PrintLevel);
- RefShaDict->Print(os);
+void Document::AddForceLoadElement (uint16_t group, uint16_t elem)
+{
+ DicomElement el;
+ el.Group = group;
+ el.Elem = elem;
+ UserForceLoadList.push_back(el);
}
-
-//-----------------------------------------------------------------------------
-// Public
/**
* \brief Get the public dictionary used
*/
}
/**
- * \brief This predicate, based on hopefully reasonable heuristics,
- * 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 Document is the one of a reasonable Dicom/Acr file,
- * false otherwise.
+ * \brief This predicate tells us whether or not the current Document
+ * was properly parsed and contains at least *one* Dicom Element
+ * (and nothing more, sorry).
+ * @return false when we're 150 % sure it's NOT a Dicom/Acr file,
+ * true otherwise.
*/
-bool Document::IsReadable()
+bool Document::IsParsable()
{
- if( Filetype == Unknown)
+ if ( Filetype == Unknown )
{
- gdcmVerboseMacro( "Wrong filetype");
+ gdcmWarningMacro( "Wrong filetype for " << GetFileName());
return false;
}
- if( TagHT.empty() )
+ if ( IsEmpty() )
{
- gdcmVerboseMacro( "No tags in internal hash table.");
+ gdcmWarningMacro( "No tag in internal hash table.");
return false;
}
return true;
}
+/**
+ * \brief This predicate tells us whether or not the current Document
+ * was properly parsed and contains at least *one* Dicom Element
+ * (and nothing more, sorry).
+ * @return false when we're 150 % sure it's NOT a Dicom/Acr file,
+ * true otherwise.
+ */
+bool Document::IsReadable()
+{
+ return IsParsable();
+}
+
+/**
+ * \brief Predicate for dicom version 3 file.
+ * @return True when the file is a dicom version 3.
+ */
+bool Document::IsDicomV3()
+{
+ // Checking if Transfer Syntax exists is enough
+ // Anyway, it's too 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 Predicate for Papyrus file
+ * Dedicated to whomsoever it may concern
+ * @return True when the file is a Papyrus file.
+ */
+bool Document::IsPapyrus()
+{
+ // check for Papyrus private Sequence
+ DocEntry *e = GetDocEntry(0x0041, 0x1050);
+ if ( !e )
+ return false;
+ // check if it's actually a Sequence
+ if ( !dynamic_cast<SeqEntry*>(e) )
+ return false;
+ return true;
+}
+
+/**
+ * \brief returns the File Type
+ * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
+ * @return the FileType code
+ */
+FileType Document::GetFileType()
+{
+ return Filetype;
+}
/**
* \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.
+ * @return The encountered Transfer Syntax of the current document, if DICOM.
+ * GDCM_UNKNOWN for ACR-NEMA files (or broken headers ...)
*/
std::string Document::GetTransferSyntax()
{
// 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) )
+
+ // Well ...
+ // (parsing and loading happen at the very same stage!)
+ //LoadDocEntrySafe(entry); //JPRx
+ if (DataEntry *dataEntry = dynamic_cast<DataEntry *>(entry) )
{
- std::string transfer = valEntry->GetValue();
+ std::string transfer = dataEntry->GetString();
// 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
+ gdcmWarningMacro( "Transfer Syntax has length = 0.");
return GDCM_UNKNOWN;
}
while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
{
transfer.erase(transfer.length()-1, 1);
+ if ( transfer.length() == 0 )
+ {
+ // for brain damaged headers
+ gdcmWarningMacro( "Transfer Syntax contains no valid character.");
+ return GDCM_UNKNOWN;
+ }
}
return transfer;
}
}
/**
- * \brief Predicate for dicom version 3 file.
- * @return True when the file is a dicom version 3.
+ * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS
+ * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
*/
-bool Document::IsDicomV3()
+std::string Document::GetTransferSyntaxName()
{
- // 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;
+ // use the TS (TS : Transfer Syntax)
+ std::string transferSyntax = GetEntryString(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 )
+ {
+ gdcmDebugMacro( "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 Swaps the bytes so they agree with the processor order
+ * @return The properly swaped 16 bits integer.
+ */
+uint16_t Document::SwapShort(uint16_t a)
+{
+ if ( SwapCode == 4321 || SwapCode == 2143 )
+ {
+ //a = ((( a << 8 ) & 0xff00 ) | (( a >> 8 ) & 0x00ff ) );
+ // Save CPU time
+ a = ( a << 8 ) | ( a >> 8 );
+ }
+ return a;
}
/**
- * \brief returns the File Type
- * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
- * @return the FileType code
+ * \brief Swaps back the bytes of 4-byte long integer accordingly to
+ * processor order.
+ * @return The properly swaped 32 bits integer.
*/
-FileType Document::GetFileType()
+uint32_t Document::SwapLong(uint32_t a)
{
- return Filetype;
+ switch (SwapCode)
+ {
+ case 1234 :
+ break;
+ case 4321 :
+// a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
+// ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
+// save CPU time
+ a=( ( a<<24) | ((a<<8) & 0x00ff0000) |
+ ((a>>8) & 0x0000ff00) | (a>>24) );
+ break;
+ case 3412 :
+// a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
+ a=( (a<<16) | (a>>16) );
+ break;
+ case 2143 :
+ a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
+ break;
+ default :
+ gdcmErrorMacro( "Unexpected swap code:" << SwapCode );
+ a = 0;
+ }
+ return a;
}
/**
- * \brief Tries to open the file \ref Document::Filename and
- * checks the preamble when existing.
- * @return The FILE pointer on success.
+ * \brief Swaps back the bytes of 8-byte long 'double' accordingly to
+ * processor order.
+ * @return The properly swaped 64 bits double.
*/
-std::ifstream *Document::OpenFile()
+double Document::SwapDouble(double a)
{
+ switch (SwapCode)
+ {
+ // There were no 'double' at ACR-NEMA time.
+ // We just have to deal with 'straight Little Endian' and
+ // 'straight Big Endian'
+ case 1234 :
+ break;
+ case 4321 :
+ {
+ char *beg = (char *)&a;
+ char *end = beg + 7;
+ char t;
+ for (unsigned int i = 0; i<7; i++)
+ {
+ t = *beg;
+ *beg = *end;
+ *end = t;
+ beg++,
+ end--;
+ }
+ }
+ break;
+ default :
+ gdcmErrorMacro( "Unexpected swap code:" << SwapCode );
+ a = 0.;
+ }
+ return a;
+}
+//
+// -----------------File I/O ---------------
+/**
+ * \brief Tries to open the file Document::Filename and
+ * checks the preamble when existing,
+ * or if the file starts with an ACR-NEMA look-like element.
+ * @return The FILE pointer on success, 0 on failure.
+ */
+std::ifstream *Document::OpenFile()
+{
HasDCMPreamble = false;
- if (Filename.length() == 0)
+ if (Filename.length() == 0)
{
return 0;
}
- if(Fp)
+ if ( Fp )
{
- gdcmVerboseMacro( "File already open: " << Filename.c_str());
+ gdcmDebugMacro( "File already open: " << Filename.c_str());
+ CloseFile();
}
Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
- if( ! *Fp )
+ if ( ! *Fp )
{
- gdcmDebugMacro( "Cannot open file: " << Filename.c_str());
+ // Don't user gdcmErrorMacro :
+ // a spurious message will appear when you use, for instance
+ // gdcm::FileHelper *fh = new gdcm::FileHelper( outputFileName );
+ // to create outputFileName.
+
+ // FIXME : if the upper comment is still usefull
+ // --> the constructor is not so good ...
+
+ gdcmWarningMacro( "Cannot open file: " << Filename.c_str());
delete Fp;
Fp = 0;
return 0;
+ //exit(1); // No function is allowed to leave the application instead
+ // of warning the caller
}
-
- uint16_t zero;
+
+ uint16_t zero = 0;
Fp->read((char*)&zero, (size_t)2);
- if( Fp->eof() )
+ if ( Fp->eof() )
{
CloseFile();
return 0;
}
-
- //ACR -- or DICOM with no Preamble; may start with a Shadow Group --
- if(
- zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 ||
- zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 ||
- zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 ||
- zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 )
- {
- std::string msg
- = Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero);
- gdcmVerboseMacro( msg.c_str() );
- return Fp;
- }
-
- //DICOM
- Fp->seekg(126L, std::ios::cur);
- char dicm[4];
+
+ //-- DICOM --
+ Fp->seekg(126L, std::ios::cur); // Once per Document
+ char dicm[4]; // = {' ',' ',' ',' '};
Fp->read(dicm, (size_t)4);
- if( Fp->eof() )
+ if ( Fp->eof() )
{
CloseFile();
return 0;
}
- if( memcmp(dicm, "DICM", 4) == 0 )
+
+ if ( memcmp(dicm, "DICM", 4) == 0 )
{
HasDCMPreamble = true;
return Fp;
}
-
+
+ //-- Broken ACR or DICOM (?) with no Preamble; may start with a Shadow Group --
+ // FIXME : We cannot be sure the preable is only zeroes..
+ // (see ACUSON-24-YBR_FULL-RLE.dcm )
+ 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 ||
+ zero == 0x0028 || 0x2800 // worse : some ACR-NEMA like files
+ // start 00028 group ?!?
+ )
+ {
+ std::string msg = Util::Format(
+ "ACR/DICOM starting by 0x(%04x) at the beginning of the file\n", zero);
+ // FIXME : is it a Warning message, or a Debug message?
+ gdcmWarningMacro( msg.c_str() );
+ return Fp;
+ }
+
+ // -- Neither ACR/No Preamble Dicom nor DICOMV3 file
CloseFile();
- gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
-
+ // Don't user Warning nor Error, not to pollute the output
+ // while directory recursive parsing ...
+ gdcmDebugMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
+ << Filename.c_str());
return 0;
}
/**
- * \brief closes the file
- * @return TRUE if the close was successfull
+ * \brief closes the file
+ * @return TRUE if the close was successfull
*/
bool Document::CloseFile()
{
- if( Fp )
+ if ( Fp )
{
Fp->close();
delete Fp;
Fp = 0;
}
-
- return true; //FIXME how do we detect a non-close ifstream ?
+ return true;
}
/**
- * \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
+ * \brief Writes in a file all the 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.
*/
-void Document::WriteContent(std::ofstream *fp, FileType filetype)
+void Document::WriteContent(std::ofstream *fp, FileType filetype, bool, bool)
{
- /// \todo move the following lines (and a lot of others, to be written)
- /// to a future function CheckAndCorrectHeader
- /// (necessary if user wants to write a DICOM V3 file
- /// starting from an ACR-NEMA (V2) Header
+ // Skip if user wants to write an ACR-NEMA file
- if ( filetype == ImplicitVR || filetype == ExplicitVR )
+ if ( filetype == ImplicitVR || filetype == ExplicitVR ||
+ filetype == JPEG || filetype == JPEG2000 )
{
// writing Dicom File Preamble
char filePreamble[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);
+ /*
+ * \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);
+ *
+ * --> Computing group length for groups with embeded Sequences
+ * --> was too much tricky / we were [in a hurry / too lazy]
+ * --> We don't write the element 0x0000 (group length)
+ */
+ // This one is recursive
+ // false : outside MetaElements
+ // false : outside Sequence
+ ElementSet::WriteContent(fp, filetype, false, false);
+}
+
+// -----------------------------------------
+// Content entries
+/**
+ * \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
*/
-
- ElementSet::WriteContent(fp, filetype); // This one is recursive
-}
-
-/**
- * \brief Modifies the value of a given Doc Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * @param value (string) Value to be set
- * @param group Group number of the Entry
- * @param elem Element number of the Entry
- * @param vr V(alue) R(epresentation) of the Entry -if private Entry-
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
- */
-ValEntry *Document::ReplaceOrCreate(std::string const &value,
- uint16_t group,
- uint16_t elem,
- TagName const &vr )
+void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
- ValEntry *valEntry = 0;
- DocEntry *currentEntry = GetDocEntry( group, elem);
-
- if (currentEntry)
+ // Search the corresponding DocEntry
+ DocEntry *docEntry = GetDocEntry(group, elem);
+ if ( !docEntry )
{
- valEntry = dynamic_cast< ValEntry* >(currentEntry);
-
- // Verify the VR
- if( valEntry )
- if( valEntry->GetVR()!=vr )
- valEntry=NULL;
-
- // if currentEntry doesn't correspond to the requested valEntry
- if( !valEntry)
- {
- if (!RemoveEntry(currentEntry))
- {
- gdcmVerboseMacro( "Removal of previous DocEntry failed.");
-
- return NULL;
- }
- }
+ gdcmDebugMacro(std::hex << group << "|" << elem
+ << " doesn't exist" );
+ return;
}
-
- // Create a new valEntry if necessary
- if (!valEntry)
+ DataEntry *dataEntry = dynamic_cast<DataEntry *>(docEntry);
+ if ( !dataEntry )
{
- valEntry = NewValEntry(group, elem, vr);
-
- if ( !AddEntry(valEntry))
- {
- gdcmVerboseMacro("AddEntry failed although this is a creation.");
-
- delete valEntry;
- return NULL;
- }
+ gdcmWarningMacro(std::hex << group << "|" << elem
+ << " is NOT a DataEntry");
+ return;
}
+ LoadEntryBinArea(dataEntry);
+}
- // Set the binEntry value
- SetEntry(value, valEntry);
- return valEntry;
-}
-
-/*
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * A copy of the binArea is made to be kept in the Document.
- * @param binArea (binary) value to be set
- * @param Group Group number of the Entry
- * @param Elem Element number of the Entry
- * @param vr V(alue) R(epresentation) of the Entry -if private Entry-
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
+/**
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
+ * @param entry Entry whose binArea is going to be loaded
*/
-BinEntry *Document::ReplaceOrCreate(uint8_t *binArea,
- int lgth,
- uint16_t group,
- uint16_t elem,
- TagName const &vr )
-{
- BinEntry *binEntry = 0;
- DocEntry *currentEntry = GetDocEntry( group, elem);
-
- // Verify the currentEntry
- if (currentEntry)
- {
- binEntry = dynamic_cast< BinEntry* >(currentEntry);
-
- // Verify the VR
- if( binEntry )
- if( binEntry->GetVR()!=vr )
- binEntry=NULL;
+void Document::LoadEntryBinArea(DataEntry *entry)
+{
+ if( entry->GetBinArea() )
+ return;
- // if currentEntry doesn't correspond to the requested valEntry
- if( !binEntry)
- {
- if (!RemoveEntry(currentEntry))
- {
- gdcmVerboseMacro( "Removal of previous DocEntry failed.");
+ bool openFile = !Fp;
+ if ( openFile )
+ OpenFile();
- return NULL;
- }
- }
- }
+ //size_t o =(size_t)entry->GetOffset();
+ Fp->seekg((size_t)entry->GetOffset(), std::ios::beg); // FIXME : for each DataEntry !
- // Create a new binEntry if necessary
- if (!binEntry)
+ size_t l = entry->GetLength();
+ uint8_t *data = new uint8_t[l];
+ if ( !data )
{
- binEntry = NewBinEntry(group, elem, vr);
-
- if ( !AddEntry(binEntry))
- {
- gdcmVerboseMacro( "AddEntry failed allthough this is a creation.");
-
- delete binEntry;
- return NULL;
- }
+ gdcmWarningMacro( "Cannot allocate DataEntry content for : "
+ << std::hex << entry->GetGroup()
+ << "|" << entry->GetElement() );
+ return;
}
- // Set the binEntry value
- uint8_t *tmpArea;
- if (lgth>0 && binArea)
- {
- tmpArea = new uint8_t[lgth];
- memcpy(tmpArea,binArea,lgth);
- }
- else
- {
- tmpArea = 0;
- }
- if (!SetEntry(tmpArea,lgth,binEntry))
+ // Read the data
+ Fp->read((char*)data, l);
+ if ( Fp->fail() || Fp->eof() )
{
- if (tmpArea)
- {
- delete[] tmpArea;
- }
+ delete[] data;
+ entry->SetState(DataEntry::STATE_UNREAD);
+ return;
}
- return binEntry;
-}
+ // Swap the data content if necessary
+ uint32_t i;
+ unsigned short vrLgth =
+ Global::GetVR()->GetAtomicElementLength(entry->GetVR());
-/*
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * when it exists. Create it when unexistant.
- * @param Group Group number of the Entry
- * @param Elem Element number of the Entry
- * \return pointer to the modified/created SeqEntry (NULL when creation
- * failed).
- */
-SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem)
-{
- SeqEntry *seqEntry = 0;
- DocEntry *currentEntry = GetDocEntry( group, elem);
+// FIXME : trouble expected if we read an ... OW Entry (LUT, etc ..)
+// if( entry->GetVR() == "OW" )
+// vrLgth = 1;
- // Verify the currentEntry
- if (currentEntry)
+ switch(vrLgth)
{
- seqEntry = dynamic_cast< SeqEntry* >(currentEntry);
-
- // Verify the VR
- if( seqEntry )
- if( seqEntry->GetVR()!="SQ" )
- seqEntry=NULL;
-
- // if currentEntry doesn't correspond to the requested valEntry
- if( !seqEntry)
+ case 1:
{
- if (!RemoveEntry(currentEntry))
- {
- gdcmVerboseMacro( "Removal of previous DocEntry failed.");
-
- return NULL;
- }
+ break;
+ }
+ case 2:
+ {
+ uint16_t *data16 = (uint16_t *)data;
+ for(i=0;i<l/vrLgth;i++)
+ data16[i] = SwapShort(data16[i]);
+ break;
}
- }
-
- // Create a new seqEntry if necessary
- if (!seqEntry)
- {
- seqEntry = NewSeqEntry(group, elem);
-
- if ( !AddEntry(seqEntry))
+ case 4:
{
- gdcmVerboseMacro( "AddEntry failed allthough this is a creation.");
-
- delete seqEntry;
- return NULL;
+ uint32_t *data32 = (uint32_t *)data;
+ for(i=0;i<l/vrLgth;i++)
+ data32[i] = SwapLong(data32[i]);
+ break;
+ }
+ case 8:
+ {
+ double *data64 = (double *)data;
+ for(i=0;i<l/vrLgth;i++)
+ data64[i] = SwapDouble(data64[i]);
+ break;
}
}
+
+ entry->SetBinArea(data);
- return seqEntry;
-}
-
-/**
- * \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 Document::ReplaceIfExist(std::string const &value,
- uint16_t group, uint16_t elem )
-{
- SetEntry(value, group, elem);
-
- return true;
-}
-
-//-----------------------------------------------------------------------------
-// Protected
+ if ( openFile ) // The file is left in the state (open/close) it was at entrance
+ CloseFile();
+}
/**
- * \brief Checks if a given Dicom Element exists within the H table
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return true is found
+ * \brief Loads the element while preserving the current
+ * underlying file position indicator as opposed to
+ * LoadDocEntry that modifies it
+ * \note seems to be unused!.
+ * @param entry DocEntry whose value will be loaded.
*/
-bool Document::CheckIfEntryExist(uint16_t group, uint16_t element )
-{
- const std::string &key = DictEntry::TranslateToKey(group, element );
- return TagHT.count(key) != 0;
-}
-
+//void Document::LoadDocEntrySafe(DocEntry *entry)
+//{
+// if ( Fp )
+// {
+// long PositionOnEntry = Fp->tellg(); // LoadDocEntrySafe is not used
+// LoadDocEntry(entry);
+// Fp->seekg(PositionOnEntry, std::ios::beg); // LoadDocEntrySafe is not used
+// }
+//}
/**
- * \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.
+ * \brief Compares two documents, according to 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'
*/
-std::string Document::GetEntry(uint16_t group, uint16_t element)
+bool Document::operator<(Document &document)
{
- TagKey key = DictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key))
+ // Patient Name
+ std::string s1 = GetEntryString(0x0010,0x0010);
+ std::string s2 = document.GetEntryString(0x0010,0x0010);
+ if (s1 < s2)
{
- return GDCM_UNFOUND;
+ return true;
}
-
- return ((ValEntry *)TagHT.find(key)->second)->GetValue();
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag..
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param group Group number of the searched tag.
- * @param element Element number of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string Document::GetEntryVR(uint16_t group, uint16_t element)
-{
- DocEntry *elem = GetDocEntry(group, element);
- if ( !elem )
+ else if ( s1 > s2 )
{
- return GDCM_UNFOUND;
+ return false;
}
- 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 Document::GetEntryLength(uint16_t group, uint16_t element)
-{
- DocEntry *elem = GetDocEntry(group, element);
- if ( !elem )
+ else
{
- return -2; //magic number
+ // Patient ID
+ s1 = GetEntryString(0x0010,0x0020);
+ s2 = document.GetEntryString(0x0010,0x0020);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if ( s1 > s2 )
+ {
+ return false;
+ }
+ else
+ {
+ // Study Instance UID
+ s1 = GetEntryString(0x0020,0x000d);
+ s2 = document.GetEntryString(0x0020,0x000d);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if ( s1 > s2 )
+ {
+ return false;
+ }
+ else
+ {
+ // Serie Instance UID
+ s1 = GetEntryString(0x0020,0x000e);
+ s2 = document.GetEntryString(0x0020,0x000e);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if ( s1 > s2 )
+ {
+ return false;
+ }
+ }
+ }
}
- return elem->GetLength();
+ return false;
}
+//-----------------------------------------------------------------------------
+// Protected
+
/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value (string) to substitute with
- * @param group group number of the Dicom Element to modify
- * @param element element number of the Dicom Element to modify
+ * \brief Reads a given length of bytes
+ * (in order to avoid to many CPU time-consuming fread-s)
+ * @param l length to read
*/
-bool Document::SetEntry(std::string const& content,
- uint16_t group, uint16_t element)
-{
- ValEntry *entry = GetValEntry(group, element);
- if (!entry )
+void Document::ReadBegBuffer(size_t l)
+ throw( FormatError )
+{
+ Fp->read (BegBuffer, (size_t)l);
+ if ( Fp->fail() )
{
- gdcmVerboseMacro( "No corresponding ValEntry (try promotion first).");
- return false;
+ throw FormatError( "Document::ReadBegBuffer()", " file error." );
}
- return SetEntry(content,entry);
-}
-
-/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value (void* -> uint8_t*) to substitute with
- * @param lgth new value length
- * @param group group number of the Dicom Element to modify
- * @param element element number of the Dicom Element to modify
- */
-bool Document::SetEntry(uint8_t*content, int lgth,
- uint16_t group, uint16_t element)
-{
- BinEntry *entry = GetBinEntry(group, element);
- if (!entry )
+ if ( Fp->eof() )
{
- gdcmVerboseMacro( "No corresponding ValEntry (try promotion first).");
- return false;
+ throw FormatError( "Document::ReadBegBuffer()", "EOF." );
}
-
- return SetEntry(content,lgth,entry);
-}
-
+ PtrBegBuffer = BegBuffer;
+ CurrentOffsetPosition+=l;
+}
/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * and modifies it's content with the given value.
- * @param content new value (string) to substitute with
- * @param entry Entry to be modified
+ * \brief Reads a supposed to be 16 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
*/
-bool Document::SetEntry(std::string const &content,ValEntry *entry)
+uint16_t Document::ReadInt16()
+ throw( FormatError )
{
- if(entry)
+ uint16_t g;
+ Fp->read ((char*)&g, (size_t)2);
+ if ( Fp->fail() )
{
- entry->SetValue(content);
- return true;
+ throw FormatError( "Document::ReadInt16()", " file error." );
}
- return false;
+ if ( Fp->eof() )
+ {
+ throw FormatError( "Document::ReadInt16()", "EOF." );
+ }
+ g = SwapShort(g);
+ return g;
}
/**
- * \brief Accesses an existing BinEntry (i.e. a Dicom Element)
- * and modifies it's content with the given value.
- * @param content new value (void* -> uint8_t*) to substitute with
- * @param entry Entry to be modified
- * @param lgth new value length
+ * \brief Gets from BegBuffer a supposed to be 16 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
*/
-bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry)
+uint16_t Document::GetInt16()
{
- if(entry)
- {
- // Hope Binary field length is *never* wrong
- /*if(lgth%2) // Non even length are padded with a space (020H).
- {
- lgth++;
- //content = content + '\0'; // fing a trick to enlarge a binary field?
- }*/
-
- entry->SetBinArea(content);
- entry->SetLength(lgth);
- entry->SetValue(GDCM_BINLOADED);
- return true;
- }
- return false;
+ uint16_t g = *((uint16_t*)PtrBegBuffer);
+ g = SwapShort(g);
+ PtrBegBuffer+=2;
+ return g;
}
-
/**
- * \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
+ * \brief Reads a supposed to be 32 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
*/
-void *Document::GetEntryBinArea(uint16_t group, uint16_t elem)
+uint32_t Document::ReadInt32()
+ throw( FormatError )
{
- DocEntry *entry = GetDocEntry(group, elem);
- if (!entry)
+ uint32_t g;
+ Fp->read ((char*)&g, (size_t)4);
+ if ( Fp->fail() )
{
- gdcmVerboseMacro( "No entry");
- return 0;
+ throw FormatError( "Document::ReadInt32()", " file error." );
}
- if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(entry) )
+ if ( Fp->eof() )
{
- return binEntry->GetBinArea();
+ throw FormatError( "Document::ReadInt32()", "EOF." );
}
-
- return 0;
+ g = SwapLong(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 Gets from BegBuffer a supposed to be 32 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
*/
-void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
+uint32_t Document::GetInt32()
{
- // Search the corresponding DocEntry
- DocEntry *docElement = GetDocEntry(group, elem);
- if ( !docElement )
- return;
-
- BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
- if( !binElement )
- return;
-
- LoadEntryBinArea(binElement);
+ uint32_t g = *((uint32_t*)PtrBegBuffer);
+ g = SwapLong(g);
+ PtrBegBuffer+=4;
+ return g;
}
/**
- * \brief Loads (from disk) the element content
- * when a string is not suitable
- * @param element Entry whose binArea is going to be loaded
+ * \brief Re-computes the length of the Dicom group 0002.
*/
-void Document::LoadEntryBinArea(BinEntry *element)
+int Document::ComputeGroup0002Length( )
{
- if(element->GetBinArea())
- return;
-
- bool openFile = !Fp;
- if(openFile)
- OpenFile();
-
- size_t o =(size_t)element->GetOffset();
- Fp->seekg(o, std::ios::beg);
-
- size_t l = element->GetLength();
- uint8_t *a = new uint8_t[l];
- if( !a )
+ uint16_t gr;
+ VRKey vr;
+
+ int groupLength = 0;
+ bool found0002 = false;
+
+ // for each zero-level Tag in the DCM Header
+ DocEntry *entry = GetFirstEntry();
+ while( entry )
{
- gdcmVerboseMacro( "Cannot allocate a");
- return;
- }
+ gr = entry->GetGroup();
- /// \todo check the result
- Fp->read((char*)a, l);
- if( Fp->fail() || Fp->eof())
- {
- delete[] a;
- return;
- }
+ if ( gr == 0x0002 )
+ {
+ found0002 = true;
- element->SetBinArea(a);
+ if ( entry->GetElement() != 0x0000 )
+ {
+ vr = entry->GetVR();
+
+ //if ( (vr == "OB")||(vr == "OW")||(vr == "UT")||(vr == "SQ"))
+ // (no SQ, OW, OL, UT in group 0x0002;)
+ if ( vr == "OB" )
+ {
+ // explicit VR AND (OB, OW, OL, SQ, UT, UN) : 4 more bytes
+ groupLength += 4;
+ }
+ groupLength += 2 + 2 + 4 + entry->GetLength();
+ }
+ }
+ else if (found0002 )
+ break;
- if(openFile)
- CloseFile();
+ entry = GetNextEntry();
+ }
+ return groupLength;
}
/**
- * \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 CallStartMethod
*/
-/*bool Document::SetEntryBinArea(uint8_t *area,
- uint16_t group, uint16_t element)
+void Document::CallStartMethod()
{
- DocEntry *currentEntry = GetDocEntry(group, element);
- if ( !currentEntry )
- {
- return false;
- }
-
- if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(currentEntry) )
- {
- binEntry->SetBinArea( area );
- return true;
- }
-
- return false;
-}*/
+ Progress = 0.0f;
+ Abort = false;
+ CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
+}
/**
- * \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 CallProgressMethod
*/
-DocEntry *Document::GetDocEntry(uint16_t group, uint16_t element)
+void Document::CallProgressMethod()
{
- TagKey key = DictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key))
- {
- return NULL;
- }
- return TagHT.find(key)->second;
+ CommandManager::ExecuteCommand(this,CMD_PROGRESS);
}
/**
- * \brief Same as \ref Document::GetDocEntry except it only
- * returns a result when the corresponding entry is of type
- * ValEntry.
- * @return When present, the corresponding ValEntry.
+ * \brief CallEndMethod
*/
-ValEntry *Document::GetValEntry(uint16_t group, uint16_t element)
+void Document::CallEndMethod()
{
- DocEntry *currentEntry = GetDocEntry(group, element);
- if ( !currentEntry )
- {
- return 0;
- }
- if ( ValEntry *entry = dynamic_cast<ValEntry*>(currentEntry) )
- {
- return entry;
- }
- gdcmVerboseMacro( "Unfound ValEntry.");
-
- return 0;
-}
-
-/**
- * \brief Same as \ref Document::GetDocEntry except it only
- * returns a result when the corresponding entry is of type
- * BinEntry.
- * @return When present, the corresponding BinEntry.
- */
-BinEntry *Document::GetBinEntry(uint16_t group, uint16_t element)
-{
- DocEntry *currentEntry = GetDocEntry(group, element);
- if ( !currentEntry )
- {
- return 0;
- }
- if ( BinEntry *entry = dynamic_cast<BinEntry*>(currentEntry) )
- {
- return entry;
- }
- gdcmVerboseMacro( "Unfound BinEntry.");
-
- return 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 will be loaded.
- * @return
- */
-void Document::LoadDocEntrySafe(DocEntry *entry)
-{
- if(Fp)
- {
- long PositionOnEntry = Fp->tellg();
- LoadDocEntry(entry);
- Fp->seekg(PositionOnEntry, std::ios::beg);
- }
-}
-
-/**
- * \brief Swaps back the bytes of 4-byte long integer accordingly to
- * processor order.
- * @return The properly swaped 32 bits integer.
- */
-uint32_t Document::SwapLong(uint32_t a)
-{
- 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;
-}
-
-/**
- * \brief Unswaps back the bytes of 4-byte long integer accordingly to
- * processor order.
- * @return The properly unswaped 32 bits integer.
- */
-uint32_t Document::UnswapLong(uint32_t a)
-{
- return SwapLong(a);
-}
-
-/**
- * \brief Swaps the bytes so they agree with the processor order
- * @return The properly swaped 16 bits integer.
- */
-uint16_t Document::SwapShort(uint16_t a)
-{
- if ( SwapCode == 4321 || SwapCode == 2143 )
- {
- a = ((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) );
- }
- return a;
+ Progress = 1.0f;
+ CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
}
+//-----------------------------------------------------------------------------
+// Private
/**
- * \brief Unswaps the bytes so they agree with the processor order
- * @return The properly unswaped 16 bits integer.
+ * \brief Loads all the needed Dictionaries
+ * \warning NOT end user intended method !
*/
-uint16_t Document::UnswapShort(uint16_t a)
+void Document::Initialize()
{
- return SwapShort(a);
+ RefPubDict = Global::GetDicts()->GetDefaultPubDict();
+ RefShaDict = NULL;
+ Filetype = Unknown;
}
-//-----------------------------------------------------------------------------
-// Private
-
/**
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
- * @return length of the parsed set.
+ * @param set DocEntrySet we are going to parse ('zero level' or a SQItem)
+ * @param offset start of parsing
+ * @param l_max length to parse (meaningless when we are in 'delimitor mode')
+ * @param delim_mode : whether we are in 'delimitor mode' (l=0xffffff) or not
*/
void Document::ParseDES(DocEntrySet *set, long offset,
long l_max, bool delim_mode)
{
- DocEntry *newDocEntry = 0;
- ValEntry *newValEntry;
- BinEntry *newBinEntry;
+ DocEntry *newDocEntry;
+ DataEntry *newDataEntry;
SeqEntry *newSeqEntry;
- VRKey vr;
- bool used=false;
-
+ //VRKey vr;
+ bool used; // will be set to false when something wrong happens to an Entry.
+ // (Entry will then be deleted)
+ bool delim_mode_intern = delim_mode;
+ bool first = true;
+ gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode
+ << " at offset " << std::hex << "0x(" << offset << ")" );
while (true)
{
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
- {
- break;
- }
+
+ ///\todo FIXME : On 64 bits processors, tellg gives unexpected results after a while ?
+ /// Probabely a bug in gdcm code somewhere (some memory erased ?)
+
+// Uncomment to track the bug
+
+ if( Debug::GetDebugFlag() )
+ std::cout << std::dec <<"(long)(Fp->tellg()) " << (long)(Fp->tellg()) // in Debug mode
+ << std::hex << " 0x(" <<(long)(Fp->tellg()) << ")" << std::endl;
+
+ // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry
+ if ( !delim_mode ) // 'and then' doesn't exist in C++ :-(
+ if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry, when no delim mode
+ {
+ break;
+ }
- used=true;
newDocEntry = ReadNextDocEntry( );
+
if ( !newDocEntry )
{
break;
}
+
+ // Uncoment this cerr line to be able to 'follow' the DocEntries
+ // when something *very* strange happens
+ if( Debug::GetDebugFlag() )
+ std::cerr<<newDocEntry->GetKey()<<" "<<newDocEntry->GetVR()<<std::endl;
+
+ // an Item Starter found elsewhere but in the first position
+ // of a SeqEntry means previous entry was a Sequence
+ // but we didn't get it (private Sequence + Implicit VR)
+ // we have to backtrack.
+ if ( !first && newDocEntry->IsItemStarter() )
+ {
+ // Debug message within the method !
+ newDocEntry = Backtrack(newDocEntry, set);
+ }
+ else
+ {
+ PreviousDocEntry = newDocEntry;
+ }
- vr = newDocEntry->GetVR();
- newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
- newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
- newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
+ used = true;
+ newDataEntry = dynamic_cast<DataEntry*>(newDocEntry);
- if ( newValEntry || newBinEntry )
+ if ( newDataEntry )
{
- if ( newBinEntry )
- {
- if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) )
- {
- ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- gdcmVerboseMacro( std::hex << newDocEntry->GetGroup()
- << "|" << newDocEntry->GetElement()
- << " : Neither Valentry, nor BinEntry."
- "Probably unknown VR.");
- }
+ //////////////////////////// DataEntry
- //////////////////// BinEntry or UNKOWN VR:
- // When "this" is a Document the Key is simply of the
- // form ( group, elem )...
- if (Document *dummy = dynamic_cast< Document* > ( set ) )
- {
- (void)dummy;
- newBinEntry->SetKey( newBinEntry->GetKey() );
- }
- // but when "this" is a SQItem, we are inserting this new
- // valEntry in a sequence item, and the kay has the
- // generalized form (refer to \ref BaseTagKey):
- if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
- {
- newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
- + newBinEntry->GetKey() );
- }
+ //vr = newDocEntry->GetVR(); // useless ?
- LoadDocEntry( newBinEntry );
- if( !set->AddEntry( newBinEntry ) )
- {
- //Expect big troubles if here
- //delete newBinEntry;
- used=false;
- }
+ if ( !set->AddEntry( newDataEntry ) )
+ {
+ gdcmDebugMacro( "in ParseDES : cannot add a DataEntry "
+ << newDataEntry->GetKey()
+ << " (at offset : 0x("
+ << newDataEntry->GetOffset() << ") )" );
+ used=false;
}
else
{
- /////////////////////// 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 (Document *dummy = dynamic_cast< Document* > ( set ) )
- {
- (void)dummy;
- newValEntry->SetKey( newValEntry->GetKey() );
- }
- // ...but when "set" is a SQItem, we are inserting this new
- // valEntry in a sequence item. Hence the key has the
- // generalized form (refer to \ref BaseTagKey):
- if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
- {
- newValEntry->SetKey( parentSQItem->GetBaseTagKey()
- + newValEntry->GetKey() );
- }
-
- 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)
+ newDataEntry->Delete();
+ // Load only if we can add (not a duplicate key)
+ LoadDocEntry( newDataEntry );
+ }
+ if ( newDataEntry->GetElement() == 0x0000 ) // if on group length
+ {
+ if ( newDataEntry->GetGroup()%2 != 0 ) // if Shadow Group
{
- if(!used)
- delete newDocEntry;
- break;
+ if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
+ {
+ std::string strLgrGroup = newDataEntry->GetString();
+
+ int lgrGroup;
+ //if ( newDataEntry->IsUnfound() ) /?!? JPR
+ {
+ lgrGroup = atoi(strLgrGroup.c_str());
+ Fp->seekg(lgrGroup, std::ios::cur); // Once per Shadow group, when NOSHADOW
+ RemoveEntry( newDocEntry ); // Remove and delete
+ continue;
+ }
+ }
}
}
- if ( ( newDocEntry->GetGroup() == 0x7fe0 )
- && ( newDocEntry->GetElement() == 0x0010 ) )
+ bool delimitor = newDataEntry->IsItemDelimitor();
+ bool outOfBounds = false;
+ if (!delim_mode )
+ if ( ((long)(Fp->tellg())-offset) >= l_max ) //Once per DataEntry when no delim mode
+ outOfBounds = true;
+
+ // 'and then', 'or else' don't exist in C++ :-(
+ // if ( (delimitor) ||
+ // (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) // Once per DataEntry
+
+ if ( delimitor || outOfBounds )
{
- std::string ts = GetTransferSyntax();
- if ( Global::GetTS()->IsRLELossless(ts) )
- {
- long positionOnEntry = Fp->tellg();
- Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
- ComputeRLEInfo();
- Fp->seekg( positionOnEntry, std::ios::beg );
- }
- else if ( Global::GetTS()->IsJPEG(ts) )
- {
- long positionOnEntry = Fp->tellg();
- Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
- ComputeJPEGFragmentInfo();
- Fp->seekg( positionOnEntry, std::ios::beg );
- }
+ if ( !used )
+ newDocEntry->Delete();
+ break;
}
// Just to make sure we are at the beginning of next entry.
- SkipToNextDocEntry(newDocEntry);
+ SkipToNextDocEntry(newDocEntry); // FIXME : once per DocEntry, segfault if commented out
}
else
{
- // VR = "SQ"
- unsigned long l = newDocEntry->GetReadLength();
- if ( l != 0 ) // don't mess the delim_mode for zero-length sequence
+ /////////////////////// SeqEntry : 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;
+ delim_mode_intern = true;
}
else
{
- delim_mode = false;
+ delim_mode_intern = false;
}
}
- // no other way to create it ...
- newSeqEntry->SetDelimitorMode( delim_mode );
+
+ if ( (LoadMode & LD_NOSHADOWSEQ) && ! delim_mode_intern )
+ {
+ // User asked to skip SeQuences *only* if they belong to Shadow Group
+ if ( newDocEntry->GetGroup()%2 != 0 )
+ {
+ Fp->seekg( l, std::ios::cur); // once per SQITEM, when NOSHADOWSEQ
+ newDocEntry->Delete(); // Delete, not in the set
+ continue;
+ }
+ }
+ if ( (LoadMode & LD_NOSEQ) && ! delim_mode_intern )
+ {
+ // User asked to skip *any* SeQuence
+ Fp->seekg( l, std::ios::cur); // Once per SQ, when NOSEQ
+ newDocEntry->Delete(); // Delete, not in the set
+ continue;
+ }
+ // delay the dynamic cast as late as possible
+ newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
+
+ // no other way to create the Delimitor ...
+ newSeqEntry->SetDelimitorMode( delim_mode_intern );
// At the top of the hierarchy, stands a Document. When "set"
// is a Document, then we are building the first depth level.
// Hence the SeqEntry we are building simply has a depth
// level of one:
- if (Document *dummy = dynamic_cast< Document* > ( set ) )
+ if ( set == this ) // ( 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 ) )
+
+ // time waste hunting
+ else 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
- ParseSQ( newSeqEntry,
- newDocEntry->GetOffset(),
- l, delim_mode);
+
+ gdcmDebugMacro( "Entry in ParseSQ, delim " << delim_mode_intern
+ << " at offset 0x(" << std::hex
+ << newDocEntry->GetOffset() << ")");
+
+ bool res = ParseSQ( newSeqEntry,
+ newDocEntry->GetOffset(),
+ l, delim_mode_intern);
+
+ gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern << " -->return : " << res);
+ }
+ if ( !set->AddEntry( newSeqEntry ) )
+ {
+ gdcmWarningMacro( "in ParseDES : cannot add a SeqEntry "
+ << newSeqEntry->GetKey()
+ << " (at offset : 0x("
+ << newSeqEntry->GetOffset() << ") )" );
+ used = false;
+ }
+ else
+ {
+ newDocEntry->Delete();
}
- set->AddEntry( newSeqEntry );
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+
+ // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry
+
+ if ( !delim_mode ) // 'and then' doesn't exist in C++ :-(
+ if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry when no delim mode
+
{
+ if ( !used )
+ newDocEntry->Delete();
break;
}
- }
+ } // end SeqEntry : VR = "SQ"
- if(!used)
- delete newDocEntry;
- }
+ if ( !used )
+ {
+ newDocEntry->Delete();
+ }
+ first = false;
+
+ if (UnexpectedEOF) // some terminator was missing
+ {
+ break;
+ }
+ } // end While
+ gdcmDebugMacro( "Exit from ParseDES, delim-mode " << delim_mode );
}
/**
* \brief Parses a Sequence ( SeqEntry after SeqEntry)
- * @return parsed length for this level
+ * @return false if expected fff0,e000 not found
*/
-void Document::ParseSQ( SeqEntry *seqEntry,
+bool Document::ParseSQ( SeqEntry *seqEntry,
long offset, long l_max, bool delim_mode)
{
int SQItemNumber = 0;
bool dlm_mod;
+ long offsetStartCurrentSQItem = offset;
while (true)
{
+ // the first time, we read the fff0,e000 of the first SQItem
DocEntry *newDocEntry = ReadNextDocEntry();
+
if ( !newDocEntry )
{
- // FIXME Should warn user
- break;
+ // The most frequent is when a SQ terminator is missing (?!?)
+ gdcmWarningMacro("in ParseSQ : should never get here!");
+ UnexpectedEOF = true;
+ return false;
}
- if( delim_mode )
+ if ( delim_mode )
{
if ( newDocEntry->IsSequenceDelimitor() )
{
- seqEntry->SetSequenceDelimitationItem( newDocEntry );
+ seqEntry->SetDelimitationItem( newDocEntry );
+ newDocEntry->Delete();
break;
}
}
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ else // ! delim_mode
{
- delete newDocEntry;
- break;
+ if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SQItem when no delim mode
+ {
+ newDocEntry->Delete();
+ break;
+ }
}
-
- SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
- std::ostringstream newBase;
- newBase << seqEntry->GetKey()
- << "/"
- << SQItemNumber
- << "#";
- itemSQ->SetBaseTagKey( newBase.str() );
+ // create the current SQItem
+ SQItem *itemSQ = SQItem::New( seqEntry->GetDepthLevel() );
unsigned int l = newDocEntry->GetReadLength();
if ( l == 0xffffffff )
{
dlm_mod = false;
}
-
- ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
- delete newDocEntry; // FIXME Why deleting fffe 000e ?!?
+
+ // avoid infinite loop when Bad assumption was made on illegal 'unknown length' UN //JPRx
+
+ if (offsetStartCurrentSQItem <= OffsetOfPreviousParseDES)
+ {
+ gdcmWarningMacro("Bad assumption was made on illegal 'unknown length' UN!" << std::endl <<
+ "OffsetOfPreviousParseDES " << std::hex << OffsetOfPreviousParseDES
+ << " offsetStartCurrentSQItem " << offsetStartCurrentSQItem);
+ /// \todo when "Bad assumption (SQ) on illegal 'unknown length' UN", Backtrack again + try OB
+ return false;
+ }
+ else
+ {
+ OffsetOfPreviousParseDES = offsetStartCurrentSQItem;
+ }
+
+ // fill up the current SQItem, starting at the beginning of fff0,e000
+ Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); // Once per SQItem
+ ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod);
+ offsetStartCurrentSQItem = Fp->tellg(); // Once per SQItem
- seqEntry->AddEntry( itemSQ, SQItemNumber );
+ seqEntry->AddSQItem( itemSQ, SQItemNumber );
+ itemSQ->Delete();
+ newDocEntry->Delete();
SQItemNumber++;
- if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
+ //if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) //JPRx
+ if ( !delim_mode && (offsetStartCurrentSQItem-offset ) >= l_max )
{
break;
}
}
+ return true;
+}
+
+/**
+ * \brief When a private Sequence + Implicit VR is encountered
+ * we cannot guess it's a Sequence till we find the first
+ * Item Starter. We then backtrack to do the job.
+ * @param docEntry Item Starter that warned us
+ * @param set DocEntrySet (ElementSet/SQItem) the DocEntry will belong
+ */
+DocEntry *Document::Backtrack(DocEntry *docEntry, DocEntrySet *set)
+{
+ // delete the Item Starter, built erroneously out of any Sequence
+ // it's not yet in the HTable/chained list
+ docEntry->Delete();
+
+ // Get all info we can from PreviousDocEntry
+ uint16_t group = PreviousDocEntry->GetGroup();
+ uint16_t elem = PreviousDocEntry->GetElement();
+ uint32_t lgt = PreviousDocEntry->GetLength();
+ long offset = PreviousDocEntry->GetOffset();
+
+ gdcmDebugMacro( "Backtrack :" << std::hex << group
+ << "|" << elem
+ << " at offset 0x(" <<offset << ")" );
+
+ set->RemoveEntry( PreviousDocEntry );
+
+ // forge the Seq Entry
+ DocEntry *newEntry = NewSeqEntry(group, elem);
+ newEntry->SetLength(lgt);
+ newEntry->SetOffset(offset);
+
+ // Move back to the beginning of the Sequence
+
+ Fp->seekg(offset, std::ios::beg); // Only for Shadow Implicit VR SQ
+ return newEntry; // It will added where it has to be!
}
/**
- * \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
+ * \brief Loads (or not) the element content depending if its length exceeds
+ * or not the value specified with Document::SetMaxSizeLoadEntry()
+ * @param entry Header Entry (Dicom Element) to be dealt with
+ * @param forceLoad whether you want to force loading of 'long' elements
*/
-void Document::LoadDocEntry(DocEntry *entry)
+void Document::LoadDocEntry(DocEntry *entry, bool forceLoad)
{
- uint16_t group = entry->GetGroup();
- std::string vr = entry->GetVR();
- uint32_t length = entry->GetLength();
+ uint16_t group = entry->GetGroup();
+ uint16_t elem = entry->GetElement();
+ const VRKey &vr = entry->GetVR();
+ uint32_t length = entry->GetLength();
- Fp->seekg((long)entry->GetOffset(), std::ios::beg);
+ // Fp->seekg((long)entry->GetOffset(), std::ios::beg); // JPRx
// 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 )
+ // (fffe 0000) is an 'impossible' tag value,
+ // found in MR-PHILIPS-16-Multi-Seq.dcm
+
+ if ( (group == 0xfffe && elem != 0x0000 ) || vr == "SQ" )
{
// NO more value field for SQ !
return;
}
- // When the length is zero things are easy:
- if ( length == 0 )
+ DataEntry *dataEntryPtr = dynamic_cast< DataEntry* >(entry);
+ if( !dataEntryPtr )
{
- ((ValEntry *)entry)->SetValue("");
- return;
- }
-
- // The elements whose length is bigger than the specified upper bound
- // are not loaded. Instead we leave a short notice of the offset of
- // the element content and it's length.
-
- std::ostringstream s;
- if (length > MaxSizeLoadEntry)
- {
- if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
- {
- //s << "gdcm::NotLoaded (BinEntry)";
- s << GDCM_NOTLOADED;
- s << " Address:" << (long)entry->GetOffset();
- s << " Length:" << entry->GetLength();
- s << " x(" << std::hex << entry->GetLength() << ")";
- binEntryPtr->SetValue(s.str());
- }
- // Be carefull : a BinEntry IS_A ValEntry ...
- else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) )
- {
- // 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 ...
- Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
- std::ios::beg);
return;
}
- // When we find a BinEntry not very much can be done :
- if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
+ // When the length is zero things are easy:
+ if ( length == 0 )
{
- s << GDCM_BINLOADED;
- binEntryPtr->SetValue(s.str());
- LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
+ dataEntryPtr->SetBinArea(NULL,true);
return;
}
- /// \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. 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++)
- {
- s << '\\';
- NewInt = ReadInt16();
- s << NewInt;
- }
- }
- }
- // 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++)
- {
- s << '\\';
- NewInt = ReadInt32();
- s << NewInt;
- }
- }
- }
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
-
- ((ValEntry *)entry)->SetValue(s.str());
- return;
- }
-
- // 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);
- gdcmVerboseMacro("Warning: bad length: " << length <<
- ",For string :" << newValue.c_str());
- // Since we change the length of string update it length
- //entry->SetReadLength(length+1);
- }
- else
- {
- newValue = Util::DicomString(str, length);
- }
- delete[] str;
+ // The elements whose length is bigger than the specified upper bound
+ // are not loaded.
- if ( ValEntry *valEntry = dynamic_cast<ValEntry* >(entry) )
+ if (!forceLoad)
{
- if ( Fp->fail() || Fp->eof())
+ if (length > MaxSizeLoadEntry)
{
- gdcmVerboseMacro("Unread element value");
- valEntry->SetValue(GDCM_UNREAD);
- return;
- }
+ dataEntryPtr->SetBinArea(NULL,true);
+ dataEntryPtr->SetState(DataEntry::STATE_NOTLOADED);
- if( vr == "UI" )
- {
- // Because of correspondance with the VR dic
- valEntry->SetValue(newValue);
- }
- else
- {
- valEntry->SetValue(newValue);
+ // to be sure we are at the end of the value ...
+ // Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
+ // std::ios::beg); //JPRx
+ return;
}
}
- else
- {
- gdcmErrorMacro( "Should have a ValEntry, here !");
- }
-}
+ /// \todo: a method that *doesn't* load anything (maybe with MaxSizeLoadEntry=0 ?)
+ /// + a ForceLoad call on the +/- 20 'usefull' fields
+ /// Allow user to tell the fields he wants to ForceLoad
+ /// during initial stage.
+ /// Later, a GetString or GetBinArea will load the value from disk, if not loaded
+ /// + a method that load *everything* that's not yet loaded
+
+ LoadEntryBinArea(dataEntryPtr); // last one, not to erase length !
+}
/**
- * \brief Find the value Length of the passed Header Entry
+ * \brief Find the value Length of the passed Doc Entry
* @param entry Header Entry whose length of the value shall be loaded.
*/
void Document::FindDocEntryLength( DocEntry *entry )
throw ( FormatError )
{
- std::string vr = entry->GetVR();
+ const VRKey &vr = entry->GetVR();
uint16_t length16;
-
if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
- if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" )
+
+ // WARNING :
+ //
+ // For some images, length of UN elements is coded on 2 bytes (instead of 4)
+ // There are *not* readable !
+ // You can make a quick and dirty patch, commenting out
+ //| vr == "UN"
+ // in the following line.
+ // (the 'straight' images will no longer be readable ...)
+
+ if ( vr == "OB" || vr == "OW" || vr == "OL" || vr == "SQ" || vr == "UT"
+ || vr == "UN" || changeFromUN == true)
{
+ changeFromUN = false;
// 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.
- Fp->seekg( 2L, std::ios::cur);
- uint32_t length32 = ReadInt32();
- if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
+ //Fp->seekg( 2L, std::ios::cur); // Once per OB,OW,OL,UT,UN,SQ DocEntry
+ uint32_t length32 = ReadInt32(); // Once per OB,OW,OL,UT,UN,SQ DocEntry
+ CurrentOffsetPosition+=4;
+ if ( (vr == "OB" || vr == "OW" || vr == "OL") && length32 == 0xffffffff )
{
uint32_t lengthOB;
try
{
- lengthOB = FindDocEntryLengthOBOrOW();
+ lengthOB = FindDocEntryLengthOBOrOW();// for encapsulation of encoded pixel
}
catch ( FormatUnexpected )
{
// chance to get the pixels by deciding the element goes
// until the end of the file. Hence we artificially fix the
// the length and proceed.
- long currentPosition = Fp->tellg();
- Fp->seekg(0L,std::ios::end);
+ gdcmWarningMacro( " Computing the length failed for " <<
+ entry->GetKey() <<" in " <<GetFileName());
+
+ long currentPosition = Fp->tellg(); // Only for gdcm-JPEG-LossLess3a.dcm-like
+ Fp->seekg(0L,std::ios::end); // Only for gdcm-JPEG-LossLess3a.dcm-like
- long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
- Fp->seekg(currentPosition, std::ios::beg);
+ long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; // Only for gdcm-JPEG-LossLess3a.dcm-like
+ Fp->seekg(currentPosition, std::ios::beg); // Only for gdcm-JPEG-LossLess3a.dcm-like
entry->SetReadLength(lengthUntilEOF);
entry->SetLength(lengthUntilEOF);
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
- // and it's value is the one of the encoding of a big endian file.
- // In order to deal with such big endian encoded files, we have
- // (at least) two strategies:
- // * when we load the "Transfer Syntax" tag with value of big endian
- // encoding, we raise the proper flags. Then we wait for the end
- // of the META group (0x0002) among which is "Transfer Syntax",
- // before switching the swap code to big endian. We have to postpone
- // the switching of the swap code since the META group is fully encoded
- // in little endian, and big endian coding only starts at the next
- // group. The corresponding code can be hard to analyse and adds
- // many additional unnecessary tests for regular tags.
- // * the second strategy consists in waiting for trouble, that shall
- // appear when we find the first group with big endian encoding. This
- // is easy to detect since the length of a "Group Length" tag (the
- // 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
- // add an additional check: we look in the already parsed elements
- // for the presence of a "Transfer Syntax" whose value has to be "big
- // 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 )
- // {
- // 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 );
-// }
-
-
+ //length16 = ReadInt16();
+ length16 = GetInt16();
// 0xffff means that we deal with 'No Length' Sequence
// or 'No Length' SQItem
if ( length16 == 0xffff)
// 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.
-
- FixDocEntryFoundLength( entry, ReadInt32() );
+
+ // Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
+ // even if Transfer Syntax is 'Implicit VR ...'
+ // --> Except for 'Implicit VR Big Endian Transfer Syntax GE Private'
+ // where Group 0x0002 is *also* encoded in Implicit VR !
+
+ FixDocEntryFoundLength( entry, GetInt32() /*ReadInt32()*/ );
return;
}
}
/**
- * \brief Find the Value Representation of the current Dicom Element.
- * @return Value Representation of the current Entry
+ * \brief Find the Length till the next sequence delimiter
+ * \warning NOT end user intended method !
+ * @return
*/
-std::string Document::FindDocEntryVR()
+uint32_t Document::FindDocEntryLengthOBOrOW()
+ throw( FormatUnexpected )
{
- if ( Filetype != ExplicitVR )
- return GDCM_UNKNOWN;
-
- 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
- // cases (see e-film filtered files) one finds implicit VR tags mixed
- // 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.
+ // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
+
+ long positionOnEntry = Fp->tellg(); // Only for OB,OW DataElements
- char vr[3];
- Fp->read (vr, (size_t)2);
- vr[2] = 0;
+ bool foundSequenceDelimiter = false;
+ uint32_t totalLength = 0;
- if( !CheckDocEntryVR(vr) )
+ while ( !foundSequenceDelimiter )
{
- 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 vr Dicom Value Representation
- * @return false if the VR is incorrect of if the VR isn't referenced
- * otherwise, it returns true
-*/
-bool Document::CheckDocEntryVR(VRKey vr)
-{
- // 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 ( !Global::GetVR()->IsValidVR(vr) )
- return false;
-
- return true;
-}
+ uint16_t group;
+ uint16_t elem;
-/**
- * \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 entry to tranform
- * @return Transformed entry value
- */
-std::string Document::GetDocEntryValue(DocEntry *entry)
-{
- if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
- {
- 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)
-
- if( vr == "US" || vr == "SS" )
+ try
+ { ///\todo make sure there is never OL encoded pixel data!
+
+ //group = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements
+ //elem = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements
+ ReadBegBuffer(4); // Once per fragment (if any) of OB,OW DataElements
+ }
+ catch ( FormatError )
{
- uint16_t newInt16;
-
- nbInt = length / 2;
- for (int i=0; i < nbInt; i++)
- {
- if( i != 0 )
- {
- s << '\\';
- }
- newInt16 = ( val[2*i+0] & 0xFF ) + ( ( val[2*i+1] & 0xFF ) << 8);
- newInt16 = SwapShort( newInt16 );
- s << newInt16;
- }
+ throw FormatError("Unexpected end of file encountered during ",
+ "Document::FindDocEntryLengthOBOrOW()");
}
+ group = GetInt16();
+ elem = GetInt16();
- // 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" )
+ // We have to decount the group and element we just read
+ totalLength += 4;
+ if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- uint32_t newInt32;
-
- nbInt = length / 4;
- for (int i=0; i < nbInt; i++)
- {
- 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;
- }
+ gdcmWarningMacro(
+ "Neither an Item tag nor a Sequence delimiter tag on :"
+ << std::hex << group << "|" << elem << ") Pos. on entry was 0x(" <<positionOnEntry<< ") "
+ );
+
+ Fp->seekg(positionOnEntry, std::ios::beg); // Once per fragment (if any) of OB,OW DataElements
+ throw FormatUnexpected(
+ "Neither an Item tag nor a Sequence delimiter tag.");
+ }
+ if ( elem == 0xe0dd )
+ {
+ foundSequenceDelimiter = true;
+ }
+ uint32_t itemLength = ReadInt32(); // Once per fragment (if any) of OB,OW DataElements
+ // We add 4 bytes since we just read the ItemLength with ReadInt32
+ totalLength += itemLength + 4;
+ SkipBytes(itemLength);
+
+ if ( foundSequenceDelimiter )
+ {
+ break;
}
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- return s.str();
}
-
- return ((ValEntry *)entry)->GetValue();
+ Fp->seekg( positionOnEntry, std::ios::beg); // Only once for OB,OW DataElements
+ return totalLength;
}
/**
- * \brief Get the reverse transformed value of the header entry. The VR
- * value is used to define the reverse transformation to operate on
- * the value
- * \warning NOT end user intended method !
- * @param entry Entry to reverse transform
- * @return Reverse transformed entry value
+ * \brief Find the Value Representation of the current Dicom Element.
+ * @return Value Representation of the current Entry
*/
-std::string Document::GetDocEntryUnvalue(DocEntry *entry)
+VRKey Document::FindDocEntryVR()
{
- if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
+ if ( Filetype != ExplicitVR )
{
- std::string vr = entry->GetVR();
- std::vector<std::string> tokens;
- std::ostringstream s;
+ return GDCM_VRUNKNOWN;
+ }
- if ( vr == "US" || vr == "SS" )
- {
- uint16_t newInt16;
+ // Delimiters (0xfffe), are not explicit VR ...
+ if ( CurrentGroup == 0xfffe )
+ return GDCM_VRUNKNOWN;
- 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 );
- }
- tokens.clear();
- }
- if ( vr == "UL" || vr == "SL")
- {
- uint32_t newInt32;
+ //long positionOnEntry;
+ //if( Debug::GetWarningFlag() )
+ // positionOnEntry = Fp->tellg(); // Only in Warning Mode
- 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++)
- {
- newInt32 = atoi(tokens[i].c_str());
- s << (char)( newInt32 & 0xFF )
- << (char)(( newInt32 >> 8 ) & 0xFF )
- << (char)(( newInt32 >> 16 ) & 0xFF )
- << (char)(( newInt32 >> 24 ) & 0xFF );
- }
- tokens.clear();
- }
+ // Warning: we believe this is explicit VR (Value Representation) because
+ // we used a heuristic that found "UL" in the first tag and/or
+ // 'Transfer Syntax' told us it is.
+ // Alas this doesn't guarantee that all the tags will be in explicit VR.
+ // In some cases one finds implicit VR tags mixed within an explicit VR file
+ // Well...
+ // 'Normaly' the only case is : group 0002 Explicit, and other groups Implicit
+ //
+ // Hence we make sure the present tag is in explicit VR and try to fix things
+ // if it happens not to be the case.
+
+ VRKey vr;
+ //Fp->read(&(vr[0]),(size_t)2);
+ vr[0] = *PtrBegBuffer++;
+ vr[1] = *PtrBegBuffer++;
+
+ //if ( !CheckDocEntryVR(vr) ) // avoid useless function call
+ if ( !Global::GetVR()->IsValidVR(vr) )
+ {
+
+ gdcmWarningMacro( "Unknown VR " << vr.GetHexaRepresentation() << std::hex
+ << " at offset : 0x(" << CurrentOffsetPosition-4
+ << ") for group " << std::hex << CurrentGroup );
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- return s.str();
+ //Fp->seekg(positionOnEntry, std::ios::beg); //JPRx
+ //Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?)
+ //see :MR_Philips_Intera_PrivateSequenceExplicitVR.dcm
+ PtrBegBuffer-=2;
+ return GDCM_VRUNKNOWN;
}
+ return vr;
+}
- return ((ValEntry *)entry)->GetValue();
+/**
+ * \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 vr Dicom Value Representation
+ * @return false if the VR is incorrect or if the VR isn't referenced
+ * otherwise, it returns true
+*/
+bool Document::CheckDocEntryVR(const VRKey &vr)
+{
+ return Global::GetVR()->IsValidVR(vr);
}
/**
* \brief Skip a given Header Entry
- * \warning NOT end user intended method !
* @param entry entry to skip
*/
void Document::SkipDocEntry(DocEntry *entry)
}
/**
- * \brief Skips to the begining of the next Header Entry
- * \warning NOT end user intended method !
+ * \brief Skips to the beginning of the next Header Entry
* @param currentDocEntry entry to skip
*/
void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
{
- Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
- Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur);
+ long l = currentDocEntry->GetReadLength();
+ if ( (uint32_t) l == (uint32_t)-1 ) // length = 0xffff shouldn't appear here ...
+ // ... but PMS imagers happen !
+ return;
+ Fp->seekg((size_t)(currentDocEntry->GetOffset()), std::ios::beg); //FIXME :each DocEntry
+ if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb
+ {
+ Fp->seekg( l,std::ios::cur); //FIXME :each DocEntry
+ }
}
/**
* the parser went Jabberwocky) one can hope improving things by
* applying some heuristics.
* @param entry entry to check
- * @param foundLength first assumption about length
+ * @param foundLength first assumption about length (before bug fix, or set to zero if =0xffffffff)
*/
void Document::FixDocEntryFoundLength(DocEntry *entry,
uint32_t foundLength)
{
- entry->SetReadLength( foundLength ); // will be updated only if a bug is found
+ entry->SetReadLength( foundLength );// will be updated only if a bug is found
+
if ( foundLength == 0xffffffff)
{
- foundLength = 0;
+ //foundLength = 0;
+ //entry->SetLength(foundLength);
+ entry->SetLength(0);
+ return; // return ASAP; don't waist time on useless tests
}
-
+
uint16_t gr = entry->GetGroup();
uint16_t elem = entry->GetElement();
if ( foundLength % 2)
{
- gdcmVerboseMacro( "Warning : Tag with uneven length " << foundLength
- << " in x(" << std::hex << gr << "," << elem <<")");
+ gdcmWarningMacro( "Warning : Tag (" << std::hex << gr << "|" << elem << ") with uneven length "
+ << std::dec << foundLength << " 0x(" << std::hex << foundLength << ") "
+ //<< " at offset x(" << offset << ")"
+ );
}
-
+
//////// 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 use (we are talking a few years, here)...
- // Note: XMedCom probably uses such a trick since it is able to read
+ // Note: XMedCon probably uses such a trick since it is able to read
// those pesky GE images ...
if ( foundLength == 13)
{
if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) )
{
foundLength = 10;
- entry->SetReadLength(10); /// \todo a bug is to be fixed !?
+ entry->SetReadLength(10); // 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 ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
+ else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
{
- foundLength = 4;
- entry->SetReadLength(4); /// \todo a bug is to be fixed !?
- }
-
+ // Ideally we should check we are in Explicit and double check
+ // that VR=UL... this is done properly in gdcm2
+ if( foundLength == 6 )
+ {
+ gdcmWarningMacro( "Replacing Length from 6 into 4" );
+ foundLength = 4;
+ entry->SetReadLength(4); // a bug is to be fixed !
+ }
+ else if ( foundLength%4 )
+ {
+ gdcmErrorMacro( "This looks like to a buggy Siemens DICOM file."
+ "The length of this tag seems to be wrong" );
+ }
+ }
+
else if ( entry->GetVR() == "SQ" )
{
- foundLength = 0; // ReadLength is unchanged
- }
-
- //////// We encountered a 'delimiter' element i.e. a tag of the form
+ 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( gr == 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 ( elem != 0x0000 )
{
foundLength = 0;
}
- }
-
+ else
+ {
+ foundLength=12; // to skip the mess that follows this bugged Tag !
+ }
+ }
entry->SetLength(foundLength);
}
*/
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();
+ uint16_t elem = entry->GetElement();
+ uint16_t group = entry->GetGroup();
+ const VRKey &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.
+ // able to swap its element value properly.
if ( elem == 0 ) // This is the group length of the group
{
if ( length == 4 )
}
else
{
- // Allthough this should never happen, still some images have a
+ // Although this should never happen, still some images have a
// corrupted group length [e.g. have a glance at offset x(8336) of
- // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm].
+ // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
// Since for dicom compliant and well behaved headers, the present
// test is useless (and might even look a bit paranoid), when we
// encounter such an ill-formed image, we simply display a warning
// message and proceed on parsing (while crossing fingers).
- long filePosition = Fp->tellg();
- gdcmVerboseMacro( "Erroneous Group Length element length on : ("
+ long filePosition = Fp->tellg(); // Only when elem 0x0000 length is not 4 (?!?)
+ (void)filePosition;
+ gdcmWarningMacro( "Erroneous Group Length element length on : ("
<< std::hex << group << " , " << elem
<< ") -before- position x(" << filePosition << ")"
<< "lgt : " << length );
return false;
}
-/**
- * \brief Find the Length till the next sequence delimiter
- * \warning NOT end user intended method !
- * @return
- */
-
-uint32_t Document::FindDocEntryLengthOBOrOW()
- throw( FormatUnexpected )
-{
- // 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();
- gdcmVerboseMacro( "Neither an Item tag nor a Sequence delimiter tag on :"
- << std::hex << group << " , " << elem
- << ") -before- position x(" << filePosition << ")" );
-
- Fp->seekg(positionOnEntry, std::ios::beg);
- throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag.");
- }
-
- if ( elem == 0xe0dd )
- {
- 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;
-}
-
-/**
- * \brief Reads a supposed to be 16 Bits integer
- * (swaps it depending on processor endianity)
- * @return read value
- */
-uint16_t Document::ReadInt16()
- throw( FormatError )
-{
- uint16_t g;
- Fp->read ((char*)&g, (size_t)2);
- if ( Fp->fail() )
- {
- throw FormatError( "Document::ReadInt16()", " file error." );
- }
- if( Fp->eof() )
- {
- throw FormatError( "Document::ReadInt16()", "EOF." );
- }
- g = SwapShort(g);
- return g;
-}
-
-/**
- * \brief Reads a supposed to be 32 Bits integer
- * (swaps it depending on processor endianity)
- * @return read value
- */
-uint32_t Document::ReadInt32()
- throw( FormatError )
-{
- uint32_t g;
- Fp->read ((char*)&g, (size_t)4);
- if ( Fp->fail() )
- {
- throw FormatError( "Document::ReadInt32()", " file error." );
- }
- if( Fp->eof() )
- {
- throw FormatError( "Document::ReadInt32()", "EOF." );
- }
- g = SwapLong(g);
- return g;
-}
-
-/**
- * \brief skips bytes inside the source file
- * \warning NOT end user intended method !
- * @return
- */
-void Document::SkipBytes(uint32_t nBytes)
-{
- //FIXME don't dump the returned value
- Fp->seekg((long)nBytes, std::ios::cur);
-}
-
-/**
- * \brief Loads all the needed Dictionaries
- * \warning NOT end user intended method !
- */
-void Document::Initialise()
-{
- RefPubDict = Global::GetDicts()->GetDefaultPubDict();
- RefShaDict = NULL;
- RLEInfo = new RLEFramesInfo;
- JPEGInfo = new JPEGFragmentsInfo;
- Filetype = Unknown;
-}
-
/**
* \brief Discover what the swap code is (among little endian, big endian,
* bad little endian, bad big endian).
* true when we hope ours assuptions are OK
*/
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...
-
- uint32_t x = 4; // x : for ntohs
- bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
+{
uint32_t s32;
uint16_t s16;
// 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) )
- {
- net2host = true;
- }
- else
- {
- net2host = false;
- }
+ bool net2host = Util::IsCurrentProcessorBigEndian();
// The easiest case is the one of a 'true' DICOM header, we just have
// to look for the string "DICM" inside the file preamble.
Fp->read(deb, 256);
char *entCur = deb + 128;
- if( memcmp(entCur, "DICM", (size_t)4) == 0 )
+ if ( memcmp(entCur, "DICM", (size_t)4) == 0 )
{
- gdcmVerboseMacro( "Looks like DICOM Version3 (preamble + DCM)" );
+ gdcmDebugMacro( "Looks like DICOM Version3 (preamble + DCM)" );
// Group 0002 should always be VR, and the first element 0000
// Let's be carefull (so many wrong headers ...)
// i.e. a total of 136 bytes.
entCur = deb + 136;
- // group 0x0002 *is always* Explicit VR Sometimes ,
+ // 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 Document::dicom_vr to test all the possibilities
// instead of just checking for UL, OB and UI !? group 0000
{
Filetype = ExplicitVR;
- gdcmVerboseMacro( "Group 0002 : Explicit Value Representation");
+ gdcmDebugMacro( "Group 0002 : Explicit Value Representation");
}
else
{
Filetype = ImplicitVR;
- gdcmVerboseMacro( "Group 0002 :Not an explicit Value Representation;"
+ gdcmWarningMacro( "Group 0002 :Not an explicit Value Representation;"
<< "Looks like a bugged Header!");
}
+ // Here, we assume that the file IS kosher Dicom !
+ // (The meta elements - group 0x0002 - ARE little endian !)
if ( net2host )
{
SwapCode = 4321;
- gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder");
+ gdcmDebugMacro( "HostByteOrder != NetworkByteOrder, SwapCode = 4321");
}
else
{
SwapCode = 1234;
- gdcmVerboseMacro( "HostByteOrder = NetworkByteOrder");
+ gdcmDebugMacro( "HostByteOrder = NetworkByteOrder, SwapCode = 1234");
}
// 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);
+
+ Fp->seekg ( 132L, std::ios::beg); // Once per Document
+ CurrentOffsetPosition = 132;
return true;
- } // End of DicomV3
+ } // ------------------------------- 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).
- gdcmVerboseMacro( "Not a DICOM Version3 file");
- Fp->seekg(0, std::ios::beg);
+
+ gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)");
+
+ Fp->seekg(0, std::ios::beg); // Once per ACR-NEMA Document
+ CurrentOffsetPosition = 0;
+ // Let's check 'No Preamble Dicom File' :
+ // Should start with group 0x0002
+ // and be Explicit Value Representation
+
+ s16 = *((uint16_t *)(deb));
+ SwapCode = 0;
+ switch ( s16 )
+ {
+ case 0x0002 :
+ SwapCode = 1234;
+ entCur = deb + 4;
+ break;
+ case 0x0200 :
+ SwapCode = 4321;
+ entCur = deb + 6;
+ }
+
+ if ( SwapCode != 0 )
+ {
+ if ( memcmp(entCur, "UL", (size_t)2) == 0 ||
+ memcmp(entCur, "OB", (size_t)2) == 0 ||
+ memcmp(entCur, "UI", (size_t)2) == 0 ||
+ memcmp(entCur, "SH", (size_t)2) == 0 ||
+ memcmp(entCur, "AE", (size_t)2) == 0 ||
+ memcmp(entCur, "OB", (size_t)2) == 0 )
+ {
+ Filetype = ExplicitVR; // FIXME : not enough to say it's Explicit
+ // Wait untill reading Transfer Syntax
+ gdcmDebugMacro( "Group 0002 : Explicit Value Representation");
+ return true;
+ }
+ }
+// ------------------------------- End of 'No Preamble' DicomV3 -------------
// 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.
+ // By clean we mean that the length of the first group is written down.
// If this is the case and since the length of the first group HAS to be
// four (bytes), then determining the proper swap code is straightforward.
// representation of a 32 bits integer. Hence the following dirty
// trick :
s32 = *((uint32_t *)(entCur));
-
switch( s32 )
{
case 0x00040000 :
// 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-)
+ // 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...
s16 = *((uint16_t *)(deb));
-
+
+ gdcmDebugMacro("not a DicomV3 nor a 'clean' ACR/NEMA;"
+ << " (->despaired wild guesses !)");
switch ( s16 )
{
case 0x0001 :
case 0x0006 :
case 0x0007 :
case 0x0008 :
+ case 0x0028 :
SwapCode = 1234;
- Filetype = ACR;
+ // Brute hack to allow reading DICOM RT files
+ //Filetype = ACR; // DICOM RT are *not* ACR-Nema files!
+ Filetype = ExplicitVR;
return true;
case 0x0100 :
case 0x0200 :
case 0x0600 :
case 0x0700 :
case 0x0800 :
+ case 0x2800 :
SwapCode = 4321;
Filetype = ACR;
return true;
default :
- gdcmVerboseMacro( "ACR/NEMA unfound swap info (Really hopeless !)");
- Filetype = Unknown;
- return false;
+
+ s16 = *((uint16_t *)(deb));
+ if (s16 != 0x0000)
+ return false;
+ s16 = *((uint16_t *)(deb+2));
+
+ Fp->seekg ( 0L, std::ios::beg); // Once per Document
+ CurrentOffsetPosition = 0;
+ switch(s16) // try an other trick!
+ // -> to be able to decode 0029|1010 DataElement
+ // -> and be not less cleaver than dcmdump ;-)
+ {
+ case 0x0004 :
+ SwapCode = 1234;
+ break;
+ case 0x0400 :
+ SwapCode = 3412;
+ break;
+ default:
+ gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)");
+ Filetype = Unknown;
+ return false;
+ }
+ // Check if next 2 bytes are a VR
+ // Probabely something more time-consuming exists with std::string
+ const char VRvalues[] = "AEASATCSDADTFLFDISLOLTPNSHSLSSSTTMUIULUSUTOBOWOLOFATUNSQRT";
+ int nbVal = 29;
+ const char *pt = VRvalues;
+ for (int i=0;i<nbVal;i++)
+ {
+ if(*(deb+4) == *pt++) {
+ if(*(deb+5) == *pt++) {
+ Filetype = ExplicitVR;
+ return true;
+ }
+ else {
+ pt++;
+ }
+ }
+ }
+ Filetype = ImplicitVR;
+ return true;
}
}
}
-
-
/**
* \brief Change the Byte Swap code.
*/
void Document::SwitchByteSwapCode()
{
- gdcmVerboseMacro( "Switching Byte Swap code from "<< SwapCode);
+ gdcmDebugMacro( "Switching Byte Swap code from "<< SwapCode
+ << " at: 0x" << std::hex << Fp->tellg() ); // Only when DEBUG
if ( SwapCode == 1234 )
{
SwapCode = 4321;
{
SwapCode = 3412;
}
+ gdcmDebugMacro( " Into: "<< SwapCode );
}
/**
- * \brief during parsing, Header Elements too long are not loaded in memory
- * @param newSize
+ * \brief during parsing, Header Elements too long are not loaded in memory
+ * @param newSize new size
*/
-void Document::SetMaxSizeLoadEntry(long newSize)
+void Document::SetMaxSizeLoadEntry(long newSize)
{
if ( newSize < 0 )
{
MaxSizeLoadEntry = newSize;
}
-
/**
- * \brief Header Elements too long will not be printed
- * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE
- * @param newSize
+ * \brief Read the next tag WITHOUT loading it's value
+ * (read the 'Group Number', the 'Element Number',
+ * gets the Dict Entry
+ * gets the VR, gets the length, gets the offset value)
+ * @return On succes : the newly created DocEntry, NULL on failure.
*/
-void Document::SetMaxSizePrintEntry(long newSize)
+DocEntry *Document::ReadNextDocEntry()
{
- //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME
- if ( newSize < 0 )
+ try
{
- return;
+ ReadBegBuffer(8); // Avoid to many time consuming freads
+ //CurrentGroup = ReadInt16();
+ //CurrentElem = ReadInt16();
}
- if ((uint32_t)newSize >= (uint32_t)0xffffffff )
- {
- MaxSizePrintEntry = 0xffffffff;
- return;
- }
- MaxSizePrintEntry = newSize;
-}
-
-
-
-/**
- * \brief Handle broken private tag from Philips NTSCAN
- * where the endianess is being switch to BigEndian for no
- * apparent reason
- * @return no return
- */
-void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
-{
- // Endian reversion. Some files contain groups of tags with reversed endianess.
- static int reversedEndian = 0;
- // try to fix endian switching in the middle of headers
- if ((group == 0xfeff) && (elem == 0x00e0))
- {
- // start endian swap mark for group found
- reversedEndian++;
- SwitchByteSwapCode();
- // fix the tag
- group = 0xfffe;
- elem = 0xe000;
- }
- else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
+ catch ( FormatError )
{
- // end of reversed endian group
- reversedEndian--;
- SwitchByteSwapCode();
+ // We reached the EOF (or an error occured) therefore
+ // header parsing has to be considered as finished.
+ return 0;
}
-}
-/**
- * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS
- * else 1.
- * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
- */
-std::string Document::GetTransferSyntaxName()
-{
- // use the TS (TS : Transfer Syntax)
- std::string transferSyntax = GetEntry(0x0002,0x0010);
+ changeFromUN = false;
+ CurrentGroup = GetInt16();
+ CurrentElem = GetInt16();
- 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 )
+ // In 'true DICOM' files Group 0002 is always little endian
+ if ( HasDCMPreamble )
{
- gdcmVerboseMacro( "Unfound Transfer Syntax (0002,0010)");
- return "Uncompressed ACR-NEMA";
- }
+ if ( !Group0002Parsed && CurrentGroup != 0x0002) // avoid calling a function when useless
+ HandleOutOfGroup0002(CurrentGroup, CurrentElem);
+ else
+ // Sometimes file contains groups of tags with reversed endianess.
+ HandleBrokenEndian(CurrentGroup, CurrentElem);
+ }
- // we do it only when we need it
- const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax );
+ VRKey vr = FindDocEntryVR();
+ VRKey realVR = vr;
- // Global::GetTS() is a global static you shall never try to delete it!
- return tsName;
-}
-
-/**
- * \brief Group 0002 is always coded Little Endian
- * whatever Transfer Syntax is
- * @return no return
- */
-void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem)
-{
- // Endian reversion. Some files contain groups of tags with reversed endianess.
- if ( !Group0002Parsed && group != 0x0002)
+ if ( vr == GDCM_VRUNKNOWN )
{
- 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) )
+ if ( CurrentElem == 0x0000 ) // Group Length
{
- gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
- return;
+ realVR = "UL"; // must be UL
}
-
- // FIXME Strangely, this works with
- //'Implicit VR Transfer Syntax (GE Private)
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
+ else if (CurrentGroup == 0xfffe) // Don't get DictEntry for Delimitors
{
- gdcmVerboseMacro("Transfer Syntax Name = ["
- << GetTransferSyntaxName() << "]" );
- SwitchByteSwapCode();
- group = SwapShort(group);
- elem = SwapShort(elem);
+ realVR = "UL";
}
- }
-}
-
-/**
- * \brief Read the next tag but WITHOUT loading it's value
- * (read the 'Group Number', the 'Element Number',
- * gets the Dict Entry
- * gets the VR, gets the length, gets the offset value)
- * @return On succes the newly created DocEntry, NULL on failure.
- */
-DocEntry *Document::ReadNextDocEntry()
-{
- 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.
- //std::cout << e;
- return 0;
+ // Was commented out in order not to generate 'Shadow Groups' where some
+ // Data Elements are Explicit VR and some other ones Implicit VR
+ // -> Better we fix the problem at Write time
+
+ else if (CurrentGroup%2 == 1 )
+ {
+ if (CurrentElem >= 0x0010 && CurrentElem <=0x00ff )
+ {
+ // DICOM PS 3-5 7.8.1 a) states that :
+ // Private Creator Data Elements numbered (gggg,0010-00FF) (gggg is odd)
+ // attributes have to be LO (Long String) and the VM shall be equal to 1
+ realVR = "LO";
+
+ // Seems not to be true
+ // Still in gdcmtk, David Clunnie disagrees, Marco Eichelberg says it's OK ...
+ // We let it for a while?
+ //(We should check length==4, for more security, but we don't have it yet !)
+ }
+ else if ( CurrentElem == 0x0001)
+ {
+ realVR = "UL"; // Private Group Length To End
+ }
+ else // check the private dictionary for shadow elements when Implicit VR!
+ {
+ DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);
+ if ( dictEntry )
+ {
+ realVR = dictEntry->GetVR();
+ dictEntry->Unregister(); // GetDictEntry registered it
+ }
+ }
+ }
+
+ else
+ {
+ DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);//only when ImplicitVR
+ if ( dictEntry )
+ {
+ realVR = dictEntry->GetVR();
+ dictEntry->Unregister(); // GetDictEntry registered it
+ }
+ }
}
- // Sometimes file contains groups of tags with reversed endianess.
- HandleBrokenEndian(group, elem);
-
-// In 'true DICOM' files Group 0002 is always little endian
- if ( HasDCMPreamble )
- HandleOutOfGroup0002(group, elem);
-
- std::string vr = FindDocEntryVR();
- std::string realVR = vr;
-
- if( vr == GDCM_UNKNOWN)
+ // if UN found, let's check the dictionary, and trust it!
+ // (maybe a private dictionary exists?)
+ else if (vr == "UN")
{
- DictEntry *dictEntry = GetDictEntry(group,elem);
- if( dictEntry )
+ DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);
+ if ( dictEntry )
+ {
realVR = dictEntry->GetVR();
+ dictEntry->Unregister(); // GetDictEntry registered it
+
+ // for VR = "UN", length is always stored on 4 bytes.
+ // remember this info, in order not to crash later
+ changeFromUN=true;
+ /// \todo : fixme If inside a vr = "UN" DataElement (but SQ according to a private dictionnary)
+ /// there is some more vr = "UN" DataElements, it will probabely fail.
+ /// --> find a -non time consuming- trick to store changeFromUN info at DataElement level,
+ /// not at the Document level.
+ /// --> ?!? JPR
+
+ }
}
DocEntry *newEntry;
- if( Global::GetVR()->IsVROfSequence(realVR) )
- newEntry = NewSeqEntry(group, elem);
- else if( Global::GetVR()->IsVROfStringRepresentable(realVR) )
- newEntry = NewValEntry(group, elem,vr);
+ //if ( Global::GetVR()->IsVROfSequence(realVR) )
+ if (realVR == "SQ")
+ {
+ newEntry = NewSeqEntry(CurrentGroup, CurrentElem);
+ }
else
- newEntry = NewBinEntry(group, elem,vr);
+ {
+ newEntry = NewDataEntry(CurrentGroup, CurrentElem, realVR);
+ static_cast<DataEntry *>(newEntry)->SetState(DataEntry::STATE_NOTLOADED);
+ }
- if( vr == GDCM_UNKNOWN )
+ if ( vr == GDCM_VRUNKNOWN )
{
- if( Filetype == ExplicitVR )
+ if ( Filetype == ExplicitVR )
{
// We thought this was explicit VR, but we end up with an
// implicit VR tag. Let's backtrack.
- if ( newEntry->GetGroup() != 0xfffe )
- {
- std::string msg;
- msg = Util::Format("Entry (%04x,%04x) should be Explicit VR\n",
- newEntry->GetGroup(), newEntry->GetElement());
- gdcmVerboseMacro( msg.c_str() );
+
+ //if ( newEntry->GetGroup() != 0xfffe )
+ if (CurrentGroup != 0xfffe)
+ {
+ int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong
+
+ gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x("
+ << std::hex << offset << ") should be Explicit VR");
}
}
newEntry->SetImplicitVR();
{
FindDocEntryLength(newEntry);
}
- catch ( FormatError e )
+ catch ( FormatError )
{
// Call it quits
- //std::cout << e;
- delete newEntry;
+ newEntry->Delete();
return 0;
}
- newEntry->SetOffset(Fp->tellg());
-
+ newEntry->SetOffset(Fp->tellg()); // for each DocEntry
return newEntry;
}
-
/**
- * \brief Generate a free TagKey i.e. a TagKey that is not present
- * in the TagHt dictionary.
- * @param group The generated tag must belong to this group.
- * @return The element of tag with given group which is fee.
- */
-uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group)
-{
- for (uint32_t elem = 0; elem < UINT32_MAX; elem++)
- {
- TagKey key = DictEntry::TranslateToKey(group, elem);
- if (TagHT.count(key) == 0)
- {
- return elem;
- }
- }
- return UINT32_MAX;
-}
-
-/**
- * \brief Assuming the internal file pointer \ref Document::Fp
- * is placed at the beginning of a tag check whether this
- * tag is (TestGroup, TestElement).
- * \warning On success the internal file pointer \ref Document::Fp
- * is modified to point after the tag.
- * On failure (i.e. when the tag wasn't the expected tag
- * (TestGroup, TestElement) the internal file pointer
- * \ref Document::Fp is restored to it's original position.
- * @param testGroup The expected group of the tag.
- * @param testElement The expected Element of the tag.
- * @return True on success, false otherwise.
+ * \brief Handle broken private tag from Philips NTSCAN
+ * where the endianess is being switched to BigEndian
+ * for no apparent reason
+ * @return no return
*/
-bool Document::ReadTag(uint16_t testGroup, uint16_t testElement)
+void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
{
- long positionOnEntry = Fp->tellg();
- long currentPosition = Fp->tellg(); // On debugging purposes
-
- //// Read the Item Tag group and element, and make
- // sure they are what we expected:
- uint16_t itemTagGroup;
- uint16_t itemTagElement;
- try
+ // for strange PMS Gyroscan Intera images
+ // Item 'starter' has a tag : 0x3f3f,0x3f00, for no apparent reason
+
+ // --- Feel free to remove this test *on your own coy of gdcm*
+ // if you are sure you'll never face this problem.
+
+ if ((group == 0x3f3f) && (elem == 0x3f00))
{
- itemTagGroup = ReadInt16();
- itemTagElement = ReadInt16();
+ // start endian swap mark for group found
+ gdcmDebugMacro( " delimiter 0x3f3f found." );
+ // fix the tag
+ group = 0xfffe;
+ elem = 0xe000;
+ return;
}
- catch ( FormatError e )
+ // --- End of removable code
+
+ // 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))
{
- //std::cerr << e << std::endl;
- return false;
- }
- if ( itemTagGroup != testGroup || itemTagElement != testElement )
+ // start endian swap mark for group found
+ gdcmDebugMacro( "Start endian swap mark found." );
+ reversedEndian++;
+ SwitchByteSwapCode();
+ // fix the tag
+ group = 0xfffe;
+ elem = 0xe000;
+ }
+ else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
{
- gdcmVerboseMacro( "Wrong Item Tag found:"
- << " We should have found tag ("
- << std::hex << testGroup << "," << testElement << ")" << std::endl
- << " but instead we encountered tag ("
- << std::hex << itemTagGroup << "," << itemTagElement << ")"
- << " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
- ) ;
- Fp->seekg(positionOnEntry, std::ios::beg);
-
- return false;
+ // end of reversed endian group
+ gdcmDebugMacro( "End of reversed endian." );
+ reversedEndian--;
+ SwitchByteSwapCode();
}
- return true;
-}
-
-/**
- * \brief Assuming the internal file pointer \ref Document::Fp
- * is placed at the beginning of a tag (TestGroup, TestElement),
- * read the length associated to the Tag.
- * \warning On success the internal file pointer \ref Document::Fp
- * is modified to point after the tag and it's length.
- * On failure (i.e. when the tag wasn't the expected tag
- * (TestGroup, TestElement) the internal file pointer
- * \ref Document::Fp is restored to it's original position.
- * @param testGroup The expected group of the tag.
- * @param testElement The expected Element of the tag.
- * @return On success returns the length associated to the tag. On failure
- * returns 0.
- */
-uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement)
-{
- long positionOnEntry = Fp->tellg();
- (void)positionOnEntry;
-
- if ( !ReadTag(testGroup, testElement) )
+ else if (group == 0xfeff && elem == 0xdde0)
{
- return 0;
+ // reversed Sequence Terminator found
+ // probabely a bug in the header !
+ // Do what you want, it breaks !
+ //reversedEndian--;
+ //SwitchByteSwapCode();
+ gdcmWarningMacro( "Should never get here! reversed Sequence Terminator!" );
+ // fix the tag
+ group = 0xfffe;
+ elem = 0xe0dd;
}
-
- //// Then read the associated Item Length
- long currentPosition = Fp->tellg();
- uint32_t itemLength = ReadInt32();
+ else if (group == 0xfffe && elem == 0xe0dd)
{
- gdcmVerboseMacro( "Basic Item Length is: "
- << itemLength << std::endl
- << " at address: " << std::hex << (unsigned int)currentPosition);
+ gdcmDebugMacro( "Straight Sequence Terminator." );
}
- return itemLength;
}
/**
- * \brief When parsing the Pixel Data of an encapsulated file, read
- * the basic offset table (when present, and BTW dump it).
+ * \brief Group 0002 is always coded Little Endian
+ * whatever Transfer Syntax is
+ * @return no return
*/
-void Document::ReadAndSkipEncapsulatedBasicOffsetTable()
+void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem)
{
- //// Read the Basic Offset Table Item Tag length...
- uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
-
- // When present, read the basic offset table itself.
- // Notes: - since the presence of this basic offset table is optional
- // we can't rely on it for the implementation, and we will simply
- // trash it's content (when present).
- // - still, when present, we could add some further checks on the
- // lengths, but we won't bother with such fuses for the time being.
- if ( itemLength != 0 )
- {
- char *basicOffsetTableItemValue = new char[itemLength + 1];
- Fp->read(basicOffsetTableItemValue, itemLength);
-
-#ifdef GDCM_DEBUG
- for (unsigned int i=0; i < itemLength; i += 4 )
- {
- uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
- uint32_t);
- gdcmVerboseMacro( "Read one length: " <<
- std::hex << individualLength );
- }
-#endif //GDCM_DEBUG
+ // Endian reversion.
+ // Some files contain groups of tags with reversed endianess.
+
+ Group0002Parsed = true;
+ // we just came out of group 0002
+ // if Transfer Syntax is Big Endian we have to change CheckSwap
- delete[] basicOffsetTableItemValue;
- }
-}
+ std::string ts = GetTransferSyntax();
+ TS::SpecialType s = Global::GetTS()->GetSpecialTransferSyntax(ts);
-/**
- * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
- * Compute the RLE extra information and store it in \ref RLEInfo
- * for later pixel retrieval usage.
- */
-void Document::ComputeRLEInfo()
-{
- std::string ts = GetTransferSyntax();
- if ( !Global::GetTS()->IsRLELossless(ts) )
- {
- return;
- }
+ // Group 0002 is always 'Explicit ...'
+ // even when Transfer Syntax says 'Implicit ..."
- // Encoded pixel data: for the time being we are only concerned with
- // Jpeg or RLE Pixel data encodings.
- // As stated in PS 3.5-2003, section 8.2 p44:
- // "If sent in Encapsulated Format (i.e. other than the Native Format) the
- // value representation OB is used".
- // Hence we expect an OB value representation. Concerning OB VR,
- // the section PS 3.5-2003, section A.4.c p 58-59, states:
- // "For the Value Representations OB and OW, the encoding shall meet the
- // following specifications depending on the Data element tag:"
- // [...snip...]
- // - the first item in the sequence of items before the encoded pixel
- // data stream shall be basic offset table item. The basic offset table
- // item value, however, is not required to be present"
-
- ReadAndSkipEncapsulatedBasicOffsetTable();
-
- // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
- // Loop on the individual frame[s] and store the information
- // on the RLE fragments in a RLEFramesInfo.
- // Note: - when only a single frame is present, this is a
- // classical image.
- // - when more than one frame are present, then we are in
- // the case of a multi-frame image.
- long frameLength;
- while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
- {
- // Parse the RLE Header and store the corresponding RLE Segment
- // Offset Table information on fragments of this current Frame.
- // Note that the fragment pixels themselves are not loaded
- // (but just skipped).
- long frameOffset = Fp->tellg();
-
- uint32_t nbRleSegments = ReadInt32();
- if ( nbRleSegments > 16 )
- {
- // There should be at most 15 segments (refer to RLEFrame class)
- gdcmVerboseMacro( "Too many segments.");
- }
-
- uint32_t rleSegmentOffsetTable[16];
- for( int k = 1; k <= 15; k++ )
+ if ( s == TS::ImplicitVRLittleEndian
+ ||
+ s == TS::ImplicitVRBigEndianPrivateGE
+ )
{
- rleSegmentOffsetTable[k] = ReadInt32();
+ Filetype = ImplicitVR;
}
-
- // Deduce from both the RLE Header and the frameLength the
- // fragment length, and again store this info in a
- // RLEFramesInfo.
- long rleSegmentLength[15];
- // skipping (not reading) RLE Segments
- if ( nbRleSegments > 1)
- {
- for(unsigned int k = 1; k <= nbRleSegments-1; k++)
- {
- rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
- - rleSegmentOffsetTable[k];
- SkipBytes(rleSegmentLength[k]);
- }
- }
-
- rleSegmentLength[nbRleSegments] = frameLength
- - rleSegmentOffsetTable[nbRleSegments];
- SkipBytes(rleSegmentLength[nbRleSegments]);
-
- // Store the collected info
- RLEFrame *newFrameInfo = new RLEFrame;
- newFrameInfo->NumberFragments = nbRleSegments;
- for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
- {
- newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk];
- newFrameInfo->Length[uk] = rleSegmentLength[uk];
- }
- RLEInfo->Frames.push_back( newFrameInfo );
- }
-
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
- if ( !ReadTag(0xfffe, 0xe0dd) )
- {
- gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence");
- }
-}
-
-/**
- * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
- * Compute the jpeg extra information (fragment[s] offset[s] and
- * length) and store it[them] in \ref JPEGInfo for later pixel
- * retrieval usage.
- */
-void Document::ComputeJPEGFragmentInfo()
-{
- // If you need to, look for comments of ComputeRLEInfo().
- std::string ts = GetTransferSyntax();
- if ( ! Global::GetTS()->IsJPEG(ts) )
- {
- return;
- }
-
- ReadAndSkipEncapsulatedBasicOffsetTable();
-
- // Loop on the fragments[s] and store the parsed information in a
- // JPEGInfo.
- long fragmentLength;
- while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
- {
- long fragmentOffset = Fp->tellg();
-
- // Store the collected info
- JPEGFragment *newFragment = new JPEGFragment;
- newFragment->Offset = fragmentOffset;
- newFragment->Length = fragmentLength;
- JPEGInfo->Fragments.push_back( newFragment );
-
- SkipBytes( fragmentLength );
- }
-
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
- if ( !ReadTag(0xfffe, 0xe0dd) )
- {
- gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence");
- }
-}
-
-/**
- * \brief Walk recursively the given \ref DocEntrySet, and feed
- * the given hash table (\ref TagDocEntryHT) with all the
- * \ref DocEntry (Dicom entries) encountered.
- * This method does the job for \ref BuildFlatHashTable.
- * @param builtHT Where to collect all the \ref DocEntry encountered
- * when recursively walking the given set.
- * @param set The structure to be traversed (recursively).
- */
-/*void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT,
- DocEntrySet *set )
-{
- if (ElementSet *elementSet = dynamic_cast< ElementSet* > ( set ) )
- {
- TagDocEntryHT const ¤tHT = elementSet->GetTagHT();
- for( TagDocEntryHT::const_iterator i = currentHT.begin();
- i != currentHT.end();
- ++i)
+
+ // FIXME Strangely, this works with
+ //'Implicit VR BigEndian Transfer Syntax' (GE Private)
+ //
+ // --> Probabely normal, since we considered we never have
+ // to trust manufacturers.
+ // (we often find 'Implicit VR' tag,
+ // even when Transfer Syntax tells us it's Explicit ...
+
+ // NEVER trust the meta elements!
+ // (see what ezDICOM does ...)
+
+ /*
+ if ( s == TS::ExplicitVRBigEndian )
{
- DocEntry *entry = i->second;
- if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
- {
- const ListSQItem& items = seqEntry->GetSQItems();
- for( ListSQItem::const_iterator item = items.begin();
- item != items.end();
- ++item)
- {
- BuildFlatHashTableRecurse( builtHT, *item );
- }
- continue;
- }
- builtHT[entry->GetKey()] = entry;
+ gdcmDebugMacro("Transfer Syntax Name = ["
+ << GetTransferSyntaxName() << "]" );
+ SwitchByteSwapCode();
+ group = SwapShort(group);
+ elem = SwapShort(elem);
}
- return;
+ */
+ //-- Broken ACR may start with a Shadow Group --
+ // worse : some ACR-NEMA like files start 00028 group ?!?
+ if ( !( (group >= 0x0001 && group <= 0x0008) || group == 0x0028 ) )
+ {
+ // We trust what we see.
+ SwitchByteSwapCode();
+ group = SwapShort(group);
+ elem = SwapShort(elem);
+ // not what we where told (by meta elements) !
+ gdcmDebugMacro("Transfer Syntax Name = ["
+ << GetTransferSyntaxName() << "]" );
}
- if (SQItem *SQItemSet = dynamic_cast< SQItem* > ( set ) )
- {
- const ListDocEntry& currentList = SQItemSet->GetDocEntries();
- for (ListDocEntry::const_iterator i = currentList.begin();
- i != currentList.end();
- ++i)
+ /// \todo find a trick to warn user and stop processing
+
+ if ( s == TS::DeflatedExplicitVRLittleEndian)
{
- DocEntry *entry = *i;
- if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
- {
- const ListSQItem& items = seqEntry->GetSQItems();
- for( ListSQItem::const_iterator item = items.begin();
- item != items.end();
- ++item)
- {
- BuildFlatHashTableRecurse( builtHT, *item );
- }
- continue;
- }
- builtHT[entry->GetKey()] = entry;
+ gdcmWarningMacro("Transfer Syntax ["
+ << GetTransferSyntaxName() << "] :"
+ << " not yet dealt with ");
+ return;
}
- }
-}*/
-
-/**
- * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current
- * Document.
- *
- * The structure used by a Document (through \ref ElementSet),
- * in order to hold the parsed entries of a Dicom header, is a recursive
- * one. This is due to the fact that the sequences (when present)
- * can be nested. Additionaly, the sequence items (represented in
- * gdcm as \ref SQItem) add an extra complexity to the data
- * structure. Hence, a gdcm user whishing to visit all the entries of
- * a Dicom header will need to dig in the gdcm internals (which
- * implies exposing all the internal data structures to the API).
- * In order to avoid this burden to the user, \ref BuildFlatHashTable
- * recursively builds a temporary hash table, which holds all the
- * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a
- * std::map<>).
- * \warning Of course there is NO integrity constrain between the
- * returned \ref TagDocEntryHT and the \ref ElementSet used
- * to build it. Hence if the underlying \ref ElementSet is
- * altered, then it is the caller responsability to invoke
- * \ref BuildFlatHashTable again...
- * @return The flat std::map<> we juste build.
- */
-/*TagDocEntryHT *Document::BuildFlatHashTable()
-{
- TagDocEntryHT *FlatHT = new TagDocEntryHT;
- BuildFlatHashTableRecurse( *FlatHT, this );
- return FlatHT;
-}*/
-
+ // The following shouldn't occur very often
+ // Let's check at the very end.
-
-/**
- * \brief Compares two documents, according to \ref DicomDir rules
- * \warning Does NOT work with ACR-NEMA files
- * \todo Find a trick to solve the pb (use RET fields ?)
- * @param document
- * @return true if 'smaller'
- */
-bool Document::operator<(Document &document)
-{
- // Patient Name
- std::string s1 = GetEntry(0x0010,0x0010);
- std::string s2 = document.GetEntry(0x0010,0x0010);
- if(s1 < s2)
- {
- return true;
- }
- else if( s1 > s2 )
- {
- return false;
- }
- else
- {
- // Patient ID
- s1 = GetEntry(0x0010,0x0020);
- s2 = document.GetEntry(0x0010,0x0020);
- if ( s1 < s2 )
+ if ( ts == GDCM_UNKNOWN )
{
- return true;
- }
- else if ( s1 > s2 )
- {
- return false;
- }
- else
- {
- // Study Instance UID
- s1 = GetEntry(0x0020,0x000d);
- s2 = document.GetEntry(0x0020,0x000d);
- if ( s1 < s2 )
- {
- return true;
- }
- else if( s1 > s2 )
- {
- return false;
- }
- else
- {
- // Serie Instance UID
- s1 = GetEntry(0x0020,0x000e);
- s2 = document.GetEntry(0x0020,0x000e);
- if ( s1 < s2 )
- {
- return true;
- }
- else if( s1 > s2 )
- {
- return false;
- }
- }
+ gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " );
+ return;
}
- }
- return false;
-}
-
-/**
- * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
- * @param filetype Type of the File to be written
- */
-int Document::ComputeGroup0002Length( FileType filetype )
-{
- uint16_t gr, el;
- std::string vr;
-
- int groupLength = 0;
- bool found0002 = false;
-
- // for each zero-level Tag in the DCM Header
- DocEntry *entry;
-
- InitTraversal();
- entry = GetNextEntry();
- while(entry)
- {
- gr = entry->GetGroup();
-
- if (gr == 0x0002)
+ if ( !Global::GetTS()->IsTransferSyntax(ts) )
{
- found0002 = true;
-
- el = entry->GetElement();
- vr = entry->GetVR();
-
- if (filetype == ExplicitVR)
- {
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
- {
- groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes
- }
- }
- groupLength += 2 + 2 + 4 + entry->GetLength();
+ gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: ["
+ << ts << "]");
+ return;
}
- else if (found0002 )
- break;
-
- entry = GetNextEntry();
- }
- return groupLength;
}
-} // end namespace gdcm
+//-----------------------------------------------------------------------------
+// Print
//-----------------------------------------------------------------------------
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff