X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=ae50bc8a2cbd31b55893e6e57c672bb5f84939d0;hb=d72e3cb0326093093f99863964f8f4df382c83e1;hp=62f5b9d211c61ca98c97cdf0fe3583977dee59f6;hpb=6d3ea6b4acd35160aaa3a23f9e47ea287059fa68;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 62f5b9d2..ae50bc8a 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/11/17 19:49:13 $ - Version: $Revision: 1.134 $ + Date: $Date: 2005/01/11 23:06:35 $ + Version: $Revision: 1.180 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,6 +23,13 @@ #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 #include @@ -36,44 +43,10 @@ namespace gdcm { -static const char *TransferSyntaxStrings[] = { - // Implicit VR Little Endian - "1.2.840.10008.1.2", - // Implicit VR Little Endian DLX G.E? - "1.2.840.113619.5.2", - // Explicit VR Little Endian - "1.2.840.10008.1.2.1", - // Deflated Explicit VR Little Endian - "1.2.840.10008.1.2.1.99", - // Explicit VR Big Endian - "1.2.840.10008.1.2.2", - // JPEG Baseline (Process 1) - "1.2.840.10008.1.2.4.50", - // JPEG Extended (Process 2 & 4) - "1.2.840.10008.1.2.4.51", - // JPEG Extended (Process 3 & 5) - "1.2.840.10008.1.2.4.52", - // JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8) - "1.2.840.10008.1.2.4.53", - // JPEG Full Progression, Non-Hierarchical (Process 10 & 12) - "1.2.840.10008.1.2.4.55", - // JPEG Lossless, Non-Hierarchical (Process 14) - "1.2.840.10008.1.2.4.57", - // JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, [Selection Value 1]) - "1.2.840.10008.1.2.4.70", - // JPEG 2000 Lossless - "1.2.840.10008.1.2.4.90", - // JPEG 2000 - "1.2.840.10008.1.2.4.91", - // RLE Lossless - "1.2.840.10008.1.2.5", - // Unknown - "Unknown Transfer Syntax" -}; //----------------------------------------------------------------------------- // Refer to Document::CheckSwap() -const unsigned int Document::HEADER_LENGTH_TO_READ = 256; +//const unsigned int Document::HEADER_LENGTH_TO_READ = 256; // Refer to Document::SetMaxSizeLoadEntry() const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 @@ -86,7 +59,7 @@ const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; * \brief constructor * @param filename file to be opened for parsing */ -Document::Document( std::string const & filename ) : ElementSet(-1) +Document::Document( std::string const &filename ) : ElementSet(-1) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; @@ -98,25 +71,26 @@ Document::Document( std::string const & filename ) : ElementSet(-1) return; } - dbg.Verbose(0, "Document::Document: starting parsing of file: ", - Filename.c_str()); - Fp->seekg( 0, std::ios_base::beg); + Group0002Parsed = false; + + gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str()); + // Fp->seekg( 0, std::ios::beg); - Fp->seekg(0, std::ios_base::end); + Fp->seekg(0, std::ios::end); long lgt = Fp->tellg(); - Fp->seekg( 0, std::ios_base::beg); + Fp->seekg( 0, std::ios::beg); CheckSwap(); long beg = Fp->tellg(); lgt -= beg; ParseDES( this, beg, lgt, false); // le Load sera fait a la volee - Fp->seekg( 0, std::ios_base::beg); + Fp->seekg( 0, std::ios::beg); // Load 'non string' values - std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + std::string PhotometricInterpretation = GetEntry(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ) { LoadEntryBinArea(0x0028,0x1200); // gray LUT @@ -162,20 +136,18 @@ Document::Document( std::string const & filename ) : ElementSet(-1) // we switch lineNumber and columnNumber // std::string RecCode; - RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code + RecCode = GetEntry(0x0008, 0x0010); // recognition code if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { Filetype = ACR_LIBIDO; - std::string rows = GetEntryByNumber(0x0028, 0x0010); - std::string columns = GetEntryByNumber(0x0028, 0x0011); - SetEntryByNumber(columns, 0x0028, 0x0010); - SetEntryByNumber(rows , 0x0028, 0x0011); + std::string rows = GetEntry(0x0028, 0x0010); + std::string columns = GetEntry(0x0028, 0x0011); + SetEntry(columns, 0x0028, 0x0010); + SetEntry(rows , 0x0028, 0x0011); } // ----------------- End of ACR-LibIDO kludge ------------------ - - PrintLevel = 1; // 'Medium' print level by default } /** @@ -188,9 +160,9 @@ Document::Document() : ElementSet(-1) SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); - SwapCode = 0; + SwapCode = 1234; Filetype = ExplicitVR; - PrintLevel = 1; // 'Medium' print level by default + Group0002Parsed = false; } /** @@ -212,8 +184,9 @@ Document::~Document () * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return */ -void Document::PrintPubDict(std::ostream & os) +void Document::PrintPubDict(std::ostream &os) { + RefPubDict->SetPrintLevel(PrintLevel); RefPubDict->Print(os); } @@ -221,8 +194,9 @@ void Document::PrintPubDict(std::ostream & os) * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ -void Document::PrintShaDict(std::ostream & os) +void Document::PrintShaDict(std::ostream &os) { + RefShaDict->SetPrintLevel(PrintLevel); RefShaDict->Print(os); } @@ -231,7 +205,7 @@ void Document::PrintShaDict(std::ostream & os) /** * \brief Get the public dictionary used */ -Dict* Document::GetPubDict() +Dict *Document::GetPubDict() { return RefPubDict; } @@ -239,14 +213,14 @@ Dict* Document::GetPubDict() /** * \brief Get the shadow dictionary used */ -Dict* Document::GetShaDict() +Dict *Document::GetShaDict() { return RefShaDict; } /** * \brief Set the shadow dictionary used - * \param dict dictionary to use in shadow + * @param dict dictionary to use in shadow */ bool Document::SetShaDict(Dict *dict) { @@ -256,9 +230,9 @@ bool Document::SetShaDict(Dict *dict) /** * \brief Set the shadow dictionary used - * \param dictName name of the dictionary to use in shadow + * @param dictName name of the dictionary to use in shadow */ -bool Document::SetShaDict(DictKey const & dictName) +bool Document::SetShaDict(DictKey const &dictName) { RefShaDict = Global::GetDicts()->GetDict(dictName); return !RefShaDict; @@ -276,14 +250,13 @@ bool Document::IsReadable() { if( Filetype == Unknown) { - dbg.Verbose(0, "Document::IsReadable: wrong filetype"); + gdcmVerboseMacro( "Wrong filetype"); return false; } if( TagHT.empty() ) { - dbg.Verbose(0, "Document::IsReadable: no tags in internal" - " hash table."); + gdcmVerboseMacro( "No tags in internal hash table."); return false; } @@ -296,18 +269,18 @@ bool Document::IsReadable() * value from disk when only parsing occured). * @return The encountered Transfer Syntax of the current document. */ -TransferSyntaxType Document::GetTransferSyntax() +std::string Document::GetTransferSyntax() { - DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); + DocEntry *entry = GetDocEntry(0x0002, 0x0010); if ( !entry ) { - return UnknownTS; + return GDCM_UNKNOWN; } // The entry might be present but not loaded (parsing and loading // happen at different stages): try loading and proceed with check... LoadDocEntrySafe(entry); - if (ValEntry* valEntry = dynamic_cast< ValEntry* >(entry) ) + if (ValEntry *valEntry = dynamic_cast< ValEntry* >(entry) ) { std::string transfer = valEntry->GetValue(); // The actual transfer (as read from disk) might be padded. We @@ -316,68 +289,15 @@ TransferSyntaxType Document::GetTransferSyntax() if ( transfer.length() == 0 ) { // for brain damaged headers - return UnknownTS; + return GDCM_UNKNOWN; } while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { transfer.erase(transfer.length()-1, 1); } - for (int i = 0; TransferSyntaxStrings[i] != NULL; i++) - { - if ( TransferSyntaxStrings[i] == transfer ) - { - return TransferSyntaxType(i); - } - } + return transfer; } - return UnknownTS; -} - -bool Document::IsJPEGLossless() -{ - TransferSyntaxType r = GetTransferSyntax(); - return r == JPEGFullProgressionProcess10_12 - || r == JPEGLosslessProcess14 - || r == JPEGLosslessProcess14_1; -} - -/** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEG2000 one - * @return True when JPEG2000 (Lossly or LossLess) found. False in all - * other cases. - */ -bool Document::IsJPEG2000() -{ - TransferSyntaxType r = GetTransferSyntax(); - return r == JPEG2000Lossless || r == JPEG2000; -} - -/** - * \brief Determines if the Transfer Syntax corresponds to any form - * of Jpeg encoded Pixel data. - * @return True when any form of JPEG found. False otherwise. - */ -bool Document::IsJPEG() -{ - TransferSyntaxType r = GetTransferSyntax(); - return r == JPEGBaselineProcess1 - || r == JPEGExtendedProcess2_4 - || r == JPEGExtendedProcess3_5 - || r == JPEGSpectralSelectionProcess6_8 - || IsJPEGLossless() - || IsJPEG2000(); -} - -/** - * \brief Determines if the Transfer Syntax corresponds to encapsulated - * of encoded Pixel Data (as opposed to native). - * @return True when encapsulated. False when native. - */ -bool Document::IsEncapsulate() -{ - TransferSyntaxType r = GetTransferSyntax(); - return IsJPEG() || r == RLELossless; + return GDCM_UNKNOWN; } /** @@ -386,11 +306,11 @@ bool Document::IsEncapsulate() */ bool Document::IsDicomV3() { - // Checking if Transfert Syntax exists is enough + // Checking if Transfer Syntax exists is enough // Anyway, it's to late check if the 'Preamble' was found ... // And ... would it be a rich idea to check ? // (some 'no Preamble' DICOM images exist !) - return GetDocEntryByNumber(0x0002, 0x0010) != NULL; + return GetDocEntry(0x0002, 0x0010) != NULL; } /** @@ -408,28 +328,36 @@ FileType Document::GetFileType() * checks the preamble when existing. * @return The FILE pointer on success. */ -std::ifstream* Document::OpenFile() +std::ifstream *Document::OpenFile() { - if (Filename.length() == 0) return 0; + + HasDCMPreamble = false; + if (Filename.length() == 0) + { + return 0; + } + if(Fp) { - dbg.Verbose( 0, - "Document::OpenFile is already opened when opening: ", - Filename.c_str()); + gdcmVerboseMacro( "File already open: " << Filename.c_str()); } Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); - - if(!Fp) + if( ! *Fp ) { - dbg.Verbose( 0, - "Document::OpenFile cannot open file: ", - Filename.c_str()); + gdcmVerboseMacro( "Cannot open file: " << Filename.c_str()); + delete Fp; + Fp = 0; return 0; } uint16_t zero; - Fp->read((char*)&zero, (size_t)2 ); + Fp->read((char*)&zero, (size_t)2); + if( Fp->eof() ) + { + CloseFile(); + return 0; + } //ACR -- or DICOM with no Preamble; may start with a Shadow Group -- if( @@ -438,22 +366,29 @@ std::ifstream* Document::OpenFile() 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_base::cur); + Fp->seekg(126L, std::ios::cur); char dicm[4]; Fp->read(dicm, (size_t)4); + if( Fp->eof() ) + { + CloseFile(); + return 0; + } if( memcmp(dicm, "DICM", 4) == 0 ) { + HasDCMPreamble = true; return Fp; } CloseFile(); - dbg.Verbose( 0, - "Document::OpenFile not DICOM/ACR (missing preamble)", - Filename.c_str()); + gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str()); return 0; } @@ -481,41 +416,22 @@ bool Document::CloseFile() * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -void Document::Write(std::ofstream* fp, FileType filetype) +void Document::WriteContent(std::ofstream *fp, FileType filetype) { /// \todo move the following lines (and a lot of others, to be written) /// to a future function CheckAndCorrectHeader /// (necessary if user wants to write a DICOM V3 file /// starting from an ACR-NEMA (V2) Header - if (filetype == ImplicitVR) - { - std::string ts = - Util::DicomString( TransferSyntaxStrings[ImplicitVRLittleEndian] ); - ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); - - /// \todo Refer to standards on page 21, chapter 6.2 - /// "Value representation": values with a VR of UI shall be - /// padded with a single trailing null - /// in the following case we have to padd manually with a 0 - - SetEntryLengthByNumber(18, 0x0002, 0x0010); - } - - if (filetype == ExplicitVR) + if ( filetype == ImplicitVR || filetype == ExplicitVR ) { - std::string ts = - Util::DicomString( TransferSyntaxStrings[ExplicitVRLittleEndian] ); - ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); //LEAK - - /// \todo Refer to standards on page 21, chapter 6.2 - /// "Value representation": values with a VR of UI shall be - /// padded with a single trailing null - /// Dans le cas suivant on doit pader manuellement avec un 0 - - SetEntryLengthByNumber(20, 0x0002, 0x0010); + // writing Dicom File Preamble + char filePreamble[128]; + memset(filePreamble, 0, 128); + fp->write(filePreamble, 128); + fp->write("DICM", 4); } - + /** * \todo rewrite later, if really usefull * - 'Group Length' element is optional in DICOM @@ -528,12 +444,11 @@ void Document::Write(std::ofstream* fp, FileType filetype) * UpdateGroupLength(true,ACR); */ - ElementSet::Write(fp, filetype); // This one is recursive - + ElementSet::WriteContent(fp, filetype); // This one is recursive } /** - * \brief Modifies the value of a given Header Entry (Dicom Element) + * \brief Modifies the value of a given Doc Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. * @param value (string) Value to be set * @param group Group number of the Entry @@ -542,79 +457,51 @@ void Document::Write(std::ofstream* fp, FileType filetype) * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ -ValEntry* Document::ReplaceOrCreateByNumber( - std::string const & value, - uint16_t group, - uint16_t elem, - TagName const & vr ) -{ - ValEntry* valEntry = 0; - DocEntry* currentEntry = GetDocEntryByNumber( group, elem); +ValEntry *Document::ReplaceOrCreate(std::string const &value, + uint16_t group, + uint16_t elem, + TagName const &vr ) +{ + ValEntry *valEntry = 0; + DocEntry *currentEntry = GetDocEntry( group, elem); - if (!currentEntry) + if (currentEntry) { - // check if (group,element) DictEntry exists - // if it doesn't, create an entry in DictSet::VirtualEntry - // and use it + valEntry = dynamic_cast< ValEntry* >(currentEntry); - // Find out if the tag we received is in the dictionaries: - Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); - DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); - if (!dictEntry) - { - currentEntry = NewDocEntryByNumber(group, elem, vr); - } - else - { - currentEntry = NewDocEntryByNumber(group, elem); - } + // Verify the VR + if( valEntry ) + if( valEntry->GetVR()!=vr ) + valEntry=NULL; - if (!currentEntry) + // if currentEntry doesn't correspond to the requested valEntry + if( !valEntry) { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; + if (!RemoveEntry(currentEntry)) + { + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + + return NULL; + } } + } - valEntry = new ValEntry(currentEntry); - delete currentEntry; + // Create a new valEntry if necessary + if (!valEntry) + { + valEntry = NewValEntry(group, elem, vr); if ( !AddEntry(valEntry)) { + gdcmVerboseMacro("AddEntry failed although this is a creation."); + delete valEntry; - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); return NULL; } } - else - { - valEntry = dynamic_cast< ValEntry* >(currentEntry); - if ( !valEntry ) // Euuuuh? It wasn't a ValEntry - // then we change it to a ValEntry ? - // Shouldn't it be considered as an error ? - { - // We need to promote the DocEntry to a ValEntry: - valEntry = new ValEntry(currentEntry); - if (!RemoveEntry(currentEntry)) - { - delete valEntry; - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); - return NULL; - } - if ( !AddEntry(valEntry)) - { - delete valEntry; - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" - " promoted ValEntry failed."); - return NULL; - } - } - } - - SetEntryByNumber(value, group, elem); + // Set the binEntry value + SetEntry(value, valEntry); return valEntry; } @@ -625,74 +512,56 @@ ValEntry* Document::ReplaceOrCreateByNumber( * @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). */ -BinEntry* Document::ReplaceOrCreateByNumber( - uint8_t* binArea, - int lgth, - uint16_t group, - uint16_t elem, - TagName const & vr ) +BinEntry *Document::ReplaceOrCreate(uint8_t *binArea, + int lgth, + uint16_t group, + uint16_t elem, + TagName const &vr ) { - BinEntry* binEntry = 0; - DocEntry* currentEntry = GetDocEntryByNumber( group, elem); - if (!currentEntry) - { - - // check if (group,element) DictEntry exists - // if it doesn't, create an entry in DictSet::VirtualEntry - // and use it - - // Find out if the tag we received is in the dictionaries: - Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); - DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem); + BinEntry *binEntry = 0; + DocEntry *currentEntry = GetDocEntry( group, elem); - if (!dictEntry) - { - currentEntry = NewDocEntryByNumber(group, elem, vr); - } - else - { - currentEntry = NewDocEntryByNumber(group, elem); - } - if (!currentEntry) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; - } - binEntry = new BinEntry(currentEntry); - if ( !AddEntry(binEntry)) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); - } - } - else + // Verify the currentEntry + if (currentEntry) { binEntry = dynamic_cast< BinEntry* >(currentEntry); - if ( !binEntry ) // Euuuuh? It wasn't a BinEntry - // then we change it to a BinEntry ? - // Shouldn't it be considered as an error ? + + // Verify the VR + if( binEntry ) + if( binEntry->GetVR()!=vr ) + binEntry=NULL; + + // if currentEntry doesn't correspond to the requested valEntry + if( !binEntry) { - // We need to promote the DocEntry to a BinEntry: - binEntry = new BinEntry(currentEntry); if (!RemoveEntry(currentEntry)) { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); - return NULL; - } - if ( !AddEntry(binEntry)) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" - " promoted BinEntry failed."); + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + return NULL; } } } + // Create a new binEntry if necessary + if (!binEntry) + { + binEntry = NewBinEntry(group, elem, vr); + + if ( !AddEntry(binEntry)) + { + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); + + delete binEntry; + return NULL; + } + } + + // Set the binEntry value uint8_t *tmpArea; if (lgth>0 && binArea) { @@ -703,7 +572,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( { tmpArea = 0; } - if (!SetEntryByNumber(tmpArea, lgth, group, elem)) + if (!SetEntry(tmpArea,lgth,binEntry)) { if (tmpArea) { @@ -714,7 +583,6 @@ BinEntry* Document::ReplaceOrCreateByNumber( return binEntry; } - /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it when unexistant. @@ -723,22 +591,48 @@ BinEntry* Document::ReplaceOrCreateByNumber( * \return pointer to the modified/created SeqEntry (NULL when creation * failed). */ -SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) +SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem) { - SeqEntry* b = 0; - DocEntry* a = GetDocEntryByNumber( group, elem); - if (!a) + SeqEntry *seqEntry = 0; + DocEntry *currentEntry = GetDocEntry( group, elem); + + // Verify the currentEntry + if (currentEntry) { - a = NewSeqEntryByNumber(group, elem); - if (!a) + seqEntry = dynamic_cast< SeqEntry* >(currentEntry); + + // Verify the VR + if( seqEntry ) + if( seqEntry->GetVR()!="SQ" ) + seqEntry=NULL; + + // if currentEntry doesn't correspond to the requested valEntry + if( !seqEntry) { - return 0; + if (!RemoveEntry(currentEntry)) + { + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + + return NULL; + } } + } - b = new SeqEntry(a, 1); // FIXME : 1 (Depth) - AddEntry(b); - } - return b; + // Create a new seqEntry if necessary + if (!seqEntry) + { + seqEntry = NewSeqEntry(group, elem); + + if ( !AddEntry(seqEntry)) + { + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); + + delete seqEntry; + return NULL; + } + } + + return seqEntry; } /** @@ -749,10 +643,10 @@ SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) * @param elem element number of the Entry * \return boolean */ -bool Document::ReplaceIfExistByNumber(std::string const & value, - uint16_t group, uint16_t elem ) +bool Document::ReplaceIfExist(std::string const &value, + uint16_t group, uint16_t elem ) { - SetEntryByNumber(value, group, elem); + SetEntry(value, group, elem); return true; } @@ -766,57 +660,12 @@ bool Document::ReplaceIfExistByNumber(std::string const & value, * @param element Element number of the searched Dicom Element * @return true is found */ -bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) +bool Document::CheckIfEntryExist(uint16_t group, uint16_t element ) { const std::string &key = DictEntry::TranslateToKey(group, element ); return TagHT.count(key) != 0; } -/** - * \brief Searches within Header Entries (Dicom Elements) parsed with - * the public and private dictionaries - * for the element value of a given tag. - * \warning Don't use any longer : use GetPubEntryByName - * @param tagName name of the searched element. - * @return Corresponding element value when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string Document::GetEntryByName(TagName const & tagName) -{ - DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) - { - return GDCM_UNFOUND; - } - - return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); -} - -/** - * \brief Searches within Header Entries (Dicom Elements) parsed with - * the public and private dictionaries - * for the element value representation of a given tag. - * - * Obtaining the VR (Value Representation) might be needed by caller - * to convert the string typed content to caller's native type - * (think of C++ vs Python). The VR is actually of a higher level - * of semantics than just the native C++ type. - * @param tagName name of the searched element. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string Document::GetEntryVRByName(TagName const& tagName) -{ - DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) - { - return GDCM_UNFOUND; - } - - DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); - return elem->GetVR(); -} /** * \brief Searches within Header Entries (Dicom Elements) parsed with @@ -827,10 +676,9 @@ std::string Document::GetEntryVRByName(TagName const& tagName) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string Document::GetEntryByNumber(uint16_t group, uint16_t element) +std::string Document::GetEntry(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); - /// \todo use map methods, instead of multimap JPR if ( !TagHT.count(key)) { return GDCM_UNFOUND; @@ -853,9 +701,9 @@ std::string Document::GetEntryByNumber(uint16_t group, uint16_t element) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element) +std::string Document::GetEntryVR(uint16_t group, uint16_t element) { - DocEntry* elem = GetDocEntryByNumber(group, element); + DocEntry *elem = GetDocEntry(group, element); if ( !elem ) { return GDCM_UNFOUND; @@ -871,33 +719,15 @@ std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element) * @param element Element number of the searched tag. * @return Corresponding element length; -2 if not found */ -int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element) +int Document::GetEntryLength(uint16_t group, uint16_t element) { - DocEntry* elem = GetDocEntryByNumber(group, element); + DocEntry *elem = GetDocEntry(group, element); if ( !elem ) { return -2; //magic number } return elem->GetLength(); } -/** - * \brief Sets the value (string) of the Header Entry (Dicom Element) - * @param content string value of the Dicom Element - * @param tagName name of the searched Dicom Element. - * @return true when found - */ -bool Document::SetEntryByName( std::string const & content, - TagName const & tagName) -{ - DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) - { - return false; - } - - return SetEntryByNumber(content,dictEntry->GetGroup(), - dictEntry->GetElement()); -} /** * \brief Accesses an existing DocEntry (i.e. a Dicom Element) @@ -907,45 +737,16 @@ bool Document::SetEntryByName( std::string const & content, * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool Document::SetEntryByNumber(std::string const& content, - uint16_t group, uint16_t element) +bool Document::SetEntry(std::string const& content, + uint16_t group, uint16_t element) { - int c; - int l; - - ValEntry* valEntry = GetValEntryByNumber(group, element); - if (!valEntry ) + ValEntry *entry = GetValEntry(group, element); + if (!entry ) { - dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding", - " ValEntry (try promotion first)."); + gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); return false; } - // Non even content must be padded with a space (020H)... - std::string finalContent = Util::DicomString( content.c_str() ); - assert( !(finalContent.size() % 2) ); - valEntry->SetValue(finalContent); - - // Integers have a special treatement for their length: - - l = finalContent.length(); - if ( l != 0) // To avoid to be cheated by 'zero length' integers - { - VRKey vr = valEntry->GetVR(); - if( vr == "US" || vr == "SS" ) - { - // for multivaluated items - c = Util::CountSubstring(content, "\\") + 1; - l = c*2; - } - else if( vr == "UL" || vr == "SL" ) - { - // for multivaluated items - c = Util::CountSubstring(content, "\\") + 1; - l = c*4;; - } - } - valEntry->SetLength(l); - return true; + return SetEntry(content,entry); } /** @@ -957,76 +758,59 @@ bool Document::SetEntryByNumber(std::string const& content, * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool Document::SetEntryByNumber(uint8_t*content, int lgth, - uint16_t group, uint16_t element) +bool Document::SetEntry(uint8_t*content, int lgth, + uint16_t group, uint16_t element) { - (void)lgth; //not used - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key)) + BinEntry *entry = GetBinEntry(group, element); + if (!entry ) { + gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); return false; } -/* Hope Binary field length is *never* wrong - if(lgth%2) // Non even length are padded with a space (020H). - { - lgth++; - //content = content + '\0'; // fing a trick to enlarge a binary field? - } -*/ - BinEntry* entry = (BinEntry *)TagHT[key]; - entry->SetBinArea(content); - entry->SetLength(lgth); - entry->SetValue(GDCM_BINLOADED); - - return true; + return SetEntry(content,lgth,entry); } /** * \brief Accesses an existing DocEntry (i.e. a Dicom Element) - * in the PubDocEntrySet of this instance - * through it's (group, element) and modifies it's length with - * the given value. - * \warning Use with extreme caution. - * @param l new length to substitute with - * @param group group number of the Entry to modify - * @param element element number of the Entry to modify - * @return true on success, false otherwise. + * and modifies it's content with the given value. + * @param content new value (string) to substitute with + * @param entry Entry to be modified */ -bool Document::SetEntryLengthByNumber(uint32_t l, - uint16_t group, uint16_t element) +bool Document::SetEntry(std::string const &content,ValEntry *entry) { - /// \todo use map methods, instead of multimap JPR - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key) ) + if(entry) { - return false; - } - if ( l % 2 ) - { - l++; // length must be even + entry->SetValue(content); + return true; } - ( ((TagHT.equal_range(key)).first)->second )->SetLength(l); - - return true ; + return false; } /** - * \brief Gets (from Header) the offset of a 'non string' element value - * (LoadElementValues has already be executed) - * @param group group number of the Entry - * @param elem element number of the Entry - * @return File Offset of the Element Value + * \brief Accesses an existing BinEntry (i.e. a Dicom Element) + * and modifies it's content with the given value. + * @param content new value (void* -> uint8_t*) to substitute with + * @param entry Entry to be modified + * @param lgth new value length */ -size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) +bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry) { - DocEntry* entry = GetDocEntryByNumber(group, elem); - if (!entry) + if(entry) { - dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present."); - return 0; + // Hope Binary field length is *never* wrong + /*if(lgth%2) // Non even length are padded with a space (020H). + { + lgth++; + //content = content + '\0'; // fing a trick to enlarge a binary field? + }*/ + + entry->SetBinArea(content); + entry->SetLength(lgth); + entry->SetValue(GDCM_BINLOADED); + return true; } - return entry->GetOffset(); + return false; } /** @@ -1036,15 +820,15 @@ size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) * @param elem element number of the Entry * @return Pointer to the 'non string' area */ -void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) +void *Document::GetEntryBinArea(uint16_t group, uint16_t elem) { - DocEntry* entry = GetDocEntryByNumber(group, elem); + DocEntry *entry = GetDocEntry(group, elem); if (!entry) { - dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry"); + gdcmVerboseMacro( "No entry"); return 0; } - if ( BinEntry* binEntry = dynamic_cast(entry) ) + if ( BinEntry *binEntry = dynamic_cast(entry) ) { return binEntry->GetBinArea(); } @@ -1061,61 +845,54 @@ void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { // Search the corresponding DocEntry - DocEntry *docElement = GetDocEntryByNumber(group, elem); + DocEntry *docElement = GetDocEntry(group, elem); if ( !docElement ) return; - size_t o =(size_t)docElement->GetOffset(); - Fp->seekg( o, std::ios_base::beg); - size_t l = docElement->GetLength(); - uint8_t* a = new uint8_t[l]; - if(!a) - { - dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); - return; - } - - // Read the value - Fp->read((char*)a, l); - if( Fp->fail() || Fp->eof() )//Fp->gcount() == 1 - { - delete[] a; + BinEntry *binElement = dynamic_cast(docElement); + if( !binElement ) return; - } - // Set the value to the DocEntry - if( !SetEntryBinAreaByNumber( a, group, elem ) ) - { - delete[] a; - dbg.Verbose(0, "Document::LoadEntryBinArea setting failed."); - } + LoadEntryBinArea(binElement); } + /** * \brief Loads (from disk) the element content * when a string is not suitable * @param element Entry whose binArea is going to be loaded */ -void Document::LoadEntryBinArea(BinEntry* element) +void Document::LoadEntryBinArea(BinEntry *element) { + if(element->GetBinArea()) + return; + + bool openFile = !Fp; + if(openFile) + OpenFile(); + size_t o =(size_t)element->GetOffset(); - Fp->seekg(o, std::ios_base::beg); + Fp->seekg(o, std::ios::beg); + size_t l = element->GetLength(); - uint8_t* a = new uint8_t[l]; + uint8_t *a = new uint8_t[l]; if( !a ) { - dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); + gdcmVerboseMacro( "Cannot allocate a"); return; } /// \todo check the result Fp->read((char*)a, l); - if( Fp->fail() || Fp->eof()) //Fp->gcount() == 1 + if( Fp->fail() || Fp->eof()) { delete[] a; return; } element->SetBinArea(a); + + if(openFile) + CloseFile(); } /** @@ -1125,89 +902,23 @@ void Document::LoadEntryBinArea(BinEntry* element) * @param element Element number of the searched Dicom Element * @return */ -bool Document::SetEntryBinAreaByNumber(uint8_t* area, - uint16_t group, uint16_t element) +/*bool Document::SetEntryBinArea(uint8_t *area, + uint16_t group, uint16_t element) { - DocEntry* currentEntry = GetDocEntryByNumber(group, element); + DocEntry *currentEntry = GetDocEntry(group, element); if ( !currentEntry ) { return false; } - if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) + if ( BinEntry *binEntry = dynamic_cast(currentEntry) ) { binEntry->SetBinArea( area ); return true; } return false; -} - -/** - * \brief Update the entries with the shadow dictionary. - * Only non even entries are analyzed - */ -void Document::UpdateShaEntries() -{ - //DictEntry *entry; - std::string vr; - - /// \todo TODO : still any use to explore recursively the whole structure? -/* - for(ListTag::iterator it=listEntries.begin(); - it!=listEntries.end(); - ++it) - { - // Odd group => from public dictionary - if((*it)->GetGroup()%2==0) - continue; - - // Peer group => search the corresponding dict entry - if(RefShaDict) - entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement()); - else - entry=NULL; - - if((*it)->IsImplicitVR()) - vr="Implicit"; - else - vr=(*it)->GetVR(); - - (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling - if(entry){ - // Set the new entry and the new value - (*it)->SetDictEntry(entry); - CheckDocEntryVR(*it,vr); - - (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling - - } - else - { - // Remove precedent value transformation - (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr)); - } - } -*/ -} - -/** - * \brief Searches within the Header Entries for a Dicom Element of - * a given tag. - * @param tagName name of the searched Dicom Element. - * @return Corresponding Dicom Element when it exists, and NULL - * otherwise. - */ -DocEntry* Document::GetDocEntryByName(TagName const & tagName) -{ - DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) - { - return NULL; - } - - return GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); -} +}*/ /** * \brief retrieves a Dicom Element (the first one) using (group, element) @@ -1219,7 +930,7 @@ DocEntry* Document::GetDocEntryByName(TagName const & tagName) * @param element Element number of the searched Dicom Element * @return */ -DocEntry* Document::GetDocEntryByNumber(uint16_t group, uint16_t element) +DocEntry *Document::GetDocEntry(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) @@ -1230,39 +941,64 @@ DocEntry* Document::GetDocEntryByNumber(uint16_t group, uint16_t element) } /** - * \brief Same as \ref Document::GetDocEntryByNumber except it only + * \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. */ -ValEntry* Document::GetValEntryByNumber(uint16_t group, uint16_t element) +ValEntry *Document::GetValEntry(uint16_t group, uint16_t element) { - DocEntry* currentEntry = GetDocEntryByNumber(group, element); + DocEntry *currentEntry = GetDocEntry(group, element); if ( !currentEntry ) { return 0; } - if ( ValEntry* valEntry = dynamic_cast(currentEntry) ) + if ( ValEntry *entry = dynamic_cast(currentEntry) ) { - return valEntry; + return entry; } - dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry."); + 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(currentEntry) ) + { + return entry; + } + gdcmVerboseMacro( "Unfound BinEntry."); return 0; } /** * \brief Loads the element while preserving the current - * underlying file position indicator as opposed to + * underlying file position indicator as opposed to * to LoadDocEntry that modifies it. * @param entry Header Entry whose value shall be loaded. * @return */ -void Document::LoadDocEntrySafe(DocEntry * entry) +void Document::LoadDocEntrySafe(DocEntry *entry) { - long PositionOnEntry = Fp->tellg(); - LoadDocEntry(entry); - Fp->seekg(PositionOnEntry, std::ios_base::beg); + if(Fp) + { + long PositionOnEntry = Fp->tellg(); + LoadDocEntry(entry); + Fp->seekg(PositionOnEntry, std::ios::beg); + } } /** @@ -1274,7 +1010,7 @@ uint32_t Document::SwapLong(uint32_t a) { switch (SwapCode) { - case 0 : + case 1234 : break; case 4321 : a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | @@ -1289,8 +1025,7 @@ uint32_t Document::SwapLong(uint32_t a) a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); break; default : - //std::cout << "swapCode= " << SwapCode << std::endl; - dbg.Error(" Document::SwapLong : unset swap code"); + gdcmErrorMacro( "Unset swap code:" << SwapCode ); a = 0; } return a; @@ -1339,6 +1074,11 @@ void Document::ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode) { DocEntry *newDocEntry = 0; + ValEntry *newValEntry; + BinEntry *newBinEntry; + SeqEntry *newSeqEntry; + VRKey vr; + bool used=false; while (true) { @@ -1346,26 +1086,61 @@ void Document::ParseDES(DocEntrySet *set, long offset, { break; } + + used=true; newDocEntry = ReadNextDocEntry( ); if ( !newDocEntry ) { break; } - VRKey vr = newDocEntry->GetVR(); - if ( vr != "SQ" ) + vr = newDocEntry->GetVR(); + newValEntry = dynamic_cast(newDocEntry); + newBinEntry = dynamic_cast(newDocEntry); + newSeqEntry = dynamic_cast(newDocEntry); + + if ( newValEntry || newBinEntry ) { - - if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) ) + if ( newBinEntry ) + { + if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) ) + { + ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR + gdcmVerboseMacro( "Neither Valentry, nor BinEntry." + "Probably unknown VR."); + } + + //////////////////// BinEntry or UNKOWN VR: + // When "this" is a Document the Key is simply of the + // form ( group, elem )... + if (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() ); + } + + LoadDocEntry( newBinEntry ); + if( !set->AddEntry( newBinEntry ) ) + { + //Expect big troubles if here + //delete newBinEntry; + used=false; + } + } + else { /////////////////////// ValEntry - ValEntry* newValEntry = - new ValEntry( newDocEntry->GetDictEntry() ); //LEAK - newValEntry->Copy( newDocEntry ); - // When "set" is a Document, then we are at the top of the // hierarchy and the Key is simply of the form ( group, elem )... - if (Document* dummy = dynamic_cast< Document* > ( set ) ) + if (Document *dummy = dynamic_cast< Document* > ( set ) ) { (void)dummy; newValEntry->SetKey( newValEntry->GetKey() ); @@ -1373,7 +1148,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, // ...but when "set" is a SQItem, we are inserting this new // valEntry in a sequence item. Hence the key has the // generalized form (refer to \ref BaseTagKey): - if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) + if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newValEntry->SetKey( parentSQItem->GetBaseTagKey() + newValEntry->GetKey() ); @@ -1384,77 +1159,44 @@ void Document::ParseDES(DocEntrySet *set, long offset, if( !set->AddEntry( newValEntry ) ) { // If here expect big troubles - delete newValEntry; //otherwise mem leak + //delete newValEntry; //otherwise mem leak + used=false; } if (delimitor) { + if(!used) + delete newDocEntry; break; } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + if(!used) + delete newDocEntry; break; } } - else - { - if ( ! Global::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) - { - ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR - dbg.Verbose(0, "Document::ParseDES: neither Valentry, " - "nor BinEntry. Probably unknown VR."); - } - - //////////////////// BinEntry or UNKOWN VR: -/* BinEntry* newBinEntry = - new BinEntry( newDocEntry->GetDictEntry() ); //LEAK - newBinEntry->Copy( newDocEntry );*/ - BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK - - // 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() ); - } - - LoadDocEntry( newBinEntry ); - if( !set->AddEntry( newBinEntry ) ) - { - //Expect big troubles if here - delete newBinEntry; - } - } if ( ( newDocEntry->GetGroup() == 0x7fe0 ) && ( newDocEntry->GetElement() == 0x0010 ) ) { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts == RLELossless ) + std::string ts = GetTransferSyntax(); + if ( Global::GetTS()->IsRLELossless(ts) ) { - long PositionOnEntry = Fp->tellg(); - Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); + long positionOnEntry = Fp->tellg(); + Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeRLEInfo(); - Fp->seekg( PositionOnEntry, std::ios_base::beg ); + Fp->seekg( positionOnEntry, std::ios::beg ); } - else if ( IsJPEG() ) + else if ( Global::GetTS()->IsJPEG(ts) ) { - long PositionOnEntry = Fp->tellg(); - Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); + long positionOnEntry = Fp->tellg(); + Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeJPEGFragmentInfo(); - Fp->seekg( PositionOnEntry, std::ios_base::beg ); + Fp->seekg( positionOnEntry, std::ios::beg ); } } - + // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); } @@ -1474,16 +1216,13 @@ void Document::ParseDES(DocEntrySet *set, long offset, } } // no other way to create it ... - SeqEntry* newSeqEntry = - new SeqEntry( newDocEntry->GetDictEntry() ); - newSeqEntry->Copy( newDocEntry ); newSeqEntry->SetDelimitorMode( delim_mode ); // At the top of the hierarchy, stands a Document. When "set" // is a Document, then we are building the first depth level. // Hence the SeqEntry we are building simply has a depth // level of one: - if (Document* dummy = dynamic_cast< Document* > ( set ) ) + if (Document *dummy = dynamic_cast< Document* > ( set ) ) { (void)dummy; newSeqEntry->SetDepthLevel( 1 ); @@ -1492,7 +1231,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, // But when "set" is allready a SQItem, we are building a nested // sequence, and hence the depth level of the new SeqEntry // we are building, is one level deeper: - if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) + if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); newSeqEntry->SetKey( parentSQItem->GetBaseTagKey() @@ -1511,7 +1250,9 @@ void Document::ParseDES(DocEntrySet *set, long offset, break; } } - delete newDocEntry; + + if(!used) + delete newDocEntry; } } @@ -1519,7 +1260,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, * \brief Parses a Sequence ( SeqEntry after SeqEntry) * @return parsed length for this level */ -void Document::ParseSQ( SeqEntry* seqEntry, +void Document::ParseSQ( SeqEntry *seqEntry, long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; @@ -1527,7 +1268,7 @@ void Document::ParseSQ( SeqEntry* seqEntry, while (true) { - DocEntry* newDocEntry = ReadNextDocEntry(); + DocEntry *newDocEntry = ReadNextDocEntry(); if ( !newDocEntry ) { // FIXME Should warn user @@ -1537,13 +1278,14 @@ void Document::ParseSQ( SeqEntry* seqEntry, { if ( newDocEntry->IsSequenceDelimitor() ) { - seqEntry->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetSequenceDelimitationItem( newDocEntry ); break; } } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - break; + delete newDocEntry; + break; } SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); @@ -1565,6 +1307,7 @@ void Document::ParseSQ( SeqEntry* seqEntry, } ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); + delete newDocEntry; seqEntry->AddEntry( itemSQ, SQItemNumber ); SQItemNumber++; @@ -1580,13 +1323,13 @@ void Document::ParseSQ( SeqEntry* seqEntry, * the value specified with Document::SetMaxSizeLoadEntry() * @param entry Header Entry (Dicom Element) to be dealt with */ -void Document::LoadDocEntry(DocEntry* entry) +void Document::LoadDocEntry(DocEntry *entry) { uint16_t group = entry->GetGroup(); std::string vr = entry->GetVR(); uint32_t length = entry->GetLength(); - Fp->seekg((long)entry->GetOffset(), std::ios_base::beg); + Fp->seekg((long)entry->GetOffset(), std::ios::beg); // A SeQuence "contains" a set of Elements. // (fffe e000) tells us an Element is beginning @@ -1612,7 +1355,7 @@ void Document::LoadDocEntry(DocEntry* entry) std::ostringstream s; if (length > MaxSizeLoadEntry) { - if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) + if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) ) { //s << "gdcm::NotLoaded (BinEntry)"; s << GDCM_NOTLOADED; @@ -1622,7 +1365,7 @@ void Document::LoadDocEntry(DocEntry* entry) binEntryPtr->SetValue(s.str()); } // Be carefull : a BinEntry IS_A ValEntry ... - else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) ) + else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { // s << "gdcm::NotLoaded. (ValEntry)"; s << GDCM_NOTLOADED; @@ -1634,25 +1377,25 @@ void Document::LoadDocEntry(DocEntry* entry) else { // fusible - std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry " - << "nor a ValEntry ?! Should never print that !" << std::endl; + gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry " + << "nor a ValEntry ?! Should never print that !" ); } // to be sure we are at the end of the value ... Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), - std::ios_base::beg); + std::ios::beg); return; } // When we find a BinEntry not very much can be done : - if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) + if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) ) { s << GDCM_BINLOADED; binEntryPtr->SetValue(s.str()); LoadEntryBinArea(binEntryPtr); // last one, not to erase length ! return; } - + /// \todo Any compacter code suggested (?) if ( IsDocEntryAnInteger(entry) ) { @@ -1711,10 +1454,10 @@ void Document::LoadDocEntry(DocEntry* entry) if( length % 2 ) { newValue = Util::DicomString(str, length+1); - //dbg.Verbose(0, "Warning: bad length: ", length ); - dbg.Verbose(0, "For string :", newValue.c_str()); + gdcmVerboseMacro("Warning: bad length: " << length << + ",For string :" << newValue.c_str()); // Since we change the length of string update it length - entry->SetReadLength(length+1); + //entry->SetReadLength(length+1); } else { @@ -1722,12 +1465,11 @@ void Document::LoadDocEntry(DocEntry* entry) } delete[] str; - if ( ValEntry* valEntry = dynamic_cast(entry) ) + if ( ValEntry *valEntry = dynamic_cast(entry) ) { - if ( Fp->fail() || Fp->eof())//Fp->gcount() == 1 + if ( Fp->fail() || Fp->eof()) { - dbg.Verbose(1, "Document::LoadDocEntry", - "unread element value"); + gdcmVerboseMacro("Unread element value"); valEntry->SetValue(GDCM_UNREAD); return; } @@ -1744,8 +1486,7 @@ void Document::LoadDocEntry(DocEntry* entry) } else { - dbg.Error(true, "Document::LoadDocEntry" - "Should have a ValEntry, here !"); + gdcmErrorMacro( "Should have a ValEntry, here !"); } } @@ -1768,7 +1509,7 @@ void Document::FindDocEntryLength( DocEntry *entry ) // 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_base::cur); + Fp->seekg( 2L, std::ios::cur); uint32_t length32 = ReadInt32(); if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) @@ -1776,9 +1517,7 @@ void Document::FindDocEntryLength( DocEntry *entry ) uint32_t lengthOB; try { - /// \todo rename that to FindDocEntryLengthOBOrOW since - /// the above test is on both OB and OW... - lengthOB = FindDocEntryLengthOB(); + lengthOB = FindDocEntryLengthOBOrOW(); } catch ( FormatUnexpected ) { @@ -1788,12 +1527,16 @@ void Document::FindDocEntryLength( DocEntry *entry ) // until the end of the file. Hence we artificially fix the // the length and proceed. long currentPosition = Fp->tellg(); - Fp->seekg(0L,std::ios_base::end); + Fp->seekg(0L,std::ios::end); + long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; - Fp->seekg(currentPosition, std::ios_base::beg); + Fp->seekg(currentPosition, std::ios::beg); + + entry->SetReadLength(lengthUntilEOF); entry->SetLength(lengthUntilEOF); return; } + entry->SetReadLength(lengthOB); entry->SetLength(lengthOB); return; } @@ -1833,21 +1576,22 @@ void Document::FindDocEntryLength( DocEntry *entry ) // big endian and proceed... if ( element == 0x0000 && length16 == 0x0400 ) { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts != ExplicitVRBigEndian ) + std::string ts = GetTransferSyntax(); + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) + != TS::ExplicitVRBigEndian ) { throw FormatError( "Document::FindDocEntryLength()", " not explicit VR." ); return; } length16 = 4; - SwitchSwapToBigEndian(); + 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 = GetDictEntryByNumber( correctGroup, - correctElem ); + DictEntry *newTag = GetDictEntry( correctGroup, correctElem ); if ( !newTag ) { // This correct tag is not in the dictionary. Create a new one. @@ -1883,16 +1627,12 @@ void Document::FindDocEntryLength( DocEntry *entry ) /** * \brief Find the Value Representation of the current Dicom Element. - * @param entry + * @return Value Representation of the current Entry */ -void Document::FindDocEntryVR( DocEntry *entry ) +std::string Document::FindDocEntryVR() { if ( Filetype != ExplicitVR ) - { - return; - } - - char vr[3]; + return GDCM_UNKNOWN; long positionOnEntry = Fp->tellg(); // Warning: we believe this is explicit VR (Value Representation) because @@ -1902,105 +1642,34 @@ void Document::FindDocEntryVR( DocEntry *entry ) // 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. - + + char vr[3]; Fp->read (vr, (size_t)2); vr[2] = 0; - if( !CheckDocEntryVR(entry, vr) ) + if( !CheckDocEntryVR(vr) ) { - Fp->seekg(positionOnEntry, std::ios_base::beg); - // When this element is known in the dictionary we shall use, e.g. for - // the semantics (see the usage of IsAnInteger), the VR proposed by the - // dictionary entry. Still we have to flag the element as implicit since - // we know now our assumption on expliciteness is not furfilled. - // avoid . - if ( entry->IsVRUnknown() ) - { - entry->SetVR("Implicit"); - } - entry->SetImplicitVR(); + Fp->seekg(positionOnEntry, std::ios::beg); + return GDCM_UNKNOWN; } + return vr; } /** * \brief Check the correspondance between the VR of the header entry * and the taken VR. If they are different, the header entry is * updated with the new VR. - * @param entry Header Entry to check * @param vr Dicom Value Representation * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ -bool Document::CheckDocEntryVR(DocEntry *entry, VRKey vr) +bool Document::CheckDocEntryVR(VRKey vr) { - std::string msg; - bool realExplicit = true; - - // Assume we are reading a falsely explicit VR file i.e. we reached - // a tag where we expect reading a VR but are in fact we read the - // first to bytes of the length. Then we will interogate (through find) - // the dicom_vr dictionary with oddities like "\004\0" which crashes - // both GCC and VC++ implementations of the STL map. Hence when the - // expected VR read happens to be non-ascii characters we consider - // we hit falsely explicit VR tag. - - if ( !isalpha((unsigned char)vr[0]) && !isalpha((unsigned char)vr[1]) ) - { - realExplicit = false; - } - // CLEANME searching the dicom_vr at each occurence is expensive. // PostPone this test in an optional integrity check at the end // of parsing or only in debug mode. - if ( realExplicit && !Global::GetVR()->Count(vr) ) - { - realExplicit = false; - } - - if ( !realExplicit ) - { - // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", - entry->GetGroup(), entry->GetElement()); - dbg.Verbose(1, "Document::FindVR: ", msg.c_str()); - - if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000) - { - // Group length is UL ! - DictEntry* newEntry = NewVirtualDictEntry( - entry->GetGroup(), entry->GetElement(), - "UL", "FIXME", "Group Length"); - entry->SetDictEntry( newEntry ); - } + if ( !Global::GetVR()->IsValidVR(vr) ) return false; - } - - if ( entry->IsVRUnknown() ) - { - // When not a dictionary entry, we can safely overwrite the VR. - if( entry->GetElement() == 0x0000 ) - { - // Group length is UL ! - entry->SetVR("UL"); - } - else - { - entry->SetVR(vr); - } - } - else if ( entry->GetVR() != vr ) - { - // The VR present in the file and the dictionary disagree. We assume - // the file writer knew best and use the VR of the file. Since it would - // be unwise to overwrite the VR of a dictionary (since it would - // compromise it's next user), we need to clone the actual DictEntry - // and change the VR for the read one. - DictEntry* newEntry = NewVirtualDictEntry( - entry->GetGroup(), entry->GetElement(), - vr, "FIXME", entry->GetName()); - entry->SetDictEntry(newEntry); - } return true; } @@ -2088,7 +1757,7 @@ std::string Document::GetDocEntryValue(DocEntry *entry) * @param entry Entry to reverse transform * @return Reverse transformed entry value */ -std::string Document::GetDocEntryUnvalue(DocEntry* entry) +std::string Document::GetDocEntryUnvalue(DocEntry *entry) { if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) { @@ -2149,12 +1818,12 @@ void Document::SkipDocEntry(DocEntry *entry) /** * \brief Skips to the begining of the next Header Entry * \warning NOT end user intended method ! - * @param entry entry to skip + * @param currentDocEntry entry to skip */ -void Document::SkipToNextDocEntry(DocEntry *entry) +void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) { - Fp->seekg((long)(entry->GetOffset()), std::ios_base::beg); - Fp->seekg( (long)(entry->GetReadLength()), std::ios_base::cur); + Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg); + Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur); } /** @@ -2162,7 +1831,7 @@ void Document::SkipToNextDocEntry(DocEntry *entry) * the parser went Jabberwocky) one can hope improving things by * applying some heuristics. * @param entry entry to check - * @param foundLength fist assumption about length + * @param foundLength first assumption about length */ void Document::FixDocEntryFoundLength(DocEntry *entry, uint32_t foundLength) @@ -2173,30 +1842,25 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, foundLength = 0; } - uint16_t gr = entry->GetGroup(); - uint16_t el = entry->GetElement(); + uint16_t gr = entry->GetGroup(); + uint16_t elem = entry->GetElement(); if ( foundLength % 2) { - std::ostringstream s; - s << "Warning : Tag with uneven length " - << foundLength - << " in x(" << std::hex << gr << "," << el <<")" << std::dec; - dbg.Verbose(0, s.str().c_str()); + gdcmVerboseMacro( "Warning : Tag with uneven length " << foundLength + << " in x(" << std::hex << gr << "," << elem <<")"); } //////// Fix for some naughty General Electric images. // Allthough not recent many such GE corrupted images are still present // on Creatis hard disks. Hence this fix shall remain when such images - // are no longer in user (we are talking a few years, here)... + // are no longer in use (we are talking a few years, here)... // Note: XMedCom probably uses such a trick since it is able to read // those pesky GE images ... if ( foundLength == 13) { // Only happens for this length ! - if ( entry->GetGroup() != 0x0008 - || ( entry->GetElement() != 0x0070 - && entry->GetElement() != 0x0080 ) ) + if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) ) { foundLength = 10; entry->SetReadLength(10); /// \todo a bug is to be fixed !? @@ -2207,9 +1871,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, // Occurence of such images is quite low (unless one leaves close to a // 'Leonardo' source. Hence, one might consider commenting out the // following fix on efficiency reasons. - else if ( entry->GetGroup() == 0x0009 - && ( entry->GetElement() == 0x1113 - || entry->GetElement() == 0x1114 ) ) + else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) ) { foundLength = 4; entry->SetReadLength(4); /// \todo a bug is to be fixed !? @@ -2223,7 +1885,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, //////// We encountered a 'delimiter' element i.e. a tag of the form // "fffe|xxxx" which is just a marker. Delimiters length should not be // taken into account. - else if( entry->GetGroup() == 0xfffe ) + else if( gr == 0xfffe ) { // According to the norm, fffe|0000 shouldn't exist. BUT the Philips // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to @@ -2234,7 +1896,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, } } - entry->SetUsableLength(foundLength); + entry->SetLength(foundLength); } /** @@ -2245,15 +1907,15 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, */ bool Document::IsDocEntryAnInteger(DocEntry *entry) { - uint16_t element = entry->GetElement(); + uint16_t elem = entry->GetElement(); uint16_t group = entry->GetGroup(); - const std::string & vr = entry->GetVR(); + const std::string &vr = entry->GetVR(); uint32_t length = entry->GetLength(); // When we have some semantics on the element we just read, and if we // a priori know we are dealing with an integer, then we shall be // able to swap it's element value properly. - if ( element == 0 ) // This is the group length of the group + if ( elem == 0 ) // This is the group length of the group { if ( length == 4 ) { @@ -2268,21 +1930,18 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) // test is useless (and might even look a bit paranoid), when we // encounter such an ill-formed image, we simply display a warning // message and proceed on parsing (while crossing fingers). - std::ostringstream s; long filePosition = Fp->tellg(); - s << "Erroneous Group Length element length on : (" \ - << std::hex << group << " , " << element + gdcmVerboseMacro( "Erroneous Group Length element length on : (" + << std::hex << group << " , " << elem << ") -before- position x(" << filePosition << ")" - << "lgt : " << length; - dbg.Verbose(0, "Document::IsDocEntryAnInteger", s.str().c_str() ); + << "lgt : " << length ); } } if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" ) { return true; - } - + } return false; } @@ -2292,7 +1951,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) * @return */ -uint32_t Document::FindDocEntryLengthOB() +uint32_t Document::FindDocEntryLengthOBOrOW() throw( FormatUnexpected ) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. @@ -2311,8 +1970,8 @@ uint32_t Document::FindDocEntryLengthOB() } catch ( FormatError ) { - throw FormatError("Document::FindDocEntryLengthOB()", - " group or element not present."); + throw FormatError("Unexpected end of file encountered during ", + "Document::FindDocEntryLengthOBOrOW()"); } // We have to decount the group and element we just read @@ -2320,12 +1979,13 @@ uint32_t Document::FindDocEntryLengthOB() if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { - dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item " - "tag nor a Sequence delimiter tag."); - Fp->seekg(positionOnEntry, std::ios_base::beg); - throw FormatUnexpected("Document::FindDocEntryLengthOB()", - "Neither an Item tag nor a Sequence " - "delimiter tag."); + long filePosition = Fp->tellg(); + gdcmVerboseMacro( "Neither an Item tag nor a Sequence delimiter tag on :" + << std::hex << group << " , " << elem + << ") -before- position x(" << filePosition << ")" ); + + Fp->seekg(positionOnEntry, std::ios::beg); + throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag."); } if ( elem == 0xe0dd ) @@ -2343,7 +2003,7 @@ uint32_t Document::FindDocEntryLengthOB() break; } } - Fp->seekg( positionOnEntry, std::ios_base::beg); + Fp->seekg( positionOnEntry, std::ios::beg); return totalLength; } @@ -2399,7 +2059,7 @@ uint32_t Document::ReadInt32() void Document::SkipBytes(uint32_t nBytes) { //FIXME don't dump the returned value - Fp->seekg((long)nBytes, std::ios_base::cur); + Fp->seekg((long)nBytes, std::ios::cur); } /** @@ -2412,6 +2072,7 @@ void Document::Initialise() RefShaDict = NULL; RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; + Filetype = Unknown; } /** @@ -2434,7 +2095,7 @@ bool Document::CheckSwap() uint32_t s32; uint16_t s16; - char deb[256]; //HEADER_LENGTH_TO_READ]; + char deb[256]; // First, compare HostByteOrder and NetworkByteOrder in order to // determine if we shall need to swap bytes (i.e. the Endian type). @@ -2449,12 +2110,12 @@ bool Document::CheckSwap() // The easiest case is the one of a DICOM header, since it possesses a // file preamble where it suffice to look for the string "DICM". - Fp->read(deb, HEADER_LENGTH_TO_READ); + Fp->read(deb, 256); char *entCur = deb + 128; if( memcmp(entCur, "DICM", (size_t)4) == 0 ) { - dbg.Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3"); + gdcmVerboseMacro( "Looks like DICOM Version3" ); // Next, determine the value representation (VR). Let's skip to the // first element (0002, 0000) and check there if we find "UL" @@ -2475,7 +2136,7 @@ bool Document::CheckSwap() // FIXME : FIXME: // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR, - // but elem 0002,0010 (Transfert Syntax) tells us the file is + // but elem 0002,0010 (Transfer Syntax) tells us the file is // *Implicit* VR. -and it is !- if( memcmp(entCur, "UL", (size_t)2) == 0 || @@ -2488,41 +2149,37 @@ bool Document::CheckSwap() // instead of just checking for UL, OB and UI !? group 0000 { Filetype = ExplicitVR; - dbg.Verbose(1, "Document::CheckSwap:", - "explicit Value Representation"); + gdcmVerboseMacro( "Explicit Value Representation"); } else { Filetype = ImplicitVR; - dbg.Verbose(1, "Document::CheckSwap:", - "not an explicit Value Representation"); + gdcmVerboseMacro( "Not an explicit Value Representation"); } if ( net2host ) { SwapCode = 4321; - dbg.Verbose(1, "Document::CheckSwap:", - "HostByteOrder != NetworkByteOrder"); + gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder"); } else { - SwapCode = 0; - dbg.Verbose(1, "Document::CheckSwap:", - "HostByteOrder = NetworkByteOrder"); + SwapCode = 1234; + gdcmVerboseMacro( "HostByteOrder = NetworkByteOrder"); } // Position the file position indicator at first tag (i.e. // after the file preamble and the "DICM" string). - Fp->seekg(0, std::ios_base::beg); - Fp->seekg ( 132L, std::ios_base::beg); + Fp->seekg(0, std::ios::beg); + Fp->seekg ( 132L, std::ios::beg); return true; } // End of DicomV3 // Alas, this is not a DicomV3 file and whatever happens there is no file // preamble. We can reset the file position indicator to where the data // is (i.e. the beginning of the file). - dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file"); - Fp->seekg(0, std::ios_base::beg); + gdcmVerboseMacro( "Not a DICOM Version3 file"); + Fp->seekg(0, std::ios::beg); // Our next best chance would be to be considering a 'clean' ACR/NEMA file. // By clean we mean that the length of the first tag is written down. @@ -2534,7 +2191,7 @@ bool Document::CheckSwap() // representation of a 32 bits integer. Hence the following dirty // trick : s32 = *((uint32_t *)(entCur)); - + switch( s32 ) { case 0x00040000 : @@ -2550,7 +2207,7 @@ bool Document::CheckSwap() Filetype = ACR; return true; case 0x00000004 : - SwapCode = 0; + SwapCode = 1234; Filetype = ACR; return true; default : @@ -2581,7 +2238,7 @@ bool Document::CheckSwap() case 0x0006 : case 0x0007 : case 0x0008 : - SwapCode = 0; + SwapCode = 1234; Filetype = ACR; return true; case 0x0100 : @@ -2596,14 +2253,13 @@ bool Document::CheckSwap() Filetype = ACR; return true; default : - dbg.Verbose(0, "Document::CheckSwap:", - "ACR/NEMA unfound swap info (Really hopeless !)"); + gdcmVerboseMacro( "ACR/NEMA unfound swap info (Really hopeless !)"); Filetype = Unknown; return false; } // Then the only info we have is the net2host one. //if (! net2host ) - // SwapCode = 0; + // SwapCode = 1234; //else // SwapCode = 4321; //return; @@ -2613,20 +2269,18 @@ bool Document::CheckSwap() /** - * \brief Restore the unproperly loaded values i.e. the group, the element - * and the dictionary entry depending on them. + * \brief Change the Byte Swap code. */ -void Document::SwitchSwapToBigEndian() +void Document::SwitchByteSwapCode() { - dbg.Verbose(1, "Document::SwitchSwapToBigEndian", - "Switching to BigEndian mode."); - if ( SwapCode == 0 ) + gdcmVerboseMacro( "Switching Byte Swap code."); + if ( SwapCode == 1234 ) { SwapCode = 4321; } else if ( SwapCode == 4321 ) { - SwapCode = 0; + SwapCode = 1234; } else if ( SwapCode == 3412 ) { @@ -2685,7 +2339,7 @@ void Document::SetMaxSizePrintEntry(long newSize) * apparent reason * @return no return */ -void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) +void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) { // Endian reversion. Some files contain groups of tags with reversed endianess. static int reversedEndian = 0; @@ -2694,28 +2348,92 @@ void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) { // start endian swap mark for group found reversedEndian++; - SwitchSwapToBigEndian(); + SwitchByteSwapCode(); // fix the tag group = 0xfffe; elem = 0xe000; } - else if ((group == 0xfffe) && (elem == 0xe00d) && reversedEndian) + else if (group == 0xfffe && elem == 0xe00d && reversedEndian) { // end of reversed endian group reversedEndian--; - SwitchSwapToBigEndian(); + SwitchByteSwapCode(); + } +} + +/** + * \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); + + if ( transferSyntax == GDCM_NOTLOADED ) + { + gdcmVerboseMacro( "Transfer Syntax not loaded. " << std::endl + << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" ); + return "Uncompressed ACR-NEMA"; + } + if ( transferSyntax == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Unfound Transfer Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; + } + + while ( ! isdigit((unsigned char)transferSyntax[transferSyntax.length()-1]) ) + { + transferSyntax.erase(transferSyntax.length()-1, 1); } + // we do it only when we need it + TS* ts = Global::GetTS(); + std::string tsName = ts->GetValue( transferSyntax ); + + // Global::GetTS() is a global static you shall never try to delete it! + return tsName; +} + +/** + * \brief Group 0002 is always coded Little Endian + * whatever Transfer Syntax is + * @return no return + */ +void Document::HandleOutOfGroup0002(uint16_t group) +{ + // Endian reversion. Some files contain groups of tags with reversed endianess. + if ( !Group0002Parsed && group != 0x0002) + { + Group0002Parsed = true; + // we just came out of group 0002 + // if Transfer syntax is Big Endian we have to change CheckSwap + + std::string ts = GetTransferSyntaxName(); + if ( !Global::GetTS()->IsTransferSyntax(ts) ) + { + gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts ); + return; + } + // FIXME Strangely, this works with + //'Implicit VR Transfer Syntax (GE Private) + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian ) + { + gdcmVerboseMacro("Tansfer Syntax = Explicit VR - Big Endian"); + SwitchByteSwapCode(); + } + } } /** * \brief Read the next tag but WITHOUT loading it's value * (read the 'Group Number', the 'Element Number', - * gets the Dict Entry + * gets the Dict Entry * gets the VR, gets the length, gets the offset value) * @return On succes the newly created DocEntry, NULL on failure. */ -DocEntry* Document::ReadNextDocEntry() +DocEntry *Document::ReadNextDocEntry() { uint16_t group; uint16_t elem; @@ -2733,9 +2451,44 @@ DocEntry* Document::ReadNextDocEntry() return 0; } + // Sometimes file contains groups of tags with reversed endianess. HandleBrokenEndian(group, elem); - DocEntry *newEntry = NewDocEntryByNumber(group, elem); - FindDocEntryVR(newEntry); + +// In 'true DICOM' files Group 0002 is allways little endian + if ( HasDCMPreamble ) + HandleOutOfGroup0002(group); + + std::string vr = FindDocEntryVR(); + std::string realVR = vr; + + if( vr == GDCM_UNKNOWN) + { + DictEntry *dictEntry = GetDictEntry(group,elem); + if( dictEntry ) + realVR = dictEntry->GetVR(); + } + + DocEntry *newEntry; + if( Global::GetVR()->IsVROfSequence(realVR) ) + newEntry = NewSeqEntry(group, elem); + else if( Global::GetVR()->IsVROfStringRepresentable(realVR) ) + newEntry = NewValEntry(group, elem,vr); + else + newEntry = NewBinEntry(group, elem,vr); + + if( vr == GDCM_UNKNOWN ) + { + if( Filetype == ExplicitVR ) + { + // We thought this was explicit VR, but we end up with an + // implicit VR tag. Let's backtrack. + std::string msg; + msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", + newEntry->GetGroup(), newEntry->GetElement()); + gdcmVerboseMacro( msg.c_str() ); + } + newEntry->SetImplicitVR(); + } try { @@ -2808,16 +2561,14 @@ bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) } if ( itemTagGroup != testGroup || itemTagElement != testElement ) { - std::ostringstream s; - s << " We should have found tag ("; - s << std::hex << testGroup << "," << testElement << ")" << std::endl; - s << " but instead we encountered tag ("; - s << std::hex << itemTagGroup << "," << itemTagElement << ")" - << std::endl; - s << " at address: " << (unsigned)currentPosition << std::endl; - dbg.Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:"); - dbg.Verbose(0, s.str().c_str()); - Fp->seekg(positionOnEntry, std::ios_base::beg); + 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; } @@ -2852,11 +2603,9 @@ uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement) long currentPosition = Fp->tellg(); uint32_t itemLength = ReadInt32(); { - std::ostringstream s; - s << "Basic Item Length is: " - << itemLength << std::endl; - s << " at address: " << (unsigned)currentPosition << std::endl; - dbg.Verbose(0, "Document::ReadItemTagLength: ", s.str().c_str()); + gdcmVerboseMacro( "Basic Item Length is: " + << itemLength << std::endl + << " at address: " << std::hex << (unsigned int)currentPosition); } return itemLength; } @@ -2878,7 +2627,7 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 ) { - char* basicOffsetTableItemValue = new char[itemLength + 1]; + char *basicOffsetTableItemValue = new char[itemLength + 1]; Fp->read(basicOffsetTableItemValue, itemLength); #ifdef GDCM_DEBUG @@ -2886,12 +2635,8 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() { uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], uint32_t); - std::ostringstream s; - s << " Read one length: "; - s << std::hex << individualLength << std::endl; - dbg.Verbose(0, - "Document::ReadAndSkipEncapsulatedBasicOffsetTable: ", - s.str().c_str()); + gdcmVerboseMacro( "Read one length: " << + std::hex << individualLength ); } #endif //GDCM_DEBUG @@ -2906,8 +2651,8 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() */ void Document::ComputeRLEInfo() { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts != RLELossless ) + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsRLELossless(ts) ) { return; } @@ -2948,7 +2693,7 @@ void Document::ComputeRLEInfo() if ( nbRleSegments > 16 ) { // There should be at most 15 segments (refer to RLEFrame class) - dbg.Verbose(0, "Document::ComputeRLEInfo: too many segments."); + gdcmVerboseMacro( "Too many segments."); } uint32_t rleSegmentOffsetTable[16]; @@ -2977,7 +2722,7 @@ void Document::ComputeRLEInfo() SkipBytes(rleSegmentLength[nbRleSegments]); // Store the collected info - RLEFrame* newFrameInfo = new RLEFrame; + RLEFrame *newFrameInfo = new RLEFrame; newFrameInfo->NumberFragments = nbRleSegments; for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) { @@ -2991,8 +2736,7 @@ void Document::ComputeRLEInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); - dbg.Verbose(0, " item at end of RLE item sequence"); + gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence"); } } @@ -3005,7 +2749,8 @@ void Document::ComputeRLEInfo() void Document::ComputeJPEGFragmentInfo() { // If you need to, look for comments of ComputeRLEInfo(). - if ( ! IsJPEG() ) + std::string ts = GetTransferSyntax(); + if ( ! Global::GetTS()->IsJPEG(ts) ) { return; } @@ -3020,7 +2765,7 @@ void Document::ComputeJPEGFragmentInfo() long fragmentOffset = Fp->tellg(); // Store the collected info - JPEGFragment* newFragment = new JPEGFragment; + JPEGFragment *newFragment = new JPEGFragment; newFragment->Offset = fragmentOffset; newFragment->Length = fragmentLength; JPEGInfo->Fragments.push_back( newFragment ); @@ -3032,8 +2777,7 @@ void Document::ComputeJPEGFragmentInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); - dbg.Verbose(0, " item at end of JPEG item sequence"); + gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence"); } } @@ -3046,18 +2790,18 @@ void Document::ComputeJPEGFragmentInfo() * when recursively walking the given set. * @param set The structure to be traversed (recursively). */ -void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, - DocEntrySet* set ) +void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, + DocEntrySet *set ) { - if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) ) + if (ElementSet *elementSet = dynamic_cast< ElementSet* > ( set ) ) { - TagDocEntryHT const & currentHT = elementSet->GetTagHT(); + TagDocEntryHT const ¤tHT = elementSet->GetTagHT(); for( TagDocEntryHT::const_iterator i = currentHT.begin(); i != currentHT.end(); ++i) { - DocEntry* entry = i->second; - if ( SeqEntry* seqEntry = dynamic_cast(entry) ) + DocEntry *entry = i->second; + if ( SeqEntry *seqEntry = dynamic_cast(entry) ) { const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); @@ -3073,15 +2817,15 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, return; } - if (SQItem* SQItemSet = dynamic_cast< SQItem* > ( set ) ) + if (SQItem *SQItemSet = dynamic_cast< SQItem* > ( set ) ) { const ListDocEntry& currentList = SQItemSet->GetDocEntries(); for (ListDocEntry::const_iterator i = currentList.begin(); i != currentList.end(); ++i) { - DocEntry* entry = *i; - if ( SeqEntry* seqEntry = dynamic_cast(entry) ) + DocEntry *entry = *i; + if ( SeqEntry *seqEntry = dynamic_cast(entry) ) { const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); @@ -3121,9 +2865,9 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, * \ref BuildFlatHashTable again... * @return The flat std::map<> we juste build. */ -TagDocEntryHT* Document::BuildFlatHashTable() +TagDocEntryHT *Document::BuildFlatHashTable() { - TagDocEntryHT* FlatHT = new TagDocEntryHT; + TagDocEntryHT *FlatHT = new TagDocEntryHT; BuildFlatHashTableRecurse( *FlatHT, this ); return FlatHT; } @@ -3140,8 +2884,8 @@ TagDocEntryHT* Document::BuildFlatHashTable() bool Document::operator<(Document &document) { // Patient Name - std::string s1 = GetEntryByNumber(0x0010,0x0010); - std::string s2 = document.GetEntryByNumber(0x0010,0x0010); + std::string s1 = GetEntry(0x0010,0x0010); + std::string s2 = document.GetEntry(0x0010,0x0010); if(s1 < s2) { return true; @@ -3153,8 +2897,8 @@ bool Document::operator<(Document &document) else { // Patient ID - s1 = GetEntryByNumber(0x0010,0x0020); - s2 = document.GetEntryByNumber(0x0010,0x0020); + s1 = GetEntry(0x0010,0x0020); + s2 = document.GetEntry(0x0010,0x0020); if ( s1 < s2 ) { return true; @@ -3166,8 +2910,8 @@ bool Document::operator<(Document &document) else { // Study Instance UID - s1 = GetEntryByNumber(0x0020,0x000d); - s2 = document.GetEntryByNumber(0x0020,0x000d); + s1 = GetEntry(0x0020,0x000d); + s2 = document.GetEntry(0x0020,0x000d); if ( s1 < s2 ) { return true; @@ -3179,8 +2923,8 @@ bool Document::operator<(Document &document) else { // Serie Instance UID - s1 = GetEntryByNumber(0x0020,0x000e); - s2 = document.GetEntryByNumber(0x0020,0x000e); + s1 = GetEntry(0x0020,0x000e); + s2 = document.GetEntry(0x0020,0x000e); if ( s1 < s2 ) { return true; @@ -3195,6 +2939,52 @@ bool Document::operator<(Document &document) 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; + + Initialize(); + entry = GetNextEntry(); + while(entry) + { + gr = entry->GetGroup(); + + if (gr == 0x0002) + { + found0002 = true; + + el = entry->GetElement(); + vr = entry->GetVR(); + + if (filetype == ExplicitVR) + { + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) + { + groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes + } + } + groupLength += 2 + 2 + 4 + entry->GetLength(); + } + else if (found0002 ) + break; + + entry = GetNextEntry(); + } + return groupLength; +} + } // end namespace gdcm //-----------------------------------------------------------------------------