X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=a252297e52f728abb71c16fadb83b91a4e18c491;hb=4976cfdaa3bb61e01e7ad0a2382d7e9622918acd;hp=08e6a9c027a5962c161aedfb643232d3143a66c7;hpb=7e9537ac534af5c5b9c5231c1b7fdd7193c2255d;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 08e6a9c0..a252297e 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2005/01/17 17:27:03 $ - Version: $Revision: 1.193 $ + Date: $Date: 2005/01/28 09:31:51 $ + Version: $Revision: 1.215 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -24,10 +24,7 @@ #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" @@ -35,9 +32,11 @@ #include // For nthos: -#if defined(_MSC_VER) || defined(__BORLANDC__) +#if defined(_MSC_VER) || defined(__BORLANDC__) || defined(__MINGW32__) #include -#else +#endif + +#ifdef CMAKE_HAVE_NETINET_IN_H #include #endif @@ -57,13 +56,13 @@ const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; /** * \brief constructor - * @param filename file to be opened for parsing + * @param filename 'Document' (File or DicomDir) to be opened for parsing */ Document::Document( std::string const &filename ) : ElementSet(-1) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; - Initialise(); + Initialize(); Fp = 0; if ( !OpenFile() ) @@ -91,7 +90,7 @@ Document::Document( std::string const &filename ) : ElementSet(-1) // Load 'non string' values - std::string PhotometricInterpretation = GetEntry(0x0028,0x0004); + std::string PhotometricInterpretation = GetEntryValue(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ) { LoadEntryBinArea(0x0028,0x1200); // gray LUT @@ -137,16 +136,16 @@ Document::Document( std::string const &filename ) : ElementSet(-1) // we switch lineNumber and columnNumber // std::string RecCode; - RecCode = GetEntry(0x0008, 0x0010); // recognition code + RecCode = GetEntryValue(0x0008, 0x0010); // recognition code (RET) if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { Filetype = 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 = GetEntryValue(0x0028, 0x0010); + std::string columns = GetEntryValue(0x0028, 0x0011); + SetValEntry(columns, 0x0028, 0x0010); + SetValEntry(rows , 0x0028, 0x0011); } // ----------------- End of ACR-LibIDO kludge ------------------ } @@ -160,7 +159,7 @@ Document::Document() : ElementSet(-1) Fp = 0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - Initialise(); + Initialize(); SwapCode = 1234; Filetype = ExplicitVR; Group0002Parsed = false; @@ -173,9 +172,6 @@ Document::~Document () { RefPubDict = NULL; RefShaDict = NULL; - - delete RLEInfo; - delete JPEGInfo; } //----------------------------------------------------------------------------- @@ -183,6 +179,7 @@ Document::~Document () /** * \brief Prints The Dict Entries of THE public Dicom Dictionary + * @param os ostream to print to * @return */ void Document::PrintPubDict(std::ostream &os) @@ -193,6 +190,7 @@ void Document::PrintPubDict(std::ostream &os) /** * \brief Prints The Dict Entries of THE shadow Dicom Dictionary + * @param os ostream to print to * @return */ void Document::PrintShaDict(std::ostream &os) @@ -255,9 +253,9 @@ bool Document::IsReadable() return false; } - if( TagHT.empty() ) + if ( IsEmpty() ) { - gdcmVerboseMacro( "No tags in internal hash table."); + gdcmVerboseMacro( "No tag in internal hash table."); return false; } @@ -314,6 +312,23 @@ bool Document::IsDicomV3() 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(e) ) + return false; + return true; +} + /** * \brief returns the File Type * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) @@ -331,7 +346,6 @@ FileType Document::GetFileType() */ std::ifstream *Document::OpenFile() { - HasDCMPreamble = false; if (Filename.length() == 0) { @@ -341,6 +355,7 @@ std::ifstream *Document::OpenFile() if(Fp) { gdcmVerboseMacro( "File already open: " << Filename.c_str()); + CloseFile(); } Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); @@ -406,8 +421,7 @@ bool Document::CloseFile() delete Fp; Fp = 0; } - - return true; //FIXME how do we detect a non-close ifstream ? + return true; //FIXME how do we detect a non-closed ifstream ? } /** @@ -415,14 +429,15 @@ bool Document::CloseFile() * @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. + * @return Always true. */ 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 + // \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 || filetype == ExplicitVR ) { @@ -433,7 +448,7 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) 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 @@ -448,397 +463,11 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) 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 ) -{ - ValEntry *valEntry = 0; - DocEntry *currentEntry = GetDocEntry( group, elem); - - if (currentEntry) - { - 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; - } - } - } - - // 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; - return NULL; - } - } - - // 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). - */ -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; - - // if currentEntry doesn't correspond to the requested valEntry - if( !binEntry) - { - if (!RemoveEntry(currentEntry)) - { - 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) - { - tmpArea = new uint8_t[lgth]; - memcpy(tmpArea,binArea,lgth); - } - else - { - tmpArea = 0; - } - if (!SetEntry(tmpArea,lgth,binEntry)) - { - if (tmpArea) - { - delete[] tmpArea; - } - } - - return binEntry; -} - -/* - * \brief Modifies the value of a given Header Entry (Dicom Element) - * when it exists. Create it when unexistant. - * @param group Group number of the Entry - * @param elem Element number of the Entry - * \return pointer to the modified/created SeqEntry (NULL when creation - * failed). - */ -SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem) -{ - SeqEntry *seqEntry = 0; - DocEntry *currentEntry = GetDocEntry( group, elem); - - // Verify the currentEntry - if (currentEntry) - { - 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) - { - if (!RemoveEntry(currentEntry)) - { - gdcmVerboseMacro( "Removal of previous DocEntry failed."); - - return NULL; - } - } - } - - // 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; -} - -/** - * \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 - /** - * \brief Checks if a given Dicom Element exists within the H table - * @param group Group number of the searched Dicom Element - * @param elem Element number of the searched Dicom Element - * @return true is found - */ -bool Document::CheckIfEntryExist(uint16_t group, uint16_t elem ) -{ - const std::string &key = DictEntry::TranslateToKey(group, elem ); - return TagHT.count(key) != 0; -} - - -/** - * \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 elem 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::GetEntry(uint16_t group, uint16_t elem) -{ - TagKey key = DictEntry::TranslateToKey(group, elem); - if ( !TagHT.count(key)) - { - return GDCM_UNFOUND; - } - - 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 elem 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 elem) -{ - DocEntry *elem = GetDocEntry(group, elem); - if ( !elem ) - { - return GDCM_UNFOUND; - } - return elem->GetVR(); -} - -/** - * \brief Searches within Header Entries (Dicom Elements) parsed with - * the public and private dictionaries - * for the value length of a given tag.. - * @param group Group number of the searched tag. - * @param elem Element number of the searched tag. - * @return Corresponding element length; -2 if not found - */ -int Document::GetEntryLength(uint16_t group, uint16_t elem) -{ - DocEntry *elem = GetDocEntry(group, elem); - if ( !elem ) - { - return -2; //magic number - } - return elem->GetLength(); -} - -/** - * \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 elem element number of the Dicom Element to modify - */ -bool Document::SetEntry(std::string const& content, - uint16_t group, uint16_t elem) -{ - ValEntry *entry = GetValEntry(group, elem); - if (!entry ) - { - gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); - return false; - } - 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 elem element number of the Dicom Element to modify - */ -bool Document::SetEntry(uint8_t*content, int lgth, - uint16_t group, uint16_t elem) -{ - BinEntry *entry = GetBinEntry(group, elem); - if (!entry ) - { - gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); - return false; - } - - return SetEntry(content,lgth,entry); -} - -/** - * \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 - */ -bool Document::SetEntry(std::string const &content,ValEntry *entry) -{ - if(entry) - { - entry->SetValue(content); - return true; - } - return false; -} - -/** - * \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 - */ -bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry) -{ - 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; -} - -/** - * \brief Gets (from Header) a 'non string' element value - * (LoadElementValues has already be executed) - * @param group group number of the Entry - * @param elem element number of the Entry - * @return Pointer to the 'non string' area - */ -void *Document::GetEntryBinArea(uint16_t group, uint16_t elem) -{ - DocEntry *entry = GetDocEntry(group, elem); - if (!entry) - { - gdcmVerboseMacro( "No entry"); - return 0; - } - if ( BinEntry *binEntry = dynamic_cast(entry) ) - { - return binEntry->GetBinArea(); - } - - return 0; -} - -/** - * \brief Loads (from disk) the element content - * when a string is not suitable + * \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 */ @@ -857,8 +486,8 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) } /** - * \brief Loads (from disk) the element content - * when a string is not suitable + * \brief Loads (from disk) the element content + * when a string is not suitable * @param elem Entry whose binArea is going to be loaded */ void Document::LoadEntryBinArea(BinEntry *elem) @@ -877,7 +506,7 @@ void Document::LoadEntryBinArea(BinEntry *elem) uint8_t *a = new uint8_t[l]; if( !a ) { - gdcmVerboseMacro( "Cannot allocate a"); + gdcmVerboseMacro( "Cannot allocate BinEntry content"); return; } @@ -920,78 +549,11 @@ void Document::LoadEntryBinArea(BinEntry *elem) return false; }*/ -/** - * \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 elem Element number of the searched Dicom Element - * @return - */ -DocEntry *Document::GetDocEntry(uint16_t group, uint16_t elem) -{ - TagKey key = DictEntry::TranslateToKey(group, elem); - if ( !TagHT.count(key)) - { - return NULL; - } - return TagHT.find(key)->second; -} - -/** - * \brief Same as \ref Document::GetDocEntry except it only - * returns a result when the corresponding entry is of type - * ValEntry. - * @param group Group number of the searched Dicom Element - * @param elem Element number of the searched Dicom Element - * @return When present, the corresponding ValEntry. - */ -ValEntry *Document::GetValEntry(uint16_t group, uint16_t elem) -{ - DocEntry *currentEntry = GetDocEntry(group, elem); - if ( !currentEntry ) - { - return 0; - } - if ( ValEntry *entry = dynamic_cast(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. - * @param group Group number of the searched Dicom Element - * @param elem Element number of the searched Dicom Element - * @return When present, the corresponding BinEntry. - */ -BinEntry *Document::GetBinEntry(uint16_t group, uint16_t elem) -{ - DocEntry *currentEntry = GetDocEntry(group, elem); - 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 - * to LoadDocEntry that modifies it. + * \brief Loads the element while preserving the current + * underlying file position indicator as opposed to + * LoadDocEntry that modifies it. * @param entry Header Entry whose value will be loaded. * @return */ @@ -1106,7 +668,8 @@ void Document::ParseDES(DocEntrySet *set, long offset, { if ( newBinEntry ) { - if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) ) + if ( Filetype == ExplicitVR && + !Global::GetVR()->IsVROfBinaryRepresentable(vr) ) { ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR gdcmVerboseMacro( std::hex << newDocEntry->GetGroup() @@ -1118,9 +681,8 @@ void Document::ParseDES(DocEntrySet *set, long offset, //////////////////// 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 ) ) + if ( dynamic_cast< Document* > ( set ) ) { - //(void)dummy; newBinEntry->SetKey( newBinEntry->GetKey() ); } // but when "this" is a SQItem, we are inserting this new @@ -1145,9 +707,8 @@ void Document::ParseDES(DocEntrySet *set, long offset, /////////////////////// 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 ) ) + if ( dynamic_cast< Document* > ( set ) ) { - //(void)dummy; newValEntry->SetKey( newValEntry->GetKey() ); } // ...but when "set" is a SQItem, we are inserting this new @@ -1182,26 +743,6 @@ void Document::ParseDES(DocEntrySet *set, long offset, } } - if ( ( newDocEntry->GetGroup() == 0x7fe0 ) - && ( newDocEntry->GetElement() == 0x0010 ) ) - { - 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 ); - } - } - // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); } @@ -1249,14 +790,19 @@ void Document::ParseDES(DocEntrySet *set, long offset, newDocEntry->GetOffset(), l, delim_mode); } - set->AddEntry( newSeqEntry ); + if( !set->AddEntry( newSeqEntry ) ) + { + used = false; + } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + if( !used ) + delete newDocEntry; break; } } - if(!used) + if( !used ) delete newDocEntry; } } @@ -1286,7 +832,7 @@ void Document::ParseSQ( SeqEntry *seqEntry, { if ( newDocEntry->IsSequenceDelimitor() ) { - seqEntry->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetDelimitationItem( newDocEntry ); break; } } @@ -1329,7 +875,7 @@ void Document::ParseSQ( SeqEntry *seqEntry, offsetStartCurrentSQItem = Fp->tellg(); // end try ----------------- - seqEntry->AddEntry( itemSQ, SQItemNumber ); + seqEntry->AddSQItem( itemSQ, SQItemNumber ); SQItemNumber++; if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) { @@ -1604,34 +1150,33 @@ void Document::FindDocEntryLength( DocEntry *entry ) // 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() ); +// 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 ) +// DictEntry *newTag = GetDictEntry( correctGroup, correctElem ); +// if ( !newTag ) // { - // This correct tag is not in the dictionary. Create a new one. +// // 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. +// // FIXME this can create a memory leaks on the old entry that be +// // left unreferenced. // entry->SetDictEntry( newTag ); // } - // 0xffff means that we deal with 'No Length' Sequence // or 'No Length' SQItem @@ -1650,6 +1195,9 @@ void Document::FindDocEntryLength( DocEntry *entry ) // on Data elements "Implicit and Explicit VR Data Elements shall // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. + + // Well ... group 0002 is always coded in 'Explicit VR Litle Endian' + // even if Transfer Syntax is 'Implicit VR ...' FixDocEntryFoundLength( entry, ReadInt32() ); return; @@ -2098,12 +1646,10 @@ void Document::SkipBytes(uint32_t nBytes) * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ -void Document::Initialise() +void Document::Initialize() { RefPubDict = Global::GetDicts()->GetDefaultPubDict(); RefShaDict = NULL; - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; Filetype = Unknown; } @@ -2291,8 +1837,6 @@ bool Document::CheckSwap() } } - - /** * \brief Change the Byte Swap code. */ @@ -2343,7 +1887,6 @@ void Document::SetMaxSizeLoadEntry(long newSize) */ void Document::SetMaxSizePrintEntry(long newSize) { - //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME if ( newSize < 0 ) { return; @@ -2388,13 +1931,12 @@ void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) /** * \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); + std::string transferSyntax = GetEntryValue(0x0002,0x0010); if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) ) { @@ -2436,6 +1978,13 @@ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) return; } + // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..." + + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian ) + { + Filetype = ImplicitVR; + } + // FIXME Strangely, this works with //'Implicit VR Transfer Syntax (GE Private) if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian ) @@ -2444,7 +1993,7 @@ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) << GetTransferSyntaxName() << "]" ); SwitchByteSwapCode(); group = SwapShort(group); - elem = SwapShort(elem); + elem = SwapShort(elem); } } } @@ -2533,279 +2082,132 @@ DocEntry *Document::ReadNextDocEntry() return newEntry; } - +//GenerateFreeTagKeyInGroup? What was it designed for ?!? /** * \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; -} +//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 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::ReadTag(uint16_t testGroup, uint16_t testElement) +bool Document::operator<(Document &document) { - 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 + // Patient Name + std::string s1 = GetEntryValue(0x0010,0x0010); + std::string s2 = document.GetEntryValue(0x0010,0x0010); + if(s1 < s2) { - itemTagGroup = ReadInt16(); - itemTagElement = ReadInt16(); + return true; } - catch ( FormatError e ) + else if( s1 > s2 ) { - //std::cerr << e << std::endl; return false; } - if ( itemTagGroup != testGroup || itemTagElement != testElement ) - { - 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; - } - 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) -{ - - if ( !ReadTag(testGroup, testElement) ) - { - return 0; - } - - //// Then read the associated Item Length - long currentPosition = Fp->tellg(); - uint32_t itemLength = ReadInt32(); - { - gdcmVerboseMacro( "Basic Item Length is: " - << itemLength << std::endl - << " at address: " << std::hex << (unsigned int)currentPosition); - } - return itemLength; -} - -/** - * \brief When parsing the Pixel Data of an encapsulated file, read - * the basic offset table (when present, and BTW dump it). - */ -void Document::ReadAndSkipEncapsulatedBasicOffsetTable() -{ - //// 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 - - delete[] basicOffsetTableItemValue; - } -} - -/** - * \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) ) + else { - return; - } - - // Encoded pixel data: for the time being we are only concerned with - // Jpeg or RLE Pixel data encodings. - // As stated in PS 3.5-2003, section 8.2 p44: - // "If sent in Encapsulated Format (i.e. other than the Native Format) the - // value representation OB is used". - // Hence we expect an OB value representation. Concerning OB VR, - // the section PS 3.5-2003, section A.4.c p 58-59, states: - // "For the Value Representations OB and OW, the encoding shall meet the - // following specifications depending on the Data element tag:" - // [...snip...] - // - the first item in the sequence of items before the encoded pixel - // data stream shall be basic offset table item. The basic offset table - // item value, however, is not required to be present" - - ReadAndSkipEncapsulatedBasicOffsetTable(); - - // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) - // Loop on the individual frame[s] and store the information - // on the RLE fragments in a RLEFramesInfo. - // Note: - when only a single frame is present, this is a - // classical image. - // - when more than one frame are present, then we are in - // the case of a multi-frame image. - long frameLength; - while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) ) - { - // Parse the RLE Header and store the corresponding RLE Segment - // Offset Table information on fragments of this current Frame. - // Note that the fragment pixels themselves are not loaded - // (but just skipped). - long frameOffset = Fp->tellg(); - - uint32_t nbRleSegments = ReadInt32(); - if ( nbRleSegments > 16 ) + // Patient ID + s1 = GetEntryValue(0x0010,0x0020); + s2 = document.GetEntryValue(0x0010,0x0020); + if ( s1 < s2 ) { - // There should be at most 15 segments (refer to RLEFrame class) - gdcmVerboseMacro( "Too many segments."); + return true; } - - uint32_t rleSegmentOffsetTable[16]; - for( int k = 1; k <= 15; k++ ) + else if ( s1 > s2 ) { - rleSegmentOffsetTable[k] = ReadInt32(); + return false; } - - // 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) + else { - for(unsigned int k = 1; k <= nbRleSegments-1; k++) + // Study Instance UID + s1 = GetEntryValue(0x0020,0x000d); + s2 = document.GetEntryValue(0x0020,0x000d); + if ( s1 < s2 ) { - 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"); + return true; + } + else if( s1 > s2 ) + { + return false; + } + else + { + // Serie Instance UID + s1 = GetEntryValue(0x0020,0x000e); + s2 = document.GetEntryValue(0x0020,0x000e); + if ( s1 < s2 ) + { + return true; + } + else if( s1 > s2 ) + { + return false; + } + } + } } + return false; } /** - * \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. + * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader + * @param filetype Type of the File to be written */ -void Document::ComputeJPEGFragmentInfo() +int Document::ComputeGroup0002Length( FileType filetype ) { - // If you need to, look for comments of ComputeRLEInfo(). - std::string ts = GetTransferSyntax(); - if ( ! Global::GetTS()->IsJPEG(ts) ) + uint16_t gr; + std::string vr; + + int groupLength = 0; + bool found0002 = false; + + // for each zero-level Tag in the DCM Header + DocEntry *entry = GetFirstEntry(); + while(entry) { - 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 ); + gr = entry->GetGroup(); - SkipBytes( fragmentLength ); - } + if (gr == 0x0002) + { + found0002 = true; + 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; - // 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"); + entry = GetNextEntry(); } + return groupLength; } -/** +/* * \brief Walk recursively the given \ref DocEntrySet, and feed * the given hash table (\ref TagDocEntryHT) with all the * \ref DocEntry (Dicom entries) encountered. @@ -2866,7 +2268,7 @@ void Document::ComputeJPEGFragmentInfo() } }*/ -/** +/* * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current * Document. * @@ -2896,119 +2298,6 @@ void Document::ComputeJPEGFragmentInfo() return FlatHT; }*/ - - -/** - * \brief Compares two documents, according to \ref DicomDir rules - * \warning Does NOT work with ACR-NEMA files - * \todo Find a trick to solve the pb (use RET fields ?) - * @param document - * @return true if 'smaller' - */ -bool 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 ) - { - 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; - } - } - } - } - 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) - { - 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 //-----------------------------------------------------------------------------