X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=d6f1cbb1e0a1f9d4c3e29fa99822fbf35da9f334;hb=70a3a0f95bf2240a6ef4b1d6523c0e6614437304;hp=08e6a9c027a5962c161aedfb643232d3143a66c7;hpb=7e9537ac534af5c5b9c5231c1b7fdd7193c2255d;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 08e6a9c0..d6f1cbb1 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: 2005/01/24 14:14:11 $ + Version: $Revision: 1.205 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -24,7 +24,6 @@ #include "gdcmUtil.h" #include "gdcmDebug.h" #include "gdcmTS.h" -#include "gdcmException.h" #include "gdcmDictSet.h" #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" @@ -35,9 +34,11 @@ #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 +58,16 @@ 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) { + RLEInfo = NULL; + JPEGInfo = NULL; + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; - Initialise(); + Initialize(); Fp = 0; if ( !OpenFile() ) @@ -137,7 +141,7 @@ Document::Document( std::string const &filename ) : ElementSet(-1) // we switch lineNumber and columnNumber // std::string RecCode; - RecCode = GetEntry(0x0008, 0x0010); // recognition code + RecCode = GetEntry(0x0008, 0x0010); // recognition code (RET) if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" @@ -157,10 +161,13 @@ Document::Document( std::string const &filename ) : ElementSet(-1) */ Document::Document() : ElementSet(-1) { + RLEInfo = NULL; + JPEGInfo = NULL; + Fp = 0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - Initialise(); + Initialize(); SwapCode = 1234; Filetype = ExplicitVR; Group0002Parsed = false; @@ -174,8 +181,10 @@ Document::~Document () RefPubDict = NULL; RefShaDict = NULL; - delete RLEInfo; - delete JPEGInfo; + if( RLEInfo ) + delete RLEInfo; + if( JPEGInfo ) + delete JPEGInfo; } //----------------------------------------------------------------------------- @@ -255,9 +264,10 @@ bool Document::IsReadable() return false; } - if( TagHT.empty() ) + //if( TagHT.empty() ) + if ( IsEmpty() ) { - gdcmVerboseMacro( "No tags in internal hash table."); + gdcmVerboseMacro( "No tag in internal hash table."); return false; } @@ -314,6 +324,23 @@ 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) @@ -407,7 +434,7 @@ bool Document::CloseFile() Fp = 0; } - return true; //FIXME how do we detect a non-close ifstream ? + return true; //FIXME how do we detect a non-closed ifstream ? } /** @@ -511,8 +538,8 @@ ValEntry *Document::ReplaceOrCreate(std::string const &value, * 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 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). @@ -618,7 +645,6 @@ SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem) } } } - // Create a new seqEntry if necessary if (!seqEntry) { @@ -632,7 +658,6 @@ SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem) return NULL; } } - return seqEntry; } @@ -655,39 +680,6 @@ bool Document::ReplaceIfExist(std::string const &value, //----------------------------------------------------------------------------- // 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 @@ -703,12 +695,12 @@ std::string Document::GetEntry(uint16_t group, uint16_t elem) */ std::string Document::GetEntryVR(uint16_t group, uint16_t elem) { - DocEntry *elem = GetDocEntry(group, elem); - if ( !elem ) + DocEntry *element = GetDocEntry(group, elem); + if ( !element ) { return GDCM_UNFOUND; } - return elem->GetVR(); + return element->GetVR(); } /** @@ -721,12 +713,12 @@ std::string Document::GetEntryVR(uint16_t group, uint16_t elem) */ int Document::GetEntryLength(uint16_t group, uint16_t elem) { - DocEntry *elem = GetDocEntry(group, elem); - if ( !elem ) + DocEntry *element = GetDocEntry(group, elem); + if ( !element ) { return -2; //magic number } - return elem->GetLength(); + return element->GetLength(); } /** @@ -777,7 +769,7 @@ bool Document::SetEntry(uint8_t*content, int lgth, * @param content new value (string) to substitute with * @param entry Entry to be modified */ -bool Document::SetEntry(std::string const &content,ValEntry *entry) +bool Document::SetEntry(std::string const &content, ValEntry *entry) { if(entry) { @@ -837,8 +829,8 @@ void *Document::GetEntryBinArea(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 group group number of the Entry * @param elem element number of the Entry */ @@ -857,8 +849,8 @@ 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 +869,7 @@ 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 +912,11 @@ 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 +1031,7 @@ 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 +1043,8 @@ 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 +1069,8 @@ 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 @@ -1286,7 +1209,7 @@ void Document::ParseSQ( SeqEntry *seqEntry, { if ( newDocEntry->IsSequenceDelimitor() ) { - seqEntry->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetDelimitationItem( newDocEntry ); break; } } @@ -1329,7 +1252,7 @@ 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 +1527,33 @@ 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 +1572,9 @@ 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; @@ -2098,7 +2023,7 @@ 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; @@ -2291,8 +2216,6 @@ bool Document::CheckSwap() } } - - /** * \brief Change the Byte Swap code. */ @@ -2343,7 +2266,6 @@ void Document::SetMaxSizeLoadEntry(long newSize) */ void Document::SetMaxSizePrintEntry(long newSize) { - //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME if ( newSize < 0 ) { return; @@ -2388,7 +2310,6 @@ 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() @@ -2436,6 +2357,13 @@ 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 +2372,7 @@ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) << GetTransferSyntaxName() << "]" ); SwitchByteSwapCode(); group = SwapShort(group); - elem = SwapShort(elem); + elem = SwapShort(elem); } } } @@ -2533,25 +2461,25 @@ 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 @@ -2805,7 +2733,7 @@ void Document::ComputeJPEGFragmentInfo() } } -/** +/* * \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 +2794,7 @@ void Document::ComputeJPEGFragmentInfo() } }*/ -/** +/* * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current * Document. * @@ -2977,10 +2905,7 @@ int Document::ComputeGroup0002Length( FileType filetype ) bool found0002 = false; // for each zero-level Tag in the DCM Header - DocEntry *entry; - - InitTraversal(); - entry = GetNextEntry(); + DocEntry *entry = GetFirstEntry(); while(entry) { gr = entry->GetGroup();