X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=3b4c2d4a7c9ccef460ac9a6274d43ec550fd797e;hb=9f596ccd6001b165eca959c6a7b104eb10ff9911;hp=4af6b8f09ac7c4985863f694e8e3935973135b8f;hpb=0b36f4932e894a1dde4a80e614755816b4b29218;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 4af6b8f0..3b4c2d4a 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -2,6 +2,10 @@ //----------------------------------------------------------------------------- #include "gdcmDocument.h" +#include "gdcmValEntry.h" +#include "gdcmBinEntry.h" +#include "gdcmSeqEntry.h" + #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" @@ -22,11 +26,9 @@ #define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1" #define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2" #define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" +#define UI1_1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5" -typedef struct { - guint32 totalSQlength; - guint32 alreadyParsedlength; -} pileElem; +#define str2num(str, typeNum) *((typeNum *)(str)) //----------------------------------------------------------------------------- // Refer to gdcmDocument::CheckSwap() @@ -57,7 +59,8 @@ const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; gdcmDocument::gdcmDocument(const char *inFilename, bool exception_on_error, bool enable_sequences, - bool ignore_shadow) { + bool ignore_shadow) + : gdcmElementSet(-1) { enableSequences=enable_sequences; ignoreShadow =ignore_shadow; @@ -67,11 +70,44 @@ gdcmDocument::gdcmDocument(const char *inFilename, if ( !OpenFile(exception_on_error)) return; + + rewind(fp); + //if (!CheckSwap()) + // return false; // to go on compiling + + fseek(fp,0L,SEEK_END); + long lgt = ftell(fp); + + rewind(fp); + CheckSwap(); + long beg = ftell(fp); + lgt -= beg; + + SQDepthLevel=0; + + long l=ParseDES( this, beg, lgt, false); // le Load sera fait a la volee + CloseFile(); + + // -------------------------------------------------------------- + // Special Patch to allow gdcm to read ACR-LibIDO formated images + // + // if recognition code tells us we deal with a LibIDO image + // we switch lineNumber and columnNumber + // + std::string RecCode; + RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code + if (RecCode == "ACRNEMA_LIBIDO_1.1" || + RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares + // with "little-endian strings" + { + filetype = gdcmACR_LIBIDO; + std::string rows = GetEntryByNumber(0x0028, 0x0010); + std::string columns = GetEntryByNumber(0x0028, 0x0011); + SetEntryByNumber(columns, 0x0028, 0x0010); + SetEntryByNumber(rows , 0x0028, 0x0011); + } + // ----------------- End of Special Patch ---------------- - LoadDocEntries(); - CloseFile(); - - wasUpdated = 0; // will be set to 1 if user adds an entry printLevel = 1; // 'Medium' print level by default } @@ -79,14 +115,14 @@ gdcmDocument::gdcmDocument(const char *inFilename, * \brief constructor * @param exception_on_error */ -gdcmDocument::gdcmDocument(bool exception_on_error) { - (void)exception_on_error; +gdcmDocument::gdcmDocument(bool exception_on_error) + :gdcmElementSet(-1) { + (void)exception_on_error; enableSequences=0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); - wasUpdated = 0; // will be set to 1 if user adds an entry printLevel = 1; // 'Medium' print level by default } @@ -101,21 +137,7 @@ gdcmDocument::~gdcmDocument (void) { //----------------------------------------------------------------------------- // Print /** - * \brief Prints the Doc Entries (Dicom Elements) - * from the chained list - * @return - */ -void gdcmDocument::PrintEntry(std::ostream & os) { - - for (ListTag::iterator i = listEntries.begin(); - i != listEntries.end(); - ++i) - { - (*i)->SetPrintLevel(printLevel); - (*i)->Print(os); - } -} - + /** * \brief Prints The Dict Entries of THE public Dicom Dictionary @@ -176,10 +198,12 @@ bool gdcmDocument::SetShaDict(DictKey dictName){ * false otherwise. */ bool gdcmDocument::IsReadable(void) { - if(filetype==Unknown) { + if(filetype==gdcmUnknown) { + std::cout << "wrong filetype" <GetValue(); + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); if ( Transfer == UI1_2_840_10008_1_2 ) return true; return false; @@ -209,12 +233,12 @@ bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) { * @return True when ExplicitVRLittleEndian found. False in all other cases. */ bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; - LoadHeaderEntrySafe(Element); + LoadDocEntrySafe(Element); - std::string Transfer = Element->GetValue(); + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); if ( Transfer == UI1_2_840_10008_1_2_1 ) return true; return false; @@ -226,12 +250,12 @@ bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) { * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; - LoadHeaderEntrySafe(Element); + LoadDocEntrySafe(Element); - std::string Transfer = Element->GetValue(); + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); if ( Transfer == UI1_2_840_10008_1_2_1_99 ) return true; return false; @@ -243,12 +267,12 @@ bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { * @return True when big endian found. False in all other cases. */ bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; - LoadHeaderEntrySafe(Element); + LoadDocEntrySafe(Element); - std::string Transfer = Element->GetValue(); + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier ! return true; return false; @@ -316,7 +340,7 @@ bool gdcmDocument::CloseFile(void) { } /** - * \brief Writes in a file all the Doc Entries (Dicom Elements) + * \brief Writes in a file all the Header Entries (Dicom Elements) * of the Chained List * @param fp file pointer on an already open file * @param type Type of the File to be written @@ -328,7 +352,7 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { /// ============== /// The stuff will have to be rewritten using the SeQuence based /// tree-like stucture instead of the chained list . -/// (so we shall remove the GroupHT from the gdcmDocument) +/// (so we shall remove the Group*HT from the gdcmDocument) /// To be checked /// ============= @@ -344,7 +368,7 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { /// a moins de se livrer a un tres complique ajout des champs manquants. /// faire un CheckAndCorrectHeader (?) - if (type == ImplicitVR) + if (type == gdcmImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); @@ -357,7 +381,7 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { SetEntryLengthByNumber(18, 0x0002, 0x0010); } - if (type == ExplicitVR) + if (type == gdcmExplicitVR) { std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); @@ -390,27 +414,28 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { /** * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. - * \warning Adds the Header Entry to the HTable, NOT to the chained List * @param Value Value to be set - * @param Group Group of the Entry - * @param Elem Element of the Entry + * @param Group Group number of the Entry + * @param Elem Element number of the Entry * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ -gdcmHeaderEntry * gdcmDocument::ReplaceOrCreateByNumber( + + +gdcmDocEntry * gdcmDocument::ReplaceOrCreateByNumber( std::string Value, guint16 Group, guint16 Elem ){ - gdcmHeaderEntry* a; - a = GetHeaderEntryByNumber( Group, Elem); + gdcmDocEntry* a; + a = GetDocEntryByNumber( Group, Elem); if (a == NULL) { - a =NewHeaderEntryByNumber(Group, Elem); + a =NewDocEntryByNumber(Group, Elem); if (a == NULL) return NULL; - AddHeaderEntry(a); + AddEntry(a); } - //CLEANME SetEntryByNumber(Value, Group, Elem); - a->SetValue(Value); + SetEntryByNumber(Value, Group, Elem); + //a->SetValue(Value); return(a); } @@ -418,8 +443,8 @@ gdcmHeaderEntry * gdcmDocument::ReplaceOrCreateByNumber( * \brief Set a new value if the invoked element exists * Seems to be useless !!! * @param Value new element value - * @param Group group of the Entry - * @param Elem element of the Entry + * @param Group group number of the Entry + * @param Elem element number of the Entry * \return boolean */ bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) @@ -433,9 +458,8 @@ bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 El // Protected /** - * \brief Checks if a given Dicom Element exists - * within the H table - * @param group Group number of the searched Dicom Element + * \brief Checks if a given Dicom Element exists within the H table + * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element * @return number of occurences */ @@ -445,7 +469,7 @@ int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \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 @@ -462,7 +486,7 @@ std::string gdcmDocument::GetEntryByName(std::string tagName) { } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag. * @@ -479,18 +503,18 @@ std::string gdcmDocument::GetEntryVRByName(std::string tagName) { if( dictEntry == NULL) return GDCM_UNFOUND; - gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); + gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), + dictEntry->GetElement()); return elem->GetVR(); } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \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 of the searched tag. - * @param element Element of the searched tag. + * @param group Group number of the searched tag. + * @param element Element number of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -498,11 +522,11 @@ std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){ TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return GDCM_UNFOUND; - return tagHT.find(key)->second->GetValue(); + return ((gdcmValEntry *)tagHT.find(key)->second)->GetValue(); } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag.. * @@ -510,28 +534,28 @@ std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){ * 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 of the searched tag. - * @param element Element of the searched tag. + * @param group Group number of the searched tag. + * @param element Element number of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ std::string gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) { - gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element); + gdcmDocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) return GDCM_UNFOUND; return elem->GetVR(); } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \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 of the searched tag. - * @param element Element of the searched tag. + * @param group Group number of the searched tag. + * @param element Element number of the searched tag. * @return Corresponding element length; -2 if not found */ int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) { - gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element); + gdcmDocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) return -2; return elem->GetLength(); @@ -552,13 +576,12 @@ bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) { } /** - * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element) + * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. - * \warning Don't use any longer : use SetPubEntryByNumber * @param content new value to substitute with - * @param group group of the Dicom Element to modify - * @param element element of the Dicom Element to modify + * @param group group number of the Dicom Element to modify + * @param element element number of the Dicom Element to modify */ bool gdcmDocument::SetEntryByNumber(std::string content, guint16 group, @@ -574,18 +597,10 @@ bool gdcmDocument::SetEntryByNumber(std::string content, content = content + '\0'; } - gdcmHeaderEntry * a; - IterHT p; - TagHeaderEntryHT::iterator p2; - // DO NOT remove the following lines : they explain the stuff - //p= tagHT.equal_range(key); // get a pair of iterators first-last synonym - //p2=p.first; // iterator on the first synonym - //a=p2->second; // H Table target column (2-nd col) - - // or, easier : - a = ((tagHT.equal_range(key)).first)->second; - - a-> SetValue(content); + gdcmDocEntry * a; + a = tagHT[key]; + + ((gdcmValEntry*)a)->SetValue(content); std::string vr = a->GetVR(); @@ -602,14 +617,14 @@ bool gdcmDocument::SetEntryByNumber(std::string content, } /** - * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element) - * in the PubHeaderEntrySet of this instance + * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) + * in the PubDocEntrySet of this instance * through it's (group, element) and modifies it's length with * the given value. * \warning Use with extreme caution. * @param l new length to substitute with - * @param group group of the Entry to modify - * @param element element of the Entry to modify + * @param group group number of the Entry to modify + * @param element element number of the Entry to modify * @return true on success, false otherwise. */ bool gdcmDocument::SetEntryLengthByNumber(guint32 l, @@ -628,17 +643,17 @@ bool gdcmDocument::SetEntryLengthByNumber(guint32 l, /** * \brief Gets (from Header) the offset of a 'non string' element value * (LoadElementValues has already be executed) - * @param Group group of the Entry - * @param Elem element of the Entry + * @param Group group number of the Entry + * @param Elem element number of the Entry * @return File Offset of the Element Value */ size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) { - gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); + gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem); if (!Entry) { - dbg.Verbose(1, "gdcmDocument::GetHeaderEntryByNumber", - "failed to Locate gdcmHeaderEntry"); + dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber", + "failed to Locate gdcmDocEntry"); return (size_t)0; } return Entry->GetOffset(); @@ -647,31 +662,31 @@ size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) /** * \brief Gets (from Header) a 'non string' element value * (LoadElementValues has already be executed) - * @param Group group of the Entry - * @param Elem element of the Entry + * @param Group group number of the Entry + * @param Elem element number of the Entry * @return Pointer to the 'non string' area */ void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) { - gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); + gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem); if (!Entry) { - dbg.Verbose(1, "gdcmDocument::GetHeaderEntryByNumber", - "failed to Locate gdcmHeaderEntry"); + dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber", + "failed to Locate gdcmDocEntry"); return (NULL); } - return Entry->GetVoidArea(); + return ((gdcmBinEntry *)Entry)->GetVoidArea(); } /** * \brief Loads (from disk) the element content * when a string is not suitable - * @param Group group of the Entry - * @param Elem element of the Entry + * @param Group group number of the Entry + * @param Elem element number of the Entry */ void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem) { - gdcmHeaderEntry * Element= GetHeaderEntryByNumber(Group, Elem); + gdcmDocEntry * Element= GetDocEntryByNumber(Group, Elem); if ( !Element ) return NULL; size_t o =(size_t)Element->GetOffset(); @@ -696,7 +711,7 @@ void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem) /** * \brief Sets a 'non string' value to a given Dicom Element * @param area - * @param group Group number of the searched Dicom Element + * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element * @return */ @@ -707,7 +722,9 @@ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; - ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area); + // This was for multimap ? + (( gdcmBinEntry *)( ((tagHT.equal_range(key)).first)->second ))->SetVoidArea(area); + return true; } @@ -718,7 +735,9 @@ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, void gdcmDocument::UpdateShaEntries(void) { gdcmDictEntry *entry; std::string vr; - + + // TODO : if still any use (?) explore recursively the whole structure +/* for(ListTag::iterator it=listEntries.begin(); it!=listEntries.end(); ++it) @@ -738,13 +757,14 @@ void gdcmDocument::UpdateShaEntries(void) { else vr=(*it)->GetVR(); - (*it)->SetValue(GetHeaderEntryUnvalue(*it)); + (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling if(entry){ // Set the new entry and the new value (*it)->SetDictEntry(entry); - CheckHeaderEntryVR(*it,vr); + CheckDocEntryVR(*it,vr); - (*it)->SetValue(GetHeaderEntryValue(*it)); + (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling + } else { @@ -752,21 +772,22 @@ void gdcmDocument::UpdateShaEntries(void) { (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr)); } } +*/ } /** - * \brief Searches within the Doc Entries for a Dicom Element of + * \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. */ - gdcmHeaderEntry *gdcmDocument::GetHeaderEntryByName(std::string tagName) { + gdcmDocEntry *gdcmDocument::GetDocEntryByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return NULL; - return(GetHeaderEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); + return(GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); } /** @@ -779,7 +800,7 @@ void gdcmDocument::UpdateShaEntries(void) { * @param element Element number of the searched Dicom Element * @return */ -gdcmHeaderEntry* gdcmDocument::GetHeaderEntryByNumber(guint16 group, guint16 element) +gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element) { TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) @@ -787,146 +808,29 @@ gdcmHeaderEntry* gdcmDocument::GetHeaderEntryByNumber(guint16 group, guint16 ele return tagHT.find(key)->second; } -/** - * \brief retrieves the Dicom Elements (all of them) using (group, element) - * @param group Group number of the searched Dicom Element. - * @param element Element number of the searched Dicom Element. - * @return a range (i.e.pair<,>) containing all elements whose key is group|element) - */ - -IterHT gdcmDocument::GetHeaderEntrySameNumber(guint16 group, guint16 element){ - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - return (tagHT.equal_range(key)); -} - /** * \brief Loads the element while preserving the current * underlying file position indicator as opposed to - * to LoadHeaderEntry that modifies it. + * to LoadDocEntry that modifies it. * @param entry Header Entry whose value shall be loaded. * @return */ -void gdcmDocument::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) { +void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) { long PositionOnEntry = ftell(fp); - LoadHeaderEntry(entry); + LoadDocEntry(entry); fseek(fp, PositionOnEntry, SEEK_SET); } -/** - * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader - * \warning : to be re-written using the chained list instead of the H table. - * \warning : DO NOT use (doesn't work any longer because of the multimap) - * \todo : to be re-written using the chained list instead of the H table - * @param SkipSequence TRUE if we don't want to write Sequences (ACR-NEMA Files) - * @param type Type of the File (ExplicitVR,ImplicitVR, ACR, ...) - */ -void gdcmDocument::UpdateGroupLength(bool SkipSequence, FileType type) { - guint16 gr, el; - std::string vr; - - gdcmHeaderEntry *elem; - char trash[10]; - std::string str_trash; - - GroupKey key; - GroupHT groupHt; // to hold the length of each group - TagKey tk; - // remember : - // typedef std::map GroupHT; - - gdcmHeaderEntry *elemZ; - - // for each Tag in the DCM Header - - for (TagHeaderEntryHT::iterator tag2 = tagHT.begin(); - tag2 != tagHT.end(); - ++tag2) - { - elem = tag2->second; - gr = elem->GetGroup(); - el = elem->GetElement(); - vr = elem->GetVR(); - - sprintf(trash, "%04x", gr); - key = trash; // generate 'group tag' - - // if the caller decided not to take SEQUENCEs into account - // e.g : he wants to write an ACR-NEMA File - - if (SkipSequence && vr == "SQ") - continue; - - // Still unsolved problem : - // we cannot find the 'Sequence Delimitation Item' - // since it's at the end of the Hash Table - // (fffe,e0dd) - - // there is SEQUENCE in ACR-NEMA - // WARNING : - // --> la descente a l'interieur' des SQ - // devrait etre faite avec une liste chainee, pas avec une HTable... - - if ( groupHt.count(key) == 0) // we just read the first elem of a given group - { - if (el == 0x0000) // the first elem is 0x0000 - { - groupHt[key] = 0; // initialize group length - } - else - { - groupHt[key] = 2 + 2 + 4 + elem->GetLength(); // non 0x0000 first group elem - } - } - else // any elem but the first - { - if (type == ExplicitVR) - { - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) - { - groupHt[key] += 4; // explicit VR AND OB, OW, SQ : 4 more bytes - } - } - groupHt[key] += 2 + 2 + 4 + elem->GetLength(); - } - } - - unsigned short int gr_bid; - - for (GroupHT::iterator g = groupHt.begin(); // for each group we found - g != groupHt.end(); - ++g) - { - // FIXME: g++ -Wall -Wstrict-prototypes reports on following line: - // warning: unsigned int format, different type arg - sscanf(g->first.c_str(),"%x",&gr_bid); //FIXME - tk = g->first + "|0000"; // generate the element full tag - - if ( tagHT.count(tk) == 0) // if element 0x0000 not found - { - gdcmDictEntry * tagZ = new gdcmDictEntry(gr_bid, 0x0000, "UL"); - elemZ = new gdcmHeaderEntry(tagZ); - elemZ->SetLength(4); - AddHeaderEntry(elemZ); // create it - } - else - { - elemZ=GetHeaderEntryByNumber(gr_bid, 0x0000); - } - sprintf(trash ,"%d",g->second); - str_trash=trash; - elemZ->SetValue(str_trash); - } -} /** * \brief Writes in a file (according to the requested format) * the group, the element, the value representation and the length - * of a single gdcmHeaderEntry passed as argument. - * @param tag pointer on the gdcmHeaderEntry to be written + * of a single gdcmDocEntry passed as argument. + * @param tag pointer on the gdcmDocEntry to be written * @param _fp already open file pointer * @param type type of the File to be written */ -void gdcmDocument::WriteEntryTagVRLength(gdcmHeaderEntry *tag, +void gdcmDocument::WriteEntryTagVRLength(gdcmDocEntry *tag, FILE *_fp, FileType type) { @@ -944,7 +848,7 @@ void gdcmDocument::WriteEntryTagVRLength(gdcmHeaderEntry *tag, fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element - if ( type == ExplicitVR ) { + if ( type == gdcmExplicitVR ) { // Special case of delimiters: if (group == 0xfffe) { @@ -982,12 +886,15 @@ void gdcmDocument::WriteEntryTagVRLength(gdcmHeaderEntry *tag, /** * \brief Writes in a file (according to the requested format) - * the value of a single gdcmHeaderEntry passed as argument. - * @param tag Pointer on the gdcmHeaderEntry to be written + * the value of a single gdcmDocEntry passed as argument. + * @param tag Pointer on the gdcmDocEntry to be written * @param _fp Already open file pointer * @param type type of the File to be written */ -void gdcmDocument::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) + + // TODO : to be re -written recursively ! + +void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type) { (void)type; guint16 group = tag->GetGroup(); @@ -1000,15 +907,23 @@ void gdcmDocument::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type if (group == 0xfffe) // Delimiters have no associated value: return; - + + //-------------------------------- + // + // FIXME + // + // ------------------------------- + + +/* // to go on compiling void *voidArea; - voidArea = tag->GetVoidArea(); + voidArea = tag->GetVoidArea(); // to go on compiling if (voidArea != NULL) { // there is a 'non string' LUT, overlay, etc fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value return; } - +*/ if (vr == "US" || vr == "SS") { // some 'Short integer' fields may be mulivaluated @@ -1016,7 +931,7 @@ void gdcmDocument::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type // we split the string and write each value as a short int std::vector tokens; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (tag->GetValue(), tokens, "\\"); + Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\"); for (unsigned int i=0; i tokens; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (tag->GetValue(), tokens, "\\"); + Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\"); for (unsigned int i=0; iGetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value + fwrite (((gdcmValEntry *)tag)->GetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value } /** * \brief Writes in a file (according to the requested format) - * a single gdcmHeaderEntry passed as argument. + * a single gdcmDocEntry passed as argument. * \sa WriteEntryValue, WriteEntryTagVRLength. - * @param tag Pointer on the gdcmHeaderEntry to be written + * @param tag Pointer on the gdcmDocEntry to be written * @param _fp Already open file pointer * @param type type of the File to be written */ -bool gdcmDocument::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type) +bool gdcmDocument::WriteEntry(gdcmDocEntry *tag, FILE *_fp,FileType type) { guint32 length = tag->GetLength(); - + gdcmValEntry * Vtag = (gdcmValEntry *) tag; +std::cout << "gdcmDocument::WriteEntry Vtag->GetValue() " << Vtag->GetValue() << std::endl; // The value of a tag MUST (see the DICOM norm) be an odd number of // bytes. When this is not the case, pad with an additional byte: if(length%2==1) { - tag->SetValue(tag->GetValue()+"\0"); - tag->SetLength(tag->GetReadLength()+1); + Vtag->SetValue(Vtag->GetValue()+"\0"); + Vtag->SetLength(Vtag->GetReadLength()+1); } - WriteEntryTagVRLength(tag, _fp, type); - WriteEntryValue(tag, _fp, type); + WriteEntryTagVRLength(Vtag, _fp, type); + std::cout << "after WriteEntryTagVRLength " << std::endl; + WriteEntryValue(Vtag, _fp, type); + std::cout << "after WriteEntryValue " << std::endl; return true; } @@ -1081,71 +999,48 @@ bool gdcmDocument::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type) * (function CheckHeaderCoherence to be written) * \warning DON'T try, right now, to write a DICOM image * from an ACR Header (meta elements will be missing!) - * \sa WriteEntriesDeprecated (Special temporary method for Theralys) * @param type type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) * @param _fp already open file pointer */ bool gdcmDocument::WriteEntries(FILE *_fp,FileType type) -{ +{ + +// FIXME : explore recursively the whole structure... + /// \todo (?) check write failures (after *each* fwrite) - - for (ListTag::iterator tag2=listEntries.begin(); - tag2 != listEntries.end(); - ++tag2) + + std::cout << "--------------------- gdcmDocument::WriteEntries " << std::endl; + for (TagDocEntryHT::iterator tag2=tagHT.begin(); + tag2 != tagHT.end(); + ++tag2) { - if ( type == ACR ){ - if ((*tag2)->GetGroup() < 0x0008) + + (*tag2).second->Print(); + + if ( type == gdcmACR ){ + if ((*tag2).second->GetGroup() < 0x0008) // Ignore pure DICOM V3 groups continue; - if ((*tag2)->GetElement() %2) + if ((*tag2).second->GetGroup() %2) // Ignore the "shadow" groups continue; - if ((*tag2)->GetVR() == "SQ" ) // ignore Sequences + if ((*tag2).second->GetVR() == "SQ" ) // ignore Sequences continue; - if ((*tag2)->GetSQDepthLevel() != 0) // Not only ignore the SQ element - continue; + //if ((*tag2).second->GetDepthLevel() != 0) // Not only ignore the SQ element + // continue; } - if (! WriteEntry(*tag2,_fp,type) ) + if (! WriteEntry((*tag2).second,_fp,type) ) { + std::cout << "Write Failure " << std::endl; return false; + } else { + + } } return true; } -/** - * \brief writes on disc according to the requested format - * (ACR-NEMA, ExplicitVR, ImplicitVR) the image, - * using only the last synonym of each mutimap H Table post. - * \warning Uses the H Table, instead of the Chained List - * in order to be compliant with the old way to proceed - * (added elements taken in to account) - * Only THERALYS, during a transitory phase is supposed - * to use this method !!! - * \warning DON'T try, right now, to write a DICOM image - * from an ACR Header (meta elements will be missing!) - * \sa WriteEntries - * @param _fp already open file pointer - * @param type type of the File to be written - * (ACR-NEMA, ExplicitVR, ImplicitVR) - */ -void gdcmDocument::WriteEntriesDeprecated(FILE *_fp,FileType type) { - - // restent a tester les echecs en ecriture (apres chaque fwrite) - - for (TagHeaderEntryHT::iterator tag2=tagHT.begin(); - tag2 != tagHT.end(); - ++tag2){ - if ( type == ACR ){ - if ((*tag2->second).GetGroup() < 0x0008) continue; // ignore pure DICOM V3 groups - if ((*tag2->second).GetElement() %2) continue; // ignore shadow groups - if ((*tag2->second).GetVR() == "SQ" ) continue; // ignore Sequences - if ((*tag2->second).GetSQDepthLevel() != 0) continue; // Not only ignore the SQ element - } - if ( ! WriteEntry(tag2->second,_fp,type)) - break; - } -} /** * \brief Swaps back the bytes of 4-byte long integer accordingly to @@ -1169,6 +1064,7 @@ guint32 gdcmDocument::SwapLong(guint32 a) { a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); break; default : + std::cout << "swapCode= " << sw << std::endl; dbg.Error(" gdcmDocument::SwapLong : unset swap code"); a=0; } @@ -1205,12 +1101,163 @@ guint16 gdcmDocument::UnswapShort(guint16 a) { //----------------------------------------------------------------------------- // Private +/** + * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) + * @return false if file is not ACR-NEMA / PAPYRUS / DICOM + */ + +long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) { + + gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; + gdcmValEntry *vl; + gdcmBinEntry *bn; + gdcmSeqEntry *sq; + VRKey vr; + long l; + int depth; + + depth = set->GetDepthLevel(); + while (true) { + + if ( !delim_mode && ftell(fp)-offset >= l_max) { + break; + } + NewDocEntry = ReadNextDocEntry( ); + if (!NewDocEntry) + break; + + vr = NewDocEntry->GetVR(); + if (vr!="SQ") { + + if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) ) + { + /////// ValEntry + vl= new gdcmValEntry(NewDocEntry->GetDictEntry()); + vl->Copy(NewDocEntry); + vl->SetDepthLevel(depth); + set->AddEntry(vl); + LoadDocEntry(vl); + if (/*!delim_mode && */vl->isItemDelimitor()) + break; + if ( !delim_mode && ftell(fp)-offset >= l_max) + { + break; + } + } + else + { + if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) + { + ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR + dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, " + "nor BinEntry. Probably unknown VR."); + } + + ////// BinEntry or UNKOWN VR: + bn = new gdcmBinEntry(NewDocEntry->GetDictEntry()); + bn->Copy(NewDocEntry); + set->AddEntry(bn); + LoadDocEntry(bn); + } + + if (NewDocEntry->GetGroup() == 0x7fe0 && + NewDocEntry->GetElement() == 0x0010 ) + { + if (NewDocEntry->GetLength()==0xffffffff) + // Broken US.3405.1.dcm + Parse7FE0(); // to skip the pixels + // (multipart JPEG/RLE are trouble makers) + } + else + { + // to be sure we are at the beginning + SkipToNextDocEntry(NewDocEntry); + l = NewDocEntry->GetFullLength(); + } + } else { // VR = "SQ" + + l=NewDocEntry->GetReadLength(); + if (l != 0) // don't mess the delim_mode for zero-length sequence + if (l == 0xffffffff) + delim_mode = true; + else + delim_mode = false; + // no other way to create it ... + sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry(), + set->GetDepthLevel()); + sq->Copy(NewDocEntry); + sq->SetDelimitorMode(delim_mode); + sq->SetDepthLevel(depth); + + if (l != 0) + { // Don't try to parse zero-length sequences + long lgt = ParseSQ( sq, + NewDocEntry->GetOffset(), + l, delim_mode); + } + // FIXME : on en fait quoi, de lgt ? + set->AddEntry(sq); + if ( !delim_mode && ftell(fp)-offset >= l_max) + { + break; + } + } + } + delete NewDocEntry; + return l; // ?? +} + +/** + * \brief Parses a Sequence ( SeqEntry after SeqEntry) + * @return parsed length for this level + */ +long gdcmDocument::ParseSQ(gdcmSeqEntry *set, long offset, long l_max, bool delim_mode) { + int SQItemNumber = 0; + gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; + gdcmSQItem *itemSQ; + bool dlm_mod; + int lgr, l, lgth; + int depth = set->GetDepthLevel(); + while (true) { + + NewDocEntry = ReadNextDocEntry(); + if(delim_mode) { + if (NewDocEntry->isSequenceDelimitor()) { + //add the Sequence Delimitor // TODO : find the trick to put it properly ! + set->SetSequenceDelimitationItem(NewDocEntry); + break; + } + } + if (!delim_mode && (ftell(fp)-offset) >= l_max) { + break; + } + itemSQ = new gdcmSQItem(set->GetDepthLevel()); + itemSQ->AddEntry(NewDocEntry); // no value, no voidArea. Think of it while printing ! + l= NewDocEntry->GetReadLength(); + + if (l ==0xffffffff) + dlm_mod = true; + else + dlm_mod=false; + + lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod); + + set->AddEntry(itemSQ); + SQItemNumber ++; // a voir + if (!delim_mode && (ftell(fp)-offset) >= l_max) { + break; + } + } + lgth = ftell(fp) - offset; + return(lgth); +} + /** * \brief Loads the element content if its length doesn't exceed * the value specified with gdcmDocument::SetMaxSizeLoadEntry() * @param Entry Header Entry (Dicom Element) to be dealt with */ -void gdcmDocument::LoadHeaderEntry(gdcmHeaderEntry *Entry) { +void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) { size_t item_read; guint16 group = Entry->GetGroup(); std::string vr= Entry->GetVR(); @@ -1223,13 +1270,16 @@ void gdcmDocument::LoadHeaderEntry(gdcmHeaderEntry *Entry) { // (fffe e00d) tells us an Element just ended // (fffe e0dd) tells us the current SeQuence just ended if( group == 0xfffe ) { - Entry->SetValue("gdcm::Skipped"); + // NO more value field for SQ ! + //Entry->SetValue("gdcm::Skipped"); + // appel recursif de Load Value + // (meme pb que pour le parsing) return; } // When the length is zero things are easy: if ( length == 0 ) { - Entry->SetValue(""); + ((gdcmValEntry *)Entry)->SetValue(""); return; } @@ -1237,17 +1287,23 @@ void gdcmDocument::LoadHeaderEntry(gdcmHeaderEntry *Entry) { // are not loaded. Instead we leave a short notice of the offset of // the element content and it's length. if (length > MaxSizeLoadEntry) { - std::ostringstream s; - s << "gdcm::NotLoaded."; - s << " Address:" << (long)Entry->GetOffset(); - s << " Length:" << Entry->GetLength(); - s << " x(" << std::hex << Entry->GetLength() << ")"; - Entry->SetValue(s.str()); + if (gdcmValEntry* ValEntryPtr = dynamic_cast< gdcmValEntry* >(Entry) ) + { + std::ostringstream s; + s << "gdcm::NotLoaded."; + s << " Address:" << (long)Entry->GetOffset(); + s << " Length:" << Entry->GetLength(); + s << " x(" << std::hex << Entry->GetLength() << ")"; + ValEntryPtr->SetValue(s.str()); + } + // to be sure we are at the end of the value ... + fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET); + return; } // Any compacter code suggested (?) - if ( IsHeaderEntryAnInteger(Entry) ) { + if ( IsDocEntryAnInteger(Entry) ) { guint32 NewInt; std::ostringstream s; int nbInt; @@ -1287,7 +1343,7 @@ void gdcmDocument::LoadHeaderEntry(gdcmHeaderEntry *Entry) { s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM - Entry->SetValue(s.str()); + ((gdcmValEntry *)Entry)->SetValue(s.str()); return; } @@ -1296,43 +1352,29 @@ void gdcmDocument::LoadHeaderEntry(gdcmHeaderEntry *Entry) { item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp); if ( item_read != 1 ) { dbg.Verbose(1, "gdcmDocument::LoadElementValue","unread element value"); - Entry->SetValue("gdcm::UnRead"); + ((gdcmValEntry *)Entry)->SetValue("gdcm::UnRead"); return; } if( (vr == "UI") ) // Because of correspondance with the VR dic - Entry->SetValue(NewValue.c_str()); + ((gdcmValEntry *)Entry)->SetValue(NewValue.c_str()); else - Entry->SetValue(NewValue); + ((gdcmValEntry *)Entry)->SetValue(NewValue); } -/** - * \brief add a new Dicom Element pointer to - * the H Table and at the end of the chained List - * \warning push_bash in listEntries ONLY during ParseHeader - * \todo something to allow further Elements addition, - * (at their right place in the chained list) - * when position to be taken care of - * @param newHeaderEntry - */ -void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { - tagHT.insert( PairHT( newHeaderEntry->GetKey(),newHeaderEntry) ); - listEntries.push_back(newHeaderEntry); - wasUpdated = 1; -} /** * \brief Find the value Length of the passed Header Entry * @param Entry Header Entry whose length of the value shall be loaded. */ - void gdcmDocument::FindHeaderEntryLength (gdcmHeaderEntry *Entry) { + void gdcmDocument::FindDocEntryLength (gdcmDocEntry *Entry) { guint16 element = Entry->GetElement(); //guint16 group = Entry->GetGroup(); //FIXME std::string vr = Entry->GetVR(); guint16 length16; - if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) ) + if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) ) { if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { @@ -1344,10 +1386,10 @@ void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { if ( (vr == "OB") && (length32 == 0xffffffff) ) { - Entry->SetLength(FindHeaderEntryLengthOB()); + Entry->SetLength(FindDocEntryLengthOB()); return; } - FixHeaderEntryFoundLength(Entry, length32); + FixDocEntryFoundLength(Entry, length32); return; } @@ -1416,7 +1458,7 @@ void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { // Actually, length= 0xffff means that we deal with // Unknown Sequence Length } - FixHeaderEntryFoundLength(Entry, (guint32)length16); + FixDocEntryFoundLength(Entry, (guint32)length16); return; } else @@ -1428,7 +1470,7 @@ void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. - FixHeaderEntryFoundLength(Entry, ReadInt32()); + FixDocEntryFoundLength(Entry, ReadInt32()); return; } } @@ -1437,9 +1479,9 @@ void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { * \brief Find the Value Representation of the current Dicom Element. * @param Entry */ -void gdcmDocument::FindHeaderEntryVR( gdcmHeaderEntry *Entry) +void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry) { - if (filetype != ExplicitVR) + if (filetype != gdcmExplicitVR) return; char VR[3]; @@ -1455,7 +1497,7 @@ void gdcmDocument::FindHeaderEntryVR( gdcmHeaderEntry *Entry) (void)fread (&VR, (size_t)2,(size_t)1, fp); VR[2]=0; - if(!CheckHeaderEntryVR(Entry,VR)) + if(!CheckDocEntryVR(Entry,VR)) { fseek(fp, PositionOnEntry, SEEK_SET); // When this element is known in the dictionary we shall use, e.g. for @@ -1478,7 +1520,7 @@ void gdcmDocument::FindHeaderEntryVR( gdcmHeaderEntry *Entry) * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ -bool gdcmDocument::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr) +bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, VRKey vr) { char msg[100]; // for sprintf bool RealExplicit = true; @@ -1547,11 +1589,11 @@ bool gdcmDocument::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr) * @param Entry * @return Transformed entry value */ -std::string gdcmDocument::GetHeaderEntryValue(gdcmHeaderEntry *Entry) +std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry) { - if ( (IsHeaderEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) + if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) { - std::string val=Entry->GetValue(); + std::string val=((gdcmValEntry *)Entry)->GetValue(); std::string vr=Entry->GetVR(); guint32 length = Entry->GetLength(); std::ostringstream s; @@ -1606,7 +1648,7 @@ std::string gdcmDocument::GetHeaderEntryValue(gdcmHeaderEntry *Entry) return(s.str()); } - return(Entry->GetValue()); + return(((gdcmValEntry *)Entry)->GetValue()); } /** @@ -1617,9 +1659,9 @@ std::string gdcmDocument::GetHeaderEntryValue(gdcmHeaderEntry *Entry) * @param Entry * @return Reverse transformed entry value */ -std::string gdcmDocument::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry) +std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry) { - if ( (IsHeaderEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) + if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) { std::string vr=Entry->GetVR(); std::ostringstream s; @@ -1630,7 +1672,7 @@ std::string gdcmDocument::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry) guint16 NewInt16; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (Entry->GetValue(), tokens, "\\"); + Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\"); for (unsigned int i=0; iGetValue(), tokens, "\\"); + Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\"); for (unsigned int i=0; iGetValue()); + return(((gdcmValEntry *)Entry)->GetValue()); } /** @@ -1667,17 +1709,38 @@ std::string gdcmDocument::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry) * \warning NOT end user intended method ! * @param entry */ -void gdcmDocument::SkipHeaderEntry(gdcmHeaderEntry *entry) +void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) { - SkipBytes(entry->GetLength()); + SkipBytes(entry->GetLength()); } +/** + * \brief Skips to the begining of the next Header Entry + * \warning NOT end user intended method ! + * @param entry + */ +void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) +{ + (void)fseek(fp, (long)(entry->GetOffset()), SEEK_SET); + (void)fseek(fp, (long)(entry->GetReadLength()), SEEK_CUR); +} + +/** + * \brief Loads the value for a a given VLEntry + * \warning NOT end user intended method ! + * @param entry + */ +void gdcmDocument::LoadVLEntry(gdcmDocEntry *entry) +{ + //SkipBytes(entry->GetLength()); + LoadDocEntry(entry); +} /** * \brief When the length of an element value is obviously wrong (because * the parser went Jabberwocky) one can hope improving things by * applying this heuristic. */ -void gdcmDocument::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 FoundLength) +void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, guint32 FoundLength) { Entry->SetReadLength(FoundLength); // will be updated only if a bug is found if ( FoundLength == 0xffffffff) { @@ -1742,7 +1805,7 @@ void gdcmDocument::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Fou * @param Entry The element value on which to apply the predicate. * @return The result of the heuristical predicate. */ -bool gdcmDocument::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { +bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { guint16 element = Entry->GetElement(); guint16 group = Entry->GetGroup(); std::string vr = Entry->GetVR(); @@ -1770,7 +1833,7 @@ bool gdcmDocument::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { // instead of giving up with an error message //std::cout << s.str().c_str() << std::endl; - // dbg.Error("gdcmDocument::IsHeaderEntryAnInteger", + // dbg.Error("gdcmDocument::IsDocEntryAnInteger", // s.str().c_str()); } } @@ -1785,7 +1848,7 @@ bool gdcmDocument::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { * @return */ - guint32 gdcmDocument::FindHeaderEntryLengthOB(void) { + guint32 gdcmDocument::FindDocEntryLengthOB(void) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. guint16 g; guint16 n; @@ -1960,13 +2023,13 @@ bool gdcmDocument::CheckSwap() { // Use gdcmDocument::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? group 0000 { - filetype = ExplicitVR; + filetype = gdcmExplicitVR; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "explicit Value Representation"); } else { - filetype = ImplicitVR; + filetype = gdcmImplicitVR; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not an explicit Value Representation"); } @@ -2011,19 +2074,19 @@ bool gdcmDocument::CheckSwap() { switch (s32) { case 0x00040000 : sw = 3412; - filetype = ACR; + filetype = gdcmACR; return true; case 0x04000000 : sw = 4321; - filetype = ACR; + filetype = gdcmACR; return true; case 0x00000400 : sw = 2143; - filetype = ACR; + filetype = gdcmACR; return true; case 0x00000004 : sw = 0; - filetype = ACR; + filetype = gdcmACR; return true; default : @@ -2049,18 +2112,18 @@ bool gdcmDocument::CheckSwap() { case 0x0004 : case 0x0008 : sw = 0; - filetype = ACR; + filetype = gdcmACR; return true; case 0x0200 : case 0x0400 : case 0x0800 : sw = 4321; - filetype = ACR; + filetype = gdcmACR; return true; default : dbg.Verbose(0, "gdcmDocument::CheckSwap:", "ACR/NEMA unfound swap info (Really hopeless !)"); - filetype = Unknown; + filetype = gdcmUnknown; return false; } @@ -2134,98 +2197,42 @@ void gdcmDocument::SetMaxSizePrintEntry(long NewSize) MaxSizePrintEntry = NewSize; } -/** - * \brief Searches both the public and the shadow dictionary (when they - * exist) for the presence of the DictEntry with given name. - * The public dictionary has precedence on the shadow one. - * @param Name name of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. - */ -gdcmDictEntry *gdcmDocument::GetDictEntryByName(std::string Name) -{ - gdcmDictEntry *found = (gdcmDictEntry *)0; - if (!RefPubDict && !RefShaDict) - { - dbg.Verbose(0, "gdcmDocument::GetDictEntry", - "we SHOULD have a default dictionary"); - } - if (RefPubDict) - { - found = RefPubDict->GetDictEntryByName(Name); - if (found) - return found; - } - if (RefShaDict) - { - found = RefShaDict->GetDictEntryByName(Name); - if (found) - return found; - } - return found; -} -/** - * \brief Searches both the public and the shadow dictionary (when they - * exist) for the presence of the DictEntry with given - * group and element. The public dictionary has precedence on the - * shadow one. - * @param group group of the searched DictEntry - * @param element element of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. - */ -gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element) -{ - gdcmDictEntry *found = (gdcmDictEntry *)0; - if (!RefPubDict && !RefShaDict) - { - dbg.Verbose(0, "gdcmDocument::GetDictEntry", - "we SHOULD have a default dictionary"); - } - if (RefPubDict) - { - found = RefPubDict->GetDictEntryByNumber(group, element); - if (found) - return found; - } - if (RefShaDict) - { - found = RefShaDict->GetDictEntryByNumber(group, element); - if (found) - return found; - } - return found; -} /** * \brief Read the next tag but WITHOUT loading it's value - * @return On succes the newly created HeaderEntry, NULL on failure. + * (read the 'Group Number', the 'Element Number', + * gets the Dict Entry + * gets the VR, gets the length, gets the offset value) + * @return On succes the newly created DocEntry, NULL on failure. */ -gdcmHeaderEntry *gdcmDocument::ReadNextHeaderEntry(void) { +gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) { guint16 g,n; - gdcmHeaderEntry *NewEntry; + gdcmDocEntry *NewEntry; g = ReadInt16(); n = ReadInt16(); if (errno == 1) // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. - return (gdcmHeaderEntry *)0; + return (gdcmDocEntry *)0; -// Pb : how to propagate the element length (used in SkipHeaderEntry) +// Pb : how to propagate the element length (used in SkipDocEntry) // direct call to SkipBytes ? // if (ignoreShadow == 1 && g%2 ==1) // if user wants to skip shadow groups // and current element *is* a shadow element // we don't create anything -// return (gdcmHeaderEntry *)1; // to tell caller it's NOT finished +// return (gdcmDocEntry *)1; // to tell caller it's NOT finished - NewEntry = NewHeaderEntryByNumber(g, n); - FindHeaderEntryVR(NewEntry); - FindHeaderEntryLength(NewEntry); + NewEntry = NewDocEntryByNumber(g, n); + FindDocEntryVR(NewEntry); + FindDocEntryLength(NewEntry); if (errno == 1) { // Call it quits + delete NewEntry; return NULL; } NewEntry->SetOffset(ftell(fp)); @@ -2238,26 +2245,26 @@ gdcmHeaderEntry *gdcmDocument::ReadNextHeaderEntry(void) { * a default one when absent. * @param Name Name of the underlying DictEntry */ -gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByName(std::string Name) +gdcmDocEntry *gdcmDocument::NewDocEntryByName(std::string Name) { gdcmDictEntry *NewTag = GetDictEntryByName(Name); if (!NewTag) NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name); - gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag); + gdcmDocEntry* NewEntry = new gdcmDocEntry(NewTag); if (!NewEntry) { - dbg.Verbose(1, "gdcmDocument::ObtainHeaderEntryByName", - "failed to allocate gdcmHeaderEntry"); - return (gdcmHeaderEntry *)0; + dbg.Verbose(1, "gdcmDocument::ObtainDocEntryByName", + "failed to allocate gdcmDocEntry"); + return (gdcmDocEntry *)0; } return NewEntry; } /** * \brief Request a new virtual dict entry to the dict set - * @param group group of the underlying DictEntry - * @param element element of the underlying DictEntry + * @param group group number of the underlying DictEntry + * @param element element number of the underlying DictEntry * @param vr VR of the underlying DictEntry * @param fourth owner group * @param name english name @@ -2274,21 +2281,21 @@ gdcmDictEntry *gdcmDocument::NewVirtualDictEntry(guint16 group, guint16 element, * \brief Build a new Element Value from all the low level arguments. * Check for existence of dictionary entry, and build * a default one when absent. - * @param Group group of the underlying DictEntry - * @param Elem element of the underlying DictEntry + * @param Group group number of the underlying DictEntry + * @param Elem element number of the underlying DictEntry */ -gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) +gdcmDocEntry *gdcmDocument::NewDocEntryByNumber(guint16 Group, guint16 Elem) { // Find out if the tag we encountered is in the dictionaries: gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); if (!DictEntry) DictEntry = NewVirtualDictEntry(Group, Elem); - gdcmHeaderEntry *NewEntry = new gdcmHeaderEntry(DictEntry); + gdcmDocEntry *NewEntry = new gdcmDocEntry(DictEntry); if (!NewEntry) { - dbg.Verbose(1, "gdcmDocument::NewHeaderEntryByNumber", - "failed to allocate gdcmHeaderEntry"); + dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber", + "failed to allocate gdcmDocEntry"); return NULL; } return NewEntry; @@ -2297,17 +2304,17 @@ gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByNumber(guint16 Group, guint16 Ele /// \todo Never used; commented out, waiting for removal. /** * \brief Small utility function that creates a new manually crafted - * (as opposed as read from the file) gdcmHeaderEntry with user + * (as opposed as read from the file) gdcmDocEntry with user * specified name and adds it to the public tag hash table. * \note A fake TagKey is generated so the PubDict can keep it's coherence. * @param NewTagName The name to be given to this new tag. * @param VR The Value Representation to be given to this new tag. * @return The newly hand crafted Element Value. */ -//gdcmHeaderEntry *gdcmDocument::NewManualHeaderEntryToPubDict(std::string NewTagName, +//gdcmDocEntry *gdcmDocument::NewManualDocEntryToPubDict(std::string NewTagName, // std::string VR) //{ -// gdcmHeaderEntry *NewEntry = NULL; +// gdcmDocEntry *NewEntry = NULL; // guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info // guint32 FreeElem = 0; // gdcmDictEntry *DictEntry = NULL; @@ -2315,15 +2322,15 @@ gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByNumber(guint16 Group, guint16 Ele // FreeElem = GenerateFreeTagKeyInGroup(StuffGroup); // if (FreeElem == UINT32_MAX) // { -// dbg.Verbose(1, "gdcmHeader::NewManualHeaderEntryToPubDict", +// dbg.Verbose(1, "gdcmHeader::NewManualDocEntryToPubDict", // "Group 0xffff in Public Dict is full"); // return NULL; // } // // DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem, // VR, "GDCM", NewTagName); -// NewEntry = new gdcmHeaderEntry(DictEntry); -// AddHeaderEntry(NewEntry); +// NewEntry = new gdcmDocEntry(DictEntry); +// AddEntry(NewEntry); // return NewEntry; //} @@ -2344,4 +2351,276 @@ guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group) return UINT32_MAX; } + +/** + * \brief Searches both the public and the shadow dictionary (when they + * exist) for the presence of the DictEntry with given name. + * The public dictionary has precedence on the shadow one. + * @param Name name of the searched DictEntry + * @return Corresponding DictEntry when it exists, NULL otherwise. + */ +gdcmDictEntry *gdcmDocument::GetDictEntryByName(std::string Name) +{ + gdcmDictEntry *found = (gdcmDictEntry *)0; + if (!RefPubDict && !RefShaDict) + { + dbg.Verbose(0, "gdcmDocument::GetDictEntry", + "we SHOULD have a default dictionary"); + } + if (RefPubDict) + { + found = RefPubDict->GetDictEntryByName(Name); + if (found) + return found; + } + if (RefShaDict) + { + found = RefShaDict->GetDictEntryByName(Name); + if (found) + return found; + } + return found; +} + +/** + * \brief Searches both the public and the shadow dictionary (when they + * exist) for the presence of the DictEntry with given + * group and element. The public dictionary has precedence on the + * shadow one. + * @param group group of the searched DictEntry + * @param element element of the searched DictEntry + * @return Corresponding DictEntry when it exists, NULL otherwise. + */ +gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element) +{ + gdcmDictEntry *found = (gdcmDictEntry *)0; + if (!RefPubDict && !RefShaDict) + { + dbg.Verbose(0, "gdcmDocument::GetDictEntry", + "we SHOULD have a default dictionary"); + } + if (RefPubDict) + { + found = RefPubDict->GetDictEntryByNumber(group, element); + if (found) + return found; + } + if (RefShaDict) + { + found = RefShaDict->GetDictEntryByNumber(group, element); + if (found) + return found; + } + return found; +} + + +/** + * \ingroup gdcmDocument + * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files + * \ No other way so 'skip' the Data + * + */ +void gdcmDocument::Parse7FE0 (void) { + + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return; + + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); + if (Transfer == UI1_2_840_10008_1_2 ) + return; + if ( Transfer == UI1_2_840_10008_1_2_1 ) + return; + if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier ! + return; + if ( Transfer == UI1_2_840_10008_1_2_1_99 ) + return; + + int nb; + std::string str_nb=GetEntryByNumber(0x0028,0x0100); + if (str_nb == GDCM_UNFOUND ) { + nb = 16; + } else { + nb = atoi(str_nb.c_str() ); + if (nb == 12) nb =16; + } + + guint16 ItemTagGr,ItemTagEl; + int ln; + long ftellRes; + + // -------------------- for Parsing : Position on begining of Jpeg/RLE Pixels + + if ( Transfer != UI1_1_2_840_10008_1_2_5 ) { // !RLELossLessTransferSyntax + // JPEG Image + ftellRes=ftell(fp); + fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr + fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El + if(GetSwapCode()) { + ItemTagGr=SwapShort(ItemTagGr); + ItemTagEl=SwapShort(ItemTagEl); + } + printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n", + (unsigned)ftellRes,ItemTagGr,ItemTagEl ); + ftellRes=ftell(fp); + fread(&ln,4,1,fp); + if(GetSwapCode()) + ln=SwapLong(ln); // Basic Offset Table Item Length + printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n", + (unsigned)ftellRes,ln,ln); + if (ln != 0) { + // What is it used for ?? + char * BasicOffsetTableItemValue= new char[ln+1]; + fread(BasicOffsetTableItemValue,ln,1,fp); + guint32 a; + for (int i=0;i1) { // skipping (not reading) RLE Segments + for(unsigned int k=1; k<=nbRleSegments-1; k++) { + RleSegmentLength[k]= RleSegmentOffsetTable[k+1] + - RleSegmentOffsetTable[k]; + ftellRes=ftell(fp); + printf (" Segment %d : Length = %d x(%x) Start at %x\n", + k,(unsigned)RleSegmentLength[k],(unsigned)RleSegmentLength[k], (unsigned)ftellRes); + fseek(fp,RleSegmentLength[k],SEEK_CUR); + } + } + RleSegmentLength[nbRleSegments]= fragmentLength + - RleSegmentOffsetTable[nbRleSegments]; + ftellRes=ftell(fp); + printf (" Segment %d : Length = %d x(%x) Start at %x\n", + nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments], + (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes); + + fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR); + + // ------------------ end of scanning fragment pixels + + ftellRes=ftell(fp); + fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr + fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El + if(GetSwapCode()) { + ItemTagGr=SwapShort(ItemTagGr); + ItemTagEl=SwapShort(ItemTagEl); + } + printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n", + (unsigned)ftellRes,ItemTagGr,ItemTagEl ); + } + } + return; +} + + + //-----------------------------------------------------------------------------