X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=e29c08bfc24dd287b2ecbacc27528ac6955d67ea;hb=65f457a97152fce4878d7aa20ec02f4ccda20705;hp=4af6b8f09ac7c4985863f694e8e3935973135b8f;hpb=0b36f4932e894a1dde4a80e614755816b4b29218;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 4af6b8f0..e29c08bf 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -1,7 +1,26 @@ -// gdcmDocument.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDocument.cxx,v $ + Language: C++ + Date: $Date: 2004/06/23 15:01:57 $ + Version: $Revision: 1.29 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ #include "gdcmDocument.h" +#include "gdcmValEntry.h" +#include "gdcmBinEntry.h" +#include "gdcmSeqEntry.h" + #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" @@ -18,15 +37,37 @@ # include +// Implicit VR Little Endian #define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" +// Explicit VR Little Endian #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" +// Deflated Explicit VR Little Endian #define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" - -typedef struct { - guint32 totalSQlength; - guint32 alreadyParsedlength; -} pileElem; +// Explicit VR Big Endian +#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2" +// JPEG Baseline (Process 1) +#define UI1_2_840_10008_1_2_4_50 "1.2.840.10008.1.2.4.50" +// JPEG Extended (Process 2 & 4) +#define UI1_2_840_10008_1_2_4_51 "1.2.840.10008.1.2.4.51" +// JPEG Extended (Process 3 & 5) +#define UI1_2_840_10008_1_2_4_52 "1.2.840.10008.1.2.4.52" +// JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8) +#define UI1_2_840_10008_1_2_4_53 "1.2.840.10008.1.2.4.53" +// JPEG Full Progression, Non-Hierarchical (Process 10 & 12) +#define UI1_2_840_10008_1_2_4_55 "1.2.840.10008.1.2.4.55" +// JPEG Lossless, Non-Hierarchical (Process 14) +#define UI1_2_840_10008_1_2_4_57 "1.2.840.10008.1.2.4.57" +// JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, +// [Selection Value 1]) +#define UI1_2_840_10008_1_2_4_70 "1.2.840.10008.1.2.4.70" +// JPEG 2000 Lossless +#define UI1_2_840_10008_1_2_4_90 "1.2.840.10008.1.2.4.90" +// JPEG 2000 +#define UI1_2_840_10008_1_2_4_91 "1.2.840.10008.1.2.4.91" +// RLE Lossless +#define UI1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5" +// UI1_1_2_840_10008_1_2_5 +#define str2num(str, typeNum) *((typeNum *)(str)) //----------------------------------------------------------------------------- // Refer to gdcmDocument::CheckSwap() @@ -54,24 +95,78 @@ const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; * with a FALSE value for the 'enable_sequence' param. * ('public elements' may be embedded in 'shadow Sequences') */ -gdcmDocument::gdcmDocument(const char *inFilename, - bool exception_on_error, - bool enable_sequences, - bool ignore_shadow) { +gdcmDocument::gdcmDocument(std::string const & inFilename, + bool exception_on_error, + bool enable_sequences, + bool ignore_shadow) + : gdcmElementSet(-1) { enableSequences=enable_sequences; - ignoreShadow =ignore_shadow; + IgnoreShadow =ignore_shadow; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - filename = inFilename; + Filename = inFilename; Initialise(); if ( !OpenFile(exception_on_error)) return; + + dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ", + Filename.c_str()); + rewind(fp); + + 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 + (void)l; //is l used anywhere ? + + rewind(fp); + + // Load 'non string' values + + std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + if( PhotometricInterpretation == "PALETTE COLOR " ) { + LoadEntryVoidArea(0x0028,0x1200); // gray LUT + LoadEntryVoidArea(0x0028,0x1201); // R LUT + LoadEntryVoidArea(0x0028,0x1202); // G LUT + LoadEntryVoidArea(0x0028,0x1203); // B LUT + + LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data + LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data + LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data + } + //FIXME later : how to use it? + LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent) + + 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 +174,14 @@ 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 } @@ -96,26 +191,17 @@ gdcmDocument::gdcmDocument(bool exception_on_error) { gdcmDocument::~gdcmDocument (void) { RefPubDict = NULL; RefShaDict = NULL; + + // Recursive clean up of sequences + for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it ) + { + delete it->second; + } + tagHT.clear(); } //----------------------------------------------------------------------------- // 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 @@ -176,48 +262,73 @@ bool gdcmDocument::SetShaDict(DictKey dictName){ * false otherwise. */ bool gdcmDocument::IsReadable(void) { - if(filetype==Unknown) { + if(Filetype==gdcmUnknown) { + dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype"); return(false); } - if(listEntries.size()<=0) { + if(!tagHT.empty()<=0) { + dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal" + " hash table."); return(false); } return(true); } + /** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a ImplicitVRLittleEndian one. - * @return True when ImplicitVRLittleEndian found. False in all other cases. + * \brief Internal function that checks whether the Transfer Syntax given + * as argument is the one present in the current document. + * @param SyntaxToCheck The transfert syntax we need to check against. + * @return True when SyntaxToCheck corresponds to the Transfer Syntax of + * the current document. False either when the document contains + * no Transfer Syntax, or when the Tranfer Syntaxes don't match. */ -bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) { - gdcmHeaderEntry *Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) +bool gdcmDocument::IsGivenTransferSyntax(const std::string & SyntaxToCheck) +{ + gdcmDocEntry *Entry = GetDocEntryByNumber(0x0002, 0x0010); + if ( !Entry ) return false; - LoadHeaderEntrySafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2 ) - return true; + // The entry might be present but not loaded (parsing and loading + // happen at differente stages): try loading and proceed with check... + LoadDocEntrySafe(Entry); + if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(Entry) ) + { + std::string Transfer = ValEntry->GetValue(); + // The actual transfer (as read from disk) might be padded. We + // first need to remove the potential padding. We can make the + // weak assumption that padding was not executed with digits... + while ( ! isdigit(Transfer[Transfer.length()-1]) ) + { + Transfer.erase(Transfer.length()-1, 1); + } + if ( Transfer == SyntaxToCheck ) + return true; + } return false; } +/** + * \brief Determines if the Transfer Syntax of the present document + * corresponds to a Implicit Value Representation of + * Little Endian. + * \sa \ref gdcmDocument::IsGivenTransferSyntax. + * @return True when ImplicitVRLittleEndian found. False in all other cases. + */ +bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2); +} + /** * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a ExplicitVRLittleEndian one. * @return True when ExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); - - std::string Transfer = Element->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_1 ) - return true; - return false; +bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1); } /** @@ -225,16 +336,9 @@ bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) { * and if it corresponds to a DeflatedExplicitVRLittleEndian one. * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); - - std::string Transfer = Element->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_1_99 ) - return true; - return false; +bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99); } /** @@ -242,16 +346,99 @@ bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { * and if it corresponds to a Explicit VR Big Endian one. * @return True when big endian found. False in all other cases. */ -bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); +bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2); +} - std::string Transfer = Element->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier ! - return true; - return false; +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGBaseLineProcess1 one. + * @return True when JPEGBaseLineProcess1found. False in all other cases. + */ +bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGExtendedProcess2-4 one. + * @return True when JPEGExtendedProcess2-4 found. False in all other cases. + */ +bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGExtendeProcess3-5 one. + * @return True when JPEGExtendedProcess3-5 found. False in all other cases. + */ +bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. + * @return True when JPEGSpectralSelectionProcess6-8 found. False in all + * other cases. + */ +bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a RLE Lossless one. + * @return True when RLE Lossless found. False in all + * other cases. + */ +bool gdcmDocument::IsRLELossLessTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); +} + +/** + * \brief Determines if Transfer Syntax was already encountered + * and if it corresponds to a JPEG Lossless one. + * @return True when RLE Lossless found. False in all + * other cases. + */ + +bool gdcmDocument::IsJPEGLossless(void) +{ + return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55) + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57) + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70) ); // was 90 +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEG2000 one + * @return True when JPEG2000 (Lossly or LossLess) found. False in all + * other cases. + */ +bool gdcmDocument::IsJPEG2000(void) +{ + return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); +} + +/** + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. + */ +bool gdcmDocument::IsDicomV3(void) { + // Checking if Transfert Syntax exists is enough + // Anyway, it's to late check if the 'Preamble' was found ... + // And ... would it be a rich idea to check ? + // (some 'no Preamble' DICOM images exist !) + return (GetDocEntryByNumber(0x0002, 0x0010) != NULL); } /** @@ -260,7 +447,7 @@ bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) { * @return the FileType code */ FileType gdcmDocument::GetFileType(void) { - return(filetype); + return Filetype; } /** @@ -271,11 +458,18 @@ FileType gdcmDocument::GetFileType(void) { FILE *gdcmDocument::OpenFile(bool exception_on_error) throw(gdcmFileError) { - fp=fopen(filename.c_str(),"rb"); - if(exception_on_error) + fp=fopen(Filename.c_str(),"rb"); + + if(!fp) { - if(!fp) - throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)"); + if(exception_on_error) + throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)"); + else + { + dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ", + Filename.c_str()); + return NULL; + } } if ( fp ) @@ -285,22 +479,22 @@ FILE *gdcmDocument::OpenFile(bool exception_on_error) //ACR -- or DICOM with no Preamble -- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200) - return(fp); + return fp; //DICOM fseek(fp, 126L, SEEK_CUR); char dicm[4]; fread(dicm, (size_t)4, (size_t)1, fp); if( memcmp(dicm, "DICM", 4) == 0 ) - return(fp); + return fp; fclose(fp); - dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", filename.c_str()); + dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", Filename.c_str()); } else { - dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", filename.c_str()); + dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", Filename.c_str()); } - return(NULL); + return NULL; } /** @@ -316,35 +510,29 @@ bool gdcmDocument::CloseFile(void) { } /** - * \brief Writes in a file all the Doc Entries (Dicom Elements) - * of the Chained List + * \brief Writes in a file all the Header Entries (Dicom Elements) * @param fp file pointer on an already open file - * @param type Type of the File to be written + * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -bool gdcmDocument::Write(FILE *fp, FileType type) { +bool gdcmDocument::WriteF(FileType filetype) { /// \todo -/// ============== -/// 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) +/// ============== +/// The stuff is rewritten using the SeQuence based +/// tree-like stucture (cf : Print ) /// To be checked /// ============= /// \todo move the following lines (and a lot of others, to be written) /// to a future function CheckAndCorrectHeader - /// \todo - /// Question : - /// Comment pourrait-on savoir si le DcmHeader vient d'un fichier - /// DicomV3 ou non (FileType est un champ de gdcmDocument ...) /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA - /// no way + /// no way (check : FileType est un champ de gdcmDocument ...) /// a moins de se livrer a un tres complique ajout des champs manquants. /// faire un CheckAndCorrectHeader (?) - if (type == ImplicitVR) + if (filetype == gdcmImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); @@ -357,7 +545,7 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { SetEntryLengthByNumber(18, 0x0002, 0x0010); } - if (type == ExplicitVR) + if (filetype == gdcmExplicitVR) { std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); @@ -372,54 +560,127 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { /** * \todo rewrite later, if really usefull + * ('Group Length' element is optional in DICOM) * - * --> Warning : un-updated odd groups lengths can causes pb + * --> Warning : un-updated odd groups lengthes can causes pb * --> (xmedcon breaks) * --> to be re- written with future org. * - * if ( (type == ImplicitVR) || (type == ExplicitVR) ) - * UpdateGroupLength(false,type); - * if ( type == ACR) + * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) ) + * UpdateGroupLength(false,filetype); + * if ( filetype == ACR) * UpdateGroupLength(true,ACR); */ + + gdcmElementSet::Write(fp,filetype); - WriteEntries(fp,type); - return(true); + /// WriteEntries(fp,type); // old stuff + return true; } /** * \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 Value (string) Value to be set + * @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( + +gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( std::string Value, guint16 Group, - guint16 Elem ){ - gdcmHeaderEntry* a; - a = GetHeaderEntryByNumber( Group, Elem); + guint16 Elem ) +{ + gdcmDocEntry* CurrentEntry; + gdcmValEntry* ValEntry; + + CurrentEntry = GetDocEntryByNumber( Group, Elem); + if (!CurrentEntry) + { + // The entry wasn't present and we simply create the required ValEntry: + CurrentEntry = NewDocEntryByNumber(Group, Elem); + if (!CurrentEntry) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" + " NewDocEntryByNumber failed."); + return NULL; + } + ValEntry = new gdcmValEntry(CurrentEntry); + if ( !AddEntry(ValEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" + " failed allthough this is a creation."); + } + } + else + { + ValEntry = dynamic_cast< gdcmValEntry* >(CurrentEntry); + if ( !ValEntry ) + { + // We need to promote the gdcmDocEntry to a gdcmValEntry: + ValEntry = new gdcmValEntry(CurrentEntry); + if (!RemoveEntry(CurrentEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" + " of previous DocEntry failed."); + return NULL; + } + if ( !AddEntry(ValEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" + " promoted ValEntry failed."); + return NULL; + } + } + } + + SetEntryByNumber(Value, Group, Elem); + + return ValEntry; +} + +/* + * \brief Modifies the value of a given Header Entry (Dicom Element) + * when it exists. Create it with the given value when unexistant. + * @param voidArea (binary) value to be set + * @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). + */ +gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( + void *voidArea, + int lgth, + guint16 Group, + guint16 Elem) +{ + gdcmDocEntry* a; + gdcmBinEntry* b; + a = GetDocEntryByNumber( Group, Elem); if (a == NULL) { - a =NewHeaderEntryByNumber(Group, Elem); + a =NewBinEntryByNumber(Group, Elem); if (a == NULL) return NULL; - AddHeaderEntry(a); + + b = new gdcmBinEntry(a); + AddEntry(b); } - //CLEANME SetEntryByNumber(Value, Group, Elem); - a->SetValue(Value); - return(a); -} + SetEntryByNumber(voidArea, lgth, Group, Elem); + b->SetVoidArea(voidArea); + + return b; +} + + /** * \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 ) @@ -433,19 +694,18 @@ 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 */ int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { std::string key = gdcmDictEntry::TranslateToKey(group, element ); - return (tagHT.count(key)); + return tagHT.count(key); } /** - * \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 @@ -458,11 +718,11 @@ std::string gdcmDocument::GetEntryByName(std::string tagName) { if( dictEntry == NULL) return GDCM_UNFOUND; - return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); + return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); } /** - * \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. * @@ -474,23 +734,23 @@ std::string gdcmDocument::GetEntryByName(std::string tagName) { * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByName(std::string tagName) { +std::string gdcmDocument::GetEntryVRByName(TagName tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(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 +758,11 @@ 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 +770,28 @@ 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(); @@ -547,69 +807,89 @@ bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) { if( dictEntry == NULL) return false; - return(SetEntryByNumber(content,dictEntry->GetGroup(), - dictEntry->GetElement())); + return SetEntryByNumber(content,dictEntry->GetGroup(), + dictEntry->GetElement()); } /** - * \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 content new value (string) to substitute with + * @param group group number of the Dicom Element to modify + * @param element element number of the Dicom Element to modify */ bool gdcmDocument::SetEntryByNumber(std::string content, guint16 group, guint16 element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + gdcmValEntry* ValEntry = GetValEntryByNumber(group, element); + if (!ValEntry) + { + dbg.Verbose(0, "gdcmDocument::SetEntryByNumber: no corresponding", + " ValEntry (try promotion first)."); return false; - int l = content.length(); - if(l%2) // Non even length are padded with a space (020H). - { - l++; - content = content + '\0'; } + + // Non even content must be padded with a space (020H). + if((content.length())%2) + 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); + ValEntry->SetValue(content); - std::string vr = a->GetVR(); - - guint32 lgr; + // Integers have a special treatement for their length: + VRKey vr = ValEntry->GetVR(); if( (vr == "US") || (vr == "SS") ) - lgr = 2; + ValEntry->SetLength(2); else if( (vr == "UL") || (vr == "SL") ) - lgr = 4; + ValEntry->SetLength(4); else - lgr = l; + ValEntry->SetLength(content.length()); - a->SetLength(lgr); return true; -} +} + +/** + * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) + * through it's (group, element) and modifies it's content with + * the given value. + * @param content new value (void *) to substitute with + * @param group group number of the Dicom Element to modify + * @param element element number of the Dicom Element to modify + */ +bool gdcmDocument::SetEntryByNumber(void *content, + int lgth, + guint16 group, + guint16 element) +{ + (void)lgth; //not used + TagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( ! tagHT.count(key)) + return false; + +/* Hope Binray 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? + } +*/ + gdcmBinEntry * a; + a = (gdcmBinEntry *)tagHT[key]; + a->SetVoidArea(content); + //a->SetLength(lgth); // ??? + return true; +} /** - * \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 +908,16 @@ 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: no entry present."); return (size_t)0; } return Entry->GetOffset(); @@ -647,40 +926,40 @@ 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: no entry"); 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(); fseek(fp, o, SEEK_SET); - size_t l=Element->GetLength(); + size_t l = Element->GetLength(); char* a = new char[l]; - if(!a) + if(!a) { + dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); return NULL; - + } SetEntryVoidAreaByNumber(a, Group, Elem); /// \todo check the result size_t l2 = fread(a, 1, l ,fp); @@ -695,8 +974,8 @@ 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 area area containing the 'non string' value + * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element * @return */ @@ -707,7 +986,9 @@ 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; } @@ -716,9 +997,11 @@ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, * Only non even entries are analyzed */ void gdcmDocument::UpdateShaEntries(void) { - gdcmDictEntry *entry; + //gdcmDictEntry *entry; std::string vr; - + + /// \todo TODO : still any use to explore recursively the whole structure? +/* for(ListTag::iterator it=listEntries.begin(); it!=listEntries.end(); ++it) @@ -738,13 +1021,14 @@ 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 +1036,22 @@ 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 +1064,7 @@ 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)) @@ -788,365 +1073,37 @@ gdcmHeaderEntry* gdcmDocument::GetHeaderEntryByNumber(guint16 group, guint16 ele } /** - * \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) + * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only + * returns a result when the corresponding entry is of type + * ValEntry. + * @return When present, the corresponding ValEntry. */ - -IterHT gdcmDocument::GetHeaderEntrySameNumber(guint16 group, guint16 element){ - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - return (tagHT.equal_range(key)); +gdcmValEntry* gdcmDocument::GetValEntryByNumber(guint16 group, guint16 element) +{ + gdcmDocEntry* CurrentEntry = GetDocEntryByNumber(group, element); + if (! CurrentEntry) + return (gdcmValEntry*)0; + if ( gdcmValEntry* ValEntry = dynamic_cast(CurrentEntry) ) + { + return ValEntry; + } + dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry."); + return (gdcmValEntry*)0; } /** * \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 - * @param _fp already open file pointer - * @param type type of the File to be written - */ -void gdcmDocument::WriteEntryTagVRLength(gdcmHeaderEntry *tag, - FILE *_fp, - FileType type) -{ - guint16 group = tag->GetGroup(); - std::string vr = tag->GetVR(); - guint16 el = tag->GetElement(); - guint32 lgr = tag->GetReadLength(); - - if ( (group == 0xfffe) && (el == 0x0000) ) - // Fix in order to make some MR PHILIPS images e-film readable - // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm: - // we just *always* ignore spurious fffe|0000 tag ! - return; - - fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group - fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element - - if ( type == ExplicitVR ) { - - // Special case of delimiters: - if (group == 0xfffe) { - // Delimiters have NO Value Representation and have NO length. - // Hence we skip writing the VR and length and we pad by writing - // 0xffffffff - - int ff=0xffffffff; - fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp); - return; - } - - guint16 z=0; - guint16 shortLgr = lgr; - if (vr == "unkn") { // Unknown was 'written' - // deal with Little Endian - fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); - fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); - } else { - fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp); - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) - { - fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); - fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); - } else { - fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); - } - } - } - else // IMPLICIT VR - { - fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); - } -} - -/** - * \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 - * @param _fp Already open file pointer - * @param type type of the File to be written - */ -void gdcmDocument::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) -{ - (void)type; - guint16 group = tag->GetGroup(); - std::string vr = tag->GetVR(); - guint32 lgr = tag->GetReadLength(); - - if (vr == "SQ") - // SeQuences have no value: - return; - if (group == 0xfffe) - // Delimiters have no associated value: - return; - - void *voidArea; - voidArea = tag->GetVoidArea(); - 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 - // each single value is separated from the next one by '\' - // 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, "\\"); - for (unsigned int i=0; i tokens; - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (tag->GetValue(), tokens, "\\"); - for (unsigned int i=0; iGetValue().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. - * \sa WriteEntryValue, WriteEntryTagVRLength. - * @param tag Pointer on the gdcmHeaderEntry 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) -{ - guint32 length = tag->GetLength(); - - // 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); - } - - WriteEntryTagVRLength(tag, _fp, type); - WriteEntryValue(tag, _fp, type); - return true; -} - -/** - * \brief writes on disc according to the requested format - * (ACR-NEMA, ExplicitVR, ImplicitVR) the image - * using the Chained List - * \warning does NOT add the missing elements in the header : - * it's up to the user doing it ! - * (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) -{ - /// \todo (?) check write failures (after *each* fwrite) - - for (ListTag::iterator tag2=listEntries.begin(); - tag2 != listEntries.end(); - ++tag2) - { - if ( type == ACR ){ - if ((*tag2)->GetGroup() < 0x0008) - // Ignore pure DICOM V3 groups - continue; - if ((*tag2)->GetElement() %2) - // Ignore the "shadow" groups - continue; - if ((*tag2)->GetVR() == "SQ" ) // ignore Sequences - continue; - if ((*tag2)->GetSQDepthLevel() != 0) // Not only ignore the SQ element - continue; - } - if (! WriteEntry(*tag2,_fp,type) ) - return false; - } - 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 * processor order. @@ -1169,11 +1126,12 @@ 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; } return(a); -} +} /** * \brief Unswaps back the bytes of 4-byte long integer accordingly to @@ -1205,12 +1163,182 @@ guint16 gdcmDocument::UnswapShort(guint16 a) { //----------------------------------------------------------------------------- // Private +/** + * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) + * @return length of the parsed set. + */ + +long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) { + + gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; + gdcmValEntry *NewValEntry = (gdcmValEntry *)0; + gdcmBinEntry *bn; + gdcmSeqEntry *sq; + VRKey vr; + unsigned 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 + NewValEntry = new gdcmValEntry(NewDocEntry->GetDictEntry()); + NewValEntry->Copy(NewDocEntry); + NewValEntry->SetDepthLevel(depth); + set->AddEntry(NewValEntry); + LoadDocEntry(NewValEntry); + if (NewValEntry->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 + { + SkipToNextDocEntry(NewDocEntry); + l = NewDocEntry->GetFullLength(); + } + } + 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); + (void)lgt; //not used... + } + // 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, lgth; + unsigned int l; + int depth = set->GetDepthLevel(); + (void)depth; //not used + + while (true) { + NewDocEntry = ReadNextDocEntry(); + if (!NewDocEntry) + break; + if(delim_mode) { + if (NewDocEntry->isSequenceDelimitor()) { + set->SetSequenceDelimitationItem(NewDocEntry); + break; + } + } + if (!delim_mode && (ftell(fp)-offset) >= l_max) { + break; + } + + itemSQ = new gdcmSQItem(set->GetDepthLevel()); + itemSQ->AddEntry(NewDocEntry); + 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); + SQItemNumber ++; + 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(); @@ -1223,31 +1351,57 @@ 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 ! return; } // When the length is zero things are easy: if ( length == 0 ) { - Entry->SetValue(""); + ((gdcmValEntry *)Entry)->SetValue(""); return; } // The elements whose length is bigger than the specified upper bound // are not loaded. Instead we leave a short notice of the offset of // the element content and it's length. + 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 (gdcmBinEntry* BinEntryPtr = dynamic_cast< gdcmBinEntry* >(Entry) ) + { + std::ostringstream s; + s << "gdcm::NotLoaded (BinEntry)"; + s << " Address:" << (long)Entry->GetOffset(); + s << " Length:" << Entry->GetLength(); + s << " x(" << std::hex << Entry->GetLength() << ")"; + BinEntryPtr->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; + // Be carefull : a BinEntry IS_A ValEntry ... + if (gdcmValEntry* ValEntryPtr = dynamic_cast< gdcmValEntry* >(Entry) ) + { + std::ostringstream s; + s << "gdcm::NotLoaded. (ValEntry)"; + 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; } + + // When we find a BinEntry not very much can be done : + if (gdcmBinEntry* BinEntryPtr = dynamic_cast< gdcmBinEntry* >(Entry) ) { + LoadEntryVoidArea (BinEntryPtr->GetGroup(),BinEntryPtr->GetElement()); + return; + } + // Any compacter code suggested (?) - if ( IsHeaderEntryAnInteger(Entry) ) { + if ( IsDocEntryAnInteger(Entry) ) { guint32 NewInt; std::ostringstream s; int nbInt; @@ -1287,7 +1441,7 @@ 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 +1450,29 @@ 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 +1484,10 @@ 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 +1556,7 @@ 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 +1568,7 @@ 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 +1577,9 @@ 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 +1595,7 @@ 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 +1618,7 @@ 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 +1687,11 @@ 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 +1746,7 @@ std::string gdcmDocument::GetHeaderEntryValue(gdcmHeaderEntry *Entry) return(s.str()); } - return(Entry->GetValue()); + return(((gdcmValEntry *)Entry)->GetValue()); } /** @@ -1617,9 +1757,9 @@ 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 +1770,7 @@ 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 +1807,29 @@ 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 When the length of an element value is obviously wrong (because * the parser went Jabberwocky) one can hope improving things by - * applying this heuristic. + * applying some heuristics. */ -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) { @@ -1689,48 +1841,61 @@ void gdcmDocument::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Fou if (FoundLength%2) { std::ostringstream s; - s << "Warning : Tag with uneven length " << FoundLength - << " in x(" << std::hex << gr << "," << el <<")" << std::dec; - dbg.Verbose(0,s.str().c_str()); + s << "Warning : Tag with uneven length " + << FoundLength + << " in x(" << std::hex << gr << "," << el <<")" << std::dec; + dbg.Verbose(0, s.str().c_str()); } - // Sorry for the patch! - // XMedCom did the trick to read some naughty GE images ... - if (FoundLength == 13) { - // The following 'if' will be removed when there is no more - // images on Creatis HDs with a 13 length for Manufacturer... - if ( (Entry->GetGroup() != 0x0008) || - ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){ - // end of remove area - FoundLength =10; - Entry->SetReadLength(10); // a bug is to be fixed + //////// Fix for some naughty General Electric images. + // Allthough not recent many such GE corrupted images are still present + // on Creatis hard disks. Hence this fix shall remain when such images + // are no longer in user (we are talking a few years, here)... + // Note: XMedCom probably uses such a trick since it is able to read + // those pesky GE images ... + if (FoundLength == 13) { // Only happens for this length ! + if ( (Entry->GetGroup() != 0x0008) + || ( (Entry->GetElement() != 0x0070) + && (Entry->GetElement() != 0x0080) ) ) + { + FoundLength = 10; + Entry->SetReadLength(10); /// \todo a bug is to be fixed !? } } - // to fix some garbage 'Leonardo' Siemens images - // May be commented out to avoid overhead - else if ( (Entry->GetGroup() == 0x0009) && - ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){ - FoundLength =4; - Entry->SetReadLength(4); // a bug is to be fixed + //////// Fix for some brain-dead 'Leonardo' Siemens images. + // Occurence of such images is quite low (unless one leaves close to a + // 'Leonardo' source. Hence, one might consider commenting out the + // following fix on efficiency reasons. + else + if ( (Entry->GetGroup() == 0x0009) + && ( (Entry->GetElement() == 0x1113) + || (Entry->GetElement() == 0x1114) ) ) + { + FoundLength = 4; + Entry->SetReadLength(4); /// \todo a bug is to be fixed !? } - // end of fix - // to try to 'go inside' SeQuences (with length), and not to skip them - else if ( Entry->GetVR() == "SQ") - { - if (enableSequences) // only if the user does want to ! - FoundLength =0; // ReadLength is unchanged + //////// Deal with sequences, but only on users request: + else + if ( ( Entry->GetVR() == "SQ") && enableSequences) + { + FoundLength = 0; // ReadLength is unchanged } - // we found a 'delimiter' element - // fffe|xxxx is just a marker, we don't take its length into account - else if(Entry->GetGroup() == 0xfffe) + //////// We encountered a 'delimiter' element i.e. a tag of the form + // "fffe|xxxx" which is just a marker. Delimiters length should not be + // taken into account. + else + if(Entry->GetGroup() == 0xfffe) { - // *normally, fffe|0000 doesn't exist ! - if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm - // causes extra troubles :-( - FoundLength =0; + // According to the norm, fffe|0000 shouldn't exist. BUT the Philips + // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to + // causes extra troubles... + if( Entry->GetElement() != 0x0000 ) + { + FoundLength = 0; + } } Entry->SetUsableLength(FoundLength); @@ -1742,11 +1907,12 @@ 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(); guint32 length = Entry->GetLength(); + // When we have some semantics on the element we just read, and if we // a priori know we are dealing with an integer, then we shall be // able to swap it's element value properly. @@ -1756,36 +1922,36 @@ bool gdcmDocument::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { return true; else { + // Allthough this should never happen, still some images have a + // corrupted group length [e.g. have a glance at offset x(8336) of + // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm]. + // Since for dicom compliant and well behaved headers, the present + // test is useless (and might even look a bit paranoid), when we + // encounter such an ill-formed image, we simply display a warning + // message and proceed on parsing (while crossing fingers). std::ostringstream s; int filePosition = ftell(fp); s << "Erroneous Group Length element length on : (" \ << std::hex << group << " , " << element << ") -before- position x(" << filePosition << ")" << "lgt : " << length; - // These 2 lines commented out : a *very dirty* patch - // to go on PrintHeader'ing gdcm-MR-PHILIPS-16-Multi-Seq.dcm. - // have a glance at offset x(8336) ... - // For *regular* headers, the test is useless.. - // lets's print a warning message and go on, - // instead of giving up with an error message - - //std::cout << s.str().c_str() << std::endl; - // dbg.Error("gdcmDocument::IsHeaderEntryAnInteger", - // s.str().c_str()); + dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() ); } } + if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) return true; return false; } + /** * \brief Find the Length till the next sequence delimiter * \warning NOT end user intended method ! * @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; @@ -1835,7 +2001,7 @@ bool gdcmDocument::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { * (swaps it depending on processor endianity) * @return read value */ -guint16 gdcmDocument::ReadInt16(void) { +guint16 gdcmDocument::ReadInt16() { guint16 g; size_t item_read; item_read = fread (&g, (size_t)2,(size_t)1, fp); @@ -1855,7 +2021,7 @@ guint16 gdcmDocument::ReadInt16(void) { * (swaps it depending on processor endianity) * @return read value */ -guint32 gdcmDocument::ReadInt32(void) { +guint32 gdcmDocument::ReadInt32() { guint32 g; size_t item_read; item_read = fread (&g, (size_t)4,(size_t)1, fp); @@ -1887,7 +2053,7 @@ void gdcmDocument::SkipBytes(guint32 NBytes) { void gdcmDocument::Initialise(void) { RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); - RefShaDict = (gdcmDict*)0; + RefShaDict = NULL; } /** @@ -1960,13 +2126,13 @@ 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 +2177,19 @@ 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 +2215,18 @@ 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; } @@ -2134,214 +2300,288 @@ 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) -// 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 - - 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)); return NewEntry; } + /** - * \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 Name Name of the underlying DictEntry + * \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. */ -gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByName(std::string Name) +guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group) { - gdcmDictEntry *NewTag = GetDictEntryByName(Name); - if (!NewTag) - NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name); + for (guint32 elem = 0; elem < UINT32_MAX; elem++) + { + TagKey key = gdcmDictEntry::TranslateToKey(group, elem); + if (tagHT.count(key) == 0) + return elem; + } + return UINT32_MAX; +} + + +/** + * \brief Assuming the internal file pointer \ref gdcmDocument::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 gdcmDocument::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 gdcmDocument::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. + */ +guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement) +{ + guint16 ItemTagGroup; + guint16 ItemTagElement; + long PositionOnEntry = ftell(fp); + long CurrentPosition = ftell(fp); // On debugging purposes - gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag); - if (!NewEntry) + //// Read the Item Tag group and element, and make + // sure they are respectively 0xfffe and 0xe000: + ItemTagGroup = ReadInt16(); + ItemTagElement = ReadInt16(); + if ( (ItemTagGroup != TestGroup) || (ItemTagElement != TestElement ) ) + { + std::ostringstream s; + s << " We should have found tag ("; + s << std::hex << TestGroup << "," << TestElement << ")" << std::endl; + s << " but instead we encountered tag ("; + s << std::hex << ItemTagGroup << "," << ItemTagElement << ")" + << std::endl; + s << " at address: " << (unsigned)CurrentPosition << std::endl; + dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:"); + dbg.Verbose(0, s.str().c_str()); + fseek(fp, PositionOnEntry, SEEK_SET); + return 0; + } + + //// Then read the associated Item Length + CurrentPosition=ftell(fp); + guint32 ItemLength; + ItemLength = ReadInt32(); { - dbg.Verbose(1, "gdcmDocument::ObtainHeaderEntryByName", - "failed to allocate gdcmHeaderEntry"); - return (gdcmHeaderEntry *)0; + std::ostringstream s; + s << "Basic Item Length is: " + << ItemLength << std::endl; + s << " at address: " << (unsigned)CurrentPosition << std::endl; + dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: ", s.str().c_str()); } - return NewEntry; -} + return ItemLength; +} /** - * \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 vr VR of the underlying DictEntry - * @param fourth owner group - * @param name english name + * \brief Read the length of an exptected Item tag i.e. (0xfffe, 0xe000). + * \sa \ref gdcmDocument::ReadTagLength + * \warning See warning of \ref gdcmDocument::ReadTagLength + * @return On success returns the length associated to the item tag. + * On failure returns 0. + */ +guint32 gdcmDocument::ReadItemTagLength(void) +{ + return ReadTagLength(0xfffe, 0xe000); +} + +/** + * \brief Read the length of an expected Sequence Delimiter tag i.e. + * (0xfffe, 0xe0dd). + * \sa \ref gdcmDocument::ReadTagLength + * \warning See warning of \ref gdcmDocument::ReadTagLength + * @return On success returns the length associated to the Sequence + * Delimiter tag. On failure returns 0. */ -gdcmDictEntry *gdcmDocument::NewVirtualDictEntry(guint16 group, guint16 element, - std::string vr, - std::string fourth, - std::string name) +guint32 gdcmDocument::ReadSequenceDelimiterTagLength(void) { - return gdcmGlobal::GetDicts()->NewVirtualDictEntry(group,element,vr,fourth,name); + return ReadTagLength(0xfffe, 0xe0dd); } + /** - * \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 + * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files + * No other way so 'skip' the Data + * */ -gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) + +void gdcmDocument::Parse7FE0 (void) { - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); - if (!DictEntry) - DictEntry = NewVirtualDictEntry(Group, Elem); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return; + + if ( IsImplicitVRLittleEndianTransferSyntax() + || IsExplicitVRLittleEndianTransferSyntax() + || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier ! + || IsDeflatedExplicitVRLittleEndianTransferSyntax() ) + return; + + // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels + + //// Read the Basic Offset Table Item Tag length... + guint32 ItemLength = ReadItemTagLength(); + + //// ... and then read length[s] itself[themselves]. We don't use + // the values read (BTW what is the purpous of those lengths ?) + if (ItemLength != 0) { + // BTW, what is the purpous of those length anyhow !? + char * BasicOffsetTableItemValue = new char[ItemLength + 1]; + fread(BasicOffsetTableItemValue, ItemLength, 1, fp); + for (unsigned int i=0; i < ItemLength; i += 4){ + guint32 IndividualLength; + IndividualLength = str2num(&BasicOffsetTableItemValue[i],guint32); + std::ostringstream s; + s << " Read one length: "; + s << std::hex << IndividualLength << std::endl; + dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str()); + } + } - gdcmHeaderEntry *NewEntry = new gdcmHeaderEntry(DictEntry); - if (!NewEntry) + if ( ! IsRLELossLessTransferSyntax() ) { - dbg.Verbose(1, "gdcmDocument::NewHeaderEntryByNumber", - "failed to allocate gdcmHeaderEntry"); - return NULL; + // JPEG Image + + //// We then skip (not reading them) all the fragments of images: + while ( (ItemLength = ReadItemTagLength()) ) + { + SkipBytes(ItemLength); + } + + } + else + { + // RLE Image + long ftellRes; + long RleSegmentLength[15], fragmentLength; + + // while 'Sequence Delimiter Item' (fffe,e0dd) not found + while ( (fragmentLength = ReadSequenceDelimiterTagLength()) ) + { + // Parse fragments of the current Fragment (Frame) + //------------------ scanning (not reading) fragment pixels + guint32 nbRleSegments = ReadInt32(); + printf(" Nb of RLE Segments : %d\n",nbRleSegments); + + //// Reading RLE Segments Offset Table + guint32 RleSegmentOffsetTable[15]; + for(int k=1; k<=15; k++) { + ftellRes=ftell(fp); + RleSegmentOffsetTable[k] = ReadInt32(); + printf(" at : %x Offset Segment %d : %d (%x)\n", + (unsigned)ftellRes,k,RleSegmentOffsetTable[k], + RleSegmentOffsetTable[k]); + } + + // skipping (not reading) RLE Segments + if (nbRleSegments>1) { + 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); + SkipBytes(RleSegmentLength[k]); + } + } + + 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); + SkipBytes(RleSegmentLength[nbRleSegments]); + } } - return NewEntry; } -/// \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 - * 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, -// std::string VR) -//{ -// gdcmHeaderEntry *NewEntry = NULL; -// guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info -// guint32 FreeElem = 0; -// gdcmDictEntry *DictEntry = NULL; -// -// FreeElem = GenerateFreeTagKeyInGroup(StuffGroup); -// if (FreeElem == UINT32_MAX) -// { -// dbg.Verbose(1, "gdcmHeader::NewManualHeaderEntryToPubDict", -// "Group 0xffff in Public Dict is full"); -// return NULL; -// } -// -// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem, -// VR, "GDCM", NewTagName); -// NewEntry = new gdcmHeaderEntry(DictEntry); -// AddHeaderEntry(NewEntry); -// return NewEntry; -//} + /** - * \brief Generate a free TagKey i.e. a TagKey that is not present - * in the TagHt dictionary. - * @param group The generated tag must belong to this group. - * @return The element of tag with given group which is fee. + * \brief Compares two documents, according to \ref gdcmDicomDir 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' */ -guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group) +bool gdcmDocument::operator<(gdcmDocument &document) { - for (guint32 elem = 0; elem < UINT32_MAX; elem++) + std::string s1,s2; + + // Patient Name + s1=this->GetEntryByNumber(0x0010,0x0010); + s2=document.GetEntryByNumber(0x0010,0x0010); + if(s1 < s2) + return true; + else if(s1 > s2) + return false; + else { - TagKey key = gdcmDictEntry::TranslateToKey(group, elem); - if (tagHT.count(key) == 0) - return elem; + // Patient ID + s1=this->GetEntryByNumber(0x0010,0x0020); + s2=document.GetEntryByNumber(0x0010,0x0020); + if (s1 < s2) + return true; + else if (s1 > s2) + return true; + else + { + // Study Instance UID + s1=this->GetEntryByNumber(0x0020,0x000d); + s2=document.GetEntryByNumber(0x0020,0x000d); + if (s1 < s2) + return true; + else if(s1 > s2) + return false; + else + { + // Serie Instance UID + s1=this->GetEntryByNumber(0x0020,0x000e); + s2=document.GetEntryByNumber(0x0020,0x000e); + if (s1 < s2) + return true; + else if(s1 > s2) + return false; + } + } } - return UINT32_MAX; + return false; } + //-----------------------------------------------------------------------------