-// gdcmDocument.cxx
-//-----------------------------------------------------------------------------
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmDocument.cxx,v $
+ Language: C++
+ Date: $Date: 2004/06/25 12:56:39 $
+ Version: $Revision: 1.33 $
+
+ 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 <iomanip>
+// 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()
const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256;
// Refer to gdcmDocument::SetMaxSizeLoadEntry()
-const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
+const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 0x7fffffff;// 4096;
-const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64;
+const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff;//64;
//-----------------------------------------------------------------------------
// Constructor / Destructor
* 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 ?
- //LoadHeaderEntries();
- long l=ParseES( (gdcmDocEntrySet *)this, 120L, 0x7fffffff, false);
- // TODO : find the right values
- CloseFile();
+ 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 ----------------
printLevel = 1; // 'Medium' print level by default
}
* \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);
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 Header 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
* \brief Get the public dictionary used
*/
gdcmDict *gdcmDocument::GetPubDict(void) {
- return(RefPubDict);
+ return RefPubDict;
}
/**
* \brief Get the shadow dictionary used
*/
gdcmDict *gdcmDocument::GetShaDict(void) {
- return(RefShaDict);
+ return RefShaDict;
}
/**
*/
bool gdcmDocument::SetShaDict(gdcmDict *dict){
RefShaDict=dict;
- return(!RefShaDict);
+ return !RefShaDict;
}
/**
*/
bool gdcmDocument::SetShaDict(DictKey dictName){
RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName);
- return(!RefShaDict);
+ return !RefShaDict;
}
/**
* false otherwise.
*/
bool gdcmDocument::IsReadable(void) {
- if(filetype==Unknown) {
- return(false);
+ if(Filetype==gdcmUnknown) {
+ dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype");
+ return false;
}
- if(listEntries.size()<=0) {
- return(false);
+ 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) {
- gdcmDocEntry *Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
+bool gdcmDocument::IsGivenTransferSyntax(const std::string & SyntaxToCheck)
+{
+ gdcmDocEntry *Entry = GetDocEntryByNumber(0x0002, 0x0010);
+ if ( !Entry )
return false;
- LoadDocEntrySafe(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) {
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadDocEntrySafe(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);
}
/**
* and if it corresponds to a DeflatedExplicitVRLittleEndian one.
* @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) {
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadDocEntrySafe(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);
}
/**
* 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) {
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadDocEntrySafe(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) );
+}
+
+/**
+ * \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);
}
/**
* @return the FileType code
*/
FileType gdcmDocument::GetFileType(void) {
- return(filetype);
+ return Filetype;
}
/**
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 )
//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;
}
/**
/**
* \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
+ * @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);
SetEntryLengthByNumber(18, 0x0002, 0x0010);
}
- if (type == ExplicitVR)
+ if (filetype == gdcmExplicitVR)
{
std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1;
ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
/**
* \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);
+ 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).
*/
-
-
-gdcmDocEntry * gdcmDocument::ReplaceOrCreateByNumber(
+
+gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
std::string Value,
guint16 Group,
- guint16 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 =NewDocEntryByNumber(Group, Elem);
+ a =NewBinEntryByNumber(Group, Elem);
if (a == NULL)
return NULL;
- AddDocEntry(a);
+
+ b = new gdcmBinEntry(a);
+ AddEntry(b);
}
- 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 )
// 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);
}
/**
if( dictEntry == NULL)
return GDCM_UNFOUND;
- return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
+ return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement());
}
/**
* @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;
gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
+ dictEntry->GetElement());
return elem->GetVR();
}
* \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.
*/
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();
}
/**
* 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.
*/
* \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) {
if( dictEntry == NULL)
return false;
- return(SetEntryByNumber(content,dictEntry->GetGroup(),
- dictEntry->GetElement()));
+ return SetEntryByNumber(content,dictEntry->GetGroup(),
+ dictEntry->GetElement());
}
/**
* \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 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';
- gdcmDocEntry * a;
- IterHT p;
- TagDocEntryHT::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 :
+ ValEntry->SetValue(content);
- // Oops ! this was for multimap, right ?
- a = ((tagHT.equal_range(key)).first)->second;
-
- ((gdcmValEntry*)a)->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 gdcmDocEntry (i.e. a Dicom Element)
* 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,
/**
* \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)
gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
if (!Entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber",
- "failed to Locate gdcmDocEntry");
+ dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry present.");
return (size_t)0;
}
return Entry->GetOffset();
/**
* \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)
gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
if (!Entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber",
- "failed to Locate gdcmDocEntry");
+ dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry");
return (NULL);
}
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)
{
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);
delete[] a;
return NULL;
}
-
+ return a;
+}
+/**
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
+ * @param Element Entry whose voidArea is going to be loaded
+ */
+void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *Element)
+{
+ size_t o =(size_t)Element->GetOffset();
+ fseek(fp, o, SEEK_SET);
+ size_t l = Element->GetLength();
+ char* a = new char[l];
+ if(!a) {
+ dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a");
+ return NULL;
+ }
+ Element->SetVoidArea((void *)a);
+ /// \todo check the result
+ size_t l2 = fread(a, 1, l ,fp);
+ if(l != l2)
+ {
+ delete[] a;
+ return NULL;
+ }
return a;
}
/**
* \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
*/
* 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)
else
vr=(*it)->GetVR();
- //(*it)->SetValue(GetDocEntryUnvalue(*it));
- // to go on compiling
+ (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling
if(entry){
// Set the new entry and the new value
(*it)->SetDictEntry(entry);
CheckDocEntryVR(*it,vr);
- //(*it)->SetValue(GetDocEntryValue(*it));
- // to go on compiling
-
+ (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling
+
}
else
{
(*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr));
}
}
+*/
}
/**
*/
gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHT.count(key))
return NULL;
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::GetDocEntrySameNumber(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 LoadDocEntry that modifies it.
- * @param entry Header Entry whose value shall be loaded.
- * @return
+ * \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.
*/
-void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) {
- long PositionOnEntry = ftell(fp);
- 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, ...)
- */
-
- /* Probabely useless, now !
-
-void gdcmDocument::UpdateGroupLength(bool SkipSequence, FileType type) {
- guint16 gr, el;
- std::string vr;
-
- gdcmDocEntry *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<GroupKey, int> GroupHT;
-
- gdcmDocEntry *elemZ;
-
- // for each Tag in the DCM Header
-
- for (TagDocEntryHT::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 gdcmDocEntry(tagZ);
- elemZ->SetLength(4);
- AddDocEntry(elemZ); // create it
- }
- else
- {
- elemZ=GetDocEntryByNumber(gr_bid, 0x0000);
- }
- sprintf(trash ,"%d",g->second);
- str_trash=trash;
- //elemZ->SetValue(str_trash); // to go on compiling
- }
-}
-
-*/
-
-/**
- * \brief Writes in a file (according to the requested format)
- * the group, the element, the value representation and the length
- * 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(gdcmDocEntry *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 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
- */
-
- // TODO : to be re -written recursively !
-
-void gdcmDocument::WriteEntryValue(gdcmDocEntry *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();
- // 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
- // each single value is separated from the next one by '\'
- // we split the string and write each value as a short int
- std::vector<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (tag->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- guint16 val_uint16 = atoi(tokens[i].c_str());
- void *ptr = &val_uint16;
- fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- return;
- }
- // some 'Integer' fields may be mulivaluated
- // each single value is separated from the next one by '\'
- // we split the string and write each value as an int
- if (vr == "UL" || vr == "SL")
- {
- std::vector<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (tag->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- guint32 val_uint32 = atoi(tokens[i].c_str());
- void *ptr = &val_uint32;
- fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- return;
- }
- fwrite (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 gdcmDocEntry passed as argument.
- * \sa WriteEntryValue, WriteEntryTagVRLength.
- * @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(gdcmDocEntry *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");
-// to go on compiling
- 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;
-}
+gdcmValEntry* gdcmDocument::GetValEntryByNumber(guint16 group, guint16 element)
+{
+ gdcmDocEntry* CurrentEntry = GetDocEntryByNumber(group, element);
+ if (! CurrentEntry)
+ return (gdcmValEntry*)0;
+ if ( gdcmValEntry* ValEntry = dynamic_cast<gdcmValEntry*>(CurrentEntry) )
+ {
+ return ValEntry;
+ }
+ dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry.");
+ return (gdcmValEntry*)0;
+}
/**
- * \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)
+ * \brief Loads the element while preserving the current
+ * underlying file position indicator as opposed to
+ * to LoadDocEntry that modifies it.
+ * @param entry Header Entry whose value shall be loaded.
+ * @return
*/
-void gdcmDocument::WriteEntriesDeprecated(FILE *_fp,FileType type) {
-
- // restent a tester les echecs en ecriture (apres chaque fwrite)
-
- for (TagDocEntryHT::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;
- }
+void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) {
+ long PositionOnEntry = ftell(fp);
+ LoadDocEntry(entry);
+ fseek(fp, PositionOnEntry, SEEK_SET);
}
/**
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);
-}
+ return a;
+}
/**
* \brief Unswaps back the bytes of 4-byte long integer accordingly to
* @return The properly unswaped 32 bits integer.
*/
guint32 gdcmDocument::UnswapLong(guint32 a) {
- return (SwapLong(a));
+ return SwapLong(a);
}
/**
guint16 gdcmDocument::SwapShort(guint16 a) {
if ( (sw==4321) || (sw==2143) )
a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
- return (a);
+ return a;
}
/**
* @return The properly unswaped 16 bits integer.
*/
guint16 gdcmDocument::UnswapShort(guint16 a) {
- return (SwapShort(a));
+ return SwapShort(a);
}
//-----------------------------------------------------------------------------
// Private
-
-
/**
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
- * @return false if file is not ACR-NEMA / PAPYRUS / DICOM
+ * @return length of the parsed set.
*/
-long gdcmDocument::ParseES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
+long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
- gdcmValEntry *vl;
+ gdcmValEntry *NewValEntry = (gdcmValEntry *)0;
+ gdcmBinEntry *bn;
gdcmSeqEntry *sq;
- long l;
+ 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;
- if (NewDocEntry->GetVR() !="SQ") {
- vl= new gdcmValEntry(NewDocEntry->GetDictEntry());
- vl->Copy(NewDocEntry);
- delete NewDocEntry;
- set->AddEntry(vl);
- if (!delim_mode && vl->isItemDelimitor())
- break;
-
- } else { // VR = "SQ"
- l=NewDocEntry->GetReadLength();
- if (l == 0xffffffff)
- delim_mode = true;
- else
- delim_mode = false;
- sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry());
- sq->Copy(NewDocEntry);
- long lgt = ParseSQ((gdcmDocEntrySet *)sq, offset, l, delim_mode);
- set->AddEntry(sq);
- if ( !delim_mode && ftell(fp)-offset >= l_max)
- break;
- }
- }
- return l; // ??
-}
+ 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->GetReadLength()==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...
+ }
+ set->AddEntry(sq);
+ if ( !delim_mode && ftell(fp)-offset >= l_max)
+ {
+ break;
+ }
+ }
+ delete NewDocEntry;
+ }
+ return l; // Probably useless
+}
-long gdcmDocument::ParseSQ(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
+/**
+ * \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 lgr, lgth;
+ unsigned int l;
+ int depth = set->GetDepthLevel();
+ (void)depth; //not used
+
while (true) {
+
+ NewDocEntry = ReadNextDocEntry();
+ if (!NewDocEntry)
+ break;
if(delim_mode) {
- NewDocEntry = ReadNextDocEntry();
- if (NewDocEntry->isSequenceDelimitor())
- // =====> ATTENTION : il faudra tout de meme ajouter
- // le Sequence Delimiter ?!?
- //set.Add(???);
- break;
- }
- if (!delim_mode && (ftell(fp)-offset) >= l_max){
- break;
- }
- itemSQ = new gdcmSQItem();
+ 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();
- l= NewDocEntry->GetLength();
- if (l ==0xffffffff)
+ if (l == 0xffffffff)
dlm_mod = true;
else
dlm_mod=false;
-
- lgr=ParseES(itemSQ, offset, l, dlm_mod);
- ((gdcmSeqEntry *)set)->AddEntry(itemSQ);
- }
- //Update(lgth); // TODO // to go on compiling
- return(lgth);
-}
-
-
-/**
- * \brief Parses the header of the file and load element values.
- * @return false if file is not ACR-NEMA / PAPYRUS / DICOM
- */
-
-/* =======================================================================
-// Replaced by ParseSQ
-
-bool gdcmDocument::LoadHeaderEntries(bool exception_on_error) throw(gdcmFormatError) {
- (void)exception_on_error;
- rewind(fp);
- if (!CheckSwap())
- return false;
-
- gdcmDocEntry *newDocEntry = (gdcmDocEntry *)0;
- while ( (newDocEntry = ReadNextDocEntry()) ) {
- SkipDocEntry(newDocEntry);
- if ( (ignoreShadow==0) || (newDocEntry->GetGroup()%2) == 0) {
- AddDocEntry(newDocEntry);
- }
- }
- rewind(fp);
- // Be carefull : merging this two loops may cause troubles ...
- for (ListTag::iterator i = GetListEntry().begin();
- i != GetListEntry().end();
- ++i)
- {
- LoadDocEntry(*i);
- }
- rewind(fp);
-
- // Load 'non string' values
-
- // --------------------------------------------------------------
- // 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 = ACR_LIBIDO;
- std::string rows = GetEntryByNumber(0x0028, 0x0010);
- std::string columns = GetEntryByNumber(0x0028, 0x0011);
- SetEntryByNumber(columns, 0x0028, 0x0010);
- SetEntryByNumber(rows , 0x0028, 0x0011);
+ lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod);
+
+ set->AddEntry(itemSQ,SQItemNumber);
+ SQItemNumber ++;
+ if (!delim_mode && (ftell(fp)-offset) >= l_max) {
+ break;
+ }
}
- // ----------------- End of Special Patch ----------------
- return true;
+ 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::LoadDocEntry(gdcmDocEntry *Entry) {
+void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry)
+{
size_t item_read;
guint16 group = Entry->GetGroup();
std::string vr= Entry->GetVR();
// (fffe e0dd) tells us the current SeQuence just ended
if( group == 0xfffe ) {
// NO more value field for SQ !
- //Entry->SetValue("gdcm::Skipped");
- // appel recursif de Load Value
- // (meme pb que pour le parsing)
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.
+
+ std::ostringstream s;
if (length > MaxSizeLoadEntry) {
- std::ostringstream s;
- s << "gdcm::NotLoaded.";
- s << " Address:" << (long)Entry->GetOffset();
- s << " Length:" << Entry->GetLength();
- s << " x(" << std::hex << Entry->GetLength() << ")";
- ((gdcmValEntry *)Entry)->SetValue(s.str());
+ if (gdcmBinEntry* BinEntryPtr = dynamic_cast< gdcmBinEntry* >(Entry) )
+ {
+ 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) )
+ {
+ 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);
+ s << "gdcm::Loaded (BinEntry)";
+ BinEntryPtr->SetValue(s.str());
return;
}
+
// Any compacter code suggested (?)
if ( IsDocEntryAnInteger(Entry) ) {
// We need an additional byte for storing \0 that is not on disk
std::string NewValue(length,0);
item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp);
- if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmDocument::LoadElementValue","unread element value");
- ((gdcmValEntry *)Entry)->SetValue("gdcm::UnRead");
- return;
+ if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(Entry) ) {
+ if ( item_read != 1 ) {
+ dbg.Verbose(1, "gdcmDocument::LoadElementValue","unread element value");
+ ValEntry->SetValue("gdcm::UnRead");
+ return;
+ }
+
+ if( (vr == "UI") ) // Because of correspondance with the VR dic
+ ValEntry->SetValue(NewValue.c_str());
+ else
+ ValEntry->SetValue(NewValue);
+ } else {
+ // fusible
+ std::cout << "Should have a ValEntry, here !" << std::endl;
}
- if( (vr == "UI") ) // Because of correspondance with the VR dic
- ((gdcmValEntry *)Entry)->SetValue(NewValue.c_str());
- else
- ((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 newDocEntry
- */
-void gdcmDocument::AddDocEntry(gdcmDocEntry *newDocEntry) {
- tagHT.insert( PairHT( newDocEntry->GetKey(),newDocEntry) );
- listEntries.push_back(newDocEntry);
-}
/**
* \brief Find the value Length of the passed Header Entry
guint16 length16;
- if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) )
+ if ( (Filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) )
{
if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") )
{
Entry->SetDictEntry(NewTag);
}
- // Heuristic: well some files are really ill-formed.
+ // Heuristic: well, some files are really ill-formed.
if ( length16 == 0xffff)
{
length16 = 0;
- //dbg.Verbose(0, "gdcmDocument::FindLength",
- // "Erroneous element length fixed.");
- // Actually, length= 0xffff means that we deal with
- // Unknown Sequence Length
+ // Length16= 0xffff means that we deal with
+ // 'Unknown Length' Sequence
}
FixDocEntryFoundLength(Entry, (guint32)length16);
return;
*/
void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry)
{
- if (filetype != ExplicitVR)
+ if (Filetype != gdcmExplicitVR)
return;
char VR[3];
"UL","FIXME","Group Length");
Entry->SetDictEntry(NewEntry);
}
- return(false);
+ return false;
}
if ( Entry->IsVRUnknown() )
vr,"FIXME",Entry->GetName());
Entry->SetDictEntry(NewEntry);
}
- return(true);
+ return true;
}
/**
{
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;
#ifdef GDCM_NO_ANSI_STRING_STREAM
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
- return(s.str());
+ return s.str();
}
- return(Entry->GetValue());
+ return ((gdcmValEntry *)Entry)->GetValue();
}
/**
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; i<tokens.size();i++)
{
NewInt16 = atoi(tokens[i].c_str());
guint32 NewInt32;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (Entry->GetValue(), tokens, "\\");
+ Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
NewInt32 = atoi(tokens[i].c_str());
#ifdef GDCM_NO_ANSI_STRING_STREAM
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
- return(s.str());
+ return s.str();
}
- return(Entry->GetValue());
+ return ((gdcmValEntry *)Entry)->GetValue();
}
/**
*/
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::FixDocEntryFoundLength(gdcmDocEntry *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) {
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);
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.
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::IsDocEntryAnInteger",
- // 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 !
* (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);
* (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);
void gdcmDocument::Initialise(void)
{
RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
- RefShaDict = (gdcmDict*)0;
+ RefShaDict = NULL;
}
/**
// 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");
}
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 :
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;
}
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
+ * (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.
*/
gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) {
// header parsing has to be considered as finished.
return (gdcmDocEntry *)0;
-// 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 (gdcmDocEntry *)1; // to tell caller it's NOT finished
-
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 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.
+ */
+guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group)
+{
+ 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 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 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.
*/
-gdcmDocEntry *gdcmDocument::NewDocEntryByName(std::string Name)
+guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement)
{
- gdcmDictEntry *NewTag = GetDictEntryByName(Name);
- if (!NewTag)
- NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name);
+ guint16 ItemTagGroup;
+ guint16 ItemTagElement;
+ long PositionOnEntry = ftell(fp);
+ long CurrentPosition = ftell(fp); // On debugging purposes
- gdcmDocEntry* NewEntry = new gdcmDocEntry(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 ) )
{
- dbg.Verbose(1, "gdcmDocument::ObtainDocEntryByName",
- "failed to allocate gdcmDocEntry");
- return (gdcmDocEntry *)0;
+ 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;
}
- return NewEntry;
-}
+
+ //// Then read the associated Item Length
+ CurrentPosition=ftell(fp);
+ guint32 ItemLength;
+ ItemLength = ReadInt32();
+ {
+ 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 ItemLength;
+}
+
+/**
+ * \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 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 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
+ *
*/
-gdcmDocEntry *gdcmDocument::NewDocEntryByNumber(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());
+ }
+ }
- gdcmDocEntry *NewEntry = new gdcmDocEntry(DictEntry);
- if (!NewEntry)
+ if ( ! IsRLELossLessTransferSyntax() )
{
- dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber",
- "failed to allocate gdcmDocEntry");
- 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) 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.
- */
-//gdcmDocEntry *gdcmDocument::NewManualDocEntryToPubDict(std::string NewTagName,
-// std::string VR)
-//{
-// gdcmDocEntry *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::NewManualDocEntryToPubDict",
-// "Group 0xffff in Public Dict is full");
-// return NULL;
-// }
-//
-// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem,
-// VR, "GDCM", NewTagName);
-// NewEntry = new gdcmDocEntry(DictEntry);
-// AddDocEntry(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;
}
+
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff