-// gdcmDocument.cxx
-//-----------------------------------------------------------------------------
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmDocument.cxx,v $
+ Language: C++
+ Date: $Date: 2004/06/23 13:02:36 $
+ Version: $Revision: 1.27 $
+
+ 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"
#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))
//-----------------------------------------------------------------------------
* 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());
+ Filename.c_str());
rewind(fp);
fseek(fp,0L,SEEK_END);
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();
// --------------------------------------------------------------
RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
// with "little-endian strings"
{
- filetype = gdcmACR_LIBIDO;
+ Filetype = gdcmACR_LIBIDO;
std::string rows = GetEntryByNumber(0x0028, 0x0010);
std::string columns = GetEntryByNumber(0x0028, 0x0011);
SetEntryByNumber(columns, 0x0028, 0x0010);
// Recursive clean up of sequences
for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it )
- {
- delete (it->second);
+ {
+ delete it->second;
}
tagHT.clear();
}
* false otherwise.
*/
bool gdcmDocument::IsReadable(void) {
- if(filetype==gdcmUnknown) {
+ if(Filetype==gdcmUnknown) {
dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype");
return(false);
}
return(true);
}
+
/**
* \brief Internal function that checks whether the Transfer Syntax given
* as argument is the one present in the current document.
* @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_90) );
+ || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70) ); // was 90
}
/**
* @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");
+ fp=fopen(Filename.c_str(),"rb");
if(!fp)
{
throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)");
else
{
- std::cout <<"gdcmDocument::OpenFile cannot open file: "
- << filename.c_str() << std::endl;
dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ",
- filename.c_str());
- return (NULL);
+ Filename.c_str());
+ return NULL;
}
}
//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 Group*HT 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 == gdcmImplicitVR)
+ if (filetype == gdcmImplicitVR)
{
std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2;
ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
SetEntryLengthByNumber(18, 0x0002, 0x0010);
}
- if (type == gdcmExplicitVR)
+ 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);
+ /// WriteEntries(fp,type); // old stuff
+ return true;
}
/**
gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
std::string Value,
guint16 Group,
- guint16 Elem ){
+ guint16 Elem )
+{
gdcmDocEntry* CurrentEntry;
gdcmValEntry* ValEntry;
{
dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
" NewDocEntryByNumber failed.");
- return (gdcmValEntry *)0;
+ return NULL;
}
ValEntry = new gdcmValEntry(CurrentEntry);
if ( !AddEntry(ValEntry))
{
dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
" of previous DocEntry failed.");
- return (gdcmValEntry *)0;
+ return NULL;
}
if ( !AddEntry(ValEntry))
{
dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
" promoted ValEntry failed.");
- return (gdcmValEntry *)0;
+ return NULL;
}
}
}
guint16 Elem)
{
gdcmDocEntry* a;
- gdcmBinEntry* b;
+ gdcmBinEntry* b;
a = GetDocEntryByNumber( Group, Elem);
if (a == NULL) {
a =NewBinEntryByNumber(Group, Elem);
if (a == NULL)
return NULL;
- b = new gdcmBinEntry(a);
+
+ b = new gdcmBinEntry(a);
AddEntry(b);
}
SetEntryByNumber(voidArea, lgth, Group, Elem);
b->SetVoidArea(voidArea);
- return (gdcmBinEntry*)b;
+
+ return b;
}
*/
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;
if( dictEntry == NULL)
return false;
- return(SetEntryByNumber(content,dictEntry->GetGroup(),
- dictEntry->GetElement()));
+ return SetEntryByNumber(content,dictEntry->GetGroup(),
+ dictEntry->GetElement());
}
/**
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).
{
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();
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();
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);
/**
* \brief Sets a 'non string' value to a given Dicom Element
- * @param area
+ * @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?
fseek(fp, PositionOnEntry, SEEK_SET);
}
-
-/**
- * \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();
- VRKey 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 == gdcmExplicitVR ) {
-
- // 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 TODO : to be re -written recursively !
-void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type)
-{
- (void)type;
- guint16 group = tag->GetGroup();
- VRKey vr = tag->GetVR();
- guint32 lgr = tag->GetReadLength();
-
- if (vr == "SQ")
- // SeQuences have no value:
- return;
- if (group == 0xfffe)
- // Delimiters have no associated value:
- return;
-
- //--------------------------------
- //
- // FIXME :right now, both value and voidArea belong to gdcmValue
- //
- // -------------------------------
-
-// if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) ) {
- void *voidArea;
- gdcmBinEntry *BinEntry= (gdcmBinEntry *)tag;;
- voidArea = BinEntry->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<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)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;
- }
- if (vr == "UL" || vr == "SL")
- {
- // Some 'Integer' fields may be multivaluated (multiple instances
- // of integers). But each single integer value is separated from the
- // next one by '\' (backslash character). Hence we split the string
- // along the '\' and write each value as an int:
- std::vector<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)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 (((gdcmValEntry *)tag)->GetValue().c_str(),
- (size_t)lgr ,(size_t)1, _fp); // Elem value
-}
-
-/**
- * \brief Writes in a file (according to the requested format)
- * a single 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();
-
- if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(tag) )
- {
- // 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) {
- ValEntry->SetValue(ValEntry->GetValue()+"\0");
- ValEntry->SetLength(ValEntry->GetReadLength()+1);
- }
- WriteEntryTagVRLength(ValEntry, _fp, type);
- WriteEntryValue(ValEntry, _fp, type);
- return true;
- }
-
- if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) )
- {
- /// \todo FIXME : when voidArea belong to gdcmBinEntry only, fix
- /// voidArea length
- //
- // 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!)
- * @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 FIXME : explore recursively the whole structure...
- /// \todo (?) check write failures (after *each* fwrite)
-
- dbg.Verbose(0, "gdcmDocument::WriteEntries: entering.");
- for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it )
- {
- gdcmDocEntry * entry = it->second;
-
- if ( type == gdcmACR ){
- if (entry->GetGroup() < 0x0008)
- // Ignore pure DICOM V3 groups
- continue;
- if (entry->GetGroup() %2)
- // Ignore the "shadow" groups
- continue;
- if (entry->GetVR() == "SQ" ) // ignore Sequences
- continue;
- }
- if (! WriteEntry(entry, _fp, type) ) {
- dbg.Verbose(0, "gdcmDocument::WriteEntries: write failure.");
- return false;
- }
- }
- return true;
-}
-
-
/**
* \brief Swaps back the bytes of 4-byte long integer accordingly to
* processor order.
a=0;
}
return(a);
-}
+}
/**
* \brief Unswaps back the bytes of 4-byte long integer accordingly to
/**
* \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::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
gdcmBinEntry *bn;
gdcmSeqEntry *sq;
VRKey vr;
- long l;
+ unsigned long l;
int depth;
depth = set->GetDepthLevel();
NewValEntry->SetDepthLevel(depth);
set->AddEntry(NewValEntry);
LoadDocEntry(NewValEntry);
- if (/*!delim_mode && */NewValEntry->isItemDelimitor())
+ if (NewValEntry->isItemDelimitor())
break;
if ( !delim_mode && ftell(fp)-offset >= l_max)
{
long lgt = ParseSQ( sq,
NewDocEntry->GetOffset(),
l, delim_mode);
+ (void)lgt; //not used...
}
// FIXME : on en fait quoi, de lgt ?
set->AddEntry(sq);
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(delim_mode) {
if (NewDocEntry->isSequenceDelimitor()) {
- /// \todo add the Sequence Delimitor
- /// \todo find the trick to put it properly !
set->SetSequenceDelimitationItem(NewDocEntry);
break;
}
itemSQ = new gdcmSQItem(set->GetDepthLevel());
itemSQ->AddEntry(NewDocEntry);
- /// \todo no value, no voidArea. Think of it while printing !
l= NewDocEntry->GetReadLength();
if (l == 0xffffffff)
lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod);
- set->AddEntry(itemSQ,SQItemNumber);
+ set->AddEntry(itemSQ,SQItemNumber);
SQItemNumber ++;
if (!delim_mode && (ftell(fp)-offset) >= l_max) {
break;
// (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.
+
if (length > MaxSizeLoadEntry) {
+ 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.";
+ 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);
-
+ 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 ( IsDocEntryAnInteger(Entry) ) {
guint16 length16;
- if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) )
+ if ( (Filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) )
{
if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") )
{
*/
void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry)
{
- if (filetype != gdcmExplicitVR)
+ if (Filetype != gdcmExplicitVR)
return;
char VR[3];
(void)fseek(fp, (long)(entry->GetReadLength()), SEEK_CUR);
}
-/**
- * \brief Loads the value for a a given VLEntry
- * \warning NOT end user intended method !
- * @param entry
- */
-void gdcmDocument::LoadVLEntry(gdcmDocEntry *entry)
-{
- //SkipBytes(entry->GetLength());
- LoadDocEntry(entry);
-}
/**
* \brief When the length of an element value is obviously wrong (because
* the parser went Jabberwocky) one can hope improving things by
* (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 = gdcmExplicitVR;
+ Filetype = gdcmExplicitVR;
dbg.Verbose(1, "gdcmDocument::CheckSwap:",
"explicit Value Representation");
}
else
{
- filetype = gdcmImplicitVR;
+ Filetype = gdcmImplicitVR;
dbg.Verbose(1, "gdcmDocument::CheckSwap:",
"not an explicit Value Representation");
}
switch (s32) {
case 0x00040000 :
sw = 3412;
- filetype = gdcmACR;
+ Filetype = gdcmACR;
return true;
case 0x04000000 :
sw = 4321;
- filetype = gdcmACR;
+ Filetype = gdcmACR;
return true;
case 0x00000400 :
sw = 2143;
- filetype = gdcmACR;
+ Filetype = gdcmACR;
return true;
case 0x00000004 :
sw = 0;
- filetype = gdcmACR;
+ Filetype = gdcmACR;
return true;
default :
case 0x0004 :
case 0x0008 :
sw = 0;
- filetype = gdcmACR;
+ Filetype = gdcmACR;
return true;
case 0x0200 :
case 0x0400 :
case 0x0800 :
sw = 4321;
- filetype = gdcmACR;
+ Filetype = gdcmACR;
return true;
default :
dbg.Verbose(0, "gdcmDocument::CheckSwap:",
"ACR/NEMA unfound swap info (Really hopeless !)");
- filetype = gdcmUnknown;
+ Filetype = gdcmUnknown;
return false;
}
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
- */
-gdcmDocEntry *gdcmDocument::NewDocEntryByName(std::string Name)
-{
- gdcmDictEntry *NewTag = GetDictEntryByName(Name);
- if (!NewTag)
- NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name);
-
- gdcmDocEntry* NewEntry = new gdcmDocEntry(NewTag);
- if (!NewEntry)
- {
- dbg.Verbose(1, "gdcmDocument::ObtainDocEntryByName",
- "failed to allocate gdcmDocEntry");
- return (gdcmDocEntry *)0;
- }
- return NewEntry;
-}
-
-/**
- * \brief Request a new virtual dict entry to the dict set
- * @param group group number of the underlying DictEntry
- * @param element element number of the underlying DictEntry
- * @param vr VR of the underlying DictEntry
- * @param fourth owner group
- * @param name english name
- */
-gdcmDictEntry *gdcmDocument::NewVirtualDictEntry(guint16 group, guint16 element,
- std::string vr,
- std::string fourth,
- std::string name)
-{
- return gdcmGlobal::GetDicts()->NewVirtualDictEntry(group,element,vr,fourth,name);
-}
-
-/**
- * \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 number of the underlying DictEntry
- * @param Elem element number of the underlying DictEntry
- */
-gdcmDocEntry* gdcmDocument::NewDocEntryByNumber(guint16 Group, guint16 Elem)
-{
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
- if (!DictEntry)
- DictEntry = NewVirtualDictEntry(Group, Elem);
-
- gdcmDocEntry *NewEntry = new gdcmDocEntry(DictEntry);
- if (!NewEntry)
- {
- dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber",
- "failed to allocate gdcmDocEntry");
- return (gdcmDocEntry*)0;
- }
- 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 Group group number of the underlying DictEntry
- * @param Elem element number of the underlying DictEntry
- */
-gdcmValEntry *gdcmDocument::NewValEntryByNumber(guint16 Group, guint16 Elem)
-{
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
- if (!DictEntry)
- DictEntry = NewVirtualDictEntry(Group, Elem);
-
- gdcmValEntry *NewEntry = new gdcmValEntry(DictEntry);
- if (!NewEntry)
- {
- dbg.Verbose(1, "gdcmDocument::NewValEntryByNumber",
- "failed to allocate gdcmValEntry");
- return NULL;
- }
- 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 Group group number of the underlying DictEntry
- * @param Elem element number of the underlying DictEntry
- */
-gdcmBinEntry *gdcmDocument::NewBinEntryByNumber(guint16 Group, guint16 Elem)
-{
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
- if (!DictEntry)
- DictEntry = NewVirtualDictEntry(Group, Elem);
-
- gdcmBinEntry *NewEntry = new gdcmBinEntry(DictEntry);
- if (!NewEntry)
- {
- dbg.Verbose(1, "gdcmDocument::NewBinEntryByNumber",
- "failed to allocate gdcmBinEntry");
- return NULL;
- }
- return NewEntry;
-}
/**
* \brief Generate a free TagKey i.e. a TagKey that is not present
}
-/**
- * \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 number of the searched DictEntry
- * @param element element number 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 Assuming the internal file pointer \ref gdcmDocument::fp
* is placed at the beginning of a tag (TestGroup, TestElement),
}
/**
- * \brief Read the length of an exptected Sequence Delimiter tag i.e.
+ * \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
* No other way so 'skip' the Data
*
*/
+
void gdcmDocument::Parse7FE0 (void)
{
gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
// BTW, what is the purpous of those length anyhow !?
char * BasicOffsetTableItemValue = new char[ItemLength + 1];
fread(BasicOffsetTableItemValue, ItemLength, 1, fp);
- for (int i=0; i < ItemLength; i += 4){
+ for (unsigned int i=0; i < ItemLength; i += 4){
guint32 IndividualLength;
IndividualLength = str2num(&BasicOffsetTableItemValue[i],guint32);
std::ostringstream s;
// JPEG Image
//// We then skip (not reading them) all the fragments of images:
- while ( ItemLength = ReadItemTagLength() )
+ while ( (ItemLength = ReadItemTagLength()) )
{
SkipBytes(ItemLength);
}
long RleSegmentLength[15], fragmentLength;
// while 'Sequence Delimiter Item' (fffe,e0dd) not found
- while ( fragmentLength = ReadSequenceDelimiterTagLength() )
+ while ( (fragmentLength = ReadSequenceDelimiterTagLength()) )
{
// Parse fragments of the current Fragment (Frame)
//------------------ scanning (not reading) fragment pixels
SkipBytes(RleSegmentLength[nbRleSegments]);
}
}
- return;
}
+
+
/**
* \brief Compares two documents, according to \ref gdcmDicomDir rules
* \warning Does NOT work with ACR-NEMA files
* @param document
* @return true if 'smaller'
*/
- bool gdcmDocument::operator<(gdcmDocument &document){
+bool gdcmDocument::operator<(gdcmDocument &document)
+{
std::string s1,s2;
// Patient Name
s1=this->GetEntryByNumber(0x0010,0x0010);
s2=document.GetEntryByNumber(0x0010,0x0010);
if(s1 < s2)
- return(true);
+ return true;
else if(s1 > s2)
- return(false);
+ return false;
else
{
// Patient ID
s1=this->GetEntryByNumber(0x0010,0x0020);
s2=document.GetEntryByNumber(0x0010,0x0020);
if (s1 < s2)
- return(true);
+ return true;
else if (s1 > s2)
- return(1);
+ return true;
else
{
// Study Instance UID
s1=this->GetEntryByNumber(0x0020,0x000d);
s2=document.GetEntryByNumber(0x0020,0x000d);
if (s1 < s2)
- return(true);
+ return true;
else if(s1 > s2)
- return(false);
+ return false;
else
{
// Serie Instance UID
s1=this->GetEntryByNumber(0x0020,0x000e);
s2=document.GetEntryByNumber(0x0020,0x000e);
if (s1 < s2)
- return(true);
+ return true;
else if(s1 > s2)
- return(false);
+ return false;
}
}
}
- return(false);
+ return false;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff