#include "gdcmParser.h"
#include "gdcmUtil.h"
#include <errno.h>
+#include <unistd.h>
// For nthos:
#ifdef _MSC_VER
//
// Other usefull abreviations :
- //Radiographic view associated with Patient Position (0018,5100).
- // Defined Terms:
+ // Radiographic view associated with Patient Position (0018,5100).
+ // Defined Terms:
//
// AP = Anterior/Posterior
// PA = Posterior/Anterior
* \ingroup gdcmParser
* \brief constructor
* @param inFilename
- * @param exception_on_error
+ * @param exception_on_error whether we throw an exception or not
* @param enable_sequences = true to allow the header
* to be parsed *inside* the SeQuences,
* when they have an actual length
enableSequences=enable_sequences;
ignoreShadow =ignore_shadow;
- SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
+ SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
filename = inFilename;
Initialise();
/**
* \ingroup gdcmParser
- * \brief Prints The Dict Entries of THE shadow Dicom Dictionnry
+ * \brief Prints The Dict Entries of THE shadow Dicom Dictionnary
* @return
*/
void gdcmParser::PrintShaDict(std::ostream & os) {
* \ingroup gdcmParser
* \brief Modifies the value of a given Header Entry (Dicom Element)
* if it exists; Creates it with the given value if it doesn't
+ * \warning : adds the Header Entry to the HTable, NOT to the chained List
* @param Value passed as a std::string
- * @param Group
- * @param Elem
- * \return false only if new element creation fails
+ * @param Group group of the Entry
+ * @param Elem element of the Entry
+ * \return pointer to the created Header Entry
+ * NULL if creation failed
*/
-bool gdcmParser::ReplaceOrCreateByNumber(std::string Value,
+gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber(
+ std::string Value,
guint16 Group,
- guint16 Elem ){
- if (CheckIfEntryExistByNumber(Group, Elem) == 0) {
+ guint16 Elem ){
+ gdcmHeaderEntry* a;
+ a = GetHeaderEntryByNumber( Group, Elem);
+ if (a == NULL) {
gdcmHeaderEntry *a =NewHeaderEntryByNumber(Group, Elem);
if (a == NULL)
- return false;
+ return NULL;
AddHeaderEntry(a);
}
- SetEntryByNumber(Value, Group, Elem);
- return(true);
+ //SetEntryByNumber(Value, Group, Elem);
+ a->SetValue(Value);
+ return(a);
}
/**
* @param Value passed as a char*
* @param Group group of the Entry
* @param Elem element of the Entry
- * \return boolean
+ * \return pointer to the created Header Entry
+ * NULL if creation failed
*
*/
-bool gdcmParser::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) {
+gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber(
+ char* Value,
+ guint16 Group,
+ guint16 Elem ) {
gdcmHeaderEntry* nvHeaderEntry=NewHeaderEntryByNumber(Group, Elem);
if(!nvHeaderEntry)
- return(false);
+ return(NULL);
AddHeaderEntry(nvHeaderEntry);
std::string v = Value;
SetEntryByNumber(v, Group, Elem);
- return(true);
+ return(nvHeaderEntry);
}
/**
/**
* \ingroup gdcmParser
* \brief Update the entries with the shadow dictionary.
- * Only non even entries are analyzed
+ * Only non even entries are analyzed
*/
void gdcmParser::UpdateShaEntries(void) {
gdcmDictEntry *entry;
/**
* \ingroup gdcmParser
* \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 temporay method for Theralys)
+ * (ACR-NEMA, ExplicitVR, ImplicitVR) ONE
+ * gdcmHeaderEntry
+ * @param tag pointer on the gdcmHeaderEntry to be written
* @param type type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* @param _fp already open file pointer
*/
-void gdcmParser::WriteEntries(FILE *_fp,FileType type)
+void gdcmParser::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
{
guint16 gr, el;
guint32 lgr;
guint16 valZero =0;
void *voidArea;
std::vector<std::string> tokens;
-
- // TODO : function CheckHeaderCoherence to be written
-
- // uses now listEntries to iterate, not TagHt!
- //
- // pb : gdcmParser.Add does NOT update listEntries
- // TODO : find a trick (in STL?) to do it, at low cost !
void *ptr;
int ff=0xffffffff;
// TODO (?) tester les echecs en ecriture (apres chaque fwrite)
int compte =0;
-
- for (ListTag::iterator tag2=listEntries.begin();
- tag2 != listEntries.end();
- ++tag2)
- {
+ itsTimeToWritePixels = false;
+
+ gr = tag->GetGroup();
+ el = tag->GetElement();
+ lgr = tag->GetReadLength();
+ val = tag->GetValue().c_str();
+ vr = tag->GetVR();
+ voidArea = tag->GetVoidArea();
+
// === Deal with the length
// --------------------
- if(((*tag2)->GetLength())%2==1)
+ if((tag->GetLength())%2==1)
{
- (*tag2)->SetValue((*tag2)->GetValue()+"\0");
- (*tag2)->SetLength((*tag2)->GetReadLength()+1);
+ tag->SetValue(tag->GetValue()+"\0");
+ tag->SetLength(tag->GetReadLength()+1);
}
-
- gr = (*tag2)->GetGroup();
- el = (*tag2)->GetElement();
- lgr = (*tag2)->GetReadLength();
- val = (*tag2)->GetValue().c_str();
- vr = (*tag2)->GetVR();
- voidArea = (*tag2)->GetVoidArea();
if ( type == ACR )
{
- if (gr < 0x0008) continue; // ignore pure DICOM V3 groups
- if (gr %2) continue; // ignore shadow groups
- if (vr == "SQ" ) continue; // ignore Sequences
+ if (gr < 0x0008) return; // ignore pure DICOM V3 groups
+ if (gr %2) return; // ignore shadow groups
+ if (vr == "SQ" ) return; // ignore Sequences
// TODO : find a trick to *skip* the SeQuences !
// Not only ignore the SQ element
- if (gr == 0xfffe ) continue; // ignore delimiters
+ if (gr == 0xfffe ) return; // ignore delimiters
}
fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group
guint16 z=0, shortLgr;
if (gr == 0xfffe) { // NO Value Representation for 'delimiters'
- // no length : write ffffffff
+ // no length : write ffffffff
+
+ // special patch to make some MR PHILIPS
+ if (el == 0x0000) return; // images e-film readable // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm
+ // from Hospital Guy de Chauliac,
+ // Montpellier
+ // we just ignore spurious fffe|0000 tag !
+
fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp);
- continue; // NO value for 'delimiters'
+ return; // NO value for 'delimiters'
}
shortLgr=lgr;
// === Deal with the value
// -------------------
- if (vr == "SQ") continue; // no "value" to write for the SEQuences
- if (gr == 0xfffe)continue; // no "value" to write for the delimiters
+ if (vr == "SQ") return; // no "value" to write for the SEQuences
+ if (gr == 0xfffe)return; // no "value" to write for the delimiters
if (voidArea != NULL)
{ // there is a 'non string' LUT, overlay, etc
fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
- continue;
+ return;
}
if (vr == "US" || vr == "SS")
{
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((*tag2)->GetValue(), tokens, "\\");
+ Tokenize (tag->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
val_uint16 = atoi(tokens[i].c_str());
fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
}
tokens.clear();
- continue;
+ return;
}
if (vr == "UL" || vr == "SL")
{
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((*tag2)->GetValue(), tokens, "\\");
+ Tokenize (tag->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
val_uint32 = atoi(tokens[i].c_str());
fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
}
tokens.clear();
- continue;
+ return;
}
// Pixels are never loaded in the element !
if ((gr == GrPixel) && (el == NumPixel) ) {
compte++;
- if (compte == countGrPixel) // we passed *all* the GrPixel,NumPixel
- break;
+ if (compte == countGrPixel) {// we passed *all* the GrPixel,NumPixel
+ itsTimeToWritePixels = true;
+ return;
+ }
}
fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
- }
}
+/**
+ * \ingroup gdcmParser
+ * \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
+ */
+
+void gdcmParser::WriteEntries(FILE *_fp,FileType type)
+{
+ // TODO (?) tester les echecs en ecriture (apres chaque fwrite)
+
+ for (ListTag::iterator tag2=listEntries.begin();
+ tag2 != listEntries.end();
+ ++tag2)
+ {
+ WriteEntry(*tag2,_fp,type);
+ if (itsTimeToWritePixels)
+ break;
+ }
+}
/**
* \ingroup gdcmParser
* (ACR-NEMA, ExplicitVR, ImplicitVR)
*/
void gdcmParser::WriteEntriesDeprecated(FILE *_fp,FileType type) {
- guint16 gr, el;
- guint32 lgr;
- const char * val;
- std::string vr;
- guint32 val_uint32;
- guint16 val_uint16;
-
- std::vector<std::string> tokens;
- void *ptr;
-
- // Tout ceci ne marche QUE parce qu'on est sur un proc Little Endian
// restent a tester les echecs en ecriture (apres chaque fwrite)
for (TagHeaderEntryHT::iterator tag2=tagHT.begin();
tag2 != tagHT.end();
++tag2){
-
- gr = tag2->second->GetGroup();
- el = tag2->second->GetElement();
- lgr = tag2->second->GetLength();
- val = tag2->second->GetValue().c_str();
- vr = tag2->second->GetVR();
-
- // std::cout << "Tag "<< std::hex << gr << " " << el << std::endl;
-
- if ( type == ACR ) {
- if (gr < 0x0008) continue; // ignore pure DICOM V3 groups
- if (gr %2) continue; // ignore shadow groups
- if (vr == "SQ" ) continue; // ignore Sequences
- if (gr == 0xfffe ) continue; // ignore delimiters
- }
-
- fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group
- fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
-
- if ( (type == ExplicitVR) && (gr <= 0x0002) ) {
- // EXPLICIT VR
- guint16 z=0, shortLgr;
- 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 {
- shortLgr=lgr;
- fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
- }
- } else { // IMPLICIT VR
- fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
- }
-
- if (vr == "US" || vr == "SS") {
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (tag2->second->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- val_uint16 = atoi(tokens[i].c_str());
- ptr = &val_uint16;
- fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- continue;
- }
- if (vr == "UL" || vr == "SL") {
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (tag2->second->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- val_uint32 = atoi(tokens[i].c_str());
- ptr = &val_uint32;
- fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- continue;
- }
- // Pixels are never loaded in the element !
- if ((gr == 0x7fe0) && (el == 0x0010) ) break;
-
- fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
+ WriteEntry(tag2->second,_fp,type);
+ if (itsTimeToWritePixels)
+ break;
}
}
-
-
-
-
-
/**
* \ingroup gdcmParser
* \brief Swaps back the bytes of 4-byte long integer accordingly to
/**
* \ingroup gdcmParser
* \brief add a new Dicom Element pointer to
- * the H Table and to the chained List
+ * 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)
}
// a SeQuence Element is beginning
- // Let's forget it's length
- // (we want to 'go inside')
-
- // Pb : *normaly* fffe|e000 is just a marker, its length *should be* zero
- // in gdcm-MR-PHILIPS-16-Multi-Seq.dcm we find lengthes as big as 28800
- // if we set the length to zero IsHeaderEntryAnInteger() breaks...
- // if we don't, we lost 28800 characters from the Header :-(
-
+ // fffe|e000 is just a marker, its length *should be* zero
else if(Entry->GetGroup() == 0xfffe)
{
- // cout << "ReadLength " <<Entry->GetReadLength() << " UsableLength " << FoundLength << endl;
- // Entry->Print();
- // sometimes, length seems to be wrong
- FoundLength =0; // some more clever checking to be done !
- // I give up!
- // only gdcm-MR-PHILIPS-16-Multi-Seq.dcm
- // causes troubles :-(
- }
-
+ // *normally, fffe|0000 doesn't exist !
+ if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm
+ // causes extra troubles :-(
+ FoundLength =0;
+ }
Entry->SetUsableLength(FoundLength);
}
/**
* \ingroup gdcmParser
- * \brief Apply some heuristics to predict wether the considered
+ * \brief Apply some heuristics to predict whether the considered
* element value contains/represents an integer or not.
* @param Entry The element value on which to apply the predicate.
* @return The result of the heuristical predicate.
/**
* \ingroup gdcmParser
- * \brief
+ * \brief skips bytes inside the source file
* \warning NOT end user intended method !
* @return
*/
/**
* \ingroup gdcmParser
- * \brief
+ * \brief Loads all the needed Dictionaries
+ * \warning NOT end user intended method !
*/
void gdcmParser::Initialise(void)
{
/**
* \ingroup gdcmParser
- * \brief
+ * \brief Restore the unproperly loaded values i.e. the group, the element
+ * and the dictionary entry depending on them.
*/
void gdcmParser::SwitchSwapToBigEndian(void)
{
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff