// gdcmDocEntrySet.cxx
//-----------------------------------------------------------------------------
//
+#include <errno.h>
+#include "gdcmDebug.h"
+#include "gdcmCommon.h"
+#include "gdcmGlobal.h"
#include "gdcmDocEntrySet.h"
#include "gdcmException.h"
+#include "gdcmDocEntry.h"
+#include "gdcmSeqEntry.h"
+#include "gdcmValEntry.h"
+#include "gdcmBinEntry.h"
//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
- * \ingroup gdcmDocEntrySEt
+ * \ingroup gdcmDocEntrySet
* \brief Constructor from a given gdcmDocEntrySet
*/
gdcmDocEntrySet::gdcmDocEntrySet() {
//-----------------------------------------------------------------------------
// Public
-
+//bool gdcmDocEntrySet::AddEntry(gdcmDocEntry *Entry){return true;}
//-----------------------------------------------------------------------------
// Protected
+
+
//-----------------------------------------------------------------------------
// Private
* \ and load element values (a voir !)
* @return false anything wrong happens
*/
+
+ /* just to keep the code
+
bool gdcmDocEntrySet::LoadDocEntrySet(bool exception_on_error)
throw(gdcmFormatError) {
(void)exception_on_error;
gdcmValEntry *newValEntry = (gdcmValEntry *)0;
gdcmBinEntry *newBinEntry = (gdcmBinEntry *)0;
gdcmSeqEntry *newSeqEntry = (gdcmSeqEntry *)0;
- //gdcmDictEntry *NewTag = (gdcmDictEntry *)0;
-
- while (newDocEntry = ReadNextDocEntry())) {
+
+ string vr;
+ while (newDocEntry = ReadNextDocEntry()) {
// TODO (?) : liberation du DocEntry ainsi cree,
// apres copie dans un ValEntry, SeqEntry, BinEntry
- vr = newDocEntry->getVR();
+ vr = newDocEntry->GetVR();
if (vr == "SQ" ) {
// --- SeqEntry
- newSeqEntry = (gdcmSeqEntry *)0;
- if (!NewSeqEntry) {
+ newSeqEntry = new gdcmSeqEntry((gdcmDictEntry*)NULL);
+ if (!newSeqEntry) {
dbg.Verbose(1, "gdcmDocEntrySet::LoadDocEntrySet",
"failed to allocate gdcmSeqEntry");
return false;
// (ensemble d' ITEMs, en fait,
// chaque ITEM etant chargé avec LoadDocEntrySet)
- SkipDocEntry(newSeqEntry); // voir ce qu'on fait pour une SeQuence
- AddDocEntry(newSeqEntry);
+ //SkipDocEntry(newSeqEntry); // voir ce qu'on fait pour une SeQuence
+ AddEntry(newSeqEntry); // on appele la fonction generique,
+ // ou une fonction spécialisée ?
} else if (vr == "AE" || vr == "AS" || vr == "DA" || vr == "PN" ||
- vr == "UI" || vr == "TM" ) {
+ vr == "UI" || vr == "TM" || vr == "SH" || vr == "LO" ||
+ vr == "CS" || vr == "IS" || vr == "LO" || vr == "LT" ||
+ vr == "SH" || vr == "ST" ||
+ vr == "SL" || vr == "SS" || vr == "UL" || vr == "US"
+ ) {
// --- ValEntry
- newValEntry = (gdcmValEntry *)0;
- if (!NewValEntry) {
+ newValEntry = new gdcmValEntry((gdcmDictEntry*)NULL);
+ if (!newValEntry) {
dbg.Verbose(1, "gdcmDocEntrySet::LoadDocEntrySet",
"failed to allocate gdcmValEntry");
return false;
}
newValEntry->Copy(newDocEntry);
- SkipDocEntry(newValEntry);
- AddDocEntry(newValEntry);
-
- } else {
+ //SkipDocEntry(newValEntry); //le skip devrait etre fait dans le Read
+ AddEntry(newValEntry); // on appele la fonction generique,
+ // ou une fonction spécialisée ?
+
+ // Maybe the following VR do correspond to a BinEntry
+
+ //AT Attribute Tag; // OK // 2 16-bit unsigned short integers
+ //FL Floating Point Single; // 32-bit IEEE 754:1985 float
+ //FD Floating Point Double; // 64-bit IEEE 754:1985 double
+ //UN Unknown; // Any length of bytes
+ //UT Unlimited Text; // At most 2^32 -1 chars
+ //OB Other Byte String; // String of bytes (VR independant)
+ //OW Other Word String; // String of 16-bit words (VR dependant)
+ } else {
// --- BinEntry
- NewBinEntry = new gdcmBinEntry(DictEntry);
- if (!NewValEntry) {
+ newBinEntry = new gdcmBinEntry((gdcmDictEntry*)NULL);
+ if (!newBinEntry) {
dbg.Verbose(1, "gdcmDocEntrySet::LoadDocEntrySet",
"failed to allocate gdcmBinEntry");
return false;
}
newBinEntry->Copy(newDocEntry);
- SkipDocEntry(newBinEntry);
- AddDocEntry(newBinEntry);
+ // SkipDocEntry(newBinEntry); //le skip devrait etre fait dans le Read
+ AddEntry(newBinEntry); // on appele la fonction generique,
+ // ou une fonction spécialisée ?
}
}
- rewind(fp);
+
// TODO : il n'y a plus de Chained List qui contient toutes les Entries
// Le chargement des valeurs devra se faire à la volée
// Be carefull : merging this two loops may cause troubles ...
+
+/*
+ rewind(fp);
for (ListTag::iterator i = GetListEntry().begin();
i != GetListEntry().end();
++i)
LoadDocEntry(*i);
}
rewind(fp);
-
+
+ */
+
+ /* TO DO : deporter den fin de parsing du DOCUMENT (pas du EntrySet)
+
// --------------------------------------------------------------
// Special Patch to allow gdcm to read ACR-LibIDO formated images
//
SetEntryByNumber(columns, 0x0028, 0x0010);
SetEntryByNumber(rows , 0x0028, 0x0011);
}
- // ----------------- End of Special Patch ----------------
+ // ----------------- End of Special Patch ----------------
+ */
+
+ /*
return true;
}
-
-
-/**
- * \brief Check the correspondance between the VR of the header entry
- * and the taken VR. If they are different, the header entry is
- * updated with the new VR.
- * @param Entry Header Entry to check
- * @param vr Dicom Value Representation
- * @return false if the VR is incorrect of if the VR isn't referenced
- * otherwise, it returns true
*/
-// NE MARCHE PAS EN L'ETAT :
-// On a besoin de VR pour 'fabriquer', au choix ValEntry, BinEntry, ou SeqEntry.
-//
-
-bool gdcmDocEntrySet::CheckEntryVR(gdcmHeaderEntry *Entry, VRKey vr)
-{
- char msg[100]; // for sprintf
- bool RealExplicit = true;
-
- // Assume we are reading a falsely explicit VR file i.e. we reached
- // a tag where we expect reading a VR but are in fact we read the
- // first to bytes of the length. Then we will interogate (through find)
- // the dicom_vr dictionary with oddities like "\004\0" which crashes
- // both GCC and VC++ implementations of the STL map. Hence when the
- // expected VR read happens to be non-ascii characters we consider
- // we hit falsely explicit VR tag.
-
- if ( (!isalpha(vr[0])) && (!isalpha(vr[1])) )
- RealExplicit = false;
-
- // CLEANME searching the dicom_vr at each occurence is expensive.
- // PostPone this test in an optional integrity check at the end
- // of parsing or only in debug mode.
- if ( RealExplicit && !gdcmGlobal::GetVR()->Count(vr) )
- RealExplicit= false;
-
- if ( !RealExplicit )
- {
- // We thought this was explicit VR, but we end up with an
- // implicit VR tag. Let's backtrack.
- sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
- Entry->GetGroup(),Entry->GetElement());
- dbg.Verbose(1, "gdcmParser::FindVR: ",msg);
- if (Entry->GetGroup()%2 && Entry->GetElement() == 0x0000) { // Group length is UL !
- gdcmDictEntry* NewEntry = NewVirtualDictEntry(
- Entry->GetGroup(),Entry->GetElement(),
- "UL","FIXME","Group Length");
- Entry->SetDictEntry(NewEntry);
- }
- return(false);
- }
-
- if ( Entry->IsVRUnknown() )
- {
- // When not a dictionary entry, we can safely overwrite the VR.
- if (Entry->GetElement() == 0x0000) { // Group length is UL !
- Entry->SetVR("UL");
- } else {
- Entry->SetVR(vr);
- }
- }
- else if ( Entry->GetVR() != vr )
- {
- // The VR present in the file and the dictionary disagree. We assume
- // the file writer knew best and use the VR of the file. Since it would
- // be unwise to overwrite the VR of a dictionary (since it would
- // compromise it's next user), we need to clone the actual DictEntry
- // and change the VR for the read one.
- gdcmDictEntry* NewEntry = NewVirtualDictEntry(
- Entry->GetGroup(),Entry->GetElement(),
- vr,"FIXME",Entry->GetName());
- Entry->SetDictEntry(NewEntry);
- }
- return(true);
-}
-
-
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
#include "gdcmDocument.h"
+#include "gdcmValEntry.h"
+#include "gdcmBinEntry.h"
+#include "gdcmSeqEntry.h"
+
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
if ( !OpenFile(exception_on_error))
return;
- rewind(fp);
- if (!CheckSwap())
- return NULL; // Du menage à faire avant de sortir ?
- LoadDocEntries();
+ //LoadHeaderEntries();
+ long l=ParseES( (gdcmDocEntrySet *)this, 120L, 0x7fffffff, false);
+ // TODO : find the right values
CloseFile();
- wasUpdated = 0; // will be set to 1 if user adds an entry
printLevel = 1; // 'Medium' print level by default
}
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Initialise();
- wasUpdated = 0; // will be set to 1 if user adds an entry
printLevel = 1; // 'Medium' print level by default
}
//-----------------------------------------------------------------------------
// Print
/**
- * \brief Prints the Doc Entries (Dicom Elements)
+ * \brief Prints the Header Entries (Dicom Elements)
* from the chained list
* @return
*/
* @return True when ImplicitVRLittleEndian found. False in all other cases.
*/
bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry *Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ gdcmDocEntry *Element = GetDocEntryByNumber(0x0002, 0x0010);
if ( !Element )
return false;
- LoadHeaderEntrySafe(Element);
+ LoadDocEntrySafe(Element);
std::string Transfer = Element->GetValue();
if ( Transfer == UI1_2_840_10008_1_2 )
* @return True when ExplicitVRLittleEndian found. False in all other cases.
*/
bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
if ( !Element )
return false;
- LoadHeaderEntrySafe(Element);
+ LoadDocEntrySafe(Element);
std::string Transfer = Element->GetValue();
if ( Transfer == UI1_2_840_10008_1_2_1 )
* @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
*/
bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
if ( !Element )
return false;
- LoadHeaderEntrySafe(Element);
+ LoadDocEntrySafe(Element);
std::string Transfer = Element->GetValue();
if ( Transfer == UI1_2_840_10008_1_2_1_99 )
* @return True when big endian found. False in all other cases.
*/
bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
if ( !Element )
return false;
- LoadHeaderEntrySafe(Element);
+ LoadDocEntrySafe(Element);
std::string Transfer = Element->GetValue();
if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier !
}
/**
- * \brief Writes in a file all the Doc Entries (Dicom Elements)
+ * \brief Writes in a file all the Header Entries (Dicom Elements)
* of the Chained List
* @param fp file pointer on an already open file
* @param type Type of the File to be written
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-gdcmHeaderEntry * gdcmDocument::ReplaceOrCreateByNumber(
+
+
+gdcmDocEntry * gdcmDocument::ReplaceOrCreateByNumber(
std::string Value,
guint16 Group,
guint16 Elem ){
- gdcmHeaderEntry* a;
- a = GetHeaderEntryByNumber( Group, Elem);
+ gdcmDocEntry* a;
+ a = GetDocEntryByNumber( Group, Elem);
if (a == NULL) {
- a =NewHeaderEntryByNumber(Group, Elem);
+ a =NewDocEntryByNumber(Group, Elem);
if (a == NULL)
return NULL;
- AddHeaderEntry(a);
+ AddDocEntry(a);
}
- //CLEANME SetEntryByNumber(Value, Group, Elem);
- a->SetValue(Value);
+ SetEntryByNumber(Value, Group, Elem);
+ //a->SetValue(Value);
return(a);
}
}
/**
- * \brief Searches within Doc Entries (Dicom Elements) parsed with
+ * \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the element value of a given tag.
* \warning Don't use any longer : use GetPubEntryByName
}
/**
- * \brief Searches within Doc Entries (Dicom Elements) parsed with
+ * \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the element value representation of a given tag.
*
if( dictEntry == NULL)
return GDCM_UNFOUND;
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(),
+ gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
dictEntry->GetElement());
return elem->GetVR();
}
/**
- * \brief Searches within Doc Entries (Dicom Elements) parsed with
+ * \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the element value representation of a given tag.
* @param group Group of the searched tag.
}
/**
- * \brief Searches within Doc Entries (Dicom Elements) parsed with
+ * \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the element value representation of a given tag..
*
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
std::string gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) {
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
+ gdcmDocEntry* elem = GetDocEntryByNumber(group, element);
if ( !elem )
return GDCM_UNFOUND;
return elem->GetVR();
}
/**
- * \brief Searches within Doc Entries (Dicom Elements) parsed with
+ * \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the value length of a given tag..
* @param group Group of the searched tag.
* @return Corresponding element length; -2 if not found
*/
int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) {
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
+ gdcmDocEntry* elem = GetDocEntryByNumber(group, element);
if ( !elem )
return -2;
return elem->GetLength();
}
/**
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
+ * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
- * \warning Don't use any longer : use SetPubEntryByNumber
* @param content new value to substitute with
* @param group group of the Dicom Element to modify
* @param element element of the Dicom Element to modify
content = content + '\0';
}
- gdcmHeaderEntry * a;
+ gdcmDocEntry * a;
IterHT p;
- TagHeaderEntryHT::iterator p2;
+ 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 :
+
+ // Oops ! this was for multimap, right ?
a = ((tagHT.equal_range(key)).first)->second;
- a-> SetValue(content);
+ ((gdcmValEntry*)a)->SetValue(content);
std::string vr = a->GetVR();
}
/**
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
- * in the PubHeaderEntrySet of this instance
+ * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * in the PubDocEntrySet of this instance
* through it's (group, element) and modifies it's length with
* the given value.
* \warning Use with extreme caution.
*/
size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem)
{
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
+ gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
if (!Entry)
{
- dbg.Verbose(1, "gdcmDocument::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
+ dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber",
+ "failed to Locate gdcmDocEntry");
return (size_t)0;
}
return Entry->GetOffset();
*/
void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem)
{
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
+ gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem);
if (!Entry)
{
- dbg.Verbose(1, "gdcmDocument::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
+ dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber",
+ "failed to Locate gdcmDocEntry");
return (NULL);
}
- return Entry->GetVoidArea();
+ return ((gdcmBinEntry *)Entry)->GetVoidArea();
}
/**
*/
void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem)
{
- gdcmHeaderEntry * Element= GetHeaderEntryByNumber(Group, Elem);
+ gdcmDocEntry * Element= GetDocEntryByNumber(Group, Elem);
if ( !Element )
return NULL;
size_t o =(size_t)Element->GetOffset();
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHT.count(key))
return false;
- ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area);
+ // This was for multimap ?
+ (( gdcmBinEntry *)( ((tagHT.equal_range(key)).first)->second ))->SetVoidArea(area);
+
return true;
}
else
vr=(*it)->GetVR();
- (*it)->SetValue(GetHeaderEntryUnvalue(*it));
+ //(*it)->SetValue(GetDocEntryUnvalue(*it));
+ // to go on compiling
if(entry){
// Set the new entry and the new value
(*it)->SetDictEntry(entry);
- CheckHeaderEntryVR(*it,vr);
+ CheckDocEntryVR(*it,vr);
- (*it)->SetValue(GetHeaderEntryValue(*it));
+ //(*it)->SetValue(GetDocEntryValue(*it));
+ // to go on compiling
+
}
else
{
}
/**
- * \brief Searches within the Doc Entries for a Dicom Element of
+ * \brief Searches within the Header Entries for a Dicom Element of
* a given tag.
* @param tagName name of the searched Dicom Element.
* @return Corresponding Dicom Element when it exists, and NULL
* otherwise.
*/
- gdcmHeaderEntry *gdcmDocument::GetHeaderEntryByName(std::string tagName) {
+ gdcmDocEntry *gdcmDocument::GetDocEntryByName(std::string tagName) {
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
return NULL;
- return(GetHeaderEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
+ return(GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
}
/**
* @param element Element number of the searched Dicom Element
* @return
*/
-gdcmHeaderEntry* gdcmDocument::GetHeaderEntryByNumber(guint16 group, guint16 element)
+gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element)
{
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHT.count(key))
* @return a range (i.e.pair<,>) containing all elements whose key is group|element)
*/
-IterHT gdcmDocument::GetHeaderEntrySameNumber(guint16 group, guint16 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 LoadHeaderEntry that modifies it.
+ * to LoadDocEntry that modifies it.
* @param entry Header Entry whose value shall be loaded.
* @return
*/
-void gdcmDocument::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) {
+void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) {
long PositionOnEntry = ftell(fp);
- LoadHeaderEntry(entry);
+ LoadDocEntry(entry);
fseek(fp, PositionOnEntry, SEEK_SET);
}
* @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;
- gdcmHeaderEntry *elem;
+ gdcmDocEntry *elem;
char trash[10];
std::string str_trash;
// remember :
// typedef std::map<GroupKey, int> GroupHT;
- gdcmHeaderEntry *elemZ;
+ gdcmDocEntry *elemZ;
// for each Tag in the DCM Header
- for (TagHeaderEntryHT::iterator tag2 = tagHT.begin();
+ for (TagDocEntryHT::iterator tag2 = tagHT.begin();
tag2 != tagHT.end();
++tag2)
{
if ( tagHT.count(tk) == 0) // if element 0x0000 not found
{
gdcmDictEntry * tagZ = new gdcmDictEntry(gr_bid, 0x0000, "UL");
- elemZ = new gdcmHeaderEntry(tagZ);
+ elemZ = new gdcmDocEntry(tagZ);
elemZ->SetLength(4);
- AddHeaderEntry(elemZ); // create it
+ AddDocEntry(elemZ); // create it
}
else
{
- elemZ=GetHeaderEntryByNumber(gr_bid, 0x0000);
+ elemZ=GetDocEntryByNumber(gr_bid, 0x0000);
}
sprintf(trash ,"%d",g->second);
str_trash=trash;
- elemZ->SetValue(str_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 gdcmHeaderEntry passed as argument.
- * @param tag pointer on the gdcmHeaderEntry to be written
+ * of a single gdcmDocEntry passed as argument.
+ * @param tag pointer on the gdcmDocEntry to be written
* @param _fp already open file pointer
* @param type type of the File to be written
*/
-void gdcmDocument::WriteEntryTagVRLength(gdcmHeaderEntry *tag,
+void gdcmDocument::WriteEntryTagVRLength(gdcmDocEntry *tag,
FILE *_fp,
FileType type)
{
/**
* \brief Writes in a file (according to the requested format)
- * the value of a single gdcmHeaderEntry passed as argument.
- * @param tag Pointer on the gdcmHeaderEntry to be written
+ * the value of a single gdcmDocEntry passed as argument.
+ * @param tag Pointer on the gdcmDocEntry to be written
* @param _fp Already open file pointer
* @param type type of the File to be written
*/
-void gdcmDocument::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
+
+ // TODO : to be re -written recursively !
+
+void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type)
{
(void)type;
guint16 group = tag->GetGroup();
return;
void *voidArea;
- voidArea = tag->GetVoidArea();
+ // voidArea = tag->GetVoidArea();
+ // to go on compiling
if (voidArea != NULL)
{ // there is a 'non string' LUT, overlay, etc
fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
/**
* \brief Writes in a file (according to the requested format)
- * a single gdcmHeaderEntry passed as argument.
+ * a single gdcmDocEntry passed as argument.
* \sa WriteEntryValue, WriteEntryTagVRLength.
- * @param tag Pointer on the gdcmHeaderEntry to be written
+ * @param tag Pointer on the gdcmDocEntry to be written
* @param _fp Already open file pointer
* @param type type of the File to be written
*/
-bool gdcmDocument::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
+bool gdcmDocument::WriteEntry(gdcmDocEntry *tag, FILE *_fp,FileType type)
{
guint32 length = tag->GetLength();
// bytes. When this is not the case, pad with an additional byte:
if(length%2==1)
{
- tag->SetValue(tag->GetValue()+"\0");
+// tag->SetValue(tag->GetValue()+"\0");
+// to go on compiling
tag->SetLength(tag->GetReadLength()+1);
}
// restent a tester les echecs en ecriture (apres chaque fwrite)
- for (TagHeaderEntryHT::iterator tag2=tagHT.begin();
+ for (TagDocEntryHT::iterator tag2=tagHT.begin();
tag2 != tagHT.end();
++tag2){
if ( type == ACR ){
//-----------------------------------------------------------------------------
// Private
+
+
+/**
+ * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
+ * @return false if file is not ACR-NEMA / PAPYRUS / DICOM
+ */
+
+long gdcmDocument::ParseES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
+
+ gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
+ gdcmValEntry *vl;
+ gdcmSeqEntry *sq;
+ long l;
+ while (true) {
+ 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; // ??
+}
+
+
+
+
+long gdcmDocument::ParseSQ(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
+
+ gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
+ gdcmSQItem *itemSQ;
+ bool dlm_mod;
+ int lgr, l, lgth;
+
+ while (true) {
+ 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();
+
+ l= NewDocEntry->GetLength();
+ 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);
+ }
+ // ----------------- End of Special Patch ----------------
+ return true;
+}
+======================================================================= */
+
+
/**
* \brief Loads the element content if its length doesn't exceed
* the value specified with gdcmDocument::SetMaxSizeLoadEntry()
* @param Entry Header Entry (Dicom Element) to be dealt with
*/
-void gdcmDocument::LoadHeaderEntry(gdcmHeaderEntry *Entry) {
+void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) {
size_t item_read;
guint16 group = Entry->GetGroup();
std::string vr= Entry->GetVR();
// (fffe e00d) tells us an Element just ended
// (fffe e0dd) tells us the current SeQuence just ended
if( group == 0xfffe ) {
- Entry->SetValue("gdcm::Skipped");
+ // NO more value field for SQ !
+ //Entry->SetValue("gdcm::Skipped");
+ // appel recursif de Load Value
+ // (meme pb que pour le parsing)
return;
}
// When the length is zero things are easy:
if ( length == 0 ) {
- Entry->SetValue("");
+ ((gdcmValEntry *)Entry)->SetValue("");
return;
}
s << " Address:" << (long)Entry->GetOffset();
s << " Length:" << Entry->GetLength();
s << " x(" << std::hex << Entry->GetLength() << ")";
- Entry->SetValue(s.str());
+ ((gdcmValEntry *)Entry)->SetValue(s.str());
return;
}
// Any compacter code suggested (?)
- if ( IsHeaderEntryAnInteger(Entry) ) {
+ if ( IsDocEntryAnInteger(Entry) ) {
guint32 NewInt;
std::ostringstream s;
int nbInt;
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
- Entry->SetValue(s.str());
+ ((gdcmValEntry *)Entry)->SetValue(s.str());
return;
}
item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp);
if ( item_read != 1 ) {
dbg.Verbose(1, "gdcmDocument::LoadElementValue","unread element value");
- Entry->SetValue("gdcm::UnRead");
+ ((gdcmValEntry *)Entry)->SetValue("gdcm::UnRead");
return;
}
if( (vr == "UI") ) // Because of correspondance with the VR dic
- Entry->SetValue(NewValue.c_str());
+ ((gdcmValEntry *)Entry)->SetValue(NewValue.c_str());
else
- Entry->SetValue(NewValue);
+ ((gdcmValEntry *)Entry)->SetValue(NewValue);
}
/**
* \todo something to allow further Elements addition,
* (at their right place in the chained list)
* when position to be taken care of
- * @param newHeaderEntry
+ * @param newDocEntry
*/
-void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) {
- tagHT.insert( PairHT( newHeaderEntry->GetKey(),newHeaderEntry) );
- listEntries.push_back(newHeaderEntry);
- wasUpdated = 1;
+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
* @param Entry Header Entry whose length of the value shall be loaded.
*/
- void gdcmDocument::FindHeaderEntryLength (gdcmHeaderEntry *Entry) {
+ void gdcmDocument::FindDocEntryLength (gdcmDocEntry *Entry) {
guint16 element = Entry->GetElement();
//guint16 group = Entry->GetGroup(); //FIXME
std::string vr = Entry->GetVR();
if ( (vr == "OB") && (length32 == 0xffffffff) )
{
- Entry->SetLength(FindHeaderEntryLengthOB());
+ Entry->SetLength(FindDocEntryLengthOB());
return;
}
- FixHeaderEntryFoundLength(Entry, length32);
+ FixDocEntryFoundLength(Entry, length32);
return;
}
// Actually, length= 0xffff means that we deal with
// Unknown Sequence Length
}
- FixHeaderEntryFoundLength(Entry, (guint32)length16);
+ FixDocEntryFoundLength(Entry, (guint32)length16);
return;
}
else
// not coexist in a Data Set and Data Sets nested within it".]
// Length is on 4 bytes.
- FixHeaderEntryFoundLength(Entry, ReadInt32());
+ FixDocEntryFoundLength(Entry, ReadInt32());
return;
}
}
* \brief Find the Value Representation of the current Dicom Element.
* @param Entry
*/
-void gdcmDocument::FindHeaderEntryVR( gdcmHeaderEntry *Entry)
+void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry)
{
if (filetype != ExplicitVR)
return;
(void)fread (&VR, (size_t)2,(size_t)1, fp);
VR[2]=0;
- if(!CheckHeaderEntryVR(Entry,VR))
+ if(!CheckDocEntryVR(Entry,VR))
{
fseek(fp, PositionOnEntry, SEEK_SET);
// When this element is known in the dictionary we shall use, e.g. for
* @return false if the VR is incorrect of if the VR isn't referenced
* otherwise, it returns true
*/
-bool gdcmDocument::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr)
+bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, VRKey vr)
{
char msg[100]; // for sprintf
bool RealExplicit = true;
* @param Entry
* @return Transformed entry value
*/
-std::string gdcmDocument::GetHeaderEntryValue(gdcmHeaderEntry *Entry)
+std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry)
{
- if ( (IsHeaderEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
+ if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
{
std::string val=Entry->GetValue();
std::string vr=Entry->GetVR();
* @param Entry
* @return Reverse transformed entry value
*/
-std::string gdcmDocument::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry)
+std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry)
{
- if ( (IsHeaderEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
+ if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
{
std::string vr=Entry->GetVR();
std::ostringstream s;
* \warning NOT end user intended method !
* @param entry
*/
-void gdcmDocument::SkipHeaderEntry(gdcmHeaderEntry *entry)
+void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry)
{
SkipBytes(entry->GetLength());
}
* the parser went Jabberwocky) one can hope improving things by
* applying this heuristic.
*/
-void gdcmDocument::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 FoundLength)
+void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, guint32 FoundLength)
{
Entry->SetReadLength(FoundLength); // will be updated only if a bug is found
if ( FoundLength == 0xffffffff) {
* @param Entry The element value on which to apply the predicate.
* @return The result of the heuristical predicate.
*/
-bool gdcmDocument::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) {
+bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) {
guint16 element = Entry->GetElement();
guint16 group = Entry->GetGroup();
std::string vr = Entry->GetVR();
// instead of giving up with an error message
//std::cout << s.str().c_str() << std::endl;
- // dbg.Error("gdcmDocument::IsHeaderEntryAnInteger",
+ // dbg.Error("gdcmDocument::IsDocEntryAnInteger",
// s.str().c_str());
}
}
* @return
*/
- guint32 gdcmDocument::FindHeaderEntryLengthOB(void) {
+ guint32 gdcmDocument::FindDocEntryLengthOB(void) {
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
guint16 g;
guint16 n;
/**
* \brief Read the next tag but WITHOUT loading it's value
- * @return On succes the newly created HeaderEntry, NULL on failure.
+ * @return On succes the newly created DocEntry, NULL on failure.
*/
-gdcmHeaderEntry *gdcmDocument::ReadNextHeaderEntry(void) {
+gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) {
guint16 g,n;
- gdcmHeaderEntry *NewEntry;
+ gdcmDocEntry *NewEntry;
g = ReadInt16();
n = ReadInt16();
if (errno == 1)
// We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
- return (gdcmHeaderEntry *)0;
+ return (gdcmDocEntry *)0;
-// Pb : how to propagate the element length (used in SkipHeaderEntry)
+// Pb : how to propagate the element length (used in SkipDocEntry)
// direct call to SkipBytes ?
// if (ignoreShadow == 1 && g%2 ==1)
// if user wants to skip shadow groups
// and current element *is* a shadow element
// we don't create anything
-// return (gdcmHeaderEntry *)1; // to tell caller it's NOT finished
+// return (gdcmDocEntry *)1; // to tell caller it's NOT finished
- NewEntry = NewHeaderEntryByNumber(g, n);
- FindHeaderEntryVR(NewEntry);
- FindHeaderEntryLength(NewEntry);
+ NewEntry = NewDocEntryByNumber(g, n);
+ FindDocEntryVR(NewEntry);
+ FindDocEntryLength(NewEntry);
if (errno == 1) {
// Call it quits
* a default one when absent.
* @param Name Name of the underlying DictEntry
*/
-gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByName(std::string Name)
+gdcmDocEntry *gdcmDocument::NewDocEntryByName(std::string Name)
{
gdcmDictEntry *NewTag = GetDictEntryByName(Name);
if (!NewTag)
NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name);
- gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag);
+ gdcmDocEntry* NewEntry = new gdcmDocEntry(NewTag);
if (!NewEntry)
{
- dbg.Verbose(1, "gdcmDocument::ObtainHeaderEntryByName",
- "failed to allocate gdcmHeaderEntry");
- return (gdcmHeaderEntry *)0;
+ dbg.Verbose(1, "gdcmDocument::ObtainDocEntryByName",
+ "failed to allocate gdcmDocEntry");
+ return (gdcmDocEntry *)0;
}
return NewEntry;
}
* @param Group group of the underlying DictEntry
* @param Elem element of the underlying DictEntry
*/
-gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByNumber(guint16 Group, guint16 Elem)
+gdcmDocEntry *gdcmDocument::NewDocEntryByNumber(guint16 Group, guint16 Elem)
{
// Find out if the tag we encountered is in the dictionaries:
gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
if (!DictEntry)
DictEntry = NewVirtualDictEntry(Group, Elem);
- gdcmHeaderEntry *NewEntry = new gdcmHeaderEntry(DictEntry);
+ gdcmDocEntry *NewEntry = new gdcmDocEntry(DictEntry);
if (!NewEntry)
{
- dbg.Verbose(1, "gdcmDocument::NewHeaderEntryByNumber",
- "failed to allocate gdcmHeaderEntry");
+ dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber",
+ "failed to allocate gdcmDocEntry");
return NULL;
}
return NewEntry;
/// \todo Never used; commented out, waiting for removal.
/**
* \brief Small utility function that creates a new manually crafted
- * (as opposed as read from the file) gdcmHeaderEntry with user
+ * (as opposed as read from the file) gdcmDocEntry with user
* specified name and adds it to the public tag hash table.
* \note A fake TagKey is generated so the PubDict can keep it's coherence.
* @param NewTagName The name to be given to this new tag.
* @param VR The Value Representation to be given to this new tag.
* @return The newly hand crafted Element Value.
*/
-//gdcmHeaderEntry *gdcmDocument::NewManualHeaderEntryToPubDict(std::string NewTagName,
+//gdcmDocEntry *gdcmDocument::NewManualDocEntryToPubDict(std::string NewTagName,
// std::string VR)
//{
-// gdcmHeaderEntry *NewEntry = NULL;
+// gdcmDocEntry *NewEntry = NULL;
// guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
// guint32 FreeElem = 0;
// gdcmDictEntry *DictEntry = NULL;
// FreeElem = GenerateFreeTagKeyInGroup(StuffGroup);
// if (FreeElem == UINT32_MAX)
// {
-// dbg.Verbose(1, "gdcmHeader::NewManualHeaderEntryToPubDict",
+// dbg.Verbose(1, "gdcmHeader::NewManualDocEntryToPubDict",
// "Group 0xffff in Public Dict is full");
// return NULL;
// }
//
// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem,
// VR, "GDCM", NewTagName);
-// NewEntry = new gdcmHeaderEntry(DictEntry);
-// AddHeaderEntry(NewEntry);
+// NewEntry = new gdcmDocEntry(DictEntry);
+// AddDocEntry(NewEntry);
// return NewEntry;
//}
projects / gdcm.git / commitdiff