Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2004/07/19 03:34:11 $
- Version: $Revision: 1.50 $
+ Date: $Date: 2004/09/17 13:11:16 $
+ Version: $Revision: 1.81 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmUtil.h"
#include "gdcmDebug.h"
-#include <errno.h>
#include <vector>
// For nthos:
/**
* \brief constructor
- * @param inFilename file to be opened for parsing
- * @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
- * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
- * @param ignore_shadow to allow skipping the shadow elements,
- * to save memory space.
- * \warning The TRUE value for this param has to be used
- * with a FALSE value for the 'enable_sequence' param.
- * ('public elements' may be embedded in 'shadow Sequences')
- */
-gdcmDocument::gdcmDocument( std::string const & filename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow)
+ * @param filename file to be opened for parsing
+ */
+gdcmDocument::gdcmDocument( std::string const & filename )
: gdcmElementSet(-1)
{
- IgnoreShadow = ignore_shadow;
- //EnableSequences=enable_sequences;
- (void)enable_sequences;
- EnableSequences = true; // JPR // TODO : remove params out of the constructor
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Filename = filename;
Initialise();
- if ( !OpenFile(exception_on_error))
+ if ( !OpenFile() )
{
return;
}
-
+
dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ",
Filename.c_str());
rewind(Fp);
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 ?
+ (void)ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
rewind(Fp);
if( PhotometricInterpretation == "PALETTE COLOR " )
{
LoadEntryVoidArea(0x0028,0x1200); // gray LUT
+ /// FIXME FIXME FIXME
+ /// The tags refered by the three following lines used to be CORRECTLY
+ /// defined as having an US Value Representation in the public
+ /// dictionnary. BUT the semantics implied by the three following
+ /// lines state that the corresponding tag contents are in fact
+ /// the ones of a gdcmBinEntry.
+ /// In order to fix things "Quick and Dirty" the dictionnary was
+ /// altered on PURPOUS but now contains a WRONG value.
+ /// In order to fix things and restore the dictionary to its
+ /// correct value, one needs to decided of the semantics by deciding
+ /// wether the following tags are either:
+ /// - multivaluated US, and hence loaded as gdcmValEntry, but afterwards
+ /// also used as gdcmBinEntry, which requires the proper conversion,
+ /// - OW, and hence loaded as gdcmBinEntry, but afterwards also used
+ /// as gdcmValEntry, which requires the proper conversion.
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
+ // Segmented Red Palette Color LUT Data
+ LoadEntryVoidArea(0x0028,0x1221);
+ // Segmented Green Palette Color LUT Data
+ LoadEntryVoidArea(0x0028,0x1222);
+ // Segmented Blue Palette Color LUT Data
+ LoadEntryVoidArea(0x0028,0x1223);
}
//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
+ // Specific code to allow gdcm to read ACR-LibIDO formated images
+ // Note: ACR-LibIDO is an extension of the ACR standard that was
+ // used at CREATIS. For the time being (say a couple years)
+ // we keep this kludge to allow a smooth move to gdcm for
+ // CREATIS developpers (sorry folks).
//
// if recognition code tells us we deal with a LibIDO image
// we switch lineNumber and columnNumber
SetEntryByNumber(columns, 0x0028, 0x0010);
SetEntryByNumber(rows , 0x0028, 0x0011);
}
- // ----------------- End of Special Patch ----------------
+ // ----------------- End of ACR-LibIDO kludge ------------------
PrintLevel = 1; // 'Medium' print level by default
}
/**
- * \brief constructor
- * @param exception_on_error
+ * \brief This default constructor doesn't parse the file. You should
+ * then invoke \ref gdcmDocument::SetFileName and then the parsing.
*/
-gdcmDocument::gdcmDocument(bool exception_on_error)
+gdcmDocument::gdcmDocument()
:gdcmElementSet(-1)
{
- (void)exception_on_error;
- //EnableSequences=0; // ?!? JPR
-
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Initialise();
-
PrintLevel = 1; // 'Medium' print level by default
}
for (TagDocEntryHT::const_iterator it = TagHT.begin();
it != TagHT.end(); ++it )
{
- delete it->second;
+ //delete it->second; //temp remove
}
TagHT.clear();
}
* \brief Set the shadow dictionary used
* \param dictName name of the dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(DictKey dictName)
+bool gdcmDocument::SetShaDict(DictKey const & dictName)
{
RefShaDict = gdcmGlobal::GetDicts()->GetDict(dictName);
return !RefShaDict;
{
if( Filetype == gdcmUnknown)
{
- std::cout << " gdcmDocument::IsReadable: Filetype " << Filetype
- << " " << "gdcmUnknown " << gdcmUnknown << std::endl; //JPR
dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype");
return false;
}
/**
* \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.
+ * @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.
+ * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match.
*/
bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck)
{
}
// The entry might be present but not loaded (parsing and loading
- // happen at differente stages): try loading and proceed with check...
+ // happen at different 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 )
- if( transfer.find( syntaxToCheck ) ) //should be faster
+ if ( transfer.length() == 0 ) { // for brain damaged headers
+ return false;
+ }
+ while ( ! isdigit(transfer[transfer.length()-1]) )
+ {
+ transfer.erase(transfer.length()-1, 1);
+ }
+ if ( transfer == syntaxToCheck )
{
return true;
}
}
/**
- * \brief opens the file
- * @param exception_on_error
- * @return
+ * \brief Tries to open the file \ref gdcmDocument::Filename and
+ * checks the preamble when existing.
+ * @return The FILE pointer on success.
*/
-FILE *gdcmDocument::OpenFile(bool exception_on_error)
- throw(gdcmFileError)
+FILE* gdcmDocument::OpenFile()
{
- Fp = fopen(Filename.c_str(),"rb");
-
- if(!Fp)
- {
- 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 )
- {
- uint16_t zero;
- fread(&zero, (size_t)2, (size_t)1, Fp);
+ Fp = fopen(Filename.c_str(),"rb");
- //ACR -- or DICOM with no Preamble --
- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 )
- {
- 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;
- }
-
- fclose(Fp);
- dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", Filename.c_str());
- }
- else
- {
- dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", Filename.c_str());
- }
-
- return 0;
+ if(!Fp)
+ {
+ dbg.Verbose( 0,
+ "gdcmDocument::OpenFile cannot open file: ",
+ Filename.c_str());
+ return 0;
+ }
+
+ uint16_t zero;
+ fread(&zero, (size_t)2, (size_t)1, Fp);
+
+ //ACR -- or DICOM with no Preamble --
+ if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 )
+ {
+ 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;
+ }
+
+ fclose(Fp);
+ dbg.Verbose( 0,
+ "gdcmDocument::OpenFile not DICOM/ACR (missing preamble)",
+ Filename.c_str());
+
+ return 0;
}
/**
bool gdcmDocument::CloseFile()
{
int closed = fclose(Fp);
- Fp = (FILE *)0;
+ Fp = 0;
return closed;
}
/**
* \brief Modifies the value of a given Header Entry (Dicom Element)
* when it exists. Create it with the given value when unexistant.
- * @param Value (string) Value to be set
- * @param Group Group number of the Entry
- * @param Elem Element number 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).
*/
-
+
+/*
gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
- std::string value,
+ std::string const & value,
uint16_t group,
uint16_t elem )
{
gdcmValEntry* valEntry = 0;
-
gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
+
if (!currentEntry)
{
// The entry wasn't present and we simply create the required ValEntry:
else
{
valEntry = dynamic_cast< gdcmValEntry* >(currentEntry);
- if ( !valEntry )
+ if ( !valEntry ) // Euuuuh? It wasn't a ValEntry
+ // then we change it to a ValEntry ?
+ // Shouldn't it be considered as an error ?
+ {
+ // 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 value (string) Value to be set
+ * @param group Group number of the Entry
+ * @param elem Element number of the Entry
+ * @param VR V(alue) R(epresentation) of the Entry -if private Entry-
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+
+ // TODO : write something clever, using default value for VR
+ // to avoid code duplication
+ // (I don't know how to tell NewDocEntryByNumber
+ // that ReplaceOrCreateByNumber was called with a default value)
+
+gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
+ std::string const & value,
+ uint16_t group,
+ uint16_t elem,
+ std::string const & VR )
+{
+ gdcmValEntry* valEntry = 0;
+ gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
+
+ if (!currentEntry)
+ {
+ // check if (group,element) DictEntry exists
+ // if it doesn't, create an entry in gdcmDictSet::VirtualEntry
+ // and use it
+
+ // Find out if the tag we received is in the dictionaries:
+ gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
+ gdcmDictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem);
+ if (!dictEntry)
+ {
+ currentEntry = NewDocEntryByNumber(group, elem,VR);
+ }
+ else
+ {
+ 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 ) // Euuuuh? It wasn't a ValEntry
+ // then we change it to a ValEntry ?
+ // Shouldn't it be considered as an error ?
{
// We need to promote the gdcmDocEntry to a gdcmValEntry:
valEntry = new gdcmValEntry(currentEntry);
gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber(
void *voidArea,
int lgth,
+ uint16_t group,
+ uint16_t elem,
+ std::string const & VR )
+{
+ gdcmBinEntry* binEntry = 0;
+ gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
+ if (!currentEntry)
+ {
+
+ // check if (group,element) DictEntry exists
+ // if it doesn't, create an entry in gdcmDictSet::VirtualEntry
+ // and use it
+
+ // Find out if the tag we received is in the dictionaries:
+ gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
+ gdcmDictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem);
+
+ if (!dictEntry)
+ {
+ currentEntry = NewDocEntryByNumber(group, elem,VR);
+ }
+ else
+ {
+ currentEntry = NewDocEntryByNumber(group, elem);
+ }
+ if (!currentEntry)
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
+ " NewDocEntryByNumber failed.");
+ return NULL;
+ }
+ binEntry = new gdcmBinEntry(currentEntry);
+ if ( !AddEntry(binEntry))
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry"
+ " failed allthough this is a creation.");
+ }
+ }
+ else
+ {
+ binEntry = dynamic_cast< gdcmBinEntry* >(currentEntry);
+ if ( !binEntry ) // Euuuuh? It wasn't a BinEntry
+ // then we change it to a BinEntry ?
+ // Shouldn't it be considered as an error ?
+ {
+ // We need to promote the gdcmDocEntry to a gdcmBinEntry:
+ binEntry = new gdcmBinEntry(currentEntry);
+ if (!RemoveEntry(currentEntry))
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
+ " of previous DocEntry failed.");
+ return NULL;
+ }
+ if ( !AddEntry(binEntry))
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
+ " promoted BinEntry failed.");
+ return NULL;
+ }
+ }
+ }
+
+ SetEntryByNumber(voidArea, lgth, group, elem);
+
+ return binEntry;
+}
+
+
+/*
+ * \brief Modifies the value of a given Header Entry (Dicom Element)
+ * when it exists. Create it when unexistant.
+ * @param Group Group number of the Entry
+ * @param Elem Element number of the Entry
+ * \return pointer to the modified/created SeqEntry (NULL when creation
+ * failed).
+ */
+gdcmSeqEntry * gdcmDocument::ReplaceOrCreateByNumber(
uint16_t group,
uint16_t elem)
{
- gdcmBinEntry* b = 0;
+ gdcmSeqEntry* b = 0;
gdcmDocEntry* a = GetDocEntryByNumber( group, elem);
if (!a)
{
- a = NewBinEntryByNumber(group, elem);
+ a = NewSeqEntryByNumber(group, elem);
if (!a)
{
return 0;
}
- b = new gdcmBinEntry(a);
+ b = new gdcmSeqEntry(a, 1); // FIXME : 1 (Depth)
AddEntry(b);
- b->SetVoidArea(voidArea);
}
- SetEntryByNumber(voidArea, lgth, group, elem);
- //b->SetVoidArea(voidArea); //what if b == 0 !!
-
return b;
-}
-
+}
+
/**
* \brief Set a new value if the invoked element exists
* Seems to be useless !!!
- * @param Value new element value
- * @param Group group number of the Entry
- * @param Elem element number of the Entry
+ * @param value new element value
+ * @param group group number of the Entry
+ * @param elem element number of the Entry
* \return boolean
*/
-bool gdcmDocument::ReplaceIfExistByNumber(const char* value, uint16_t group,
- uint16_t elem )
+bool gdcmDocument::ReplaceIfExistByNumber(std::string const & value,
+ uint16_t group, uint16_t elem )
{
- const std::string v = value;
- SetEntryByNumber(v, group, elem);
+ SetEntryByNumber(value, group, elem);
return true;
}
* \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
+ * @return true is found
*/
-int gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
+bool gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
{
- std::string key = gdcmDictEntry::TranslateToKey(group, element );
+ const std::string &key = gdcmDictEntry::TranslateToKey(group, element );
return TagHT.count(key);
}
* @return Corresponding element value when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryByName(TagName tagName)
+std::string gdcmDocument::GetEntryByName(TagName const & tagName)
{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( !dictEntry )
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryVRByName(TagName tagName)
+std::string gdcmDocument::GetEntryVRByName(TagName const & tagName)
{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
return GDCM_UNFOUND;
}
- gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
+ gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
+ dictEntry->GetElement());
return elem->GetVR();
}
* @param tagName name of the searched Dicom Element.
* @return true when found
*/
-bool gdcmDocument::SetEntryByName(std::string content,std::string tagName)
+bool gdcmDocument::SetEntryByName(std::string const & content,std::string const & tagName)
{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( !dictEntry )
* @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,
+bool gdcmDocument::SetEntryByNumber(std::string const & content,
uint16_t group,
uint16_t element)
{
+ int c;
+ int l;
+
gdcmValEntry* valEntry = GetValEntryByNumber(group, element);
if (!valEntry )
{
" ValEntry (try promotion first).");
return false;
}
- // Non even content must be padded with a space (020H).
- if( content.length() % 2 )
+ // Non even content must be padded with a space (020H)...
+ std::string finalContent = content;
+ if( finalContent.length() % 2 )
{
- content += '\0';
+ finalContent += '\0'; // ... therefore we padd with (000H) .!?!
}
- valEntry->SetValue(content);
+ valEntry->SetValue(finalContent);
// Integers have a special treatement for their length:
- gdcmVRKey vr = valEntry->GetVR();
- if( vr == "US" || vr == "SS" )
- {
- valEntry->SetLength(2);
- }
- else if( vr == "UL" || vr == "SL" )
- {
- valEntry->SetLength(4);
- }
- else
- {
- valEntry->SetLength(content.length());
- }
+ l = finalContent.length();
+ if ( l != 0) // To avoid to be cheated by 'zero length' integers
+ {
+ gdcmVRKey vr = valEntry->GetVR();
+ if( vr == "US" || vr == "SS" )
+ {
+ c = CountSubstring(content, "\\") + 1; // for multivaluated items
+ l = c*2;
+ }
+ else if( vr == "UL" || vr == "SL" )
+ {
+ c = CountSubstring(content, "\\") + 1; // for multivaluated items
+ l = c*4;;
+ }
+ }
+ valEntry->SetLength(l);
return true;
}
return false;
}
-/* Hope Binaray field length is *never* wrong
+/* Hope Binary 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];
+ gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key];
a->SetVoidArea(content);
- //a->SetLength(lgth); // ???
+ a->SetLength(lgth);
+
return true;
}
/**
* \brief Gets (from Header) the offset of a 'non string' element value
* (LoadElementValues has already be executed)
- * @param Group group number of the Entry
- * @param Elem element number 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(uint16_t group, uint16_t elem)
/**
* \brief Gets (from Header) a 'non string' element value
* (LoadElementValues has already be executed)
- * @param Group group number of the Entry
- * @param Elem element number 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(uint16_t group, uint16_t elem)
/**
* \brief Loads (from disk) the element content
* when a string is not suitable
- * @param Group group number of the Entry
- * @param Elem element number of the Entry
+ * @param group group number of the Entry
+ * @param elem element number of the Entry
*/
-void *gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem)
+void* gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem)
{
gdcmDocEntry *docElement = GetDocEntryByNumber(group, elem);
if ( !docElement )
return NULL;
}
/// \todo Drop any already existing void area! JPR
- SetEntryVoidAreaByNumber(a, group, elem);
+ if( !SetEntryVoidAreaByNumber( a, group, elem ) );
+ {
+ dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea setting failed.");
+ }
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
+ * @param element Entry whose voidArea is going to be loaded
*/
void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element)
{
uint16_t group,
uint16_t element)
{
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key))
+ gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ if ( !currentEntry )
{
return false;
}
- // This was for multimap ?
- (( gdcmBinEntry *)( ((TagHT.equal_range(key)).first)->second ))->SetVoidArea(area);
-
+ if ( gdcmBinEntry* binEntry = dynamic_cast<gdcmBinEntry*>(currentEntry) )
+ {
+ binEntry->SetVoidArea( area );
+ return true;
+ }
return true;
}
a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
break;
default :
- std::cout << "swapCode= " << SwapCode << std::endl;
+ //std::cout << "swapCode= " << SwapCode << std::endl;
dbg.Error(" gdcmDocument::SwapLong : unset swap code");
- a=0;
+ a = 0;
}
return a;
}
{
if ( SwapCode == 4321 || SwapCode == 2143 )
{
- a =((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) );
+ a = ((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) );
}
return a;
}
bool delim_mode)
{
gdcmDocEntry *newDocEntry = 0;
- gdcmValEntry *newValEntry = 0;
unsigned long l = 0;
- int depth = set->GetDepthLevel();
while (true)
{
if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
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())
+ /////////////////////// ValEntry
+ gdcmValEntry* newValEntry =
+ new gdcmValEntry( newDocEntry->GetDictEntry() );
+ newValEntry->Copy( newDocEntry );
+
+ // When "set" is a gdcmDocument, then we are at the top of the
+ // hierarchy and the Key is simply of the form ( group, elem )...
+ if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ {
+ newValEntry->SetKey( newValEntry->GetKey() );
+ }
+ // ...but when "set" is a gdcmSQItem, we are inserting this new
+ // valEntry in a sequence item. Hence the key has the
+ // generalized form (refer to \ref gdcmBaseTagKey):
+ if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ {
+ newValEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newValEntry->GetKey() );
+ }
+
+ set->AddEntry( newValEntry );
+ LoadDocEntry( newValEntry );
+ if (newValEntry->IsItemDelimitor())
{
break;
}
"nor BinEntry. Probably unknown VR.");
}
- ////// BinEntry or UNKOWN VR:
- gdcmBinEntry *bn = new gdcmBinEntry(newDocEntry->GetDictEntry());
- bn->Copy(newDocEntry);
- set->AddEntry(bn);
- LoadDocEntry(bn);
+ //////////////////// BinEntry or UNKOWN VR:
+ gdcmBinEntry* newBinEntry =
+ new gdcmBinEntry( newDocEntry->GetDictEntry() );
+ newBinEntry->Copy( newDocEntry );
+
+ // When "this" is a gdcmDocument the Key is simply of the
+ // form ( group, elem )...
+ if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ {
+ newBinEntry->SetKey( newBinEntry->GetKey() );
+ }
+ // but when "this" is a SQItem, we are inserting this new
+ // valEntry in a sequence item, and the kay has the
+ // generalized form (refer to \ref gdcmBaseTagKey):
+ if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ {
+ newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newBinEntry->GetKey() );
+ }
+
+ set->AddEntry( newBinEntry );
+ LoadDocEntry( newBinEntry );
}
if (newDocEntry->GetGroup() == 0x7fe0 &&
}
}
// no other way to create it ...
- gdcmSeqEntry *sq = new gdcmSeqEntry(newDocEntry->GetDictEntry(),
- set->GetDepthLevel());
- sq->Copy(newDocEntry);
- sq->SetDelimitorMode(delim_mode);
- sq->SetDepthLevel(depth);
+ gdcmSeqEntry* newSeqEntry =
+ new gdcmSeqEntry( newDocEntry->GetDictEntry() );
+ newSeqEntry->Copy( newDocEntry );
+ newSeqEntry->SetDelimitorMode( delim_mode );
+
+ // At the top of the hierarchy, stands a gdcmDocument. When "set"
+ // is a gdcmDocument, then we are building the first depth level.
+ // Hence the gdcmSeqEntry we are building simply has a depth
+ // level of one:
+ if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ {
+ newSeqEntry->SetDepthLevel( 1 );
+ newSeqEntry->SetKey( newSeqEntry->GetKey() );
+ }
+ // But when "set" is allready a SQItem, we are building a nested
+ // sequence, and hence the depth level of the new gdcmSeqEntry
+ // we are building, is one level deeper:
+ if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ {
+ newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
+ newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newSeqEntry->GetKey() );
+ }
if ( l != 0 )
{ // Don't try to parse zero-length sequences
- long lgt = ParseSQ( sq,
- newDocEntry->GetOffset(),
- l, delim_mode);
- (void)lgt; //not used...
+ (void)ParseSQ( newSeqEntry,
+ newDocEntry->GetOffset(),
+ l, delim_mode);
}
- set->AddEntry(sq);
+ set->AddEntry( newSeqEntry );
if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
{
break;
}
delete newDocEntry;
}
-
return l; // Probably useless
}
* \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)
+long gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry,
+ long offset, long l_max, bool delim_mode)
{
int SQItemNumber = 0;
bool dlm_mod;
- //int depth = set->GetDepthLevel();
- //(void)depth; //not used
while (true)
{
- gdcmDocEntry *newDocEntry = ReadNextDocEntry();
+ gdcmDocEntry* newDocEntry = ReadNextDocEntry();
if ( !newDocEntry )
{
// FIXME Should warn user
}
if( delim_mode )
{
- if ( newDocEntry->isSequenceDelimitor() )
+ if ( newDocEntry->IsSequenceDelimitor() )
{
- set->SetSequenceDelimitationItem( newDocEntry );
+ seqEntry->SetSequenceDelimitationItem( newDocEntry );
break;
}
}
break;
}
- gdcmSQItem *itemSQ = new gdcmSQItem(set->GetDepthLevel());
- itemSQ->AddEntry(newDocEntry);
+ gdcmSQItem *itemSQ = new gdcmSQItem( seqEntry->GetDepthLevel() );
+ std::ostringstream newBase;
+ newBase << seqEntry->GetKey()
+ << "/"
+ << SQItemNumber
+ << "#";
+ itemSQ->SetBaseTagKey( newBase.str() );
unsigned int l = newDocEntry->GetReadLength();
if ( l == 0xffffffff )
dlm_mod = false;
}
- int lgr = ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+ (void)ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
- set->AddEntry(itemSQ, SQItemNumber);
+ seqEntry->AddEntry( itemSQ, SQItemNumber );
SQItemNumber++;
- if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
+ if ( !delim_mode && ( ftell(Fp) - offset ) >= l_max )
{
break;
}
/**
* \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
+ * @param entry Header Entry (Dicom Element) to be dealt with
*/
void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry)
{
if (length > MaxSizeLoadEntry)
{
if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) )
- {
- s << "gdcm::NotLoaded (BinEntry)";
+ {
+ //s << "gdcm::NotLoaded (BinEntry)";
+ s << GDCM_NOTLOADED;
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; //FIXME FIXME FIXME FIXME ????
-
// Be carefull : a BinEntry IS_A ValEntry ...
- if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) )
+ else if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) )
{
- s << "gdcm::NotLoaded. (ValEntry)";
+ // s << "gdcm::NotLoaded. (ValEntry)";
+ s << GDCM_NOTLOADED;
s << " Address:" << (long)entry->GetOffset();
s << " Length:" << entry->GetLength();
s << " x(" << std::hex << entry->GetLength() << ")";
valEntryPtr->SetValue(s.str());
}
+ else
+ {
+ // fusible
+ std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry "
+ << "nor a ValEntry ?! Should never print that !" << std::endl;
+ }
+
// 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());
+ LoadEntryVoidArea(binEntryPtr); // last one, not to erase length !
return;
}
if ( IsDocEntryAnInteger(entry) )
{
uint32_t NewInt;
- std::ostringstream s;
int nbInt;
// When short integer(s) are expected, read and convert the following
// n *two characters properly i.e. consider them as short integers as
//std::string newValue(length,0);
//item_read = fread(&(newValue[0]), (size_t)length, (size_t)1, Fp);
//rah !! I can't believe it could work, normally this is a const char* !!!
- char str[length];
+ char *str = new char[length+1];
item_read = fread(str, (size_t)length, (size_t)1, Fp);
+ str[length] = '\0';
std::string newValue = str;
- newValue += '\0';
+ delete[] str;
if ( gdcmValEntry* valEntry = dynamic_cast<gdcmValEntry* >(entry) )
{
if ( item_read != 1 )
{
dbg.Verbose(1, "gdcmDocument::LoadDocEntry",
"unread element value");
- valEntry->SetValue("gdcm::UnRead");
+ valEntry->SetValue(GDCM_UNREAD);
return;
}
/**
* \brief Find the value Length of the passed Header Entry
- * @param Entry Header Entry whose length of the value shall be loaded.
+ * @param entry Header Entry whose length of the value shall be loaded.
*/
-void gdcmDocument::FindDocEntryLength (gdcmDocEntry *entry)
+void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry )
+ throw ( gdcmFormatError )
{
uint16_t element = entry->GetElement();
std::string vr = entry->GetVR();
- uint16_t length16;
-
+ uint16_t length16;
if ( Filetype == gdcmExplicitVR && !entry->IsImplicitVR() )
{
if ( vr == "OB" && length32 == 0xffffffff )
{
- uint32_t lengthOB = FindDocEntryLengthOB();
- if ( errno == 1 )
+ uint32_t lengthOB;
+ try
+ {
+ lengthOB = FindDocEntryLengthOB();
+ }
+ catch ( gdcmFormatUnexpected )
{
// Computing the length failed (this happens with broken
// files like gdcm-JPEG-LossLess3a.dcm). We still have a
long lengthUntilEOF = ftell(Fp) - currentPosition;
fseek(Fp, currentPosition, SEEK_SET);
entry->SetLength(lengthUntilEOF);
- errno = 0;
return;
}
entry->SetLength(lengthOB);
// endian encoding". When this is the case, chances are we have got our
// hands on a big endian encoded file: we switch the swap code to
// big endian and proceed...
- if ( (element == 0x0000) && (length16 == 0x0400) )
+ if ( element == 0x0000 && length16 == 0x0400 )
{
- if ( ! IsExplicitVRBigEndianTransferSyntax() )
+ if ( !IsExplicitVRBigEndianTransferSyntax() )
{
- dbg.Verbose(0, "gdcmDocument::FindLength", "not explicit VR");
- errno = 1;
+ throw gdcmFormatError( "gdcmDocument::FindDocEntryLength()",
+ " not explicit VR." );
return;
}
length16 = 4;
// Heuristic: well, some files are really ill-formed.
if ( length16 == 0xffff)
{
+ // 0xffff means that we deal with 'Unknown Length' Sequence
length16 = 0;
- // Length16= 0xffff means that we deal with
- // 'Unknown Length' Sequence
}
- FixDocEntryFoundLength(entry, (uint32_t)length16);
+ FixDocEntryFoundLength( entry, (uint32_t)length16 );
return;
}
else
// not coexist in a Data Set and Data Sets nested within it".]
// Length is on 4 bytes.
- FixDocEntryFoundLength(entry, ReadInt32());
+ FixDocEntryFoundLength( entry, ReadInt32() );
return;
}
}
/**
* \brief Find the Value Representation of the current Dicom Element.
- * @param Entry
+ * @param entry
*/
void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry )
{
// is in explicit VR and try to fix things if it happens not to be
// the case.
- fread (&vr, (size_t)2,(size_t)1, Fp);
+ fread (vr, (size_t)2,(size_t)1, Fp);
vr[2] = 0;
if( !CheckDocEntryVR(entry, vr) )
* \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 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
// expected VR read happens to be non-ascii characters we consider
// we hit falsely explicit VR tag.
- if ( (!isalpha(vr[0])) && (!isalpha(vr[1])) )
+ if ( !isalpha(vr[0]) && !isalpha(vr[1]) )
{
realExplicit = false;
}
* \brief Get the transformed value of the header entry. The VR value
* is used to define the transformation to operate on the value
* \warning NOT end user intended method !
- * @param Entry
+ * @param entry entry to tranform
* @return Transformed entry value
*/
std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *entry)
* value is used to define the reverse transformation to operate on
* the value
* \warning NOT end user intended method !
- * @param Entry
+ * @param entry Entry to reverse transform
* @return Reverse transformed entry value
*/
std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* entry)
/**
* \brief Skip a given Header Entry
* \warning NOT end user intended method !
- * @param entry
+ * @param entry entry to skip
*/
void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry)
{
/**
* \brief Skips to the begining of the next Header Entry
* \warning NOT end user intended method !
- * @param entry
+ * @param entry entry to skip
*/
void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry)
{
* \brief When the length of an element value is obviously wrong (because
* the parser went Jabberwocky) one can hope improving things by
* applying some heuristics.
+ * @param entry entry to check
+ * @param foundLength fist assumption about length
*/
void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry,
uint32_t foundLength)
entry->SetReadLength(4); /// \todo a bug is to be fixed !?
}
- //////// Deal with sequences, but only on users request:
- else if ( entry->GetVR() == "SQ" && EnableSequences)
+ else if ( entry->GetVR() == "SQ" )
{
foundLength = 0; // ReadLength is unchanged
}
/**
* \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.
+ * @param entry The element value on which to apply the predicate.
* @return The result of the heuristical predicate.
*/
bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *entry)
*/
uint32_t gdcmDocument::FindDocEntryLengthOB()
+ throw( gdcmFormatUnexpected )
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
long positionOnEntry = ftell(Fp);
while ( !foundSequenceDelimiter )
{
- uint16_t g = ReadInt16();
- uint16_t n = ReadInt16();
- if ( errno == 1 )
+ uint16_t group;
+ uint16_t elem;
+ try
{
- return 0;
+ group = ReadInt16();
+ elem = ReadInt16();
+ }
+ catch ( gdcmFormatError )
+ {
+ throw gdcmFormatError("gdcmDocument::FindDocEntryLengthOB()",
+ " group or element not present.");
}
// We have to decount the group and element we just read
totalLength += 4;
- if ( g != 0xfffe || ( n != 0xe0dd && n != 0xe000 ) )
+ if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- dbg.Verbose(1, "gdcmDocument::FindLengthOB: neither an Item tag "
- "nor a Sequence delimiter tag.");
+ dbg.Verbose(1, "gdcmDocument::FindDocEntryLengthOB: neither an Item "
+ "tag nor a Sequence delimiter tag.");
fseek(Fp, positionOnEntry, SEEK_SET);
- errno = 1;
- return 0;
+ throw gdcmFormatUnexpected("gdcmDocument::FindDocEntryLengthOB()",
+ "Neither an Item tag nor a Sequence "
+ "delimiter tag.");
}
- if ( n == 0xe0dd )
+ if ( elem == 0xe0dd )
{
foundSequenceDelimiter = true;
}
* @return read value
*/
uint16_t gdcmDocument::ReadInt16()
+ throw( gdcmFormatError )
{
uint16_t g;
size_t item_read = fread (&g, (size_t)2,(size_t)1, Fp);
{
if( ferror(Fp) )
{
- dbg.Verbose(0, "gdcmDocument::ReadInt16", " File Error");
+ throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
}
- errno = 1;
- return 0;
+ throw gdcmFormatError( "gdcmDocument::ReadInt16()", "EOF." );
}
- errno = 0;
g = SwapShort(g);
return g;
}
* @return read value
*/
uint32_t gdcmDocument::ReadInt32()
+ throw( gdcmFormatError )
{
uint32_t g;
size_t item_read = fread (&g, (size_t)4,(size_t)1, Fp);
{
if( ferror(Fp) )
{
- dbg.Verbose(0, "gdcmDocument::ReadInt32", " File Error");
+ throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
}
- errno = 1;
- return 0;
+ throw gdcmFormatError( "gdcmDocument::ReadInt32()", "EOF." );
}
- errno = 0;
g = SwapLong(g);
return g;
}
// The easiest case is the one of a DICOM header, since it possesses a
// file preamble where it suffice to look for the string "DICM".
int lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, Fp);
+ (void)lgrLue; //FIXME not used
char *entCur = deb + 128;
if( memcmp(entCur, "DICM", (size_t)4) == 0 )
/**
* \brief during parsing, Header Elements too long are not loaded in memory
- * @param NewSize
+ * @param newSize
*/
void gdcmDocument::SetMaxSizeLoadEntry(long newSize)
{
/**
* \brief Header Elements too long will not be printed
* \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE
- * @param NewSize
+ * @param newSize
*/
void gdcmDocument::SetMaxSizePrintEntry(long newSize)
{
* gets the VR, gets the length, gets the offset value)
* @return On succes the newly created DocEntry, NULL on failure.
*/
-gdcmDocEntry *gdcmDocument::ReadNextDocEntry()
+gdcmDocEntry* gdcmDocument::ReadNextDocEntry()
{
- if (errno == 1)
+ uint16_t group;
+ uint16_t elem;
+
+ try
+ {
+ group = ReadInt16();
+ elem = ReadInt16();
+ }
+ catch ( gdcmFormatError e )
{
// We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
+ //std::cout << e;
return 0;
}
- uint16_t g = ReadInt16();
- uint16_t n = ReadInt16();
- gdcmDocEntry *newEntry = NewDocEntryByNumber(g, n);
-
+ gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem);
FindDocEntryVR(newEntry);
- FindDocEntryLength(newEntry);
- if (errno == 1)
+ try
+ {
+ FindDocEntryLength(newEntry);
+ }
+ catch ( gdcmFormatError e )
{
// Call it quits
+ //std::cout << e;
delete newEntry;
- return NULL;
+ return 0;
}
+
newEntry->SetOffset(ftell(Fp));
return newEntry;
}
/**
- * \brief Assuming the internal file pointer \ref gdcmDocument::fp
+ * \brief Assuming the internal file pointer \ref gdcmDocument::Fp
* is placed at the beginning of a tag check whether this
* tag is (TestGroup, TestElement).
- * \warning On success the internal file pointer \ref gdcmDocument::fp
+ * \warning On success the internal file pointer \ref gdcmDocument::Fp
* is modified to point after the tag.
* 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.
+ * \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 True on success, false otherwise.
*/
bool gdcmDocument::ReadTag(uint16_t testGroup, uint16_t testElement)
}
/**
- * \brief Assuming the internal file pointer \ref gdcmDocument::fp
+ * \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
+ * \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.
+ * \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.
*/
uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement)
{
- long PositionOnEntry = ftell(Fp);
- (void)PositionOnEntry;
+ long positionOnEntry = ftell(Fp);
+ (void)positionOnEntry;
if ( !ReadTag(testGroup, testElement) )
{
/**
* \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files
* No other way so 'skip' the Data
- *
*/
void gdcmDocument::Parse7FE0 ()
{
s << " Read one length: ";
s << std::hex << individualLength << std::endl;
dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str());
- }
+ }
+ delete[] basicOffsetTableItemValue;
}
if ( ! IsRLELossLessTransferSyntax() )
// Make sure that at the end of the item we encounter a 'Sequence
// Delimiter Item':
- if ( ! ReadTag(0xfffe, 0xe0dd) )
+ if ( !ReadTag(0xfffe, 0xe0dd) )
{
dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item");
dbg.Verbose(0, " at end of RLE item sequence");
}
}
+/**
+ * \brief Walk recursively the given \ref gdcmDocEntrySet, and feed
+ * the given hash table (\ref TagDocEntryHT) with all the
+ * \ref gdcmDocEntry (Dicom entries) encountered.
+ * This method does the job for \ref BuildFlatHashTable.
+ * @param builtHT Where to collect all the \ref gdcmDocEntry encountered
+ * when recursively walking the given set.
+ * @param set The structure to be traversed (recursively).
+ */
+void gdcmDocument::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT,
+ gdcmDocEntrySet* set )
+{
+ if (gdcmElementSet* elementSet = dynamic_cast< gdcmElementSet* > ( set ) )
+ {
+ TagDocEntryHT* currentHT = elementSet->GetTagHT();
+ for( TagDocEntryHT::const_iterator i = currentHT->begin();
+ i != currentHT->end();
+ ++i)
+ {
+ gdcmDocEntry* entry = i->second;
+ if ( gdcmSeqEntry* seqEntry = dynamic_cast<gdcmSeqEntry*>(entry) )
+ {
+ ListSQItem& items = seqEntry->GetSQItems();
+ for( ListSQItem::const_iterator item = items.begin();
+ item != items.end();
+ ++item)
+ {
+ BuildFlatHashTableRecurse( builtHT, *item );
+ }
+ continue;
+ }
+ builtHT[entry->GetKey()] = entry;
+ }
+ return;
+ }
+
+ if (gdcmSQItem* SQItemSet = dynamic_cast< gdcmSQItem* > ( set ) )
+ {
+ ListDocEntry& currentList = SQItemSet->GetDocEntries();
+ for (ListDocEntry::iterator i = currentList.begin();
+ i != currentList.end();
+ ++i)
+ {
+ gdcmDocEntry* entry = *i;
+ if ( gdcmSeqEntry* seqEntry = dynamic_cast<gdcmSeqEntry*>(entry) )
+ {
+ ListSQItem& items = seqEntry->GetSQItems();
+ for( ListSQItem::const_iterator item = items.begin();
+ item != items.end();
+ ++item)
+ {
+ BuildFlatHashTableRecurse( builtHT, *item );
+ }
+ continue;
+ }
+ builtHT[entry->GetKey()] = entry;
+ }
+
+ }
+}
+
+/**
+ * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current
+ * gdcmDocument.
+ *
+ * The structure used by a gdcmDocument (through \ref gdcmElementSet),
+ * in order to old the parsed entries of a Dicom header, is a recursive
+ * one. This is due to the fact that the sequences (when present)
+ * can be nested. Additionaly, the sequence items (represented in
+ * gdcm as \ref gdcmSQItem) add an extra complexity to the data
+ * structure. Hence, a gdcm user whishing to visit all the entries of
+ * a Dicom header will need to dig in the gdcm internals (which
+ * implies exposing all the internal data structures to the API).
+ * In order to avoid this burden to the user, \ref BuildFlatHashTable
+ * recursively builds a temporary hash table, which olds all the
+ * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a
+ * std::map<>).
+ * \warning Of course there is NO integrity constrain between the
+ * returned \ref TagDocEntryHT and the \ref gdcmElemenSet used
+ * to build it. Hence if the underlying \ref gdcmElemenSet is
+ * altered, then it is the caller responsability to invoke
+ * \ref BuildFlatHashTable again...
+ * @return The flat std::map<> we juste build.
+ */
+TagDocEntryHT* gdcmDocument::BuildFlatHashTable()
+{
+ TagDocEntryHT* FlatHT = new TagDocEntryHT;
+ BuildFlatHashTableRecurse( *FlatHT, this );
+ return FlatHT;
+}
+
/**
bool gdcmDocument::operator<(gdcmDocument &document)
{
// Patient Name
- std::string s1 = this->GetEntryByNumber(0x0010,0x0010);
+ std::string s1 = GetEntryByNumber(0x0010,0x0010);
std::string s2 = document.GetEntryByNumber(0x0010,0x0010);
if(s1 < s2)
{
return true;
}
- else if(s1 > s2)
+ else if( s1 > s2 )
{
return false;
}
else
{
// Patient ID
- s1 = this->GetEntryByNumber(0x0010,0x0020);
+ s1 = GetEntryByNumber(0x0010,0x0020);
s2 = document.GetEntryByNumber(0x0010,0x0020);
if ( s1 < s2 )
{
}
else if ( s1 > s2 )
{
- return true;
+ return false;
}
else
{
// Study Instance UID
- s1 = this->GetEntryByNumber(0x0020,0x000d);
+ s1 = GetEntryByNumber(0x0020,0x000d);
s2 = document.GetEntryByNumber(0x0020,0x000d);
if ( s1 < s2 )
{
else
{
// Serie Instance UID
- s1 = this->GetEntryByNumber(0x0020,0x000e);
- s2 = document.GetEntryByNumber(0x0020,0x000e);
+ s1 = GetEntryByNumber(0x0020,0x000e);
+ s2 = document.GetEntryByNumber(0x0020,0x000e);
if ( s1 < s2 )
{
return true;
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff