Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2004/11/16 10:25:53 $
- Version: $Revision: 1.125 $
+ Date: $Date: 2005/01/06 15:36:48 $
+ Version: $Revision: 1.157 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
+#include "gdcmTS.h"
+#include "gdcmException.h"
+#include "gdcmDictSet.h"
+#include "gdcmRLEFramesInfo.h"
+#include "gdcmJPEGFragmentsInfo.h"
+#include "gdcmDocEntrySet.h"
+#include "gdcmSQItem.h"
#include <vector>
#include <iomanip>
namespace gdcm
{
+//-----------------------------------------------------------------------------
static const char *TransferSyntaxStrings[] = {
// Implicit VR Little Endian
"1.2.840.10008.1.2",
+ // Implicit VR Little Endian DLX G.E?
+ "1.2.840.113619.5.2",
// Explicit VR Little Endian
"1.2.840.10008.1.2.1",
// Deflated Explicit VR Little Endian
// Unknown
"Unknown Transfer Syntax"
};
-
+
//-----------------------------------------------------------------------------
// Refer to Document::CheckSwap()
-const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
+//const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
// Refer to Document::SetMaxSizeLoadEntry()
const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
dbg.Verbose(0, "Document::Document: starting parsing of file: ",
Filename.c_str());
- Fp->seekg( 0, std::ios_base::beg);
+ Fp->seekg( 0, std::ios::beg);
- Fp->seekg(0, std::ios_base::end);
+ Fp->seekg(0, std::ios::end);
long lgt = Fp->tellg();
- Fp->seekg( 0, std::ios_base::beg);
+ Fp->seekg( 0, std::ios::beg);
CheckSwap();
long beg = Fp->tellg();
lgt -= beg;
ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
- Fp->seekg( 0, std::ios_base::beg);
+ Fp->seekg( 0, std::ios::beg);
// Load 'non string' values
SetEntryByNumber(rows , 0x0028, 0x0011);
}
// ----------------- End of ACR-LibIDO kludge ------------------
-
- PrintLevel = 1; // 'Medium' print level by default
}
/**
Initialise();
SwapCode = 0;
Filetype = ExplicitVR;
- PrintLevel = 1; // 'Medium' print level by default
}
/**
RefPubDict = NULL;
RefShaDict = NULL;
- // Recursive clean up of sequences
- for (TagDocEntryHT::const_iterator it = TagHT.begin();
- it != TagHT.end(); ++it )
- {
- //delete it->second; //temp remove
- }
- TagHT.clear();
delete RLEInfo;
delete JPEGInfo;
}
*/
void Document::PrintPubDict(std::ostream & os)
{
+ RefPubDict->SetPrintLevel(PrintLevel);
RefPubDict->Print(os);
}
*/
void Document::PrintShaDict(std::ostream & os)
{
+ RefShaDict->SetPrintLevel(PrintLevel);
RefShaDict->Print(os);
}
// for brain damaged headers
return UnknownTS;
}
- while ( !isdigit(transfer[transfer.length()-1]) )
+ while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
{
transfer.erase(transfer.length()-1, 1);
}
*/
std::ifstream* Document::OpenFile()
{
- if (Filename.length() == 0) return 0;
+ if (Filename.length() == 0)
+ {
+ return 0;
+ }
+
if(Fp)
{
dbg.Verbose( 0,
}
Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
-
- if(!Fp)
+ if( ! *Fp )
{
dbg.Verbose( 0,
"Document::OpenFile cannot open file: ",
Filename.c_str());
+ delete Fp;
+ Fp = 0;
return 0;
}
uint16_t zero;
- Fp->read((char*)&zero, (size_t)2 );
+ Fp->read((char*)&zero, (size_t)2);
+ if( Fp->eof() )
+ {
+ CloseFile();
+ return 0;
+ }
- //ACR -- or DICOM with no Preamble --
- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 )
+ //ACR -- or DICOM with no Preamble; may start with a Shadow Group --
+ if(
+ zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 ||
+ zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 ||
+ zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 ||
+ zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 )
{
return Fp;
}
//DICOM
- Fp->seekg(126L, std::ios_base::cur);
+ Fp->seekg(126L, std::ios::cur);
char dicm[4];
Fp->read(dicm, (size_t)4);
+ if( Fp->eof() )
+ {
+ CloseFile();
+ return 0;
+ }
if( memcmp(dicm, "DICM", 4) == 0 )
{
return Fp;
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* \return Always true.
*/
-void Document::Write(std::ofstream* fp, FileType filetype)
+void Document::WriteContent(std::ofstream* fp, FileType filetype)
{
/// \todo move the following lines (and a lot of others, to be written)
/// to a future function CheckAndCorrectHeader
/// (necessary if user wants to write a DICOM V3 file
/// starting from an ACR-NEMA (V2) Header
- if (filetype == ImplicitVR)
- {
- std::string ts =
- Util::DicomString( TransferSyntaxStrings[ImplicitVRLittleEndian] );
- ReplaceOrCreateByNumber(ts, 0x0002, 0x0010);
-
- /// \todo Refer to standards on page 21, chapter 6.2
- /// "Value representation": values with a VR of UI shall be
- /// padded with a single trailing null
- /// in the following case we have to padd manually with a 0
-
- SetEntryLengthByNumber(18, 0x0002, 0x0010);
- }
-
- if (filetype == ExplicitVR)
+ if ( filetype == ImplicitVR || filetype == ExplicitVR )
{
- std::string ts =
- Util::DicomString( TransferSyntaxStrings[ExplicitVRLittleEndian] );
- ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); //LEAK
-
- /// \todo Refer to standards on page 21, chapter 6.2
- /// "Value representation": values with a VR of UI shall be
- /// padded with a single trailing null
- /// Dans le cas suivant on doit pader manuellement avec un 0
-
- SetEntryLengthByNumber(20, 0x0002, 0x0010);
+ // writing Dicom File Preamble
+ char filePreamble[128];
+ memset(filePreamble, 0, 128);
+ fp->write(filePreamble, 128);
+ fp->write("DICM", 4);
}
-
+
/**
* \todo rewrite later, if really usefull
* - 'Group Length' element is optional in DICOM
* UpdateGroupLength(true,ACR);
*/
- ElementSet::Write(fp, filetype); // This one is recursive
-
+ ElementSet::WriteContent(fp, filetype); // This one is recursive
}
/**
- * \brief Modifies the value of a given Header Entry (Dicom Element)
+ * \brief Modifies the value of a given Doc 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
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-ValEntry* Document::ReplaceOrCreateByNumber(
- std::string const & value,
- uint16_t group,
- uint16_t elem,
- TagName const & vr )
+ValEntry* Document::ReplaceOrCreateByNumber(std::string const & value,
+ uint16_t group,
+ uint16_t elem,
+ TagName const & vr )
{
ValEntry* valEntry = 0;
DocEntry* currentEntry = GetDocEntryByNumber( group, elem);
- if (!currentEntry)
+ if (currentEntry)
{
- // check if (group,element) DictEntry exists
- // if it doesn't, create an entry in DictSet::VirtualEntry
- // and use it
+ valEntry = dynamic_cast< ValEntry* >(currentEntry);
- // Find out if the tag we received is in the dictionaries:
- Dict *pubDict = Global::GetDicts()->GetDefaultPubDict();
- DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem);
- if (!dictEntry)
- {
- currentEntry = NewDocEntryByNumber(group, elem, vr);
- }
- else
- {
- currentEntry = NewDocEntryByNumber(group, elem);
- }
+ // Verify the VR
+ if( valEntry )
+ if( valEntry->GetVR()!=vr )
+ valEntry=NULL;
- if (!currentEntry)
+ // if currentEntry doesn't correspond to the requested valEntry
+ if( !valEntry)
{
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to"
- " NewDocEntryByNumber failed.");
- return NULL;
- }
- valEntry = new ValEntry(currentEntry);
- if ( !AddEntry(valEntry))
- {
- delete valEntry;
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
- " failed allthough this is a creation.");
- }
- // This is the reason why NewDocEntryByNumber are a real
- // bad habit !!! FIXME
- delete currentEntry;
- }
- else
- {
- valEntry = dynamic_cast< ValEntry* >(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 DocEntry to a ValEntry:
- valEntry = new ValEntry(currentEntry);
if (!RemoveEntry(currentEntry))
{
- delete valEntry;
dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
" of previous DocEntry failed.");
- return NULL;
- }
- if ( !AddEntry(valEntry))
- {
- delete valEntry;
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding"
- " promoted ValEntry failed.");
+
return NULL;
}
}
}
- SetEntryByNumber(value, group, elem);
+ // Create a new valEntry if necessary
+ if (!valEntry)
+ {
+ valEntry = NewValEntryByNumber(group, elem, vr);
+ if ( !AddEntry(valEntry))
+ {
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
+ " failed allthough this is a creation.");
+
+ delete valEntry;
+ return NULL;
+ }
+ }
+
+ // Set the binEntry value
+ SetEntry(value, valEntry);
return valEntry;
}
/*
* \brief Modifies the value of a given Header Entry (Dicom Element)
* when it exists. Create it with the given value when unexistant.
+ * A copy of the binArea is made to be kept in the Document.
* @param binArea (binary) 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).
*/
-BinEntry* Document::ReplaceOrCreateByNumber(
- uint8_t* binArea,
- int lgth,
- uint16_t group,
- uint16_t elem,
- TagName const & vr )
+BinEntry* Document::ReplaceOrCreateByNumber(uint8_t* binArea,
+ int lgth,
+ uint16_t group,
+ uint16_t elem,
+ TagName const & vr )
{
BinEntry* binEntry = 0;
DocEntry* currentEntry = GetDocEntryByNumber( group, elem);
- if (!currentEntry)
- {
- // check if (group,element) DictEntry exists
- // if it doesn't, create an entry in DictSet::VirtualEntry
- // and use it
+ // Verify the currentEntry
+ if (currentEntry)
+ {
+ binEntry = dynamic_cast< BinEntry* >(currentEntry);
- // Find out if the tag we received is in the dictionaries:
- Dict *pubDict = Global::GetDicts()->GetDefaultPubDict();
- DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem);
+ // Verify the VR
+ if( binEntry )
+ if( binEntry->GetVR()!=vr )
+ binEntry=NULL;
- if (!dictEntry)
+ // if currentEntry doesn't correspond to the requested valEntry
+ if( !binEntry)
{
- currentEntry = NewDocEntryByNumber(group, elem, vr);
- }
- else
- {
- currentEntry = NewDocEntryByNumber(group, elem);
- }
- if (!currentEntry)
- {
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to"
- " NewDocEntryByNumber failed.");
- return NULL;
+ if (!RemoveEntry(currentEntry))
+ {
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
+ " of previous DocEntry failed.");
+
+ return NULL;
+ }
}
- binEntry = new BinEntry(currentEntry);
+ }
+
+ // Create a new binEntry if necessary
+ if (!binEntry)
+ {
+ binEntry = NewBinEntryByNumber(group, elem, vr);
+
if ( !AddEntry(binEntry))
{
dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
" failed allthough this is a creation.");
+
+ delete binEntry;
+ return NULL;
}
}
+
+ // Set the binEntry value
+ uint8_t *tmpArea;
+ if (lgth>0 && binArea)
+ {
+ tmpArea = new uint8_t[lgth];
+ memcpy(tmpArea,binArea,lgth);
+ }
else
{
- binEntry = dynamic_cast< BinEntry* >(currentEntry);
- if ( !binEntry ) // Euuuuh? It wasn't a BinEntry
- // then we change it to a BinEntry ?
- // Shouldn't it be considered as an error ?
+ tmpArea = 0;
+ }
+ if (!SetEntry(tmpArea,lgth,binEntry))
+ {
+ if (tmpArea)
{
- // We need to promote the DocEntry to a BinEntry:
- binEntry = new BinEntry(currentEntry);
- if (!RemoveEntry(currentEntry))
- {
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
- " of previous DocEntry failed.");
- return NULL;
- }
- if ( !AddEntry(binEntry))
- {
- dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding"
- " promoted BinEntry failed.");
- return NULL;
- }
+ delete[] tmpArea;
}
}
- SetEntryByNumber(binArea, lgth, group, elem);
-
return binEntry;
}
-
/*
* \brief Modifies the value of a given Header Entry (Dicom Element)
* when it exists. Create it when unexistant.
*/
SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem)
{
- SeqEntry* b = 0;
- DocEntry* a = GetDocEntryByNumber( group, elem);
- if (!a)
+ SeqEntry* seqEntry = 0;
+ DocEntry* currentEntry = GetDocEntryByNumber( group, elem);
+
+ // Verify the currentEntry
+ if (currentEntry)
+ {
+ seqEntry = dynamic_cast< SeqEntry* >(currentEntry);
+
+ // Verify the VR
+ if( seqEntry )
+ if( seqEntry->GetVR()!="SQ" )
+ seqEntry=NULL;
+
+ // if currentEntry doesn't correspond to the requested valEntry
+ if( !seqEntry)
+ {
+ if (!RemoveEntry(currentEntry))
+ {
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
+ " of previous DocEntry failed.");
+
+ return NULL;
+ }
+ }
+ }
+
+ // Create a new seqEntry if necessary
+ if (!seqEntry)
{
- a = NewSeqEntryByNumber(group, elem);
- if (!a)
+ seqEntry = NewSeqEntryByNumber(group, elem);
+
+ if ( !AddEntry(seqEntry))
{
- return 0;
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
+ " failed allthough this is a creation.");
+
+ delete seqEntry;
+ return NULL;
}
+ }
- b = new SeqEntry(a, 1); // FIXME : 1 (Depth)
- AddEntry(b);
- }
- return b;
+ return seqEntry;
}
/**
return true;
}
+std::string Document::GetTransferSyntaxValue(TransferSyntaxType type)
+{
+ return TransferSyntaxStrings[type];
+}
+
//-----------------------------------------------------------------------------
// Protected
std::string Document::GetEntryByNumber(uint16_t group, uint16_t element)
{
TagKey key = DictEntry::TranslateToKey(group, element);
- /// \todo use map methods, instead of multimap JPR
if ( !TagHT.count(key))
{
return GDCM_UNFOUND;
bool Document::SetEntryByNumber(std::string const& content,
uint16_t group, uint16_t element)
{
- int c;
- int l;
-
- ValEntry* valEntry = GetValEntryByNumber(group, element);
- if (!valEntry )
+ ValEntry* entry = GetValEntryByNumber(group, element);
+ if (!entry )
{
dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding",
" ValEntry (try promotion first).");
return false;
}
- // Non even content must be padded with a space (020H)...
- std::string finalContent = Util::DicomString( content.c_str() );
- assert( !(finalContent.size() % 2) );
- valEntry->SetValue(finalContent);
-
- // Integers have a special treatement for their length:
-
- l = finalContent.length();
- if ( l != 0) // To avoid to be cheated by 'zero length' integers
- {
- VRKey vr = valEntry->GetVR();
- if( vr == "US" || vr == "SS" )
- {
- // for multivaluated items
- c = Util::CountSubstring(content, "\\") + 1;
- l = c*2;
- }
- else if( vr == "UL" || vr == "SL" )
- {
- // for multivaluated items
- c = Util::CountSubstring(content, "\\") + 1;
- l = c*4;;
- }
- }
- valEntry->SetLength(l);
- return true;
+ return SetEntry(content,entry);
}
/**
bool Document::SetEntryByNumber(uint8_t*content, int lgth,
uint16_t group, uint16_t element)
{
- (void)lgth; //not used
- TagKey key = DictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key))
+ BinEntry* entry = GetBinEntryByNumber(group, element);
+ if (!entry )
{
+ dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding",
+ " ValEntry (try promotion first).");
return false;
}
-/* 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?
- }
-*/
- BinEntry* a = (BinEntry *)TagHT[key];
- a->SetBinArea(content);
- a->SetLength(lgth);
- a->SetValue(GDCM_BINLOADED);
-
- return true;
+ return SetEntry(content,lgth,entry);
}
/**
* \brief Accesses an existing DocEntry (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.
- * @param l new length to substitute with
- * @param group group number of the Entry to modify
- * @param element element number of the Entry to modify
- * @return true on success, false otherwise.
+ * and modifies it's content with the given value.
+ * @param content new value (string) to substitute with
*/
-bool Document::SetEntryLengthByNumber(uint32_t l,
- uint16_t group, uint16_t element)
+bool Document::SetEntry(std::string const & content,ValEntry* entry)
{
- /// \todo use map methods, instead of multimap JPR
- TagKey key = DictEntry::TranslateToKey(group, element);
- if ( !TagHT.count(key) )
- {
- return false;
- }
- if ( l % 2 )
+ if(entry)
{
- l++; // length must be even
+ entry->SetValue(content);
+ return true;
}
- ( ((TagHT.equal_range(key)).first)->second )->SetLength(l);
-
- return true ;
+ return false;
}
/**
- * \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
- * @return File Offset of the Element Value
+ * \brief Accesses an existing BinEntry (i.e. a Dicom Element)
+ * and modifies it's content with the given value.
+ * @param content new value (void* -> uint8_t*) to substitute with
+ * @param lgth new value length
*/
-size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem)
+bool Document::SetEntry(uint8_t* content, int lgth,BinEntry* entry)
{
- DocEntry* entry = GetDocEntryByNumber(group, elem);
- if (!entry)
+ if(entry)
{
- dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present.");
- return 0;
+ // 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?
+ }*/
+
+ entry->SetBinArea(content);
+ entry->SetLength(lgth);
+ entry->SetValue(GDCM_BINLOADED);
+ return true;
}
- return entry->GetOffset();
+ return false;
}
/**
if ( !docElement )
return;
- size_t o =(size_t)docElement->GetOffset();
- Fp->seekg( o, std::ios_base::beg);
- size_t l = docElement->GetLength();
- uint8_t* a = new uint8_t[l];
- if(!a)
- {
- dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a");
- return;
- }
-
- // Read the value
- Fp->read((char*)a, l);
- if( Fp->fail() || Fp->eof() )//Fp->gcount() == 1
- {
- delete[] a;
+ BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
+ if( !binElement )
return;
- }
- // Set the value to the DocEntry
- if( !SetEntryBinAreaByNumber( a, group, elem ) )
- {
- delete[] a;
- dbg.Verbose(0, "Document::LoadEntryBinArea setting failed.");
- }
+ LoadEntryBinArea(binElement);
}
+
/**
* \brief Loads (from disk) the element content
* when a string is not suitable
*/
void Document::LoadEntryBinArea(BinEntry* element)
{
+ if(element->GetBinArea())
+ return;
+
+ bool openFile = !Fp;
+ if(openFile)
+ OpenFile();
+
size_t o =(size_t)element->GetOffset();
- Fp->seekg(o, std::ios_base::beg);
+ Fp->seekg(o, std::ios::beg);
+
size_t l = element->GetLength();
uint8_t* a = new uint8_t[l];
if( !a )
return;
}
- element->SetBinArea((uint8_t*)a);
+ element->SetBinArea(a);
+
+ if(openFile)
+ CloseFile();
}
/**
* @param element Element number of the searched Dicom Element
* @return
*/
-bool Document::SetEntryBinAreaByNumber(uint8_t* area,
+/*bool Document::SetEntryBinAreaByNumber(uint8_t* area,
uint16_t group, uint16_t element)
{
DocEntry* currentEntry = GetDocEntryByNumber(group, element);
}
return false;
-}
-
-/**
- * \brief Update the entries with the shadow dictionary.
- * Only non even entries are analyzed
- */
-void Document::UpdateShaEntries()
-{
- //DictEntry *entry;
- std::string vr;
-
- /// \todo TODO : still any use to explore recursively the whole structure?
-/*
- for(ListTag::iterator it=listEntries.begin();
- it!=listEntries.end();
- ++it)
- {
- // Odd group => from public dictionary
- if((*it)->GetGroup()%2==0)
- continue;
-
- // Peer group => search the corresponding dict entry
- if(RefShaDict)
- entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement());
- else
- entry=NULL;
-
- if((*it)->IsImplicitVR())
- vr="Implicit";
- else
- vr=(*it)->GetVR();
-
- (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling
- if(entry){
- // Set the new entry and the new value
- (*it)->SetDictEntry(entry);
- CheckDocEntryVR(*it,vr);
-
- (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling
-
- }
- else
- {
- // Remove precedent value transformation
- (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr));
- }
- }
-*/
-}
+}*/
/**
* \brief Searches within the Header Entries for a Dicom Element of
{
return 0;
}
- if ( ValEntry* valEntry = dynamic_cast<ValEntry*>(currentEntry) )
+ if ( ValEntry* entry = dynamic_cast<ValEntry*>(currentEntry) )
{
- return valEntry;
+ return entry;
}
dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry.");
return 0;
}
+/**
+ * \brief Same as \ref Document::GetDocEntryByNumber except it only
+ * returns a result when the corresponding entry is of type
+ * BinEntry.
+ * @return When present, the corresponding BinEntry.
+ */
+BinEntry* Document::GetBinEntryByNumber(uint16_t group, uint16_t element)
+{
+ DocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ if ( !currentEntry )
+ {
+ return 0;
+ }
+ if ( BinEntry* entry = dynamic_cast<BinEntry*>(currentEntry) )
+ {
+ return entry;
+ }
+ dbg.Verbose(0, "Document::GetBinEntryByNumber: unfound BinEntry.");
+
+ return 0;
+}
+
/**
* \brief Loads the element while preserving the current
* underlying file position indicator as opposed to
*/
void Document::LoadDocEntrySafe(DocEntry * entry)
{
- long PositionOnEntry = Fp->tellg();
- LoadDocEntry(entry);
- Fp->seekg(PositionOnEntry, std::ios_base::beg);
+ if(Fp)
+ {
+ long PositionOnEntry = Fp->tellg();
+ LoadDocEntry(entry);
+ Fp->seekg(PositionOnEntry, std::ios::beg);
+ }
}
/**
long l_max, bool delim_mode)
{
DocEntry *newDocEntry = 0;
-
+
while (true)
- {
- if ( !delim_mode && (Fp->tellg()-offset) >= l_max)
+ {
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
break;
}
+ newValEntry->GetKey() );
}
+ LoadDocEntry( newValEntry );
+ bool delimitor=newValEntry->IsItemDelimitor();
if( !set->AddEntry( newValEntry ) )
{
// If here expect big troubles
delete newValEntry; //otherwise mem leak
}
- LoadDocEntry( newValEntry );
- if (newValEntry->IsItemDelimitor())
+
+ if (delimitor)
{
+ delete newDocEntry;
break;
}
- if ( !delim_mode && (Fp->tellg()-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
+ delete newDocEntry;
break;
}
}
}
//////////////////// BinEntry or UNKOWN VR:
- BinEntry* newBinEntry =
- new BinEntry( newDocEntry->GetDictEntry() ); //LEAK
- newBinEntry->Copy( newDocEntry );
+ BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK
// When "this" is a Document the Key is simply of the
// form ( group, elem )...
+ newBinEntry->GetKey() );
}
+ LoadDocEntry( newBinEntry );
if( !set->AddEntry( newBinEntry ) )
{
//Expect big troubles if here
delete newBinEntry;
}
- LoadDocEntry( newBinEntry );
}
if ( ( newDocEntry->GetGroup() == 0x7fe0 )
if ( ts == RLELossless )
{
long PositionOnEntry = Fp->tellg();
- Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg );
+ Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
ComputeRLEInfo();
- Fp->seekg( PositionOnEntry, std::ios_base::beg );
+ Fp->seekg( PositionOnEntry, std::ios::beg );
}
else if ( IsJPEG() )
{
long PositionOnEntry = Fp->tellg();
- Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg );
+ Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
ComputeJPEGFragmentInfo();
- Fp->seekg( PositionOnEntry, std::ios_base::beg );
+ Fp->seekg( PositionOnEntry, std::ios::beg );
}
}
// Just to make sure we are at the beginning of next entry.
SkipToNextDocEntry(newDocEntry);
+ //delete newDocEntry;
}
else
{
l, delim_mode);
}
set->AddEntry( newSeqEntry );
- if ( !delim_mode && (Fp->tellg()-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
+ delete newDocEntry;
break;
}
}
{
if ( newDocEntry->IsSequenceDelimitor() )
{
- seqEntry->SetSequenceDelimitationItem( newDocEntry );
+ seqEntry->SetSequenceDelimitationItem( newDocEntry );
break;
}
}
- if ( !delim_mode && (Fp->tellg()-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- break;
+ delete newDocEntry;
+ break;
}
SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
}
ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+ delete newDocEntry;
seqEntry->AddEntry( itemSQ, SQItemNumber );
SQItemNumber++;
- if ( !delim_mode && ( Fp->tellg() - offset ) >= l_max )
+ if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
{
break;
}
std::string vr = entry->GetVR();
uint32_t length = entry->GetLength();
- Fp->seekg((long)entry->GetOffset(), std::ios_base::beg);
+ Fp->seekg((long)entry->GetOffset(), std::ios::beg);
// A SeQuence "contains" a set of Elements.
// (fffe e000) tells us an Element is beginning
// to be sure we are at the end of the value ...
Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
- std::ios_base::beg);
+ std::ios::beg);
return;
}
// The following reserved two bytes (see PS 3.5-2003, section
// "7.1.2 Data element structure with explicit vr", p 27) must be
// skipped before proceeding on reading the length on 4 bytes.
- Fp->seekg( 2L, std::ios_base::cur);
+ Fp->seekg( 2L, std::ios::cur);
uint32_t length32 = ReadInt32();
if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
// until the end of the file. Hence we artificially fix the
// the length and proceed.
long currentPosition = Fp->tellg();
- Fp->seekg(0L,std::ios_base::end);
- long lengthUntilEOF = Fp->tellg() - currentPosition;
- Fp->seekg(currentPosition, std::ios_base::beg);
+ Fp->seekg(0L,std::ios::end);
+ long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
+ Fp->seekg(currentPosition, std::ios::beg);
entry->SetLength(lengthUntilEOF);
return;
}
* \brief Find the Value Representation of the current Dicom Element.
* @param entry
*/
-void Document::FindDocEntryVR( DocEntry *entry )
+std::string Document::FindDocEntryVR()
{
if ( Filetype != ExplicitVR )
- {
- return;
- }
-
- char vr[3];
+ return(GDCM_UNKNOWN);
long positionOnEntry = Fp->tellg();
// Warning: we believe this is explicit VR (Value Representation) because
// within an explicit VR file. Hence we make sure the present tag
// is in explicit VR and try to fix things if it happens not to be
// the case.
-
+
+ char vr[3];
Fp->read (vr, (size_t)2);
vr[2] = 0;
- if( !CheckDocEntryVR(entry, vr) )
+ if( !CheckDocEntryVR(vr) )
{
- Fp->seekg(positionOnEntry, std::ios_base::beg);
- // When this element is known in the dictionary we shall use, e.g. for
- // the semantics (see the usage of IsAnInteger), the VR proposed by the
- // dictionary entry. Still we have to flag the element as implicit since
- // we know now our assumption on expliciteness is not furfilled.
- // avoid .
- if ( entry->IsVRUnknown() )
- {
- entry->SetVR("Implicit");
- }
- entry->SetImplicitVR();
+ Fp->seekg(positionOnEntry, std::ios::beg);
+ return(GDCM_UNKNOWN);
}
+ return(vr);
}
/**
* @return false if the VR is incorrect of if the VR isn't referenced
* otherwise, it returns true
*/
-bool Document::CheckDocEntryVR(DocEntry *entry, VRKey vr)
+bool Document::CheckDocEntryVR(VRKey vr)
{
- std::string msg;
- 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 && !Global::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.
- msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n",
- entry->GetGroup(), entry->GetElement());
- dbg.Verbose(1, "Document::FindVR: ", msg.c_str());
-
- if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000)
- {
- // Group length is UL !
- DictEntry* newEntry = NewVirtualDictEntry(
- entry->GetGroup(), entry->GetElement(),
- "UL", "FIXME", "Group Length");
- entry->SetDictEntry( newEntry );
- }
+ if ( !Global::GetVR()->IsValidVR(vr) )
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.
- DictEntry* newEntry = NewVirtualDictEntry(
- entry->GetGroup(), entry->GetElement(),
- vr, "FIXME", entry->GetName());
- entry->SetDictEntry(newEntry);
- }
return true;
}
*/
void Document::SkipToNextDocEntry(DocEntry *entry)
{
- Fp->seekg((long)(entry->GetOffset()), std::ios_base::beg);
- Fp->seekg( (long)(entry->GetReadLength()), std::ios_base::cur);
+ Fp->seekg((long)(entry->GetOffset()), std::ios::beg);
+ Fp->seekg( (long)(entry->GetReadLength()), std::ios::cur);
}
/**
if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" )
{
return true;
- }
-
+ }
return false;
}
{
dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item "
"tag nor a Sequence delimiter tag.");
- Fp->seekg(positionOnEntry, std::ios_base::beg);
+ Fp->seekg(positionOnEntry, std::ios::beg);
throw FormatUnexpected("Document::FindDocEntryLengthOB()",
"Neither an Item tag nor a Sequence "
"delimiter tag.");
break;
}
}
- Fp->seekg( positionOnEntry, std::ios_base::beg);
+ Fp->seekg( positionOnEntry, std::ios::beg);
return totalLength;
}
void Document::SkipBytes(uint32_t nBytes)
{
//FIXME don't dump the returned value
- Fp->seekg((long)nBytes, std::ios_base::cur);
+ Fp->seekg((long)nBytes, std::ios::cur);
}
/**
RefShaDict = NULL;
RLEInfo = new RLEFramesInfo;
JPEGInfo = new JPEGFragmentsInfo;
+ Filetype = Unknown;
}
/**
uint32_t s32;
uint16_t s16;
- char deb[256]; //HEADER_LENGTH_TO_READ];
+ char deb[256];
// First, compare HostByteOrder and NetworkByteOrder in order to
// determine if we shall need to swap bytes (i.e. the Endian type).
// 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".
- Fp->read(deb, HEADER_LENGTH_TO_READ);
+ Fp->read(deb, 256);
char *entCur = deb + 128;
if( memcmp(entCur, "DICM", (size_t)4) == 0 )
// Position the file position indicator at first tag (i.e.
// after the file preamble and the "DICM" string).
- Fp->seekg(0, std::ios_base::beg);
- Fp->seekg ( 132L, std::ios_base::beg);
+ Fp->seekg(0, std::ios::beg);
+ Fp->seekg ( 132L, std::ios::beg);
return true;
} // End of DicomV3
// preamble. We can reset the file position indicator to where the data
// is (i.e. the beginning of the file).
dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file");
- Fp->seekg(0, std::ios_base::beg);
+ Fp->seekg(0, std::ios::beg);
// Our next best chance would be to be considering a 'clean' ACR/NEMA file.
// By clean we mean that the length of the first tag is written down.
// representation of a 32 bits integer. Hence the following dirty
// trick :
s32 = *((uint32_t *)(entCur));
-
+
switch( s32 )
{
case 0x00040000 :
// So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA,
// i.e. the 'group length' element is not present :
- // check the supposed to be 'group number'
- // 0x0002 or 0x0004 or 0x0008
+ // check the supposed-to-be 'group number'
+ // in ( 0x0001 .. 0x0008 )
// to determine ' SwapCode' value .
// Only 0 or 4321 will be possible
// (no oportunity to check for the formerly well known
// ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
- // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -4, 8-)
+ // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -3, 4, ..., 8-)
// the file IS NOT ACR-NEMA nor DICOM V3
// Find a trick to tell it the caller...
switch ( s16 )
{
+ case 0x0001 :
case 0x0002 :
+ case 0x0003 :
case 0x0004 :
- case 0x0008 :
+ case 0x0005 :
+ case 0x0006 :
+ case 0x0007 :
+ case 0x0008 :
SwapCode = 0;
Filetype = ACR;
return true;
+ case 0x0100 :
case 0x0200 :
+ case 0x0300 :
case 0x0400 :
- case 0x0800 :
+ case 0x0500 :
+ case 0x0600 :
+ case 0x0700 :
+ case 0x0800 :
SwapCode = 4321;
Filetype = ACR;
return true;
default :
dbg.Verbose(0, "Document::CheckSwap:",
- "ACR/NEMA unfound swap info (Really hopeless !)");
- Filetype = Unknown;
+ "ACR/NEMA unfound swap info (Really hopeless !)");
+ Filetype = Unknown;
return false;
}
// Then the only info we have is the net2host one.
}
}
+
+
/**
* \brief Restore the unproperly loaded values i.e. the group, the element
* and the dictionary entry depending on them.
reversedEndian--;
SwitchSwapToBigEndian();
}
-
}
/**
}
HandleBrokenEndian(group, elem);
- DocEntry *newEntry = NewDocEntryByNumber(group, elem);
- FindDocEntryVR(newEntry);
+ std::string vr=FindDocEntryVR();
+
+ DocEntry *newEntry = NewDocEntryByNumber(group, elem, vr);
+ if( vr == GDCM_UNKNOWN )
+ {
+ if( Filetype == ExplicitVR )
+ {
+ // We thought this was explicit VR, but we end up with an
+ // implicit VR tag. Let's backtrack.
+ std::string msg;
+ msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n",
+ newEntry->GetGroup(), newEntry->GetElement());
+ dbg.Verbose(1, "Document::FindVR: ", msg.c_str());
+ }
+ newEntry->SetImplicitVR();
+ }
try
{
s << " at address: " << (unsigned)currentPosition << std::endl;
dbg.Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:");
dbg.Verbose(0, s.str().c_str());
- Fp->seekg(positionOnEntry, std::ios_base::beg);
+ Fp->seekg(positionOnEntry, std::ios::beg);
return false;
}
dbg.Verbose(0, "Document::ComputeRLEInfo: too many segments.");
}
- uint32_t rleSegmentOffsetTable[15];
+ uint32_t rleSegmentOffsetTable[16];
for( int k = 1; k <= 15; k++ )
{
rleSegmentOffsetTable[k] = ReadInt32();
* Document.
*
* The structure used by a Document (through \ref ElementSet),
- * in order to old the parsed entries of a Dicom header, is a recursive
+ * in order to hold 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 SQItem) add an extra complexity to the data
return false;
}
+
+/**
+ * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
+ * @param filetype Type of the File to be written
+ */
+int Document::ComputeGroup0002Length( FileType filetype )
+{
+ uint16_t gr, el;
+ std::string vr;
+
+ int groupLength = 0;
+ bool found0002 = false;
+
+ // for each zero-level Tag in the DCM Header
+ DocEntry *entry;
+
+ Initialize();
+ entry = GetNextEntry();
+ while(entry)
+ {
+ gr = entry->GetGroup();
+
+ if (gr == 0x0002)
+ {
+ found0002 = true;
+
+ el = entry->GetElement();
+ vr = entry->GetVR();
+
+ if (filetype == ExplicitVR)
+ {
+ if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
+ {
+ groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes
+ }
+ }
+ groupLength += 2 + 2 + 4 + entry->GetLength();
+ }
+ else if (found0002 )
+ break;
+
+ entry = GetNextEntry();
+ }
+ return groupLength;
+}
+
} // end namespace gdcm
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff