Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2006/02/07 17:15:28 $
- Version: $Revision: 1.339 $
+ Date: $Date: 2006/03/01 10:15:12 $
+ Version: $Revision: 1.343 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
return DoTheLoadingDocumentJob( );
}
+#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief Loader. (DEPRECATED : not to break the API)
+ * @param fileName 'Document' (File or DicomDir) to be open for parsing
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool Document::Load( std::string const &fileName )
+{
+ Filename = fileName;
+ return DoTheLoadingDocumentJob( );
+}
+#endif
+
/**
* \brief Performs the Loading Job (internal use only)
* @return false if file cannot be open or no swap info was found,
Group0002Parsed = false;
gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str());
-
+
// Computes the total length of the file
- Fp->seekg(0, std::ios::end); // Once for a given Document !
- long lgt = Fp->tellg(); // Once for a given Document !
- Fp->seekg(0, std::ios::beg); // Once for a given Document !
+ Fp->seekg(0, std::ios::end); // Once per Document !
+ long lgt = Fp->tellg(); // Once per Document !
+ Fp->seekg(0, std::ios::beg); // Once per Document !
// CheckSwap returns a boolean
// (false if no swap info of any kind was found)
}
IsDocumentAlreadyLoaded = true;
- Fp->seekg( 0, std::ios::beg); // Once per Document
+ //Fp->seekg(0, std::ios::beg); // Once per Document!
// Load 'non string' values
}
//FIXME later : how to use it?
- SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000);
+ SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000); // Modality LUT Sequence
if ( modLutSeq !=0 )
{
SQItem *sqi= modLutSeq->GetFirstSQItem();
if ( sqi != 0 )
{
- DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006);
+ DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006); // LUT Data
if ( dataEntry != 0 )
{
if ( dataEntry->GetLength() != 0 )
if ( d == NULL)
{
- gdcmWarningMacro( "You asked toForce Load " << std::hex
+ gdcmWarningMacro( "You asked to ForceLoad " << std::hex
<< (*it).Group <<"|"<< (*it).Elem
<< " that doesn't exist" );
continue;
}
//-- DICOM --
- Fp->seekg(126L, std::ios::cur); // Once for a given Document
+ Fp->seekg(126L, std::ios::cur); // Once per Document
char dicm[4]; // = {' ',' ',' ',' '};
Fp->read(dicm, (size_t)4);
if ( Fp->eof() )
// -- Neither ACR/No Preamble Dicom nor DICOMV3 file
CloseFile();
- // Don't user Warning nor Error, not to polute the output
+ // Don't user Warning nor Error, not to pollute the output
// while directory recursive parsing ...
gdcmDebugMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
<< Filename.c_str());
* @param entry Entry whose binArea is going to be loaded
*/
void Document::LoadEntryBinArea(DataEntry *entry)
-{
+{
if( entry->GetBinArea() )
return;
-// to be coherent with LoadEntryBinArea(uint16_t group, uint16_t elem)
-// (and save time !)
-// :-(
-// TestAllReadCompareDicom hangs on rle16sti.dcm
bool openFile = !Fp;
if ( openFile )
OpenFile();
-// -------
- size_t o =(size_t)entry->GetOffset();
- Fp->seekg(o, std::ios::beg); // FIXME : for each BinEntry LoadEntryBinArea
+
+ //size_t o =(size_t)entry->GetOffset();
+ Fp->seekg((size_t)entry->GetOffset(), std::ios::beg); // FIXME : for each DataEntry !
size_t l = entry->GetLength();
uint8_t *data = new uint8_t[l];
}
entry->SetBinArea(data);
-
-// to be coherent with LoadEntryBinArea(uint16_t group, uint16_t elem)
-// (and save time !)
- if ( openFile )
+ if ( openFile ) // The file is left in the state (open/close) it was at entrance
CloseFile();
-// ---------------
}
/**
* \note seems to be unused!.
* @param entry DocEntry whose value will be loaded.
*/
-void Document::LoadDocEntrySafe(DocEntry *entry)
-{
- if ( Fp )
- {
- long PositionOnEntry = Fp->tellg(); // LoadDocEntrySafe is not used
- LoadDocEntry(entry);
- Fp->seekg(PositionOnEntry, std::ios::beg); // LoadDocEntrySafe is not used
- }
-}
+//void Document::LoadDocEntrySafe(DocEntry *entry)
+//{
+// if ( Fp )
+// {
+// long PositionOnEntry = Fp->tellg(); // LoadDocEntrySafe is not used
+// LoadDocEntry(entry);
+// Fp->seekg(PositionOnEntry, std::ios::beg); // LoadDocEntrySafe is not used
+// }
+//}
/**
* \brief Compares two documents, according to \ref DicomDir rules
// explicit VR AND (OB, OW, SQ, UT) : 4 more bytes
groupLength += 4;
}
-
groupLength += 2 + 2 + 4 + entry->GetLength();
}
}
// Private
/**
* \brief Loads all the needed Dictionaries
+ * \warning NOT end user intended method !
*/
void Document::Initialize()
{
<< " at offset " << std::hex << "0x(" << offset << ")" );
while (true)
{
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry
- {
- break;
- }
+
+ ///\todo FIXME : On 64 bits processors, tellg gives unexpected results after a while ?
+ /// Probabely a bug in gdcm code somwhere (some memory erased ?)
+
+// Uncomment to track the bug
+/*
+ if( Debug::GetDebugFlag() )
+ std::cout << std::dec <<"(long)(Fp->tellg()) " << (long)(Fp->tellg())
+ << std::hex << " 0x(" <<(long)(Fp->tellg()) << ")" << std::endl;
+*/
+ // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry
+ if ( !delim_mode ) // 'and then' doesn't exist in C++ :-(
+ if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry, when no delim mode
+ {
+ break;
+ }
newDocEntry = ReadNextDocEntry( );
// Uncoment this cerr line to be able to 'follow' the DocEntries
// but we didn't get it (private Sequence + Implicit VR)
// we have to backtrack.
if ( !first && newDocEntry->IsItemStarter() )
- {
- // Debug message within the method !
- newDocEntry = Backtrack(newDocEntry);
+ {
+ // Debug message within the method !
+ newDocEntry = Backtrack(newDocEntry);
}
else
{
if ( !set->AddEntry( newDataEntry ) )
{
gdcmDebugMacro( "in ParseDES : cannot add a DataEntry "
- << newDataEntry->GetKey()
+ << newDataEntry->GetKey()
<< " (at offset : 0x("
<< newDataEntry->GetOffset() << ") )" );
used=false;
//if ( newDataEntry->IsUnfound() ) /?!? JPR
{
lgrGroup = atoi(strLgrGroup.c_str());
- Fp->seekg(lgrGroup, std::ios::cur); // Only when NOSHADOW
+ Fp->seekg(lgrGroup, std::ios::cur); // Once per Shadow group, when NOSHADOW
RemoveEntry( newDocEntry ); // Remove and delete
continue;
}
}
}
- bool delimitor = newDataEntry->IsItemDelimitor();
+ bool delimitor = newDataEntry->IsItemDelimitor();
+ bool outOfBounds = false;
+ if (!delim_mode )
+ if ( ((long)(Fp->tellg())-offset) >= l_max ) //Once per DataEntry when no delim mode
+ outOfBounds = true;
+
+ // 'and then', 'or else' don't exist in C++ :-(
+ // if ( (delimitor) ||
+ // (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) // Once per DataEntry
- if ( (delimitor) ||
- (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) // Once per DataEntry
+ if ( delimitor || outOfBounds )
{
if ( !used )
newDocEntry->Delete();
}
// Just to make sure we are at the beginning of next entry.
- SkipToNextDocEntry(newDocEntry); // FIXME : once per DocEntry, segfault if commented out
+ SkipToNextDocEntry(newDocEntry); // FIXME : once per DocEntry, segfault if commented out
}
else
{
{
newDocEntry->Delete();
}
+
+ // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry
+ if ( !delim_mode ) // 'and then' doesn't exist in C++ :-(
+ if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry when no delim mode
+
{
if ( !used )
newDocEntry->Delete();
break;
}
}
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per SQItem
- {
- newDocEntry->Delete();
- break;
- }
+ if ( !delim_mode ) // andthen doesn't exist in C++ :-(
+ if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SQItem when no delim mode
+ {
+ newDocEntry->Delete();
+ break;
+ }
// create the current SQItem
SQItem *itemSQ = SQItem::New( seqEntry->GetDepthLevel() );
unsigned int l = newDocEntry->GetReadLength();
newEntry->SetOffset(offset);
// Move back to the beginning of the Sequence
- // Fp->seekg( 0, std::ios::beg); // JPRx
- // Fp->seekg(offset, std::ios::cur); // JPRx
+
Fp->seekg(offset, std::ios::beg); // Only for Shadow Implicit VR SQ
return newEntry;
}
// (fffe e000) tells us an Element is beginning
// (fffe e00d) tells us an Element just ended
// (fffe e0dd) tells us the current SeQuence just ended
- //
// (fffe 0000) is an 'impossible' tag value,
// found in MR-PHILIPS-16-Multi-Seq.dcm
// The elements whose length is bigger than the specified upper bound
// are not loaded.
- std::ostringstream s;
-
if (!forceLoad)
{
if (length > MaxSizeLoadEntry)
dataEntryPtr->SetBinArea(NULL,true);
dataEntryPtr->SetState(DataEntry::STATE_NOTLOADED);
- // to be sure we are at the end of the value ...
+ // to be sure we are at the end of the value ...
// Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
// std::ios::beg); //JPRx
return;
}
}
-
+
+ /// \todo: a method that *doesn't* load anything (maybe with MaxSizeLoadEntry=0 ?)
+ /// + a ForceLoad call on the +/- 20 'usefull' fields
+ /// Allow user to tell the fields he wants to ForceLoad
+ /// during initial stage.
+ /// Later, a GetString or GetBinArea will load the value from disk, if not loaded
+ /// + a method that load *everything* that's not yet loaded
+
LoadEntryBinArea(dataEntryPtr); // last one, not to erase length !
}
// 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::cur); // Once per OW,OB,SQ DocEntry
uint32_t length32 = ReadInt32();
// Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
// even if Transfer Syntax is 'Implicit VR ...'
// --> Except for 'Implicit VR Big Endian Transfer Syntax GE Private'
+ // where Group 0x0002 is *also* encoded in Implicit VR !
FixDocEntryFoundLength( entry, ReadInt32() );
return;
/**
* \brief Find the Length till the next sequence delimiter
+ * \warning NOT end user intended method !
* @return
*/
uint32_t Document::FindDocEntryLengthOBOrOW()
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
long positionOnEntry = Fp->tellg(); // Only for OB,OW DataElements
-
+
bool foundSequenceDelimiter = false;
uint32_t totalLength = 0;
totalLength += 4;
if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- // long filePosition = Fp->tellg(); JPRx
gdcmWarningMacro(
"Neither an Item tag nor a Sequence delimiter tag on :"
<< std::hex << group << " , " << elem
- //<< ") -before- position x(" << filePosition // JPRx
<< ")" );
- Fp->seekg(positionOnEntry, std::ios::beg); // Oncd per fragment (if any) of OB,OW DataElements
+ Fp->seekg(positionOnEntry, std::ios::beg); // Once per fragment (if any) of OB,OW DataElements
throw FormatUnexpected(
"Neither an Item tag nor a Sequence delimiter tag.");
}
if ( Filetype != ExplicitVR )
return GDCM_VRUNKNOWN;
- //long positionOnEntry = Fp->tellg(); // JPRx
+ // Delimiters (0xfffe), are not explicit VR ...
+ if ( CurrentGroup == 0xfffe )
+ return GDCM_VRUNKNOWN;
+
+ long positionOnEntry;
+ if( Debug::GetWarningFlag() )
+ positionOnEntry = Fp->tellg(); // Only in Warning Mode
// Warning: we believe this is explicit VR (Value Representation) because
// we used a heuristic that found "UL" in the first tag and/or
if ( !CheckDocEntryVR(vr) )
{
- // Don't warn user with useless messages
- // Often, delimiters (0xfffe), are not explicit VR ...
- if ( CurrentGroup != 0xfffe )
- gdcmWarningMacro( "Unknown VR " << std::hex << "0x("
+/*
+ std::cout << "================================================================Unknown VR"
+ << std::hex << "0x("
+ << (unsigned int)vr[0] << "|" << (unsigned int)vr[1]
+ << ")" << "for : " << CurrentGroup
+ << " at offset : 0x(" << positionOnEntry << ")"
+ << std::endl;
+*/
+ gdcmWarningMacro( "Unknown VR " << std::hex << "0x("
<< (unsigned int)vr[0] << "|" << (unsigned int)vr[1]
<< ")"
- //<< "at offset : 0x(" << positionOnEntry<< ")"
+ << " at offset : 0x(" << positionOnEntry<< ") for group " << CurrentGroup
);
//Fp->seekg(positionOnEntry, std::ios::beg); //JPRx
- Fp->seekg((long)-2, std::ios::cur);// FIXME : for each VR !
+ Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?)
+ //see :MR_Philips_Intera_PrivateSequenceExplicitVR.dcm
return GDCM_VRUNKNOWN;
}
return vr;
if ( l == -1 ) // length = 0xffff shouldn't appear here ...
// ... but PMS imagers happen !
return;
- Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg); //FIXME :each DocEntry
+ Fp->seekg((size_t)(currentDocEntry->GetOffset()), std::ios::beg); //FIXME :each DocEntry
if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb
{
- //Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur);
- Fp->seekg( l,std::ios::cur); //FIXME :each DocEntry
+ Fp->seekg( l,std::ios::cur); //FIXME :each DocEntry
}
}
* the parser went Jabberwocky) one can hope improving things by
* applying some heuristics.
* @param entry entry to check
- * @param foundLength first assumption about length
+ * @param foundLength first assumption about length (before bug fix, or set to zero if =0xffffffff)
*/
void Document::FixDocEntryFoundLength(DocEntry *entry,
uint32_t foundLength)
{
entry->SetReadLength( foundLength );// will be updated only if a bug is found
+
if ( foundLength == 0xffffffff)
{
- foundLength = 0;
+ //foundLength = 0;
+ //entry->SetLength(foundLength);
+ entry->SetLength(0);
+ return; // return ASAP; don't waist time on useless tests
}
-
+
uint16_t gr = entry->GetGroup();
uint16_t elem = entry->GetElement();
// Occurence of such images is quite low (unless one leaves close to a
// 'Leonardo' source. Hence, one might consider commenting out the
// following fix on efficiency reasons.
- else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
+ else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
{
foundLength = 4;
entry->SetReadLength(4); // a bug is to be fixed !
// According to the norm, fffe|0000 shouldn't exist. BUT the Philips
// image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to
// causes extra troubles...
- if ( entry->GetElement() != 0x0000 )
+ if ( elem != 0x0000 )
{
foundLength = 0;
}
// Position the file position indicator at first tag
// (i.e. after the file preamble and the "DICM" string).
- //Fp->seekg(0, std::ios::beg); // JPRx
-
Fp->seekg ( 132L, std::ios::beg); // Once per Document
return true;
} // ------------------------------- End of DicomV3 ----------------
memcmp(entCur, "AE", (size_t)2) == 0 ||
memcmp(entCur, "OB", (size_t)2) == 0 )
{
- Filetype = ExplicitVR;
+ Filetype = ExplicitVR; // FIXME : not enough to say it's Explicit
+ // Wait untill reading Transfer Syntax
gdcmDebugMacro( "Group 0002 : Explicit Value Representation");
return true;
}
return 0;
}
- // Sometimes file contains groups of tags with reversed endianess.
- HandleBrokenEndian(CurrentGroup, CurrentElem);
-
// In 'true DICOM' files Group 0002 is always little endian
if ( HasDCMPreamble )
- HandleOutOfGroup0002(CurrentGroup, CurrentElem);
-
+ {
+ if ( !Group0002Parsed && CurrentGroup != 0x0002) // avoid calling a function when useless
+ HandleOutOfGroup0002(CurrentGroup, CurrentElem);
+ else
+ // Sometimes file contains groups of tags with reversed endianess.
+ HandleBrokenEndian(CurrentGroup, CurrentElem);
+ }
+
VRKey vr = FindDocEntryVR();
VRKey realVR = vr;
}
}
}
- // gdcmDebugMacro( "Found VR: " << vr << " / Real VR: " << realVR );
DocEntry *newEntry;
- if ( Global::GetVR()->IsVROfSequence(realVR) )
+ //if ( Global::GetVR()->IsVROfSequence(realVR) )
+ if (realVR == "SQ")
newEntry = NewSeqEntry(CurrentGroup, CurrentElem);
else
{
if ( newEntry->GetGroup() != 0xfffe )
{
std::string msg;
- int offset = Fp->tellg(); // FIXME : Only when heuristic for Explicit/Implicit was wrong
+ int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong
msg = Util::Format(
"Entry (%04x,%04x) at x(%x) should be Explicit VR\n",
newEntry->GetGroup(), newEntry->GetElement(), offset );
{
// Endian reversion.
// Some files contain groups of tags with reversed endianess.
- if ( !Group0002Parsed && group != 0x0002)
- {
+
Group0002Parsed = true;
// we just came out of group 0002
// if Transfer Syntax is Big Endian we have to change CheckSwap
std::string ts = GetTransferSyntax();
+ TS::SpecialType s = Global::GetTS()->GetSpecialTransferSyntax(ts);
// Group 0002 is always 'Explicit ...'
// even when Transfer Syntax says 'Implicit ..."
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
- TS::ImplicitVRLittleEndian )
+ if ( s == TS::ImplicitVRLittleEndian
+ ||
+ s == TS::ImplicitVRBigEndianPrivateGE
+ )
{
Filetype = ImplicitVR;
}
// to trust manufacturers.
// (we find very often 'Implicit VR' tag,
// even when Transfer Syntax tells us it's Explicit ...
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
- TS::ExplicitVRBigEndian )
+
+ if ( s == TS::ExplicitVRBigEndian )
{
gdcmDebugMacro("Transfer Syntax Name = ["
<< GetTransferSyntaxName() << "]" );
group = SwapShort(group);
elem = SwapShort(elem);
}
-
+
/// \todo find a trick to warn user and stop processing
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
- TS::DeflatedExplicitVRLittleEndian)
+ if ( s == TS::DeflatedExplicitVRLittleEndian)
{
gdcmWarningMacro("Transfer Syntax ["
<< GetTransferSyntaxName() << "] :"
<< ts << "]");
return;
}
- }
}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff