Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/11/04 15:33:35 $
- Version: $Revision: 1.324 $
+ Date: $Date: 2006/05/05 22:13:55 $
+ Version: $Revision: 1.347 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <ctype.h> // for isdigit
#include <stdlib.h> // for atoi
+#if defined(__BORLANDC__)
+ #include <mem.h> // for memset
+#endif
+
namespace gdcm
{
//-----------------------------------------------------------------------------
return false;
}
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
Filename = fileName;
return DoTheLoadingDocumentJob( );
}
+#endif
/**
* \brief Performs the Loading Job (internal use only)
gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str());
- Fp->seekg(0, std::ios::end);
- long lgt = Fp->tellg(); // total length of the file
-
- Fp->seekg(0, std::ios::beg);
+ // Computes the total length of the file
+ 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);
+ //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;
* @return false when we're 150 % sure it's NOT a Dicom/Acr file,
* true otherwise.
*/
-bool Document::IsReadable()
+bool Document::IsParsable()
{
if ( Filetype == Unknown )
{
- gdcmErrorMacro( "Wrong filetype for " << GetFileName());
+ gdcmWarningMacro( "Wrong filetype for " << GetFileName());
return false;
}
if ( IsEmpty() )
{
- gdcmErrorMacro( "No tag in internal hash table.");
+ gdcmWarningMacro( "No tag in internal hash table.");
return false;
}
return true;
}
+/**
+ * \brief This predicate tells us whether or not the current Document
+ * was properly parsed and contains at least *one* Dicom Element
+ * (and nothing more, sorry).
+ * @return false when we're 150 % sure it's NOT a Dicom/Acr file,
+ * true otherwise.
+ */
+bool Document::IsReadable()
+{
+ return IsParsable();
+}
/**
* \brief Predicate for dicom version 3 file.
// The entry might be present but not loaded (parsing and loading
// happen at different stages): try loading and proceed with check...
- LoadDocEntrySafe(entry);
+
+ // Well ...
+ // (parsing and loading happen at the very same stage!)
+ //LoadDocEntrySafe(entry); //JPRx
if (DataEntry *dataEntry = dynamic_cast<DataEntry *>(entry) )
{
std::string transfer = dataEntry->GetString();
return 0;
}
- //-- ACR or DICOM with no Preamble; may start with a Shadow Group --
+ //-- Broken ACR or DICOM with no Preamble; may start with a Shadow Group --
+
+ // FIXME : We cannot be sure the preable is only zeroes..
+ // (see ACUSON-24-YBR_FULL-RLE.dcm )
if (
zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 ||
zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 ||
}
//-- DICOM --
- Fp->seekg(126L, std::ios::cur);
+ 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());
fp->write(filePreamble, 128);
fp->write("DICM", 4);
}
-
/*
* \todo rewrite later, if really usefull
* - 'Group Length' element is optional in DICOM
DocEntry *docEntry = GetDocEntry(group, elem);
if ( !docEntry )
{
- gdcmWarningMacro(std::hex << group << "|" << elem
- << "doesn't exist" );
+ gdcmDebugMacro(std::hex << group << "|" << elem
+ << " doesn't exist" );
return;
}
DataEntry *dataEntry = dynamic_cast<DataEntry *>(docEntry);
if ( !dataEntry )
{
gdcmWarningMacro(std::hex << group << "|" << elem
- << "is NOT a DataEntry");
+ << " is NOT a DataEntry");
return;
}
LoadEntryBinArea(dataEntry);
* @param entry Entry whose binArea is going to be loaded
*/
void Document::LoadEntryBinArea(DataEntry *entry)
-{
+{
if( entry->GetBinArea() )
return;
if ( openFile )
OpenFile();
- size_t o =(size_t)entry->GetOffset();
- Fp->seekg(o, std::ios::beg);
+ //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);
- if ( openFile )
+ if ( openFile ) // The file is left in the state (open/close) it was at entrance
CloseFile();
}
/**
* \brief Loads the element while preserving the current
* underlying file position indicator as opposed to
- * LoadDocEntry that modifies it.
+ * LoadDocEntry that modifies it
+ * \note seems to be unused!.
* @param entry DocEntry whose value will be loaded.
*/
-void Document::LoadDocEntrySafe(DocEntry *entry)
-{
- if ( Fp )
- {
- long PositionOnEntry = Fp->tellg();
- LoadDocEntry(entry);
- Fp->seekg(PositionOnEntry, std::ios::beg);
- }
-}
+//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
return g;
}
-/**
- * \brief skips bytes inside the source file
- * \warning NOT end user intended method !
- * @return
- */
-void Document::SkipBytes(uint32_t nBytes)
-{
- //FIXME don't dump the returned value
- Fp->seekg((long)nBytes, std::ios::cur);
-}
-
/**
* \brief Re-computes the length of the Dicom group 0002.
*/
// explicit VR AND (OB, OW, SQ, UT) : 4 more bytes
groupLength += 4;
}
-
groupLength += 2 + 2 + 4 + entry->GetLength();
}
}
return groupLength;
}
+/**
+ * \brief CallStartMethod
+ */
+void Document::CallStartMethod()
+{
+ Progress = 0.0f;
+ Abort = false;
+ CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
+}
+
+/**
+ * \brief CallProgressMethod
+ */
+void Document::CallProgressMethod()
+{
+ CommandManager::ExecuteCommand(this,CMD_PROGRESS);
+}
+
+/**
+ * \brief CallEndMethod
+ */
+void Document::CallEndMethod()
+{
+ Progress = 1.0f;
+ CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
+}
+
//-----------------------------------------------------------------------------
// Private
/**
* \brief Loads all the needed Dictionaries
- * \warning NOT end user intended method !
+ * \warning NOT end user intended method !
*/
void Document::Initialize()
{
bool delim_mode_intern = delim_mode;
bool first = true;
gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode
- << " at offset " << std::hex << offset );
+ << " at offset " << std::hex << "0x(" << offset << ")" );
while (true)
{
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
- {
- 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()) // in Debug mode
+ << 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
}
// an Item Starter found elsewhere but the first position
- // of a SeqEntry means previous entry was a Sequence
+ // of a SeqEntry means previous entry was a Sequence
// 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()
- << " (at offset : "
- << newDataEntry->GetOffset() << " )" );
+ << newDataEntry->GetKey()
+ << " (at offset : 0x("
+ << newDataEntry->GetOffset() << ") )" );
used=false;
}
else
// Load only if we can add (not a duplicate key)
LoadDocEntry( newDataEntry );
}
-
if ( newDataEntry->GetElement() == 0x0000 ) // if on group length
{
if ( newDataEntry->GetGroup()%2 != 0 ) // if Shadow Group
if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
{
std::string strLgrGroup = newDataEntry->GetString();
+
int lgrGroup;
- if ( newDataEntry->IsUnfound() )
+ //if ( newDataEntry->IsUnfound() ) /?!? JPR
{
lgrGroup = atoi(strLgrGroup.c_str());
- Fp->seekg(lgrGroup, std::ios::cur);
- //used = false; // never used
+ Fp->seekg(lgrGroup, std::ios::cur); // Once per Shadow group, when NOSHADOW
RemoveEntry( newDocEntry ); // Remove and delete
- // bcc 5.5 is right "assigned a value that's never used"
- // newDocEntry = 0;
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;
- if ( (delimitor) ||
- (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) )
+ // 'and then', 'or else' don't exist in C++ :-(
+ // 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);
+ SkipToNextDocEntry(newDocEntry); // FIXME : once per DocEntry, segfault if commented out
}
else
{
// User asked to skip SeQuences *only* if they belong to Shadow Group
if ( newDocEntry->GetGroup()%2 != 0 )
{
- Fp->seekg( l, std::ios::cur);
+ Fp->seekg( l, std::ios::cur); // once per SQITEM, when NOSHADOWSEQ
newDocEntry->Delete(); // Delete, not in the set
continue;
}
if ( (LoadMode & LD_NOSEQ) && ! delim_mode_intern )
{
// User asked to skip *any* SeQuence
- Fp->seekg( l, std::ios::cur);
+ Fp->seekg( l, std::ios::cur); // Once per SQ, when NOSEQ
newDocEntry->Delete(); // Delete, not in the set
continue;
}
{ // Don't try to parse zero-length sequences
gdcmDebugMacro( "Entry in ParseSQ, delim " << delim_mode_intern
- << " at offset " << std::hex
- << newDocEntry->GetOffset() );
+ << " at offset 0x(" << std::hex
+ << newDocEntry->GetOffset() << ")");
ParseSQ( newSeqEntry,
newDocEntry->GetOffset(),
l, delim_mode_intern);
gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern);
-
}
if ( !set->AddEntry( newSeqEntry ) )
{
gdcmWarningMacro( "in ParseDES : cannot add a SeqEntry "
<< newSeqEntry->GetKey()
- << " (at offset : "
- << newSeqEntry->GetOffset() << " )" );
+ << " (at offset : 0x("
+ << newSeqEntry->GetOffset() << ") )" );
used = false;
}
else
{
newDocEntry->Delete();
}
+
+ // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ 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)
+ else // ! delim_mode
{
- newDocEntry->Delete();
- break;
+ 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() );
{
dlm_mod = false;
}
-
- // remove fff0,e000, created out of the SQItem
- Fp->seekg(offsetStartCurrentSQItem, std::ios::beg);
+
// fill up the current SQItem, starting at the beginning of fff0,e000
-
+
+ Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); // Once per SQItem
ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod);
-
- offsetStartCurrentSQItem = Fp->tellg();
+ offsetStartCurrentSQItem = Fp->tellg(); // Once per SQItem
seqEntry->AddSQItem( itemSQ, SQItemNumber );
itemSQ->Delete();
newDocEntry->Delete();
SQItemNumber++;
- if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
+ //if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) //JPRx
+ if ( !delim_mode && (offsetStartCurrentSQItem-offset ) >= l_max )
{
break;
}
long offset = PreviousDocEntry->GetOffset();
gdcmDebugMacro( "Backtrack :" << std::hex << group
- << "|" << elem
- << " at offset " << offset );
+ << "|" << elem
+ << " at offset 0x(" <<offset << ")" );
RemoveEntry( PreviousDocEntry );
// forge the Seq Entry
newEntry->SetOffset(offset);
// Move back to the beginning of the Sequence
- Fp->seekg( 0, std::ios::beg);
- Fp->seekg(offset, std::ios::cur);
+ Fp->seekg(offset, std::ios::beg); // Only for Shadow Implicit VR SQ
return newEntry;
}
const VRKey &vr = entry->GetVR();
uint32_t length = entry->GetLength();
- Fp->seekg((long)entry->GetOffset(), std::ios::beg);
+ // Fp->seekg((long)entry->GetOffset(), std::ios::beg); // JPRx
// A SeQuence "contains" a set of Elements.
// (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 ...
- Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
- std::ios::beg);
+ // 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);
+
+ Fp->seekg( 2L, std::ios::cur); // Once per OW,OB,SQ DocEntry
uint32_t length32 = ReadInt32();
if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
uint32_t lengthOB;
try
{
- lengthOB = FindDocEntryLengthOBOrOW();
+ lengthOB = FindDocEntryLengthOBOrOW();// for encapsulation of encoded pixel
}
catch ( FormatUnexpected )
{
gdcmWarningMacro( " Computing the length failed for " <<
entry->GetKey() <<" in " <<GetFileName());
- long currentPosition = Fp->tellg();
- Fp->seekg(0L,std::ios::end);
+ long currentPosition = Fp->tellg(); // Only for gdcm-JPEG-LossLess3a.dcm-like
+ Fp->seekg(0L,std::ios::end); // Only for gdcm-JPEG-LossLess3a.dcm-like
- long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
- Fp->seekg(currentPosition, std::ios::beg);
+ long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; // Only for gdcm-JPEG-LossLess3a.dcm-like
+ Fp->seekg(currentPosition, std::ios::beg); // Only for gdcm-JPEG-LossLess3a.dcm-like
entry->SetReadLength(lengthUntilEOF);
entry->SetLength(lengthUntilEOF);
// 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;
throw( FormatUnexpected )
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
- long positionOnEntry = Fp->tellg();
+ 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();
gdcmWarningMacro(
"Neither an Item tag nor a Sequence delimiter tag on :"
<< std::hex << group << " , " << elem
- << ") -before- position x(" << filePosition << ")" );
+ << ")" );
- Fp->seekg(positionOnEntry, std::ios::beg);
+ 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.");
}
break;
}
}
- Fp->seekg( positionOnEntry, std::ios::beg);
+ Fp->seekg( positionOnEntry, std::ios::beg); // Only for OB,OW DataElements
return totalLength;
}
VRKey Document::FindDocEntryVR()
{
if ( Filetype != ExplicitVR )
+ {
return GDCM_VRUNKNOWN;
+ }
- long positionOnEntry = Fp->tellg();
+ // 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
// 'Transfer Syntax' told us it is.
// Alas this doesn't guarantee that all the tags will be in explicit VR.
- // In some cases one finds implicit VR tags mixed within an explicit VR file.
+ // In some cases one finds implicit VR tags mixed within an explicit VR file
+ // Well...
+ // 'Normaly' the only case is : group 0002 Explicit, and other groups Implicit
+ //
// Hence we make sure the present tag is in explicit VR and try to fix things
// if it happens not to be the case.
if ( !CheckDocEntryVR(vr) )
{
- // Don't warn user with useless messages
- if ( (unsigned char)vr[0] != 0xff || (unsigned char)vr[1] != 0xff )
- gdcmWarningMacro( "Unknown VR " << std::hex << "0x("
+/*
+// std::cout << "================================================================Unknown VR"
+ << std::hex << "0x("
<< (unsigned int)vr[0] << "|" << (unsigned int)vr[1]
- << ") at offset :" << positionOnEntry );
- Fp->seekg(positionOnEntry, std::ios::beg);
+ << ")" << "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<< ") for group " << CurrentGroup
+ );
+
+ //Fp->seekg(positionOnEntry, std::ios::beg); //JPRx
+ Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?)
+ //see :MR_Philips_Intera_PrivateSequenceExplicitVR.dcm
return GDCM_VRUNKNOWN;
}
return vr;
/**
* \brief Skip a given Header Entry
- * \warning NOT end user intended method !
* @param entry entry to skip
*/
void Document::SkipDocEntry(DocEntry *entry)
/**
* \brief Skips to the beginning of the next Header Entry
- * \warning NOT end user intended method !
* @param currentDocEntry entry to skip
*/
void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
{
- int l = currentDocEntry->GetReadLength();
+ long l = currentDocEntry->GetReadLength();
if ( l == -1 ) // length = 0xffff shouldn't appear here ...
// ... but PMS imagers happen !
return;
- Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
+ 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
}
}
* 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 ) )
- {
- foundLength = 4;
- entry->SetReadLength(4); // a bug is to be fixed !
- }
-
+ else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
+ {
+ // Ideally we should check we are in Explicit and double check
+ // that VR=UL... this is done properly in gdcm2
+ if( foundLength == 6 )
+ {
+ gdcmWarningMacro( "Replacing Length from 6 into 4" );
+ foundLength = 4;
+ entry->SetReadLength(4); // a bug is to be fixed !
+ }
+ else if ( foundLength%4 )
+ {
+ gdcmErrorMacro( "This looks like to a buggy Siemens DICOM file."
+ "The length of this tag seems to be wrong" );
+ }
+ }
+
else if ( entry->GetVR() == "SQ" )
{
- foundLength = 0; // ReadLength is unchanged
- }
-
- //////// We encountered a 'delimiter' element i.e. a tag of the form
+ foundLength = 0; // ReadLength is unchanged
+ }
+
+ //////// We encountered a 'delimiter' element i.e. a tag of the form
// "fffe|xxxx" which is just a marker. Delimiters length should not be
// taken into account.
else if ( gr == 0xfffe )
- {
+ {
// 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;
}
{
foundLength=12; // to skip the mess that follows this bugged Tag !
}
- }
+ }
entry->SetLength(foundLength);
}
// test is useless (and might even look a bit paranoid), when we
// encounter such an ill-formed image, we simply display a warning
// message and proceed on parsing (while crossing fingers).
- long filePosition = Fp->tellg();
+ long filePosition = Fp->tellg(); // Only when elem 0x0000 length is not 4 (?!?)
gdcmWarningMacro( "Erroneous Group Length element length on : ("
<< std::hex << group << " , " << elem
<< ") -before- position x(" << filePosition << ")"
// Position the file position indicator at first tag
// (i.e. after the file preamble and the "DICM" string).
- Fp->seekg(0, std::ios::beg); // FIXME : Is it usefull?
-
- Fp->seekg ( 132L, std::ios::beg);
+ Fp->seekg ( 132L, std::ios::beg); // Once per Document
return true;
} // ------------------------------- End of DicomV3 ----------------
gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)");
- Fp->seekg(0, std::ios::beg);
+ Fp->seekg(0, std::ios::beg); // Once per ACR-NEMA Document
// Let's check 'No Preamble Dicom File' :
// Should start with group 0x0002
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;
}
void Document::SwitchByteSwapCode()
{
gdcmDebugMacro( "Switching Byte Swap code from "<< SwapCode
- << " at: 0x" << std::hex << Fp->tellg() );
+ << " at: 0x" << std::hex << Fp->tellg() ); // Only when DEBUG
if ( SwapCode == 1234 )
{
SwapCode = 4321;
* \brief during parsing, Header Elements too long are not loaded in memory
* @param newSize new size
*/
-void Document::SetMaxSizeLoadEntry(long newSize)
+void Document::SetMaxSizeLoadEntry(long newSize)
{
if ( newSize < 0 )
{
* (read the 'Group Number', the 'Element Number',
* gets the Dict Entry
* gets the VR, gets the length, gets the offset value)
- * @return On succes : the newly created DocEntry, NULL on failure.
+ * @return On succes : the newly created DocEntry, NULL on failure.
*/
DocEntry *Document::ReadNextDocEntry()
{
- uint16_t group;
- uint16_t elem;
-
try
{
- group = ReadInt16();
- elem = ReadInt16();
+ CurrentGroup = ReadInt16();
+ CurrentElem = ReadInt16();
}
catch ( FormatError )
{
- // We reached the EOF (or an error occured) therefore
+ // We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
return 0;
}
- // Sometimes file contains groups of tags with reversed endianess.
- HandleBrokenEndian(group, elem);
-
// In 'true DICOM' files Group 0002 is always little endian
if ( HasDCMPreamble )
- HandleOutOfGroup0002(group, elem);
-
+ {
+ 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;
if ( vr == GDCM_VRUNKNOWN )
{
- if ( elem == 0x0000 ) // Group Length
+ if ( CurrentElem == 0x0000 ) // Group Length
{
realVR = "UL"; // must be UL
}
- else if (group%2 == 1 && (elem >= 0x0010 && elem <=0x00ff ))
+ else if (CurrentGroup == 0xfffe) // Don't get DictEntry for Delimitors
+ {
+ realVR = "UL";
+ }
+
+ // Commented out in order not to generate 'Shadow Groups' where some
+ // Data Elements are Explicit VR and some other ones Implicit VR
+ // (Stupid MatLab DICOM Reader couldn't read gdcm-written images)
+ /*
+ else if (CurrentGroup%2 == 1 &&
+ (CurrentElem >= 0x0010 && CurrentElem <=0x00ff ))
{
// DICOM PS 3-5 7.8.1 a) states that those
// (gggg-0010->00FF where gggg is odd) attributes have to be LO
realVR = "LO";
}
+ */
else
{
- DictEntry *dictEntry = GetDictEntry(group,elem);
+ DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);//only when ImplicitVR
if ( dictEntry )
{
realVR = dictEntry->GetVR();
- dictEntry->Unregister();
+ dictEntry->Unregister(); // GetDictEntry registered it
}
}
}
- // gdcmDebugMacro( "Found VR: " << vr << " / Real VR: " << realVR );
DocEntry *newEntry;
- if ( Global::GetVR()->IsVROfSequence(realVR) )
- newEntry = NewSeqEntry(group, elem);
- else
+ //if ( Global::GetVR()->IsVROfSequence(realVR) )
+ if (realVR == "SQ")
{
- newEntry = NewDataEntry(group, elem, realVR);
+ newEntry = NewSeqEntry(CurrentGroup, CurrentElem);
+ }
+ else
+ {
+ newEntry = NewDataEntry(CurrentGroup, CurrentElem, realVR);
static_cast<DataEntry *>(newEntry)->SetState(DataEntry::STATE_NOTLOADED);
}
{
// We thought this was explicit VR, but we end up with an
// implicit VR tag. Let's backtrack.
- if ( newEntry->GetGroup() != 0xfffe )
+
+ //if ( newEntry->GetGroup() != 0xfffe )
+ if (CurrentGroup != 0xfffe )
{
- std::string msg;
- int offset = Fp->tellg();
- msg = Util::Format(
- "Entry (%04x,%04x) at x(%x) should be Explicit VR\n",
- newEntry->GetGroup(), newEntry->GetElement(), offset );
- gdcmWarningMacro( msg.c_str() );
+ int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong
+
+ gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x("
+ << offset << ") should be Explicit VR");
}
}
newEntry->SetImplicitVR();
return 0;
}
- newEntry->SetOffset(Fp->tellg());
+ newEntry->SetOffset(Fp->tellg()); // for each DocEntry
return newEntry;
}
if ((group == 0xfeff) && (elem == 0x00e0))
{
// start endian swap mark for group found
+ gdcmDebugMacro( "Start endian swap mark found." );
reversedEndian++;
SwitchByteSwapCode();
// fix the tag
else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
{
// end of reversed endian group
+ gdcmDebugMacro( "End of reversed endian." );
reversedEndian--;
SwitchByteSwapCode();
}
{
// 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();
- if ( ts == GDCM_UNKNOWN )
- {
- gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " );
- return;
- }
- if ( !Global::GetTS()->IsTransferSyntax(ts) )
- {
- gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: ["
- << ts << "]");
- return;
- }
+ 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;
}
// FIXME Strangely, this works with
- //'Implicit VR BigEndian Transfer Syntax (GE Private)
+ //'Implicit VR BigEndian Transfer Syntax' (GE Private)
//
// --> Probabely normal, since we considered we never have
// 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 ( s == TS::DeflatedExplicitVRLittleEndian)
+ {
+ gdcmWarningMacro("Transfer Syntax ["
+ << GetTransferSyntaxName() << "] :"
+ << " not yet dealt with ");
+ return;
+ }
+
+ // The following shouldn't occur very often
+ // Let's check at the very end.
+
+ if ( ts == GDCM_UNKNOWN )
+ {
+ gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " );
+ return;
+ }
+
+ if ( !Global::GetTS()->IsTransferSyntax(ts) )
+ {
+ gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: ["
+ << ts << "]");
+ return;
+ }
}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff