Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2006/02/09 10:48:04 $
- Version: $Revision: 1.341 $
+ Date: $Date: 2006/06/15 14:22:33 $
+ Version: $Revision: 1.350 $
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 per Document !
long lgt = Fp->tellg(); // Once per Document !
LoadDocEntry(d, true);
}
- CloseFile();
+ CloseFile();
// ----------------------------
// Specific code to allow gdcm to read ACR-LibIDO formated images
}
//-- 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 (
// -- 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
// 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()
{
DocEntry *newDocEntry;
DataEntry *newDataEntry;
SeqEntry *newSeqEntry;
- VRKey vr;
+ //VRKey vr;
bool used; // will be set to false when something wrong happens to an Entry.
// (Entry will then be deleted)
bool delim_mode_intern = delim_mode;
bool first = true;
gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode
- << " at offset " << std::hex << "0x(" << offset << ")" );
+ << " at offset " << std::hex << "0x(" << offset << ")" );
while (true)
{
- // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry
+ ///\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
- // when something *very* strange happens
- if( Debug::GetDebugFlag() )
- std::cerr<<newDocEntry->GetKey()<<" "<<newDocEntry->GetVR()<<std::endl;
+ newDocEntry = ReadNextDocEntry( );
if ( !newDocEntry )
{
break;
}
+
+ // Uncoment this cerr line to be able to 'follow' the DocEntries
+ // when something *very* strange happens
+ if( Debug::GetDebugFlag() )
+ std::cerr<<newDocEntry->GetKey()<<" "<<newDocEntry->GetVR()<<std::endl;
- // an Item Starter found elsewhere but the first position
+ // an Item Starter found elsewhere but in the first position
// 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
{
{
//////////////////////////// DataEntry
- vr = newDocEntry->GetVR();
+ //vr = newDocEntry->GetVR(); // useless ?
if ( !set->AddEntry( newDataEntry ) )
{
l, delim_mode_intern);
gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern);
-
}
if ( !set->AddEntry( newSeqEntry ) )
{
break;
}
}
- if ( !delim_mode ) // andthen doesn't exist in C++ :-(
+ else // ! delim_mode
+ {
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();
{
dlm_mod = false;
}
-
- // remove fff0,e000, created out of the SQItem
-
- //Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); //JPRx
-
+
// 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(); // Once per SQItem
+ offsetStartCurrentSQItem = Fp->tellg(); // Once per SQItem
seqEntry->AddSQItem( itemSQ, SQItemNumber );
itemSQ->Delete();
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;
}
*/
void Document::LoadDocEntry(DocEntry *entry, bool forceLoad)
{
- uint16_t group = entry->GetGroup();
- uint16_t elem = entry->GetElement();
+ uint16_t group = entry->GetGroup();
+ uint16_t elem = entry->GetElement();
const VRKey &vr = entry->GetVR();
- uint32_t length = entry->GetLength();
+ uint32_t length = entry->GetLength();
// Fp->seekg((long)entry->GetOffset(), std::ios::beg); // JPRx
// (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 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); // Once per fragment (if any) of OB,OW DataElements
VRKey Document::FindDocEntryVR()
{
if ( Filetype != ExplicitVR )
+ {
return GDCM_VRUNKNOWN;
+ }
// Delimiters (0xfffe), are not explicit VR ...
if ( CurrentGroup == 0xfffe )
if ( !CheckDocEntryVR(vr) )
{
/*
- std::cout << "================================================================Unknown VR"
+// std::cout << "================================================================Unknown VR"
<< std::hex << "0x("
<< (unsigned int)vr[0] << "|" << (unsigned int)vr[1]
<< ")" << "for : " << CurrentGroup
* 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);
}
// encounter such an ill-formed image, we simply display a warning
// message and proceed on parsing (while crossing fingers).
long filePosition = Fp->tellg(); // Only when elem 0x0000 length is not 4 (?!?)
+ (void)filePosition;
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); // JPRx
-
Fp->seekg ( 132L, std::ios::beg); // Once per Document
return true;
} // ------------------------------- End of DicomV3 ----------------
* \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()
{
}
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;
}
// In 'true DICOM' files Group 0002 is always little endian
- if ( HasDCMPreamble )
+ if ( HasDCMPreamble )
{
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);
+ HandleBrokenEndian(CurrentGroup, CurrentElem);
}
-
+
VRKey vr = FindDocEntryVR();
-
VRKey realVR = vr;
if ( vr == GDCM_VRUNKNOWN )
{
realVR = "UL"; // must be UL
}
+ 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 couln't read gdcm-written images)
+ // (Stupid MatLab DICOM Reader couldn't read gdcm-written images)
/*
else if (CurrentGroup%2 == 1 &&
(CurrentElem >= 0x0010 && CurrentElem <=0x00ff ))
*/
else
{
- DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);
+ DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);//only when ImplicitVR
if ( dictEntry )
{
realVR = dictEntry->GetVR();
- dictEntry->Unregister();
+ dictEntry->Unregister(); // GetDictEntry registered it
}
}
}
-
+
DocEntry *newEntry;
//if ( Global::GetVR()->IsVROfSequence(realVR) )
if (realVR == "SQ")
+ {
newEntry = NewSeqEntry(CurrentGroup, CurrentElem);
- else
+ }
+ 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();//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 );
- gdcmWarningMacro( msg.c_str() );
+
+ gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x("
+ << offset << ") should be Explicit VR");
}
}
newEntry->SetImplicitVR();
}
newEntry->SetOffset(Fp->tellg()); // for each DocEntry
-
return newEntry;
}
*/
void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
{
+ // for strange PMS Gyroscan Intera images
+ // Item 'starter' has a tag : 0x3f3f,0x3f00, for no apparent reason
+
+ // --- Feel free to remove this test *on your own coy of gdcm*
+ // if you are sure you'll never face this problem.
+
+ if ((group == 0x3f3f) && (elem == 0x3f00))
+ {
+ // start endian swap mark for group found
+ gdcmDebugMacro( " delimiter 0x3f3f found." );
+ // fix the tag
+ group = 0xfffe;
+ elem = 0xe000;
+ return;
+ }
+ // --- End of removable code
+
// Endian reversion.
// Some files contain groups of tags with reversed endianess.
static int reversedEndian = 0;
group = SwapShort(group);
elem = SwapShort(elem);
}
-
+
/// \todo find a trick to warn user and stop processing
if ( s == TS::DeflatedExplicitVRLittleEndian)