Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2006/03/01 10:15:12 $
- Version: $Revision: 1.343 $
+ Date: $Date: 2006/06/21 14:06:56 $
+ Version: $Revision: 1.351 $
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
+
+//#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
+*/
+//#endif
/**
* \brief Performs the Loading Job (internal use only)
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 (
fp->write(filePreamble, 128);
fp->write("DICM", 4);
}
-
/*
* \todo rewrite later, if really usefull
* - 'Group Length' element is optional in DICOM
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)
{
// Uncomment to track the bug
/*
if( Debug::GetDebugFlag() )
- std::cout << std::dec <<"(long)(Fp->tellg()) " << (long)(Fp->tellg())
+ 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.
{
//////////////////////////// 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();
*/
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
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
// '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 !
- }
-
+ {
+ // 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...
{
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 << ")"
// Find a trick to tell it the caller...
s16 = *((uint16_t *)(deb));
+
+ gdcmDebugMacro("not a DicomV3 nor a 'clean' ACR/NEMA;"
+ << " (->despaired wild guesses !)");
switch ( s16 )
{
* \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;
}
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;
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff