Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2010/04/09 15:32:39 $
- Version: $Revision: 1.382 $
+ Date: $Date: 2010/06/24 04:34:20 $
+ Version: $Revision: 1.383 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
std::string RecCode;
RecCode = GetEntryString(0x0008, 0x0010); // recognition code (RET)
-
+
if(RecCode.find("ACRNEMA_LIBIDO") == 0 || // any version
RecCode.find("CANRME_AILIBOD") == 0) // for brain-damaged softwares
// with "little-endian strings"
// happen at different stages): try loading and proceed with check...
// Well ...
- // (parsing and loading happen at the very same stage!)
+ // (parsing and loading happen at the very same stage!)
//LoadDocEntrySafe(entry); //JPRx
if (DataEntry *dataEntry = dynamic_cast<DataEntry *>(entry) )
{
// save CPU time
a=( ( a<<24) | ((a<<8) & 0x00ff0000) |
((a>>8) & 0x0000ff00) | (a>>24) );
- break;
+ break;
case 3412 :
// a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
a=( (a<<16) | (a>>16) );
- break;
+ break;
case 2143 :
a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
break;
a = 0;
}
return a;
-}
+}
/**
* \brief Swaps back the bytes of 8-byte long 'double' accordingly to
* \brief Tries to open the file Document::Filename and
* checks the preamble when existing,
* or if the file starts with an ACR-NEMA look-like element.
- * @return The FILE pointer on success, 0 on failure.
+ * @return The FILE pointer on success, 0 on failure.
*/
std::ifstream *Document::OpenFile()
{
HasDCMPreamble = false;
- if (Filename.length() == 0)
+ if (Filename.length() == 0)
{
return 0;
}
if ( ! *Fp )
{
// Don't user gdcmErrorMacro :
- // a spurious message will appear when you use, for instance
+ // a spurious message will appear when you use, for instance
// gdcm::FileHelper *fh = new gdcm::FileHelper( outputFileName );
// to create outputFileName.
-
- // FIXME : if the upper comment is still usefull
+
+ // FIXME : if the upper comment is still usefull
// --> the constructor is not so good ...
-
+
gdcmWarningMacro( "Cannot open file: " << Filename.c_str());
delete Fp;
Fp = 0;
//exit(1); // No function is allowed to leave the application instead
// of warning the caller
}
-
+
uint16_t zero = 0;
Fp->read((char*)&zero, (size_t)2);
if ( Fp->eof() )
CloseFile();
return 0;
}
-
+
//-- DICOM --
Fp->seekg(126L, std::ios::cur); // Once per Document
char dicm[4]; // = {' ',' ',' ',' '};
CloseFile();
return 0;
}
-
+
if ( memcmp(dicm, "DICM", 4) == 0 )
{
HasDCMPreamble = true;
//-- 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 (
+ 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 ||
zero == 0x0028 || 0x2800 // worse : some ACR-NEMA like files
- // start 00028 group ?!?
+ // start 00028 group ?!?
)
{
std::string msg = Util::Format(
gdcmWarningMacro( msg.c_str() );
return Fp;
}
-
+
// -- Neither ACR/No Preamble Dicom nor DICOMV3 file
CloseFile();
// 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());
+ << Filename.c_str());
return 0;
}
/**
- * \brief closes the file
- * @return TRUE if the close was successfull
+ * \brief closes the file
+ * @return TRUE if the close was successfull
*/
bool Document::CloseFile()
{
}
/**
- * \brief Writes in a file all the Entries (Dicom Elements)
+ * \brief Writes in a file all the Entries (Dicom Elements)
* @param fp file pointer on an already open file (actually: Output File Stream)
- * @param filetype Type of the File to be written
+ * @param filetype Type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
*/
void Document::WriteContent(std::ofstream *fp, FileType filetype, bool, bool)
uint32_t Document::GetInt32()
{
uint32_t g = *((uint32_t*)PtrBegBuffer);
- g = SwapLong(g);
+ g = SwapLong(g);
PtrBegBuffer+=4;
return g;
}
/**
* \brief Re-computes the length of the Dicom group 0002.
*/
-int Document::ComputeGroup0002Length( )
+int Document::ComputeGroup0002Length( )
{
uint16_t gr;
VRKey vr;
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)
{
/// Probabely a bug in gdcm code somewhere (some memory erased ?)
// Uncomment to track the bug
-
- if( Debug::GetDebugFlag() )
+
+ 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
// Uncoment this cerr line to be able to 'follow' the DocEntries
// when something *very* strange happens
- if( Debug::GetDebugFlag() )
+ if( Debug::GetDebugFlag() )
std::cerr<<newDocEntry->GetKey()<<" "<<newDocEntry->GetVR()<<std::endl;
// an Item Starter found elsewhere but in the first position
newDocEntry = Backtrack(newDocEntry, set);
}
else
- {
- PreviousDocEntry = newDocEntry;
+ {
+ PreviousDocEntry = newDocEntry;
}
-
+
used = true;
newDataEntry = dynamic_cast<DataEntry*>(newDocEntry);
- if ( newDataEntry )
+ if ( newDataEntry )
{
//////////////////////////// DataEntry
-
+
//vr = newDocEntry->GetVR(); // useless ?
if ( !set->AddEntry( newDataEntry ) )
}
}
- 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
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();
DocEntry *newDocEntry = ReadNextDocEntry();
if ( !newDocEntry )
- {
+ {
// The most frequent is when a SQ terminator is missing (?!?)
gdcmWarningMacro("in ParseSQ : should never get here!");
UnexpectedEOF = true;
{
dlm_mod = false;
}
-
+
// avoid infinite loop when Bad assumption was made on illegal 'unknown length' UN //JPRx
if (offsetStartCurrentSQItem <= OffsetOfPreviousParseDES)
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
uint16_t length16;
if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
-
+
// WARNING :
//
// For some images, length of UN elements is coded on 2 bytes (instead of 4)
//| vr == "UN"
// in the following line.
// (the 'straight' images will no longer be readable ...)
-
+
if ( vr == "OB" || vr == "OW" || vr == "OL" || vr == "SQ" || vr == "UT"
|| vr == "UN" || changeFromUN == true)
{
// Delimiters (0xfffe), are not explicit VR ...
if ( CurrentGroup == 0xfffe )
return GDCM_VRUNKNOWN;
-
- //long positionOnEntry;
- //if( Debug::GetWarningFlag() )
+
+ //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.
//Fp->read(&(vr[0]),(size_t)2);
vr[0] = *PtrBegBuffer++;
vr[1] = *PtrBegBuffer++;
-
+
//if ( !CheckDocEntryVR(vr) ) // avoid useless function call
if ( !Global::GetVR()->IsValidVR(vr) )
- {
+ {
gdcmWarningMacro( "Unknown VR " << vr.GetHexaRepresentation() << std::hex
<< " at offset : 0x(" << CurrentOffsetPosition-4
<< ") for group " << std::hex << CurrentGroup );
-
+
//Fp->seekg(positionOnEntry, std::ios::beg); //JPRx
- //Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?)
+ //Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?)
//see :MR_Philips_Intera_PrivateSequenceExplicitVR.dcm
PtrBegBuffer-=2;
return GDCM_VRUNKNOWN;
entry->SetLength(0);
return; // return ASAP; don't waist time on useless tests
}
-
+
uint16_t gr = entry->GetGroup();
uint16_t elem = entry->GetElement();
// 'Leonardo' source. Hence, one might consider commenting out the
// following fix on efficiency reasons.
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."
// 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 : ("
+ gdcmWarningMacro( "Erroneous Group Length element length on : ("
<< std::hex << group << " , " << elem
<< ") -before- position x(" << filePosition << ")"
<< "lgt : " << length );
// 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 )
Filetype = ACR;
return true;
default :
-
+
s16 = *((uint16_t *)(deb));
if (s16 != 0x0000)
return false;
break;
case 0x0400 :
SwapCode = 3412;
- break;
+ break;
default:
gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)");
Filetype = Unknown;
}
}
Filetype = ImplicitVR;
- return true;
+ return true;
}
}
}
// header parsing has to be considered as finished.
return 0;
}
-
+
changeFromUN = false;
CurrentGroup = GetInt16();
CurrentElem = GetInt16();
-
+
// In 'true DICOM' files Group 0002 is always little endian
if ( HasDCMPreamble )
{
HandleBrokenEndian(CurrentGroup, CurrentElem);
}
- VRKey vr = FindDocEntryVR();
- VRKey realVR = vr;
+ //VRKey vr = FindDocEntryVR();
+ //VRKey realVR = vr;
+
+ std::string vr, realVR;
+ if (group == 0xfffe && (elem == 0xe000 || elem == 0xe00d || elem == 0xe0dd))
+ {
+ // DICOM PS 3.6-2009, page 117 states:
+ // The VR for Data Elements, Item (FFFE,E000), Item Delimitation
+ // Item (FFFE,E00D), and Sequence Delimitation Item (FFFE,E0DD)
+ // do not exist. See PS 3.5 for explanation.
+ vr = GDCM_UNKNOWN;
+ realVR = GDCM_UNKNOWN;
+ }
+ else
+ {
+ vr = FindDocEntryVR();
+ realVR = vr;
+ }
if ( vr == GDCM_VRUNKNOWN )
{
// -> Better we fix the problem at Write time
else if (CurrentGroup%2 == 1 )
- {
+ {
if (CurrentElem >= 0x0010 && CurrentElem <=0x00ff )
{
// DICOM PS 3-5 7.8.1 a) states that :
}
// if UN found, let's check the dictionary, and trust it!
- // (maybe a private dictionary exists?)
+ // (maybe a private dictionary exists?)
else if (vr == "UN")
{
DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);
if ( dictEntry )
{
- realVR = dictEntry->GetVR();
+ realVR = dictEntry->GetVR();
dictEntry->Unregister(); // GetDictEntry registered it
// for VR = "UN", length is always stored on 4 bytes.
{
// 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)
- {
+ {
int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong
gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x("
if ( s == TS::ImplicitVRLittleEndian
||
- s == TS::ImplicitVRBigEndianPrivateGE
+ s == TS::ImplicitVRBigEndianPrivateGE
)
{
Filetype = ImplicitVR;
// to trust manufacturers.
// (we often find 'Implicit VR' tag,
// even when Transfer Syntax tells us it's Explicit ...
-
+
// NEVER trust the meta elements!
// (see what ezDICOM does ...)
-
+
/*
if ( s == TS::ExplicitVRBigEndian )
{
elem = SwapShort(elem);
// not what we where told (by meta elements) !
gdcmDebugMacro("Transfer Syntax Name = ["
- << GetTransferSyntaxName() << "]" );
+ << GetTransferSyntaxName() << "]" );
}
-
+
/// \todo find a trick to warn user and stop processing
-
+
if ( s == TS::DeflatedExplicitVRLittleEndian)
{
gdcmWarningMacro("Transfer Syntax ["
<< GetTransferSyntaxName() << "] :"
<< " not yet dealt with ");
- return;
+ 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;
+ return;
}
-
+
if ( !Global::GetTS()->IsTransferSyntax(ts) )
{
gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: ["
<< ts << "]");
return;
- }
+ }
}
//-----------------------------------------------------------------------------
projects / gdcm.git / commitdiff