Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/01/07 16:45:51 $
- Version: $Revision: 1.164 $
+ Date: $Date: 2005/01/11 16:44:43 $
+ Version: $Revision: 1.174 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
namespace gdcm
{
-//-----------------------------------------------------------------------------
-static const char *TransferSyntaxStrings[] = {
- // Implicit VR Little Endian
- "1.2.840.10008.1.2",
- // Implicit VR Big Endian DLX G.E?
- "1.2.840.113619.5.2",
- // Explicit VR Little Endian
- "1.2.840.10008.1.2.1",
- // Deflated Explicit VR Little Endian
- "1.2.840.10008.1.2.1.99",
- // Explicit VR Big Endian
- "1.2.840.10008.1.2.2",
- // JPEG Baseline (Process 1)
- "1.2.840.10008.1.2.4.50",
- // JPEG Extended (Process 2 & 4)
- "1.2.840.10008.1.2.4.51",
- // JPEG Extended (Process 3 & 5)
- "1.2.840.10008.1.2.4.52",
- // JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8)
- "1.2.840.10008.1.2.4.53",
- // JPEG Full Progression, Non-Hierarchical (Process 10 & 12)
- "1.2.840.10008.1.2.4.55",
- // JPEG Lossless, Non-Hierarchical (Process 14)
- "1.2.840.10008.1.2.4.57",
- // JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, [Selection Value 1])
- "1.2.840.10008.1.2.4.70",
- // JPEG 2000 Lossless
- "1.2.840.10008.1.2.4.90",
- // JPEG 2000
- "1.2.840.10008.1.2.4.91",
- // RLE Lossless
- "1.2.840.10008.1.2.5",
- // Unknown
- "Unknown Transfer Syntax"
-};
//-----------------------------------------------------------------------------
// Refer to Document::CheckSwap()
return;
}
- Debug::Verbose(0, "Document::Document: starting parsing of file: ",
- Filename.c_str());
- Fp->seekg( 0, std::ios::beg);
+ Group0002Parsed = false;
+
+ gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str());
+ // Fp->seekg( 0, std::ios::beg);
Fp->seekg(0, std::ios::end);
long lgt = Fp->tellg();
// Load 'non string' values
- std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
+ std::string PhotometricInterpretation = GetEntry(0x0028,0x0004);
if( PhotometricInterpretation == "PALETTE COLOR " )
{
LoadEntryBinArea(0x0028,0x1200); // gray LUT
// we switch lineNumber and columnNumber
//
std::string RecCode;
- RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code
+ RecCode = GetEntry(0x0008, 0x0010); // recognition code
if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
// with "little-endian strings"
{
Filetype = ACR_LIBIDO;
- std::string rows = GetEntryByNumber(0x0028, 0x0010);
- std::string columns = GetEntryByNumber(0x0028, 0x0011);
- SetEntryByNumber(columns, 0x0028, 0x0010);
- SetEntryByNumber(rows , 0x0028, 0x0011);
+ std::string rows = GetEntry(0x0028, 0x0010);
+ std::string columns = GetEntry(0x0028, 0x0011);
+ SetEntry(columns, 0x0028, 0x0010);
+ SetEntry(rows , 0x0028, 0x0011);
}
// ----------------- End of ACR-LibIDO kludge ------------------
}
Initialise();
SwapCode = 0;
Filetype = ExplicitVR;
+ Group0002Parsed = false;
}
/**
{
if( Filetype == Unknown)
{
- Debug::Verbose(0, "Document::IsReadable: wrong filetype");
+ gdcmVerboseMacro( "Wrong filetype");
return false;
}
if( TagHT.empty() )
{
- Debug::Verbose(0, "Document::IsReadable: no tags in internal"
- " hash table.");
+ gdcmVerboseMacro( "No tags in internal hash table.");
return false;
}
* value from disk when only parsing occured).
* @return The encountered Transfer Syntax of the current document.
*/
-TransferSyntaxType Document::GetTransferSyntax()
+std::string Document::GetTransferSyntax()
{
- DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010);
+ DocEntry *entry = GetDocEntry(0x0002, 0x0010);
if ( !entry )
{
- return UnknownTS;
+ return GDCM_UNKNOWN;
}
// The entry might be present but not loaded (parsing and loading
if ( transfer.length() == 0 )
{
// for brain damaged headers
- return UnknownTS;
+ return GDCM_UNKNOWN;
}
while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
{
transfer.erase(transfer.length()-1, 1);
}
- for (int i = 0; TransferSyntaxStrings[i] != NULL; i++)
- {
- if ( TransferSyntaxStrings[i] == transfer )
- {
- return TransferSyntaxType(i);
- }
- }
+ return transfer;
}
- return UnknownTS;
-}
-
-bool Document::IsJPEGLossless()
-{
- TransferSyntaxType r = GetTransferSyntax();
- return r == JPEGFullProgressionProcess10_12
- || r == JPEGLosslessProcess14
- || r == JPEGLosslessProcess14_1;
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEG2000 one
- * @return True when JPEG2000 (Lossly or LossLess) found. False in all
- * other cases.
- */
-bool Document::IsJPEG2000()
-{
- TransferSyntaxType r = GetTransferSyntax();
- return r == JPEG2000Lossless || r == JPEG2000;
-}
-
-/**
- * \brief Determines if the Transfer Syntax corresponds to any form
- * of Jpeg encoded Pixel data.
- * @return True when any form of JPEG found. False otherwise.
- */
-bool Document::IsJPEG()
-{
- TransferSyntaxType r = GetTransferSyntax();
- return r == JPEGBaselineProcess1
- || r == JPEGExtendedProcess2_4
- || r == JPEGExtendedProcess3_5
- || r == JPEGSpectralSelectionProcess6_8
- || IsJPEGLossless()
- || IsJPEG2000();
-}
-
-/**
- * \brief Determines if the Transfer Syntax corresponds to encapsulated
- * of encoded Pixel Data (as opposed to native).
- * @return True when encapsulated. False when native.
- */
-bool Document::IsEncapsulate()
-{
- TransferSyntaxType r = GetTransferSyntax();
- return IsJPEG() || r == RLELossless;
+ return GDCM_UNKNOWN;
}
/**
*/
bool Document::IsDicomV3()
{
- // Checking if Transfert Syntax exists is enough
+ // Checking if Transfer Syntax exists is enough
// Anyway, it's to late check if the 'Preamble' was found ...
// And ... would it be a rich idea to check ?
// (some 'no Preamble' DICOM images exist !)
- return GetDocEntryByNumber(0x0002, 0x0010) != NULL;
+ return GetDocEntry(0x0002, 0x0010) != NULL;
}
/**
*/
std::ifstream *Document::OpenFile()
{
+
+ HasDCMPreamble = false;
if (Filename.length() == 0)
{
return 0;
if(Fp)
{
- Debug::Verbose( 0,
- "Document::OpenFile is already opened when opening: ",
- Filename.c_str());
+ gdcmVerboseMacro( "File already open: " << Filename.c_str());
}
Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
if( ! *Fp )
{
- Debug::Verbose( 0,
- "Document::OpenFile cannot open file: ",
- Filename.c_str());
+ gdcmVerboseMacro( "Cannot open file: " << Filename.c_str());
delete Fp;
Fp = 0;
return 0;
zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 ||
zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 )
{
+ std::string msg
+ = Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero);
+ gdcmVerboseMacro( msg.c_str() );
return Fp;
}
}
if( memcmp(dicm, "DICM", 4) == 0 )
{
+ HasDCMPreamble = true;
return Fp;
}
CloseFile();
- Debug::Verbose( 0,
- "Document::OpenFile not DICOM/ACR (missing preamble)",
- Filename.c_str());
+ gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
return 0;
}
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-ValEntry *Document::ReplaceOrCreateByNumber(std::string const &value,
- uint16_t group,
- uint16_t elem,
- TagName const &vr )
+ValEntry *Document::ReplaceOrCreate(std::string const &value,
+ uint16_t group,
+ uint16_t elem,
+ TagName const &vr )
{
ValEntry *valEntry = 0;
- DocEntry *currentEntry = GetDocEntryByNumber( group, elem);
+ DocEntry *currentEntry = GetDocEntry( group, elem);
if (currentEntry)
{
{
if (!RemoveEntry(currentEntry))
{
- Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
- " of previous DocEntry failed.");
+ gdcmVerboseMacro( "Removal of previous DocEntry failed.");
return NULL;
}
// Create a new valEntry if necessary
if (!valEntry)
{
- valEntry = NewValEntryByNumber(group, elem, vr);
+ valEntry = NewValEntry(group, elem, vr);
if ( !AddEntry(valEntry))
{
- Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
- " failed allthough this is a creation.");
+ gdcmVerboseMacro("AddEntry failed although this is a creation.");
delete valEntry;
return NULL;
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-BinEntry *Document::ReplaceOrCreateByNumber(uint8_t *binArea,
- int lgth,
- uint16_t group,
- uint16_t elem,
- TagName const &vr )
+BinEntry *Document::ReplaceOrCreate(uint8_t *binArea,
+ int lgth,
+ uint16_t group,
+ uint16_t elem,
+ TagName const &vr )
{
BinEntry *binEntry = 0;
- DocEntry *currentEntry = GetDocEntryByNumber( group, elem);
+ DocEntry *currentEntry = GetDocEntry( group, elem);
// Verify the currentEntry
if (currentEntry)
{
if (!RemoveEntry(currentEntry))
{
- Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
- " of previous DocEntry failed.");
+ gdcmVerboseMacro( "Removal of previous DocEntry failed.");
return NULL;
}
// Create a new binEntry if necessary
if (!binEntry)
{
- binEntry = NewBinEntryByNumber(group, elem, vr);
+ binEntry = NewBinEntry(group, elem, vr);
if ( !AddEntry(binEntry))
{
- Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
- " failed allthough this is a creation.");
+ gdcmVerboseMacro( "AddEntry failed allthough this is a creation.");
delete binEntry;
return NULL;
* \return pointer to the modified/created SeqEntry (NULL when creation
* failed).
*/
-SeqEntry *Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem)
+SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem)
{
SeqEntry *seqEntry = 0;
- DocEntry *currentEntry = GetDocEntryByNumber( group, elem);
+ DocEntry *currentEntry = GetDocEntry( group, elem);
// Verify the currentEntry
if (currentEntry)
{
if (!RemoveEntry(currentEntry))
{
- Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
- " of previous DocEntry failed.");
+ gdcmVerboseMacro( "Removal of previous DocEntry failed.");
return NULL;
}
// Create a new seqEntry if necessary
if (!seqEntry)
{
- seqEntry = NewSeqEntryByNumber(group, elem);
+ seqEntry = NewSeqEntry(group, elem);
if ( !AddEntry(seqEntry))
{
- Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
- " failed allthough this is a creation.");
+ gdcmVerboseMacro( "AddEntry failed allthough this is a creation.");
delete seqEntry;
return NULL;
* @param elem element number of the Entry
* \return boolean
*/
-bool Document::ReplaceIfExistByNumber(std::string const &value,
- uint16_t group, uint16_t elem )
+bool Document::ReplaceIfExist(std::string const &value,
+ uint16_t group, uint16_t elem )
{
- SetEntryByNumber(value, group, elem);
+ SetEntry(value, group, elem);
return true;
}
-std::string Document::GetTransferSyntaxValue(TransferSyntaxType type)
-{
- return TransferSyntaxStrings[type];
-}
-
//-----------------------------------------------------------------------------
// Protected
* @param element Element number of the searched Dicom Element
* @return true is found
*/
-bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
+bool Document::CheckIfEntryExist(uint16_t group, uint16_t element )
{
const std::string &key = DictEntry::TranslateToKey(group, element );
return TagHT.count(key) != 0;
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string Document::GetEntryByNumber(uint16_t group, uint16_t element)
+std::string Document::GetEntry(uint16_t group, uint16_t element)
{
TagKey key = DictEntry::TranslateToKey(group, element);
if ( !TagHT.count(key))
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element)
+std::string Document::GetEntryVR(uint16_t group, uint16_t element)
{
- DocEntry *elem = GetDocEntryByNumber(group, element);
+ DocEntry *elem = GetDocEntry(group, element);
if ( !elem )
{
return GDCM_UNFOUND;
* @param element Element number of the searched tag.
* @return Corresponding element length; -2 if not found
*/
-int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element)
+int Document::GetEntryLength(uint16_t group, uint16_t element)
{
- DocEntry *elem = GetDocEntryByNumber(group, element);
+ DocEntry *elem = GetDocEntry(group, element);
if ( !elem )
{
return -2; //magic number
* @param group group number of the Dicom Element to modify
* @param element element number of the Dicom Element to modify
*/
-bool Document::SetEntryByNumber(std::string const& content,
- uint16_t group, uint16_t element)
+bool Document::SetEntry(std::string const& content,
+ uint16_t group, uint16_t element)
{
- ValEntry *entry = GetValEntryByNumber(group, element);
+ ValEntry *entry = GetValEntry(group, element);
if (!entry )
{
- Debug::Verbose(0, "Document::SetEntryByNumber: no corresponding",
- " ValEntry (try promotion first).");
+ gdcmVerboseMacro( "No corresponding ValEntry (try promotion first).");
return false;
}
return SetEntry(content,entry);
* @param group group number of the Dicom Element to modify
* @param element element number of the Dicom Element to modify
*/
-bool Document::SetEntryByNumber(uint8_t*content, int lgth,
- uint16_t group, uint16_t element)
+bool Document::SetEntry(uint8_t*content, int lgth,
+ uint16_t group, uint16_t element)
{
- BinEntry *entry = GetBinEntryByNumber(group, element);
+ BinEntry *entry = GetBinEntry(group, element);
if (!entry )
{
- Debug::Verbose(0, "Document::SetEntryByNumber: no corresponding",
- " ValEntry (try promotion first).");
+ gdcmVerboseMacro( "No corresponding ValEntry (try promotion first).");
return false;
}
* @param elem element number of the Entry
* @return Pointer to the 'non string' area
*/
-void *Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem)
+void *Document::GetEntryBinArea(uint16_t group, uint16_t elem)
{
- DocEntry *entry = GetDocEntryByNumber(group, elem);
+ DocEntry *entry = GetDocEntry(group, elem);
if (!entry)
{
- Debug::Verbose(1, "Document::GetDocEntryByNumber: no entry");
+ gdcmVerboseMacro( "No entry");
return 0;
}
if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(entry) )
void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
// Search the corresponding DocEntry
- DocEntry *docElement = GetDocEntryByNumber(group, elem);
+ DocEntry *docElement = GetDocEntry(group, elem);
if ( !docElement )
return;
uint8_t *a = new uint8_t[l];
if( !a )
{
- Debug::Verbose(0, "Document::LoadEntryBinArea cannot allocate a");
+ gdcmVerboseMacro( "Cannot allocate a");
return;
}
/// \todo check the result
Fp->read((char*)a, l);
- if( Fp->fail() || Fp->eof()) //Fp->gcount() == 1
+ if( Fp->fail() || Fp->eof())
{
delete[] a;
return;
* @param element Element number of the searched Dicom Element
* @return
*/
-/*bool Document::SetEntryBinAreaByNumber(uint8_t *area,
- uint16_t group, uint16_t element)
+/*bool Document::SetEntryBinArea(uint8_t *area,
+ uint16_t group, uint16_t element)
{
- DocEntry *currentEntry = GetDocEntryByNumber(group, element);
+ DocEntry *currentEntry = GetDocEntry(group, element);
if ( !currentEntry )
{
return false;
* @param element Element number of the searched Dicom Element
* @return
*/
-DocEntry *Document::GetDocEntryByNumber(uint16_t group, uint16_t element)
+DocEntry *Document::GetDocEntry(uint16_t group, uint16_t element)
{
TagKey key = DictEntry::TranslateToKey(group, element);
if ( !TagHT.count(key))
}
/**
- * \brief Same as \ref Document::GetDocEntryByNumber except it only
+ * \brief Same as \ref Document::GetDocEntry except it only
* returns a result when the corresponding entry is of type
* ValEntry.
* @return When present, the corresponding ValEntry.
*/
-ValEntry *Document::GetValEntryByNumber(uint16_t group, uint16_t element)
+ValEntry *Document::GetValEntry(uint16_t group, uint16_t element)
{
- DocEntry *currentEntry = GetDocEntryByNumber(group, element);
+ DocEntry *currentEntry = GetDocEntry(group, element);
if ( !currentEntry )
{
return 0;
{
return entry;
}
- Debug::Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry.");
+ gdcmVerboseMacro( "Unfound ValEntry.");
return 0;
}
/**
- * \brief Same as \ref Document::GetDocEntryByNumber except it only
+ * \brief Same as \ref Document::GetDocEntry except it only
* returns a result when the corresponding entry is of type
* BinEntry.
* @return When present, the corresponding BinEntry.
*/
-BinEntry *Document::GetBinEntryByNumber(uint16_t group, uint16_t element)
+BinEntry *Document::GetBinEntry(uint16_t group, uint16_t element)
{
- DocEntry *currentEntry = GetDocEntryByNumber(group, element);
+ DocEntry *currentEntry = GetDocEntry(group, element);
if ( !currentEntry )
{
return 0;
{
return entry;
}
- Debug::Verbose(0, "Document::GetBinEntryByNumber: unfound BinEntry.");
+ gdcmVerboseMacro( "Unfound BinEntry.");
return 0;
}
a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
break;
default :
- //std::cout << "swapCode= " << SwapCode << std::endl;
- Debug::Error(" Document::SwapLong : unset swap code");
+ gdcmErrorMacro( "Unset swap code:" << SwapCode );
a = 0;
}
return a;
if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) )
{
////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- Debug::Verbose(0, "Document::ParseDES: neither Valentry, "
- "nor BinEntry. Probably unknown VR.");
+ gdcmVerboseMacro( "Neither Valentry, nor BinEntry."
+ "Probably unknown VR.");
}
//////////////////// BinEntry or UNKOWN VR:
if ( ( newDocEntry->GetGroup() == 0x7fe0 )
&& ( newDocEntry->GetElement() == 0x0010 ) )
{
- TransferSyntaxType ts = GetTransferSyntax();
- if ( ts == RLELossless )
+ std::string ts = GetTransferSyntax();
+ if ( Global::GetTS()->IsRLELossless(ts) )
{
long positionOnEntry = Fp->tellg();
Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
ComputeRLEInfo();
Fp->seekg( positionOnEntry, std::ios::beg );
}
- else if ( IsJPEG() )
+ else if ( Global::GetTS()->IsJPEG(ts) )
{
long positionOnEntry = Fp->tellg();
Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
else
{
// fusible
- std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry "
- << "nor a ValEntry ?! Should never print that !" << std::endl;
+ gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry "
+ << "nor a ValEntry ?! Should never print that !" );
}
// to be sure we are at the end of the value ...
if( length % 2 )
{
newValue = Util::DicomString(str, length+1);
- //Debug::Verbose(0, "Warning: bad length: ", length );
- Debug::Verbose(0, "For string :", newValue.c_str());
+ gdcmVerboseMacro("Warning: bad length: " << length <<
+ ",For string :" << newValue.c_str());
// Since we change the length of string update it length
//entry->SetReadLength(length+1);
}
if ( ValEntry *valEntry = dynamic_cast<ValEntry* >(entry) )
{
- if ( Fp->fail() || Fp->eof())//Fp->gcount() == 1
+ if ( Fp->fail() || Fp->eof())
{
- Debug::Verbose(1, "Document::LoadDocEntry",
- "unread element value");
+ gdcmVerboseMacro("Unread element value");
valEntry->SetValue(GDCM_UNREAD);
return;
}
}
else
{
- Debug::Error(true, "Document::LoadDocEntry"
- "Should have a ValEntry, here !");
+ gdcmErrorMacro( "Should have a ValEntry, here !");
}
}
// big endian and proceed...
if ( element == 0x0000 && length16 == 0x0400 )
{
- TransferSyntaxType ts = GetTransferSyntax();
- if ( ts != ExplicitVRBigEndian )
+ std::string ts = GetTransferSyntax();
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) != TS::ExplicitVRBigEndian )
{
throw FormatError( "Document::FindDocEntryLength()",
" not explicit VR." );
return;
}
length16 = 4;
- SwitchSwapToBigEndian();
+ SwitchByteSwapCode();
// Restore the unproperly loaded values i.e. the group, the element
// and the dictionary entry depending on them.
uint16_t correctGroup = SwapShort( entry->GetGroup() );
uint16_t correctElem = SwapShort( entry->GetElement() );
- DictEntry *newTag = GetDictEntryByNumber( correctGroup,
- correctElem );
+ DictEntry *newTag = GetDictEntry( correctGroup, correctElem );
if ( !newTag )
{
// This correct tag is not in the dictionary. Create a new one.
std::string Document::FindDocEntryVR()
{
if ( Filetype != ExplicitVR )
- return(GDCM_UNKNOWN);
+ return GDCM_UNKNOWN;
long positionOnEntry = Fp->tellg();
// Warning: we believe this is explicit VR (Value Representation) because
if( !CheckDocEntryVR(vr) )
{
Fp->seekg(positionOnEntry, std::ios::beg);
- return(GDCM_UNKNOWN);
+ return GDCM_UNKNOWN;
}
- return(vr);
+ return vr;
}
/**
/**
* \brief Skips to the begining of the next Header Entry
* \warning NOT end user intended method !
- * @param offset start of skipping
- * @param readLgth length to skip
-
+ * @param currentDocEntry entry to skip
*/
-void Document::SkipToNextDocEntry(DocEntry *newDocEntry)
+void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
{
- Fp->seekg((long)(newDocEntry->GetOffset()), std::ios::beg);
- Fp->seekg( (long)(newDocEntry->GetReadLength()),std::ios::cur);
+ Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
+ Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur);
}
/**
* the parser went Jabberwocky) one can hope improving things by
* applying some heuristics.
* @param entry entry to check
- * @param foundLength fist assumption about length
+ * @param foundLength first assumption about length
*/
void Document::FixDocEntryFoundLength(DocEntry *entry,
uint32_t foundLength)
if ( foundLength % 2)
{
- std::ostringstream s;
- s << "Warning : Tag with uneven length "
- << foundLength
- << " in x(" << std::hex << gr << "," << elem <<")" << std::dec;
- Debug::Verbose(0, s.str().c_str());
+ gdcmVerboseMacro( "Warning : Tag with uneven length " << foundLength
+ << " in x(" << std::hex << gr << "," << elem <<")");
}
//////// Fix for some naughty General Electric images.
// Allthough not recent many such GE corrupted images are still present
// on Creatis hard disks. Hence this fix shall remain when such images
- // are no longer in user (we are talking a few years, here)...
+ // are no longer in use (we are talking a few years, here)...
// Note: XMedCom probably uses such a trick since it is able to read
// those pesky GE images ...
if ( foundLength == 13)
*/
bool Document::IsDocEntryAnInteger(DocEntry *entry)
{
- uint16_t element = entry->GetElement();
+ uint16_t elem = entry->GetElement();
uint16_t group = entry->GetGroup();
const std::string &vr = entry->GetVR();
uint32_t length = entry->GetLength();
// When we have some semantics on the element we just read, and if we
// a priori know we are dealing with an integer, then we shall be
// able to swap it's element value properly.
- if ( element == 0 ) // This is the group length of the group
+ if ( elem == 0 ) // This is the group length of the group
{
if ( length == 4 )
{
// 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).
- std::ostringstream s;
long filePosition = Fp->tellg();
- s << "Erroneous Group Length element length on : (" \
- << std::hex << group << " , " << element
+ gdcmVerboseMacro( "Erroneous Group Length element length on : ("
+ << std::hex << group << " , " << elem
<< ") -before- position x(" << filePosition << ")"
- << "lgt : " << length;
- Debug::Verbose(0, "Document::IsDocEntryAnInteger", s.str().c_str() );
+ << "lgt : " << length );
}
}
}
catch ( FormatError )
{
- throw FormatError("Document::FindDocEntryLengthOBOrOW()",
- " group or element not present.");
+ throw FormatError("Unexpected end of file encountered during ",
+ "Document::FindDocEntryLengthOBOrOW()");
}
// We have to decount the group and element we just read
if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- Debug::Verbose(1, "Document::FindDocEntryLengthOBOrOW: neither an Item "
- "tag nor a Sequence delimiter tag.");
+ long filePosition = Fp->tellg();
+ gdcmVerboseMacro( "Neither an Item tag nor a Sequence delimiter tag on :"
+ << std::hex << group << " , " << elem
+ << ") -before- position x(" << filePosition << ")" );
+
Fp->seekg(positionOnEntry, std::ios::beg);
- throw FormatUnexpected("Document::FindDocEntryLengthOBOrOW()",
- "Neither an Item tag nor a Sequence "
- "delimiter tag.");
+ throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag.");
}
if ( elem == 0xe0dd )
char *entCur = deb + 128;
if( memcmp(entCur, "DICM", (size_t)4) == 0 )
{
- Debug::Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3");
+ gdcmVerboseMacro( "Looks like DICOM Version3" );
// Next, determine the value representation (VR). Let's skip to the
// first element (0002, 0000) and check there if we find "UL"
// FIXME : FIXME:
// Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR,
- // but elem 0002,0010 (Transfert Syntax) tells us the file is
+ // but elem 0002,0010 (Transfer Syntax) tells us the file is
// *Implicit* VR. -and it is !-
if( memcmp(entCur, "UL", (size_t)2) == 0 ||
// instead of just checking for UL, OB and UI !? group 0000
{
Filetype = ExplicitVR;
- Debug::Verbose(1, "Document::CheckSwap:",
- "explicit Value Representation");
+ gdcmVerboseMacro( "Explicit Value Representation");
}
else
{
Filetype = ImplicitVR;
- Debug::Verbose(1, "Document::CheckSwap:",
- "not an explicit Value Representation");
+ gdcmVerboseMacro( "Not an explicit Value Representation");
}
if ( net2host )
{
SwapCode = 4321;
- Debug::Verbose(1, "Document::CheckSwap:",
- "HostByteOrder != NetworkByteOrder");
+ gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder");
}
else
{
SwapCode = 0;
- Debug::Verbose(1, "Document::CheckSwap:",
- "HostByteOrder = NetworkByteOrder");
+ gdcmVerboseMacro( "HostByteOrder = NetworkByteOrder");
}
// Position the file position indicator at first tag (i.e.
// Alas, this is not a DicomV3 file and whatever happens there is no file
// preamble. We can reset the file position indicator to where the data
// is (i.e. the beginning of the file).
- Debug::Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file");
+ gdcmVerboseMacro( "Not a DICOM Version3 file");
Fp->seekg(0, std::ios::beg);
// Our next best chance would be to be considering a 'clean' ACR/NEMA file.
Filetype = ACR;
return true;
default :
- Debug::Verbose(0, "Document::CheckSwap:",
- "ACR/NEMA unfound swap info (Really hopeless !)");
+ gdcmVerboseMacro( "ACR/NEMA unfound swap info (Really hopeless !)");
Filetype = Unknown;
return false;
}
/**
- * \brief Restore the unproperly loaded values i.e. the group, the element
- * and the dictionary entry depending on them.
+ * \brief Change the Byte Swap code.
*/
-void Document::SwitchSwapToBigEndian()
+void Document::SwitchByteSwapCode()
{
- Debug::Verbose(1, "Document::SwitchSwapToBigEndian",
- "Switching to BigEndian mode.");
+ gdcmVerboseMacro( "Switching Byte Swap code.");
if ( SwapCode == 0 )
{
SwapCode = 4321;
{
// start endian swap mark for group found
reversedEndian++;
- SwitchSwapToBigEndian();
+ SwitchByteSwapCode();
// fix the tag
group = 0xfffe;
elem = 0xe000;
}
- else if ((group == 0xfffe) && (elem == 0xe00d) && reversedEndian)
+ else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
{
// end of reversed endian group
reversedEndian--;
- SwitchSwapToBigEndian();
+ SwitchByteSwapCode();
+ }
+}
+
+/**
+ * \brief Group 0002 is always coded Little Endian
+ * whatever Transfer Syntax is
+ * @return no return
+ */
+void Document::HandleOutOfGroup0002(uint16_t group)
+{
+ // 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
+
+ TagKey key = DictEntry::TranslateToKey(0x0002, 0x0010);
+ if ( !TagHT.count(key))
+ {
+ gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax ?!?");
+ return;
+ }
+
+ // FIXME Strangely, this works with
+ //'Implicit VR Transfer Syntax (GE Private)
+
+ if ( ((ValEntry *)TagHT.find(key)->second)->GetValue()
+ == "Explicit VR - Big Endian" )
+ {
+ gdcmVerboseMacro("Tansfer Syntax = Explicit VR - Big Endian");
+ SwitchByteSwapCode();
+ }
}
}
/**
* \brief Read the next tag but WITHOUT loading it's value
* (read the 'Group Number', the 'Element Number',
- * gets the Dict Entry
+ * 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 0;
}
+ // Sometimes file contains groups of tags with reversed endianess.
HandleBrokenEndian(group, elem);
+
+// In 'true DICOM' files Group 0002 is allways little endian
+ if ( HasDCMPreamble )
+ HandleOutOfGroup0002(group);
+
std::string vr = FindDocEntryVR();
std::string realVR = vr;
if( vr == GDCM_UNKNOWN)
{
- DictEntry *dictEntry = GetDictEntryByNumber(group,elem);
+ DictEntry *dictEntry = GetDictEntry(group,elem);
if( dictEntry )
realVR = dictEntry->GetVR();
}
DocEntry *newEntry;
if( Global::GetVR()->IsVROfSequence(realVR) )
- newEntry = NewSeqEntryByNumber(group, elem);
+ newEntry = NewSeqEntry(group, elem);
else if( Global::GetVR()->IsVROfStringRepresentable(realVR) )
- newEntry = NewValEntryByNumber(group, elem,vr);
+ newEntry = NewValEntry(group, elem,vr);
else
- newEntry = NewBinEntryByNumber(group, elem,vr);
+ newEntry = NewBinEntry(group, elem,vr);
if( vr == GDCM_UNKNOWN )
{
std::string msg;
msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n",
newEntry->GetGroup(), newEntry->GetElement());
- Debug::Verbose(1, "Document::FindVR: ", msg.c_str());
+ gdcmVerboseMacro( msg.c_str() );
}
newEntry->SetImplicitVR();
}
}
if ( itemTagGroup != testGroup || itemTagElement != testElement )
{
- std::ostringstream s;
- s << " We should have found tag (";
- s << std::hex << testGroup << "," << testElement << ")" << std::endl;
- s << " but instead we encountered tag (";
- s << std::hex << itemTagGroup << "," << itemTagElement << ")"
- << std::endl;
- s << " at address: " << (unsigned)currentPosition << std::endl;
- Debug::Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:");
- Debug::Verbose(0, s.str().c_str());
+ gdcmVerboseMacro( "Wrong Item Tag found:"
+ << " We should have found tag ("
+ << std::hex << testGroup << "," << testElement << ")" << std::endl
+ << " but instead we encountered tag ("
+ << std::hex << itemTagGroup << "," << itemTagElement << ")"
+ << std::dec
+ << " at address: " << (unsigned int)currentPosition
+ << std::hex
+ << " 0x(" << (unsigned int)currentPosition << ")"
+ ) ;
Fp->seekg(positionOnEntry, std::ios::beg);
return false;
long currentPosition = Fp->tellg();
uint32_t itemLength = ReadInt32();
{
- std::ostringstream s;
- s << "Basic Item Length is: "
- << itemLength << std::endl;
- s << " at address: " << (unsigned)currentPosition << std::endl;
- Debug::Verbose(0, "Document::ReadItemTagLength: ", s.str().c_str());
+ gdcmVerboseMacro( "Basic Item Length is: "
+ << itemLength << std::endl
+ << " at address: " << (unsigned int)currentPosition);
}
return itemLength;
}
{
uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
uint32_t);
- std::ostringstream s;
- s << " Read one length: ";
- s << std::hex << individualLength << std::endl;
- Debug::Verbose(0,
- "Document::ReadAndSkipEncapsulatedBasicOffsetTable: ",
- s.str().c_str());
+ gdcmVerboseMacro( "Read one length: " <<
+ std::hex << individualLength );
}
#endif //GDCM_DEBUG
*/
void Document::ComputeRLEInfo()
{
- TransferSyntaxType ts = GetTransferSyntax();
- if ( ts != RLELossless )
+ std::string ts = GetTransferSyntax();
+ if ( Global::GetTS()->IsRLELossless(ts) )
{
return;
}
if ( nbRleSegments > 16 )
{
// There should be at most 15 segments (refer to RLEFrame class)
- Debug::Verbose(0, "Document::ComputeRLEInfo: too many segments.");
+ gdcmVerboseMacro( "Too many segments.");
}
uint32_t rleSegmentOffsetTable[16];
// Delimiter Item':
if ( !ReadTag(0xfffe, 0xe0dd) )
{
- Debug::Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
- Debug::Verbose(0, " item at end of RLE item sequence");
+ gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence");
}
}
void Document::ComputeJPEGFragmentInfo()
{
// If you need to, look for comments of ComputeRLEInfo().
- if ( ! IsJPEG() )
+ std::string ts = GetTransferSyntax();
+ if ( ! Global::GetTS()->IsJPEG(ts) )
{
return;
}
// Delimiter Item':
if ( !ReadTag(0xfffe, 0xe0dd) )
{
- Debug::Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
- Debug::Verbose(0, " item at end of JPEG item sequence");
+ gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence");
}
}
bool Document::operator<(Document &document)
{
// Patient Name
- std::string s1 = GetEntryByNumber(0x0010,0x0010);
- std::string s2 = document.GetEntryByNumber(0x0010,0x0010);
+ std::string s1 = GetEntry(0x0010,0x0010);
+ std::string s2 = document.GetEntry(0x0010,0x0010);
if(s1 < s2)
{
return true;
else
{
// Patient ID
- s1 = GetEntryByNumber(0x0010,0x0020);
- s2 = document.GetEntryByNumber(0x0010,0x0020);
+ s1 = GetEntry(0x0010,0x0020);
+ s2 = document.GetEntry(0x0010,0x0020);
if ( s1 < s2 )
{
return true;
else
{
// Study Instance UID
- s1 = GetEntryByNumber(0x0020,0x000d);
- s2 = document.GetEntryByNumber(0x0020,0x000d);
+ s1 = GetEntry(0x0020,0x000d);
+ s2 = document.GetEntry(0x0020,0x000d);
if ( s1 < s2 )
{
return true;
else
{
// Serie Instance UID
- s1 = GetEntryByNumber(0x0020,0x000e);
- s2 = document.GetEntryByNumber(0x0020,0x000e);
+ s1 = GetEntry(0x0020,0x000e);
+ s2 = document.GetEntry(0x0020,0x000e);
if ( s1 < s2 )
{
return true;
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff