Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/01/06 15:36:48 $
- Version: $Revision: 1.157 $
+ Date: $Date: 2005/01/11 23:06:35 $
+ Version: $Revision: 1.180 $
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 Little 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()
//const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
* \brief constructor
* @param filename file to be opened for parsing
*/
-Document::Document( std::string const & filename ) : ElementSet(-1)
+Document::Document( std::string const &filename ) : ElementSet(-1)
{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Filename = filename;
return;
}
- dbg.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 ------------------
}
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Initialise();
- SwapCode = 0;
+ SwapCode = 1234;
Filetype = ExplicitVR;
+ Group0002Parsed = false;
}
/**
* \brief Prints The Dict Entries of THE public Dicom Dictionary
* @return
*/
-void Document::PrintPubDict(std::ostream & os)
+void Document::PrintPubDict(std::ostream &os)
{
RefPubDict->SetPrintLevel(PrintLevel);
RefPubDict->Print(os);
* \brief Prints The Dict Entries of THE shadow Dicom Dictionary
* @return
*/
-void Document::PrintShaDict(std::ostream & os)
+void Document::PrintShaDict(std::ostream &os)
{
RefShaDict->SetPrintLevel(PrintLevel);
RefShaDict->Print(os);
/**
* \brief Get the public dictionary used
*/
-Dict* Document::GetPubDict()
+Dict *Document::GetPubDict()
{
return RefPubDict;
}
/**
* \brief Get the shadow dictionary used
*/
-Dict* Document::GetShaDict()
+Dict *Document::GetShaDict()
{
return RefShaDict;
}
/**
* \brief Set the shadow dictionary used
- * \param dict dictionary to use in shadow
+ * @param dict dictionary to use in shadow
*/
bool Document::SetShaDict(Dict *dict)
{
/**
* \brief Set the shadow dictionary used
- * \param dictName name of the dictionary to use in shadow
+ * @param dictName name of the dictionary to use in shadow
*/
-bool Document::SetShaDict(DictKey const & dictName)
+bool Document::SetShaDict(DictKey const &dictName)
{
RefShaDict = Global::GetDicts()->GetDict(dictName);
return !RefShaDict;
{
if( Filetype == Unknown)
{
- dbg.Verbose(0, "Document::IsReadable: wrong filetype");
+ gdcmVerboseMacro( "Wrong filetype");
return false;
}
if( TagHT.empty() )
{
- dbg.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
// happen at different stages): try loading and proceed with check...
LoadDocEntrySafe(entry);
- if (ValEntry* valEntry = dynamic_cast< ValEntry* >(entry) )
+ if (ValEntry *valEntry = dynamic_cast< ValEntry* >(entry) )
{
std::string transfer = valEntry->GetValue();
// The actual transfer (as read from disk) might be padded. We
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;
}
/**
* checks the preamble when existing.
* @return The FILE pointer on success.
*/
-std::ifstream* Document::OpenFile()
+std::ifstream *Document::OpenFile()
{
+
+ HasDCMPreamble = false;
if (Filename.length() == 0)
{
return 0;
if(Fp)
{
- dbg.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 )
{
- dbg.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();
- dbg.Verbose( 0,
- "Document::OpenFile not DICOM/ACR (missing preamble)",
- Filename.c_str());
+ gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
return 0;
}
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* \return Always true.
*/
-void Document::WriteContent(std::ofstream* fp, FileType filetype)
+void Document::WriteContent(std::ofstream *fp, FileType filetype)
{
/// \todo move the following lines (and a lot of others, to be written)
/// to a future function CheckAndCorrectHeader
* \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);
+ ValEntry *valEntry = 0;
+ DocEntry *currentEntry = GetDocEntry( group, elem);
if (currentEntry)
{
{
if (!RemoveEntry(currentEntry))
{
- dbg.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))
{
- dbg.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);
+ BinEntry *binEntry = 0;
+ DocEntry *currentEntry = GetDocEntry( group, elem);
// Verify the currentEntry
if (currentEntry)
{
if (!RemoveEntry(currentEntry))
{
- dbg.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))
{
- dbg.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);
+ SeqEntry *seqEntry = 0;
+ DocEntry *currentEntry = GetDocEntry( group, elem);
// Verify the currentEntry
if (currentEntry)
{
if (!RemoveEntry(currentEntry))
{
- dbg.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))
{
- dbg.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;
}
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value of a given tag.
- * \warning Don't use any longer : use GetPubEntryByName
- * @param tagName name of the searched element.
- * @return Corresponding element value when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string Document::GetEntryByName(TagName const & tagName)
-{
- DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( !dictEntry )
- {
- return GDCM_UNFOUND;
- }
-
- return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement());
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param tagName name of the searched element.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string Document::GetEntryVRByName(TagName const& tagName)
-{
- DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- {
- return GDCM_UNFOUND;
- }
-
- DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
- return elem->GetVR();
-}
/**
* \brief Searches within Header Entries (Dicom Elements) parsed with
* @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
}
return elem->GetLength();
}
-/**
- * \brief Sets the value (string) of the Header Entry (Dicom Element)
- * @param content string value of the Dicom Element
- * @param tagName name of the searched Dicom Element.
- * @return true when found
- */
-bool Document::SetEntryByName( std::string const & content,
- TagName const & tagName)
-{
- DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( !dictEntry )
- {
- return false;
- }
-
- return SetEntryByNumber(content,dictEntry->GetGroup(),
- dictEntry->GetElement());
-}
/**
* \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* @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 )
{
- dbg.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 )
{
- dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding",
- " ValEntry (try promotion first).");
+ gdcmVerboseMacro( "No corresponding ValEntry (try promotion first).");
return false;
}
/**
* \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* and modifies it's content with the given value.
- * @param content new value (string) to substitute with
+ * @param content new value (string) to substitute with
+ * @param entry Entry to be modified
*/
-bool Document::SetEntry(std::string const & content,ValEntry* entry)
+bool Document::SetEntry(std::string const &content,ValEntry *entry)
{
if(entry)
{
* \brief Accesses an existing BinEntry (i.e. a Dicom Element)
* and modifies it's content with the given value.
* @param content new value (void* -> uint8_t*) to substitute with
+ * @param entry Entry to be modified
* @param lgth new value length
*/
-bool Document::SetEntry(uint8_t* content, int lgth,BinEntry* entry)
+bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry)
{
if(entry)
{
* @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)
{
- dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry");
+ gdcmVerboseMacro( "No entry");
return 0;
}
- if ( BinEntry* binEntry = dynamic_cast<BinEntry*>(entry) )
+ if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(entry) )
{
return binEntry->GetBinArea();
}
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;
* when a string is not suitable
* @param element Entry whose binArea is going to be loaded
*/
-void Document::LoadEntryBinArea(BinEntry* element)
+void Document::LoadEntryBinArea(BinEntry *element)
{
if(element->GetBinArea())
return;
Fp->seekg(o, std::ios::beg);
size_t l = element->GetLength();
- uint8_t* a = new uint8_t[l];
+ uint8_t *a = new uint8_t[l];
if( !a )
{
- dbg.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;
}
- if ( BinEntry* binEntry = dynamic_cast<BinEntry*>(currentEntry) )
+ if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(currentEntry) )
{
binEntry->SetBinArea( area );
return true;
return false;
}*/
-/**
- * \brief Searches within the Header Entries for a Dicom Element of
- * a given tag.
- * @param tagName name of the searched Dicom Element.
- * @return Corresponding Dicom Element when it exists, and NULL
- * otherwise.
- */
-DocEntry* Document::GetDocEntryByName(TagName const & tagName)
-{
- DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( !dictEntry )
- {
- return NULL;
- }
-
- return GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement());
-}
-
/**
* \brief retrieves a Dicom Element (the first one) using (group, element)
* \warning (group, element) IS NOT an identifier inside the Dicom Header
* @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;
}
- if ( ValEntry* entry = dynamic_cast<ValEntry*>(currentEntry) )
+ if ( ValEntry *entry = dynamic_cast<ValEntry*>(currentEntry) )
{
return entry;
}
- dbg.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;
}
- if ( BinEntry* entry = dynamic_cast<BinEntry*>(currentEntry) )
+ if ( BinEntry *entry = dynamic_cast<BinEntry*>(currentEntry) )
{
return entry;
}
- dbg.Verbose(0, "Document::GetBinEntryByNumber: unfound BinEntry.");
+ gdcmVerboseMacro( "Unfound BinEntry.");
return 0;
}
/**
* \brief Loads the element while preserving the current
- * underlying file position indicator as opposed to
+ * underlying file position indicator as opposed to
* to LoadDocEntry that modifies it.
* @param entry Header Entry whose value shall be loaded.
* @return
*/
-void Document::LoadDocEntrySafe(DocEntry * entry)
+void Document::LoadDocEntrySafe(DocEntry *entry)
{
if(Fp)
{
{
switch (SwapCode)
{
- case 0 :
+ case 1234 :
break;
case 4321 :
a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
break;
default :
- //std::cout << "swapCode= " << SwapCode << std::endl;
- dbg.Error(" Document::SwapLong : unset swap code");
+ gdcmErrorMacro( "Unset swap code:" << SwapCode );
a = 0;
}
return a;
long l_max, bool delim_mode)
{
DocEntry *newDocEntry = 0;
+ ValEntry *newValEntry;
+ BinEntry *newBinEntry;
+ SeqEntry *newSeqEntry;
+ VRKey vr;
+ bool used=false;
while (true)
{
{
break;
}
+
+ used=true;
newDocEntry = ReadNextDocEntry( );
if ( !newDocEntry )
{
break;
}
- VRKey vr = newDocEntry->GetVR();
- if ( vr != "SQ" )
+ vr = newDocEntry->GetVR();
+ newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
+ newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
+ newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
+
+ if ( newValEntry || newBinEntry )
{
-
- if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) )
+ if ( newBinEntry )
+ {
+ if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) )
+ {
+ ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
+ gdcmVerboseMacro( "Neither Valentry, nor BinEntry."
+ "Probably unknown VR.");
+ }
+
+ //////////////////// BinEntry or UNKOWN VR:
+ // When "this" is a Document the Key is simply of the
+ // form ( group, elem )...
+ if (Document *dummy = dynamic_cast< Document* > ( set ) )
+ {
+ (void)dummy;
+ newBinEntry->SetKey( newBinEntry->GetKey() );
+ }
+ // but when "this" is a SQItem, we are inserting this new
+ // valEntry in a sequence item, and the kay has the
+ // generalized form (refer to \ref BaseTagKey):
+ if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ {
+ newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newBinEntry->GetKey() );
+ }
+
+ LoadDocEntry( newBinEntry );
+ if( !set->AddEntry( newBinEntry ) )
+ {
+ //Expect big troubles if here
+ //delete newBinEntry;
+ used=false;
+ }
+ }
+ else
{
/////////////////////// ValEntry
- ValEntry* newValEntry =
- new ValEntry( newDocEntry->GetDictEntry() ); //LEAK
- newValEntry->Copy( newDocEntry );
-
// When "set" is a Document, then we are at the top of the
// hierarchy and the Key is simply of the form ( group, elem )...
- if (Document* dummy = dynamic_cast< Document* > ( set ) )
+ if (Document *dummy = dynamic_cast< Document* > ( set ) )
{
(void)dummy;
newValEntry->SetKey( newValEntry->GetKey() );
// ...but when "set" is a SQItem, we are inserting this new
// valEntry in a sequence item. Hence the key has the
// generalized form (refer to \ref BaseTagKey):
- if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newValEntry->SetKey( parentSQItem->GetBaseTagKey()
+ newValEntry->GetKey() );
if( !set->AddEntry( newValEntry ) )
{
// If here expect big troubles
- delete newValEntry; //otherwise mem leak
+ //delete newValEntry; //otherwise mem leak
+ used=false;
}
if (delimitor)
{
- delete newDocEntry;
+ if(!used)
+ delete newDocEntry;
break;
}
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- delete newDocEntry;
+ if(!used)
+ delete newDocEntry;
break;
}
}
- else
- {
- if ( ! Global::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
- {
- ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- dbg.Verbose(0, "Document::ParseDES: neither Valentry, "
- "nor BinEntry. Probably unknown VR.");
- }
-
- //////////////////// BinEntry or UNKOWN VR:
- BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK
-
- // When "this" is a Document the Key is simply of the
- // form ( group, elem )...
- if (Document* dummy = dynamic_cast< Document* > ( set ) )
- {
- (void)dummy;
- newBinEntry->SetKey( newBinEntry->GetKey() );
- }
- // but when "this" is a SQItem, we are inserting this new
- // valEntry in a sequence item, and the kay has the
- // generalized form (refer to \ref BaseTagKey):
- if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) )
- {
- newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
- + newBinEntry->GetKey() );
- }
-
- LoadDocEntry( newBinEntry );
- if( !set->AddEntry( newBinEntry ) )
- {
- //Expect big troubles if here
- delete newBinEntry;
- }
- }
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();
+ long positionOnEntry = Fp->tellg();
Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
ComputeRLEInfo();
- Fp->seekg( PositionOnEntry, std::ios::beg );
+ Fp->seekg( positionOnEntry, std::ios::beg );
}
- else if ( IsJPEG() )
+ else if ( Global::GetTS()->IsJPEG(ts) )
{
- long PositionOnEntry = Fp->tellg();
+ long positionOnEntry = Fp->tellg();
Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
ComputeJPEGFragmentInfo();
- Fp->seekg( PositionOnEntry, std::ios::beg );
+ Fp->seekg( positionOnEntry, std::ios::beg );
}
}
-
+
// Just to make sure we are at the beginning of next entry.
SkipToNextDocEntry(newDocEntry);
- //delete newDocEntry;
}
else
{
}
}
// no other way to create it ...
- SeqEntry* newSeqEntry =
- new SeqEntry( newDocEntry->GetDictEntry() );
- newSeqEntry->Copy( newDocEntry );
newSeqEntry->SetDelimitorMode( delim_mode );
// At the top of the hierarchy, stands a Document. When "set"
// is a Document, then we are building the first depth level.
// Hence the SeqEntry we are building simply has a depth
// level of one:
- if (Document* dummy = dynamic_cast< Document* > ( set ) )
+ if (Document *dummy = dynamic_cast< Document* > ( set ) )
{
(void)dummy;
newSeqEntry->SetDepthLevel( 1 );
// But when "set" is allready a SQItem, we are building a nested
// sequence, and hence the depth level of the new SeqEntry
// we are building, is one level deeper:
- if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
set->AddEntry( newSeqEntry );
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- delete newDocEntry;
break;
}
}
- delete newDocEntry;
+
+ if(!used)
+ delete newDocEntry;
}
}
* \brief Parses a Sequence ( SeqEntry after SeqEntry)
* @return parsed length for this level
*/
-void Document::ParseSQ( SeqEntry* seqEntry,
+void Document::ParseSQ( SeqEntry *seqEntry,
long offset, long l_max, bool delim_mode)
{
int SQItemNumber = 0;
while (true)
{
- DocEntry* newDocEntry = ReadNextDocEntry();
+ DocEntry *newDocEntry = ReadNextDocEntry();
if ( !newDocEntry )
{
// FIXME Should warn user
* the value specified with Document::SetMaxSizeLoadEntry()
* @param entry Header Entry (Dicom Element) to be dealt with
*/
-void Document::LoadDocEntry(DocEntry* entry)
+void Document::LoadDocEntry(DocEntry *entry)
{
uint16_t group = entry->GetGroup();
std::string vr = entry->GetVR();
std::ostringstream s;
if (length > MaxSizeLoadEntry)
{
- if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) )
+ if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
{
//s << "gdcm::NotLoaded (BinEntry)";
s << GDCM_NOTLOADED;
binEntryPtr->SetValue(s.str());
}
// Be carefull : a BinEntry IS_A ValEntry ...
- else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) )
+ else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) )
{
// s << "gdcm::NotLoaded. (ValEntry)";
s << GDCM_NOTLOADED;
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 ...
}
// When we find a BinEntry not very much can be done :
- if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) )
+ if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
{
s << GDCM_BINLOADED;
binEntryPtr->SetValue(s.str());
LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
return;
}
-
+
/// \todo Any compacter code suggested (?)
if ( IsDocEntryAnInteger(entry) )
{
if( length % 2 )
{
newValue = Util::DicomString(str, length+1);
- //dbg.Verbose(0, "Warning: bad length: ", length );
- dbg.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);
+ //entry->SetReadLength(length+1);
}
else
{
}
delete[] str;
- if ( ValEntry* valEntry = dynamic_cast<ValEntry* >(entry) )
+ if ( ValEntry *valEntry = dynamic_cast<ValEntry* >(entry) )
{
- if ( Fp->fail() || Fp->eof())//Fp->gcount() == 1
+ if ( Fp->fail() || Fp->eof())
{
- dbg.Verbose(1, "Document::LoadDocEntry",
- "unread element value");
+ gdcmVerboseMacro("Unread element value");
valEntry->SetValue(GDCM_UNREAD);
return;
}
}
else
{
- dbg.Error(true, "Document::LoadDocEntry"
- "Should have a ValEntry, here !");
+ gdcmErrorMacro( "Should have a ValEntry, here !");
}
}
uint32_t lengthOB;
try
{
- /// \todo rename that to FindDocEntryLengthOBOrOW since
- /// the above test is on both OB and OW...
- lengthOB = FindDocEntryLengthOB();
+ lengthOB = FindDocEntryLengthOBOrOW();
}
catch ( FormatUnexpected )
{
// the length and proceed.
long currentPosition = Fp->tellg();
Fp->seekg(0L,std::ios::end);
+
long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
Fp->seekg(currentPosition, std::ios::beg);
+
+ entry->SetReadLength(lengthUntilEOF);
entry->SetLength(lengthUntilEOF);
return;
}
+ entry->SetReadLength(lengthOB);
entry->SetLength(lengthOB);
return;
}
// 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.
/**
* \brief Find the Value Representation of the current Dicom Element.
- * @param entry
+ * @return Value Representation of the current Entry
*/
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 Check the correspondance between the VR of the header entry
* and the taken VR. If they are different, the header entry is
* updated with the new VR.
- * @param entry Header Entry to check
* @param vr Dicom Value Representation
* @return false if the VR is incorrect of if the VR isn't referenced
* otherwise, it returns true
* @param entry Entry to reverse transform
* @return Reverse transformed entry value
*/
-std::string Document::GetDocEntryUnvalue(DocEntry* entry)
+std::string Document::GetDocEntryUnvalue(DocEntry *entry)
{
if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
/**
* \brief Skips to the begining of the next Header Entry
* \warning NOT end user intended method !
- * @param entry entry to skip
+ * @param currentDocEntry entry to skip
*/
-void Document::SkipToNextDocEntry(DocEntry *entry)
+void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
{
- Fp->seekg((long)(entry->GetOffset()), std::ios::beg);
- Fp->seekg( (long)(entry->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)
foundLength = 0;
}
- uint16_t gr = entry->GetGroup();
- uint16_t el = entry->GetElement();
+ uint16_t gr = entry->GetGroup();
+ uint16_t elem = entry->GetElement();
if ( foundLength % 2)
{
- std::ostringstream s;
- s << "Warning : Tag with uneven length "
- << foundLength
- << " in x(" << std::hex << gr << "," << el <<")" << std::dec;
- dbg.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)
{
// Only happens for this length !
- if ( entry->GetGroup() != 0x0008
- || ( entry->GetElement() != 0x0070
- && entry->GetElement() != 0x0080 ) )
+ if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) )
{
foundLength = 10;
entry->SetReadLength(10); /// \todo a bug is to be fixed !?
// 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 ( entry->GetGroup() == 0x0009
- && ( entry->GetElement() == 0x1113
- || entry->GetElement() == 0x1114 ) )
+ else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
{
foundLength = 4;
entry->SetReadLength(4); /// \todo a bug is to be fixed !?
//////// 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( entry->GetGroup() == 0xfffe )
+ 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
}
}
- entry->SetUsableLength(foundLength);
+ entry->SetLength(foundLength);
}
/**
*/
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();
+ 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;
- dbg.Verbose(0, "Document::IsDocEntryAnInteger", s.str().c_str() );
+ << "lgt : " << length );
}
}
* @return
*/
-uint32_t Document::FindDocEntryLengthOB()
+uint32_t Document::FindDocEntryLengthOBOrOW()
throw( FormatUnexpected )
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
}
catch ( FormatError )
{
- throw FormatError("Document::FindDocEntryLengthOB()",
- " 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 ) ) )
{
- dbg.Verbose(1, "Document::FindDocEntryLengthOB: 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::FindDocEntryLengthOB()",
- "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 )
{
- dbg.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;
- dbg.Verbose(1, "Document::CheckSwap:",
- "explicit Value Representation");
+ gdcmVerboseMacro( "Explicit Value Representation");
}
else
{
Filetype = ImplicitVR;
- dbg.Verbose(1, "Document::CheckSwap:",
- "not an explicit Value Representation");
+ gdcmVerboseMacro( "Not an explicit Value Representation");
}
if ( net2host )
{
SwapCode = 4321;
- dbg.Verbose(1, "Document::CheckSwap:",
- "HostByteOrder != NetworkByteOrder");
+ gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder");
}
else
{
- SwapCode = 0;
- dbg.Verbose(1, "Document::CheckSwap:",
- "HostByteOrder = NetworkByteOrder");
+ SwapCode = 1234;
+ 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).
- dbg.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;
case 0x00000004 :
- SwapCode = 0;
+ SwapCode = 1234;
Filetype = ACR;
return true;
default :
case 0x0006 :
case 0x0007 :
case 0x0008 :
- SwapCode = 0;
+ SwapCode = 1234;
Filetype = ACR;
return true;
case 0x0100 :
Filetype = ACR;
return true;
default :
- dbg.Verbose(0, "Document::CheckSwap:",
- "ACR/NEMA unfound swap info (Really hopeless !)");
+ gdcmVerboseMacro( "ACR/NEMA unfound swap info (Really hopeless !)");
Filetype = Unknown;
return false;
}
// Then the only info we have is the net2host one.
//if (! net2host )
- // SwapCode = 0;
+ // SwapCode = 1234;
//else
// SwapCode = 4321;
//return;
/**
- * \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()
{
- dbg.Verbose(1, "Document::SwitchSwapToBigEndian",
- "Switching to BigEndian mode.");
- if ( SwapCode == 0 )
+ gdcmVerboseMacro( "Switching Byte Swap code.");
+ if ( SwapCode == 1234 )
{
SwapCode = 4321;
}
else if ( SwapCode == 4321 )
{
- SwapCode = 0;
+ SwapCode = 1234;
}
else if ( SwapCode == 3412 )
{
* apparent reason
* @return no return
*/
-void Document::HandleBrokenEndian(uint16_t group, uint16_t elem)
+void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
{
// Endian reversion. Some files contain groups of tags with reversed endianess.
static int reversedEndian = 0;
{
// 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 Accesses the info from 0002,0010 : Transfer Syntax and TS
+ * else 1.
+ * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
+ */
+std::string Document::GetTransferSyntaxName()
+{
+ // use the TS (TS : Transfer Syntax)
+ std::string transferSyntax = GetEntry(0x0002,0x0010);
+
+ if ( transferSyntax == GDCM_NOTLOADED )
+ {
+ gdcmVerboseMacro( "Transfer Syntax not loaded. " << std::endl
+ << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" );
+ return "Uncompressed ACR-NEMA";
+ }
+ if ( transferSyntax == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Transfer Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
+ }
+
+ while ( ! isdigit((unsigned char)transferSyntax[transferSyntax.length()-1]) )
+ {
+ transferSyntax.erase(transferSyntax.length()-1, 1);
+ }
+ // we do it only when we need it
+ TS* ts = Global::GetTS();
+ std::string tsName = ts->GetValue( transferSyntax );
+
+ // Global::GetTS() is a global static you shall never try to delete it!
+ return tsName;
+}
+
+/**
+ * \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
+
+ std::string ts = GetTransferSyntaxName();
+ if ( !Global::GetTS()->IsTransferSyntax(ts) )
+ {
+ gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
+ return;
+ }
+
+ // FIXME Strangely, this works with
+ //'Implicit VR Transfer Syntax (GE Private)
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
+ {
+ 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.
*/
-DocEntry* Document::ReadNextDocEntry()
+DocEntry *Document::ReadNextDocEntry()
{
uint16_t group;
uint16_t elem;
return 0;
}
+ // Sometimes file contains groups of tags with reversed endianess.
HandleBrokenEndian(group, elem);
- std::string vr=FindDocEntryVR();
- DocEntry *newEntry = NewDocEntryByNumber(group, elem, vr);
+// 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 = GetDictEntry(group,elem);
+ if( dictEntry )
+ realVR = dictEntry->GetVR();
+ }
+
+ DocEntry *newEntry;
+ if( Global::GetVR()->IsVROfSequence(realVR) )
+ newEntry = NewSeqEntry(group, elem);
+ else if( Global::GetVR()->IsVROfStringRepresentable(realVR) )
+ newEntry = NewValEntry(group, elem,vr);
+ else
+ newEntry = NewBinEntry(group, elem,vr);
+
if( vr == GDCM_UNKNOWN )
{
if( Filetype == ExplicitVR )
std::string msg;
msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n",
newEntry->GetGroup(), newEntry->GetElement());
- dbg.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;
- dbg.Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:");
- dbg.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 << ")"
+ << " at address: " << " 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;
- dbg.Verbose(0, "Document::ReadItemTagLength: ", s.str().c_str());
+ gdcmVerboseMacro( "Basic Item Length is: "
+ << itemLength << std::endl
+ << " at address: " << std::hex << (unsigned int)currentPosition);
}
return itemLength;
}
// lengths, but we won't bother with such fuses for the time being.
if ( itemLength != 0 )
{
- char* basicOffsetTableItemValue = new char[itemLength + 1];
+ char *basicOffsetTableItemValue = new char[itemLength + 1];
Fp->read(basicOffsetTableItemValue, itemLength);
#ifdef GDCM_DEBUG
{
uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
uint32_t);
- std::ostringstream s;
- s << " Read one length: ";
- s << std::hex << individualLength << std::endl;
- dbg.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)
- dbg.Verbose(0, "Document::ComputeRLEInfo: too many segments.");
+ gdcmVerboseMacro( "Too many segments.");
}
uint32_t rleSegmentOffsetTable[16];
SkipBytes(rleSegmentLength[nbRleSegments]);
// Store the collected info
- RLEFrame* newFrameInfo = new RLEFrame;
+ RLEFrame *newFrameInfo = new RLEFrame;
newFrameInfo->NumberFragments = nbRleSegments;
for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
{
// Delimiter Item':
if ( !ReadTag(0xfffe, 0xe0dd) )
{
- dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
- dbg.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;
}
long fragmentOffset = Fp->tellg();
// Store the collected info
- JPEGFragment* newFragment = new JPEGFragment;
+ JPEGFragment *newFragment = new JPEGFragment;
newFragment->Offset = fragmentOffset;
newFragment->Length = fragmentLength;
JPEGInfo->Fragments.push_back( newFragment );
// Delimiter Item':
if ( !ReadTag(0xfffe, 0xe0dd) )
{
- dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
- dbg.Verbose(0, " item at end of JPEG item sequence");
+ gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence");
}
}
* when recursively walking the given set.
* @param set The structure to be traversed (recursively).
*/
-void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT,
- DocEntrySet* set )
+void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT,
+ DocEntrySet *set )
{
- if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) )
+ if (ElementSet *elementSet = dynamic_cast< ElementSet* > ( set ) )
{
- TagDocEntryHT const & currentHT = elementSet->GetTagHT();
+ TagDocEntryHT const ¤tHT = elementSet->GetTagHT();
for( TagDocEntryHT::const_iterator i = currentHT.begin();
i != currentHT.end();
++i)
{
- DocEntry* entry = i->second;
- if ( SeqEntry* seqEntry = dynamic_cast<SeqEntry*>(entry) )
+ DocEntry *entry = i->second;
+ if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
{
const ListSQItem& items = seqEntry->GetSQItems();
for( ListSQItem::const_iterator item = items.begin();
return;
}
- if (SQItem* SQItemSet = dynamic_cast< SQItem* > ( set ) )
+ if (SQItem *SQItemSet = dynamic_cast< SQItem* > ( set ) )
{
const ListDocEntry& currentList = SQItemSet->GetDocEntries();
for (ListDocEntry::const_iterator i = currentList.begin();
i != currentList.end();
++i)
{
- DocEntry* entry = *i;
- if ( SeqEntry* seqEntry = dynamic_cast<SeqEntry*>(entry) )
+ DocEntry *entry = *i;
+ if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
{
const ListSQItem& items = seqEntry->GetSQItems();
for( ListSQItem::const_iterator item = items.begin();
* \ref BuildFlatHashTable again...
* @return The flat std::map<> we juste build.
*/
-TagDocEntryHT* Document::BuildFlatHashTable()
+TagDocEntryHT *Document::BuildFlatHashTable()
{
- TagDocEntryHT* FlatHT = new TagDocEntryHT;
+ TagDocEntryHT *FlatHT = new TagDocEntryHT;
BuildFlatHashTableRecurse( *FlatHT, this );
return FlatHT;
}
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