Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/10/10 10:49:24 $
- Version: $Revision: 1.286 $
+ Date: $Date: 2008/09/15 15:49:22 $
+ Version: $Revision: 1.381 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
#include "gdcmDocument.h"
-#include "gdcmValEntry.h"
-#include "gdcmBinEntry.h"
#include "gdcmSeqEntry.h"
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDictSet.h"
#include "gdcmDocEntrySet.h"
#include "gdcmSQItem.h"
+#include "gdcmDataEntry.h"
#include <vector>
#include <iomanip>
#include <ctype.h> // for isdigit
#include <stdlib.h> // for atoi
-namespace gdcm
+#if defined(__BORLANDC__)
+ #include <mem.h> // for memset
+#endif
+
+namespace GDCM_NAME_SPACE
{
//-----------------------------------------------------------------------------
/**
* \brief This default constructor neither loads nor parses the file.
- * You should then invoke \ref Document::Load.
+ * You should then invoke Document::Load.
*
*/
Document::Document()
- :ElementSet(-1)
+ :ElementSet()
{
Fp = 0;
Initialize();
SwapCode = 1234;
Filetype = ExplicitVR;
+ CurrentOffsetPosition = 0;
+ OffsetOfPreviousParseDES =0;
// Load will set it to true if sucessfull
Group0002Parsed = false;
IsDocumentAlreadyLoaded = false;
IsDocumentModified = true;
LoadMode = LD_ALL; // default : load everything, later
+
SetFileName("");
+ changeFromUN=false;
+ UnexpectedEOF=false;
}
-/**
- * \brief Constructor (DEPRECATED : not to break the API)
- * @param fileName 'Document' (File or DicomDir) to be open for parsing
- */
-Document::Document( std::string const &fileName )
- :ElementSet(-1)
-{
- Fp = 0;
-
- SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialize();
- SwapCode = 1234;
- Filetype = ExplicitVR;
- Group0002Parsed = false;
- LoadMode = LD_ALL; // Load everything, later
-
- // Load will set it to true if sucessfull
- IsDocumentAlreadyLoaded = false;
- IsDocumentModified = true;
-
- SetFileName(fileName);
- Load( );
-}
/**
* \brief Canonical destructor.
*/
//-----------------------------------------------------------------------------
// Public
-
/**
* \brief Loader. use SetLoadMode(), SetFileName() before !
* @return false if file cannot be open or no swap info was found,
return false;
}
return DoTheLoadingDocumentJob( );
-}
+}
+
+
+//#ifndef GDCM_LEGACY_REMOVE
/**
* \brief Loader. (DEPRECATED : not to break the API)
* @param fileName 'Document' (File or DicomDir) to be open for parsing
* @return false if file cannot be open or no swap info was found,
* or no tag was found.
*/
+ /*
bool Document::Load( std::string const &fileName )
{
Filename = fileName;
return DoTheLoadingDocumentJob( );
}
+*/
+//#endif
/**
* \brief Performs the Loading Job (internal use only)
if ( ! IsDocumentModified ) // Nothing to do !
return true;
- // if ( Filename == fileName )
- // {
- // gdcmWarningMacro( "The file was already parsed inside this "
- // << "gdcm::Document (its name is: "
- // << Filename.c_str() );
- // return true;
- // }
-
- //gdcmWarningMacro( "A file was already parsed inside this "
- // << "gdcm::Document (previous name was: "
- // << Filename.c_str() << ". New name is :"
- // << fileName );
- // clean out the Entries, if already parsed
- // (probabely a mistake from the user)
-
ClearEntry();
Fp = 0;
if ( !OpenFile() )
{
// warning already performed in OpenFile()
- //gdcmWarningMacro( "Unable to open as an ACR/DICOM file: "
- // << Filename.c_str() );
Filetype = Unknown;
return false;
}
Group0002Parsed = false;
- gdcmWarningMacro( "Starting parsing of file: " << Filename.c_str());
+ gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str());
- Fp->seekg(0, std::ios::end);
- long lgt = Fp->tellg(); // total length of the file
-
- Fp->seekg(0, std::ios::beg);
+ // Computes the total length of the file
+ Fp->seekg(0, std::ios::end); // Once per Document !
+ long lgt = Fp->tellg(); // Once per Document !
+ Fp->seekg(0, std::ios::beg); // Once per Document !
// CheckSwap returns a boolean
// (false if no swap info of any kind was found)
// Recursive call.
// Loading is done during parsing
+ OffsetOfPreviousParseDES = beg;
ParseDES( this, beg, lgt, false); // delim_mode is first defaulted to false
if ( IsEmpty() )
{
- gdcmWarningMacro( "No tag in internal hash table for: "
+ gdcmErrorMacro( "No tag in internal hash table for: "
<< Filename.c_str());
CloseFile();
return false;
}
IsDocumentAlreadyLoaded = true;
- Fp->seekg( 0, std::ios::beg);
+ //Fp->seekg(0, std::ios::beg); // Once per Document!
// Load 'non string' values
- std::string PhotometricInterpretation = GetEntryValue(0x0028,0x0004);
+ std::string PhotometricInterpretation = GetEntryString(0x0028,0x0004);
if ( PhotometricInterpretation == "PALETTE COLOR " )
{
// FIXME
LoadEntryBinArea(0x0028,0x1200); // gray LUT
/// FIXME
+ /// --> FIXME : The difference between BinEntry and DataEntry
+ /// --> no longer exists, but the alteration of Dicom Dictionary remains.
+ /// --> Old comment restored on purpose.
+ /// --> New one (replacing both BinEntry and ValEntry by DataEntry)
+ /// --> had absolutely no meaning.
+ /// --> The whole comment will be removed when the stuff is cleaned !
+ /// -->
/// The tags refered by the three following lines used to be CORRECTLY
/// defined as having an US Value Representation in the public
/// dictionary. BUT the semantics implied by the three following
/// In order to fix things "Quick and Dirty" the dictionary was
/// altered on PURPOSE but now contains a WRONG value.
/// In order to fix things and restore the dictionary to its
- /// correct value, one needs to decided of the semantics by deciding
+ /// correct value, one needs to decide of the semantics by deciding
/// whether the following tags are either :
/// - multivaluated US, and hence loaded as ValEntry, but afterwards
/// also used as BinEntry, which requires the proper conversion,
/// - OW, and hence loaded as BinEntry, but afterwards also used
/// as ValEntry, which requires the proper conversion.
+
+ // --> OB (byte aray) or OW (short int aray)
+ // The actual VR has to be deduced from other entries.
+ // Our way of loading them may fail in some cases :
+ // We must or not SwapByte depending on other field values.
+
LoadEntryBinArea(0x0028,0x1201); // R LUT
LoadEntryBinArea(0x0028,0x1202); // G LUT
LoadEntryBinArea(0x0028,0x1203); // B LUT
}
//FIXME later : how to use it?
- SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000);
+ SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000); // Modality LUT Sequence
if ( modLutSeq !=0 )
{
SQItem *sqi= modLutSeq->GetFirstSQItem();
if ( sqi != 0 )
{
- BinEntry *b = sqi->GetBinEntry(0x0028,0x3006);
- if ( b != 0 )
+ DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006); // LUT Data
+ if ( dataEntry != 0 )
{
- if ( b->GetLength() != 0 )
+ if ( dataEntry->GetLength() != 0 )
{
- LoadEntryBinArea(b); //LUT Data (CTX dependent)
+ // FIXME : CTX dependent means : contexted dependant.
+ // see upper comment.
+ LoadEntryBinArea(dataEntry); //LUT Data (CTX dependent)
}
}
}
// Force Loading some more elements if user asked to.
- gdcm::DocEntry *d;
+ GDCM_NAME_SPACE::DocEntry *d;
for (ListElements::iterator it = UserForceLoadList.begin();
it != UserForceLoadList.end();
++it)
{
- gdcmWarningMacro( "Force Load " << std::hex
+ gdcmDebugMacro( "Force Load " << std::hex
<< (*it).Group << "|" <<(*it).Elem );
d = GetDocEntry( (*it).Group, (*it).Elem);
if ( d == NULL)
{
- gdcmWarningMacro( "You asked toForce Load " << std::hex
+ gdcmWarningMacro( "You asked to ForceLoad " << std::hex
<< (*it).Group <<"|"<< (*it).Elem
<< " that doesn't exist" );
continue;
}
- if ( dynamic_cast<ValEntry *>(d) )
- {
- LoadDocEntry(d, true);
- continue;
- }
-
- BinEntry *b = dynamic_cast<BinEntry *>(d);
- if ( b )
- {
- LoadEntryBinArea(b);
- b->SetValue(GDCM_BINLOADED);
- continue;
- }
-
- if ( dynamic_cast<SeqEntry *>(d) )
- {
- gdcmWarningMacro( "You cannot 'ForceLoad' a SeqEntry :" << std::hex
- << (*it).Group <<"|"<< (*it).Elem );
- continue;
- }
+ LoadDocEntry(d, true);
}
- CloseFile();
+ CloseFile();
// ----------------------------
// Specific code to allow gdcm to read ACR-LibIDO formated images
// we switch lineNumber and columnNumber
//
std::string RecCode;
- RecCode = GetEntryValue(0x0008, 0x0010); // recognition code (RET)
- if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
- RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
- // with "little-endian strings"
+ 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"
{
+
Filetype = ACR_LIBIDO;
- std::string rows = GetEntryValue(0x0028, 0x0010);
- std::string columns = GetEntryValue(0x0028, 0x0011);
- SetValEntry(columns, 0x0028, 0x0010);
- SetValEntry(rows , 0x0028, 0x0011);
+ std::string rows = GetEntryString(0x0028, 0x0010);
+ std::string columns = GetEntryString(0x0028, 0x0011);
+ SetEntryString(columns, 0x0028, 0x0010);
+ SetEntryString(rows , 0x0028, 0x0011);
}
// --- End of ACR-LibIDO kludge ---
return true;
*/
void Document::AddForceLoadElement (uint16_t group, uint16_t elem)
{
- Element el;
+ DicomElement el;
el.Group = group;
el.Elem = elem;
UserForceLoadList.push_back(el);
* @return false when we're 150 % sure it's NOT a Dicom/Acr file,
* true otherwise.
*/
-bool Document::IsReadable()
+bool Document::IsParsable()
{
if ( Filetype == Unknown )
{
- gdcmWarningMacro( "Wrong filetype");
+ gdcmWarningMacro( "Wrong filetype for " << GetFileName());
return false;
}
return true;
}
+/**
+ * \brief This predicate tells us whether or not the current Document
+ * was properly parsed and contains at least *one* Dicom Element
+ * (and nothing more, sorry).
+ * @return false when we're 150 % sure it's NOT a Dicom/Acr file,
+ * true otherwise.
+ */
+bool Document::IsReadable()
+{
+ return IsParsable();
+}
/**
* \brief Predicate for dicom version 3 file.
* \brief Accessor to the Transfer Syntax (when present) of the
* current document (it internally handles reading the
* value from disk when only parsing occured).
- * @return The encountered Transfer Syntax of the current document.
+ * @return The encountered Transfer Syntax of the current document, if DICOM.
+ * GDCM_UNKNOWN for ACR-NEMA files (or broken headers ...)
*/
std::string Document::GetTransferSyntax()
{
// 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) )
+
+ // Well ...
+ // (parsing and loading happen at the very same stage!)
+ //LoadDocEntrySafe(entry); //JPRx
+ if (DataEntry *dataEntry = dynamic_cast<DataEntry *>(entry) )
{
- std::string transfer = valEntry->GetValue();
+ std::string transfer = dataEntry->GetString();
// The actual transfer (as read from disk) might be padded. We
// first need to remove the potential padding. We can make the
// weak assumption that padding was not executed with digits...
if ( transfer.length() == 0 )
{
// for brain damaged headers
+ gdcmWarningMacro( "Transfer Syntax has length = 0.");
return GDCM_UNKNOWN;
}
while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
{
transfer.erase(transfer.length()-1, 1);
+ if ( transfer.length() == 0 )
+ {
+ // for brain damaged headers
+ gdcmWarningMacro( "Transfer Syntax contains no valid character.");
+ return GDCM_UNKNOWN;
+ }
}
return transfer;
}
std::string Document::GetTransferSyntaxName()
{
// use the TS (TS : Transfer Syntax)
- std::string transferSyntax = GetEntryValue(0x0002,0x0010);
+ std::string transferSyntax = GetEntryString(0x0002,0x0010);
if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) )
{
}
if ( transferSyntax == GDCM_UNFOUND )
{
- gdcmWarningMacro( "Unfound Transfer Syntax (0002,0010)");
+ gdcmDebugMacro( "Unfound Transfer Syntax (0002,0010)");
return "Uncompressed ACR-NEMA";
}
a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
break;
default :
- gdcmErrorMacro( "Unset swap code:" << SwapCode );
+ gdcmErrorMacro( "Unexpected swap code:" << SwapCode );
a = 0;
}
return a;
}
+/**
+ * \brief Swaps back the bytes of 8-byte long 'double' accordingly to
+ * processor order.
+ * @return The properly swaped 64 bits double.
+ */
+double Document::SwapDouble(double a)
+{
+ switch (SwapCode)
+ {
+ // There were no 'double' at ACR-NEMA time.
+ // We just have to deal with 'straight Little Endian' and
+ // 'straight Big Endian'
+ case 1234 :
+ break;
+ case 4321 :
+ {
+ char *beg = (char *)&a;
+ char *end = beg + 7;
+ char t;
+ for (unsigned int i = 0; i<7; i++)
+ {
+ t = *beg;
+ *beg = *end;
+ *end = t;
+ beg++,
+ end--;
+ }
+ }
+ break;
+ default :
+ gdcmErrorMacro( "Unexpected swap code:" << SwapCode );
+ a = 0.;
+ }
+ return a;
+}
+
//
// -----------------File I/O ---------------
/**
- * \brief Tries to open the file \ref Document::Filename and
- * checks the preamble when existing.
- * @return The FILE pointer on success.
+ * \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.
*/
std::ifstream *Document::OpenFile()
{
if ( Fp )
{
- gdcmWarningMacro( "File already open: " << Filename.c_str());
+ gdcmDebugMacro( "File already open: " << Filename.c_str());
CloseFile();
}
// 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
+ // --> the constructor is not so good ...
+
gdcmWarningMacro( "Cannot open file: " << Filename.c_str());
delete Fp;
Fp = 0;
return 0;
}
- //-- ACR or DICOM with no Preamble; may start with a Shadow Group --
- 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 )
- {
- std::string msg = Util::Format(
- "ACR/DICOM starting at the beginning of the file:(%04x)\n", zero);
- gdcmWarningMacro( msg.c_str() );
- return Fp;
- }
-
//-- DICOM --
- Fp->seekg(126L, std::ios::cur);
+ Fp->seekg(126L, std::ios::cur); // Once per Document
char dicm[4]; // = {' ',' ',' ',' '};
Fp->read(dicm, (size_t)4);
if ( Fp->eof() )
CloseFile();
return 0;
}
+
if ( memcmp(dicm, "DICM", 4) == 0 )
{
HasDCMPreamble = true;
return Fp;
}
+ //-- 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 (
+ 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 ?!?
+ )
+ {
+ std::string msg = Util::Format(
+ "ACR/DICOM starting by 0x(%04x) at the beginning of the file\n", zero);
+ // FIXME : is it a Warning message, or a Debug message?
+ gdcmWarningMacro( msg.c_str() );
+ return Fp;
+ }
+
// -- Neither ACR/No Preamble Dicom nor DICOMV3 file
CloseFile();
- gdcmWarningMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
+ // 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());
return 0;
}
* @param filetype Type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
*/
-void Document::WriteContent(std::ofstream *fp, FileType filetype)
+void Document::WriteContent(std::ofstream *fp, FileType filetype, bool, bool)
{
// Skip if user wants to write an ACR-NEMA file
- if ( filetype == ImplicitVR || filetype == ExplicitVR )
+ if ( filetype == ImplicitVR || filetype == ExplicitVR ||
+ filetype == JPEG || filetype == JPEG2000 )
{
// writing Dicom File Preamble
char filePreamble[128];
fp->write(filePreamble, 128);
fp->write("DICM", 4);
}
-
/*
* \todo rewrite later, if really usefull
* - 'Group Length' element is optional in DICOM
* UpdateGroupLength(false,filetype);
* if ( filetype == ACR)
* UpdateGroupLength(true,ACR);
+ *
+ * --> Computing group length for groups with embeded Sequences
+ * --> was too much tricky / we were [in a hurry / too lazy]
+ * --> We don't write the element 0x0000 (group length)
*/
-
- ElementSet::WriteContent(fp, filetype); // This one is recursive
+ // This one is recursive
+ // false : outside MetaElements
+ // false : outside Sequence
+ ElementSet::WriteContent(fp, filetype, false, false);
}
// -----------------------------------------
void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
// Search the corresponding DocEntry
- DocEntry *docElement = GetDocEntry(group, elem);
- if ( !docElement )
+ DocEntry *docEntry = GetDocEntry(group, elem);
+ if ( !docEntry )
{
- gdcmWarningMacro(std::hex << group << "|" << elem
- << "doesn't exist" );
+ gdcmDebugMacro(std::hex << group << "|" << elem
+ << " doesn't exist" );
return;
}
- BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
- if ( !binElement )
+ DataEntry *dataEntry = dynamic_cast<DataEntry *>(docEntry);
+ if ( !dataEntry )
{
gdcmWarningMacro(std::hex << group << "|" << elem
- << "is NOT a BinEntry");
+ << " is NOT a DataEntry");
return;
}
- LoadEntryBinArea(binElement);
+ LoadEntryBinArea(dataEntry);
}
/**
* \brief Loads (from disk) the element content
* when a string is not suitable
- * @param elem Entry whose binArea is going to be loaded
+ * @param entry Entry whose binArea is going to be loaded
*/
-void Document::LoadEntryBinArea(BinEntry *elem)
-{
- if (elem->GetBinArea() )
+void Document::LoadEntryBinArea(DataEntry *entry)
+{
+ if( entry->GetBinArea() )
return;
bool openFile = !Fp;
if ( openFile )
OpenFile();
- size_t o =(size_t)elem->GetOffset();
- Fp->seekg(o, std::ios::beg);
+ //size_t o =(size_t)entry->GetOffset();
+ Fp->seekg((size_t)entry->GetOffset(), std::ios::beg); // FIXME : for each DataEntry !
- size_t l = elem->GetLength();
- uint8_t *a = new uint8_t[l];
- if ( !a )
+ size_t l = entry->GetLength();
+ uint8_t *data = new uint8_t[l];
+ if ( !data )
{
- gdcmWarningMacro( "Cannot allocate BinEntry content for : "
- << std::hex << elem->GetGroup()
- << "|" << elem->GetElement() );
+ gdcmWarningMacro( "Cannot allocate DataEntry content for : "
+ << std::hex << entry->GetGroup()
+ << "|" << entry->GetElement() );
return;
}
- Fp->read((char*)a, l);
+ // Read the data
+ Fp->read((char*)data, l);
if ( Fp->fail() || Fp->eof() )
{
- delete[] a;
+ delete[] data;
+ entry->SetState(DataEntry::STATE_UNREAD);
return;
}
- elem->SetBinArea(a);
+ // Swap the data content if necessary
+ uint32_t i;
+ unsigned short vrLgth =
+ Global::GetVR()->GetAtomicElementLength(entry->GetVR());
- if ( openFile )
+// FIXME : trouble expected if we read an ... OW Entry (LUT, etc ..)
+// if( entry->GetVR() == "OW" )
+// vrLgth = 1;
+
+ switch(vrLgth)
+ {
+ case 1:
+ {
+ break;
+ }
+ case 2:
+ {
+ uint16_t *data16 = (uint16_t *)data;
+ for(i=0;i<l/vrLgth;i++)
+ data16[i] = SwapShort(data16[i]);
+ break;
+ }
+ case 4:
+ {
+ uint32_t *data32 = (uint32_t *)data;
+ for(i=0;i<l/vrLgth;i++)
+ data32[i] = SwapLong(data32[i]);
+ break;
+ }
+ case 8:
+ {
+ double *data64 = (double *)data;
+ for(i=0;i<l/vrLgth;i++)
+ data64[i] = SwapDouble(data64[i]);
+ break;
+ }
+ }
+
+ entry->SetBinArea(data);
+
+ if ( openFile ) // The file is left in the state (open/close) it was at entrance
CloseFile();
}
/**
* \brief Loads the element while preserving the current
* underlying file position indicator as opposed to
- * LoadDocEntry that modifies it.
+ * LoadDocEntry that modifies it
+ * \note seems to be unused!.
* @param entry DocEntry whose value will be loaded.
*/
-void Document::LoadDocEntrySafe(DocEntry *entry)
-{
- if ( Fp )
- {
- long PositionOnEntry = Fp->tellg();
- LoadDocEntry(entry);
- Fp->seekg(PositionOnEntry, std::ios::beg);
- }
-}
+//void Document::LoadDocEntrySafe(DocEntry *entry)
+//{
+// if ( Fp )
+// {
+// long PositionOnEntry = Fp->tellg(); // LoadDocEntrySafe is not used
+// LoadDocEntry(entry);
+// Fp->seekg(PositionOnEntry, std::ios::beg); // LoadDocEntrySafe is not used
+// }
+//}
/**
- * \brief Compares two documents, according to \ref DicomDir rules
+ * \brief Compares two documents, according to DicomDir rules
* \warning Does NOT work with ACR-NEMA files
* \todo Find a trick to solve the pb (use RET fields ?)
* @param document to compare with current one
bool Document::operator<(Document &document)
{
// Patient Name
- std::string s1 = GetEntryValue(0x0010,0x0010);
- std::string s2 = document.GetEntryValue(0x0010,0x0010);
+ std::string s1 = GetEntryString(0x0010,0x0010);
+ std::string s2 = document.GetEntryString(0x0010,0x0010);
if (s1 < s2)
{
return true;
else
{
// Patient ID
- s1 = GetEntryValue(0x0010,0x0020);
- s2 = document.GetEntryValue(0x0010,0x0020);
+ s1 = GetEntryString(0x0010,0x0020);
+ s2 = document.GetEntryString(0x0010,0x0020);
if ( s1 < s2 )
{
return true;
else
{
// Study Instance UID
- s1 = GetEntryValue(0x0020,0x000d);
- s2 = document.GetEntryValue(0x0020,0x000d);
+ s1 = GetEntryString(0x0020,0x000d);
+ s2 = document.GetEntryString(0x0020,0x000d);
if ( s1 < s2 )
{
return true;
else
{
// Serie Instance UID
- s1 = GetEntryValue(0x0020,0x000e);
- s2 = document.GetEntryValue(0x0020,0x000e);
+ s1 = GetEntryString(0x0020,0x000e);
+ s2 = document.GetEntryString(0x0020,0x000e);
if ( s1 < s2 )
{
return true;
//-----------------------------------------------------------------------------
// Protected
+
+/**
+ * \brief Reads a given length of bytes
+ * (in order to avoid to many CPU time-consuming fread-s)
+ * @param l length to read
+ */
+void Document::ReadBegBuffer(size_t l)
+ throw( FormatError )
+{
+ Fp->read (BegBuffer, (size_t)l);
+ if ( Fp->fail() )
+ {
+ throw FormatError( "Document::ReadBegBuffer()", " file error." );
+ }
+ if ( Fp->eof() )
+ {
+ throw FormatError( "Document::ReadBegBuffer()", "EOF." );
+ }
+ PtrBegBuffer = BegBuffer;
+ CurrentOffsetPosition+=l;
+}
/**
* \brief Reads a supposed to be 16 Bits integer
* (swaps it depending on processor endianness)
return g;
}
+/**
+ * \brief Gets from BegBuffer a supposed to be 16 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
+ */
+uint16_t Document::GetInt16()
+{
+ uint16_t g = *((uint16_t*)PtrBegBuffer);
+ g = SwapShort(g);
+ PtrBegBuffer+=2;
+ return g;
+}
/**
* \brief Reads a supposed to be 32 Bits integer
* (swaps it depending on processor endianness)
}
/**
- * \brief skips bytes inside the source file
- * \warning NOT end user intended method !
- * @return
+ * \brief Gets from BegBuffer a supposed to be 32 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
*/
-void Document::SkipBytes(uint32_t nBytes)
+uint32_t Document::GetInt32()
{
- //FIXME don't dump the returned value
- Fp->seekg((long)nBytes, std::ios::cur);
+ uint32_t g = *((uint32_t*)PtrBegBuffer);
+ g = SwapLong(g);
+ PtrBegBuffer+=4;
+ return g;
}
/**
- * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
+ * \brief Re-computes the length of the Dicom group 0002.
*/
-int Document::ComputeGroup0002Length( /*FileType filetype*/ )
+int Document::ComputeGroup0002Length( )
{
uint16_t gr;
- std::string vr;
+ VRKey vr;
int groupLength = 0;
bool found0002 = false;
{
vr = entry->GetVR();
- // FIXME : group 0x0002 is *always* Explicit VR!
-
- //if ( filetype == ExplicitVR )
- //{
- // if ( (vr == "OB") || (vr == "OW") || (vr == "UT") || (vr == "SQ") )
- // (no SQ, OW, UT in group 0x0002;)
+ //if ( (vr == "OB")||(vr == "OW")||(vr == "UT")||(vr == "SQ"))
+ // (no SQ, OW, OL, UT in group 0x0002;)
if ( vr == "OB" )
{
- // explicit VR AND OB, OW, SQ, UT : 4 more bytes
+ // explicit VR AND (OB, OW, OL, SQ, UT, UN) : 4 more bytes
groupLength += 4;
}
- //}
groupLength += 2 + 2 + 4 + entry->GetLength();
}
}
return groupLength;
}
+/**
+ * \brief CallStartMethod
+ */
+void Document::CallStartMethod()
+{
+ Progress = 0.0f;
+ Abort = false;
+ CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
+}
+
+/**
+ * \brief CallProgressMethod
+ */
+void Document::CallProgressMethod()
+{
+ CommandManager::ExecuteCommand(this,CMD_PROGRESS);
+}
+
+/**
+ * \brief CallEndMethod
+ */
+void Document::CallEndMethod()
+{
+ Progress = 1.0f;
+ CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
+}
+
//-----------------------------------------------------------------------------
// Private
/**
* \brief Loads all the needed Dictionaries
- * \warning NOT end user intended method !
+ * \warning NOT end user intended method !
*/
void Document::Initialize()
{
long l_max, bool delim_mode)
{
DocEntry *newDocEntry;
- ValEntry *newValEntry;
- BinEntry *newBinEntry;
+ DataEntry *newDataEntry;
SeqEntry *newSeqEntry;
- VRKey vr;
+ //VRKey vr;
bool used; // will be set to false when something wrong happens to an Entry.
// (Entry will then be deleted)
bool delim_mode_intern = delim_mode;
bool first = true;
- gdcmWarningMacro( "Enter in ParseDES, delim-mode " << delim_mode
- << " at offset " << std::hex << offset );
+ gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode
+ << " at offset " << std::hex << "0x(" << offset << ")" );
while (true)
{
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
- {
- break;
- }
-
- newDocEntry = ReadNextDocEntry( );
-
- // FIXME :
- // Private tag, in IMplicit VR are defaulted as a BinEntry,
- // Very often they are only composed of Printable characters,
- // and could be defaulted as a ValEntry.
- // It's too late to do the Job
- // (we should check the value, but we know it after LoadDocEntry ...)
- // --> in next gdcm major release let's unify ValEntry and BinEntry !
+
+ ///\todo FIXME : On 64 bits processors, tellg gives unexpected results after a while ?
+ /// Probabely a bug in gdcm code somewhere (some memory erased ?)
- // Uncoment this printf line to be able to 'follow' the DocEntries
- // when something *very* strange happens
+// Uncomment to track the bug
+
+ if( Debug::GetDebugFlag() )
+ std::cout << std::dec <<"(long)(Fp->tellg()) " << (long)(Fp->tellg()) // in Debug mode
+ << std::hex << " 0x(" <<(long)(Fp->tellg()) << ")" << std::endl;
+
+
+ // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry
+ if ( !delim_mode ) // 'and then' doesn't exist in C++ :-(
+ if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry, when no delim mode
+ {
+ break;
+ }
- //printf( "%04x|%04x %s\n",newDocEntry->GetGroup(),
- // newDocEntry->GetElement(),
- // newDocEntry->GetVR().c_str() );
+ newDocEntry = ReadNextDocEntry( );
if ( !newDocEntry )
{
break;
}
+
+ // Uncoment this cerr line to be able to 'follow' the DocEntries
+ // when something *very* strange happens
+ if( Debug::GetDebugFlag() )
+ std::cerr<<newDocEntry->GetKey()<<" "<<newDocEntry->GetVR()<<std::endl;
- // an Item Starter found elsewhere but the first position
- // of a SeqEntry means previous entry was a Sequence
+ // an Item Starter found elsewhere but in the first position
+ // of a SeqEntry means previous entry was a Sequence
// but we didn't get it (private Sequence + Implicit VR)
// we have to backtrack.
if ( !first && newDocEntry->IsItemStarter() )
{
- newDocEntry = Backtrack(newDocEntry);
+ // Debug message within the method !
+ newDocEntry = Backtrack(newDocEntry, set);
}
else
{
}
used = true;
- newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
- newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
+ newDataEntry = dynamic_cast<DataEntry*>(newDocEntry);
- if ( newValEntry || newBinEntry )
+ if ( newDataEntry )
{
- //////////////////////////// ContentEntry
- if ( newBinEntry )
- {
- vr = newDocEntry->GetVR();
- if ( Filetype == ExplicitVR &&
- !Global::GetVR()->IsVROfBinaryRepresentable(vr) )
- {
- ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- gdcmWarningMacro( std::hex << newDocEntry->GetGroup()
- << "|" << newDocEntry->GetElement()
- << " : Neither Valentry, nor BinEntry."
- "Probably unknown VR.");
- }
+ //////////////////////////// DataEntry
+
+ //vr = newDocEntry->GetVR(); // useless ?
- //////////////////// BinEntry or UNKOWN VR:
-
- // When "this" is a Document the Key is simply of the
- // form ( group, elem )...
- //if ( set == this ) // ( dynamic_cast< Document* > ( set ) )
- //{
- // newBinEntry->SetKey( newBinEntry->GetKey() );
- //}
- // but when "this" is a SQItem, we are inserting this new
- // valEntry in a sequence item, and the key has the
- // generalized form (refer to \ref BaseTagKey):
-
- // time waste hunting
- //if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
- //{
- // newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
- // + newBinEntry->GetKey() );
- //}
-
- if ( !set->AddEntry( newBinEntry ) )
- {
- gdcmWarningMacro( "in ParseDES : cannot add a BinEntry "
- << newBinEntry->GetKey()
- << " (at offset : "
- << newBinEntry->GetOffset() << " )" );
- used=false;
- }
- else
- {
- // Load only if we can add (not a duplicate key)
- LoadDocEntry( newBinEntry );
- }
- } // end BinEntry
+ if ( !set->AddEntry( newDataEntry ) )
+ {
+ gdcmDebugMacro( "in ParseDES : cannot add a DataEntry "
+ << newDataEntry->GetKey()
+ << " (at offset : 0x("
+ << newDataEntry->GetOffset() << ") )" );
+ used=false;
+ }
else
{
- /////////////////////// ValEntry
-
- // 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 ( set == this ) // ( dynamic_cast< Document* > ( set ) )
- //{
- // 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):
-
- // time waste hunting
- //if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
- //{
- // newValEntry->SetKey( parentSQItem->GetBaseTagKey()
- // + newValEntry->GetKey() );
- //}
-
- if ( !set->AddEntry( newValEntry ) )
- {
- gdcmWarningMacro( "in ParseDES : cannot add a ValEntry "
- << newValEntry->GetKey()
- << " (at offset : "
- << newValEntry->GetOffset() << " )" );
- used=false;
- }
- else
- {
- // Load only if we can add (not a duplicate key)
- LoadDocEntry( newValEntry );
- }
-
- if ( newValEntry->GetElement() == 0x0000 ) // if on group length
+ newDataEntry->Delete();
+ // Load only if we can add (not a duplicate key)
+ LoadDocEntry( newDataEntry );
+ }
+ if ( newDataEntry->GetElement() == 0x0000 ) // if on group length
+ {
+ if ( newDataEntry->GetGroup()%2 != 0 ) // if Shadow Group
{
- if ( newValEntry->GetGroup()%2 != 0 ) // if Shadow Group
+ if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
{
- if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
+ std::string strLgrGroup = newDataEntry->GetString();
+
+ int lgrGroup;
+ //if ( newDataEntry->IsUnfound() ) /?!? JPR
{
- std::string strLgrGroup = newValEntry->GetValue();
- int lgrGroup;
- if ( strLgrGroup != GDCM_UNFOUND)
- {
- lgrGroup = atoi(strLgrGroup.c_str());
- Fp->seekg(lgrGroup, std::ios::cur);
- //used = false; // never used
- RemoveEntry( newDocEntry ); // Remove and delete
- // bcc 5.5 is right "assigned a value that's never used"
- // newDocEntry = 0;
- continue;
- }
+ lgrGroup = atoi(strLgrGroup.c_str());
+ Fp->seekg(lgrGroup, std::ios::cur); // Once per Shadow group, when NOSHADOW
+ RemoveEntry( newDocEntry ); // Remove and delete
+ continue;
}
}
}
+ }
- bool delimitor = newValEntry->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
+ outOfBounds = true;
- if ( (delimitor) ||
- (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) )
- {
- if ( !used )
- delete newDocEntry;
- break;
- }
+ // 'and then', 'or else' don't exist in C++ :-(
+ // if ( (delimitor) ||
+ // (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) // Once per DataEntry
+
+ if ( delimitor || outOfBounds )
+ {
+ if ( !used )
+ newDocEntry->Delete();
+ break;
}
// Just to make sure we are at the beginning of next entry.
- SkipToNextDocEntry(newDocEntry);
+ SkipToNextDocEntry(newDocEntry); // FIXME : once per DocEntry, segfault if commented out
}
else
{
/////////////////////// SeqEntry : VR = "SQ"
- unsigned long l = newDocEntry->GetReadLength();
+ unsigned long l = newDocEntry->GetReadLength();
if ( l != 0 ) // don't mess the delim_mode for 'zero-length sequence'
{
if ( l == 0xffffffff )
// User asked to skip SeQuences *only* if they belong to Shadow Group
if ( newDocEntry->GetGroup()%2 != 0 )
{
- Fp->seekg( l, std::ios::cur);
- RemoveEntry( newDocEntry ); // Remove and delete
- //used = false; // never used
+ Fp->seekg( l, std::ios::cur); // once per SQITEM, when NOSHADOWSEQ
+ newDocEntry->Delete(); // Delete, not in the set
continue;
}
}
if ( (LoadMode & LD_NOSEQ) && ! delim_mode_intern )
{
// User asked to skip *any* SeQuence
- Fp->seekg( l, std::ios::cur);
- //used = false; // never used
- RemoveEntry( newDocEntry ); // Remove and delete
+ Fp->seekg( l, std::ios::cur); // Once per SQ, when NOSEQ
+ newDocEntry->Delete(); // Delete, not in the set
continue;
}
// delay the dynamic cast as late as possible
// is a Document, then we are building the first depth level.
// Hence the SeqEntry we are building simply has a depth
// level of one:
-// SQItem *parentSQItem = dynamic_cast< SQItem* > ( set );
if ( set == this ) // ( dynamic_cast< Document* > ( set ) )
{
newSeqEntry->SetDepthLevel( 1 );
- // newSeqEntry->SetKey( newSeqEntry->GetKey() );
}
// But when "set" is already a SQItem, we are building a nested
// sequence, and hence the depth level of the new SeqEntry
else if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
-
- // newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
- // + newSeqEntry->GetKey() );
}
if ( l != 0 )
{ // Don't try to parse zero-length sequences
- gdcmWarningMacro( "Entry in ParseSQ, delim " << delim_mode_intern
- << " at offset " << std::hex
- << newDocEntry->GetOffset() );
+ gdcmDebugMacro( "Entry in ParseSQ, delim " << delim_mode_intern
+ << " at offset 0x(" << std::hex
+ << newDocEntry->GetOffset() << ")");
- ParseSQ( newSeqEntry,
- newDocEntry->GetOffset(),
- l, delim_mode_intern);
+ bool res = ParseSQ( newSeqEntry,
+ newDocEntry->GetOffset(),
+ l, delim_mode_intern);
- gdcmWarningMacro( "Exit from ParseSQ, delim " << delim_mode_intern);
-
+ gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern << " -->return : " << res);
}
if ( !set->AddEntry( newSeqEntry ) )
{
gdcmWarningMacro( "in ParseDES : cannot add a SeqEntry "
<< newSeqEntry->GetKey()
- << " (at offset : "
- << newSeqEntry->GetOffset() << " )" );
+ << " (at offset : 0x("
+ << newSeqEntry->GetOffset() << ") )" );
used = false;
}
+ else
+ {
+ newDocEntry->Delete();
+ }
+
+ // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ 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 )
- delete newDocEntry;
- break;
+ newDocEntry->Delete();
+ break;
}
} // end SeqEntry : VR = "SQ"
if ( !used )
{
- delete newDocEntry;
+ newDocEntry->Delete();
}
first = false;
+
+ if (UnexpectedEOF) // some terminator was missing
+ {
+ break;
+ }
} // end While
- gdcmWarningMacro( "Exit from ParseDES, delim-mode " << delim_mode );
+ gdcmDebugMacro( "Exit from ParseDES, delim-mode " << delim_mode );
}
/**
* \brief Parses a Sequence ( SeqEntry after SeqEntry)
- * @return parsed length for this level
+ * @return false if expected fff0,e000 not found
*/
-void Document::ParseSQ( SeqEntry *seqEntry,
+bool Document::ParseSQ( SeqEntry *seqEntry,
long offset, long l_max, bool delim_mode)
{
int SQItemNumber = 0;
DocEntry *newDocEntry = ReadNextDocEntry();
if ( !newDocEntry )
- {
- // FIXME Should warn user
+ {
+ // The most frequent is when a SQ terminator is missing (?!?)
gdcmWarningMacro("in ParseSQ : should never get here!");
- break;
+ UnexpectedEOF = true;
+ return false;
}
if ( delim_mode )
{
if ( newDocEntry->IsSequenceDelimitor() )
{
seqEntry->SetDelimitationItem( newDocEntry );
+ newDocEntry->Delete();
break;
}
}
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ else // ! delim_mode
{
- delete newDocEntry;
- break;
+ if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SQItem when no delim mode
+ {
+ newDocEntry->Delete();
+ break;
+ }
}
// create the current SQItem
- SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
-/*
- std::ostringstream newBase;
- newBase << seqEntry->GetKey()
- << "/"
- << SQItemNumber
- << "#";
- itemSQ->SetBaseTagKey( newBase.str() );
-*/
+ SQItem *itemSQ = SQItem::New( seqEntry->GetDepthLevel() );
unsigned int l = newDocEntry->GetReadLength();
if ( l == 0xffffffff )
{
dlm_mod = false;
}
+
+ // avoid infinite loop when Bad assumption was made on illegal 'unknown length' UN //JPRx
+
+ if (offsetStartCurrentSQItem <= OffsetOfPreviousParseDES)
+ {
+ gdcmWarningMacro("Bad assumption was made on illegal 'unknown length' UN!" << std::endl <<
+ "OffsetOfPreviousParseDES " << std::hex << OffsetOfPreviousParseDES
+ << " offsetStartCurrentSQItem " << offsetStartCurrentSQItem);
+ /// \todo when "Bad assumption (SQ) on illegal 'unknown length' UN", Backtrack again + try OB
+ return false;
+ }
+ else
+ {
+ OffsetOfPreviousParseDES = offsetStartCurrentSQItem;
+ }
- // Let's try :------------
- // remove fff0,e000, created out of the SQItem
- delete newDocEntry;
- Fp->seekg(offsetStartCurrentSQItem, std::ios::beg);
// fill up the current SQItem, starting at the beginning of fff0,e000
-
+ Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); // Once per SQItem
ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod);
-
- offsetStartCurrentSQItem = Fp->tellg();
- // end try -----------------
+ offsetStartCurrentSQItem = Fp->tellg(); // Once per SQItem
seqEntry->AddSQItem( itemSQ, SQItemNumber );
+ itemSQ->Delete();
+ newDocEntry->Delete();
SQItemNumber++;
- if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
+ //if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) //JPRx
+ if ( !delim_mode && (offsetStartCurrentSQItem-offset ) >= l_max )
{
break;
}
}
+ return true;
}
/**
* \brief When a private Sequence + Implicit VR is encountered
* we cannot guess it's a Sequence till we find the first
* Item Starter. We then backtrack to do the job.
- * @param docEntry Item Starter that warned us
+ * @param docEntry Item Starter that warned us
+ * @param set DocEntrySet (ElementSet/SQItem) the DocEntry will belong
*/
-DocEntry *Document::Backtrack(DocEntry *docEntry)
+DocEntry *Document::Backtrack(DocEntry *docEntry, DocEntrySet *set)
{
// delete the Item Starter, built erroneously out of any Sequence
// it's not yet in the HTable/chained list
- delete docEntry;
+ docEntry->Delete();
// Get all info we can from PreviousDocEntry
uint16_t group = PreviousDocEntry->GetGroup();
uint32_t lgt = PreviousDocEntry->GetLength();
long offset = PreviousDocEntry->GetOffset();
- gdcmWarningMacro( "Backtrack :" << std::hex << group
- << "|" << elem
- << " at offset " << offset );
- RemoveEntry( PreviousDocEntry );
+ gdcmDebugMacro( "Backtrack :" << std::hex << group
+ << "|" << elem
+ << " at offset 0x(" <<offset << ")" );
+
+ set->RemoveEntry( PreviousDocEntry );
// forge the Seq Entry
DocEntry *newEntry = NewSeqEntry(group, elem);
newEntry->SetOffset(offset);
// Move back to the beginning of the Sequence
- Fp->seekg( 0, std::ios::beg);
- Fp->seekg(offset, std::ios::cur);
-return newEntry;
+ Fp->seekg(offset, std::ios::beg); // Only for Shadow Implicit VR SQ
+ return newEntry; // It will added where it has to be!
}
/**
*/
void Document::LoadDocEntry(DocEntry *entry, bool forceLoad)
{
- uint16_t group = entry->GetGroup();
- std::string vr = entry->GetVR();
- uint32_t length = entry->GetLength();
+ uint16_t group = entry->GetGroup();
+ uint16_t elem = entry->GetElement();
+ const VRKey &vr = entry->GetVR();
+ uint32_t length = entry->GetLength();
- Fp->seekg((long)entry->GetOffset(), std::ios::beg);
+ // Fp->seekg((long)entry->GetOffset(), std::ios::beg); // JPRx
// A SeQuence "contains" a set of Elements.
// (fffe e000) tells us an Element is beginning
// (fffe e00d) tells us an Element just ended
// (fffe e0dd) tells us the current SeQuence just ended
- if ( group == 0xfffe )
+ // (fffe 0000) is an 'impossible' tag value,
+ // found in MR-PHILIPS-16-Multi-Seq.dcm
+
+ if ( (group == 0xfffe && elem != 0x0000 ) || vr == "SQ" )
{
// NO more value field for SQ !
return;
}
+ DataEntry *dataEntryPtr = dynamic_cast< DataEntry* >(entry);
+ if( !dataEntryPtr )
+ {
+ return;
+ }
+
// When the length is zero things are easy:
if ( length == 0 )
{
- ((ValEntry *)entry)->SetValue("");
+ dataEntryPtr->SetBinArea(NULL,true);
return;
}
// The elements whose length is bigger than the specified upper bound
- // are not loaded. Instead we leave a short notice on the offset of
- // the element content and it's length.
-
- std::ostringstream s;
+ // are not loaded.
if (!forceLoad)
{
if (length > MaxSizeLoadEntry)
{
- if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
- {
- s << GDCM_NOTLOADED;
- s << " Ad.:" << (long)entry->GetOffset();
- s << " x(" << std::hex << entry->GetOffset() << ")";
- s << std::dec;
- s << " Lgt:" << entry->GetLength();
- s << " x(" << std::hex << entry->GetLength() << ")";
- binEntryPtr->SetValue(s.str());
- }
- else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) )
- {
- s << GDCM_NOTLOADED;
- s << " Address:" << (long)entry->GetOffset();
- s << " Length:" << entry->GetLength();
- s << " x(" << std::hex << entry->GetLength() << ")";
- valEntryPtr->SetValue(s.str());
- }
- else
- {
- // fusible
- gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry "
- << "nor a ValEntry ?! Should never print that !" );
- }
+ dataEntryPtr->SetBinArea(NULL,true);
+ dataEntryPtr->SetState(DataEntry::STATE_NOTLOADED);
- // to be sure we are at the end of the value ...
- Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
- std::ios::beg);
+ // to be sure we are at the end of the value ...
+ // Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
+ // std::ios::beg); //JPRx
return;
}
}
-
- // When we find a BinEntry not very much can be done :
- if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
- {
- s << GDCM_BINLOADED;
- binEntryPtr->SetValue(s.str());
- LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
- return;
- }
-
- if ( IsDocEntryAnInteger(entry) )
- {
- uint32_t NewInt;
- int nbInt;
- // When short integer(s) are expected, read and convert the following
- // (n * 2) characters properly i.e. consider them as short integers as
- // opposed to strings.
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- if (vr == "US" || vr == "SS")
- {
- nbInt = length / 2;
- NewInt = ReadInt16();
- s << NewInt;
- if (nbInt > 1)
- {
- for (int i=1; i < nbInt; i++)
- {
- s << '\\';
- NewInt = ReadInt16();
- s << NewInt;
- }
- }
- }
- // See above comment on multiple integers (mutatis mutandis).
- else if (vr == "UL" || vr == "SL")
- {
- nbInt = length / 4;
- NewInt = ReadInt32();
- s << NewInt;
- if (nbInt > 1)
- {
- for (int i=1; i < nbInt; i++)
- {
- s << '\\';
- NewInt = ReadInt32();
- s << NewInt;
- }
- }
- }
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
-
- ((ValEntry *)entry)->SetValue(s.str());
- return;
- }
- // FIXME: We need an additional byte for storing \0 that is not on disk
- char *str = new char[length+1];
- Fp->read(str, (size_t)length);
- str[length] = '\0'; //this is only useful when length is odd
- // Special DicomString call to properly handle \0 and even length
- std::string newValue;
- if ( length % 2 )
- {
- newValue = Util::DicomString(str, length+1);
- gdcmWarningMacro("Warning: bad length: " << length <<
- " For string :" << newValue.c_str());
- // Since we change the length of string update it length
- //entry->SetReadLength(length+1);
- }
- else
- {
- newValue = Util::DicomString(str, length);
- }
- delete[] str;
-
- if ( ValEntry *valEntry = dynamic_cast<ValEntry* >(entry) )
- {
- if ( Fp->fail() || Fp->eof())
- {
- if ( Fp->fail() )
- gdcmWarningMacro("--> fail");
-
- gdcmWarningMacro("Unread element value " << valEntry->GetKey()
- << " lgt : " << valEntry->GetReadLength()
- << " at " << std::hex << valEntry->GetOffset());
- valEntry->SetValue(GDCM_UNREAD);
- return;
- }
-
- if ( vr == "UI" )
- {
- // Because of correspondance with the VR dic
- valEntry->SetValue(newValue);
- }
- else
- {
- valEntry->SetValue(newValue);
- }
- }
- else
- {
- gdcmWarningMacro("Should have a ValEntry, here ! " << valEntry->GetKey()
- << " lgt : " << valEntry->GetReadLength()
- << " at " << std::hex << valEntry->GetOffset());
- }
+ /// \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
+ /// during initial stage.
+ /// Later, a GetString or GetBinArea will load the value from disk, if not loaded
+ /// + a method that load *everything* that's not yet loaded
+
+ LoadEntryBinArea(dataEntryPtr); // last one, not to erase length !
}
/**
void Document::FindDocEntryLength( DocEntry *entry )
throw ( FormatError )
{
- std::string vr = entry->GetVR();
+ const VRKey &vr = entry->GetVR();
uint16_t length16;
-
if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
- if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT"
- /*|| vr == "UN"*/ )
+
+ // WARNING :
+ //
+ // For some images, length of UN elements is coded on 2 bytes (instead of 4)
+ // There are *not* readable !
+ // You can make a quick and dirty patch, commenting out
+ //| 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)
{
+ changeFromUN = false;
// The following reserved two bytes (see PS 3.5-2003, section
// "7.1.2 Data element structure with explicit vr", p 27) must be
// skipped before proceeding on reading the length on 4 bytes.
- Fp->seekg( 2L, std::ios::cur);
- uint32_t length32 = ReadInt32();
- if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
+ //Fp->seekg( 2L, std::ios::cur); // Once per OB,OW,OL,UT,UN,SQ DocEntry
+ uint32_t length32 = ReadInt32(); // Once per OB,OW,OL,UT,UN,SQ DocEntry
+ CurrentOffsetPosition+=4;
+ if ( (vr == "OB" || vr == "OW" || vr == "OL") && length32 == 0xffffffff )
{
uint32_t lengthOB;
try
{
- lengthOB = FindDocEntryLengthOBOrOW();
+ lengthOB = FindDocEntryLengthOBOrOW();// for encapsulation of encoded pixel
}
catch ( FormatUnexpected )
{
gdcmWarningMacro( " Computing the length failed for " <<
entry->GetKey() <<" in " <<GetFileName());
- long currentPosition = Fp->tellg();
- Fp->seekg(0L,std::ios::end);
+ long currentPosition = Fp->tellg(); // Only for gdcm-JPEG-LossLess3a.dcm-like
+ Fp->seekg(0L,std::ios::end); // Only for gdcm-JPEG-LossLess3a.dcm-like
- long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
- Fp->seekg(currentPosition, std::ios::beg);
+ long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; // Only for gdcm-JPEG-LossLess3a.dcm-like
+ Fp->seekg(currentPosition, std::ios::beg); // Only for gdcm-JPEG-LossLess3a.dcm-like
entry->SetReadLength(lengthUntilEOF);
entry->SetLength(lengthUntilEOF);
FixDocEntryFoundLength(entry, length32);
return;
}
-
// Length is encoded on 2 bytes.
- length16 = ReadInt16();
-
+ //length16 = ReadInt16();
+ length16 = GetInt16();
// 0xffff means that we deal with 'No Length' Sequence
// or 'No Length' SQItem
if ( length16 == 0xffff)
// Length is on 4 bytes.
// Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
- // even if Transfer Syntax is 'Implicit VR ...'
-
- FixDocEntryFoundLength( entry, ReadInt32() );
+ // even if Transfer Syntax is 'Implicit VR ...'
+ // --> Except for 'Implicit VR Big Endian Transfer Syntax GE Private'
+ // where Group 0x0002 is *also* encoded in Implicit VR !
+
+ FixDocEntryFoundLength( entry, GetInt32() /*ReadInt32()*/ );
return;
}
}
throw( FormatUnexpected )
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
- long positionOnEntry = Fp->tellg();
+
+ long positionOnEntry = Fp->tellg(); // Only for OB,OW DataElements
+
bool foundSequenceDelimiter = false;
uint32_t totalLength = 0;
{
uint16_t group;
uint16_t elem;
+
try
- {
- group = ReadInt16();
- elem = ReadInt16();
+ { ///\todo make sure there is never OL encoded pixel data!
+
+ //group = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements
+ //elem = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements
+ ReadBegBuffer(4); // Once per fragment (if any) of OB,OW DataElements
}
catch ( FormatError )
{
throw FormatError("Unexpected end of file encountered during ",
"Document::FindDocEntryLengthOBOrOW()");
}
+ group = GetInt16();
+ elem = GetInt16();
+
// We have to decount the group and element we just read
totalLength += 4;
if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- long filePosition = Fp->tellg();
gdcmWarningMacro(
"Neither an Item tag nor a Sequence delimiter tag on :"
- << std::hex << group << " , " << elem
- << ") -before- position x(" << filePosition << ")" );
+ << std::hex << group << "|" << elem << ") Pos. on entry was 0x(" <<positionOnEntry<< ") "
+ );
- Fp->seekg(positionOnEntry, std::ios::beg);
+ Fp->seekg(positionOnEntry, std::ios::beg); // Once per fragment (if any) of OB,OW DataElements
throw FormatUnexpected(
"Neither an Item tag nor a Sequence delimiter tag.");
}
{
foundSequenceDelimiter = true;
}
- uint32_t itemLength = ReadInt32();
+ uint32_t itemLength = ReadInt32(); // Once per fragment (if any) of OB,OW DataElements
// We add 4 bytes since we just read the ItemLength with ReadInt32
totalLength += itemLength + 4;
SkipBytes(itemLength);
break;
}
}
- Fp->seekg( positionOnEntry, std::ios::beg);
+ Fp->seekg( positionOnEntry, std::ios::beg); // Only once for OB,OW DataElements
return totalLength;
}
* \brief Find the Value Representation of the current Dicom Element.
* @return Value Representation of the current Entry
*/
-std::string Document::FindDocEntryVR()
+VRKey Document::FindDocEntryVR()
{
if ( Filetype != ExplicitVR )
- return GDCM_UNKNOWN;
+ {
+ return GDCM_VRUNKNOWN;
+ }
- long positionOnEntry = Fp->tellg();
+ // Delimiters (0xfffe), are not explicit VR ...
+ if ( CurrentGroup == 0xfffe )
+ return GDCM_VRUNKNOWN;
+
+ //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. Alas this
- // doesn't guarantee that all the tags will be in explicit VR. In some
- // cases (see e-film filtered files) one finds implicit VR tags mixed
- // within an explicit VR file. Hence we make sure the present tag
- // is in explicit VR and try to fix things if it happens not to be
- // the case.
+ // we used a heuristic that found "UL" in the first tag and/or
+ // 'Transfer Syntax' told us it is.
+ // Alas this doesn't guarantee that all the tags will be in explicit VR.
+ // In some cases one finds implicit VR tags mixed within an explicit VR file
+ // Well...
+ // 'Normaly' the only case is : group 0002 Explicit, and other groups Implicit
+ //
+ // Hence we make sure the present tag is in explicit VR and try to fix things
+ // if it happens not to be the case.
- char vr[3];
- Fp->read (vr, (size_t)2);
- vr[2] = 0;
+ VRKey vr;
+ //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) )
+ {
- if ( !CheckDocEntryVR(vr) )
- {
- Fp->seekg(positionOnEntry, std::ios::beg);
- return GDCM_UNKNOWN;
+ 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 (?!?)
+ //see :MR_Philips_Intera_PrivateSequenceExplicitVR.dcm
+ PtrBegBuffer-=2;
+ return GDCM_VRUNKNOWN;
}
return vr;
}
* @return false if the VR is incorrect or if the VR isn't referenced
* otherwise, it returns true
*/
-bool Document::CheckDocEntryVR(VRKey vr)
+bool Document::CheckDocEntryVR(const VRKey &vr)
{
- if ( !Global::GetVR()->IsValidVR(vr) )
- return false;
-
- return true;
-}
-
-/**
- * \brief Get the transformed value of the header entry. The VR value
- * is used to define the transformation to operate on the value
- * \warning NOT end user intended method !
- * @param entry entry to tranform
- * @return Transformed entry value
- */
-std::string Document::GetDocEntryValue(DocEntry *entry)
-{
- if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
- {
- std::string val = ((ValEntry *)entry)->GetValue();
- std::string vr = entry->GetVR();
- uint32_t length = entry->GetLength();
- std::ostringstream s;
- int nbInt;
-
- // When short integer(s) are expected, read and convert the following
- // n * 2 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // as usual for standard multivaluated filels
- // Elements with Value Multiplicity > 1
- // contain a set of short integers (not a single one)
-
- if ( vr == "US" || vr == "SS" )
- {
- uint16_t newInt16;
-
- nbInt = length / 2;
- for (int i=0; i < nbInt; i++)
- {
- if ( i != 0 )
- {
- s << '\\';
- }
- newInt16 = ( val[2*i+0] & 0xFF ) + ( ( val[2*i+1] & 0xFF ) << 8);
- newInt16 = SwapShort( newInt16 );
- s << newInt16;
- }
- }
-
- // When integer(s) are expected, read and convert the following
- // n * 4 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // as usual for standard multivaluated filels
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- else if ( vr == "UL" || vr == "SL" )
- {
- uint32_t newInt32;
-
- nbInt = length / 4;
- for (int i=0; i < nbInt; i++)
- {
- if ( i != 0)
- {
- s << '\\';
- }
- newInt32 = ( val[4*i+0] & 0xFF )
- + (( val[4*i+1] & 0xFF ) << 8 )
- + (( val[4*i+2] & 0xFF ) << 16 )
- + (( val[4*i+3] & 0xFF ) << 24 );
- newInt32 = SwapLong( newInt32 );
- s << newInt32;
- }
- }
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- return s.str();
- }
- return ((ValEntry *)entry)->GetValue();
-}
-
-/**
- * \brief Get the reverse transformed value of the header entry. The VR
- * value is used to define the reverse transformation to operate on
- * the value
- * \warning NOT end user intended method !
- * @param entry Entry to reverse transform
- * @return Reverse transformed entry value
- */
-std::string Document::GetDocEntryUnvalue(DocEntry *entry)
-{
- if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
- {
- std::string vr = entry->GetVR();
- std::vector<std::string> tokens;
- std::ostringstream s;
-
- if ( vr == "US" || vr == "SS" )
- {
- uint16_t newInt16;
-
- tokens.erase( tokens.begin(), tokens.end()); // clean any previous value
- Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size(); i++)
- {
- newInt16 = atoi(tokens[i].c_str());
- s << ( newInt16 & 0xFF )
- << (( newInt16 >> 8 ) & 0xFF );
- }
- tokens.clear();
- }
- if ( vr == "UL" || vr == "SL")
- {
- uint32_t newInt32;
-
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- newInt32 = atoi(tokens[i].c_str());
- s << (char)( newInt32 & 0xFF )
- << (char)(( newInt32 >> 8 ) & 0xFF )
- << (char)(( newInt32 >> 16 ) & 0xFF )
- << (char)(( newInt32 >> 24 ) & 0xFF );
- }
- tokens.clear();
- }
-
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- return s.str();
- }
-
- return ((ValEntry *)entry)->GetValue();
+ return Global::GetVR()->IsValidVR(vr);
}
/**
* \brief Skip a given Header Entry
- * \warning NOT end user intended method !
* @param entry entry to skip
*/
void Document::SkipDocEntry(DocEntry *entry)
/**
* \brief Skips to the beginning of the next Header Entry
- * \warning NOT end user intended method !
* @param currentDocEntry entry to skip
*/
void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
{
- int l = currentDocEntry->GetReadLength();
- if ( l == -1 ) // length = 0xffff shouldn't appear here ...
+ long l = currentDocEntry->GetReadLength();
+ if ( (uint32_t) l == (uint32_t)-1 ) // length = 0xffff shouldn't appear here ...
// ... but PMS imagers happen !
return;
- Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
+ Fp->seekg((size_t)(currentDocEntry->GetOffset()), std::ios::beg); //FIXME :each DocEntry
if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb
{
- Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur);
+ Fp->seekg( l,std::ios::cur); //FIXME :each DocEntry
}
}
* the parser went Jabberwocky) one can hope improving things by
* applying some heuristics.
* @param entry entry to check
- * @param foundLength first assumption about length
+ * @param foundLength first assumption about length (before bug fix, or set to zero if =0xffffffff)
*/
void Document::FixDocEntryFoundLength(DocEntry *entry,
uint32_t foundLength)
{
- entry->SetReadLength( foundLength ); // will be updated only if a bug is found
+ entry->SetReadLength( foundLength );// will be updated only if a bug is found
+
if ( foundLength == 0xffffffff)
{
- foundLength = 0;
+ //foundLength = 0;
+ //entry->SetLength(foundLength);
+ entry->SetLength(0);
+ return; // return ASAP; don't waist time on useless tests
}
-
+
uint16_t gr = entry->GetGroup();
uint16_t elem = entry->GetElement();
if ( foundLength % 2)
{
- gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength
- << " in x(" << std::hex << gr << "," << elem <<")");
+ gdcmWarningMacro( "Warning : Tag (" << std::hex << gr << "|" << elem << ") with uneven length "
+ << std::dec << foundLength << " 0x(" << std::hex << foundLength << ") "
+ //<< " at offset x(" << offset << ")"
+ );
}
-
+
//////// 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
// Occurence of such images is quite low (unless one leaves close to a
// 'Leonardo' source. Hence, one might consider commenting out the
// following fix on efficiency reasons.
- else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
- {
- foundLength = 4;
- entry->SetReadLength(4); // a bug is to be fixed !?
- }
-
+ else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
+ {
+ // Ideally we should check we are in Explicit and double check
+ // that VR=UL... this is done properly in gdcm2
+ if( foundLength == 6 )
+ {
+ gdcmWarningMacro( "Replacing Length from 6 into 4" );
+ foundLength = 4;
+ entry->SetReadLength(4); // a bug is to be fixed !
+ }
+ else if ( foundLength%4 )
+ {
+ gdcmErrorMacro( "This looks like to a buggy Siemens DICOM file."
+ "The length of this tag seems to be wrong" );
+ }
+ }
+
else if ( entry->GetVR() == "SQ" )
{
- foundLength = 0; // ReadLength is unchanged
- }
-
- //////// We encountered a 'delimiter' element i.e. a tag of the form
+ foundLength = 0; // ReadLength is unchanged
+ }
+
+ //////// We encountered a 'delimiter' element i.e. a tag of the form
// "fffe|xxxx" which is just a marker. Delimiters length should not be
// taken into account.
else if ( gr == 0xfffe )
- {
+ {
// According to the norm, fffe|0000 shouldn't exist. BUT the Philips
// image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to
// causes extra troubles...
- if ( entry->GetElement() != 0x0000 )
+ if ( elem != 0x0000 )
{
foundLength = 0;
}
- }
+ else
+ {
+ foundLength=12; // to skip the mess that follows this bugged Tag !
+ }
+ }
entry->SetLength(foundLength);
}
{
uint16_t elem = entry->GetElement();
uint16_t group = entry->GetGroup();
- const std::string &vr = entry->GetVR();
+ const VRKey &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.
+ // able to swap its element value properly.
if ( elem == 0 ) // This is the group length of the group
{
if ( length == 4 )
}
else
{
- // Allthough this should never happen, still some images have a
+ // Although this should never happen, still some images have a
// corrupted group length [e.g. have a glance at offset x(8336) of
- // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm].
+ // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
// Since for dicom compliant and well behaved headers, the present
// 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).
- long filePosition = Fp->tellg();
+ long filePosition = Fp->tellg(); // Only when elem 0x0000 length is not 4 (?!?)
+ (void)filePosition;
gdcmWarningMacro( "Erroneous Group Length element length on : ("
<< std::hex << group << " , " << elem
<< ") -before- position x(" << filePosition << ")"
char *entCur = deb + 128;
if ( memcmp(entCur, "DICM", (size_t)4) == 0 )
{
- gdcmWarningMacro( "Looks like DICOM Version3 (preamble + DCM)" );
+ gdcmDebugMacro( "Looks like DICOM Version3 (preamble + DCM)" );
// Group 0002 should always be VR, and the first element 0000
// Let's be carefull (so many wrong headers ...)
// i.e. a total of 136 bytes.
entCur = deb + 136;
- // group 0x0002 *is always* Explicit VR Sometimes ,
+ // group 0x0002 *is always* Explicit VR Sometimes,
// even if elem 0002,0010 (Transfer Syntax) tells us the file is
// *Implicit* VR (see former 'gdcmData/icone.dcm')
// instead of just checking for UL, OB and UI !? group 0000
{
Filetype = ExplicitVR;
- gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
+ gdcmDebugMacro( "Group 0002 : Explicit Value Representation");
}
else
{
<< "Looks like a bugged Header!");
}
+ // Here, we assume that the file IS kosher Dicom !
+ // (The meta elements - group 0x0002 - ARE little endian !)
if ( net2host )
{
SwapCode = 4321;
- gdcmWarningMacro( "HostByteOrder != NetworkByteOrder");
+ gdcmDebugMacro( "HostByteOrder != NetworkByteOrder, SwapCode = 4321");
}
else
{
SwapCode = 1234;
- gdcmWarningMacro( "HostByteOrder = NetworkByteOrder");
+ gdcmDebugMacro( "HostByteOrder = NetworkByteOrder, SwapCode = 1234");
}
// Position the file position indicator at first tag
// (i.e. after the file preamble and the "DICM" string).
- Fp->seekg(0, std::ios::beg); // FIXME : Is it usefull?
-
- Fp->seekg ( 132L, std::ios::beg);
+ Fp->seekg ( 132L, std::ios::beg); // Once per Document
+ CurrentOffsetPosition = 132;
return true;
} // ------------------------------- End of DicomV3 ----------------
gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)");
- Fp->seekg(0, std::ios::beg);
-
+ Fp->seekg(0, std::ios::beg); // Once per ACR-NEMA Document
+ CurrentOffsetPosition = 0;
// Let's check 'No Preamble Dicom File' :
// Should start with group 0x0002
// and be Explicit Value Representation
memcmp(entCur, "AE", (size_t)2) == 0 ||
memcmp(entCur, "OB", (size_t)2) == 0 )
{
- Filetype = ExplicitVR;
- gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
+ Filetype = ExplicitVR; // FIXME : not enough to say it's Explicit
+ // Wait untill reading Transfer Syntax
+ gdcmDebugMacro( "Group 0002 : Explicit Value Representation");
return true;
}
}
// Only 0 or 4321 will be possible
// (no oportunity to check for the formerly well known
// ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
- // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -3, 4, ..., 8-)
+ // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc-3, 4, ..., 8-)
// the file IS NOT ACR-NEMA nor DICOM V3
// 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 )
{
case 0x0001 :
case 0x0006 :
case 0x0007 :
case 0x0008 :
+ case 0x0028 :
SwapCode = 1234;
Filetype = ACR;
return true;
case 0x0600 :
case 0x0700 :
case 0x0800 :
+ case 0x2800 :
SwapCode = 4321;
Filetype = ACR;
return true;
default :
- gdcmWarningMacro("ACR/NEMA unfound swap info (Really hopeless !)");
- Filetype = Unknown;
- return false;
+
+ s16 = *((uint16_t *)(deb));
+ if (s16 != 0x0000)
+ return false;
+ s16 = *((uint16_t *)(deb+2));
+
+ Fp->seekg ( 0L, std::ios::beg); // Once per Document
+ CurrentOffsetPosition = 0;
+ switch(s16) // try an other trick!
+ // -> to be able to decode 0029|1010 DataElement
+ // -> and be not less cleaver than dcmdump ;-)
+ {
+ case 0x0004 :
+ SwapCode = 1234;
+ break;
+ case 0x0400 :
+ SwapCode = 3412;
+ break;
+ default:
+ gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)");
+ Filetype = Unknown;
+ return false;
+ }
+ // Check if next 2 bytes are a VR
+ // Probabely something more time-consuming exists with std::string
+ const char VRvalues[] = "AEASATCSDADTFLFDISLOLTPNSHSLSSSTTMUIULUSUTOBOWOLOFATUNSQRT";
+ int nbVal = 29;
+ const char *pt = VRvalues;
+ for (int i=0;i<nbVal;i++)
+ {
+ if(*(deb+4) == *pt++) {
+ if(*(deb+5) == *pt++) {
+ Filetype = ExplicitVR;
+ return true;
+ }
+ else {
+ pt++;
+ }
+ }
+ }
+ Filetype = ImplicitVR;
+ return true;
}
}
}
*/
void Document::SwitchByteSwapCode()
{
- gdcmWarningMacro( "Switching Byte Swap code from "<< SwapCode
- << " at :" <<std::hex << Fp->tellg() );
+ gdcmDebugMacro( "Switching Byte Swap code from "<< SwapCode
+ << " at: 0x" << std::hex << Fp->tellg() ); // Only when DEBUG
if ( SwapCode == 1234 )
{
SwapCode = 4321;
{
SwapCode = 3412;
}
+ gdcmDebugMacro( " Into: "<< SwapCode );
}
/**
* \brief during parsing, Header Elements too long are not loaded in memory
* @param newSize new size
*/
-void Document::SetMaxSizeLoadEntry(long newSize)
+void Document::SetMaxSizeLoadEntry(long newSize)
{
if ( newSize < 0 )
{
* (read the 'Group Number', the 'Element Number',
* gets the Dict Entry
* gets the VR, gets the length, gets the offset value)
- * @return On succes : the newly created DocEntry, NULL on failure.
+ * @return On succes : the newly created DocEntry, NULL on failure.
*/
DocEntry *Document::ReadNextDocEntry()
{
- uint16_t group;
- uint16_t elem;
-
try
{
- group = ReadInt16();
- elem = ReadInt16();
+ ReadBegBuffer(8); // Avoid to many time consuming freads
+ //CurrentGroup = ReadInt16();
+ //CurrentElem = ReadInt16();
}
catch ( FormatError )
{
- // We reached the EOF (or an error occured) therefore
+ // We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
return 0;
}
-
- // Sometimes file contains groups of tags with reversed endianess.
- HandleBrokenEndian(group, elem);
-
+
+ changeFromUN = false;
+ CurrentGroup = GetInt16();
+ CurrentElem = GetInt16();
+
// In 'true DICOM' files Group 0002 is always little endian
if ( HasDCMPreamble )
- HandleOutOfGroup0002(group, elem);
-
- std::string vr = FindDocEntryVR();
- std::string realVR = vr;
+ {
+ if ( !Group0002Parsed && CurrentGroup != 0x0002) // avoid calling a function when useless
+ HandleOutOfGroup0002(CurrentGroup, CurrentElem);
+ else
+ // Sometimes file contains groups of tags with reversed endianess.
+ HandleBrokenEndian(CurrentGroup, CurrentElem);
+ }
+
+ VRKey vr = FindDocEntryVR();
+ VRKey realVR = vr;
- if ( vr == GDCM_UNKNOWN )
+ if ( vr == GDCM_VRUNKNOWN )
{
- if ( elem == 0x0000 ) // Group Length
+ if ( CurrentElem == 0x0000 ) // Group Length
{
realVR = "UL"; // must be UL
}
- else if (group%2 == 1 && (elem >= 0x0010 && elem <=0x00ff ))
- {
- // DICOM PS 3-5 7.8.1 a) states that those
- // (gggg-0010->00FF where gggg is odd) attributes have to be LO
- realVR = "LO";
+ else if (CurrentGroup == 0xfffe) // Don't get DictEntry for Delimitors
+ {
+ realVR = "UL";
+ }
+
+ // Was commented out in order not to generate 'Shadow Groups' where some
+ // Data Elements are Explicit VR and some other ones Implicit VR
+ // -> 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 :
+ // Private Creator Data Elements numbered (gggg,0010-00FF) (gggg is odd)
+ // attributes have to be LO (Long String) and the VM shall be equal to 1
+ realVR = "LO";
+
+ // Seems not to be true
+ // Still in gdcmtk, David Clunnie disagrees, Marco Eichelberg says it's OK ...
+ // We let it for a while?
+ //(We should check length==4, for more security, but we don't have it yet !)
+ }
+ else if ( CurrentElem == 0x0001)
+ {
+ realVR = "UL"; // Private Group Length To End
+ }
+ else // check the private dictionary for shadow elements when Implicit VR!
+ {
+ DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);
+ if ( dictEntry )
+ {
+ realVR = dictEntry->GetVR();
+ dictEntry->Unregister(); // GetDictEntry registered it
+ }
+ }
}
+
else
{
- DictEntry *dictEntry = GetDictEntry(group,elem);
+ DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);//only when ImplicitVR
if ( dictEntry )
{
realVR = dictEntry->GetVR();
+ dictEntry->Unregister(); // GetDictEntry registered it
}
}
}
+ // if UN found, let's check the dictionary, and trust it!
+ // (maybe a private dictionary exists?)
+ else if (vr == "UN")
+ {
+ DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);
+ if ( dictEntry )
+ {
+ realVR = dictEntry->GetVR();
+ dictEntry->Unregister(); // GetDictEntry registered it
+
+ // for VR = "UN", length is always stored on 4 bytes.
+ // remember this info, in order not to crash later
+ changeFromUN=true;
+ /// \todo : fixme If inside a vr = "UN" DataElement (but SQ according to a private dictionnary)
+ /// there is some more vr = "UN" DataElements, it will probabely fail.
+ /// --> find a -non time consuming- trick to store changeFromUN info at DataElement level,
+ /// not at the Document level.
+ /// --> ?!? JPR
+
+ }
+ }
+
DocEntry *newEntry;
- if ( Global::GetVR()->IsVROfSequence(realVR) )
- newEntry = NewSeqEntry(group, elem);
- else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) )
- newEntry = NewValEntry(group, elem, realVR);
+ //if ( Global::GetVR()->IsVROfSequence(realVR) )
+ if (realVR == "SQ")
+ {
+ newEntry = NewSeqEntry(CurrentGroup, CurrentElem);
+ }
else
- newEntry = NewBinEntry(group, elem, realVR);
+ {
+ newEntry = NewDataEntry(CurrentGroup, CurrentElem, realVR);
+ static_cast<DataEntry *>(newEntry)->SetState(DataEntry::STATE_NOTLOADED);
+ }
- if ( vr == GDCM_UNKNOWN )
+ if ( vr == GDCM_VRUNKNOWN )
{
if ( Filetype == ExplicitVR )
{
// We thought this was explicit VR, but we end up with an
// implicit VR tag. Let's backtrack.
- if ( newEntry->GetGroup() != 0xfffe )
+
+ //if ( newEntry->GetGroup() != 0xfffe )
+ if (CurrentGroup != 0xfffe)
{
- std::string msg;
- int offset = Fp->tellg();
- msg = Util::Format("Entry (%04x,%04x) at 0x(%x) should be Explicit VR\n",
- newEntry->GetGroup(), newEntry->GetElement(), offset );
- gdcmWarningMacro( msg.c_str() );
+ int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong
+
+ gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x("
+ << std::hex << offset << ") should be Explicit VR");
}
}
newEntry->SetImplicitVR();
catch ( FormatError )
{
// Call it quits
- delete newEntry;
+ newEntry->Delete();
return 0;
}
- newEntry->SetOffset(Fp->tellg());
-
+ newEntry->SetOffset(Fp->tellg()); // for each DocEntry
return newEntry;
}
*/
void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
{
- // Endian reversion. Some files contain groups of tags with reversed endianess.
+ // for strange PMS Gyroscan Intera images
+ // Item 'starter' has a tag : 0x3f3f,0x3f00, for no apparent reason
+
+ // --- Feel free to remove this test *on your own coy of gdcm*
+ // if you are sure you'll never face this problem.
+
+ if ((group == 0x3f3f) && (elem == 0x3f00))
+ {
+ // start endian swap mark for group found
+ gdcmDebugMacro( " delimiter 0x3f3f found." );
+ // fix the tag
+ group = 0xfffe;
+ elem = 0xe000;
+ return;
+ }
+ // --- End of removable code
+
+ // Endian reversion.
+ // Some files contain groups of tags with reversed endianess.
static int reversedEndian = 0;
// try to fix endian switching in the middle of headers
if ((group == 0xfeff) && (elem == 0x00e0))
{
// start endian swap mark for group found
+ gdcmDebugMacro( "Start endian swap mark found." );
reversedEndian++;
SwitchByteSwapCode();
// fix the tag
else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
{
// end of reversed endian group
+ gdcmDebugMacro( "End of reversed endian." );
reversedEndian--;
SwitchByteSwapCode();
}
// Do what you want, it breaks !
//reversedEndian--;
//SwitchByteSwapCode();
- gdcmWarningMacro( "Should never get here! reversed Sequence Terminator!" );
+ gdcmWarningMacro( "Should never get here! reversed Sequence Terminator!" );
// fix the tag
group = 0xfffe;
elem = 0xe0dd;
}
else if (group == 0xfffe && elem == 0xe0dd)
{
- gdcmWarningMacro( "Straight Sequence Terminator." );
+ gdcmDebugMacro( "Straight Sequence Terminator." );
}
}
*/
void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem)
{
- // Endian reversion. Some files contain groups of tags with reversed endianess.
- if ( !Group0002Parsed && group != 0x0002)
- {
+ // Endian reversion.
+ // Some files contain groups of tags with reversed endianess.
+
Group0002Parsed = true;
// we just came out of group 0002
- // if Transfer syntax is Big Endian we have to change CheckSwap
+ // if Transfer Syntax is Big Endian we have to change CheckSwap
std::string ts = GetTransferSyntax();
- if ( !Global::GetTS()->IsTransferSyntax(ts) )
- {
- gdcmWarningMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
- return;
- }
+ TS::SpecialType s = Global::GetTS()->GetSpecialTransferSyntax(ts);
- // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..."
+ // Group 0002 is always 'Explicit ...'
+ // even when Transfer Syntax says 'Implicit ..."
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian )
- {
- Filetype = ImplicitVR;
- }
+ if ( s == TS::ImplicitVRLittleEndian
+ ||
+ s == TS::ImplicitVRBigEndianPrivateGE
+ )
+ {
+ Filetype = ImplicitVR;
+ }
// FIXME Strangely, this works with
- //'Implicit VR Transfer Syntax (GE Private)
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
+ //'Implicit VR BigEndian Transfer Syntax' (GE Private)
+ //
+ // --> Probabely normal, since we considered we never have
+ // 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 )
{
- gdcmWarningMacro("Transfer Syntax Name = ["
+ gdcmDebugMacro("Transfer Syntax Name = ["
<< GetTransferSyntaxName() << "]" );
SwitchByteSwapCode();
group = SwapShort(group);
elem = SwapShort(elem);
}
- }
+ */
+ //-- Broken ACR may start with a Shadow Group --
+ // worse : some ACR-NEMA like files start 00028 group ?!?
+ if ( !( (group >= 0x0001 && group <= 0x0008) || group == 0x0028 ) )
+ {
+ // We trust what we see.
+ SwitchByteSwapCode();
+ group = SwapShort(group);
+ elem = SwapShort(elem);
+ // not what we where told (by meta elements) !
+ gdcmDebugMacro("Transfer Syntax Name = ["
+ << GetTransferSyntaxName() << "]" );
+ }
+
+ /// \todo find a trick to warn user and stop processing
+
+ if ( s == TS::DeflatedExplicitVRLittleEndian)
+ {
+ gdcmWarningMacro("Transfer Syntax ["
+ << GetTransferSyntaxName() << "] :"
+ << " not yet dealt with ");
+ 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;
+ }
+
+ if ( !Global::GetTS()->IsTransferSyntax(ts) )
+ {
+ gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: ["
+ << ts << "]");
+ return;
+ }
}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff