Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/02/02 18:13:57 $
- Version: $Revision: 1.221 $
+ Date: $Date: 2005/06/29 15:58:33 $
+ Version: $Revision: 1.252 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <vector>
#include <iomanip>
-
-// For nthos:
-#if defined(_MSC_VER) || defined(__BORLANDC__) || defined(__MINGW32__)
- #include <winsock.h>
-#endif
-
-#ifdef CMAKE_HAVE_NETINET_IN_H
- #include <netinet/in.h>
-#endif
+#include <fstream>
namespace gdcm
{
//-----------------------------------------------------------------------------
-// Refer to Document::CheckSwap()
-//const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
// Refer to Document::SetMaxSizeLoadEntry()
const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
-const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff;
//-----------------------------------------------------------------------------
// Constructor / Destructor
// Constructors and destructors are protected to avoid user to invoke directly
+
/**
- * \brief constructor
- * @param filename 'Document' (File or DicomDir) to be opened for parsing
+ * \brief This default constructor neither loads nor parses the file.
+ * You should then invoke \ref Document::Load.
+ *
*/
-Document::Document( std::string const &filename )
+Document::Document()
:ElementSet(-1)
{
- SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Filename = filename;
+ Fp = 0;
+
+ SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
+ Initialize();
+ SwapCode = 1234;
+ Filetype = ExplicitVR;
+ // Load will set it to true if sucessfull
+ Group0002Parsed = false;
+ IsDocumentAlreadyLoaded = false;
+ LoadMode = 0x00000000; // default : load everything, later
+}
+
+/**
+ * \brief Constructor (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 = 0x00000000; // Load everything
+
+ // Load will set it to true if sucessfull
+ IsDocumentAlreadyLoaded = false;
+
+ Load(fileName);
+}
+/**
+ * \brief Canonical destructor.
+ */
+Document::~Document ()
+{
+ RefPubDict = NULL;
+ RefShaDict = NULL;
+}
+
+//-----------------------------------------------------------------------------
+// Public
+
+/**
+ * \brief Loader
+ * @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 )
+{
+ // We should clean out anything that already exists.
+ // Check IsDocumentAlreadyLoaded to be sure.
+ if ( IsDocumentAlreadyLoaded )
+ {
+ gdcmWarningMacro( "A file was already parsed inside this "
+ << "gdcm::Document (previous name was: "
+ << Filename.c_str() << ". New name is :"
+ << fileName );
+ // todo : clean out the 'Document'
+ // Should we call ClearEntry() on the parent object ?!?
+ }
+
+ Filename = fileName;
Fp = 0;
if ( !OpenFile() )
{
- return;
+ // warning already performed in OpenFile()
+ //gdcmWarningMacro( "Unable to open as an ACR/DICOM file: "
+ // << Filename.c_str() );
+ Filetype = Unknown;
+ return false;
}
Group0002Parsed = false;
- gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str());
- // Fp->seekg( 0, std::ios::beg);
-
+ gdcmWarningMacro( "Starting parsing of file: " << Filename.c_str());
+
Fp->seekg(0, std::ios::end);
- long lgt = Fp->tellg();
-
+ long lgt = Fp->tellg(); // total length of the file
+
Fp->seekg(0, std::ios::beg);
- CheckSwap();
- long beg = Fp->tellg();
- lgt -= beg;
-
+ // CheckSwap returns a boolean
+ // (false if no swap info of any kind was found)
+ if (! CheckSwap() )
+ {
+ gdcmWarningMacro( "Neither a DICOM V3 nor an ACR-NEMA file: "
+ << Filename.c_str());
+ CloseFile();
+ return false;
+ }
+
+ long beg = Fp->tellg(); // just after DICOM preamble (if any)
+
+ lgt -= beg; // remaining length to parse
+
ParseDES( this, beg, lgt, false); // Loading is done during parsing
- Fp->seekg( 0, std::ios::beg);
+ if ( IsEmpty() )
+ {
+ gdcmWarningMacro( "No tag in internal hash table for: "
+ << Filename.c_str());
+ CloseFile();
+ return false;
+ }
+ IsDocumentAlreadyLoaded = true;
+
+ Fp->seekg( 0, std::ios::beg);
// Load 'non string' values
std::string PhotometricInterpretation = GetEntryValue(0x0028,0x0004);
- if( PhotometricInterpretation == "PALETTE COLOR " )
+ if ( PhotometricInterpretation == "PALETTE COLOR " )
{
- LoadEntryBinArea(0x0028,0x1200); // gray LUT
- /// FIXME FIXME FIXME
+ // FIXME
+ // Probabely this line should be outside the 'if'
+ // Try to find an image sample holding a 'gray LUT'
+ LoadEntryBinArea(0x0028,0x1200); // gray LUT
+
+ /// FIXME
/// 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
LoadEntryBinArea(0x0028,0x1222);
// Segmented Blue Palette Color LUT Data
LoadEntryBinArea(0x0028,0x1223);
- }
+ }
+
//FIXME later : how to use it?
- LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent)
+ SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000);
+ if ( modLutSeq !=0 )
+ {
+ SQItem *sqi= modLutSeq->GetFirstSQItem();
+ if ( sqi != 0 )
+ {
+ BinEntry *b = sqi->GetBinEntry(0x0028,0x3006);
+ if ( b != 0 )
+ {
+ if ( b->GetLength() != 0 )
+ {
+ LoadEntryBinArea(b); //LUT Data (CTX dependent)
+ }
+ }
+ }
+ }
CloseFile();
// Specific code to allow gdcm to read ACR-LibIDO formated images
// Note: ACR-LibIDO is an extension of the ACR standard that was
// used at CREATIS. For the time being (say a couple years)
- // we keep this kludge to allow a smooth move to gdcm for
- // CREATIS developpers (sorry folks).
+ // we keep this kludge to allow CREATIS users
+ // reading their old images.
//
// if recognition code tells us we deal with a LibIDO image
// we switch lineNumber and columnNumber
SetValEntry(rows , 0x0028, 0x0011);
}
// --- End of ACR-LibIDO kludge ---
-}
-
-/**
- * \brief This default constructor doesn't parse the file. You should
- * then invoke \ref Document::SetFileName and then the parsing.
- */
-Document::Document()
- :ElementSet(-1)
-{
- Fp = 0;
- SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialize();
- SwapCode = 1234;
- Filetype = ExplicitVR;
- Group0002Parsed = false;
-}
-
-/**
- * \brief Canonical destructor.
- */
-Document::~Document ()
-{
- RefPubDict = NULL;
- RefShaDict = NULL;
+ return true;
}
-//-----------------------------------------------------------------------------
-// Public
/**
* \brief Get the public dictionary used
*/
}
/**
- * \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current Document was properly parsed
- * and contains the mandatory information for being considered as
- * a well formed and usable Dicom/Acr File.
- * @return true when Document is the one of a reasonable Dicom/Acr file,
- * false otherwise.
+ * \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()
{
- if( Filetype == Unknown)
+ if ( Filetype == Unknown )
{
- gdcmVerboseMacro( "Wrong filetype");
+ gdcmWarningMacro( "Wrong filetype");
return false;
}
if ( IsEmpty() )
{
- gdcmVerboseMacro( "No tag in internal hash table.");
+ gdcmWarningMacro( "No tag in internal hash table.");
return false;
}
bool Document::IsDicomV3()
{
// Checking if Transfer Syntax exists is enough
- // Anyway, it's to late check if the 'Preamble' was found ...
+ // Anyway, it's too late check if the 'Preamble' was found ...
// And ... would it be a rich idea to check ?
// (some 'no Preamble' DICOM images exist !)
return GetDocEntry(0x0002, 0x0010) != NULL;
}
if ( transferSyntax == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Unfound Transfer Syntax (0002,0010)");
+ gdcmWarningMacro( "Unfound Transfer Syntax (0002,0010)");
return "Uncompressed ACR-NEMA";
}
{
if ( SwapCode == 4321 || SwapCode == 2143 )
{
- a = ((( a << 8 ) & 0xff00 ) | (( a >> 8 ) & 0x00ff ) );
+ //a = ((( a << 8 ) & 0xff00 ) | (( a >> 8 ) & 0x00ff ) );
+ // Save CPU time
+ a = ( a << 8 ) | ( a >> 8 );
}
return a;
}
case 1234 :
break;
case 4321 :
- a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
- ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
+// a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
+// ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
+// save CPU time
+ a=( ( a<<24) | ((a<<8) & 0x00ff0000) |
+ ((a>>8) & 0x0000ff00) | (a>>24) );
break;
case 3412 :
- a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
+// a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
+ a=( (a<<16) | (a>>16) );
break;
case 2143 :
a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
return 0;
}
- if(Fp)
+ if ( Fp )
{
- gdcmVerboseMacro( "File already open: " << Filename.c_str());
+ gdcmWarningMacro( "File already open: " << Filename.c_str());
CloseFile();
}
Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
- if( ! *Fp )
+ if ( ! *Fp )
{
- gdcmDebugMacro( "Cannot open file: " << Filename.c_str());
+ // Don't user gdcmErrorMacro :
+ // a spurious message will appear when you use, for instance
+ // gdcm::FileHelper *fh = new gdcm::FileHelper( outputFileName );
+ // to create outputFileName.
+ gdcmWarningMacro( "Cannot open file: " << Filename.c_str());
delete Fp;
Fp = 0;
return 0;
+ //exit(1); // No function is allowed to leave the application instead
+ // of warning the caller
}
- uint16_t zero;
+ uint16_t zero = 0;
Fp->read((char*)&zero, (size_t)2);
- if( Fp->eof() )
+ if ( Fp->eof() )
{
CloseFile();
return 0;
}
- //ACR -- or DICOM with no Preamble; may start with a Shadow Group --
- if(
+ //-- 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 with no preamble: (%04x)\n", zero);
- gdcmVerboseMacro( msg.c_str() );
+ std::string msg = Util::Format(
+ "ACR/DICOM starting at the begining of the file:(%04x)\n", zero);
+ gdcmWarningMacro( msg.c_str() );
return Fp;
}
- //DICOM
+ //-- DICOM --
Fp->seekg(126L, std::ios::cur);
- char dicm[4];
+ char dicm[4] = {' ',' ',' ',' '};
Fp->read(dicm, (size_t)4);
- if( Fp->eof() )
+ if ( Fp->eof() )
{
CloseFile();
return 0;
}
- if( memcmp(dicm, "DICM", 4) == 0 )
+ if ( memcmp(dicm, "DICM", 4) == 0 )
{
HasDCMPreamble = true;
return Fp;
}
-
+
+ // -- Neither ACR/No Preamble Dicom nor DICOMV3 file
CloseFile();
- gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
-
+ gdcmWarningMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
+ << Filename.c_str());
return 0;
}
*/
bool Document::CloseFile()
{
- if( Fp )
+ if ( Fp )
{
Fp->close();
delete Fp;
Fp = 0;
}
- return true; //FIXME how do we detect a non-closed ifstream ?
+ return true;
}
/**
return;
BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
- if( !binElement )
+ if ( !binElement )
return;
LoadEntryBinArea(binElement);
*/
void Document::LoadEntryBinArea(BinEntry *elem)
{
- if(elem->GetBinArea())
+ if (elem->GetBinArea() )
return;
bool openFile = !Fp;
- if(openFile)
+ if ( openFile )
OpenFile();
size_t o =(size_t)elem->GetOffset();
size_t l = elem->GetLength();
uint8_t *a = new uint8_t[l];
- if( !a )
+ if ( !a )
{
- gdcmVerboseMacro( "Cannot allocate BinEntry content");
+ gdcmWarningMacro( "Cannot allocate BinEntry content");
return;
}
- /// \todo check the result
Fp->read((char*)a, l);
- if( Fp->fail() || Fp->eof())
+ if ( Fp->fail() || Fp->eof() )
{
delete[] a;
return;
elem->SetBinArea(a);
- if(openFile)
+ if ( openFile )
CloseFile();
}
* \brief Loads the element while preserving the current
* underlying file position indicator as opposed to
* LoadDocEntry that modifies it.
- * @param entry Header Entry whose value will be loaded.
- * @return
+ * @param entry DocEntry whose value will be loaded.
*/
void Document::LoadDocEntrySafe(DocEntry *entry)
{
- if(Fp)
+ if ( Fp )
{
long PositionOnEntry = Fp->tellg();
LoadDocEntry(entry);
* \brief Compares two documents, according to \ref DicomDir rules
* \warning Does NOT work with ACR-NEMA files
* \todo Find a trick to solve the pb (use RET fields ?)
- * @param document
+ * @param document to compare with current one
* @return true if 'smaller'
*/
bool Document::operator<(Document &document)
// Patient Name
std::string s1 = GetEntryValue(0x0010,0x0010);
std::string s2 = document.GetEntryValue(0x0010,0x0010);
- if(s1 < s2)
+ if (s1 < s2)
{
return true;
}
- else if( s1 > s2 )
+ else if ( s1 > s2 )
{
return false;
}
{
return true;
}
- else if( s1 > s2 )
+ else if ( s1 > s2 )
{
return false;
}
{
return true;
}
- else if( s1 > s2 )
+ else if ( s1 > s2 )
{
return false;
}
// Protected
/**
* \brief Reads a supposed to be 16 Bits integer
- * (swaps it depending on processor endianity)
+ * (swaps it depending on processor endianness)
* @return read value
*/
uint16_t Document::ReadInt16()
{
throw FormatError( "Document::ReadInt16()", " file error." );
}
- if( Fp->eof() )
+ if ( Fp->eof() )
{
throw FormatError( "Document::ReadInt16()", "EOF." );
}
/**
* \brief Reads a supposed to be 32 Bits integer
- * (swaps it depending on processor endianity)
+ * (swaps it depending on processor endianness)
* @return read value
*/
uint32_t Document::ReadInt32()
{
throw FormatError( "Document::ReadInt32()", " file error." );
}
- if( Fp->eof() )
+ if ( Fp->eof() )
{
throw FormatError( "Document::ReadInt32()", "EOF." );
}
{
gr = entry->GetGroup();
- if( gr == 0x0002 )
+ if ( gr == 0x0002 )
{
found0002 = true;
- if( entry->GetElement() != 0x0000 )
+ if ( entry->GetElement() != 0x0000 )
{
vr = entry->GetVR();
- if( filetype == ExplicitVR )
+ if ( filetype == ExplicitVR )
{
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
+ if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || (vr == "UT") )
{
- // explicit VR AND OB, OW, SQ : 4 more bytes
+ // explicit VR AND OB, OW, SQ, UT : 4 more bytes
groupLength += 4;
}
}
/**
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
- * @return length of the parsed set.
+ * @param set DocEntrySet we are going to parse ('zero level' or a SQItem)
+ * @param offset start of parsing
+ * @param l_max length to parse
+ * @param delim_mode : whether we are in 'delimitor mode' (l=0xffffff) or not
*/
void Document::ParseDES(DocEntrySet *set, long offset,
long l_max, bool delim_mode)
{
- DocEntry *newDocEntry = 0;
+ DocEntry *newDocEntry;
ValEntry *newValEntry;
BinEntry *newBinEntry;
SeqEntry *newSeqEntry;
VRKey vr;
- bool used = false;
+ bool used;
while (true)
{
!Global::GetVR()->IsVROfBinaryRepresentable(vr) )
{
////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- gdcmVerboseMacro( std::hex << newDocEntry->GetGroup()
+ gdcmWarningMacro( std::hex << newDocEntry->GetGroup()
<< "|" << newDocEntry->GetElement()
<< " : Neither Valentry, nor BinEntry."
"Probably unknown VR.");
}
LoadDocEntry( newBinEntry );
- if( !set->AddEntry( newBinEntry ) )
+ if ( !set->AddEntry( newBinEntry ) )
{
//Expect big troubles if here
//delete newBinEntry;
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 ( dynamic_cast< Document* > ( set ) )
LoadDocEntry( newValEntry );
bool delimitor=newValEntry->IsItemDelimitor();
- if( !set->AddEntry( newValEntry ) )
+
+ if ( LoadMode & NO_SHADOW ) // User asked to skip, if possible,
+ // shadow groups ( if possible :
+ // whether element 0x0000 exits)
+ {
+ if ( newValEntry->GetGroup()%2 != 0 )
+ {
+ if ( newValEntry->GetElement() == 0x0000 )
+ {
+ std::string strLgrGroup = newValEntry->GetValue();
+ int lgrGroup;
+ if ( strLgrGroup != GDCM_UNFOUND)
+ {
+ lgrGroup = atoi(strLgrGroup.c_str());
+ Fp->seekg(lgrGroup, std::ios::cur);
+ used = false;
+ continue;
+ }
+ }
+ }
+ }
+
+ if ( !set->AddEntry( newValEntry ) )
{
// If here expect big troubles
- //delete newValEntry; //otherwise mem leak
+ // delete newValEntry; //otherwise mem leak
used=false;
}
if (delimitor)
{
- if(!used)
+ if ( !used )
delete newDocEntry;
break;
}
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max )
{
- if(!used)
+ if ( !used )
delete newDocEntry;
break;
}
}
else
{
- // VR = "SQ"
- unsigned long l = newDocEntry->GetReadLength();
+ /////////////////////// SeqEntry : VR = "SQ"
+
+ unsigned long l = newDocEntry->GetReadLength();
if ( l != 0 ) // don't mess the delim_mode for zero-length sequence
{
if ( l == 0xffffffff )
delim_mode = false;
}
}
+
+ if ( (LoadMode & NO_SHADOWSEQ) && ! delim_mode )
+ {
+ // User asked to skip SQ only if they belong to Shadow group
+ if ( newDocEntry->GetGroup()%2 != 0 )
+ {
+ Fp->seekg( l, std::ios::cur);
+ used = false;
+ continue;
+ }
+ }
+
+ if ( (LoadMode & NO_SEQ) && ! delim_mode )
+ {
+ // User asked to skip *any* SeQuence
+ Fp->seekg( l, std::ios::cur);
+ used = false;
+ continue;
+ }
+
// no other way to create it ...
newSeqEntry->SetDelimitorMode( delim_mode );
// 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 ( dynamic_cast< Document* > ( set ) )
{
- //(void)dummy;
newSeqEntry->SetDepthLevel( 1 );
newSeqEntry->SetKey( newSeqEntry->GetKey() );
}
newDocEntry->GetOffset(),
l, delim_mode);
}
- if( !set->AddEntry( newSeqEntry ) )
+ if ( !set->AddEntry( newSeqEntry ) )
{
used = false;
}
+
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- if( !used )
+ if ( !used )
delete newDocEntry;
break;
}
}
- if( !used )
+ if ( !used )
delete newDocEntry;
}
}
// FIXME Should warn user
break;
}
- if( delim_mode )
+ if ( delim_mode )
{
if ( newDocEntry->IsSequenceDelimitor() )
{
{
dlm_mod = false;
}
- // FIXME, TODO
- // when we're here, element fffe,e000 is already passed.
- // it's lost for the SQItem we're going to process !!
-
- //ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
- //delete newDocEntry; // FIXME well ... it's too late to use it !
// Let's try :------------
// remove fff0,e000, created out of the SQItem
// (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 )
+ if ( group == 0xfffe )
{
// NO more value field for SQ !
return;
{
if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
{
- //s << "gdcm::NotLoaded (BinEntry)";
s << GDCM_NOTLOADED;
- s << " Address:" << (long)entry->GetOffset();
- s << " Length:" << entry->GetLength();
+ 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());
}
- // Be carefull : a BinEntry IS_A ValEntry ...
else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) )
{
- // s << "gdcm::NotLoaded. (ValEntry)";
s << GDCM_NOTLOADED;
s << " Address:" << (long)entry->GetOffset();
s << " Length:" << entry->GetLength();
return;
}
- /// \todo Any compacter code suggested (?)
if ( IsDocEntryAnInteger(entry) )
{
uint32_t NewInt;
int nbInt;
// When short integer(s) are expected, read and convert the following
- // n *two characters properly i.e. consider them as short integers as
+ // (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)
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 )
+ if ( length % 2 )
{
newValue = Util::DicomString(str, length+1);
- gdcmVerboseMacro("Warning: bad length: " << length <<
- ",For string :" << newValue.c_str());
+ gdcmWarningMacro("Warning: bad length: " << length <<
+ " For string :" << newValue.c_str());
// Since we change the length of string update it length
//entry->SetReadLength(length+1);
}
{
if ( Fp->fail() || Fp->eof())
{
- gdcmVerboseMacro("Unread element value");
+ 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" )
+ if ( vr == "UI" )
{
// Because of correspondance with the VR dic
valEntry->SetValue(newValue);
}
else
{
- gdcmErrorMacro( "Should have a ValEntry, here !");
+ gdcmWarningMacro("Should have a ValEntry, here ! " << valEntry->GetKey()
+ << " lgt : " << valEntry->GetReadLength()
+ << " at " << std::hex << valEntry->GetOffset());
}
}
if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
- if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" )
+ if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT" || vr == "UN" )
{
// The following reserved two bytes (see PS 3.5-2003, section
// "7.1.2 Data element structure with explicit vr", p 27) must be
// Length is encoded on 2 bytes.
length16 = ReadInt16();
-
- // FIXME : This heuristic supposes that the first group following
- // group 0002 *has* and element 0000.
- // BUT ... Element 0000 is optionnal :-(
-
-
- // Fixed using : HandleOutOfGroup0002()
- // (first hereafter strategy ...)
-
- // We can tell the current file is encoded in big endian (like
- // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag
- // and it's value is the one of the encoding of a big endian file.
- // In order to deal with such big endian encoded files, we have
- // (at least) two strategies:
- // * when we load the "Transfer Syntax" tag with value of big endian
- // encoding, we raise the proper flags. Then we wait for the end
- // of the META group (0x0002) among which is "Transfer Syntax",
- // before switching the swap code to big endian. We have to postpone
- // the switching of the swap code since the META group is fully encoded
- // in little endian, and big endian coding only starts at the next
- // group. The corresponding code can be hard to analyse and adds
- // many additional unnecessary tests for regular tags.
- // * the second strategy consists in waiting for trouble, that shall
- // appear when we find the first group with big endian encoding. This
- // is easy to detect since the length of a "Group Length" tag (the
- // ones with zero as element number) has to be of 4 (0x0004). When we
- // encounter 1024 (0x0400) chances are the encoding changed and we
- // found a group with big endian encoding.
- //---> Unfortunately, element 0000 is optional.
- //---> This will not work when missing!
- // We shall use this second strategy. In order to make sure that we
- // can interpret the presence of an apparently big endian encoded
- // length of a "Group Length" without committing a big mistake, we
- // add an additional check: we look in the already parsed elements
- // for the presence of a "Transfer Syntax" whose value has to be "big
- // endian encoding". When this is the case, chances are we have got our
- // hands on a big endian encoded file: we switch the swap code to
- // big endian and proceed...
-
-// if ( element == 0x0000 && length16 == 0x0400 )
-// {
-// std::string ts = GetTransferSyntax();
-// if ( Global::GetTS()->GetSpecialTransferSyntax(ts)
-// != TS::ExplicitVRBigEndian )
-// {
-// throw FormatError( "Document::FindDocEntryLength()",
-// " not explicit VR." );
-// return;
-// }
-// length16 = 4;
-// 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 = GetDictEntry( correctGroup, correctElem );
-// if ( !newTag )
-// {
-// // This correct tag is not in the dictionary. Create a new one.
-// newTag = NewVirtualDictEntry(correctGroup, correctElem);
-// }
-// // FIXME this can create a memory leaks on the old entry that be
-// // left unreferenced.
-// entry->SetDictEntry( newTag );
-// }
// 0xffff means that we deal with 'No Length' Sequence
// or 'No Length' SQItem
if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
long filePosition = Fp->tellg();
- gdcmVerboseMacro( "Neither an Item tag nor a Sequence delimiter tag on :"
+ gdcmWarningMacro(
+ "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( "Neither an Item tag nor a Sequence delimiter tag.");
+ throw FormatUnexpected(
+ "Neither an Item tag nor a Sequence delimiter tag.");
}
if ( elem == 0xe0dd )
{
Fp->read (vr, (size_t)2);
vr[2] = 0;
- if( !CheckDocEntryVR(vr) )
+ if ( !CheckDocEntryVR(vr) )
{
Fp->seekg(positionOnEntry, std::ios::beg);
return GDCM_UNKNOWN;
// Elements with Value Multiplicity > 1
// contain a set of short integers (not a single one)
- if( vr == "US" || vr == "SS" )
+ if ( vr == "US" || vr == "SS" )
{
uint16_t newInt16;
nbInt = length / 2;
for (int i=0; i < nbInt; i++)
{
- if( i != 0 )
+ if ( i != 0 )
{
s << '\\';
}
// 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" )
+ else if ( vr == "UL" || vr == "SL" )
{
uint32_t newInt32;
nbInt = length / 4;
for (int i=0; i < nbInt; i++)
{
- if( i != 0)
+ if ( i != 0)
{
s << '\\';
}
if ( foundLength % 2)
{
- gdcmVerboseMacro( "Warning : Tag with uneven length " << foundLength
+ gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength
<< " in x(" << std::hex << gr << "," << elem <<")");
}
// 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 use (we are talking a few years, here)...
- // Note: XMedCom probably uses such a trick since it is able to read
+ // Note: XMedCon probably uses such a trick since it is able to read
// those pesky GE images ...
if ( foundLength == 13)
{
if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) )
{
foundLength = 10;
- entry->SetReadLength(10); /// \todo a bug is to be fixed !?
+ entry->SetReadLength(10); // a bug is to be fixed !?
}
}
else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
{
foundLength = 4;
- entry->SetReadLength(4); /// \todo a bug is to be fixed !?
+ entry->SetReadLength(4); // a bug is to be fixed !?
}
else if ( entry->GetVR() == "SQ" )
//////// 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 )
+ 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 ( entry->GetElement() != 0x0000 )
{
foundLength = 0;
}
*/
bool Document::IsDocEntryAnInteger(DocEntry *entry)
{
- uint16_t elem = entry->GetElement();
- uint16_t group = entry->GetGroup();
- const std::string &vr = entry->GetVR();
- uint32_t length = entry->GetLength();
+ uint16_t elem = entry->GetElement();
+ uint16_t group = entry->GetGroup();
+ const std::string &vr = entry->GetVR();
+ uint32_t length = entry->GetLength();
// When we have some semantics on the element we just read, and if we
// a priori know we are dealing with an integer, then we shall be
// encounter such an ill-formed image, we simply display a warning
// message and proceed on parsing (while crossing fingers).
long filePosition = Fp->tellg();
- gdcmVerboseMacro( "Erroneous Group Length element length on : ("
+ gdcmWarningMacro( "Erroneous Group Length element length on : ("
<< std::hex << group << " , " << elem
<< ") -before- position x(" << filePosition << ")"
<< "lgt : " << length );
* true when we hope ours assuptions are OK
*/
bool Document::CheckSwap()
-{
- // The only guaranted way of finding the swap code is to find a
- // group tag since we know it's length has to be of four bytes i.e.
- // 0x00000004. Finding the swap code in then straigthforward. Trouble
- // occurs when we can't find such group...
-
- uint32_t x = 4; // x : for ntohs
- bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
+{
uint32_t s32;
uint16_t s16;
// First, compare HostByteOrder and NetworkByteOrder in order to
// determine if we shall need to swap bytes (i.e. the Endian type).
- if ( x == ntohs(x) )
- {
- net2host = true;
- }
- else
- {
- net2host = false;
- }
+ bool net2host = Util::IsCurrentProcessorBigEndian();
// The easiest case is the one of a 'true' DICOM header, we just have
// to look for the string "DICM" inside the file preamble.
Fp->read(deb, 256);
char *entCur = deb + 128;
- if( memcmp(entCur, "DICM", (size_t)4) == 0 )
+ if ( memcmp(entCur, "DICM", (size_t)4) == 0 )
{
- gdcmVerboseMacro( "Looks like DICOM Version3 (preamble + DCM)" );
+ gdcmWarningMacro( "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 ...)
// even if elem 0002,0010 (Transfer Syntax) tells us the file is
// *Implicit* VR (see former 'gdcmData/icone.dcm')
- if( memcmp(entCur, "UL", (size_t)2) == 0 ||
- memcmp(entCur, "OB", (size_t)2) == 0 ||
- memcmp(entCur, "UI", (size_t)2) == 0 ||
- memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later
- // when Write DCM *adds*
+ if ( memcmp(entCur, "UL", (size_t)2) == 0 ||
+ memcmp(entCur, "OB", (size_t)2) == 0 ||
+ memcmp(entCur, "UI", (size_t)2) == 0 ||
+ memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later
+ // when Write DCM *adds*
// FIXME
// Use Document::dicom_vr to test all the possibilities
// instead of just checking for UL, OB and UI !? group 0000
{
Filetype = ExplicitVR;
- gdcmVerboseMacro( "Group 0002 : Explicit Value Representation");
+ gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
}
else
{
Filetype = ImplicitVR;
- gdcmVerboseMacro( "Group 0002 :Not an explicit Value Representation;"
+ gdcmWarningMacro( "Group 0002 :Not an explicit Value Representation;"
<< "Looks like a bugged Header!");
}
if ( net2host )
{
SwapCode = 4321;
- gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder");
+ gdcmWarningMacro( "HostByteOrder != NetworkByteOrder");
}
else
{
SwapCode = 1234;
- gdcmVerboseMacro( "HostByteOrder = NetworkByteOrder");
+ gdcmWarningMacro( "HostByteOrder = NetworkByteOrder");
}
// Position the file position indicator at first tag
// (i.e. after the file preamble and the "DICM" string).
- Fp->seekg(0, std::ios::beg);
+
+ Fp->seekg(0, std::ios::beg); // FIXME : Is it usefull?
+
Fp->seekg ( 132L, std::ios::beg);
return true;
- } // End of DicomV3
+ } // ------------------------------- End of DicomV3 ----------------
// 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).
- gdcmVerboseMacro( "Not a DICOM Version3 file");
+
+ gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)");
+
Fp->seekg(0, std::ios::beg);
+ // Let's check 'No Preamble Dicom File' :
+ // Should start with group 0x0002
+ // and be Explicit Value Representation
+
+ s16 = *((uint16_t *)(deb));
+ SwapCode = 0;
+ switch ( s16 )
+ {
+ case 0x0002 :
+ SwapCode = 1234;
+ entCur = deb + 4;
+ break;
+ case 0x0200 :
+ SwapCode = 4321;
+ entCur = deb + 6;
+ }
+
+ if ( SwapCode != 0 )
+ {
+ if ( memcmp(entCur, "UL", (size_t)2) == 0 ||
+ memcmp(entCur, "OB", (size_t)2) == 0 ||
+ memcmp(entCur, "UI", (size_t)2) == 0 ||
+ memcmp(entCur, "SH", (size_t)2) == 0 ||
+ memcmp(entCur, "AE", (size_t)2) == 0 ||
+ memcmp(entCur, "OB", (size_t)2) == 0 )
+ {
+ Filetype = ExplicitVR;
+ gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
+ return true;
+ }
+ }
+// ------------------------------- End of 'No Preamble' DicomV3 -------------
+
// Our next best chance would be to be considering a 'clean' ACR/NEMA file.
- // By clean we mean that the length of the first tag is written down.
+ // By clean we mean that the length of the first group is written down.
// If this is the case and since the length of the first group HAS to be
// four (bytes), then determining the proper swap code is straightforward.
// representation of a 32 bits integer. Hence the following dirty
// trick :
s32 = *((uint32_t *)(entCur));
-
switch( s32 )
{
case 0x00040000 :
Filetype = ACR;
return true;
default :
- gdcmVerboseMacro( "ACR/NEMA unfound swap info (Really hopeless !)");
+ gdcmWarningMacro( "ACR/NEMA unfound swap info (Really hopeless !)");
Filetype = Unknown;
return false;
}
*/
void Document::SwitchByteSwapCode()
{
- gdcmVerboseMacro( "Switching Byte Swap code from "<< SwapCode);
+ gdcmWarningMacro( "Switching Byte Swap code from "<< SwapCode
+ << " at :" <<std::hex << Fp->tellg() );
if ( SwapCode == 1234 )
{
SwapCode = 4321;
/**
* \brief during parsing, Header Elements too long are not loaded in memory
- * @param newSize
+ * @param newSize new size
*/
void Document::SetMaxSizeLoadEntry(long newSize)
{
MaxSizeLoadEntry = newSize;
}
-/**
- * \brief Header Elements too long will not be printed
- * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE
- * @param newSize
- */
-void Document::SetMaxSizePrintEntry(long newSize)
-{
- if ( newSize < 0 )
- {
- return;
- }
- if ((uint32_t)newSize >= (uint32_t)0xffffffff )
- {
- MaxSizePrintEntry = 0xffffffff;
- return;
- }
- MaxSizePrintEntry = newSize;
-}
-
-
/**
* \brief Read the next tag but WITHOUT loading it's value
* (read the 'Group Number', the 'Element Number',
std::string vr = FindDocEntryVR();
std::string realVR = vr;
- if( vr == GDCM_UNKNOWN)
+ if ( vr == GDCM_UNKNOWN )
{
- DictEntry *dictEntry = GetDictEntry(group,elem);
- if( dictEntry )
- realVR = dictEntry->GetVR();
+ if ( elem == 0x0000 ) // Group Length
+ realVR = "UL"; // must be UL
+ else
+ {
+ DictEntry *dictEntry = GetDictEntry(group,elem);
+ if ( dictEntry )
+ realVR = dictEntry->GetVR();
+ }
}
DocEntry *newEntry;
- if( Global::GetVR()->IsVROfSequence(realVR) )
+ if ( Global::GetVR()->IsVROfSequence(realVR) )
newEntry = NewSeqEntry(group, elem);
- else if( Global::GetVR()->IsVROfStringRepresentable(realVR) )
+ else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) )
newEntry = NewValEntry(group, elem,vr);
else
newEntry = NewBinEntry(group, elem,vr);
- if( vr == GDCM_UNKNOWN )
+ if ( vr == GDCM_UNKNOWN )
{
- if( Filetype == ExplicitVR )
+ 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 )
{
std::string msg;
- msg = Util::Format("Entry (%04x,%04x) should be Explicit VR\n",
- newEntry->GetGroup(), newEntry->GetElement());
- gdcmVerboseMacro( msg.c_str() );
+ int offset = Fp->tellg();
+ msg = Util::Format("Entry (%04x,%04x) at %x should be Explicit VR\n",
+ newEntry->GetGroup(), newEntry->GetElement(), offset );
+ gdcmWarningMacro( msg.c_str() );
}
}
newEntry->SetImplicitVR();
catch ( FormatError e )
{
// Call it quits
- //std::cout << e;
delete newEntry;
return 0;
}
/**
* \brief Handle broken private tag from Philips NTSCAN
- * where the endianess is being switch to BigEndian for no
+ * where the endianess is being switched to BigEndian for no
* apparent reason
* @return no return
*/
std::string ts = GetTransferSyntax();
if ( !Global::GetTS()->IsTransferSyntax(ts) )
{
- gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
+ gdcmWarningMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
return;
}
//'Implicit VR Transfer Syntax (GE Private)
if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
{
- gdcmVerboseMacro("Transfer Syntax Name = ["
+ gdcmWarningMacro("Transfer Syntax Name = ["
<< GetTransferSyntaxName() << "]" );
SwitchByteSwapCode();
group = SwapShort(group);
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff