Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/01/28 09:31:51 $
- Version: $Revision: 1.215 $
+ Date: $Date: 2005/02/07 09:51:03 $
+ Version: $Revision: 1.225 $
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>
+#include <fstream>
// For nthos:
#if defined(_MSC_VER) || defined(__BORLANDC__) || defined(__MINGW32__)
namespace gdcm
{
-
//-----------------------------------------------------------------------------
// Refer to Document::CheckSwap()
//const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
//-----------------------------------------------------------------------------
// 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
*/
-Document::Document( std::string const &filename ) : ElementSet(-1)
+Document::Document( std::string const &filename )
+ :ElementSet(-1)
{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Filename = filename;
Group0002Parsed = false;
- gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str());
+ gdcmWarningMacro( "Starting parsing of file: " << Filename.c_str());
// Fp->seekg( 0, std::ios::beg);
- Fp->seekg(0, std::ios::end);
+ Fp->seekg(0, std::ios::end);
long lgt = Fp->tellg();
- Fp->seekg( 0, std::ios::beg);
+ Fp->seekg(0, std::ios::beg);
CheckSwap();
long beg = Fp->tellg();
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)
SetValEntry(columns, 0x0028, 0x0010);
SetValEntry(rows , 0x0028, 0x0011);
}
- // ----------------- End of ACR-LibIDO kludge ------------------
+ // --- 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)
+Document::Document()
+ :ElementSet(-1)
{
Fp = 0;
RefShaDict = NULL;
}
-//-----------------------------------------------------------------------------
-// Print
-
-/**
- * \brief Prints The Dict Entries of THE public Dicom Dictionary
- * @param os ostream to print to
- * @return
- */
-void Document::PrintPubDict(std::ostream &os)
-{
- RefPubDict->SetPrintLevel(PrintLevel);
- RefPubDict->Print(os);
-}
-
-/**
- * \brief Prints The Dict Entries of THE shadow Dicom Dictionary
- * @param os ostream to print to
- * @return
- */
-void Document::PrintShaDict(std::ostream &os)
-{
- RefShaDict->SetPrintLevel(PrintLevel);
- RefShaDict->Print(os);
-}
-
//-----------------------------------------------------------------------------
// Public
/**
{
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;
}
return true;
}
+/**
+ * \brief Predicate for dicom version 3 file.
+ * @return True when the file is a dicom version 3.
+ */
+bool Document::IsDicomV3()
+{
+ // Checking if Transfer Syntax exists is enough
+ // Anyway, it's to late check if the 'Preamble' was found ...
+ // And ... would it be a rich idea to check ?
+ // (some 'no Preamble' DICOM images exist !)
+ return GetDocEntry(0x0002, 0x0010) != NULL;
+}
+
+/**
+ * \brief Predicate for Papyrus file
+ * Dedicated to whomsoever it may concern
+ * @return True when the file is a Papyrus file.
+ */
+bool Document::IsPapyrus()
+{
+ // check for Papyrus private Sequence
+ DocEntry *e = GetDocEntry(0x0041, 0x1050);
+ if ( !e )
+ return false;
+ // check if it's actually a Sequence
+ if ( !dynamic_cast<SeqEntry*>(e) )
+ return false;
+ return true;
+}
+
+/**
+ * \brief returns the File Type
+ * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
+ * @return the FileType code
+ */
+FileType Document::GetFileType()
+{
+ return Filetype;
+}
+
/**
* \brief Accessor to the Transfer Syntax (when present) of the
* current document (it internally handles reading the
}
/**
- * \brief Predicate for dicom version 3 file.
- * @return True when the file is a dicom version 3.
+ * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS
+ * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
*/
-bool Document::IsDicomV3()
+std::string Document::GetTransferSyntaxName()
{
- // Checking if Transfer Syntax exists is enough
- // Anyway, it's to late check if the 'Preamble' was found ...
- // And ... would it be a rich idea to check ?
- // (some 'no Preamble' DICOM images exist !)
- return GetDocEntry(0x0002, 0x0010) != NULL;
-}
+ // use the TS (TS : Transfer Syntax)
+ std::string transferSyntax = GetEntryValue(0x0002,0x0010);
+
+ if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) )
+ {
+ gdcmErrorMacro( "Transfer Syntax not loaded. " << std::endl
+ << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" );
+ return "Uncompressed ACR-NEMA";
+ }
+ if ( transferSyntax == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Unfound Transfer Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
+ }
+ // we do it only when we need it
+ const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax );
+
+ // Global::GetTS() is a global static you shall never try to delete it!
+ return tsName;
+}
+//
+// --------------- Swap Code ------------------
/**
- * \brief Predicate for Papyrus file
- * Dedicated to whomsoever it may concern
- * @return True when the file is a Papyrus file.
+ * \brief Swaps the bytes so they agree with the processor order
+ * @return The properly swaped 16 bits integer.
*/
-bool Document::IsPapyrus()
+uint16_t Document::SwapShort(uint16_t a)
{
- // check for Papyrus private Sequence
- DocEntry *e = GetDocEntry(0x0041, 0x1050);
- if ( !e )
- return false;
- // check if it's actually a Sequence
- if ( !dynamic_cast<SeqEntry*>(e) )
- return false;
- return true;
+ if ( SwapCode == 4321 || SwapCode == 2143 )
+ {
+ a = ((( a << 8 ) & 0xff00 ) | (( a >> 8 ) & 0x00ff ) );
+ }
+ return a;
}
/**
- * \brief returns the File Type
- * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
- * @return the FileType code
+ * \brief Swaps back the bytes of 4-byte long integer accordingly to
+ * processor order.
+ * @return The properly swaped 32 bits integer.
*/
-FileType Document::GetFileType()
+uint32_t Document::SwapLong(uint32_t a)
{
- return Filetype;
-}
+ switch (SwapCode)
+ {
+ case 1234 :
+ break;
+ case 4321 :
+ a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
+ ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
+ break;
+ case 3412 :
+ a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
+ break;
+ case 2143 :
+ a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
+ break;
+ default :
+ gdcmErrorMacro( "Unset 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.
if(Fp)
{
- gdcmVerboseMacro( "File already open: " << Filename.c_str());
+ gdcmWarningMacro( "File already open: " << Filename.c_str());
CloseFile();
}
return 0;
}
- uint16_t zero;
+ uint16_t zero = 0;
Fp->read((char*)&zero, (size_t)2);
if( Fp->eof() )
{
{
std::string msg
= Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero);
- gdcmVerboseMacro( msg.c_str() );
+ gdcmWarningMacro( msg.c_str() );
return Fp;
}
//DICOM
Fp->seekg(126L, std::ios::cur);
- char dicm[4];
+ char dicm[4] = {' ',' ',' ',' '};
Fp->read(dicm, (size_t)4);
if( Fp->eof() )
{
}
CloseFile();
- gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
+ gdcmWarningMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
return 0;
}
fp->write("DICM", 4);
}
-/*
- * \todo rewrite later, if really usefull
- * - 'Group Length' element is optional in DICOM
- * - but un-updated odd groups lengthes can causes pb
- * (xmedcon breaker)
- *
- * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) )
- * UpdateGroupLength(false,filetype);
- * if ( filetype == ACR)
- * UpdateGroupLength(true,ACR);
- */
-
+ /*
+ * \todo rewrite later, if really usefull
+ * - 'Group Length' element is optional in DICOM
+ * - but un-updated odd groups lengthes can causes pb
+ * (xmedcon breaker)
+ *
+ * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) )
+ * UpdateGroupLength(false,filetype);
+ * if ( filetype == ACR)
+ * UpdateGroupLength(true,ACR);
+ */
+
ElementSet::WriteContent(fp, filetype); // This one is recursive
}
-//-----------------------------------------------------------------------------
-// Protected
+// -----------------------------------------
+// Content entries
/**
* \brief Loads (from disk) the element content
* when a string is not suitable
uint8_t *a = new uint8_t[l];
if( !a )
{
- gdcmVerboseMacro( "Cannot allocate BinEntry content");
+ gdcmWarningMacro( "Cannot allocate BinEntry content");
return;
}
CloseFile();
}
-/**
- * \brief Sets a 'non string' value to a given Dicom Element
- * @param area area containing the 'non string' value
- * @param group Group number of the searched Dicom Element
- * @param elem Element number of the searched Dicom Element
- * @return
- */
-/*bool Document::SetEntryBinArea(uint8_t *area,
- uint16_t group, uint16_t elem)
-{
- DocEntry *currentEntry = GetDocEntry(group, elem);
- if ( !currentEntry )
- {
- return false;
- }
-
- if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(currentEntry) )
- {
- binEntry->SetBinArea( area );
- return true;
- }
-
- return false;
-}*/
-
-
/**
* \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)
{
}
/**
- * \brief Swaps back the bytes of 4-byte long integer accordingly to
- * processor order.
- * @return The properly swaped 32 bits integer.
+ * \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 to compare with current one
+ * @return true if 'smaller'
*/
-uint32_t Document::SwapLong(uint32_t a)
+bool Document::operator<(Document &document)
{
- switch (SwapCode)
+ // Patient Name
+ std::string s1 = GetEntryValue(0x0010,0x0010);
+ std::string s2 = document.GetEntryValue(0x0010,0x0010);
+ if(s1 < s2)
{
- case 1234 :
- break;
- case 4321 :
- a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
- ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
- break;
- case 3412 :
- a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
- break;
- case 2143 :
- a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
- break;
- default :
- gdcmErrorMacro( "Unset swap code:" << SwapCode );
- a = 0;
+ return true;
}
- return a;
-}
-
-/**
- * \brief Unswaps back the bytes of 4-byte long integer accordingly to
- * processor order.
- * @return The properly unswaped 32 bits integer.
- */
-uint32_t Document::UnswapLong(uint32_t a)
-{
- return SwapLong(a);
-}
-
-/**
- * \brief Swaps the bytes so they agree with the processor order
- * @return The properly swaped 16 bits integer.
- */
-uint16_t Document::SwapShort(uint16_t a)
-{
- if ( SwapCode == 4321 || SwapCode == 2143 )
+ else if( s1 > s2 )
{
- a = ((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) );
+ return false;
}
- return a;
-}
-
-/**
- * \brief Unswaps the bytes so they agree with the processor order
- * @return The properly unswaped 16 bits integer.
- */
-uint16_t Document::UnswapShort(uint16_t a)
-{
- return SwapShort(a);
-}
-
-//-----------------------------------------------------------------------------
-// Private
-
-/**
- * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
- * @return length of the parsed set.
- */
-void Document::ParseDES(DocEntrySet *set, long offset,
- long l_max, bool delim_mode)
-{
- DocEntry *newDocEntry = 0;
- ValEntry *newValEntry;
- BinEntry *newBinEntry;
- SeqEntry *newSeqEntry;
- VRKey vr;
- bool used = false;
-
- while (true)
+ else
{
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ // Patient ID
+ s1 = GetEntryValue(0x0010,0x0020);
+ s2 = document.GetEntryValue(0x0010,0x0020);
+ if ( s1 < s2 )
{
- break;
+ return true;
}
-
- used = true;
- newDocEntry = ReadNextDocEntry( );
-
- if ( !newDocEntry )
+ else if ( s1 > s2 )
{
- break;
+ return false;
}
-
- vr = newDocEntry->GetVR();
- newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
- newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
- newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
-
- if ( newValEntry || newBinEntry )
+ else
{
- if ( newBinEntry )
- {
+ // Study Instance UID
+ s1 = GetEntryValue(0x0020,0x000d);
+ s2 = document.GetEntryValue(0x0020,0x000d);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
+ else
+ {
+ // Serie Instance UID
+ s1 = GetEntryValue(0x0020,0x000e);
+ s2 = document.GetEntryValue(0x0020,0x000e);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
+ }
+ }
+ }
+ return false;
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \brief Reads a supposed to be 16 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
+ */
+uint16_t Document::ReadInt16()
+ throw( FormatError )
+{
+ uint16_t g;
+ Fp->read ((char*)&g, (size_t)2);
+ if ( Fp->fail() )
+ {
+ throw FormatError( "Document::ReadInt16()", " file error." );
+ }
+ if( Fp->eof() )
+ {
+ throw FormatError( "Document::ReadInt16()", "EOF." );
+ }
+ g = SwapShort(g);
+ return g;
+}
+
+/**
+ * \brief Reads a supposed to be 32 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
+ */
+uint32_t Document::ReadInt32()
+ throw( FormatError )
+{
+ uint32_t g;
+ Fp->read ((char*)&g, (size_t)4);
+ if ( Fp->fail() )
+ {
+ throw FormatError( "Document::ReadInt32()", " file error." );
+ }
+ if( Fp->eof() )
+ {
+ throw FormatError( "Document::ReadInt32()", "EOF." );
+ }
+ g = SwapLong(g);
+ return g;
+}
+
+/**
+ * \brief skips bytes inside the source file
+ * \warning NOT end user intended method !
+ * @return
+ */
+void Document::SkipBytes(uint32_t nBytes)
+{
+ //FIXME don't dump the returned value
+ Fp->seekg((long)nBytes, std::ios::cur);
+}
+
+/**
+ * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
+ * @param filetype Type of the File to be written
+ */
+int Document::ComputeGroup0002Length( FileType filetype )
+{
+ uint16_t gr;
+ std::string vr;
+
+ int groupLength = 0;
+ bool found0002 = false;
+
+ // for each zero-level Tag in the DCM Header
+ DocEntry *entry = GetFirstEntry();
+ while( entry )
+ {
+ gr = entry->GetGroup();
+
+ if( gr == 0x0002 )
+ {
+ found0002 = true;
+
+ if( entry->GetElement() != 0x0000 )
+ {
+ vr = entry->GetVR();
+
+ if( filetype == ExplicitVR )
+ {
+ if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
+ {
+ // explicit VR AND OB, OW, SQ : 4 more bytes
+ groupLength += 4;
+ }
+ }
+ groupLength += 2 + 2 + 4 + entry->GetLength();
+ }
+ }
+ else if (found0002 )
+ break;
+
+ entry = GetNextEntry();
+ }
+ return groupLength;
+}
+
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \brief Loads all the needed Dictionaries
+ * \warning NOT end user intended method !
+ */
+void Document::Initialize()
+{
+ RefPubDict = Global::GetDicts()->GetDefaultPubDict();
+ RefShaDict = NULL;
+ Filetype = Unknown;
+}
+
+/**
+ * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
+ * @return length of the parsed set.
+ */
+void Document::ParseDES(DocEntrySet *set, long offset,
+ long l_max, bool delim_mode)
+{
+ DocEntry *newDocEntry = 0;
+ ValEntry *newValEntry;
+ BinEntry *newBinEntry;
+ SeqEntry *newSeqEntry;
+ VRKey vr;
+ bool used = false;
+
+ while (true)
+ {
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ {
+ break;
+ }
+
+ used = true;
+ newDocEntry = ReadNextDocEntry( );
+
+ if ( !newDocEntry )
+ {
+ break;
+ }
+
+ vr = newDocEntry->GetVR();
+ newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
+ newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
+ newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
+
+ if ( newValEntry || newBinEntry )
+ {
+ if ( newBinEntry )
+ {
if ( Filetype == ExplicitVR &&
!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.");
}
/**
- * \brief Loads the element content if its length doesn't exceed
- * the value specified with Document::SetMaxSizeLoadEntry()
- * @param entry Header Entry (Dicom Element) to be dealt with
+ * \brief Loads the element content if its length doesn't exceed
+ * the value specified with Document::SetMaxSizeLoadEntry()
+ * @param entry Header Entry (Dicom Element) to be dealt with
*/
void Document::LoadDocEntry(DocEntry *entry)
{
if( length % 2 )
{
newValue = Util::DicomString(str, length+1);
- gdcmVerboseMacro("Warning: bad length: " << length <<
+ 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");
+ gdcmWarningMacro("Unread element value");
valEntry->SetValue(GDCM_UNREAD);
return;
}
}
}
-
/**
* \brief Find the value Length of the passed Header Entry
* @param entry Header Entry whose length of the value shall be loaded.
}
}
+/**
+ * \brief Find the Length till the next sequence delimiter
+ * \warning NOT end user intended method !
+ * @return
+ */
+uint32_t Document::FindDocEntryLengthOBOrOW()
+ throw( FormatUnexpected )
+{
+ // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
+ long positionOnEntry = Fp->tellg();
+ bool foundSequenceDelimiter = false;
+ uint32_t totalLength = 0;
+
+ while ( !foundSequenceDelimiter )
+ {
+ uint16_t group;
+ uint16_t elem;
+ try
+ {
+ group = ReadInt16();
+ elem = ReadInt16();
+ }
+ catch ( FormatError )
+ {
+ throw FormatError("Unexpected end of file encountered during ",
+ "Document::FindDocEntryLengthOBOrOW()");
+ }
+ // 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 << ")" );
+
+ Fp->seekg(positionOnEntry, std::ios::beg);
+ throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag.");
+ }
+ if ( elem == 0xe0dd )
+ {
+ foundSequenceDelimiter = true;
+ }
+ uint32_t itemLength = ReadInt32();
+ // We add 4 bytes since we just read the ItemLength with ReadInt32
+ totalLength += itemLength + 4;
+ SkipBytes(itemLength);
+
+ if ( foundSequenceDelimiter )
+ {
+ break;
+ }
+ }
+ Fp->seekg( positionOnEntry, std::ios::beg);
+ return totalLength;
+}
+
/**
* \brief Find the Value Representation of the current Dicom Element.
* @return Value Representation of the current Entry
*/
bool Document::CheckDocEntryVR(VRKey vr)
{
- // CLEANME searching the dicom_vr at each occurence is expensive.
- // PostPone this test in an optional integrity check at the end
- // of parsing or only in debug mode.
if ( !Global::GetVR()->IsValidVR(vr) )
return false;
#endif //GDCM_NO_ANSI_STRING_STREAM
return s.str();
}
-
return ((ValEntry *)entry)->GetValue();
}
}
/**
- * \brief Skips to the begining of the next Header Entry
+ * \brief Skips to the beginning of the next Header Entry
* \warning NOT end user intended method !
* @param currentDocEntry entry to skip
*/
if ( foundLength % 2)
{
- gdcmVerboseMacro( "Warning : Tag with uneven length " << foundLength
+ gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength
<< " in x(" << std::hex << gr << "," << elem <<")");
}
{
foundLength = 0;
}
- }
-
+ }
entry->SetLength(foundLength);
}
*/
bool Document::IsDocEntryAnInteger(DocEntry *entry)
{
- uint16_t elem = entry->GetElement();
- uint16_t group = entry->GetGroup();
+ uint16_t elem = entry->GetElement();
+ uint16_t group = entry->GetGroup();
const std::string &vr = entry->GetVR();
- uint32_t length = entry->GetLength();
+ 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 );
}
/**
- * \brief Find the Length till the next sequence delimiter
- * \warning NOT end user intended method !
- * @return
+ * \brief Discover what the swap code is (among little endian, big endian,
+ * bad little endian, bad big endian).
+ * sw is set
+ * @return false when we are absolutely sure
+ * it's neither ACR-NEMA nor DICOM
+ * true when we hope ours assuptions are OK
*/
-
-uint32_t Document::FindDocEntryLengthOBOrOW()
- throw( FormatUnexpected )
-{
- // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
- long positionOnEntry = Fp->tellg();
- bool foundSequenceDelimiter = false;
- uint32_t totalLength = 0;
-
- while ( !foundSequenceDelimiter )
- {
- uint16_t group;
- uint16_t elem;
- try
- {
- group = ReadInt16();
- elem = ReadInt16();
- }
- catch ( FormatError )
- {
- throw FormatError("Unexpected end of file encountered during ",
- "Document::FindDocEntryLengthOBOrOW()");
- }
-
- // We have to decount the group and element we just read
- totalLength += 4;
-
- if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
- {
- long filePosition = Fp->tellg();
- gdcmVerboseMacro( "Neither an Item tag nor a Sequence delimiter tag on :"
- << std::hex << group << " , " << elem
- << ") -before- position x(" << filePosition << ")" );
-
- Fp->seekg(positionOnEntry, std::ios::beg);
- throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag.");
- }
-
- if ( elem == 0xe0dd )
- {
- foundSequenceDelimiter = true;
- }
-
- uint32_t itemLength = ReadInt32();
- // We add 4 bytes since we just read the ItemLength with ReadInt32
- totalLength += itemLength + 4;
- SkipBytes(itemLength);
-
- if ( foundSequenceDelimiter )
- {
- break;
- }
- }
- Fp->seekg( positionOnEntry, std::ios::beg);
- return totalLength;
-}
-
-/**
- * \brief Reads a supposed to be 16 Bits integer
- * (swaps it depending on processor endianity)
- * @return read value
- */
-uint16_t Document::ReadInt16()
- throw( FormatError )
-{
- uint16_t g;
- Fp->read ((char*)&g, (size_t)2);
- if ( Fp->fail() )
- {
- throw FormatError( "Document::ReadInt16()", " file error." );
- }
- if( Fp->eof() )
- {
- throw FormatError( "Document::ReadInt16()", "EOF." );
- }
- g = SwapShort(g);
- return g;
-}
-
-/**
- * \brief Reads a supposed to be 32 Bits integer
- * (swaps it depending on processor endianity)
- * @return read value
- */
-uint32_t Document::ReadInt32()
- throw( FormatError )
-{
- uint32_t g;
- Fp->read ((char*)&g, (size_t)4);
- if ( Fp->fail() )
- {
- throw FormatError( "Document::ReadInt32()", " file error." );
- }
- if( Fp->eof() )
- {
- throw FormatError( "Document::ReadInt32()", "EOF." );
- }
- g = SwapLong(g);
- return g;
-}
-
-/**
- * \brief skips bytes inside the source file
- * \warning NOT end user intended method !
- * @return
- */
-void Document::SkipBytes(uint32_t nBytes)
-{
- //FIXME don't dump the returned value
- Fp->seekg((long)nBytes, std::ios::cur);
-}
-
-/**
- * \brief Loads all the needed Dictionaries
- * \warning NOT end user intended method !
- */
-void Document::Initialize()
-{
- RefPubDict = Global::GetDicts()->GetDefaultPubDict();
- RefShaDict = NULL;
- Filetype = Unknown;
-}
-
-/**
- * \brief Discover what the swap code is (among little endian, big endian,
- * bad little endian, bad big endian).
- * sw is set
- * @return false when we are absolutely sure
- * it's neither ACR-NEMA nor DICOM
- * true when we hope ours assuptions are OK
- */
-bool Document::CheckSwap()
+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.
char *entCur = deb + 128;
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 ...)
// 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
// 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 DICOM Version3 file");
Fp->seekg(0, std::ios::beg);
// Our next best chance would be to be considering a 'clean' ACR/NEMA file.
Filetype = ACR;
return true;
default :
- 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);
if ( SwapCode == 1234 )
{
SwapCode = 4321;
MaxSizeLoadEntry = newSize;
}
-
/**
* \brief Header Elements too long will not be printed
* \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE
}
-
-/**
- * \brief Handle broken private tag from Philips NTSCAN
- * where the endianess is being switch to BigEndian for no
- * apparent reason
- * @return no return
- */
-void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
-{
- // 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
- reversedEndian++;
- SwitchByteSwapCode();
- // fix the tag
- group = 0xfffe;
- elem = 0xe000;
- }
- else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
- {
- // end of reversed endian group
- reversedEndian--;
- SwitchByteSwapCode();
- }
-}
-
-/**
- * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS
- * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
- */
-std::string Document::GetTransferSyntaxName()
-{
- // use the TS (TS : Transfer Syntax)
- std::string transferSyntax = GetEntryValue(0x0002,0x0010);
-
- if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) )
- {
- gdcmErrorMacro( "Transfer Syntax not loaded. " << std::endl
- << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" );
- return "Uncompressed ACR-NEMA";
- }
- if ( transferSyntax == GDCM_UNFOUND )
- {
- gdcmVerboseMacro( "Unfound Transfer Syntax (0002,0010)");
- return "Uncompressed ACR-NEMA";
- }
-
- // we do it only when we need it
- const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax );
-
- // Global::GetTS() is a global static you shall never try to delete it!
- return tsName;
-}
-
-/**
- * \brief Group 0002 is always coded Little Endian
- * whatever Transfer Syntax is
- * @return no return
- */
-void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem)
-{
- // Endian reversion. Some files contain groups of tags with reversed endianess.
- if ( !Group0002Parsed && group != 0x0002)
- {
- Group0002Parsed = true;
- // we just came out of group 0002
- // if Transfer syntax is Big Endian we have to change CheckSwap
-
- std::string ts = GetTransferSyntax();
- if ( !Global::GetTS()->IsTransferSyntax(ts) )
- {
- gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
- return;
- }
-
- // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..."
-
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian )
- {
- Filetype = ImplicitVR;
- }
-
- // FIXME Strangely, this works with
- //'Implicit VR Transfer Syntax (GE Private)
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
- {
- gdcmVerboseMacro("Transfer Syntax Name = ["
- << GetTransferSyntaxName() << "]" );
- SwitchByteSwapCode();
- group = SwapShort(group);
- elem = SwapShort(elem);
- }
- }
-}
-
/**
* \brief Read the next tag but WITHOUT loading it's value
* (read the 'Group Number', the 'Element Number',
{
// We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
- //std::cout << e;
return 0;
}
// Sometimes file contains groups of tags with reversed endianess.
HandleBrokenEndian(group, elem);
-// In 'true DICOM' files Group 0002 is always little endian
+ // In 'true DICOM' files Group 0002 is always little endian
if ( HasDCMPreamble )
HandleOutOfGroup0002(group, elem);
std::string msg;
msg = Util::Format("Entry (%04x,%04x) should be Explicit VR\n",
newEntry->GetGroup(), newEntry->GetElement());
- gdcmVerboseMacro( msg.c_str() );
+ gdcmWarningMacro( msg.c_str() );
}
}
newEntry->SetImplicitVR();
return newEntry;
}
-//GenerateFreeTagKeyInGroup? What was it designed for ?!?
-/**
- * \brief Generate a free TagKey i.e. a TagKey that is not present
- * in the TagHt dictionary.
- * @param group The generated tag must belong to this group.
- * @return The element of tag with given group which is fee.
- */
-//uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group)
-//{
-// for (uint32_t elem = 0; elem < UINT32_MAX; elem++)
-// {
-// TagKey key = DictEntry::TranslateToKey(group, elem);
-// if (TagHT.count(key) == 0)
-// {
-// return elem;
-// }
-// }
-// return UINT32_MAX;
-//}
-
/**
- * \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
- * @return true if 'smaller'
+ * \brief Handle broken private tag from Philips NTSCAN
+ * where the endianess is being switch to BigEndian for no
+ * apparent reason
+ * @return no return
*/
-bool Document::operator<(Document &document)
+void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
{
- // Patient Name
- std::string s1 = GetEntryValue(0x0010,0x0010);
- std::string s2 = document.GetEntryValue(0x0010,0x0010);
- if(s1 < s2)
- {
- return true;
- }
- else if( s1 > s2 )
+ // 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))
{
- return false;
- }
- else
+ // start endian swap mark for group found
+ reversedEndian++;
+ SwitchByteSwapCode();
+ // fix the tag
+ group = 0xfffe;
+ elem = 0xe000;
+ }
+ else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
{
- // Patient ID
- s1 = GetEntryValue(0x0010,0x0020);
- s2 = document.GetEntryValue(0x0010,0x0020);
- if ( s1 < s2 )
- {
- return true;
- }
- else if ( s1 > s2 )
- {
- return false;
- }
- else
- {
- // Study Instance UID
- s1 = GetEntryValue(0x0020,0x000d);
- s2 = document.GetEntryValue(0x0020,0x000d);
- if ( s1 < s2 )
- {
- return true;
- }
- else if( s1 > s2 )
- {
- return false;
- }
- else
- {
- // Serie Instance UID
- s1 = GetEntryValue(0x0020,0x000e);
- s2 = document.GetEntryValue(0x0020,0x000e);
- if ( s1 < s2 )
- {
- return true;
- }
- else if( s1 > s2 )
- {
- return false;
- }
- }
- }
+ // end of reversed endian group
+ reversedEndian--;
+ SwitchByteSwapCode();
}
- return false;
}
/**
- * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
- * @param filetype Type of the File to be written
+ * \brief Group 0002 is always coded Little Endian
+ * whatever Transfer Syntax is
+ * @return no return
*/
-int Document::ComputeGroup0002Length( FileType filetype )
+void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem)
{
- uint16_t gr;
- std::string vr;
-
- int groupLength = 0;
- bool found0002 = false;
-
- // for each zero-level Tag in the DCM Header
- DocEntry *entry = GetFirstEntry();
- while(entry)
+ // Endian reversion. Some files contain groups of tags with reversed endianess.
+ if ( !Group0002Parsed && group != 0x0002)
{
- gr = entry->GetGroup();
+ Group0002Parsed = true;
+ // we just came out of group 0002
+ // if Transfer syntax is Big Endian we have to change CheckSwap
- if (gr == 0x0002)
+ std::string ts = GetTransferSyntax();
+ if ( !Global::GetTS()->IsTransferSyntax(ts) )
{
- found0002 = true;
- vr = entry->GetVR();
-
- if (filetype == ExplicitVR)
- {
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
- {
- groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes
- }
- }
- groupLength += 2 + 2 + 4 + entry->GetLength();
+ gdcmWarningMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
+ return;
}
- else if (found0002 )
- break;
- entry = GetNextEntry();
- }
- return groupLength;
-}
+ // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..."
-/*
- * \brief Walk recursively the given \ref DocEntrySet, and feed
- * the given hash table (\ref TagDocEntryHT) with all the
- * \ref DocEntry (Dicom entries) encountered.
- * This method does the job for \ref BuildFlatHashTable.
- * @param builtHT Where to collect all the \ref DocEntry encountered
- * when recursively walking the given set.
- * @param set The structure to be traversed (recursively).
- */
-/*void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT,
- DocEntrySet *set )
-{
- if (ElementSet *elementSet = dynamic_cast< ElementSet* > ( set ) )
- {
- TagDocEntryHT const ¤tHT = elementSet->GetTagHT();
- for( TagDocEntryHT::const_iterator i = currentHT.begin();
- i != currentHT.end();
- ++i)
- {
- DocEntry *entry = i->second;
- if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian )
{
- const ListSQItem& items = seqEntry->GetSQItems();
- for( ListSQItem::const_iterator item = items.begin();
- item != items.end();
- ++item)
- {
- BuildFlatHashTableRecurse( builtHT, *item );
- }
- continue;
+ Filetype = ImplicitVR;
}
- builtHT[entry->GetKey()] = entry;
- }
- return;
- }
-
- if (SQItem *SQItemSet = dynamic_cast< SQItem* > ( set ) )
- {
- const ListDocEntry& currentList = SQItemSet->GetDocEntries();
- for (ListDocEntry::const_iterator i = currentList.begin();
- i != currentList.end();
- ++i)
+
+ // FIXME Strangely, this works with
+ //'Implicit VR Transfer Syntax (GE Private)
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
{
- DocEntry *entry = *i;
- if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
- {
- const ListSQItem& items = seqEntry->GetSQItems();
- for( ListSQItem::const_iterator item = items.begin();
- item != items.end();
- ++item)
- {
- BuildFlatHashTableRecurse( builtHT, *item );
- }
- continue;
- }
- builtHT[entry->GetKey()] = entry;
+ gdcmWarningMacro("Transfer Syntax Name = ["
+ << GetTransferSyntaxName() << "]" );
+ SwitchByteSwapCode();
+ group = SwapShort(group);
+ elem = SwapShort(elem);
}
-
}
-}*/
-
-/*
- * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current
- * Document.
- *
- * The structure used by a Document (through \ref ElementSet),
- * in order to hold the parsed entries of a Dicom header, is a recursive
- * one. This is due to the fact that the sequences (when present)
- * can be nested. Additionaly, the sequence items (represented in
- * gdcm as \ref SQItem) add an extra complexity to the data
- * structure. Hence, a gdcm user whishing to visit all the entries of
- * a Dicom header will need to dig in the gdcm internals (which
- * implies exposing all the internal data structures to the API).
- * In order to avoid this burden to the user, \ref BuildFlatHashTable
- * recursively builds a temporary hash table, which holds all the
- * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a
- * std::map<>).
- * \warning Of course there is NO integrity constrain between the
- * returned \ref TagDocEntryHT and the \ref ElementSet used
- * to build it. Hence if the underlying \ref ElementSet is
- * altered, then it is the caller responsability to invoke
- * \ref BuildFlatHashTable again...
- * @return The flat std::map<> we juste build.
- */
-/*TagDocEntryHT *Document::BuildFlatHashTable()
-{
- TagDocEntryHT *FlatHT = new TagDocEntryHT;
- BuildFlatHashTableRecurse( *FlatHT, this );
- return FlatHT;
-}*/
+}
-} // end namespace gdcm
+//-----------------------------------------------------------------------------
+// Print
//-----------------------------------------------------------------------------
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff