Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2006/05/30 08:10:19 $
- Version: $Revision: 1.349 $
+ Date: $Date: 2007/04/12 13:22:49 $
+ Version: $Revision: 1.357 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
Initialize();
SwapCode = 1234;
Filetype = ExplicitVR;
+ CurrentOffsetPosition = 0;
// Load will set it to true if sucessfull
Group0002Parsed = false;
IsDocumentAlreadyLoaded = false;
IsDocumentModified = true;
LoadMode = LD_ALL; // default : load everything, later
+
SetFileName("");
}
// -----------------File I/O ---------------
/**
* \brief Tries to open the file \ref Document::Filename and
- * checks the preamble when existing.
- * @return The FILE pointer on success.
+ * 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()
{
return 0;
}
- //-- 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 )
- {
- 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;
- }
-
//-- DICOM --
Fp->seekg(126L, std::ios::cur); // Once per Document
char dicm[4]; // = {' ',' ',' ',' '};
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();
// Don't user Warning nor Error, not to pollute the output
// Skip if user wants to write an ACR-NEMA file
if ( filetype == ImplicitVR || filetype == ExplicitVR ||
- filetype == JPEG )
+ filetype == JPEG || filetype == JPEG2000 )
{
// writing Dicom File Preamble
char filePreamble[128];
//-----------------------------------------------------------------------------
// 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)
return g;
}
+/**
+ * \brief Gets from BegBuffer a supposed to be 32 Bits integer
+ * (swaps it depending on processor endianness)
+ * @return read value
+ */
+uint32_t Document::GetInt32()
+{
+ uint32_t g = *((uint32_t*)PtrBegBuffer);
+ g = SwapLong(g);
+ PtrBegBuffer+=4;
+ return g;
+}
+
/**
* \brief Re-computes the length of the Dicom group 0002.
*/
// "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); // Once per OW,OB,SQ DocEntry
- uint32_t length32 = ReadInt32();
-
+ //Fp->seekg( 2L, std::ios::cur); // Once per OW,OB,SQ DocEntry
+ uint32_t length32 = ReadInt32(); // Once per OW,OB,SQ DocEntry
+ CurrentOffsetPosition+=4;
if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
{
uint32_t lengthOB;
}
// 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)
// 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, ReadInt32() );
+
+ 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(); // Only for OB,OW DataElements
bool foundSequenceDelimiter = false;
{
uint16_t group;
uint16_t elem;
+
try
{
- group = ReadInt16();
- elem = ReadInt16();
+ //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 ) ) )
{
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); // Only for OB,OW DataElements
+ Fp->seekg( positionOnEntry, std::ios::beg); // Only once for OB,OW DataElements
return totalLength;
}
if ( CurrentGroup == 0xfffe )
return GDCM_VRUNKNOWN;
- long positionOnEntry;
- if( Debug::GetWarningFlag() )
- positionOnEntry = Fp->tellg(); // Only in Warning Mode
+ //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 and/or
// if it happens not to be the case.
VRKey vr;
- Fp->read(&(vr[0]),(size_t)2);
-
- if ( !CheckDocEntryVR(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) )
{
/*
// std::cout << "================================================================Unknown VR"
gdcmWarningMacro( "Unknown VR " << std::hex << "0x("
<< (unsigned int)vr[0] << "|" << (unsigned int)vr[1]
<< ")"
- << " at offset : 0x(" << positionOnEntry<< ") for group " << CurrentGroup
+ << " at offset : 0x(" << CurrentOffsetPosition-4<< ") for group " << CurrentGroup
);
//Fp->seekg(positionOnEntry, std::ios::beg); //JPRx
- Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?)
+ //Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?)
//see :MR_Philips_Intera_PrivateSequenceExplicitVR.dcm
+ PtrBegBuffer-=2;
return GDCM_VRUNKNOWN;
}
return vr;
// 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 )
// 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')
<< "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;
// (i.e. after the file preamble and the "DICM" string).
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); // Once per ACR-NEMA Document
-
+ CurrentOffsetPosition = 0;
// Let's check 'No Preamble Dicom File' :
// Should start with group 0x0002
// and be Explicit Value Representation
// 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 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;
{
try
{
- CurrentGroup = ReadInt16();
- CurrentElem = ReadInt16();
+ ReadBegBuffer(8); // Avoid to many time consuming freads
+ //CurrentGroup = ReadInt16();
+ //CurrentElem = ReadInt16();
}
catch ( FormatError )
{
// header parsing has to be considered as finished.
return 0;
}
-
+
+ CurrentGroup = GetInt16();
+ CurrentElem = GetInt16();
+
// In 'true DICOM' files Group 0002 is always little endian
if ( HasDCMPreamble )
{
// We thought this was explicit VR, but we end up with an
// implicit VR tag. Let's backtrack.
- //if ( newEntry->GetGroup() != 0xfffe )
- if (CurrentGroup != 0xfffe )
+ //if ( newEntry->GetGroup() != 0xfffe )
+ if (CurrentGroup != 0xfffe)
{
int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong
}
newEntry->SetOffset(Fp->tellg()); // for each DocEntry
-
return newEntry;
}
*/
void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
{
+ // 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;
//
// --> Probabely normal, since we considered we never have
// to trust manufacturers.
- // (we find very often 'Implicit VR' tag,
+ // (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 )
{
gdcmDebugMacro("Transfer Syntax Name = ["
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)
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff