Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/10/26 06:34:03 $
- Version: $Revision: 1.309 $
+ Date: $Date: 2005/11/21 16:28:06 $
+ Version: $Revision: 1.331 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
//-----------------------------------------------------------------------------
// Public
-
/**
* \brief Loader. use SetLoadMode(), SetFileName() before !
* @return false if file cannot be open or no swap info was found,
return false;
}
return DoTheLoadingDocumentJob( );
-}
-/**
- * \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.
- */
+}
+
+/*
+//#ifndef GDCM_LEGACY_REMOVE
bool Document::Load( std::string const &fileName )
{
Filename = fileName;
return DoTheLoadingDocumentJob( );
}
+//#endif
+*/
/**
* \brief Performs the Loading Job (internal use only)
if ( !OpenFile() )
{
// warning already performed in OpenFile()
- //gdcmWarningMacro( "Unable to open as an ACR/DICOM file: "
- // << Filename.c_str() );
Filetype = Unknown;
return 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;
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
/// lines state that the corresponding tag contents are in fact
- /// the ones of a DataEntry.
+ /// the ones of a BinEntry.
/// 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 DataEntry, but afterwards
- /// also used as DataEntry, which requires the proper conversion,
- /// - OW, and hence loaded as DataEntry, but afterwards also used
- /// as DataEntry, which requires the proper conversion.
+ /// - 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
{
if ( dataEntry->GetLength() != 0 )
{
+ // FIXME : CTX dependent means : contexted dependant.
+ // see upper comment.
LoadEntryBinArea(dataEntry); //LUT Data (CTX dependent)
}
}
it != UserForceLoadList.end();
++it)
{
- gdcmWarningMacro( "Force Load " << std::hex
+ gdcmDebugMacro( "Force Load " << std::hex
<< (*it).Group << "|" <<(*it).Elem );
d = GetDocEntry( (*it).Group, (*it).Elem);
* @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.
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]) )
if ( transfer.length() == 0 )
{
// for brain damaged headers
+ gdcmWarningMacro( "Transfer Syntax contains no valid character.");
return GDCM_UNKNOWN;
}
}
}
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 ---------------
/**
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 --
+ //-- 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 == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 )
{
std::string msg = Util::Format(
- "ACR/DICOM starting at the beginning of the file:(%04x)\n", zero);
+ "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 polute the output
+ // while directory recursive parsing ...
+ gdcmDebugMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
<< Filename.c_str());
return 0;
}
* 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
DocEntry *docEntry = GetDocEntry(group, elem);
if ( !docEntry )
{
- gdcmWarningMacro(std::hex << group << "|" << elem
- << "doesn't exist" );
+ gdcmDebugMacro(std::hex << group << "|" << elem
+ << " doesn't exist" );
return;
}
DataEntry *dataEntry = dynamic_cast<DataEntry *>(docEntry);
if ( !dataEntry )
{
gdcmWarningMacro(std::hex << group << "|" << elem
- << "is NOT a DataEntry");
+ << " is NOT a DataEntry");
return;
}
LoadEntryBinArea(dataEntry);
uint32_t i;
unsigned short vrLgth =
Global::GetVR()->GetAtomicElementLength(entry->GetVR());
- if( entry->GetVR() == "OW" )
- vrLgth = 1;
+
+// 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;
}
case 8:
{
- gdcmWarningMacro("Can't swap 64 bits data");
-/* uint64_t *data64 = (uint64_t *)data;
+ double *data64 = (double *)data;
for(i=0;i<l/vrLgth;i++)
- data64[i] = SwapLongLong(data64[i]);*/
+ data64[i] = SwapDouble(data64[i]);
break;
}
}
/**
* \brief skips bytes inside the source file
- * \warning NOT end user intended method !
* @return
*/
void Document::SkipBytes(uint32_t nBytes)
}
/**
- * \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( )
{
{
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" )
// explicit VR AND (OB, OW, SQ, UT) : 4 more bytes
groupLength += 4;
}
- //}
+
groupLength += 2 + 2 + 4 + entry->GetLength();
}
}
// Private
/**
* \brief Loads all the needed Dictionaries
- * \warning NOT end user intended method !
*/
void Document::Initialize()
{
// (Entry will then be deleted)
bool delim_mode_intern = delim_mode;
bool first = true;
- gdcmWarningMacro( "Enter in ParseDES, delim-mode " << delim_mode
+ gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode
<< " at offset " << std::hex << offset );
while (true)
{
newDocEntry = ReadNextDocEntry( );
- // FIXME :
- // Private tag, in IMplicit VR are defaulted as a DataEntry,
- // Very often they are only composed of Printable characters,
- // and could be defaulted as a DataEntry.
- // It's too late to do the Job
- // (we should check the value, but we know it after LoadDocEntry ...)
-
- // Uncoment this printf line to be able to 'follow' the DocEntries
+ // Uncoment this cerr line to be able to 'follow' the DocEntries
// when something *very* strange happens
-
- //printf( "%04x|%04x %s\n",newDocEntry->GetGroup(),
- // newDocEntry->GetElement(),
- // newDocEntry->GetVR().c_str() );
+ if( Debug::GetDebugFlag() )
+ std::cerr<<newDocEntry->GetKey()<<" "<<newDocEntry->GetVR()<<std::endl;
if ( !newDocEntry )
{
// 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);
}
else
{
//////////////////////////// DataEntry
vr = newDocEntry->GetVR();
-
- // Useless checking, now !
- /*
- if ( Filetype == ExplicitVR &&
- !Global::GetVR()->IsVROfBinaryRepresentable(vr) )
- {
- ////// No DataEntry: should mean UNKOWN VR
- gdcmWarningMacro( std::hex << newDocEntry->GetGroup()
- << "|" << newDocEntry->GetElement()
- << " : unknown VR."
- " Probably 'Implicit VR' entry within "
- "an explicit VR 'document'.");
- }
- */
if ( !set->AddEntry( newDataEntry ) )
{
- gdcmWarningMacro( "in ParseDES : cannot add a DataEntry "
+ gdcmDebugMacro( "in ParseDES : cannot add a DataEntry "
<< newDataEntry->GetKey()
<< " (at offset : "
<< newDataEntry->GetOffset() << " )" );
if ( l != 0 )
{ // Don't try to parse zero-length sequences
- gdcmWarningMacro( "Entry in ParseSQ, delim " << delim_mode_intern
+ gdcmDebugMacro( "Entry in ParseSQ, delim " << delim_mode_intern
<< " at offset " << std::hex
<< newDocEntry->GetOffset() );
newDocEntry->GetOffset(),
l, delim_mode_intern);
- gdcmWarningMacro( "Exit from ParseSQ, delim " << delim_mode_intern);
+ gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern);
}
if ( !set->AddEntry( newSeqEntry ) )
if ( !newDocEntry )
{
- // FIXME Should warn user
gdcmWarningMacro("in ParseSQ : should never get here!");
break;
}
dlm_mod = false;
}
- // Let's try :------------
// remove fff0,e000, created out of the SQItem
Fp->seekg(offsetStartCurrentSQItem, std::ios::beg);
// fill up the current SQItem, starting at the beginning of fff0,e000
ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod);
offsetStartCurrentSQItem = Fp->tellg();
- // end try -----------------
seqEntry->AddSQItem( itemSQ, SQItemNumber );
itemSQ->Delete();
uint32_t lgt = PreviousDocEntry->GetLength();
long offset = PreviousDocEntry->GetOffset();
- gdcmWarningMacro( "Backtrack :" << std::hex << group
+ gdcmDebugMacro( "Backtrack :" << std::hex << group
<< "|" << elem
<< " at offset " << offset );
RemoveEntry( PreviousDocEntry );
}
// 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.
+ // are not loaded.
std::ostringstream s;
// Length is on 4 bytes.
// Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
- // even if Transfer Syntax is 'Implicit VR ...'
+ // even if Transfer Syntax is 'Implicit VR ...'
+ // --> Except for 'Implicit VR Big Endian Transfer Syntax GE Private'
FixDocEntryFoundLength( entry, ReadInt32() );
return;
/**
* \brief Find the Length till the next sequence delimiter
- * \warning NOT end user intended method !
* @return
*/
uint32_t Document::FindDocEntryLengthOBOrOW()
long positionOnEntry = Fp->tellg();
// 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.
+ // Hence we make sure the present tag is in explicit VR and try to fix things
+ // if it happens not to be the case.
VRKey vr;
Fp->read(&(vr[0]),(size_t)2);
- //gdcmDebugMacro( "--> VR: " << vr )
if ( !CheckDocEntryVR(vr) )
{
- gdcmWarningMacro( "Unknown VR '" << vr << "'" )
+ // Don't warn user with useless messages
+ // Often, delimiters (0xfffe), are not explicit VR ...
+ if ( CurrentGroup != 0xfffe )
+ gdcmWarningMacro( "Unknown VR " << std::hex << "0x("
+ << (unsigned int)vr[0] << "|" << (unsigned int)vr[1]
+ << ") at offset :" << positionOnEntry );
Fp->seekg(positionOnEntry, std::ios::beg);
return GDCM_VRUNKNOWN;
}
/**
* \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)
{
uint16_t elem = entry->GetElement();
uint16_t group = entry->GetGroup();
- const VRKey &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
else
{
Filetype = ImplicitVR;
- gdcmErrorMacro( "Group 0002 :Not an explicit Value Representation;"
+ gdcmWarningMacro( "Group 0002 :Not an explicit Value Representation;"
<< "Looks like a bugged Header!");
}
if ( net2host )
{
SwapCode = 4321;
- gdcmDebugMacro( "HostByteOrder != NetworkByteOrder");
+ gdcmDebugMacro( "HostByteOrder != NetworkByteOrder, SwapCode = 4321");
}
else
{
SwapCode = 1234;
- gdcmDebugMacro( "HostByteOrder = NetworkByteOrder");
+ gdcmDebugMacro( "HostByteOrder = NetworkByteOrder, SwapCode = 1234");
}
// Position the file position indicator at first tag
*/
DocEntry *Document::ReadNextDocEntry()
{
- uint16_t group;
- uint16_t elem;
-
try
{
- group = ReadInt16();
- elem = ReadInt16();
+ CurrentGroup = ReadInt16();
+ CurrentElem = ReadInt16();
}
catch ( FormatError )
{
}
// Sometimes file contains groups of tags with reversed endianess.
- HandleBrokenEndian(group, elem);
+ HandleBrokenEndian(CurrentGroup, CurrentElem);
// In 'true DICOM' files Group 0002 is always little endian
if ( HasDCMPreamble )
- HandleOutOfGroup0002(group, elem);
+ HandleOutOfGroup0002(CurrentGroup, CurrentElem);
VRKey vr = FindDocEntryVR();
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 ))
+ else if (CurrentGroup%2 == 1 &&
+ (CurrentElem >= 0x0010 && CurrentElem <=0x00ff ))
{
// DICOM PS 3-5 7.8.1 a) states that those
// (gggg-0010->00FF where gggg is odd) attributes have to be LO
}
else
{
- DictEntry *dictEntry = GetDictEntry(group,elem);
+ DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);
if ( dictEntry )
{
realVR = dictEntry->GetVR();
DocEntry *newEntry;
if ( Global::GetVR()->IsVROfSequence(realVR) )
- newEntry = NewSeqEntry(group, elem);
+ newEntry = NewSeqEntry(CurrentGroup, CurrentElem);
else
{
- newEntry = NewDataEntry(group, elem, realVR);
+ newEntry = NewDataEntry(CurrentGroup, CurrentElem, realVR);
static_cast<DataEntry *>(newEntry)->SetState(DataEntry::STATE_NOTLOADED);
}
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();
}
}
else if (group == 0xfffe && elem == 0xe0dd)
{
- gdcmWarningMacro( "Straight Sequence Terminator." );
+ gdcmDebugMacro( "Straight Sequence Terminator." );
}
}
{
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 ( ts == GDCM_UNKNOWN )
+ {
+ gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " );
+ return;
+ }
if ( !Global::GetTS()->IsTransferSyntax(ts) )
{
- gdcmWarningMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
+ gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: ["
+ << ts << "]");
return;
}
if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
TS::ImplicitVRLittleEndian )
- {
- Filetype = ImplicitVR;
- }
+ {
+ Filetype = ImplicitVR;
+ }
// FIXME Strangely, this works with
//'Implicit VR BigEndian Transfer Syntax (GE Private)
if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
TS::ExplicitVRBigEndian )
{
- gdcmWarningMacro("Transfer Syntax Name = ["
+ gdcmDebugMacro("Transfer Syntax Name = ["
<< GetTransferSyntaxName() << "]" );
SwitchByteSwapCode();
group = SwapShort(group);
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff