Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/02/25 15:49:55 $
- Version: $Revision: 1.231 $
+ Date: $Date: 2005/04/26 16:18:23 $
+ Version: $Revision: 1.237 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// 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 opened 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 opened for parsing
+ */
+void 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'
+ // We should call ClearEntry() on the parent object ?!?
+ }
+
+ Filename = filename;
Fp = 0;
if ( !OpenFile() )
{
+ // warning already performed in OpenFile()
+ //gdcmWarningMacro( "Unable to open as an ACR/DICOM file: "
+ // << Filename.c_str() );
+ Filetype = Unknown;
return;
}
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 ;
+ }
+
+ 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 ;
+ }
+ IsDocumentAlreadyLoaded = true;
+
+ Fp->seekg( 0, std::ios::beg);
// Load 'non string' values
// 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
// --- 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;
-}
-
-//-----------------------------------------------------------------------------
-// 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()
{
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;
Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
if( ! *Fp )
{
- gdcmDebugMacro( "Cannot open file: " << Filename.c_str());
+ gdcmErrorMacro( "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 = 0;
return 0;
}
- //ACR -- or DICOM with no Preamble; may start with a Shadow Group --
+ //-- 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);
+ 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] = {' ',' ',' ',' '};
Fp->read(dicm, (size_t)4);
HasDCMPreamble = true;
return Fp;
}
-
+
+ // -- Neither ACR/No Preamble Dicom nor DICOMV3 file
CloseFile();
- gdcmWarningMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str());
-
+ gdcmWarningMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
+ << Filename.c_str());
return 0;
}
/**
* \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)
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 ( 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;
}
else
{
// VR = "SQ"
- unsigned long l = newDocEntry->GetReadLength();
+ unsigned long l = newDocEntry->GetReadLength();
if ( l != 0 ) // don't mess the delim_mode for zero-length sequence
{
if ( l == 0xffffffff )
delim_mode = false;
}
}
+
+ if ( (LoadMode & NO_SEQ) && ! delim_mode ) // User asked to skip SQ
+ {
+ 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() );
}
{
used = false;
}
+
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
if( !used )
{
//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());
}
// 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();
- gdcmWarningMacro( "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 )
{
*/
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
Fp->seekg(0, std::ios::beg);
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).
+
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.
- // 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 :
MaxSizeLoadEntry = newSize;
}
-/**
- * \brief Header Elements too long will not be printed
- * See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE
- * @param newSize new size
- */
-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',
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;
catch ( FormatError e )
{
// Call it quits
- //std::cout << e;
delete newEntry;
return 0;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff