Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/06/03 16:05:23 $
- Version: $Revision: 1.243 $
+ Date: $Date: 2005/09/22 14:41:24 $
+ Version: $Revision: 1.284 $
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>
+#include <ctype.h> // for isdigit
+#include <stdlib.h> // for atoi
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
// Load will set it to true if sucessfull
Group0002Parsed = false;
IsDocumentAlreadyLoaded = false;
- LoadMode = 0x00000000; // default : load everything, later
+ IsDocumentModified = true;
+ LoadMode = LD_ALL; // default : load everything, later
+ SetFileName("");
}
/**
- * \brief Constructor (not to break the API)
- * @param fileName 'Document' (File or DicomDir) to be opened for parsing
+ * \brief Constructor (DEPRECATED : not to break the API)
+ * @param fileName 'Document' (File or DicomDir) to be open for parsing
*/
Document::Document( std::string const &fileName )
:ElementSet(-1)
SwapCode = 1234;
Filetype = ExplicitVR;
Group0002Parsed = false;
- LoadMode = 0x00000000; // Load everything
+ LoadMode = LD_ALL; // Load everything, later
// Load will set it to true if sucessfull
IsDocumentAlreadyLoaded = false;
+ IsDocumentModified = true;
- Load(fileName);
-
- // Normaly (?) Fp should be already deleted by CloseFile()
- if ( Fp != 0 )
- delete Fp;
- Fp = 0;
+ SetFileName(fileName);
+ Load( );
}
/**
* \brief Canonical destructor.
*/
Document::~Document ()
{
- RefPubDict = NULL;
- RefShaDict = NULL;
+ CloseFile();
}
//-----------------------------------------------------------------------------
// Public
/**
- * \brief Loader
- * @param fileName 'Document' (File or DicomDir) to be opened for parsing
+ * \brief Loader. use SetLoadMode(), SetFileName() before !
* @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 )
+bool Document::Load( )
{
- // We should clean out anything that already exists.
- // Check IsDocumentAlreadyLoaded to be sure.
- if( IsDocumentAlreadyLoaded )
+ if ( GetFileName() == "" )
{
- 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 ?!?
+ gdcmWarningMacro( "Use SetFileName, before !" );
+ 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.
+ */
+bool Document::Load( std::string const &fileName )
+{
Filename = fileName;
+ return DoTheLoadingDocumentJob( );
+}
+
+/**
+ * \brief Performs the Loading Job (internal use only)
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool Document::DoTheLoadingDocumentJob( )
+{
+ if ( ! IsDocumentModified ) // Nothing to do !
+ return true;
+
+ // if ( Filename == fileName )
+ // {
+ // gdcmWarningMacro( "The file was already parsed inside this "
+ // << "gdcm::Document (its name is: "
+ // << Filename.c_str() );
+ // return true;
+ // }
+
+ //gdcmWarningMacro( "A file was already parsed inside this "
+ // << "gdcm::Document (previous name was: "
+ // << Filename.c_str() << ". New name is :"
+ // << fileName );
+ // clean out the Entries, if already parsed
+ // (probabely a mistake from the user)
+
+ ClearEntry();
Fp = 0;
if ( !OpenFile() )
lgt -= beg; // remaining length to parse
- ParseDES( this, beg, lgt, false); // Loading is done during parsing
+ // Recursive call.
+ // Loading is done during parsing
+ ParseDES( this, beg, lgt, false); // delim_mode is first defaulted to false
if ( IsEmpty() )
{
// 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
/// 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
- /// whether the following tags are either:
+ /// whether the following tags are either :
/// - 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
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)
+ }
+ }
+ }
+ }
+
+ // Force Loading some more elements if user asked to.
+
+ gdcm::DocEntry *d;
+ for (ListElements::iterator it = UserForceLoadList.begin();
+ it != UserForceLoadList.end();
+ ++it)
+ {
+ gdcmWarningMacro( "Force Load " << std::hex
+ << (*it).Group << "|" <<(*it).Elem );
+
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( d == NULL)
+ {
+ gdcmWarningMacro( "You asked toForce Load " << std::hex
+ << (*it).Group <<"|"<< (*it).Elem
+ << " that doesn't exist" );
+ continue;
+ }
+
+ if ( dynamic_cast<ValEntry *>(d) )
+ {
+ LoadDocEntry(d, true);
+ continue;
+ }
+
+ BinEntry *b = dynamic_cast<BinEntry *>(d);
+ if ( b )
+ {
+ LoadEntryBinArea(b);
+ b->SetValue(GDCM_BINLOADED);
+ continue;
+ }
+
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'ForceLoad' a SeqEntry :" << std::hex
+ << (*it).Group <<"|"<< (*it).Elem );
+ continue;
+ }
+ }
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)
+ // used at CREATIS. For the time being (say a couple of years)
// we keep this kludge to allow CREATIS users
// reading their old images.
//
SetValEntry(rows , 0x0028, 0x0011);
}
// --- End of ACR-LibIDO kludge ---
-
return true;
}
+
+/**
+ * \brief Adds a new element we want to load anyway
+ * @param group Group number of the target tag.
+ * @param elem Element number of the target tag.
+ */
+void Document::AddForceLoadElement (uint16_t group, uint16_t elem)
+{
+ Element el;
+ el.Group = group;
+ el.Elem = elem;
+ UserForceLoadList.push_back(el);
+}
/**
* \brief Get the public dictionary used
*/
*/
bool Document::IsReadable()
{
- if( Filetype == Unknown)
+ if ( Filetype == Unknown )
{
gdcmWarningMacro( "Wrong filetype");
return false;
return 0;
}
- if(Fp)
+ if ( Fp )
{
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 )
{
// Don't user gdcmErrorMacro :
// a spurious message will appear when you use, for instance
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(
+ 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 at the begining of the file:(%04x)\n", zero);
+ "ACR/DICOM starting at the beginning of the file:(%04x)\n", zero);
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() )
+ if ( Fp->eof() )
{
CloseFile();
return 0;
}
- if( memcmp(dicm, "DICM", 4) == 0 )
+ if ( memcmp(dicm, "DICM", 4) == 0 )
{
HasDCMPreamble = true;
return Fp;
*/
bool Document::CloseFile()
{
- if( Fp )
+ if ( Fp )
{
Fp->close();
delete Fp;
}
/**
- * \brief Writes in a file all the Header Entries (Dicom Elements)
+ * \brief Writes in a file all the Entries (Dicom Elements)
* @param fp file pointer on an already open file (actually: Output File Stream)
* @param filetype Type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
- * @return Always true.
*/
void Document::WriteContent(std::ofstream *fp, FileType filetype)
{
- // \TODO move the following lines (and a lot of others, to be written)
- // to a future function CheckAndCorrectHeader
-
- // (necessary if user wants to write a DICOM V3 file
- // starting from an ACR-NEMA (V2) Header
+ // Skip if user wants to write an ACR-NEMA file
if ( filetype == ImplicitVR || filetype == ExplicitVR )
{
// Search the corresponding DocEntry
DocEntry *docElement = GetDocEntry(group, elem);
if ( !docElement )
+ {
+ gdcmWarningMacro(std::hex << group << "|" << elem
+ << "doesn't exist" );
return;
-
+ }
BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
- if( !binElement )
+ if ( !binElement )
+ {
+ gdcmWarningMacro(std::hex << group << "|" << elem
+ << "is NOT a BinEntry");
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 )
{
- gdcmWarningMacro( "Cannot allocate BinEntry content");
+ gdcmWarningMacro( "Cannot allocate BinEntry content for : "
+ << std::hex << elem->GetGroup()
+ << "|" << elem->GetElement() );
return;
}
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();
}
*/
void Document::LoadDocEntrySafe(DocEntry *entry)
{
- if(Fp)
+ if ( Fp )
{
long PositionOnEntry = Fp->tellg();
LoadDocEntry(entry);
// 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;
}
{
throw FormatError( "Document::ReadInt16()", " file error." );
}
- if( Fp->eof() )
+ if ( Fp->eof() )
{
throw FormatError( "Document::ReadInt16()", "EOF." );
}
{
throw FormatError( "Document::ReadInt32()", " file error." );
}
- if( Fp->eof() )
+ if ( Fp->eof() )
{
throw FormatError( "Document::ReadInt32()", "EOF." );
}
/**
* \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 )
+int Document::ComputeGroup0002Length( /*FileType filetype*/ )
{
uint16_t gr;
std::string vr;
{
gr = entry->GetGroup();
- if( gr == 0x0002 )
+ if ( gr == 0x0002 )
{
found0002 = true;
- if( entry->GetElement() != 0x0000 )
+ if ( entry->GetElement() != 0x0000 )
{
vr = entry->GetVR();
+
+ // FIXME : group 0x0002 is *always* Explicit VR!
- if( filetype == ExplicitVR )
- {
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || (vr == "UT") )
+ //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();
}
}
/**
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
- * @param set DocEntrySet we are going to parse ('zero level' or a SQItem)
+ * @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 l_max length to parse (meaningless when we are in 'delimitor mode')
* @param delim_mode : whether we are in 'delimitor mode' (l=0xffffff) or not
*/
void Document::ParseDES(DocEntrySet *set, long offset,
BinEntry *newBinEntry;
SeqEntry *newSeqEntry;
VRKey vr;
- bool used;
-
+ bool used; // will be set to false when something wrong happens to an Entry.
+ // (Entry will then be deleted)
+ bool delim_mode_intern = delim_mode;
+ bool first = true;
while (true)
{
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
break;
}
- used = true;
newDocEntry = ReadNextDocEntry( );
+ // FIXME :
+ // Private tag, in IMplicit VR are defaulted as a BinEntry,
+ // Very often they are only composed of Printable characters,
+ // and could be defaulted as a ValEntry.
+ // It's too late to do the Job
+ // (we should check the value, but we know it after LoadDocEntry ...)
+ // --> in next gdcm major release let's unify ValEntry and BinEntry !
+
+ // Uncoment this printf 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 ( !newDocEntry )
{
break;
}
- vr = newDocEntry->GetVR();
+ // an Item Starter found elsewhere but the first position
+ // of a SeqEntry means previous entry was a Sequence
+ // but we didn't get it (private Sequence + Implicit VR)
+ // we have to backtrack.
+ if ( !first && newDocEntry->IsItemStarter() )
+ {
+ newDocEntry = Backtrack(newDocEntry);
+ }
+ else
+ {
+ PreviousDocEntry = newDocEntry;
+ }
+
+ used = true;
newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
- newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
- if ( newValEntry || newBinEntry )
+ if ( newValEntry || newBinEntry )
{
+ //////////////////////////// ContentEntry
if ( newBinEntry )
{
+ vr = newDocEntry->GetVR();
if ( Filetype == ExplicitVR &&
!Global::GetVR()->IsVROfBinaryRepresentable(vr) )
{
}
//////////////////// BinEntry or UNKOWN VR:
+
// When "this" is a Document the Key is simply of the
// form ( group, elem )...
- if ( dynamic_cast< Document* > ( set ) )
- {
- newBinEntry->SetKey( newBinEntry->GetKey() );
- }
+ //if ( set == this ) // ( dynamic_cast< Document* > ( set ) )
+ //{
+ // newBinEntry->SetKey( newBinEntry->GetKey() );
+ //}
// but when "this" is a SQItem, we are inserting this new
// valEntry in a sequence item, and the key has the
// generalized form (refer to \ref BaseTagKey):
- if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+
+ // time waste hunting
+ //if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ //{
+ // newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
+ // + newBinEntry->GetKey() );
+ //}
+
+ if ( !set->AddEntry( newBinEntry ) )
{
- newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
- + newBinEntry->GetKey() );
+ gdcmWarningMacro( "in ParseDES : cannot add a BinEntry "
+ << newBinEntry->GetKey()
+ << " (at offset : "
+ << newBinEntry->GetOffset() << " )" );
+ used=false;
}
-
- LoadDocEntry( newBinEntry );
- if( !set->AddEntry( newBinEntry ) )
+ else
{
- //Expect big troubles if here
- //delete newBinEntry;
- used=false;
+ // Load only if we can add (not a duplicate key)
+ LoadDocEntry( newBinEntry );
}
- }
+ } // end BinEntry
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 ) )
- {
- newValEntry->SetKey( newValEntry->GetKey() );
- }
+ //if ( set == this ) // ( dynamic_cast< Document* > ( set ) )
+ //{
+ // newValEntry->SetKey( newValEntry->GetKey() );
+ //}
// ...but when "set" is a SQItem, we are inserting this new
// valEntry in a sequence item. Hence the key has the
// generalized form (refer to \ref BaseTagKey):
- if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+
+ // time waste hunting
+ //if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ //{
+ // newValEntry->SetKey( parentSQItem->GetBaseTagKey()
+ // + newValEntry->GetKey() );
+ //}
+
+ if ( !set->AddEntry( newValEntry ) )
+ {
+ gdcmWarningMacro( "in ParseDES : cannot add a ValEntry "
+ << newValEntry->GetKey()
+ << " (at offset : "
+ << newValEntry->GetOffset() << " )" );
+ used=false;
+ }
+ else
{
- newValEntry->SetKey( parentSQItem->GetBaseTagKey()
- + newValEntry->GetKey() );
+ // Load only if we can add (not a duplicate key)
+ LoadDocEntry( newValEntry );
}
-
- 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->GetElement() == 0x0000 ) // if on group length
{
- if ( newValEntry->GetGroup()%2 != 0 )
+ if ( newValEntry->GetGroup()%2 != 0 ) // if Shadow Group
{
- if ( newValEntry->GetElement() == 0x0000 )
+ if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
{
std::string strLgrGroup = newValEntry->GetValue();
int lgrGroup;
if ( strLgrGroup != GDCM_UNFOUND)
{
lgrGroup = atoi(strLgrGroup.c_str());
- Fp->seekg(lgrGroup , std::ios::cur);
- used = false;
+ Fp->seekg(lgrGroup, std::ios::cur);
+ //used = false; // never used
+ RemoveEntry( newDocEntry ); // Remove and delete
+ // bcc 5.5 is right "assigned a value that's never used"
+ // newDocEntry = 0;
continue;
}
}
}
- }
-
- if( !set->AddEntry( newValEntry ) )
- {
- // If here expect big troubles
- // delete newValEntry; //otherwise mem leak
- used=false;
}
- if (delimitor)
- {
- if(!used)
- delete newDocEntry;
- break;
- }
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ bool delimitor = newValEntry->IsItemDelimitor();
+
+ if ( (delimitor) ||
+ (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) )
{
- if(!used)
+ if ( !used )
delete newDocEntry;
break;
}
}
else
{
- // VR = "SQ"
+ /////////////////////// SeqEntry : VR = "SQ"
+
unsigned long l = newDocEntry->GetReadLength();
- if ( l != 0 ) // don't mess the delim_mode for zero-length sequence
+ if ( l != 0 ) // don't mess the delim_mode for 'zero-length sequence'
{
if ( l == 0xffffffff )
{
- delim_mode = true;
+ delim_mode_intern = true;
}
else
{
- delim_mode = false;
+ delim_mode_intern = false;
}
}
-
- if ( (LoadMode & NO_SEQ) && ! delim_mode ) // User asked to skip SQ
+
+ if ( (LoadMode & LD_NOSHADOWSEQ) && ! delim_mode_intern )
+ {
+ // User asked to skip SeQuences *only* if they belong to Shadow Group
+ if ( newDocEntry->GetGroup()%2 != 0 )
+ {
+ Fp->seekg( l, std::ios::cur);
+ RemoveEntry( newDocEntry ); // Remove and delete
+ //used = false; // never used
+ continue;
+ }
+ }
+ if ( (LoadMode & LD_NOSEQ) && ! delim_mode_intern )
{
+ // User asked to skip *any* SeQuence
Fp->seekg( l, std::ios::cur);
- used = false;
+ //used = false; // never used
+ RemoveEntry( newDocEntry ); // Remove and delete
continue;
- }
+ }
+ // delay the dynamic cast as late as possible
+ newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
- // no other way to create it ...
- newSeqEntry->SetDelimitorMode( delim_mode );
+ // no other way to create the Delimitor ...
+ newSeqEntry->SetDelimitorMode( delim_mode_intern );
// At the top of the hierarchy, stands a Document. When "set"
// 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 ( dynamic_cast< Document* > ( set ) )
+// SQItem *parentSQItem = dynamic_cast< SQItem* > ( set );
+ if ( set == this ) // ( dynamic_cast< Document* > ( set ) )
{
newSeqEntry->SetDepthLevel( 1 );
- newSeqEntry->SetKey( newSeqEntry->GetKey() );
+ // newSeqEntry->SetKey( newSeqEntry->GetKey() );
}
// But when "set" is already a SQItem, we are building a nested
// sequence, and hence the depth level of the new SeqEntry
// we are building, is one level deeper:
- if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+
+ // time waste hunting
+ else if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
- newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
- + newSeqEntry->GetKey() );
+
+ // newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
+ // + newSeqEntry->GetKey() );
}
if ( l != 0 )
{ // Don't try to parse zero-length sequences
ParseSQ( newSeqEntry,
newDocEntry->GetOffset(),
- l, delim_mode);
+ l, delim_mode_intern);
}
- if( !set->AddEntry( newSeqEntry ) )
+ if ( !set->AddEntry( newSeqEntry ) )
{
+ gdcmWarningMacro( "in ParseDES : cannot add a SeqEntry "
+ << newSeqEntry->GetKey()
+ << " (at offset : "
+ << newSeqEntry->GetOffset() << " )" );
used = false;
}
-
+
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- if( !used )
- delete newDocEntry;
- break;
+ if ( !used )
+ delete newDocEntry;
+ break;
}
- }
+ } // end SeqEntry : VR = "SQ"
- if( !used )
+ if ( !used )
+ {
delete newDocEntry;
- }
+ }
+ first = false;
+ } // end While
}
/**
if ( !newDocEntry )
{
// FIXME Should warn user
+ gdcmWarningMacro("in ParseSQ : should never get here!");
break;
}
- if( delim_mode )
+ if ( delim_mode )
{
if ( newDocEntry->IsSequenceDelimitor() )
{
}
// create the current SQItem
SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
+/*
std::ostringstream newBase;
newBase << seqEntry->GetKey()
<< "/"
<< SQItemNumber
<< "#";
itemSQ->SetBaseTagKey( newBase.str() );
+*/
unsigned int l = newDocEntry->GetReadLength();
if ( l == 0xffffffff )
delete newDocEntry;
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 -----------------
}
/**
- * \brief Loads the element content if its length doesn't exceed
- * the value specified with Document::SetMaxSizeLoadEntry()
+ * \brief When a private Sequence + Implicit VR is encountered
+ * we cannot guess it's a Sequence till we find the first
+ * Item Starter. We then backtrack to do the job.
+ * @param docEntry Item Starter that warned us
+ */
+DocEntry *Document::Backtrack(DocEntry *docEntry)
+{
+ // delete the Item Starter, built erroneously out of any Sequence
+ // it's not yet in the HTable/chained list
+ delete docEntry;
+
+ // Get all info we can from PreviousDocEntry
+ uint16_t group = PreviousDocEntry->GetGroup();
+ uint16_t elem = PreviousDocEntry->GetElement();
+ uint32_t lgt = PreviousDocEntry->GetLength();
+ long offset = PreviousDocEntry->GetOffset();
+
+ gdcmWarningMacro( "Backtrack :" << std::hex << group
+ << "|" << elem
+ << " at offset " << offset );
+ RemoveEntry( PreviousDocEntry );
+
+ // forge the Seq Entry
+ DocEntry *newEntry = NewSeqEntry(group, elem);
+ newEntry->SetLength(lgt);
+ newEntry->SetOffset(offset);
+
+ // Move back to the beginning of the Sequence
+ Fp->seekg( 0, std::ios::beg);
+ Fp->seekg(offset, std::ios::cur);
+
+return newEntry;
+}
+
+/**
+ * \brief Loads (or not) the element content depending if its length exceeds
+ * or not the value specified with Document::SetMaxSizeLoadEntry()
* @param entry Header Entry (Dicom Element) to be dealt with
*/
-void Document::LoadDocEntry(DocEntry *entry)
+void Document::LoadDocEntry(DocEntry *entry, bool forceLoad)
{
uint16_t group = entry->GetGroup();
std::string vr = entry->GetVR();
// (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;
}
// The elements whose length is bigger than the specified upper bound
- // are not loaded. Instead we leave a short notice of the offset of
+ // are not loaded. Instead we leave a short notice on the offset of
// the element content and it's length.
std::ostringstream s;
- if (length > MaxSizeLoadEntry)
+
+ if (!forceLoad)
{
- if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
- {
- //s << "gdcm::NotLoaded (BinEntry)";
- s << GDCM_NOTLOADED;
- 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();
- s << " x(" << std::hex << entry->GetLength() << ")";
- valEntryPtr->SetValue(s.str());
- }
- else
+ if (length > MaxSizeLoadEntry)
{
- // fusible
- gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry "
- << "nor a ValEntry ?! Should never print that !" );
- }
+ if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
+ {
+ s << GDCM_NOTLOADED;
+ 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());
+ }
+ else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) )
+ {
+ s << GDCM_NOTLOADED;
+ s << " Address:" << (long)entry->GetOffset();
+ s << " Length:" << entry->GetLength();
+ s << " x(" << std::hex << entry->GetLength() << ")";
+ valEntryPtr->SetValue(s.str());
+ }
+ else
+ {
+ // fusible
+ gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry "
+ << "nor a ValEntry ?! Should never print that !" );
+ }
- // to be sure we are at the end of the value ...
- Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
- std::ios::beg);
- return;
+ // to be sure we are at the end of the value ...
+ Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
+ std::ios::beg);
+ return;
+ }
}
// When we find a BinEntry not very much can be done :
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);
gdcmWarningMacro("Warning: bad length: " << length <<
- ",For string :" << newValue.c_str());
+ " For string :" << newValue.c_str());
// Since we change the length of string update it length
//entry->SetReadLength(length+1);
}
{
if ( Fp->fail() || Fp->eof())
{
- gdcmWarningMacro("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());
}
}
/**
- * \brief Find the value Length of the passed Header Entry
+ * \brief Find the value Length of the passed Doc Entry
* @param entry Header Entry whose length of the value shall be loaded.
*/
void Document::FindDocEntryLength( DocEntry *entry )
if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
- if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT" || 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
// chance to get the pixels by deciding the element goes
// until the end of the file. Hence we artificially fix the
// the length and proceed.
+ gdcmWarningMacro( " Computing the length failed for " <<
+ entry->GetKey() <<" in " <<GetFileName());
+
long currentPosition = Fp->tellg();
Fp->seekg(0L,std::ios::end);
Fp->read (vr, (size_t)2);
vr[2] = 0;
- if( !CheckDocEntryVR(vr) )
+ if ( !CheckDocEntryVR(vr) )
{
Fp->seekg(positionOnEntry, std::ios::beg);
return GDCM_UNKNOWN;
* and the taken VR. If they are different, the header entry is
* updated with the new VR.
* @param vr Dicom Value Representation
- * @return false if the VR is incorrect of if the VR isn't referenced
+ * @return false if the VR is incorrect or if the VR isn't referenced
* otherwise, it returns true
*/
bool Document::CheckDocEntryVR(VRKey vr)
// 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 << '\\';
}
*/
void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
{
- Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
+ int l = currentDocEntry->GetReadLength();
+ if ( l == -1 ) // length = 0xffff shouldn't appear here ...
+ // ... but PMS imagers happen !
+ return;
+ Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb
+ {
Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur);
+ }
}
/**
//////// 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;
}
* 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 s32;
uint16_t s16;
Fp->read(deb, 256);
char *entCur = deb + 128;
- if( memcmp(entCur, "DICM", (size_t)4) == 0 )
+ if ( memcmp(entCur, "DICM", (size_t)4) == 0 )
{
gdcmWarningMacro( "Looks like DICOM Version3 (preamble + DCM)" );
// 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
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 )
+ 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");
Filetype = ACR;
return true;
default :
- gdcmWarningMacro( "ACR/NEMA unfound swap info (Really hopeless !)");
+ gdcmWarningMacro("ACR/NEMA unfound swap info (Really hopeless !)");
Filetype = Unknown;
return false;
}
*/
void Document::SwitchByteSwapCode()
{
- gdcmWarningMacro( "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
+ * \brief during parsing, Header Elements too long are not loaded in memory
* @param newSize new size
*/
void Document::SetMaxSizeLoadEntry(long newSize)
}
/**
- * \brief Read the next tag but WITHOUT loading it's value
+ * \brief Read the next tag WITHOUT loading it's value
* (read the 'Group Number', the 'Element Number',
* gets the Dict Entry
* gets the VR, gets the length, gets the offset value)
- * @return On succes the newly created DocEntry, NULL on failure.
+ * @return On succes : the newly created DocEntry, NULL on failure.
*/
DocEntry *Document::ReadNextDocEntry()
{
group = ReadInt16();
elem = ReadInt16();
}
- catch ( FormatError e )
+ catch ( FormatError )
{
// We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
std::string vr = FindDocEntryVR();
std::string realVR = vr;
- if( vr == GDCM_UNKNOWN)
+ if ( vr == GDCM_UNKNOWN )
{
if ( elem == 0x0000 ) // Group Length
+ {
realVR = "UL"; // must be UL
+ }
+ else if (group%2 == 1 && (elem >= 0x0010 && elem <=0x00ff ))
+ {
+ // DICOM PS 3-5 7.8.1 a) states that those
+ // (gggg-0010->00FF where gggg is odd) attributes have to be LO
+ realVR = "LO";
+ }
else
{
DictEntry *dictEntry = GetDictEntry(group,elem);
- if( dictEntry )
+ 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) )
- newEntry = NewValEntry(group, elem,vr);
+ else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) )
+ newEntry = NewValEntry(group, elem, realVR);
else
- newEntry = NewBinEntry(group, elem,vr);
+ newEntry = NewBinEntry(group, elem, realVR);
- 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());
+ int offset = Fp->tellg();
+ msg = Util::Format("Entry (%04x,%04x) at 0x(%x) should be Explicit VR\n",
+ newEntry->GetGroup(), newEntry->GetElement(), offset );
gdcmWarningMacro( msg.c_str() );
}
}
{
FindDocEntryLength(newEntry);
}
- catch ( FormatError e )
+ catch ( FormatError )
{
// Call it quits
delete newEntry;
}
newEntry->SetOffset(Fp->tellg());
-
+
return newEntry;
}
/**
* \brief Handle broken private tag from Philips NTSCAN
- * where the endianess is being switch to BigEndian for no
- * apparent reason
+ * where the endianess is being switched to BigEndian
+ * for no apparent reason
* @return no return
*/
void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff