Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/08/23 12:57:49 $
- Version: $Revision: 1.265 $
+ 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
Group0002Parsed = false;
IsDocumentAlreadyLoaded = false;
IsDocumentModified = true;
- LoadMode = 0x00000000; // default : load everything, later
+ LoadMode = LD_ALL; // default : load everything, later
SetFileName("");
}
SwapCode = 1234;
Filetype = ExplicitVR;
Group0002Parsed = false;
- LoadMode = 0x00000000; // Load everything, later
+ LoadMode = LD_ALL; // Load everything, later
// Load will set it to true if sucessfull
IsDocumentAlreadyLoaded = false;
*/
Document::~Document ()
{
- RefPubDict = NULL;
- RefShaDict = NULL;
+ CloseFile();
}
//-----------------------------------------------------------------------------
}
}
+ // 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();
// ----------------------------
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
*/
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() )
{
}
/**
- * \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 )
+ {
+ gdcmWarningMacro(std::hex << group << "|" << elem
+ << "is NOT a BinEntry");
return;
-
+ }
LoadEntryBinArea(binElement);
}
uint8_t *a = new uint8_t[l];
if ( !a )
{
- gdcmWarningMacro( "Cannot allocate BinEntry content");
+ gdcmWarningMacro( "Cannot allocate BinEntry content for : "
+ << std::hex << elem->GetGroup()
+ << "|" << elem->GetElement() );
return;
}
/**
* \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;
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();
}
}
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)
newDocEntry = ReadNextDocEntry( );
- if ( !newDocEntry )
- {
- break;
- }
+ // 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;
+ }
+
+ // 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);
// 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):
// 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 ( newValEntry->GetGroup()%2 != 0 ) // if Shadow Group
{
- if ( LoadMode & NO_SHADOW ) // if user asked to skip shad.gr
+ if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
{
std::string strLgrGroup = newValEntry->GetValue();
int lgrGroup;
{
lgrGroup = atoi(strLgrGroup.c_str());
Fp->seekg(lgrGroup, std::ios::cur);
- used = false;
- RemoveEntry( newDocEntry );
- newDocEntry = 0;
+ //used = false; // never used
+ RemoveEntry( newDocEntry ); // Remove and delete
+ // bcc 5.5 is right "assigned a value that's never used"
+ // newDocEntry = 0;
continue;
}
}
}
- }
-
- bool delimitor=newValEntry->IsItemDelimitor();
-
- // FIXME : Brutal patch, waiting till we find a clever way to guess
- // if a doc entry is a Sequence,
- // - when it's odd number
- // - and the file is Implicit VR Transfert Syntax
- //
- // '&& offset!=132' is a very fierce way to guess
- // if we are at zero level (Probabely not enough ...).
- // We want to go on parsing.
- if ( (delimitor && offset!=132) ||
+ }
+
+ bool delimitor = newValEntry->IsItemDelimitor();
+
+ if ( (delimitor) ||
(!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) )
{
- if (offset!=132)
- {
- gdcmWarningMacro( "in ParseDES : Item found out of a Sequence "
- << newValEntry->GetKey()
- << " (at offset : "
- << newValEntry->GetOffset() << " )" );
- }
if ( !used )
delete newDocEntry;
break;
}
}
- if ( (LoadMode & NO_SHADOWSEQ) && ! delim_mode_intern )
+ 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);
- used = false;
+ RemoveEntry( newDocEntry ); // Remove and delete
+ //used = false; // never used
continue;
}
}
- if ( (LoadMode & NO_SEQ) && ! delim_mode_intern )
+ 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
// 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:
// time waste hunting
- if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
+ else if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
{
delete newDocEntry;
}
+ first = false;
} // end While
}
}
/**
- * \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();
// 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;
- 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
+ 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 :
}
/**
- * \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);
* 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)
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;
}
}
/**
- * \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)
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.
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 ( Global::GetVR()->IsVROfSequence(realVR) )
newEntry = NewSeqEntry(group, elem);
else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) )
- newEntry = NewValEntry(group, elem,vr);
+ newEntry = NewValEntry(group, elem, realVR);
else
- newEntry = NewBinEntry(group, elem,vr);
+ newEntry = NewBinEntry(group, elem, realVR);
if ( vr == GDCM_UNKNOWN )
{
{
FindDocEntryLength(newEntry);
}
- catch ( FormatError e )
+ catch ( FormatError )
{
// Call it quits
delete newEntry;
}
newEntry->SetOffset(Fp->tellg());
-
+
return newEntry;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff