Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/09/20 15:11:19 $
- Version: $Revision: 1.281 $
+ Date: $Date: 2005/10/25 09:22:15 $
+ Version: $Revision: 1.305 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
#include "gdcmDocument.h"
-#include "gdcmValEntry.h"
-#include "gdcmBinEntry.h"
#include "gdcmSeqEntry.h"
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDictSet.h"
#include "gdcmDocEntrySet.h"
#include "gdcmSQItem.h"
+#include "gdcmDataEntry.h"
#include <vector>
#include <iomanip>
*
*/
Document::Document()
- :ElementSet(-1)
+ :ElementSet()
{
Fp = 0;
SetFileName("");
}
-/**
- * \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)
-{
- Fp = 0;
-
- SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialize();
- SwapCode = 1234;
- Filetype = ExplicitVR;
- Group0002Parsed = false;
- LoadMode = LD_ALL; // Load everything, later
-
- // Load will set it to true if sucessfull
- IsDocumentAlreadyLoaded = false;
- IsDocumentModified = true;
-
- SetFileName(fileName);
- Load( );
-}
/**
* \brief Canonical destructor.
*/
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;
Group0002Parsed = false;
- gdcmWarningMacro( "Starting parsing of file: " << Filename.c_str());
+ gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str());
Fp->seekg(0, std::ios::end);
long lgt = Fp->tellg(); // total length of the file
// Load 'non string' values
- std::string PhotometricInterpretation = GetEntryValue(0x0028,0x0004);
+ std::string PhotometricInterpretation = GetEntryString(0x0028,0x0004);
if ( PhotometricInterpretation == "PALETTE COLOR " )
{
// FIXME
/// 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 BinEntry.
+ /// the ones of a DataEntry.
/// 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
/// 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
- /// as ValEntry, which requires the proper conversion.
+ /// - 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.
LoadEntryBinArea(0x0028,0x1201); // R LUT
LoadEntryBinArea(0x0028,0x1202); // G LUT
LoadEntryBinArea(0x0028,0x1203); // B LUT
SQItem *sqi= modLutSeq->GetFirstSQItem();
if ( sqi != 0 )
{
- BinEntry *b = sqi->GetBinEntry(0x0028,0x3006);
- if ( b != 0 )
+ DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006);
+ if ( dataEntry != 0 )
{
- if ( b->GetLength() != 0 )
+ if ( dataEntry->GetLength() != 0 )
{
- LoadEntryBinArea(b); //LUT Data (CTX dependent)
+ LoadEntryBinArea(dataEntry); //LUT Data (CTX dependent)
}
}
}
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;
- }
+ LoadDocEntry(d, true);
}
CloseFile();
// we switch lineNumber and columnNumber
//
std::string RecCode;
- RecCode = GetEntryValue(0x0008, 0x0010); // recognition code (RET)
+ RecCode = GetEntryString(0x0008, 0x0010); // recognition code (RET)
if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
// with "little-endian strings"
{
Filetype = ACR_LIBIDO;
- std::string rows = GetEntryValue(0x0028, 0x0010);
- std::string columns = GetEntryValue(0x0028, 0x0011);
- SetValEntry(columns, 0x0028, 0x0010);
- SetValEntry(rows , 0x0028, 0x0011);
+ std::string rows = GetEntryString(0x0028, 0x0010);
+ std::string columns = GetEntryString(0x0028, 0x0011);
+ SetEntryString(columns, 0x0028, 0x0010);
+ SetEntryString(rows , 0x0028, 0x0011);
}
// --- End of ACR-LibIDO kludge ---
return true;
*/
void Document::AddForceLoadElement (uint16_t group, uint16_t elem)
{
- Element el;
+ DicomElement el;
el.Group = group;
el.Elem = elem;
UserForceLoadList.push_back(el);
// The entry might be present but not loaded (parsing and loading
// happen at different stages): try loading and proceed with check...
LoadDocEntrySafe(entry);
- if (ValEntry *valEntry = dynamic_cast< ValEntry* >(entry) )
+ if (DataEntry *dataEntry = dynamic_cast<DataEntry *>(entry) )
{
- std::string transfer = valEntry->GetValue();
+ std::string transfer = dataEntry->GetString();
// The actual transfer (as read from disk) might be padded. We
// first need to remove the potential padding. We can make the
// weak assumption that padding was not executed with digits...
while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
{
transfer.erase(transfer.length()-1, 1);
+ if ( transfer.length() == 0 )
+ {
+ // for brain damaged headers
+ return GDCM_UNKNOWN;
+ }
}
return transfer;
}
std::string Document::GetTransferSyntaxName()
{
// use the TS (TS : Transfer Syntax)
- std::string transferSyntax = GetEntryValue(0x0002,0x0010);
+ std::string transferSyntax = GetEntryString(0x0002,0x0010);
if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) )
{
}
/**
- * \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)
{
// Skip if user wants to write an ACR-NEMA file
- if ( filetype == ImplicitVR || filetype == ExplicitVR )
+ if ( filetype == ImplicitVR || filetype == ExplicitVR ||
+ filetype == JPEG )
{
// writing Dicom File Preamble
char filePreamble[128];
void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
// Search the corresponding DocEntry
- DocEntry *docElement = GetDocEntry(group, elem);
- if ( !docElement )
+ DocEntry *docEntry = GetDocEntry(group, elem);
+ if ( !docEntry )
{
gdcmWarningMacro(std::hex << group << "|" << elem
<< "doesn't exist" );
return;
}
- BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
- if ( !binElement )
+ DataEntry *dataEntry = dynamic_cast<DataEntry *>(docEntry);
+ if ( !dataEntry )
{
gdcmWarningMacro(std::hex << group << "|" << elem
- << "is NOT a BinEntry");
+ << "is NOT a DataEntry");
return;
}
- LoadEntryBinArea(binElement);
+ LoadEntryBinArea(dataEntry);
}
/**
* \brief Loads (from disk) the element content
* when a string is not suitable
- * @param elem Entry whose binArea is going to be loaded
+ * @param entry Entry whose binArea is going to be loaded
*/
-void Document::LoadEntryBinArea(BinEntry *elem)
+void Document::LoadEntryBinArea(DataEntry *entry)
{
- if (elem->GetBinArea() )
+ if( entry->GetBinArea() )
return;
bool openFile = !Fp;
if ( openFile )
OpenFile();
- size_t o =(size_t)elem->GetOffset();
+ size_t o =(size_t)entry->GetOffset();
Fp->seekg(o, std::ios::beg);
- size_t l = elem->GetLength();
- uint8_t *a = new uint8_t[l];
- if ( !a )
+ size_t l = entry->GetLength();
+ uint8_t *data = new uint8_t[l];
+ if ( !data )
{
- gdcmWarningMacro( "Cannot allocate BinEntry content for : "
- << std::hex << elem->GetGroup()
- << "|" << elem->GetElement() );
+ gdcmWarningMacro( "Cannot allocate DataEntry content for : "
+ << std::hex << entry->GetGroup()
+ << "|" << entry->GetElement() );
return;
}
- Fp->read((char*)a, l);
+ // Read the data
+ Fp->read((char*)data, l);
if ( Fp->fail() || Fp->eof() )
{
- delete[] a;
+ delete[] data;
+ entry->SetState(DataEntry::STATE_UNREAD);
return;
}
- elem->SetBinArea(a);
+ // Swap the data content if necessary
+ uint32_t i;
+ unsigned short vrLgth =
+ Global::GetVR()->GetAtomicElementLength(entry->GetVR());
+ if( entry->GetVR() == "OW" )
+ vrLgth = 1;
+
+ switch(vrLgth)
+ {
+ case 2:
+ {
+ uint16_t *data16 = (uint16_t *)data;
+ for(i=0;i<l/vrLgth;i++)
+ data16[i] = SwapShort(data16[i]);
+ break;
+ }
+ case 4:
+ {
+ uint32_t *data32 = (uint32_t *)data;
+ for(i=0;i<l/vrLgth;i++)
+ data32[i] = SwapLong(data32[i]);
+ break;
+ }
+ case 8:
+ {
+ gdcmWarningMacro("Can't swap 64 bits data");
+/* uint64_t *data64 = (uint64_t *)data;
+ for(i=0;i<l/vrLgth;i++)
+ data64[i] = SwapLongLong(data64[i]);*/
+ break;
+ }
+ }
+
+ entry->SetBinArea(data);
if ( openFile )
CloseFile();
bool Document::operator<(Document &document)
{
// Patient Name
- std::string s1 = GetEntryValue(0x0010,0x0010);
- std::string s2 = document.GetEntryValue(0x0010,0x0010);
+ std::string s1 = GetEntryString(0x0010,0x0010);
+ std::string s2 = document.GetEntryString(0x0010,0x0010);
if (s1 < s2)
{
return true;
else
{
// Patient ID
- s1 = GetEntryValue(0x0010,0x0020);
- s2 = document.GetEntryValue(0x0010,0x0020);
+ s1 = GetEntryString(0x0010,0x0020);
+ s2 = document.GetEntryString(0x0010,0x0020);
if ( s1 < s2 )
{
return true;
else
{
// Study Instance UID
- s1 = GetEntryValue(0x0020,0x000d);
- s2 = document.GetEntryValue(0x0020,0x000d);
+ s1 = GetEntryString(0x0020,0x000d);
+ s2 = document.GetEntryString(0x0020,0x000d);
if ( s1 < s2 )
{
return true;
else
{
// Serie Instance UID
- s1 = GetEntryValue(0x0020,0x000e);
- s2 = document.GetEntryValue(0x0020,0x000e);
+ s1 = GetEntryString(0x0020,0x000e);
+ s2 = document.GetEntryString(0x0020,0x000e);
if ( s1 < s2 )
{
return true;
/**
* \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
*/
-int Document::ComputeGroup0002Length( /*FileType filetype*/ )
+int Document::ComputeGroup0002Length( )
{
uint16_t gr;
- std::string vr;
+ VRKey vr;
int groupLength = 0;
bool found0002 = false;
//if ( filetype == ExplicitVR )
//{
- // if ( (vr == "OB") || (vr == "OW") || (vr == "UT") || (vr == "SQ") )
+ //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
+ // explicit VR AND (OB, OW, SQ, UT) : 4 more bytes
groupLength += 4;
}
//}
long l_max, bool delim_mode)
{
DocEntry *newDocEntry;
- ValEntry *newValEntry;
- BinEntry *newBinEntry;
+ DataEntry *newDataEntry;
SeqEntry *newSeqEntry;
VRKey vr;
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;
+ bool first = true;
+ gdcmWarningMacro( "Enter in ParseDES, delim-mode " << delim_mode
+ << " at offset " << std::hex << offset );
while (true)
{
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
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
// when something *very* strange happens
break;
}
- // an Item Starter found elsewhere but the first postition
+ // 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.
}
used = true;
- newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
- newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
+ newDataEntry = dynamic_cast<DataEntry*>(newDocEntry);
- if ( newValEntry || newBinEntry )
+ if ( newDataEntry )
{
- //////////////////////////// ContentEntry
- if ( newBinEntry )
- {
- vr = newDocEntry->GetVR();
- if ( Filetype == ExplicitVR &&
- !Global::GetVR()->IsVROfBinaryRepresentable(vr) )
- {
- ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- gdcmWarningMacro( std::hex << newDocEntry->GetGroup()
- << "|" << newDocEntry->GetElement()
- << " : Neither Valentry, nor BinEntry."
- "Probably unknown VR.");
- }
-
- //////////////////// BinEntry or UNKOWN VR:
-
- // When "this" is a Document the Key is simply of the
- // form ( group, elem )...
- //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):
+ //////////////////////////// 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'.");
+ }
+ */
- // time waste hunting
- //if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
- //{
- // newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
- // + newBinEntry->GetKey() );
- //}
-
- if ( !set->AddEntry( newBinEntry ) )
- {
- gdcmWarningMacro( "in ParseDES : cannot add a BinEntry "
- << newBinEntry->GetKey()
- << " (at offset : "
- << newBinEntry->GetOffset() << " )" );
- used=false;
- }
- else
- {
- // Load only if we can add (not a duplicate key)
- LoadDocEntry( newBinEntry );
- }
- } // end BinEntry
+ if ( !set->AddEntry( newDataEntry ) )
+ {
+ gdcmWarningMacro( "in ParseDES : cannot add a DataEntry "
+ << newDataEntry->GetKey()
+ << " (at offset : "
+ << newDataEntry->GetOffset() << " )" );
+ used=false;
+ }
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 ( 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):
-
- // 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
- {
- // Load only if we can add (not a duplicate key)
- LoadDocEntry( newValEntry );
- }
+ newDataEntry->Delete();
+ // Load only if we can add (not a duplicate key)
+ LoadDocEntry( newDataEntry );
+ }
- if ( newValEntry->GetElement() == 0x0000 ) // if on group length
+ if ( newDataEntry->GetElement() == 0x0000 ) // if on group length
+ {
+ if ( newDataEntry->GetGroup()%2 != 0 ) // if Shadow Group
{
- if ( newValEntry->GetGroup()%2 != 0 ) // if Shadow Group
+ if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
{
- if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
+ std::string strLgrGroup = newDataEntry->GetString();
+ int lgrGroup;
+ if ( newDataEntry->IsUnfound() )
{
- std::string strLgrGroup = newValEntry->GetValue();
- int lgrGroup;
- if ( strLgrGroup != GDCM_UNFOUND)
- {
- lgrGroup = atoi(strLgrGroup.c_str());
- Fp->seekg(lgrGroup, std::ios::cur);
- used = false;
- RemoveEntry( newDocEntry );
- // bcc 5.5 is right "assigned a value that's never used"
- // newDocEntry = 0;
- continue;
- }
+ lgrGroup = atoi(strLgrGroup.c_str());
+ 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;
}
}
}
+ }
- bool delimitor = newValEntry->IsItemDelimitor();
+ bool delimitor = newDataEntry->IsItemDelimitor();
- if ( (delimitor) ||
- (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) )
- {
- if ( !used )
- delete newDocEntry;
- break;
- }
+ if ( (delimitor) ||
+ (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) )
+ {
+ if ( !used )
+ newDocEntry->Delete();
+ break;
}
// Just to make sure we are at the beginning of next entry.
if ( newDocEntry->GetGroup()%2 != 0 )
{
Fp->seekg( l, std::ios::cur);
- used = false;
+ newDocEntry->Delete(); // Delete, not in the set
continue;
}
}
{
// User asked to skip *any* SeQuence
Fp->seekg( l, std::ios::cur);
- used = false;
+ newDocEntry->Delete(); // Delete, not in the set
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:
-// SQItem *parentSQItem = dynamic_cast< SQItem* > ( set );
if ( set == this ) // ( dynamic_cast< Document* > ( set ) )
{
newSeqEntry->SetDepthLevel( 1 );
- // 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
else if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
-
- // newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
- // + newSeqEntry->GetKey() );
}
if ( l != 0 )
{ // Don't try to parse zero-length sequences
+
+ gdcmWarningMacro( "Entry in ParseSQ, delim " << delim_mode_intern
+ << " at offset " << std::hex
+ << newDocEntry->GetOffset() );
+
ParseSQ( newSeqEntry,
newDocEntry->GetOffset(),
l, delim_mode_intern);
+
+ gdcmWarningMacro( "Exit from ParseSQ, delim " << delim_mode_intern);
+
}
if ( !set->AddEntry( newSeqEntry ) )
{
<< newSeqEntry->GetOffset() << " )" );
used = false;
}
+ else
+ {
+ newDocEntry->Delete();
+ }
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
if ( !used )
- delete newDocEntry;
- break;
+ newDocEntry->Delete();
+ break;
}
} // end SeqEntry : VR = "SQ"
if ( !used )
{
- delete newDocEntry;
+ newDocEntry->Delete();
}
first = false;
} // end While
+ gdcmDebugMacro( "Exit from ParseDES, delim-mode " << delim_mode );
}
/**
if ( newDocEntry->IsSequenceDelimitor() )
{
seqEntry->SetDelimitationItem( newDocEntry );
+ newDocEntry->Delete();
break;
}
}
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- delete newDocEntry;
+ newDocEntry->Delete();
break;
}
// 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 )
// Let's try :------------
// remove fff0,e000, created out of the SQItem
- delete newDocEntry;
Fp->seekg(offsetStartCurrentSQItem, std::ios::beg);
// fill up the current SQItem, starting at the beginning of fff0,e000
// end try -----------------
seqEntry->AddSQItem( itemSQ, SQItemNumber );
+ newDocEntry->Delete();
SQItemNumber++;
if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
{
{
// delete the Item Starter, built erroneously out of any Sequence
// it's not yet in the HTable/chained list
- delete docEntry;
+ docEntry->Delete();
// Get all info we can from PreviousDocEntry
uint16_t group = PreviousDocEntry->GetGroup();
Fp->seekg( 0, std::ios::beg);
Fp->seekg(offset, std::ios::cur);
-return newEntry;
+ 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
+ * @param forceLoad whether you want to force loading of 'long' elements
*/
void Document::LoadDocEntry(DocEntry *entry, bool forceLoad)
{
uint16_t group = entry->GetGroup();
- std::string vr = entry->GetVR();
+ uint16_t elem = entry->GetElement();
+ const VRKey &vr = entry->GetVR();
uint32_t length = entry->GetLength();
Fp->seekg((long)entry->GetOffset(), std::ios::beg);
// (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 )
+ //
+ // (fffe 0000) is an 'impossible' tag value,
+ // found in MR-PHILIPS-16-Multi-Seq.dcm
+
+ if ( (group == 0xfffe && elem != 0x0000 ) || vr == "SQ" )
{
// NO more value field for SQ !
return;
}
+ DataEntry *dataEntryPtr = dynamic_cast< DataEntry* >(entry);
+ if( !dataEntryPtr )
+ {
+ return;
+ }
+
// When the length is zero things are easy:
if ( length == 0 )
{
- ((ValEntry *)entry)->SetValue("");
+ dataEntryPtr->SetBinArea(NULL,true);
return;
}
{
if (length > MaxSizeLoadEntry)
{
- 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 !" );
- }
+ dataEntryPtr->SetBinArea(NULL,true);
+ dataEntryPtr->SetState(DataEntry::STATE_NOTLOADED);
// to be sure we are at the end of the value ...
Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
}
}
- // When we find a BinEntry not very much can be done :
- if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
- {
- s << GDCM_BINLOADED;
- binEntryPtr->SetValue(s.str());
- LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
- return;
- }
-
- if ( IsDocEntryAnInteger(entry) )
- {
- uint32_t NewInt;
- int nbInt;
- // When short integer(s) are expected, read and convert the following
- // (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)
- if (vr == "US" || vr == "SS")
- {
- nbInt = length / 2;
- NewInt = ReadInt16();
- s << NewInt;
- if (nbInt > 1)
- {
- for (int i=1; i < nbInt; i++)
- {
- s << '\\';
- NewInt = ReadInt16();
- s << NewInt;
- }
- }
- }
- // See above comment on multiple integers (mutatis mutandis).
- else if (vr == "UL" || vr == "SL")
- {
- nbInt = length / 4;
- NewInt = ReadInt32();
- s << NewInt;
- if (nbInt > 1)
- {
- for (int i=1; i < nbInt; i++)
- {
- s << '\\';
- NewInt = ReadInt32();
- s << NewInt;
- }
- }
- }
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
-
- ((ValEntry *)entry)->SetValue(s.str());
- return;
- }
-
- // FIXME: We need an additional byte for storing \0 that is not on disk
- char *str = new char[length+1];
- Fp->read(str, (size_t)length);
- 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 )
- {
- newValue = Util::DicomString(str, length+1);
- gdcmWarningMacro("Warning: bad length: " << length <<
- " For string :" << newValue.c_str());
- // Since we change the length of string update it length
- //entry->SetReadLength(length+1);
- }
- else
- {
- newValue = Util::DicomString(str, length);
- }
- delete[] str;
-
- if ( ValEntry *valEntry = dynamic_cast<ValEntry* >(entry) )
- {
- if ( Fp->fail() || Fp->eof())
- {
- 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" )
- {
- // Because of correspondance with the VR dic
- valEntry->SetValue(newValue);
- }
- else
- {
- valEntry->SetValue(newValue);
- }
- }
- else
- {
- gdcmWarningMacro("Should have a ValEntry, here ! " << valEntry->GetKey()
- << " lgt : " << valEntry->GetReadLength()
- << " at " << std::hex << valEntry->GetOffset());
- }
+ LoadEntryBinArea(dataEntryPtr); // last one, not to erase length !
}
/**
void Document::FindDocEntryLength( DocEntry *entry )
throw ( FormatError )
{
- std::string vr = entry->GetVR();
+ const VRKey &vr = entry->GetVR();
uint16_t length16;
if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT"
- /*|| vr == "UN"*/ )
+ || 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
* \brief Find the Value Representation of the current Dicom Element.
* @return Value Representation of the current Entry
*/
-std::string Document::FindDocEntryVR()
+VRKey Document::FindDocEntryVR()
{
if ( Filetype != ExplicitVR )
- return GDCM_UNKNOWN;
+ return GDCM_VRUNKNOWN;
long positionOnEntry = Fp->tellg();
// Warning: we believe this is explicit VR (Value Representation) because
// is in explicit VR and try to fix things if it happens not to be
// the case.
- char vr[3];
- Fp->read (vr, (size_t)2);
- vr[2] = 0;
+ VRKey vr;
+ Fp->read(&(vr[0]),(size_t)2);
+ gdcmDebugMacro( "--> VR: " << vr )
if ( !CheckDocEntryVR(vr) )
{
+ gdcmWarningMacro( "Unknown VR '" << vr << "'" )
Fp->seekg(positionOnEntry, std::ios::beg);
- return GDCM_UNKNOWN;
+ return GDCM_VRUNKNOWN;
}
return vr;
}
* @return false if the VR is incorrect or if the VR isn't referenced
* otherwise, it returns true
*/
-bool Document::CheckDocEntryVR(VRKey vr)
+bool Document::CheckDocEntryVR(const VRKey &vr)
{
- if ( !Global::GetVR()->IsValidVR(vr) )
- return false;
-
- return true;
-}
-
-/**
- * \brief Get the transformed value of the header entry. The VR value
- * is used to define the transformation to operate on the value
- * \warning NOT end user intended method !
- * @param entry entry to tranform
- * @return Transformed entry value
- */
-std::string Document::GetDocEntryValue(DocEntry *entry)
-{
- if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
- {
- std::string val = ((ValEntry *)entry)->GetValue();
- std::string vr = entry->GetVR();
- uint32_t length = entry->GetLength();
- std::ostringstream s;
- int nbInt;
-
- // When short integer(s) are expected, read and convert the following
- // n * 2 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // as usual for standard multivaluated filels
- // Elements with Value Multiplicity > 1
- // contain a set of short integers (not a single one)
-
- if ( vr == "US" || vr == "SS" )
- {
- uint16_t newInt16;
-
- nbInt = length / 2;
- for (int i=0; i < nbInt; i++)
- {
- if ( i != 0 )
- {
- s << '\\';
- }
- newInt16 = ( val[2*i+0] & 0xFF ) + ( ( val[2*i+1] & 0xFF ) << 8);
- newInt16 = SwapShort( newInt16 );
- s << newInt16;
- }
- }
-
- // When integer(s) are expected, read and convert the following
- // n * 4 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // 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" )
- {
- uint32_t newInt32;
-
- nbInt = length / 4;
- for (int i=0; i < nbInt; i++)
- {
- if ( i != 0)
- {
- s << '\\';
- }
- newInt32 = ( val[4*i+0] & 0xFF )
- + (( val[4*i+1] & 0xFF ) << 8 )
- + (( val[4*i+2] & 0xFF ) << 16 )
- + (( val[4*i+3] & 0xFF ) << 24 );
- newInt32 = SwapLong( newInt32 );
- s << newInt32;
- }
- }
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- return s.str();
- }
- return ((ValEntry *)entry)->GetValue();
-}
-
-/**
- * \brief Get the reverse transformed value of the header entry. The VR
- * value is used to define the reverse transformation to operate on
- * the value
- * \warning NOT end user intended method !
- * @param entry Entry to reverse transform
- * @return Reverse transformed entry value
- */
-std::string Document::GetDocEntryUnvalue(DocEntry *entry)
-{
- if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
- {
- std::string vr = entry->GetVR();
- std::vector<std::string> tokens;
- std::ostringstream s;
-
- if ( vr == "US" || vr == "SS" )
- {
- uint16_t newInt16;
-
- tokens.erase( tokens.begin(), tokens.end()); // clean any previous value
- Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size(); i++)
- {
- newInt16 = atoi(tokens[i].c_str());
- s << ( newInt16 & 0xFF )
- << (( newInt16 >> 8 ) & 0xFF );
- }
- tokens.clear();
- }
- if ( vr == "UL" || vr == "SL")
- {
- uint32_t newInt32;
-
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- newInt32 = atoi(tokens[i].c_str());
- s << (char)( newInt32 & 0xFF )
- << (char)(( newInt32 >> 8 ) & 0xFF )
- << (char)(( newInt32 >> 16 ) & 0xFF )
- << (char)(( newInt32 >> 24 ) & 0xFF );
- }
- tokens.clear();
- }
-
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- return s.str();
- }
-
- return ((ValEntry *)entry)->GetValue();
+ return Global::GetVR()->IsValidVR(vr);
}
/**
void Document::FixDocEntryFoundLength(DocEntry *entry,
uint32_t foundLength)
{
- entry->SetReadLength( foundLength ); // will be updated only if a bug is found
+ entry->SetReadLength( foundLength );// will be updated only if a bug is found
if ( foundLength == 0xffffffff)
{
foundLength = 0;
if ( foundLength % 2)
{
- gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength
+ gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength
<< " in x(" << std::hex << gr << "," << elem <<")");
}
else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
{
foundLength = 4;
- entry->SetReadLength(4); // a bug is to be fixed !?
+ entry->SetReadLength(4); // a bug is to be fixed !
}
else if ( entry->GetVR() == "SQ" )
{
foundLength = 0;
}
- }
+ else
+ {
+ foundLength=12; // to skip the mess that follows this bugged Tag !
+ }
+ }
entry->SetLength(foundLength);
}
{
uint16_t elem = entry->GetElement();
uint16_t group = entry->GetGroup();
- const std::string &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
{
- // Allthough this should never happen, still some images have a
+ // Although this should never happen, still some images have a
// corrupted group length [e.g. have a glance at offset x(8336) of
- // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm].
+ // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
// Since for dicom compliant and well behaved headers, the present
// test is useless (and might even look a bit paranoid), when we
// encounter such an ill-formed image, we simply display a warning
char *entCur = deb + 128;
if ( memcmp(entCur, "DICM", (size_t)4) == 0 )
{
- gdcmWarningMacro( "Looks like DICOM Version3 (preamble + DCM)" );
+ gdcmDebugMacro( "Looks like DICOM Version3 (preamble + DCM)" );
// Group 0002 should always be VR, and the first element 0000
// Let's be carefull (so many wrong headers ...)
// instead of just checking for UL, OB and UI !? group 0000
{
Filetype = ExplicitVR;
- gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
+ gdcmDebugMacro( "Group 0002 : Explicit Value Representation");
}
else
{
Filetype = ImplicitVR;
- gdcmWarningMacro( "Group 0002 :Not an explicit Value Representation;"
+ gdcmErrorMacro( "Group 0002 :Not an explicit Value Representation;"
<< "Looks like a bugged Header!");
}
if ( net2host )
{
SwapCode = 4321;
- gdcmWarningMacro( "HostByteOrder != NetworkByteOrder");
+ gdcmDebugMacro( "HostByteOrder != NetworkByteOrder");
}
else
{
SwapCode = 1234;
- gdcmWarningMacro( "HostByteOrder = NetworkByteOrder");
+ gdcmDebugMacro( "HostByteOrder = NetworkByteOrder");
}
// Position the file position indicator at first tag
memcmp(entCur, "OB", (size_t)2) == 0 )
{
Filetype = ExplicitVR;
- gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
+ gdcmDebugMacro( "Group 0002 : Explicit Value Representation");
return true;
}
}
// Only 0 or 4321 will be possible
// (no oportunity to check for the formerly well known
// ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
- // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -3, 4, ..., 8-)
+ // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc-3, 4, ..., 8-)
// the file IS NOT ACR-NEMA nor DICOM V3
// Find a trick to tell it the caller...
Filetype = ACR;
return true;
default :
- gdcmWarningMacro("ACR/NEMA unfound swap info (Really hopeless !)");
+ gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)");
Filetype = Unknown;
return false;
}
*/
void Document::SwitchByteSwapCode()
{
- gdcmWarningMacro( "Switching Byte Swap code from "<< SwapCode
- << " at :" <<std::hex << Fp->tellg() );
+ gdcmDebugMacro( "Switching Byte Swap code from "<< SwapCode
+ << " at: 0x" << std::hex << Fp->tellg() );
if ( SwapCode == 1234 )
{
SwapCode = 4321;
{
SwapCode = 3412;
}
+ gdcmDebugMacro( " Into: "<< SwapCode );
}
/**
if ( HasDCMPreamble )
HandleOutOfGroup0002(group, elem);
- std::string vr = FindDocEntryVR();
- std::string realVR = vr;
+ VRKey vr = FindDocEntryVR();
+
+ VRKey realVR = vr;
- if ( vr == GDCM_UNKNOWN )
+ if ( vr == GDCM_VRUNKNOWN )
{
if ( elem == 0x0000 ) // Group Length
{
}
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";
+ // 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
{
if ( dictEntry )
{
realVR = dictEntry->GetVR();
+ dictEntry->Unregister();
}
}
}
+ gdcmDebugMacro( "Found VR: " << vr << " / Real VR: " << realVR );
DocEntry *newEntry;
if ( Global::GetVR()->IsVROfSequence(realVR) )
newEntry = NewSeqEntry(group, elem);
- else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) )
- newEntry = NewValEntry(group, elem, vr);
- else
- newEntry = NewBinEntry(group, elem, vr);
+ else
+ {
+ newEntry = NewDataEntry(group, elem, realVR);
+ static_cast<DataEntry *>(newEntry)->SetState(DataEntry::STATE_NOTLOADED);
+ }
- if ( vr == GDCM_UNKNOWN )
+ if ( vr == GDCM_VRUNKNOWN )
{
if ( Filetype == ExplicitVR )
{
{
std::string msg;
int offset = Fp->tellg();
- msg = Util::Format("Entry (%04x,%04x) at 0x(%x) should be Explicit VR\n",
- newEntry->GetGroup(), newEntry->GetElement(), offset );
+ msg = Util::Format(
+ "Entry (%04x,%04x) at x(%x) should be Explicit VR\n",
+ newEntry->GetGroup(), newEntry->GetElement(), offset );
gdcmWarningMacro( msg.c_str() );
}
}
catch ( FormatError )
{
// Call it quits
- delete newEntry;
+ newEntry->Delete();
return 0;
}
*/
void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
{
- // Endian reversion. Some files contain groups of tags with reversed endianess.
+ // Endian reversion.
+ // Some files contain groups of tags with reversed endianess.
static int reversedEndian = 0;
// try to fix endian switching in the middle of headers
if ((group == 0xfeff) && (elem == 0x00e0))
reversedEndian--;
SwitchByteSwapCode();
}
+ else if (group == 0xfeff && elem == 0xdde0)
+ {
+ // reversed Sequence Terminator found
+ // probabely a bug in the header !
+ // Do what you want, it breaks !
+ //reversedEndian--;
+ //SwitchByteSwapCode();
+ gdcmWarningMacro( "Should never get here! reversed Sequence Terminator!" );
+ // fix the tag
+ group = 0xfffe;
+ elem = 0xe0dd;
+ }
+ else if (group == 0xfffe && elem == 0xe0dd)
+ {
+ gdcmWarningMacro( "Straight Sequence Terminator." );
+ }
}
/**
*/
void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem)
{
- // Endian reversion. Some files contain groups of tags with reversed endianess.
+ // Endian reversion.
+ // Some files contain groups of tags with reversed endianess.
if ( !Group0002Parsed && group != 0x0002)
{
Group0002Parsed = true;
return;
}
- // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..."
+ // Group 0002 is always 'Explicit ...'
+ // even when Transfer Syntax says 'Implicit ..."
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian )
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
+ TS::ImplicitVRLittleEndian )
{
Filetype = ImplicitVR;
}
// FIXME Strangely, this works with
- //'Implicit VR Transfer Syntax (GE Private)
- if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
+ //'Implicit VR BigEndian Transfer Syntax (GE Private)
+ //
+ // --> Probabely normal, since we considered we never have
+ // to trust manufacturers.
+ // (we find very often 'Implicit VR' tag,
+ // even when Transfer Syntax tells us it's Explicit ...
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
+ TS::ExplicitVRBigEndian )
{
gdcmWarningMacro("Transfer Syntax Name = ["
<< GetTransferSyntaxName() << "]" );
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff