Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/11/14 14:23:44 $
- Version: $Revision: 1.327 $
+ Date: $Date: 2006/02/07 12:37:19 $
+ Version: $Revision: 1.338 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <ctype.h> // for isdigit
#include <stdlib.h> // for atoi
+#if defined(__BORLANDC__)
+ #include <mem.h> // for memset
+#endif
+
namespace gdcm
{
//-----------------------------------------------------------------------------
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( );
}
/**
Group0002Parsed = false;
gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str());
-
- Fp->seekg(0, std::ios::end);
- long lgt = Fp->tellg(); // total length of the file
-
- Fp->seekg(0, std::ios::beg);
+
+ // Computes the total length of the file
+ Fp->seekg(0, std::ios::end); // Once for a given Document !
+ long lgt = Fp->tellg(); // Once for a given Document !
+ Fp->seekg(0, std::ios::beg); // Once for a given Document !
// CheckSwap returns a boolean
// (false if no swap info of any kind was found)
}
IsDocumentAlreadyLoaded = true;
- Fp->seekg( 0, std::ios::beg);
+ Fp->seekg( 0, std::ios::beg); // Once per Document
// Load 'non string' values
* @return false when we're 150 % sure it's NOT a Dicom/Acr file,
* true otherwise.
*/
-bool Document::IsReadable()
+bool Document::IsParsable()
{
if ( Filetype == Unknown )
{
- gdcmErrorMacro( "Wrong filetype for " << GetFileName());
+ gdcmWarningMacro( "Wrong filetype for " << GetFileName());
return false;
}
if ( IsEmpty() )
{
- gdcmErrorMacro( "No tag in internal hash table.");
+ gdcmWarningMacro( "No tag in internal hash table.");
return false;
}
return true;
}
+/**
+ * \brief This predicate tells us whether or not the current Document
+ * was properly parsed and contains at least *one* Dicom Element
+ * (and nothing more, sorry).
+ * @return false when we're 150 % sure it's NOT a Dicom/Acr file,
+ * true otherwise.
+ */
+bool Document::IsReadable()
+{
+ return IsParsable();
+}
/**
* \brief Predicate for dicom version 3 file.
// The entry might be present but not loaded (parsing and loading
// happen at different stages): try loading and proceed with check...
- LoadDocEntrySafe(entry);
+
+ // Well ...
+ // (parsing and loading happen at the very same stage!)
+ //LoadDocEntrySafe(entry); //JPRx
if (DataEntry *dataEntry = dynamic_cast<DataEntry *>(entry) )
{
std::string transfer = dataEntry->GetString();
}
//-- DICOM --
- Fp->seekg(126L, std::ios::cur);
+ Fp->seekg(126L, std::ios::cur); // Once for a given Document
char dicm[4]; // = {' ',' ',' ',' '};
Fp->read(dicm, (size_t)4);
if ( Fp->eof() )
{
if( entry->GetBinArea() )
return;
+// to be coherent with LoadEntryBinArea(uint16_t group, uint16_t elem)
+// (and save time !)
+// :-(
+// TestAllReadCompareDicom hangs on rle16sti.dcm
bool openFile = !Fp;
if ( openFile )
OpenFile();
-
+// -------
size_t o =(size_t)entry->GetOffset();
- Fp->seekg(o, std::ios::beg);
+ Fp->seekg(o, std::ios::beg); // FIXME : for each BinEntry LoadEntryBinArea
size_t l = entry->GetLength();
uint8_t *data = new uint8_t[l];
}
entry->SetBinArea(data);
+
+// to be coherent with LoadEntryBinArea(uint16_t group, uint16_t elem)
+// (and save time !)
if ( openFile )
CloseFile();
+// ---------------
}
/**
* \brief Loads the element while preserving the current
* underlying file position indicator as opposed to
- * LoadDocEntry that modifies it.
+ * LoadDocEntry that modifies it
+ * \note seems to be unused!.
* @param entry DocEntry whose value will be loaded.
*/
void Document::LoadDocEntrySafe(DocEntry *entry)
{
if ( Fp )
{
- long PositionOnEntry = Fp->tellg();
+ long PositionOnEntry = Fp->tellg(); // LoadDocEntrySafe is not used
LoadDocEntry(entry);
- Fp->seekg(PositionOnEntry, std::ios::beg);
+ Fp->seekg(PositionOnEntry, std::ios::beg); // LoadDocEntrySafe is not used
}
}
return g;
}
-/**
- * \brief skips bytes inside the source file
- * @return
- */
-void Document::SkipBytes(uint32_t nBytes)
-{
- //FIXME don't dump the returned value
- Fp->seekg((long)nBytes, std::ios::cur);
-}
-
/**
* \brief Re-computes the length of the Dicom group 0002.
*/
return groupLength;
}
+/**
+ * \brief CallStartMethod
+ */
+void Document::CallStartMethod()
+{
+ Progress = 0.0f;
+ Abort = false;
+ CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
+}
+
+/**
+ * \brief CallProgressMethod
+ */
+void Document::CallProgressMethod()
+{
+ CommandManager::ExecuteCommand(this,CMD_PROGRESS);
+}
+
+/**
+ * \brief CallEndMethod
+ */
+void Document::CallEndMethod()
+{
+ Progress = 1.0f;
+ CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
+}
+
//-----------------------------------------------------------------------------
// Private
/**
bool delim_mode_intern = delim_mode;
bool first = true;
gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode
- << " at offset " << std::hex << offset );
+ << " at offset " << std::hex << "0x(" << offset << ")" );
while (true)
{
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry
{
break;
}
{
gdcmDebugMacro( "in ParseDES : cannot add a DataEntry "
<< newDataEntry->GetKey()
- << " (at offset : "
- << newDataEntry->GetOffset() << " )" );
+ << " (at offset : 0x("
+ << newDataEntry->GetOffset() << ") )" );
used=false;
}
else
// Load only if we can add (not a duplicate key)
LoadDocEntry( newDataEntry );
}
-
if ( newDataEntry->GetElement() == 0x0000 ) // if on group length
{
if ( newDataEntry->GetGroup()%2 != 0 ) // if Shadow Group
if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
{
std::string strLgrGroup = newDataEntry->GetString();
+
int lgrGroup;
- if ( newDataEntry->IsUnfound() )
+ //if ( newDataEntry->IsUnfound() ) /?!? JPR
{
lgrGroup = atoi(strLgrGroup.c_str());
- Fp->seekg(lgrGroup, std::ios::cur);
+ Fp->seekg(lgrGroup, std::ios::cur); // Only when NOSHADOW
//used = false; // never used
RemoveEntry( newDocEntry ); // Remove and delete
// bcc 5.5 is right "assigned a value that's never used"
bool delimitor = newDataEntry->IsItemDelimitor();
if ( (delimitor) ||
- (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) )
+ (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) // Once per DataEntry
{
if ( !used )
newDocEntry->Delete();
// User asked to skip SeQuences *only* if they belong to Shadow Group
if ( newDocEntry->GetGroup()%2 != 0 )
{
- Fp->seekg( l, std::ios::cur);
+ Fp->seekg( l, std::ios::cur); // once per SQITEM, when NOSHADOWSEQ
newDocEntry->Delete(); // Delete, not in the set
continue;
}
if ( (LoadMode & LD_NOSEQ) && ! delim_mode_intern )
{
// User asked to skip *any* SeQuence
- Fp->seekg( l, std::ios::cur);
+ Fp->seekg( l, std::ios::cur); // Once per SQ, when NOSEQ
newDocEntry->Delete(); // Delete, not in the set
continue;
}
{ // Don't try to parse zero-length sequences
gdcmDebugMacro( "Entry in ParseSQ, delim " << delim_mode_intern
- << " at offset " << std::hex
- << newDocEntry->GetOffset() );
+ << " at offset 0x(" << std::hex
+ << newDocEntry->GetOffset() << ")");
ParseSQ( newSeqEntry,
newDocEntry->GetOffset(),
{
gdcmWarningMacro( "in ParseDES : cannot add a SeqEntry "
<< newSeqEntry->GetKey()
- << " (at offset : "
- << newSeqEntry->GetOffset() << " )" );
+ << " (at offset : 0x("
+ << 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) // Once per SeqEntry
{
if ( !used )
newDocEntry->Delete();
break;
}
}
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per SQItem
{
newDocEntry->Delete();
break;
}
// remove fff0,e000, created out of the SQItem
- Fp->seekg(offsetStartCurrentSQItem, std::ios::beg);
+
+ //Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); //JPRx
+
// fill up the current SQItem, starting at the beginning of fff0,e000
ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod);
- offsetStartCurrentSQItem = Fp->tellg();
+ offsetStartCurrentSQItem = Fp->tellg(); // Once per SQItem
seqEntry->AddSQItem( itemSQ, SQItemNumber );
itemSQ->Delete();
newDocEntry->Delete();
SQItemNumber++;
- if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
+ //if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) //JPRx
+ if ( !delim_mode && (offsetStartCurrentSQItem-offset ) >= l_max )
{
break;
}
long offset = PreviousDocEntry->GetOffset();
gdcmDebugMacro( "Backtrack :" << std::hex << group
- << "|" << elem
- << " at offset " << offset );
+ << "|" << elem
+ << " at offset 0x(" <<offset << ")" );
RemoveEntry( PreviousDocEntry );
// forge the Seq Entry
newEntry->SetOffset(offset);
// Move back to the beginning of the Sequence
- Fp->seekg( 0, std::ios::beg);
- Fp->seekg(offset, std::ios::cur);
+ Fp->seekg( 0, std::ios::beg); // Only for Shadow Implicit VR SQ
+ Fp->seekg(offset, std::ios::cur); // Only for Shadow Implicit VR SQ
return newEntry;
}
const VRKey &vr = entry->GetVR();
uint32_t length = entry->GetLength();
- Fp->seekg((long)entry->GetOffset(), std::ios::beg);
+ // Fp->seekg((long)entry->GetOffset(), std::ios::beg); // JPRx
// A SeQuence "contains" a set of Elements.
// (fffe e000) tells us an Element is beginning
dataEntryPtr->SetState(DataEntry::STATE_NOTLOADED);
// to be sure we are at the end of the value ...
- Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
- std::ios::beg);
+ // Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
+ // std::ios::beg); //JPRx
return;
}
}
// The following reserved two bytes (see PS 3.5-2003, section
// "7.1.2 Data element structure with explicit vr", p 27) must be
// skipped before proceeding on reading the length on 4 bytes.
- Fp->seekg( 2L, std::ios::cur);
+
+ Fp->seekg( 2L, std::ios::cur); // Once per OW,OB,SQ DocEntry
uint32_t length32 = ReadInt32();
if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
uint32_t lengthOB;
try
{
- lengthOB = FindDocEntryLengthOBOrOW();
+ lengthOB = FindDocEntryLengthOBOrOW();// for encapsulation of encoded pixel
}
catch ( FormatUnexpected )
{
gdcmWarningMacro( " Computing the length failed for " <<
entry->GetKey() <<" in " <<GetFileName());
- long currentPosition = Fp->tellg();
- Fp->seekg(0L,std::ios::end);
+ long currentPosition = Fp->tellg(); // Only for gdcm-JPEG-LossLess3a.dcm-like
+ Fp->seekg(0L,std::ios::end); // Only for gdcm-JPEG-LossLess3a.dcm-like
- long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
- Fp->seekg(currentPosition, std::ios::beg);
+ long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; // Only for gdcm-JPEG-LossLess3a.dcm-like
+ Fp->seekg(currentPosition, std::ios::beg); // Only for gdcm-JPEG-LossLess3a.dcm-like
entry->SetReadLength(lengthUntilEOF);
entry->SetLength(lengthUntilEOF);
throw( FormatUnexpected )
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
- long positionOnEntry = Fp->tellg();
+ long positionOnEntry = Fp->tellg(); // Only for OB,OW DataElements
+
bool foundSequenceDelimiter = false;
uint32_t totalLength = 0;
totalLength += 4;
if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- long filePosition = Fp->tellg();
+ // long filePosition = Fp->tellg(); JPRx
gdcmWarningMacro(
"Neither an Item tag nor a Sequence delimiter tag on :"
<< std::hex << group << " , " << elem
- << ") -before- position x(" << filePosition << ")" );
+ //<< ") -before- position x(" << filePosition // JPRx
+ << ")" );
- Fp->seekg(positionOnEntry, std::ios::beg);
+ Fp->seekg(positionOnEntry, std::ios::beg); // Oncd per fragment (if any) of OB,OW DataElements
throw FormatUnexpected(
"Neither an Item tag nor a Sequence delimiter tag.");
}
break;
}
}
- Fp->seekg( positionOnEntry, std::ios::beg);
+ Fp->seekg( positionOnEntry, std::ios::beg); // Only for OB,OW DataElements
return totalLength;
}
if ( Filetype != ExplicitVR )
return GDCM_VRUNKNOWN;
- long positionOnEntry = Fp->tellg();
+ long positionOnEntry = Fp->tellg(); // FIXME : for each VR !
// Warning: we believe this is explicit VR (Value Representation) because
// we used a heuristic that found "UL" in the first tag and/or
// 'Transfer Syntax' told us it is.
// Alas this doesn't guarantee that all the tags will be in explicit VR.
- // In some cases one finds implicit VR tags mixed within an explicit VR file.
+ // In some cases one finds implicit VR tags mixed within an explicit VR file
+ // Well...
+ // 'Normaly' the only case is : group 0002 Explicit, and other groups Implicit
+ //
// Hence we make sure the present tag is in explicit VR and try to fix things
// if it happens not to be the case.
if ( CurrentGroup != 0xfffe )
gdcmWarningMacro( "Unknown VR " << std::hex << "0x("
<< (unsigned int)vr[0] << "|" << (unsigned int)vr[1]
- << ") at offset :" << positionOnEntry );
- Fp->seekg(positionOnEntry, std::ios::beg);
+ << ") at offset : 0x(" << positionOnEntry<< ")" );
+ Fp->seekg(positionOnEntry, std::ios::beg); // FIXME : for each VR !
return GDCM_VRUNKNOWN;
}
return vr;
// test is useless (and might even look a bit paranoid), when we
// encounter such an ill-formed image, we simply display a warning
// message and proceed on parsing (while crossing fingers).
- long filePosition = Fp->tellg();
+ long filePosition = Fp->tellg(); // Only when elem 0x0000 length is not 0 (?!?)
gdcmWarningMacro( "Erroneous Group Length element length on : ("
<< std::hex << group << " , " << elem
<< ") -before- position x(" << filePosition << ")"
// Position the file position indicator at first tag
// (i.e. after the file preamble and the "DICM" string).
- Fp->seekg(0, std::ios::beg); // FIXME : Is it usefull?
+ //Fp->seekg(0, std::ios::beg); // FIXME : Is it usefull?
- Fp->seekg ( 132L, std::ios::beg);
+ Fp->seekg ( 132L, std::ios::beg); // Once per Document
return true;
} // ------------------------------- End of DicomV3 ----------------
gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)");
- Fp->seekg(0, std::ios::beg);
+ Fp->seekg(0, std::ios::beg); // Once per ACR-NEMA Document
// Let's check 'No Preamble Dicom File' :
// Should start with group 0x0002
void Document::SwitchByteSwapCode()
{
gdcmDebugMacro( "Switching Byte Swap code from "<< SwapCode
- << " at: 0x" << std::hex << Fp->tellg() );
+ << " at: 0x" << std::hex << Fp->tellg() ); // Only when DEBUG
if ( SwapCode == 1234 )
{
SwapCode = 4321;
{
realVR = "UL"; // must be UL
}
+ // Commented out in order not to generate 'Shadow Groups' where some
+ // Data Elements are Explicit VR and some other ones Implicit VR
+ // (Stupid MatLab DICOM Reader couln't read gdcm-written images)
+ /*
else if (CurrentGroup%2 == 1 &&
(CurrentElem >= 0x0010 && CurrentElem <=0x00ff ))
{
// (gggg-0010->00FF where gggg is odd) attributes have to be LO
realVR = "LO";
}
+ */
else
{
DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);
if ( newEntry->GetGroup() != 0xfffe )
{
std::string msg;
- int offset = Fp->tellg();
+ int offset = Fp->tellg(); // FIXME : Only when heuristic for Explicit/Implicit was wrong
msg = Util::Format(
"Entry (%04x,%04x) at x(%x) should be Explicit VR\n",
newEntry->GetGroup(), newEntry->GetElement(), offset );
return 0;
}
- newEntry->SetOffset(Fp->tellg());
+ newEntry->SetOffset(Fp->tellg()); // for each DocEntry
return newEntry;
}
// if Transfer Syntax is Big Endian we have to change CheckSwap
std::string ts = GetTransferSyntax();
- if ( ts == GDCM_UNKNOWN )
- {
- gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " );
- return;
- }
- if ( !Global::GetTS()->IsTransferSyntax(ts) )
- {
- gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: ["
- << ts << "]");
- return;
- }
// Group 0002 is always 'Explicit ...'
// even when Transfer Syntax says 'Implicit ..."
}
// FIXME Strangely, this works with
- //'Implicit VR BigEndian Transfer Syntax (GE Private)
+ //'Implicit VR BigEndian Transfer Syntax' (GE Private)
//
// --> Probabely normal, since we considered we never have
// to trust manufacturers.
group = SwapShort(group);
elem = SwapShort(elem);
}
+
+ /// \todo find a trick to warn user and stop processing
+
+ if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
+ TS::DeflatedExplicitVRLittleEndian)
+ {
+ gdcmWarningMacro("Transfer Syntax ["
+ << GetTransferSyntaxName() << "] :"
+ << " not yet dealt with ");
+ return;
+ }
+
+ // The following shouldn't occur very often
+ // Let's check at the very end.
+
+ if ( ts == GDCM_UNKNOWN )
+ {
+ gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " );
+ return;
+ }
+
+ if ( !Global::GetTS()->IsTransferSyntax(ts) )
+ {
+ gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: ["
+ << ts << "]");
+ return;
+ }
}
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff