Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/06/22 08:01:41 $
- Version: $Revision: 1.249 $
+ Date: $Date: 2005/07/06 00:15:11 $
+ Version: $Revision: 1.256 $
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
{
SwapCode = 1234;
Filetype = ExplicitVR;
Group0002Parsed = false;
- LoadMode = 0x00000000; // Load everything
+ LoadMode = 0x00000000; // Load everything, later
// Load will set it to true if sucessfull
IsDocumentAlreadyLoaded = false;
{
// We should clean out anything that already exists.
// Check IsDocumentAlreadyLoaded to be sure.
- if( IsDocumentAlreadyLoaded )
+ if ( IsDocumentAlreadyLoaded )
{
gdcmWarningMacro( "A file was already parsed inside this "
<< "gdcm::Document (previous name was: "
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 " )
{
// FIXME
// Probabely this line should be outside the 'if'
/// 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
// ----------------------------
// 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.
//
*/
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 ||
Fp->seekg(126L, std::ios::cur);
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;
return;
BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
- if( !binElement )
+ if ( !binElement )
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");
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." );
}
{
gr = entry->GetGroup();
- if( gr == 0x0002 )
+ if ( gr == 0x0002 )
{
found0002 = true;
- if( entry->GetElement() != 0x0000 )
+ if ( entry->GetElement() != 0x0000 )
{
vr = entry->GetVR();
- if( filetype == ExplicitVR )
+ if ( filetype == ExplicitVR )
{
if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || (vr == "UT") )
{
/**
* \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 delim_mode : whether we are in 'delimitor mode' (l=0xffffff) or not
SeqEntry *newSeqEntry;
VRKey vr;
bool used;
+ bool delim_mode_intern = delim_mode;
while (true)
{
}
LoadDocEntry( newBinEntry );
- if( !set->AddEntry( newBinEntry ) )
+ if ( !set->AddEntry( newBinEntry ) )
{
//Expect big troubles if here
//delete newBinEntry;
+ gdcmWarningMacro("in ParseDES : shouldn't get here !");
used=false;
}
}
}
}
- if( !set->AddEntry( newValEntry ) )
+ if ( !set->AddEntry( newValEntry ) )
{
// If here expect big troubles
// delete newValEntry; //otherwise mem leak
if (delimitor)
{
- if(!used)
+ if ( !used )
delete newDocEntry;
break;
}
- if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
+ if ( !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 & NO_SHADOWSEQ) && ! 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;
+ continue;
+ }
+ }
+ if ( (LoadMode & NO_SEQ) && ! delim_mode_intern )
{
+ // User asked to skip *any* SeQuence
Fp->seekg( l, std::ios::cur);
used = false;
continue;
- }
+ }
// no other way to create it ...
- newSeqEntry->SetDelimitorMode( delim_mode );
+ 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.
{ // 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 ) )
{
used = false;
}
-
+
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
- if( !used )
+ if ( !used )
delete newDocEntry;
break;
}
}
- if( !used )
+ if ( !used )
delete newDocEntry;
}
}
if ( !newDocEntry )
{
// FIXME Should warn user
+ gdcmWarningMacro("in ParseSQ : should never get here!");
break;
}
- if( delim_mode )
+ if ( delim_mode )
{
if ( newDocEntry->IsSequenceDelimitor() )
{
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 -----------------
// (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;
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 <<
return;
}
- if( vr == "UI" )
+ if ( vr == "UI" )
{
// Because of correspondance with the VR dic
valEntry->SetValue(newValue);
Fp->read (vr, (size_t)2);
vr[2] = 0;
- if( !CheckDocEntryVR(vr) )
+ if ( !CheckDocEntryVR(vr) )
{
Fp->seekg(positionOnEntry, std::ios::beg);
return GDCM_UNKNOWN;
// 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 << '\\';
}
//////// 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");
*/
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 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()
{
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
{
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) )
+ else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) )
newEntry = NewValEntry(group, elem,vr);
else
newEntry = NewBinEntry(group, elem,vr);
- 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() );
}
}
/**
* \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