Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/04/29 15:10:55 $
- Version: $Revision: 1.238 $
+ Date: $Date: 2005/07/02 16:51:16 $
+ Version: $Revision: 1.253 $
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
/**
* \brief Constructor (not to break the API)
- * @param filename 'Document' (File or DicomDir) to be opened for parsing
+ * @param fileName 'Document' (File or DicomDir) to be open for parsing
*/
Document::Document( std::string const &fileName )
:ElementSet(-1)
// Load will set it to true if sucessfull
IsDocumentAlreadyLoaded = false;
- Load(fileName);
+ Load(fileName);
}
/**
* \brief Canonical destructor.
/**
* \brief Loader
- * @param filename 'Document' (File or DicomDir) to be opened for parsing
+ * @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.
*/
-void Document::Load( std::string const &fileName )
+bool Document::Load( std::string const &fileName )
{
// 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: "
- << Filename.c_str() << ". New name is :"
- << fileName );
+ 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 ?!?
+ // Should we call ClearEntry() on the parent object ?!?
}
Filename = fileName;
//gdcmWarningMacro( "Unable to open as an ACR/DICOM file: "
// << Filename.c_str() );
Filetype = Unknown;
- return;
+ return false;
}
Group0002Parsed = false;
gdcmWarningMacro( "Neither a DICOM V3 nor an ACR-NEMA file: "
<< Filename.c_str());
CloseFile();
- return ;
+ return false;
}
long beg = Fp->tellg(); // just after DICOM preamble (if any)
gdcmWarningMacro( "No tag in internal hash table for: "
<< Filename.c_str());
CloseFile();
- return ;
+ return false;
}
IsDocumentAlreadyLoaded = true;
// 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
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)
+ }
+ }
+ }
+ }
CloseFile();
SetValEntry(rows , 0x0028, 0x0011);
}
// --- End of ACR-LibIDO kludge ---
+
+ return true;
}
/**
*/
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") )
+ if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || (vr == "UT") )
{
- // explicit VR AND OB, OW, SQ : 4 more bytes
+ // explicit VR AND OB, OW, SQ, UT : 4 more bytes
groupLength += 4;
}
}
}
LoadDocEntry( newBinEntry );
- if( !set->AddEntry( newBinEntry ) )
+ if ( !set->AddEntry( newBinEntry ) )
{
//Expect big troubles if here
//delete newBinEntry;
if ( strLgrGroup != GDCM_UNFOUND)
{
lgrGroup = atoi(strLgrGroup.c_str());
- Fp->seekg(lgrGroup , std::ios::cur);
+ Fp->seekg(lgrGroup, std::ios::cur);
used = false;
continue;
}
}
}
- 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 ( (LoadMode & NO_SEQ) && ! delim_mode ) // User asked to skip SQ
+ if ( (LoadMode & NO_SHADOWSEQ) && ! delim_mode )
+ {
+ // User asked to skip SQ 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 )
{
+ // User asked to skip *any* SeQuence
Fp->seekg( l, std::ios::cur);
used = false;
continue;
newDocEntry->GetOffset(),
l, delim_mode);
}
- 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;
}
}
// FIXME Should warn user
break;
}
- if( delim_mode )
+ if ( delim_mode )
{
if ( newDocEntry->IsSequenceDelimitor() )
{
// (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;
{
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 << " 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();
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());
}
}
if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
- if ( vr == "OB" || vr == "OW" || vr == "SQ" || 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
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 << '\\';
}
// Allthough not recent many such GE corrupted images are still present
// on Creatis hard disks. Hence this fix shall remain when such images
// are no longer in use (we are talking a few years, here)...
- // Note: XMedCom probably uses such a trick since it is able to read
+ // Note: XMedCon probably uses such a trick since it is able to read
// those pesky GE images ...
if ( foundLength == 13)
{
//////// 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
// Position the file position indicator at first tag
// (i.e. after the file preamble and the "DICM" string).
- Fp->seekg(0, std::ios::beg);
+
+ Fp->seekg(0, std::ios::beg); // FIXME : Is it usefull?
+
Fp->seekg ( 132L, std::ios::beg);
return true;
} // ------------------------------- End of DicomV3 ----------------
// preamble. We can reset the file position indicator to where the data
// is (i.e. the beginning of the file).
- gdcmWarningMacro( "Not a DICOM Version3 file");
+ gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)");
Fp->seekg(0, std::ios::beg);
+ // Let's check 'No Preamble Dicom File' :
+ // Should start with group 0x0002
+ // and be Explicit Value Representation
+
+ s16 = *((uint16_t *)(deb));
+ SwapCode = 0;
+ switch ( s16 )
+ {
+ case 0x0002 :
+ SwapCode = 1234;
+ entCur = deb + 4;
+ break;
+ case 0x0200 :
+ SwapCode = 4321;
+ entCur = deb + 6;
+ }
+
+ 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 )
+ {
+ Filetype = ExplicitVR;
+ gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
+ return true;
+ }
+ }
+// ------------------------------- End of 'No Preamble' DicomV3 -------------
+
// Our next best chance would be to be considering a 'clean' ACR/NEMA file.
// By clean we mean that the length of the first group is written down.
// If this is the case and since the length of the first group HAS to be
*/
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;
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 %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
+ * where the endianess is being switched to BigEndian for no
* apparent reason
* @return no return
*/
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff