Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2004/07/19 03:34:11 $
- Version: $Revision: 1.50 $
+ Date: $Date: 2004/08/02 16:42:14 $
+ Version: $Revision: 1.65 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmUtil.h"
#include "gdcmDebug.h"
-#include <errno.h>
#include <vector>
// For nthos:
/**
* \brief constructor
* @param inFilename file to be opened for parsing
- * @param exception_on_error whether we throw an exception or not
- * @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences,
- * when they have an actual length
- * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
- * @param ignore_shadow to allow skipping the shadow elements,
- * to save memory space.
- * \warning The TRUE value for this param has to be used
- * with a FALSE value for the 'enable_sequence' param.
- * ('public elements' may be embedded in 'shadow Sequences')
- */
-gdcmDocument::gdcmDocument( std::string const & filename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow)
+ */
+gdcmDocument::gdcmDocument( std::string const & filename )
: gdcmElementSet(-1)
{
- IgnoreShadow = ignore_shadow;
- //EnableSequences=enable_sequences;
- (void)enable_sequences;
- EnableSequences = true; // JPR // TODO : remove params out of the constructor
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Filename = filename;
Initialise();
- if ( !OpenFile(exception_on_error))
+ if ( !OpenFile() )
{
return;
}
long beg = ftell(Fp);
lgt -= beg;
- SQDepthLevel=0;
+ SQDepthLevel = 0;
long l = ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
(void)l; //is l used anywhere ?
CloseFile();
// --------------------------------------------------------------
- // Special Patch to allow gdcm to read ACR-LibIDO formated images
+ // 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)
+ // we keep this kludge to allow a smooth move to gdcm for
+ // CREATIS developpers (sorry folks).
//
// if recognition code tells us we deal with a LibIDO image
// we switch lineNumber and columnNumber
SetEntryByNumber(columns, 0x0028, 0x0010);
SetEntryByNumber(rows , 0x0028, 0x0011);
}
- // ----------------- End of Special Patch ----------------
+ // ----------------- End of ACR-LibIDO kludge ------------------
PrintLevel = 1; // 'Medium' print level by default
}
/**
- * \brief constructor
- * @param exception_on_error
+ * \brief This default constructor doesn't parse the file. You should
+ * then invoke \ref gdcmDocument::SetFileName and then the parsing.
*/
-gdcmDocument::gdcmDocument(bool exception_on_error)
+gdcmDocument::gdcmDocument()
:gdcmElementSet(-1)
{
- (void)exception_on_error;
- //EnableSequences=0; // ?!? JPR
-
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Initialise();
-
PrintLevel = 1; // 'Medium' print level by default
}
* \brief Set the shadow dictionary used
* \param dictName name of the dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(DictKey dictName)
+bool gdcmDocument::SetShaDict(DictKey const & dictName)
{
RefShaDict = gdcmGlobal::GetDicts()->GetDict(dictName);
return !RefShaDict;
* @param SyntaxToCheck The transfert syntax we need to check against.
* @return True when SyntaxToCheck corresponds to the Transfer Syntax of
* the current document. False either when the document contains
- * no Transfer Syntax, or when the Tranfer Syntaxes don't match.
+ * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match.
*/
bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck)
{
}
// The entry might be present but not loaded (parsing and loading
- // happen at differente stages): try loading and proceed with check...
+ // happen at different stages): try loading and proceed with check...
LoadDocEntrySafe(entry);
if (gdcmValEntry* valEntry = dynamic_cast< gdcmValEntry* >(entry) )
{
std::string transfer = valEntry->GetValue();
-
// 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(transfer[transfer.length()-1]) )
-// {
-// transfer.erase(transfer.length()-1, 1);
-// }
-// if ( transfer == syntaxToCheck )
- if( transfer.find( syntaxToCheck ) ) //should be faster
+ if ( transfer.length() == 0 ) { // for brain damaged headers
+ return false;
+ }
+ while ( ! isdigit(transfer[transfer.length()-1]) )
+ {
+ transfer.erase(transfer.length()-1, 1);
+ }
+ if ( transfer == syntaxToCheck )
{
return true;
}
}
/**
- * \brief opens the file
- * @param exception_on_error
- * @return
+ * \brief Tries to open the file \ref gdcmDocument::Filename and
+ * checks the preamble when existing.
+ * @return The FILE pointer on success.
*/
-FILE *gdcmDocument::OpenFile(bool exception_on_error)
- throw(gdcmFileError)
+FILE* gdcmDocument::OpenFile()
{
- Fp = fopen(Filename.c_str(),"rb");
-
- if(!Fp)
- {
- if(exception_on_error)
- {
- throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)");
- }
- else
- {
- dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ",
- Filename.c_str());
- return NULL;
- }
- }
-
- if ( Fp )
- {
- uint16_t zero;
- fread(&zero, (size_t)2, (size_t)1, Fp);
+ Fp = fopen(Filename.c_str(),"rb");
- //ACR -- or DICOM with no Preamble --
- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 )
- {
- return Fp;
- }
-
- //DICOM
- fseek(Fp, 126L, SEEK_CUR);
- char dicm[4];
- fread(dicm, (size_t)4, (size_t)1, Fp);
- if( memcmp(dicm, "DICM", 4) == 0 )
- {
- return Fp;
- }
-
- fclose(Fp);
- dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", Filename.c_str());
- }
- else
- {
- dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", Filename.c_str());
- }
-
- return 0;
+ if(!Fp)
+ {
+ dbg.Verbose( 0,
+ "gdcmDocument::OpenFile cannot open file: ",
+ Filename.c_str());
+ return 0;
+ }
+
+ uint16_t zero;
+ fread(&zero, (size_t)2, (size_t)1, Fp);
+
+ //ACR -- or DICOM with no Preamble --
+ if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 )
+ {
+ return Fp;
+ }
+
+ //DICOM
+ fseek(Fp, 126L, SEEK_CUR);
+ char dicm[4];
+ fread(dicm, (size_t)4, (size_t)1, Fp);
+ if( memcmp(dicm, "DICM", 4) == 0 )
+ {
+ return Fp;
+ }
+
+ fclose(Fp);
+ dbg.Verbose( 0,
+ "gdcmDocument::OpenFile not DICOM/ACR (missing preamble)",
+ Filename.c_str());
+
+ return 0;
}
/**
bool gdcmDocument::CloseFile()
{
int closed = fclose(Fp);
- Fp = (FILE *)0;
+ Fp = 0;
return closed;
}
*/
gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
- std::string value,
+ std::string const & value,
uint16_t group,
uint16_t elem )
{
* @param Elem element number of the Entry
* \return boolean
*/
-bool gdcmDocument::ReplaceIfExistByNumber(const char* value, uint16_t group,
- uint16_t elem )
+bool gdcmDocument::ReplaceIfExistByNumber(std::string const & value,
+ uint16_t group, uint16_t elem )
{
- const std::string v = value;
- SetEntryByNumber(v, group, elem);
+ SetEntryByNumber(value, group, elem);
return true;
}
*/
int gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
{
- std::string key = gdcmDictEntry::TranslateToKey(group, element );
+ const std::string &key = gdcmDictEntry::TranslateToKey(group, element );
return TagHT.count(key);
}
* @return Corresponding element value when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryByName(TagName tagName)
+std::string gdcmDocument::GetEntryByName(TagName const & tagName)
{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( !dictEntry )
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryVRByName(TagName tagName)
+std::string gdcmDocument::GetEntryVRByName(TagName const & tagName)
{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
return GDCM_UNFOUND;
}
- gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
+ gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
+ dictEntry->GetElement());
return elem->GetVR();
}
* @param tagName name of the searched Dicom Element.
* @return true when found
*/
-bool gdcmDocument::SetEntryByName(std::string content,std::string tagName)
+bool gdcmDocument::SetEntryByName(std::string const & content,std::string const & tagName)
{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( !dictEntry )
* @param group group number of the Dicom Element to modify
* @param element element number of the Dicom Element to modify
*/
-bool gdcmDocument::SetEntryByNumber(std::string content,
+bool gdcmDocument::SetEntryByNumber(std::string const & content,
uint16_t group,
uint16_t element)
{
" ValEntry (try promotion first).");
return false;
}
- // Non even content must be padded with a space (020H).
- if( content.length() % 2 )
+ // Non even content must be padded with a space (020H)...
+ std::string evenContent = content;
+ if( evenContent.length() % 2 )
{
- content += '\0';
+ evenContent += '\0'; // ... therefore we padd with (000H) .!?!
}
- valEntry->SetValue(content);
+ valEntry->SetValue(evenContent);
// Integers have a special treatement for their length:
gdcmVRKey vr = valEntry->GetVR();
}
else
{
- valEntry->SetLength(content.length());
+ valEntry->SetLength(evenContent.length());
}
return true;
return false;
}
-/* Hope Binaray field length is *never* wrong
+/* Hope Binary field length is *never* wrong
if(lgth%2) // Non even length are padded with a space (020H).
{
lgth++;
//content = content + '\0'; // fing a trick to enlarge a binary field?
}
*/
- gdcmBinEntry * a;
- a = (gdcmBinEntry *)TagHT[key];
+ gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key];
a->SetVoidArea(content);
//a->SetLength(lgth); // ???
+
return true;
}
{
return false;
}
- // This was for multimap ?
- (( gdcmBinEntry *)( ((TagHT.equal_range(key)).first)->second ))->SetVoidArea(area);
+
+ // This was for multimap ?
+ (( gdcmBinEntry *)( ((TagHT.equal_range(key)).first)->second ))->SetVoidArea(area);
return true;
}
default :
std::cout << "swapCode= " << SwapCode << std::endl;
dbg.Error(" gdcmDocument::SwapLong : unset swap code");
- a=0;
+ a = 0;
}
return a;
}
{
if ( SwapCode == 4321 || SwapCode == 2143 )
{
- a =((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) );
+ a = ((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) );
}
return a;
}
newValEntry->SetDepthLevel(depth);
set->AddEntry(newValEntry);
LoadDocEntry(newValEntry);
- if (newValEntry->isItemDelimitor())
+ if (newValEntry->IsItemDelimitor())
{
break;
}
}
if( delim_mode )
{
- if ( newDocEntry->isSequenceDelimitor() )
+ if ( newDocEntry->IsSequenceDelimitor() )
{
set->SetSequenceDelimitationItem( newDocEntry );
break;
}
int lgr = ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+ (void)lgr; //FIXME not used
set->AddEntry(itemSQ, SQItemNumber);
SQItemNumber++;
}
// to be sure we are at the end of the value ...
fseek(Fp, (long)entry->GetOffset()+(long)entry->GetLength(), SEEK_SET);
-
- return; //FIXME FIXME FIXME FIXME ????
+ // Following return introduced by JPR on version 1.25. Since the
+ // treatement of a ValEntry is never executed (doh!) this means
+ // we were lucky up to now because we NEVER encountered a ValEntry
+ // whose length was bigger thant MaxSizeLoadEntry !? I can't believe
+ // this could ever work...
+ return; //FIXME FIXME FIXME FIXME JPR ????
// Be carefull : a BinEntry IS_A ValEntry ...
if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) )
//std::string newValue(length,0);
//item_read = fread(&(newValue[0]), (size_t)length, (size_t)1, Fp);
//rah !! I can't believe it could work, normally this is a const char* !!!
- char str[length];
+ char *str = new char[length+1];
item_read = fread(str, (size_t)length, (size_t)1, Fp);
+ str[length] = '\0';
std::string newValue = str;
- newValue += '\0';
+ delete[] str;
if ( gdcmValEntry* valEntry = dynamic_cast<gdcmValEntry* >(entry) )
{
if ( item_read != 1 )
* \brief Find the value Length of the passed Header Entry
* @param Entry Header Entry whose length of the value shall be loaded.
*/
-void gdcmDocument::FindDocEntryLength (gdcmDocEntry *entry)
+void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry )
+ throw ( gdcmFormatError )
{
uint16_t element = entry->GetElement();
std::string vr = entry->GetVR();
if ( vr == "OB" && length32 == 0xffffffff )
{
- uint32_t lengthOB = FindDocEntryLengthOB();
- if ( errno == 1 )
+ uint32_t lengthOB;
+ try
+ {
+ lengthOB = FindDocEntryLengthOB();
+ }
+ catch ( gdcmFormatUnexpected )
{
// Computing the length failed (this happens with broken
// files like gdcm-JPEG-LossLess3a.dcm). We still have a
long lengthUntilEOF = ftell(Fp) - currentPosition;
fseek(Fp, currentPosition, SEEK_SET);
entry->SetLength(lengthUntilEOF);
- errno = 0;
return;
}
entry->SetLength(lengthOB);
// endian encoding". When this is the case, chances are we have got our
// hands on a big endian encoded file: we switch the swap code to
// big endian and proceed...
- if ( (element == 0x0000) && (length16 == 0x0400) )
+ if ( element == 0x0000 && length16 == 0x0400 )
{
- if ( ! IsExplicitVRBigEndianTransferSyntax() )
+ if ( !IsExplicitVRBigEndianTransferSyntax() )
{
- dbg.Verbose(0, "gdcmDocument::FindLength", "not explicit VR");
- errno = 1;
+ throw gdcmFormatError( "gdcmDocument::FindDocEntryLength()",
+ " not explicit VR." );
return;
}
length16 = 4;
// Heuristic: well, some files are really ill-formed.
if ( length16 == 0xffff)
{
+ // 0xffff means that we deal with 'Unknown Length' Sequence
length16 = 0;
- // Length16= 0xffff means that we deal with
- // 'Unknown Length' Sequence
}
- FixDocEntryFoundLength(entry, (uint32_t)length16);
+ FixDocEntryFoundLength( entry, (uint32_t)length16 );
return;
}
else
// not coexist in a Data Set and Data Sets nested within it".]
// Length is on 4 bytes.
- FixDocEntryFoundLength(entry, ReadInt32());
+ FixDocEntryFoundLength( entry, ReadInt32() );
return;
}
}
// is in explicit VR and try to fix things if it happens not to be
// the case.
- fread (&vr, (size_t)2,(size_t)1, Fp);
+ fread (vr, (size_t)2,(size_t)1, Fp);
vr[2] = 0;
if( !CheckDocEntryVR(entry, vr) )
// expected VR read happens to be non-ascii characters we consider
// we hit falsely explicit VR tag.
- if ( (!isalpha(vr[0])) && (!isalpha(vr[1])) )
+ if ( !isalpha(vr[0]) && !isalpha(vr[1]) )
{
realExplicit = false;
}
entry->SetReadLength(4); /// \todo a bug is to be fixed !?
}
- //////// Deal with sequences, but only on users request:
- else if ( entry->GetVR() == "SQ" && EnableSequences)
+ else if ( entry->GetVR() == "SQ" )
{
foundLength = 0; // ReadLength is unchanged
}
*/
uint32_t gdcmDocument::FindDocEntryLengthOB()
+ throw( gdcmFormatUnexpected )
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
long positionOnEntry = ftell(Fp);
while ( !foundSequenceDelimiter )
{
- uint16_t g = ReadInt16();
- uint16_t n = ReadInt16();
- if ( errno == 1 )
+ uint16_t group;
+ uint16_t elem;
+ try
{
- return 0;
+ group = ReadInt16();
+ elem = ReadInt16();
+ }
+ catch ( gdcmFormatError )
+ {
+ throw gdcmFormatError("gdcmDocument::FindDocEntryLengthOB()",
+ " group or element not present.");
}
// We have to decount the group and element we just read
totalLength += 4;
- if ( g != 0xfffe || ( n != 0xe0dd && n != 0xe000 ) )
+ if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- dbg.Verbose(1, "gdcmDocument::FindLengthOB: neither an Item tag "
- "nor a Sequence delimiter tag.");
+ dbg.Verbose(1, "gdcmDocument::FindDocEntryLengthOB: neither an Item "
+ "tag nor a Sequence delimiter tag.");
fseek(Fp, positionOnEntry, SEEK_SET);
- errno = 1;
- return 0;
+ throw gdcmFormatUnexpected("gdcmDocument::FindDocEntryLengthOB()",
+ "Neither an Item tag nor a Sequence "
+ "delimiter tag.");
}
- if ( n == 0xe0dd )
+ if ( elem == 0xe0dd )
{
foundSequenceDelimiter = true;
}
* @return read value
*/
uint16_t gdcmDocument::ReadInt16()
+ throw( gdcmFormatError )
{
uint16_t g;
size_t item_read = fread (&g, (size_t)2,(size_t)1, Fp);
{
if( ferror(Fp) )
{
- dbg.Verbose(0, "gdcmDocument::ReadInt16", " File Error");
+ throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
}
- errno = 1;
- return 0;
+ throw gdcmFormatError( "gdcmDocument::ReadInt16()", "EOF." );
}
- errno = 0;
g = SwapShort(g);
return g;
}
* @return read value
*/
uint32_t gdcmDocument::ReadInt32()
+ throw( gdcmFormatError )
{
uint32_t g;
size_t item_read = fread (&g, (size_t)4,(size_t)1, Fp);
{
if( ferror(Fp) )
{
- dbg.Verbose(0, "gdcmDocument::ReadInt32", " File Error");
+ throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
}
- errno = 1;
- return 0;
+ throw gdcmFormatError( "gdcmDocument::ReadInt32()", "EOF." );
}
- errno = 0;
g = SwapLong(g);
return g;
}
// The easiest case is the one of a DICOM header, since it possesses a
// file preamble where it suffice to look for the string "DICM".
int lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, Fp);
+ (void)lgrLue; //FIXME not used
char *entCur = deb + 128;
if( memcmp(entCur, "DICM", (size_t)4) == 0 )
* gets the VR, gets the length, gets the offset value)
* @return On succes the newly created DocEntry, NULL on failure.
*/
-gdcmDocEntry *gdcmDocument::ReadNextDocEntry()
+gdcmDocEntry* gdcmDocument::ReadNextDocEntry()
{
- if (errno == 1)
+ uint16_t group;
+ uint16_t elem;
+
+ try
+ {
+ group = ReadInt16();
+ elem = ReadInt16();
+ }
+ catch ( gdcmFormatError e )
{
// We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
+ std::cout << e;
return 0;
}
- uint16_t g = ReadInt16();
- uint16_t n = ReadInt16();
- gdcmDocEntry *newEntry = NewDocEntryByNumber(g, n);
-
+ gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem);
FindDocEntryVR(newEntry);
- FindDocEntryLength(newEntry);
- if (errno == 1)
+ try
+ {
+ FindDocEntryLength(newEntry);
+ }
+ catch ( gdcmFormatError e )
{
// Call it quits
+ std::cout << e;
delete newEntry;
- return NULL;
+ return 0;
}
+
newEntry->SetOffset(ftell(Fp));
return newEntry;
*/
uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement)
{
- long PositionOnEntry = ftell(Fp);
- (void)PositionOnEntry;
+ long positionOnEntry = ftell(Fp);
+ (void)positionOnEntry;
if ( !ReadTag(testGroup, testElement) )
{
s << " Read one length: ";
s << std::hex << individualLength << std::endl;
dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str());
- }
+ }
+ delete[] basicOffsetTableItemValue;
}
if ( ! IsRLELossLessTransferSyntax() )
// Make sure that at the end of the item we encounter a 'Sequence
// Delimiter Item':
- if ( ! ReadTag(0xfffe, 0xe0dd) )
+ if ( !ReadTag(0xfffe, 0xe0dd) )
{
dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item");
dbg.Verbose(0, " at end of RLE item sequence");
bool gdcmDocument::operator<(gdcmDocument &document)
{
// Patient Name
- std::string s1 = this->GetEntryByNumber(0x0010,0x0010);
+ std::string s1 = GetEntryByNumber(0x0010,0x0010);
std::string s2 = document.GetEntryByNumber(0x0010,0x0010);
if(s1 < s2)
{
else
{
// Patient ID
- s1 = this->GetEntryByNumber(0x0010,0x0020);
+ s1 = GetEntryByNumber(0x0010,0x0020);
s2 = document.GetEntryByNumber(0x0010,0x0020);
if ( s1 < s2 )
{
else
{
// Study Instance UID
- s1 = this->GetEntryByNumber(0x0020,0x000d);
+ s1 = GetEntryByNumber(0x0020,0x000d);
s2 = document.GetEntryByNumber(0x0020,0x000d);
if ( s1 < s2 )
{
else
{
// Serie Instance UID
- s1 = this->GetEntryByNumber(0x0020,0x000e);
+ s1 = GetEntryByNumber(0x0020,0x000e);
s2 = document.GetEntryByNumber(0x0020,0x000e);
if ( s1 < s2 )
{
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff