Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/01/17 17:27:03 $
- Version: $Revision: 1.193 $
+ Date: $Date: 2005/01/28 09:31:51 $
+ Version: $Revision: 1.215 $
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 "gdcmTS.h"
-#include "gdcmException.h"
#include "gdcmDictSet.h"
-#include "gdcmRLEFramesInfo.h"
-#include "gdcmJPEGFragmentsInfo.h"
#include "gdcmDocEntrySet.h"
#include "gdcmSQItem.h"
#include <iomanip>
// For nthos:
-#if defined(_MSC_VER) || defined(__BORLANDC__)
+#if defined(_MSC_VER) || defined(__BORLANDC__) || defined(__MINGW32__)
#include <winsock.h>
-#else
+#endif
+
+#ifdef CMAKE_HAVE_NETINET_IN_H
#include <netinet/in.h>
#endif
/**
* \brief constructor
- * @param filename file to be opened for parsing
+ * @param filename 'Document' (File or DicomDir) to be opened for parsing
*/
Document::Document( std::string const &filename ) : ElementSet(-1)
{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Filename = filename;
- Initialise();
+ Initialize();
Fp = 0;
if ( !OpenFile() )
// Load 'non string' values
- std::string PhotometricInterpretation = GetEntry(0x0028,0x0004);
+ std::string PhotometricInterpretation = GetEntryValue(0x0028,0x0004);
if( PhotometricInterpretation == "PALETTE COLOR " )
{
LoadEntryBinArea(0x0028,0x1200); // gray LUT
// we switch lineNumber and columnNumber
//
std::string RecCode;
- RecCode = GetEntry(0x0008, 0x0010); // recognition code
+ RecCode = GetEntryValue(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 = GetEntry(0x0028, 0x0010);
- std::string columns = GetEntry(0x0028, 0x0011);
- SetEntry(columns, 0x0028, 0x0010);
- SetEntry(rows , 0x0028, 0x0011);
+ std::string rows = GetEntryValue(0x0028, 0x0010);
+ std::string columns = GetEntryValue(0x0028, 0x0011);
+ SetValEntry(columns, 0x0028, 0x0010);
+ SetValEntry(rows , 0x0028, 0x0011);
}
// ----------------- End of ACR-LibIDO kludge ------------------
}
Fp = 0;
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialise();
+ Initialize();
SwapCode = 1234;
Filetype = ExplicitVR;
Group0002Parsed = false;
{
RefPubDict = NULL;
RefShaDict = NULL;
-
- delete RLEInfo;
- delete JPEGInfo;
}
//-----------------------------------------------------------------------------
/**
* \brief Prints The Dict Entries of THE public Dicom Dictionary
+ * @param os ostream to print to
* @return
*/
void Document::PrintPubDict(std::ostream &os)
/**
* \brief Prints The Dict Entries of THE shadow Dicom Dictionary
+ * @param os ostream to print to
* @return
*/
void Document::PrintShaDict(std::ostream &os)
return false;
}
- if( TagHT.empty() )
+ if ( IsEmpty() )
{
- gdcmVerboseMacro( "No tags in internal hash table.");
+ gdcmVerboseMacro( "No tag in internal hash table.");
return false;
}
return GetDocEntry(0x0002, 0x0010) != NULL;
}
+/**
+ * \brief Predicate for Papyrus file
+ * Dedicated to whomsoever it may concern
+ * @return True when the file is a Papyrus file.
+ */
+bool Document::IsPapyrus()
+{
+ // check for Papyrus private Sequence
+ DocEntry *e = GetDocEntry(0x0041, 0x1050);
+ if ( !e )
+ return false;
+ // check if it's actually a Sequence
+ if ( !dynamic_cast<SeqEntry*>(e) )
+ return false;
+ return true;
+}
+
/**
* \brief returns the File Type
* (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
*/
std::ifstream *Document::OpenFile()
{
-
HasDCMPreamble = false;
if (Filename.length() == 0)
{
if(Fp)
{
gdcmVerboseMacro( "File already open: " << Filename.c_str());
+ CloseFile();
}
Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
delete Fp;
Fp = 0;
}
-
- return true; //FIXME how do we detect a non-close ifstream ?
+ return true; //FIXME how do we detect a non-closed ifstream ?
}
/**
* @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.
+ * @return Always true.
*/
void Document::WriteContent(std::ofstream *fp, FileType filetype)
{
- /// \todo move the following lines (and a lot of others, to be written)
- /// to a future function CheckAndCorrectHeader
- /// (necessary if user wants to write a DICOM V3 file
- /// starting from an ACR-NEMA (V2) Header
+ // \TODO move the following lines (and a lot of others, to be written)
+ // to a future function CheckAndCorrectHeader
+
+ // (necessary if user wants to write a DICOM V3 file
+ // starting from an ACR-NEMA (V2) Header
if ( filetype == ImplicitVR || filetype == ExplicitVR )
{
fp->write("DICM", 4);
}
-/**
+/*
* \todo rewrite later, if really usefull
* - 'Group Length' element is optional in DICOM
* - but un-updated odd groups lengthes can causes pb
ElementSet::WriteContent(fp, filetype); // This one is recursive
}
-/**
- * \brief Modifies the value of a given Doc Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * @param value (string) Value to be set
- * @param group Group number of the Entry
- * @param elem Element number of the Entry
- * @param vr V(alue) R(epresentation) of the Entry -if private Entry-
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
- */
-ValEntry *Document::ReplaceOrCreate(std::string const &value,
- uint16_t group,
- uint16_t elem,
- TagName const &vr )
-{
- ValEntry *valEntry = 0;
- DocEntry *currentEntry = GetDocEntry( group, elem);
-
- if (currentEntry)
- {
- valEntry = dynamic_cast< ValEntry* >(currentEntry);
-
- // Verify the VR
- if( valEntry )
- if( valEntry->GetVR()!=vr )
- valEntry=NULL;
-
- // if currentEntry doesn't correspond to the requested valEntry
- if( !valEntry)
- {
- if (!RemoveEntry(currentEntry))
- {
- gdcmVerboseMacro( "Removal of previous DocEntry failed.");
-
- return NULL;
- }
- }
- }
-
- // Create a new valEntry if necessary
- if (!valEntry)
- {
- valEntry = NewValEntry(group, elem, vr);
-
- if ( !AddEntry(valEntry))
- {
- gdcmVerboseMacro("AddEntry failed although this is a creation.");
-
- delete valEntry;
- return NULL;
- }
- }
-
- // Set the binEntry value
- SetEntry(value, valEntry);
- return valEntry;
-}
-
-/*
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * A copy of the binArea is made to be kept in the Document.
- * @param binArea (binary) value to be set
- * @param Group Group number of the Entry
- * @param Elem Element number of the Entry
- * @param vr V(alue) R(epresentation) of the Entry -if private Entry-
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
- */
-BinEntry *Document::ReplaceOrCreate(uint8_t *binArea,
- int lgth,
- uint16_t group,
- uint16_t elem,
- TagName const &vr )
-{
- BinEntry *binEntry = 0;
- DocEntry *currentEntry = GetDocEntry( group, elem);
-
- // Verify the currentEntry
- if (currentEntry)
- {
- binEntry = dynamic_cast< BinEntry* >(currentEntry);
-
- // Verify the VR
- if( binEntry )
- if( binEntry->GetVR()!=vr )
- binEntry=NULL;
-
- // if currentEntry doesn't correspond to the requested valEntry
- if( !binEntry)
- {
- if (!RemoveEntry(currentEntry))
- {
- gdcmVerboseMacro( "Removal of previous DocEntry failed.");
-
- return NULL;
- }
- }
- }
-
- // Create a new binEntry if necessary
- if (!binEntry)
- {
- binEntry = NewBinEntry(group, elem, vr);
-
- if ( !AddEntry(binEntry))
- {
- gdcmVerboseMacro( "AddEntry failed allthough this is a creation.");
-
- delete binEntry;
- return NULL;
- }
- }
-
- // Set the binEntry value
- uint8_t *tmpArea;
- if (lgth>0 && binArea)
- {
- tmpArea = new uint8_t[lgth];
- memcpy(tmpArea,binArea,lgth);
- }
- else
- {
- tmpArea = 0;
- }
- if (!SetEntry(tmpArea,lgth,binEntry))
- {
- if (tmpArea)
- {
- delete[] tmpArea;
- }
- }
-
- return binEntry;
-}
-
-/*
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * when it exists. Create it when unexistant.
- * @param group Group number of the Entry
- * @param elem Element number of the Entry
- * \return pointer to the modified/created SeqEntry (NULL when creation
- * failed).
- */
-SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem)
-{
- SeqEntry *seqEntry = 0;
- DocEntry *currentEntry = GetDocEntry( group, elem);
-
- // Verify the currentEntry
- if (currentEntry)
- {
- seqEntry = dynamic_cast< SeqEntry* >(currentEntry);
-
- // Verify the VR
- if( seqEntry )
- if( seqEntry->GetVR()!="SQ" )
- seqEntry=NULL;
-
- // if currentEntry doesn't correspond to the requested valEntry
- if( !seqEntry)
- {
- if (!RemoveEntry(currentEntry))
- {
- gdcmVerboseMacro( "Removal of previous DocEntry failed.");
-
- return NULL;
- }
- }
- }
-
- // Create a new seqEntry if necessary
- if (!seqEntry)
- {
- seqEntry = NewSeqEntry(group, elem);
-
- if ( !AddEntry(seqEntry))
- {
- gdcmVerboseMacro( "AddEntry failed allthough this is a creation.");
-
- delete seqEntry;
- return NULL;
- }
- }
-
- return seqEntry;
-}
-
-/**
- * \brief Set a new value if the invoked element exists
- * Seems to be useless !!!
- * @param value new element value
- * @param group group number of the Entry
- * @param elem element number of the Entry
- * \return boolean
- */
-bool Document::ReplaceIfExist(std::string const &value,
- uint16_t group, uint16_t elem )
-{
- SetEntry(value, group, elem);
-
- return true;
-}
-
//-----------------------------------------------------------------------------
// Protected
-
/**
- * \brief Checks if a given Dicom Element exists within the H table
- * @param group Group number of the searched Dicom Element
- * @param elem Element number of the searched Dicom Element
- * @return true is found
- */
-bool Document::CheckIfEntryExist(uint16_t group, uint16_t elem )
-{
- const std::string &key = DictEntry::TranslateToKey(group, elem );
- return TagHT.count(key) != 0;
-}
-
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- * @param group Group number of the searched tag.
- * @param elem Element number of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string Document::GetEntry(uint16_t group, uint16_t elem)
-{
- TagKey key = DictEntry::TranslateToKey(group, elem);
- if ( !TagHT.count(key))
- {
- return GDCM_UNFOUND;
- }
-
- return ((ValEntry *)TagHT.find(key)->second)->GetValue();
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag..
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param group Group number of the searched tag.
- * @param elem Element number of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string Document::GetEntryVR(uint16_t group, uint16_t elem)
-{
- DocEntry *elem = GetDocEntry(group, elem);
- if ( !elem )
- {
- return GDCM_UNFOUND;
- }
- return elem->GetVR();
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the value length of a given tag..
- * @param group Group number of the searched tag.
- * @param elem Element number of the searched tag.
- * @return Corresponding element length; -2 if not found
- */
-int Document::GetEntryLength(uint16_t group, uint16_t elem)
-{
- DocEntry *elem = GetDocEntry(group, elem);
- if ( !elem )
- {
- return -2; //magic number
- }
- return elem->GetLength();
-}
-
-/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value (string) to substitute with
- * @param group group number of the Dicom Element to modify
- * @param elem element number of the Dicom Element to modify
- */
-bool Document::SetEntry(std::string const& content,
- uint16_t group, uint16_t elem)
-{
- ValEntry *entry = GetValEntry(group, elem);
- if (!entry )
- {
- gdcmVerboseMacro( "No corresponding ValEntry (try promotion first).");
- return false;
- }
- return SetEntry(content,entry);
-}
-
-/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value (void* -> uint8_t*) to substitute with
- * @param lgth new value length
- * @param group group number of the Dicom Element to modify
- * @param elem element number of the Dicom Element to modify
- */
-bool Document::SetEntry(uint8_t*content, int lgth,
- uint16_t group, uint16_t elem)
-{
- BinEntry *entry = GetBinEntry(group, elem);
- if (!entry )
- {
- gdcmVerboseMacro( "No corresponding ValEntry (try promotion first).");
- return false;
- }
-
- return SetEntry(content,lgth,entry);
-}
-
-/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * and modifies it's content with the given value.
- * @param content new value (string) to substitute with
- * @param entry Entry to be modified
- */
-bool Document::SetEntry(std::string const &content,ValEntry *entry)
-{
- if(entry)
- {
- entry->SetValue(content);
- return true;
- }
- return false;
-}
-
-/**
- * \brief Accesses an existing BinEntry (i.e. a Dicom Element)
- * and modifies it's content with the given value.
- * @param content new value (void* -> uint8_t*) to substitute with
- * @param entry Entry to be modified
- * @param lgth new value length
- */
-bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry)
-{
- if(entry)
- {
- // 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?
- }*/
-
- entry->SetBinArea(content);
- entry->SetLength(lgth);
- entry->SetValue(GDCM_BINLOADED);
- return true;
- }
- return false;
-}
-
-/**
- * \brief Gets (from Header) a 'non string' element value
- * (LoadElementValues has already be executed)
- * @param group group number of the Entry
- * @param elem element number of the Entry
- * @return Pointer to the 'non string' area
- */
-void *Document::GetEntryBinArea(uint16_t group, uint16_t elem)
-{
- DocEntry *entry = GetDocEntry(group, elem);
- if (!entry)
- {
- gdcmVerboseMacro( "No entry");
- return 0;
- }
- if ( BinEntry *binEntry = dynamic_cast<BinEntry*>(entry) )
- {
- return binEntry->GetBinArea();
- }
-
- return 0;
-}
-
-/**
- * \brief Loads (from disk) the element content
- * when a string is not suitable
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
* @param group group number of the Entry
* @param elem element number of the Entry
*/
}
/**
- * \brief Loads (from disk) the element content
- * when a string is not suitable
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
* @param elem Entry whose binArea is going to be loaded
*/
void Document::LoadEntryBinArea(BinEntry *elem)
uint8_t *a = new uint8_t[l];
if( !a )
{
- gdcmVerboseMacro( "Cannot allocate a");
+ gdcmVerboseMacro( "Cannot allocate BinEntry content");
return;
}
return false;
}*/
-/**
- * \brief retrieves a Dicom Element (the first one) using (group, element)
- * \warning (group, element) IS NOT an identifier inside the Dicom Header
- * if you think it's NOT UNIQUE, check the count number
- * and use iterators to retrieve ALL the Dicoms Elements within
- * a given couple (group, element)
- * @param group Group number of the searched Dicom Element
- * @param elem Element number of the searched Dicom Element
- * @return
- */
-DocEntry *Document::GetDocEntry(uint16_t group, uint16_t elem)
-{
- TagKey key = DictEntry::TranslateToKey(group, elem);
- if ( !TagHT.count(key))
- {
- return NULL;
- }
- return TagHT.find(key)->second;
-}
-
-/**
- * \brief Same as \ref Document::GetDocEntry except it only
- * returns a result when the corresponding entry is of type
- * ValEntry.
- * @param group Group number of the searched Dicom Element
- * @param elem Element number of the searched Dicom Element
- * @return When present, the corresponding ValEntry.
- */
-ValEntry *Document::GetValEntry(uint16_t group, uint16_t elem)
-{
- DocEntry *currentEntry = GetDocEntry(group, elem);
- if ( !currentEntry )
- {
- return 0;
- }
- if ( ValEntry *entry = dynamic_cast<ValEntry*>(currentEntry) )
- {
- return entry;
- }
- gdcmVerboseMacro( "Unfound ValEntry.");
-
- return 0;
-}
-
-/**
- * \brief Same as \ref Document::GetDocEntry except it only
- * returns a result when the corresponding entry is of type
- * BinEntry.
- * @param group Group number of the searched Dicom Element
- * @param elem Element number of the searched Dicom Element
- * @return When present, the corresponding BinEntry.
- */
-BinEntry *Document::GetBinEntry(uint16_t group, uint16_t elem)
-{
- DocEntry *currentEntry = GetDocEntry(group, elem);
- if ( !currentEntry )
- {
- return 0;
- }
- if ( BinEntry *entry = dynamic_cast<BinEntry*>(currentEntry) )
- {
- return entry;
- }
- gdcmVerboseMacro( "Unfound BinEntry.");
-
- return 0;
-}
/**
- * \brief Loads the element while preserving the current
- * underlying file position indicator as opposed to
- * to LoadDocEntry that modifies it.
+ * \brief Loads the element while preserving the current
+ * underlying file position indicator as opposed to
+ * LoadDocEntry that modifies it.
* @param entry Header Entry whose value will be loaded.
* @return
*/
{
if ( newBinEntry )
{
- if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) )
+ if ( Filetype == ExplicitVR &&
+ !Global::GetVR()->IsVROfBinaryRepresentable(vr) )
{
////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
gdcmVerboseMacro( std::hex << newDocEntry->GetGroup()
//////////////////// BinEntry or UNKOWN VR:
// When "this" is a Document the Key is simply of the
// form ( group, elem )...
- if (/*Document *dummy =*/ dynamic_cast< Document* > ( set ) )
+ if ( dynamic_cast< Document* > ( set ) )
{
- //(void)dummy;
newBinEntry->SetKey( newBinEntry->GetKey() );
}
// but when "this" is a SQItem, we are inserting this new
/////////////////////// 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 (/*Document *dummy =*/ dynamic_cast< Document* > ( set ) )
+ if ( dynamic_cast< Document* > ( set ) )
{
- //(void)dummy;
newValEntry->SetKey( newValEntry->GetKey() );
}
// ...but when "set" is a SQItem, we are inserting this new
}
}
- if ( ( newDocEntry->GetGroup() == 0x7fe0 )
- && ( newDocEntry->GetElement() == 0x0010 ) )
- {
- std::string ts = GetTransferSyntax();
- if ( Global::GetTS()->IsRLELossless(ts) )
- {
- long positionOnEntry = Fp->tellg();
- Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
- ComputeRLEInfo();
- Fp->seekg( positionOnEntry, std::ios::beg );
- }
- else if ( Global::GetTS()->IsJPEG(ts) )
- {
- long positionOnEntry = Fp->tellg();
- Fp->seekg( newDocEntry->GetOffset(), std::ios::beg );
- ComputeJPEGFragmentInfo();
- Fp->seekg( positionOnEntry, std::ios::beg );
- }
- }
-
// Just to make sure we are at the beginning of next entry.
SkipToNextDocEntry(newDocEntry);
}
newDocEntry->GetOffset(),
l, delim_mode);
}
- set->AddEntry( newSeqEntry );
+ if( !set->AddEntry( newSeqEntry ) )
+ {
+ used = false;
+ }
if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
{
+ if( !used )
+ delete newDocEntry;
break;
}
}
- if(!used)
+ if( !used )
delete newDocEntry;
}
}
{
if ( newDocEntry->IsSequenceDelimitor() )
{
- seqEntry->SetSequenceDelimitationItem( newDocEntry );
+ seqEntry->SetDelimitationItem( newDocEntry );
break;
}
}
offsetStartCurrentSQItem = Fp->tellg();
// end try -----------------
- seqEntry->AddEntry( itemSQ, SQItemNumber );
+ seqEntry->AddSQItem( itemSQ, SQItemNumber );
SQItemNumber++;
if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
{
// hands on a big endian encoded file: we switch the swap code to
// big endian and proceed...
- //
- // if ( element == 0x0000 && length16 == 0x0400 )
- // {
- // std::string ts = GetTransferSyntax();
- // if ( Global::GetTS()->GetSpecialTransferSyntax(ts)
- // != TS::ExplicitVRBigEndian )
- // {
- // throw FormatError( "Document::FindDocEntryLength()",
- // " not explicit VR." );
- // return;
- // }
- // length16 = 4;
- // SwitchByteSwapCode();
-
- // Restore the unproperly loaded values i.e. the group, the element
- // and the dictionary entry depending on them.
-// uint16_t correctGroup = SwapShort( entry->GetGroup() );
+// if ( element == 0x0000 && length16 == 0x0400 )
+// {
+// std::string ts = GetTransferSyntax();
+// if ( Global::GetTS()->GetSpecialTransferSyntax(ts)
+// != TS::ExplicitVRBigEndian )
+// {
+// throw FormatError( "Document::FindDocEntryLength()",
+// " not explicit VR." );
+// return;
+// }
+// length16 = 4;
+// SwitchByteSwapCode();
+//
+// // Restore the unproperly loaded values i.e. the group, the element
+// // and the dictionary entry depending on them.
+// uint16_t correctGroup = SwapShort( entry->GetGroup() );
// uint16_t correctElem = SwapShort( entry->GetElement() );
-// DictEntry *newTag = GetDictEntry( correctGroup, correctElem ); if ( !newTag )
+// DictEntry *newTag = GetDictEntry( correctGroup, correctElem );
+// if ( !newTag )
// {
- // This correct tag is not in the dictionary. Create a new one.
+// // This correct tag is not in the dictionary. Create a new one.
// newTag = NewVirtualDictEntry(correctGroup, correctElem);
// }
- // FIXME this can create a memory leaks on the old entry that be
- // left unreferenced.
+// // FIXME this can create a memory leaks on the old entry that be
+// // left unreferenced.
// entry->SetDictEntry( newTag );
// }
-
// 0xffff means that we deal with 'No Length' Sequence
// or 'No Length' SQItem
// on Data elements "Implicit and Explicit VR Data Elements shall
// not coexist in a Data Set and Data Sets nested within it".]
// Length is on 4 bytes.
+
+ // Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
+ // even if Transfer Syntax is 'Implicit VR ...'
FixDocEntryFoundLength( entry, ReadInt32() );
return;
* \brief Loads all the needed Dictionaries
* \warning NOT end user intended method !
*/
-void Document::Initialise()
+void Document::Initialize()
{
RefPubDict = Global::GetDicts()->GetDefaultPubDict();
RefShaDict = NULL;
- RLEInfo = new RLEFramesInfo;
- JPEGInfo = new JPEGFragmentsInfo;
Filetype = Unknown;
}
}
}
-
-
/**
* \brief Change the Byte Swap code.
*/
*/
void Document::SetMaxSizePrintEntry(long newSize)
{
- //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME
if ( newSize < 0 )
{
return;
/**
* \brief Accesses the info from 0002,0010 : Transfer Syntax and TS
- * else 1.
* @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
*/
std::string Document::GetTransferSyntaxName()
{
// use the TS (TS : Transfer Syntax)
- std::string transferSyntax = GetEntry(0x0002,0x0010);
+ std::string transferSyntax = GetEntryValue(0x0002,0x0010);
if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) )
{
return;
}
+ // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..."
+
+ 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 )
<< GetTransferSyntaxName() << "]" );
SwitchByteSwapCode();
group = SwapShort(group);
- elem = SwapShort(elem);
+ elem = SwapShort(elem);
}
}
}
return newEntry;
}
-
+//GenerateFreeTagKeyInGroup? What was it designed for ?!?
/**
* \brief Generate a free TagKey i.e. a TagKey that is not present
* in the TagHt dictionary.
* @param group The generated tag must belong to this group.
* @return The element of tag with given group which is fee.
*/
-uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group)
-{
- for (uint32_t elem = 0; elem < UINT32_MAX; elem++)
- {
- TagKey key = DictEntry::TranslateToKey(group, elem);
- if (TagHT.count(key) == 0)
- {
- return elem;
- }
- }
- return UINT32_MAX;
-}
+//uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group)
+//{
+// for (uint32_t elem = 0; elem < UINT32_MAX; elem++)
+// {
+// TagKey key = DictEntry::TranslateToKey(group, elem);
+// if (TagHT.count(key) == 0)
+// {
+// return elem;
+// }
+// }
+// return UINT32_MAX;
+//}
/**
- * \brief Assuming the internal file pointer \ref Document::Fp
- * is placed at the beginning of a tag check whether this
- * tag is (TestGroup, TestElement).
- * \warning On success the internal file pointer \ref Document::Fp
- * is modified to point after the tag.
- * On failure (i.e. when the tag wasn't the expected tag
- * (TestGroup, TestElement) the internal file pointer
- * \ref Document::Fp is restored to it's original position.
- * @param testGroup The expected group of the tag.
- * @param testElement The expected Element of the tag.
- * @return True on success, false otherwise.
+ * \brief Compares two documents, according to \ref DicomDir rules
+ * \warning Does NOT work with ACR-NEMA files
+ * \todo Find a trick to solve the pb (use RET fields ?)
+ * @param document
+ * @return true if 'smaller'
*/
-bool Document::ReadTag(uint16_t testGroup, uint16_t testElement)
+bool Document::operator<(Document &document)
{
- long positionOnEntry = Fp->tellg();
- long currentPosition = Fp->tellg(); // On debugging purposes
-
- //// Read the Item Tag group and element, and make
- // sure they are what we expected:
- uint16_t itemTagGroup;
- uint16_t itemTagElement;
- try
+ // Patient Name
+ std::string s1 = GetEntryValue(0x0010,0x0010);
+ std::string s2 = document.GetEntryValue(0x0010,0x0010);
+ if(s1 < s2)
{
- itemTagGroup = ReadInt16();
- itemTagElement = ReadInt16();
+ return true;
}
- catch ( FormatError e )
+ else if( s1 > s2 )
{
- //std::cerr << e << std::endl;
return false;
}
- if ( itemTagGroup != testGroup || itemTagElement != testElement )
- {
- gdcmVerboseMacro( "Wrong Item Tag found:"
- << " We should have found tag ("
- << std::hex << testGroup << "," << testElement << ")" << std::endl
- << " but instead we encountered tag ("
- << std::hex << itemTagGroup << "," << itemTagElement << ")"
- << " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
- ) ;
- Fp->seekg(positionOnEntry, std::ios::beg);
-
- return false;
- }
- return true;
-}
-
-/**
- * \brief Assuming the internal file pointer \ref Document::Fp
- * is placed at the beginning of a tag (TestGroup, TestElement),
- * read the length associated to the Tag.
- * \warning On success the internal file pointer \ref Document::Fp
- * is modified to point after the tag and it's length.
- * On failure (i.e. when the tag wasn't the expected tag
- * (TestGroup, TestElement) the internal file pointer
- * \ref Document::Fp is restored to it's original position.
- * @param testGroup The expected group of the tag.
- * @param testElement The expected Element of the tag.
- * @return On success returns the length associated to the tag. On failure
- * returns 0.
- */
-uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement)
-{
-
- if ( !ReadTag(testGroup, testElement) )
- {
- return 0;
- }
-
- //// Then read the associated Item Length
- long currentPosition = Fp->tellg();
- uint32_t itemLength = ReadInt32();
- {
- gdcmVerboseMacro( "Basic Item Length is: "
- << itemLength << std::endl
- << " at address: " << std::hex << (unsigned int)currentPosition);
- }
- return itemLength;
-}
-
-/**
- * \brief When parsing the Pixel Data of an encapsulated file, read
- * the basic offset table (when present, and BTW dump it).
- */
-void Document::ReadAndSkipEncapsulatedBasicOffsetTable()
-{
- //// Read the Basic Offset Table Item Tag length...
- uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
-
- // When present, read the basic offset table itself.
- // Notes: - since the presence of this basic offset table is optional
- // we can't rely on it for the implementation, and we will simply
- // trash it's content (when present).
- // - still, when present, we could add some further checks on the
- // lengths, but we won't bother with such fuses for the time being.
- if ( itemLength != 0 )
- {
- char *basicOffsetTableItemValue = new char[itemLength + 1];
- Fp->read(basicOffsetTableItemValue, itemLength);
-
-#ifdef GDCM_DEBUG
- for (unsigned int i=0; i < itemLength; i += 4 )
- {
- uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
- uint32_t);
- gdcmVerboseMacro( "Read one length: " <<
- std::hex << individualLength );
- }
-#endif //GDCM_DEBUG
-
- delete[] basicOffsetTableItemValue;
- }
-}
-
-/**
- * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
- * Compute the RLE extra information and store it in \ref RLEInfo
- * for later pixel retrieval usage.
- */
-void Document::ComputeRLEInfo()
-{
- std::string ts = GetTransferSyntax();
- if ( !Global::GetTS()->IsRLELossless(ts) )
+ else
{
- return;
- }
-
- // Encoded pixel data: for the time being we are only concerned with
- // Jpeg or RLE Pixel data encodings.
- // As stated in PS 3.5-2003, section 8.2 p44:
- // "If sent in Encapsulated Format (i.e. other than the Native Format) the
- // value representation OB is used".
- // Hence we expect an OB value representation. Concerning OB VR,
- // the section PS 3.5-2003, section A.4.c p 58-59, states:
- // "For the Value Representations OB and OW, the encoding shall meet the
- // following specifications depending on the Data element tag:"
- // [...snip...]
- // - the first item in the sequence of items before the encoded pixel
- // data stream shall be basic offset table item. The basic offset table
- // item value, however, is not required to be present"
-
- ReadAndSkipEncapsulatedBasicOffsetTable();
-
- // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
- // Loop on the individual frame[s] and store the information
- // on the RLE fragments in a RLEFramesInfo.
- // Note: - when only a single frame is present, this is a
- // classical image.
- // - when more than one frame are present, then we are in
- // the case of a multi-frame image.
- long frameLength;
- while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
- {
- // Parse the RLE Header and store the corresponding RLE Segment
- // Offset Table information on fragments of this current Frame.
- // Note that the fragment pixels themselves are not loaded
- // (but just skipped).
- long frameOffset = Fp->tellg();
-
- uint32_t nbRleSegments = ReadInt32();
- if ( nbRleSegments > 16 )
+ // Patient ID
+ s1 = GetEntryValue(0x0010,0x0020);
+ s2 = document.GetEntryValue(0x0010,0x0020);
+ if ( s1 < s2 )
{
- // There should be at most 15 segments (refer to RLEFrame class)
- gdcmVerboseMacro( "Too many segments.");
+ return true;
}
-
- uint32_t rleSegmentOffsetTable[16];
- for( int k = 1; k <= 15; k++ )
+ else if ( s1 > s2 )
{
- rleSegmentOffsetTable[k] = ReadInt32();
+ return false;
}
-
- // Deduce from both the RLE Header and the frameLength the
- // fragment length, and again store this info in a
- // RLEFramesInfo.
- long rleSegmentLength[15];
- // skipping (not reading) RLE Segments
- if ( nbRleSegments > 1)
+ else
{
- for(unsigned int k = 1; k <= nbRleSegments-1; k++)
+ // Study Instance UID
+ s1 = GetEntryValue(0x0020,0x000d);
+ s2 = document.GetEntryValue(0x0020,0x000d);
+ if ( s1 < s2 )
{
- rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
- - rleSegmentOffsetTable[k];
- SkipBytes(rleSegmentLength[k]);
- }
- }
-
- rleSegmentLength[nbRleSegments] = frameLength
- - rleSegmentOffsetTable[nbRleSegments];
- SkipBytes(rleSegmentLength[nbRleSegments]);
-
- // Store the collected info
- RLEFrame *newFrameInfo = new RLEFrame;
- newFrameInfo->NumberFragments = nbRleSegments;
- for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
- {
- newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk];
- newFrameInfo->Length[uk] = rleSegmentLength[uk];
- }
- RLEInfo->Frames.push_back( newFrameInfo );
- }
-
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
- if ( !ReadTag(0xfffe, 0xe0dd) )
- {
- gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence");
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
+ else
+ {
+ // Serie Instance UID
+ s1 = GetEntryValue(0x0020,0x000e);
+ s2 = document.GetEntryValue(0x0020,0x000e);
+ if ( s1 < s2 )
+ {
+ return true;
+ }
+ else if( s1 > s2 )
+ {
+ return false;
+ }
+ }
+ }
}
+ return false;
}
/**
- * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
- * Compute the jpeg extra information (fragment[s] offset[s] and
- * length) and store it[them] in \ref JPEGInfo for later pixel
- * retrieval usage.
+ * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
+ * @param filetype Type of the File to be written
*/
-void Document::ComputeJPEGFragmentInfo()
+int Document::ComputeGroup0002Length( FileType filetype )
{
- // If you need to, look for comments of ComputeRLEInfo().
- std::string ts = GetTransferSyntax();
- if ( ! Global::GetTS()->IsJPEG(ts) )
+ uint16_t gr;
+ std::string vr;
+
+ int groupLength = 0;
+ bool found0002 = false;
+
+ // for each zero-level Tag in the DCM Header
+ DocEntry *entry = GetFirstEntry();
+ while(entry)
{
- return;
- }
-
- ReadAndSkipEncapsulatedBasicOffsetTable();
-
- // Loop on the fragments[s] and store the parsed information in a
- // JPEGInfo.
- long fragmentLength;
- while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
- {
- long fragmentOffset = Fp->tellg();
-
- // Store the collected info
- JPEGFragment *newFragment = new JPEGFragment;
- newFragment->Offset = fragmentOffset;
- newFragment->Length = fragmentLength;
- JPEGInfo->Fragments.push_back( newFragment );
+ gr = entry->GetGroup();
- SkipBytes( fragmentLength );
- }
+ if (gr == 0x0002)
+ {
+ found0002 = true;
+ vr = entry->GetVR();
+
+ if (filetype == ExplicitVR)
+ {
+ if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
+ {
+ groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes
+ }
+ }
+ groupLength += 2 + 2 + 4 + entry->GetLength();
+ }
+ else if (found0002 )
+ break;
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
- if ( !ReadTag(0xfffe, 0xe0dd) )
- {
- gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence");
+ entry = GetNextEntry();
}
+ return groupLength;
}
-/**
+/*
* \brief Walk recursively the given \ref DocEntrySet, and feed
* the given hash table (\ref TagDocEntryHT) with all the
* \ref DocEntry (Dicom entries) encountered.
}
}*/
-/**
+/*
* \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current
* Document.
*
return FlatHT;
}*/
-
-
-/**
- * \brief Compares two documents, according to \ref DicomDir rules
- * \warning Does NOT work with ACR-NEMA files
- * \todo Find a trick to solve the pb (use RET fields ?)
- * @param document
- * @return true if 'smaller'
- */
-bool Document::operator<(Document &document)
-{
- // Patient Name
- std::string s1 = GetEntry(0x0010,0x0010);
- std::string s2 = document.GetEntry(0x0010,0x0010);
- if(s1 < s2)
- {
- return true;
- }
- else if( s1 > s2 )
- {
- return false;
- }
- else
- {
- // Patient ID
- s1 = GetEntry(0x0010,0x0020);
- s2 = document.GetEntry(0x0010,0x0020);
- if ( s1 < s2 )
- {
- return true;
- }
- else if ( s1 > s2 )
- {
- return false;
- }
- else
- {
- // Study Instance UID
- s1 = GetEntry(0x0020,0x000d);
- s2 = document.GetEntry(0x0020,0x000d);
- if ( s1 < s2 )
- {
- return true;
- }
- else if( s1 > s2 )
- {
- return false;
- }
- else
- {
- // Serie Instance UID
- s1 = GetEntry(0x0020,0x000e);
- s2 = document.GetEntry(0x0020,0x000e);
- if ( s1 < s2 )
- {
- return true;
- }
- else if( s1 > s2 )
- {
- return false;
- }
- }
- }
- }
- return false;
-}
-
-
-/**
- * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
- * @param filetype Type of the File to be written
- */
-int Document::ComputeGroup0002Length( FileType filetype )
-{
- uint16_t gr, el;
- std::string vr;
-
- int groupLength = 0;
- bool found0002 = false;
-
- // for each zero-level Tag in the DCM Header
- DocEntry *entry;
-
- InitTraversal();
- entry = GetNextEntry();
- while(entry)
- {
- gr = entry->GetGroup();
-
- if (gr == 0x0002)
- {
- found0002 = true;
-
- el = entry->GetElement();
- vr = entry->GetVR();
-
- if (filetype == ExplicitVR)
- {
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
- {
- groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes
- }
- }
- groupLength += 2 + 2 + 4 + entry->GetLength();
- }
- else if (found0002 )
- break;
-
- entry = GetNextEntry();
- }
- return groupLength;
-}
-
} // end namespace gdcm
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff