Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2004/09/15 03:50:48 $
- Version: $Revision: 1.78 $
+ Date: $Date: 2004/10/08 08:38:54 $
+ Version: $Revision: 1.98 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
- http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details.
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
#include "gdcmValEntry.h"
#include "gdcmBinEntry.h"
#include "gdcmSeqEntry.h"
-
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
long beg = ftell(Fp);
lgt -= beg;
- SQDepthLevel = 0;
-
- (void)ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
+ ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
rewind(Fp);
std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
if( PhotometricInterpretation == "PALETTE COLOR " )
{
- LoadEntryVoidArea(0x0028,0x1200); // gray LUT
+ LoadEntryBinArea(0x0028,0x1200); // gray LUT
/// FIXME FIXME FIXME
/// The tags refered by the three following lines used to be CORRECTLY
/// defined as having an US Value Representation in the public
/// also used as gdcmBinEntry, which requires the proper conversion,
/// - OW, and hence loaded as gdcmBinEntry, but afterwards also used
/// as gdcmValEntry, which requires the proper conversion.
- LoadEntryVoidArea(0x0028,0x1201); // R LUT
- LoadEntryVoidArea(0x0028,0x1202); // G LUT
- LoadEntryVoidArea(0x0028,0x1203); // B LUT
+ LoadEntryBinArea(0x0028,0x1201); // R LUT
+ LoadEntryBinArea(0x0028,0x1202); // G LUT
+ LoadEntryBinArea(0x0028,0x1203); // B LUT
// Segmented Red Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1221);
+ LoadEntryBinArea(0x0028,0x1221);
// Segmented Green Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1222);
+ LoadEntryBinArea(0x0028,0x1222);
// Segmented Blue Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1223);
+ LoadEntryBinArea(0x0028,0x1223);
}
//FIXME later : how to use it?
- LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent)
+ LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent)
CloseFile();
/**
* \brief Get the public dictionary used
*/
-gdcmDict *gdcmDocument::GetPubDict()
+gdcmDict* gdcmDocument::GetPubDict()
{
return RefPubDict;
}
/**
* \brief Get the shadow dictionary used
*/
-gdcmDict *gdcmDocument::GetShaDict()
+gdcmDict* gdcmDocument::GetShaDict()
{
return RefShaDict;
}
|| IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) );
}
+/**
+ * \brief Determines if the Transfer Syntax corresponds to encapsulated
+ * of encoded Pixel Data (as opposed to native).
+ * @return True when encapsulated. False when native.
+ */
+bool gdcmDocument::IsEncapsulateTransferSyntax()
+{
+ return ( IsJPEGBaseLineProcess1TransferSyntax()
+ || IsJPEGExtendedProcess2_4TransferSyntax()
+ || IsJPEGExtendedProcess3_5TransferSyntax()
+ || IsJPEGSpectralSelectionProcess6_8TransferSyntax()
+ || IsRLELossLessTransferSyntax()
+ || IsJPEGLossless()
+ || IsJPEG2000() );
+}
+
/**
* \brief Predicate for dicom version 3 file.
* @return True when the file is a dicom version 3.
void gdcmDocument::Write(FILE* fp,FileType filetype)
{
/// \todo move the following lines (and a lot of others, to be written)
- /// to a future function CheckAndCorrectHeader
-
- /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA
- /// no way (check : FileType est un champ de gdcmDocument ...)
- /// a moins de se livrer a un tres complique ajout des champs manquants.
- /// faire un CheckAndCorrectHeader (?)
-
+ /// to a future function CheckAndCorrectHeader
+ /// (necessary if user wants to write a DICOM V3 file
+ /// starting from an ACR-NEMA (V2) gdcmHeader
+
if (filetype == gdcmImplicitVR)
{
std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2;
* @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).
- */
-
-gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
+ */
+gdcmValEntry* gdcmDocument::ReplaceOrCreateByNumber(
std::string const & value,
uint16_t group,
- uint16_t elem )
+ uint16_t elem,
+ std::string const & VR )
{
gdcmValEntry* valEntry = 0;
gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
if (!currentEntry)
{
- // The entry wasn't present and we simply create the required ValEntry:
- currentEntry = NewDocEntryByNumber(group, elem);
+ // check if (group,element) DictEntry exists
+ // if it doesn't, create an entry in gdcmDictSet::VirtualEntry
+ // and use it
+
+ // Find out if the tag we received is in the dictionaries:
+ gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
+ gdcmDictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem);
+ if (!dictEntry)
+ {
+ currentEntry = NewDocEntryByNumber(group, elem,VR);
+ }
+ else
+ {
+ currentEntry = NewDocEntryByNumber(group, elem);
+ }
+
if (!currentEntry)
{
dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
return valEntry;
}
-/**
+/*
* \brief Modifies the value of a given Header 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-
+ * @param binArea (binary) value to be set
+ * @param Group Group number of the Entry
+ * @param Elem Element number of the Entry
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-
- // TODO : write something clever, using default value for VR
- // to avoid code duplication
- // (I don't know how to tell NewDocEntryByNumber
- // that ReplaceOrCreateByNumber was called with a default value)
-
-gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
- std::string const & value,
+gdcmBinEntry* gdcmDocument::ReplaceOrCreateByNumber(
+ uint8_t* binArea,
+ int lgth,
uint16_t group,
uint16_t elem,
- std::string const & VR )
+ std::string const& VR )
{
- gdcmValEntry* valEntry = 0;
+ gdcmBinEntry* binEntry = 0;
gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
-
if (!currentEntry)
{
+
// check if (group,element) DictEntry exists
// if it doesn't, create an entry in gdcmDictSet::VirtualEntry
// and use it
// Find out if the tag we received is in the dictionaries:
gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
gdcmDictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem);
+
if (!dictEntry)
{
- currentEntry = NewDocEntryByNumber(group, elem,VR);
+ currentEntry = NewDocEntryByNumber(group, elem, VR);
}
else
{
currentEntry = NewDocEntryByNumber(group, elem);
}
-
if (!currentEntry)
{
dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
" NewDocEntryByNumber failed.");
return NULL;
}
- valEntry = new gdcmValEntry(currentEntry);
- if ( !AddEntry(valEntry))
+ binEntry = new gdcmBinEntry(currentEntry);
+ if ( !AddEntry(binEntry))
{
dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry"
" failed allthough this is a creation.");
}
else
{
- valEntry = dynamic_cast< gdcmValEntry* >(currentEntry);
- if ( !valEntry ) // Euuuuh? It wasn't a ValEntry
- // then we change it to a ValEntry ?
+ binEntry = dynamic_cast< gdcmBinEntry* >(currentEntry);
+ if ( !binEntry ) // Euuuuh? It wasn't a BinEntry
+ // then we change it to a BinEntry ?
// Shouldn't it be considered as an error ?
{
- // We need to promote the gdcmDocEntry to a gdcmValEntry:
- valEntry = new gdcmValEntry(currentEntry);
+ // We need to promote the gdcmDocEntry to a gdcmBinEntry:
+ binEntry = new gdcmBinEntry(currentEntry);
if (!RemoveEntry(currentEntry))
{
dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
" of previous DocEntry failed.");
return NULL;
}
- if ( !AddEntry(valEntry))
+ if ( !AddEntry(binEntry))
{
dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
- " promoted ValEntry failed.");
+ " promoted BinEntry failed.");
return NULL;
}
}
}
- SetEntryByNumber(value, group, elem);
-
- return valEntry;
-}
-
-/*
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * @param voidArea (binary) value to be set
- * @param Group Group number of the Entry
- * @param Elem Element number of the Entry
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
- */
-gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber(
- void *voidArea,
- int lgth,
- uint16_t group,
- uint16_t elem)
-{
- gdcmBinEntry* b = 0;
- gdcmDocEntry* a = GetDocEntryByNumber( group, elem);
- if (!a)
- {
- a = NewBinEntryByNumber(group, elem);
- if (!a)
- {
- return 0;
- }
-
- b = new gdcmBinEntry(a);
- AddEntry(b);
- b->SetVoidArea(voidArea);
- }
-
- SetEntryByNumber(voidArea, lgth, group, elem);
+ SetEntryByNumber(binArea, lgth, group, elem);
- return b;
+ return binEntry;
}
* \return pointer to the modified/created SeqEntry (NULL when creation
* failed).
*/
-gdcmSeqEntry * gdcmDocument::ReplaceOrCreateByNumber(
+gdcmSeqEntry* gdcmDocument::ReplaceOrCreateByNumber(
uint16_t group,
uint16_t elem)
{
* @return Corresponding element value when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryByName(TagName const & tagName)
+std::string gdcmDocument::GetEntryByName(TagName const& tagName)
{
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
+ gdcmDictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( !dictEntry )
{
return GDCM_UNFOUND;
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryVRByName(TagName const & tagName)
+std::string gdcmDocument::GetEntryVRByName(TagName const& tagName)
{
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
return elem->GetVR();
}
-
/**
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* @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 const & content,
+bool gdcmDocument::SetEntryByNumber(std::string const& content,
uint16_t group,
uint16_t element)
{
* \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
- * @param content new value (void *) to substitute with
+ * @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 element element number of the Dicom Element to modify
*/
-bool gdcmDocument::SetEntryByNumber(void *content,
+bool gdcmDocument::SetEntryByNumber(uint8_t*content,
int lgth,
uint16_t group,
uint16_t element)
}
*/
gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key];
- a->SetVoidArea(content);
+ a->SetBinArea(content);
a->SetLength(lgth);
+ a->SetValue(GDCM_BINLOADED);
return true;
}
* @param elem element number of the Entry
* @return Pointer to the 'non string' area
*/
-void * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem)
+void* gdcmDocument::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem)
{
gdcmDocEntry* entry = GetDocEntryByNumber(group, elem);
if (!entry)
dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry");
return 0;
}
- return ((gdcmBinEntry *)entry)->GetVoidArea();
+ return ((gdcmBinEntry *)entry)->GetBinArea();
}
/**
* @param group group number of the Entry
* @param elem element number of the Entry
*/
-void* gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem)
+void* gdcmDocument::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
gdcmDocEntry *docElement = GetDocEntryByNumber(group, elem);
if ( !docElement )
size_t o =(size_t)docElement->GetOffset();
fseek(Fp, o, SEEK_SET);
size_t l = docElement->GetLength();
- char* a = new char[l];
+ uint8_t* a = new uint8_t[l];
if(!a)
{
- dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a");
+ dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea cannot allocate a");
return NULL;
}
size_t l2 = fread(a, 1, l , Fp);
delete[] a;
return NULL;
}
- /// \TODO Drop any already existing void area! JPR
- if( !SetEntryVoidAreaByNumber( a, group, elem ) );
+ /// \todo Drop any already existing void area! JPR
+ if( !SetEntryBinAreaByNumber( a, group, elem ) );
{
- dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea setting failed.");
+ dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea setting failed.");
}
-
return a;
}
/**
* \brief Loads (from disk) the element content
* when a string is not suitable
- * @param element Entry whose voidArea is going to be loaded
+ * @param element Entry whose binArea is going to be loaded
*/
-void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element)
+void* gdcmDocument::LoadEntryBinArea(gdcmBinEntry* element)
{
size_t o =(size_t)element->GetOffset();
fseek(Fp, o, SEEK_SET);
size_t l = element->GetLength();
- char* a = new char[l];
+ uint8_t* a = new uint8_t[l];
if( !a )
{
- dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a");
+ dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea cannot allocate a");
return NULL;
}
- element->SetVoidArea((void *)a);
+ element->SetBinArea((uint8_t*)a);
/// \todo check the result
size_t l2 = fread(a, 1, l , Fp);
if( l != l2 )
* @param element Element number of the searched Dicom Element
* @return
*/
-bool gdcmDocument::SetEntryVoidAreaByNumber(void * area,
+bool gdcmDocument::SetEntryBinAreaByNumber(uint8_t* area,
uint16_t group,
uint16_t element)
{
}
if ( gdcmBinEntry* binEntry = dynamic_cast<gdcmBinEntry*>(currentEntry) )
{
- binEntry->SetVoidArea( area );
+ binEntry->SetBinArea( area );
return true;
}
return true;
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
* @return length of the parsed set.
*/
-
-long gdcmDocument::ParseDES(gdcmDocEntrySet *set,
+void gdcmDocument::ParseDES(gdcmDocEntrySet *set,
long offset,
long l_max,
bool delim_mode)
{
gdcmDocEntry *newDocEntry = 0;
- unsigned long l = 0;
- int depth = set->GetDepthLevel();
while (true)
{
if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) )
{
- /////// ValEntry
+ /////////////////////// ValEntry
gdcmValEntry* newValEntry =
new gdcmValEntry( newDocEntry->GetDictEntry() );
newValEntry->Copy( newDocEntry );
- newValEntry->SetKey( set->GetBaseTagKey() + newValEntry->GetKey() );
+
+ // When "set" is a gdcmDocument, then we are at the top of the
+ // hierarchy and the Key is simply of the form ( group, elem )...
+ if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ {
+ (void)dummy;
+ newValEntry->SetKey( newValEntry->GetKey() );
+ }
+ // ...but when "set" is a gdcmSQItem, we are inserting this new
+ // valEntry in a sequence item. Hence the key has the
+ // generalized form (refer to \ref gdcmBaseTagKey):
+ if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ {
+ newValEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newValEntry->GetKey() );
+ }
+
set->AddEntry( newValEntry );
LoadDocEntry( newValEntry );
if (newValEntry->IsItemDelimitor())
"nor BinEntry. Probably unknown VR.");
}
- ////// BinEntry or UNKOWN VR:
+ //////////////////// BinEntry or UNKOWN VR:
gdcmBinEntry* newBinEntry =
new gdcmBinEntry( newDocEntry->GetDictEntry() );
newBinEntry->Copy( newDocEntry );
- newBinEntry->SetKey( set->GetBaseTagKey() + newBinEntry->GetKey() );
+
+ // When "this" is a gdcmDocument the Key is simply of the
+ // form ( group, elem )...
+ if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ {
+ newBinEntry->SetKey( newBinEntry->GetKey() );
+ }
+ // but when "this" is a SQItem, we are inserting this new
+ // valEntry in a sequence item, and the kay has the
+ // generalized form (refer to \ref gdcmBaseTagKey):
+ if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ {
+ newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newBinEntry->GetKey() );
+ }
+
set->AddEntry( newBinEntry );
LoadDocEntry( newBinEntry );
}
if (newDocEntry->GetGroup() == 0x7fe0 &&
newDocEntry->GetElement() == 0x0010 )
{
- if (newDocEntry->GetReadLength()==0xffffffff)
+ if ( IsRLELossLessTransferSyntax() )
{
- // Broken US.3405.1.dcm
- Parse7FE0(); // to skip the pixels
- // (multipart JPEG/RLE are trouble makers)
+ long PositionOnEntry = ftell(Fp);
+ fseek(Fp, newDocEntry->GetOffset(), SEEK_SET);
+ ComputeRLEInfo();
+ fseek(Fp, PositionOnEntry, SEEK_SET);
}
else
{
SkipToNextDocEntry(newDocEntry);
- l = newDocEntry->GetFullLength();
}
}
else
{
// to be sure we are at the beginning
SkipToNextDocEntry(newDocEntry);
- l = newDocEntry->GetFullLength();
}
}
else
{
// VR = "SQ"
- l = newDocEntry->GetReadLength();
+ unsigned long l = newDocEntry->GetReadLength();
if ( l != 0 ) // don't mess the delim_mode for zero-length sequence
{
if ( l == 0xffffffff )
}
// no other way to create it ...
gdcmSeqEntry* newSeqEntry =
- new gdcmSeqEntry( newDocEntry->GetDictEntry(),
- set->GetDepthLevel() );
+ new gdcmSeqEntry( newDocEntry->GetDictEntry() );
newSeqEntry->Copy( newDocEntry );
newSeqEntry->SetDelimitorMode( delim_mode );
- newSeqEntry->SetDepthLevel( depth );
- newSeqEntry->SetKey( set->GetBaseTagKey() + newSeqEntry->GetKey() );
+
+ // At the top of the hierarchy, stands a gdcmDocument. When "set"
+ // is a gdcmDocument, then we are building the first depth level.
+ // Hence the gdcmSeqEntry we are building simply has a depth
+ // level of one:
+ if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ {
+ (void)dummy;
+ newSeqEntry->SetDepthLevel( 1 );
+ newSeqEntry->SetKey( newSeqEntry->GetKey() );
+ }
+ // But when "set" is allready a SQItem, we are building a nested
+ // sequence, and hence the depth level of the new gdcmSeqEntry
+ // we are building, is one level deeper:
+ if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ {
+ newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
+ newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
+ + newSeqEntry->GetKey() );
+ }
if ( l != 0 )
{ // Don't try to parse zero-length sequences
- (void)ParseSQ( newSeqEntry,
- newDocEntry->GetOffset(),
- l, delim_mode);
+ ParseSQ( newSeqEntry,
+ newDocEntry->GetOffset(),
+ l, delim_mode);
}
set->AddEntry( newSeqEntry );
if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
}
delete newDocEntry;
}
- return l; // Probably useless
}
/**
* \brief Parses a Sequence ( SeqEntry after SeqEntry)
* @return parsed length for this level
*/
-long gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry,
+void gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry,
long offset, long l_max, bool delim_mode)
{
int SQItemNumber = 0;
dlm_mod = false;
}
- (void)ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+ ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
seqEntry->AddEntry( itemSQ, SQItemNumber );
SQItemNumber++;
break;
}
}
-
- int lgth = ftell(Fp) - offset;
- return lgth;
}
/**
// When we find a BinEntry not very much can be done :
if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) )
{
- s << "gdcm::Loaded (BinEntry)";
+ s << GDCM_BINLOADED;
binEntryPtr->SetValue(s.str());
- LoadEntryVoidArea(binEntryPtr); // last one, not to erase length !
+ LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
return;
}
{
if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" )
{
- // The following reserved two bytes (see PS 3.5-2001, section
- // 7.1.2 Data element structure with explicit vr p27) must be
+ // 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.
fseek(Fp, 2L, SEEK_CUR);
uint32_t length32 = ReadInt32();
- if ( vr == "OB" && length32 == 0xffffffff )
+ if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
{
uint32_t lengthOB;
try
{
+ /// \todo rename that to FindDocEntryLengthOBOrOW since
+ /// the above test is on both OB and OW...
lengthOB = FindDocEntryLengthOB();
}
catch ( gdcmFormatUnexpected )
}
/**
- * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files
- * No other way so 'skip' the Data
- *
+ * \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 gdcmDocument::Parse7FE0 ()
+void gdcmDocument::ComputeRLEInfo()
{
- gdcmDocEntry* element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !element )
- {
- // Should warn user FIXME
- return;
- }
-
- if ( IsImplicitVRLittleEndianTransferSyntax()
- || IsExplicitVRLittleEndianTransferSyntax()
- || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier !
- || IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+ if ( ! IsRLELossLessTransferSyntax() )
{
return;
}
-
- // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels
+ // 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"
//// Read the Basic Offset Table Item Tag length...
uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
- //// ... and then read length[s] itself[themselves]. We don't use
- // the values read (BTW what is the purpous of those lengths ?)
+ // 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 )
{
- // BTW, what is the purpous of those length anyhow !?
char* basicOffsetTableItemValue = new char[itemLength + 1];
fread(basicOffsetTableItemValue, itemLength, 1, Fp);
for (unsigned int i=0; i < itemLength; i += 4 )
{
- uint32_t individualLength = str2num(&basicOffsetTableItemValue[i],uint32_t);
+ uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
+ uint32_t);
std::ostringstream s;
s << " Read one length: ";
s << std::hex << individualLength << std::endl;
- dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str());
+ dbg.Verbose(0, "gdcmDocument::ComputeRLEInfo: ", s.str().c_str());
}
delete[] basicOffsetTableItemValue;
}
- if ( ! IsRLELossLessTransferSyntax() )
- {
- // JPEG Image
-
- //// We then skip (not reading them) all the fragments of images:
- while ( (itemLength = ReadTagLength(0xfffe, 0xe000)) )
+ // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
+ // Loop on the frame[s] and store the parsed information in a
+ // gdcmRLEFramesInfo.
+ long frameLength;
+
+ // Loop on the individual frame[s] and store the information
+ // on the RLE fragments in a gdcmRLEFramesInfo.
+ // 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.
+ 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 = ftell(Fp);
+
+ uint32_t nbRleSegments = ReadInt32();
+
+ uint32_t rleSegmentOffsetTable[15];
+ for( int k = 1; k <= 15; k++ )
{
- SkipBytes(itemLength);
+ rleSegmentOffsetTable[k] = ReadInt32();
}
+
+ // Deduce from both the RLE Header and the frameLength the
+ // fragment length, and again store this info in a
+ // gdcmRLEFramesInfo.
+ long rleSegmentLength[15];
+ // skipping (not reading) RLE Segments
+ if ( nbRleSegments > 1)
+ {
+ for(unsigned int k = 1; k <= nbRleSegments-1; k++)
+ {
+ rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
+ - rleSegmentOffsetTable[k];
+ SkipBytes(rleSegmentLength[k]);
+ }
+ }
+
+ rleSegmentLength[nbRleSegments] = frameLength
+ - rleSegmentOffsetTable[nbRleSegments];
+ SkipBytes(rleSegmentLength[nbRleSegments]);
+
+ // Store the collected info
+ gdcmRLEFrame* newFrameInfo = new gdcmRLEFrame;
+ 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 );
}
- else
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
{
- // RLE Image
- long ftellRes;
- long rleSegmentLength[15], fragmentLength;
+ dbg.Verbose(0, "gdcmDocument::ComputeRLEInfo: no sequence delimiter ");
+ dbg.Verbose(0, " item at end of RLE item sequence");
+ }
+}
- // While we find some items:
- while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
- {
- // Parse fragments of the current Fragment (Frame)
- //------------------ scanning (not reading) fragment pixels
- uint32_t nbRleSegments = ReadInt32();
-
- //// Reading RLE Segments Offset Table
- uint32_t rleSegmentOffsetTable[15];
- for(int k=1; k<=15; k++)
+/**
+ * \brief Walk recursively the given \ref gdcmDocEntrySet, and feed
+ * the given hash table (\ref TagDocEntryHT) with all the
+ * \ref gdcmDocEntry (Dicom entries) encountered.
+ * This method does the job for \ref BuildFlatHashTable.
+ * @param builtHT Where to collect all the \ref gdcmDocEntry encountered
+ * when recursively walking the given set.
+ * @param set The structure to be traversed (recursively).
+ */
+void gdcmDocument::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT,
+ gdcmDocEntrySet* set )
+{
+ if (gdcmElementSet* elementSet = dynamic_cast< gdcmElementSet* > ( set ) )
+ {
+ TagDocEntryHT* currentHT = elementSet->GetTagHT();
+ for( TagDocEntryHT::const_iterator i = currentHT->begin();
+ i != currentHT->end();
+ ++i)
+ {
+ gdcmDocEntry* entry = i->second;
+ if ( gdcmSeqEntry* seqEntry = dynamic_cast<gdcmSeqEntry*>(entry) )
{
- ftellRes = ftell(Fp);
- rleSegmentOffsetTable[k] = ReadInt32();
+ ListSQItem& items = seqEntry->GetSQItems();
+ for( ListSQItem::const_iterator item = items.begin();
+ item != items.end();
+ ++item)
+ {
+ BuildFlatHashTableRecurse( builtHT, *item );
+ }
+ continue;
}
+ builtHT[entry->GetKey()] = entry;
+ }
+ return;
+ }
- // skipping (not reading) RLE Segments
- if ( nbRleSegments > 1)
+ if (gdcmSQItem* SQItemSet = dynamic_cast< gdcmSQItem* > ( set ) )
+ {
+ ListDocEntry& currentList = SQItemSet->GetDocEntries();
+ for (ListDocEntry::iterator i = currentList.begin();
+ i != currentList.end();
+ ++i)
+ {
+ gdcmDocEntry* entry = *i;
+ if ( gdcmSeqEntry* seqEntry = dynamic_cast<gdcmSeqEntry*>(entry) )
{
- for(unsigned int k = 1; k <= nbRleSegments-1; k++)
+ ListSQItem& items = seqEntry->GetSQItems();
+ for( ListSQItem::const_iterator item = items.begin();
+ item != items.end();
+ ++item)
{
- rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
- - rleSegmentOffsetTable[k];
- ftellRes = ftell(Fp);
- SkipBytes(rleSegmentLength[k]);
- }
- }
-
- rleSegmentLength[nbRleSegments] = fragmentLength
- - rleSegmentOffsetTable[nbRleSegments];
- ftellRes = ftell(Fp);
- SkipBytes(rleSegmentLength[nbRleSegments]);
+ BuildFlatHashTableRecurse( builtHT, *item );
+ }
+ continue;
+ }
+ builtHT[entry->GetKey()] = entry;
}
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
- if ( !ReadTag(0xfffe, 0xe0dd) )
- {
- dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item");
- dbg.Verbose(0, " at end of RLE item sequence");
- }
}
}
+/**
+ * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current
+ * gdcmDocument.
+ *
+ * The structure used by a gdcmDocument (through \ref gdcmElementSet),
+ * in order to old the parsed entries of a Dicom header, is a recursive
+ * one. This is due to the fact that the sequences (when present)
+ * can be nested. Additionaly, the sequence items (represented in
+ * gdcm as \ref gdcmSQItem) add an extra complexity to the data
+ * structure. Hence, a gdcm user whishing to visit all the entries of
+ * a Dicom header will need to dig in the gdcm internals (which
+ * implies exposing all the internal data structures to the API).
+ * In order to avoid this burden to the user, \ref BuildFlatHashTable
+ * recursively builds a temporary hash table, which holds all the
+ * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a
+ * std::map<>).
+ * \warning Of course there is NO integrity constrain between the
+ * returned \ref TagDocEntryHT and the \ref gdcmElementSet used
+ * to build it. Hence if the underlying \ref gdcmElementSet is
+ * altered, then it is the caller responsability to invoke
+ * \ref BuildFlatHashTable again...
+ * @return The flat std::map<> we juste build.
+ */
+TagDocEntryHT* gdcmDocument::BuildFlatHashTable()
+{
+ TagDocEntryHT* FlatHT = new TagDocEntryHT;
+ BuildFlatHashTableRecurse( *FlatHT, this );
+ return FlatHT;
+}
+
/**
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff