-/**
- * \brief Read the next tag but WITHOUT loading it's value
- * (read the 'Group Number', the 'Element Number',
- * gets the Dict Entry
- * gets the VR, gets the length, gets the offset value)
- * @return On succes the newly created DocEntry, NULL on failure.
- */
-DocEntry *Document::ReadNextDocEntry()
-{
- uint16_t group;
- uint16_t elem;
-
- try
- {
- group = ReadInt16();
- elem = ReadInt16();
- }
- catch ( FormatError e )
- {
- // We reached the EOF (or an error occured) therefore
- // header parsing has to be considered as finished.
- //std::cout << e;
- return 0;
- }
-
- // Sometimes file contains groups of tags with reversed endianess.
- HandleBrokenEndian(group, elem);
-
-// In 'true DICOM' files Group 0002 is always little endian
- if ( HasDCMPreamble )
- HandleOutOfGroup0002(group, elem);
-
- std::string vr = FindDocEntryVR();
- std::string realVR = vr;
-
- if( vr == GDCM_UNKNOWN)
- {
- DictEntry *dictEntry = GetDictEntry(group,elem);
- if( dictEntry )
- realVR = dictEntry->GetVR();
- }
-
- DocEntry *newEntry;
- if( Global::GetVR()->IsVROfSequence(realVR) )
- newEntry = NewSeqEntry(group, elem);
- else if( Global::GetVR()->IsVROfStringRepresentable(realVR) )
- newEntry = NewValEntry(group, elem,vr);
- else
- newEntry = NewBinEntry(group, elem,vr);
-
- if( vr == GDCM_UNKNOWN )
- {
- 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());
- gdcmVerboseMacro( msg.c_str() );
- }
- }
- newEntry->SetImplicitVR();
- }
-
- try
- {
- FindDocEntryLength(newEntry);
- }
- catch ( FormatError e )
- {
- // Call it quits
- //std::cout << e;
- delete newEntry;
- return 0;
- }
-
- newEntry->SetOffset(Fp->tellg());
-
- return newEntry;
-}
-
-
-/**
- * \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;
-}
-
-/**
- * \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.
- */
-bool Document::ReadTag(uint16_t testGroup, uint16_t testElement)
-{
- 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
- {
- itemTagGroup = ReadInt16();
- itemTagElement = ReadInt16();
- }
- catch ( FormatError e )
- {
- //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) )
- {
- 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 )
- {
- // There should be at most 15 segments (refer to RLEFrame class)
- gdcmVerboseMacro( "Too many segments.");
- }
-
- uint32_t rleSegmentOffsetTable[16];
- for( int k = 1; k <= 15; k++ )
- {
- rleSegmentOffsetTable[k] = ReadInt32();
- }
-
- // 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)
- {
- 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
- 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");
- }
-}
-
-/**
- * \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.
- */
-void Document::ComputeJPEGFragmentInfo()
-{
- // If you need to, look for comments of ComputeRLEInfo().
- std::string ts = GetTransferSyntax();
- if ( ! Global::GetTS()->IsJPEG(ts) )
- {
- 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 );
-
- SkipBytes( fragmentLength );
- }
-
- // 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");
- }
-}
-
-/**
- * \brief Walk recursively the given \ref DocEntrySet, and feed
- * the given hash table (\ref TagDocEntryHT) with all the
- * \ref DocEntry (Dicom entries) encountered.
- * This method does the job for \ref BuildFlatHashTable.
- * @param builtHT Where to collect all the \ref DocEntry encountered
- * when recursively walking the given set.
- * @param set The structure to be traversed (recursively).
- */
-/*void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT,
- DocEntrySet *set )
-{
- if (ElementSet *elementSet = dynamic_cast< ElementSet* > ( set ) )
- {
- TagDocEntryHT const ¤tHT = elementSet->GetTagHT();
- for( TagDocEntryHT::const_iterator i = currentHT.begin();
- i != currentHT.end();
- ++i)
- {
- DocEntry *entry = i->second;
- if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
- {
- const ListSQItem& items = seqEntry->GetSQItems();
- for( ListSQItem::const_iterator item = items.begin();
- item != items.end();
- ++item)
- {
- BuildFlatHashTableRecurse( builtHT, *item );
- }
- continue;
- }
- builtHT[entry->GetKey()] = entry;
- }
- return;
- }
-
- if (SQItem *SQItemSet = dynamic_cast< SQItem* > ( set ) )
- {
- const ListDocEntry& currentList = SQItemSet->GetDocEntries();
- for (ListDocEntry::const_iterator i = currentList.begin();
- i != currentList.end();
- ++i)
- {
- DocEntry *entry = *i;
- if ( SeqEntry *seqEntry = dynamic_cast<SeqEntry*>(entry) )
- {
- const ListSQItem& items = seqEntry->GetSQItems();
- for( ListSQItem::const_iterator item = items.begin();
- item != items.end();
- ++item)
- {
- BuildFlatHashTableRecurse( builtHT, *item );
- }
- continue;
- }
- builtHT[entry->GetKey()] = entry;
- }
-
- }
-}*/
-
-/**
- * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current
- * Document.
- *
- * The structure used by a Document (through \ref ElementSet),
- * in order to hold 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 SQItem) 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 ElementSet used
- * to build it. Hence if the underlying \ref ElementSet is
- * altered, then it is the caller responsability to invoke
- * \ref BuildFlatHashTable again...
- * @return The flat std::map<> we juste build.
- */
-/*TagDocEntryHT *Document::BuildFlatHashTable()
-{
- TagDocEntryHT *FlatHT = new TagDocEntryHT;
- BuildFlatHashTableRecurse( *FlatHT, this );
- 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 = GetFirstEntry();
- 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