Example/exExtractSegmentedPalette.cxx

   1 /*=========================================================================
   2
   3   Program:   gdcm
   4   Module:    $RCSfile: exExtractSegmentedPalette.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2007/10/03 08:50:48 $
   7   Version:   $Revision: 1.2 $
   8
   9   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
  10   l'Image). All rights reserved. See Doc/License.txt or
  11   http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
  12
  13      This software is distributed WITHOUT ANY WARRANTY; without even
  14      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15      PURPOSE.  See the above copyright notices for more information.
  16
  17 =========================================================================*/
  18
  19 #include <gdcm.h>
  20 // Ref:
  21 // http://blog.goo.ne.jp/satomi_takeo/e/3643e5249b2a9650f9e10ef1c830e8b8
  22 // I bet the code was compiled on VS6. Make it compile on other platform:
  23 // * typedef are not inherited
  24 // * need to explicitely add typename keyword
  25 // * Uint8 / Uint16 are neither C nor C++
  26 // * replace all dcmtk code with identical gdcm code
  27
  28 #include <assert.h>
  29 #include <algorithm>
  30 #include <deque>
  31 #include <map>
  32 #include <vector>
  33 #include <iterator>
  34
  35 namespace {
  36     // abstract class for segment.
  37     template <typename EntryType>
  38     class Segment {
  39     public:
  40         typedef std::map<const EntryType*, const Segment*> SegmentMap;
  41         virtual bool Expand(const SegmentMap& instances,
  42             std::vector<EntryType>& expanded) const = 0;
  43         const EntryType* First() const { return _first; }
  44         const EntryType* Last() const { return _last; }
  45         struct ToMap {
  46             std::pair<
  47                 typename SegmentMap::key_type,
  48                 typename SegmentMap::mapped_type
  49             >
  50                 operator()(const Segment* segment) const
  51             { return std::make_pair(segment->First(), segment); }
  52         };
  53     protected:
  54         Segment(const EntryType* first, const EntryType* last) {
  55             _first = first; _last = last;
  56         }
  57         const EntryType* _first;
  58         const EntryType* _last;
  59     };
  60
  61     // discrete segment (opcode = 0)
  62     template <typename EntryType>
  63     class DiscreteSegment : public Segment<EntryType> {
  64     public:
  65         typedef typename Segment<EntryType>::SegmentMap SegmentMap;
  66         DiscreteSegment(const EntryType* first)
  67             : Segment<EntryType>(first, first+2+*(first+1)) {}
  68         virtual bool Expand(const SegmentMap&,
  69             std::vector<EntryType>& expanded) const
  70         {
  71             std::copy(this->_first + 2, this->_last, std::back_inserter(expanded));
  72             return true;
  73         }
  74     };
  75
  76     // linear segment (opcode = 1)
  77     template <typename EntryType>
  78     class LinearSegment : public Segment<EntryType> {
  79     public:
  80         typedef typename Segment<EntryType>::SegmentMap SegmentMap;
  81         LinearSegment(const EntryType* first)
  82             : Segment<EntryType>(first, first+3) {}
  83         virtual bool Expand(const SegmentMap&,
  84             std::vector<EntryType>& expanded) const
  85         {
  86             if ( expanded.empty() ) {
  87                 // linear segment can't be the first segment.
  88                 return false;
  89             }
  90             EntryType length = *(this->_first + 1);
  91             EntryType y0 = expanded.back();
  92             EntryType y1 = *(this->_first + 2);
  93             double y01 = y1 - y0;
  94             for ( EntryType i = 0; i <length; ++i ) {
  95                 double value_float
  96                     = static_cast<double>(y0)
  97                     + (static_cast<double>(i)/static_cast<double>(length)) * y01;
  98                 EntryType value_int = static_cast<EntryType>(value_float + 0.5);
  99                 expanded.push_back(value_int);
 100             }
 101             return true;
 102         }
 103     };
 104
 105     // indirect segment (opcode = 2)
 106     template <typename EntryType>
 107     class IndirectSegment : public Segment<EntryType> {
 108     public:
 109         typedef typename Segment<EntryType>::SegmentMap SegmentMap;
 110         IndirectSegment(const EntryType* first)
 111             : Segment<EntryType>(first, first+2+4/sizeof(EntryType)) {}
 112         virtual bool Expand(const SegmentMap& instances,
 113             std::vector<EntryType>& expanded) const
 114         {
 115             if ( instances.empty() ) {
 116                 // some other segments are required as references.
 117                 return false;
 118             }
 119             const EntryType* first_segment = instances.begin()->first;
 120             const unsigned short* pOffset
 121                 = reinterpret_cast<const unsigned short*>(this->_first + 2);
 122             unsigned long offsetBytes
 123                 = (*pOffset) | (static_cast<unsigned long>(*(pOffset + 1)) << 16);
 124             const EntryType* copied_part_head
 125                 = first_segment + offsetBytes / sizeof(EntryType);
 126             typename SegmentMap::const_iterator ppHeadSeg = instances.find(copied_part_head);
 127             if ( ppHeadSeg == instances.end() ) {
 128                 // referred segment not found
 129                 return false;
 130             }
 131             EntryType nNumCopies = *(this->_first + 1);
 132             typename SegmentMap::const_iterator ppSeg = ppHeadSeg;
 133             while ( std::distance(ppHeadSeg, ppSeg) <nNumCopies ) {
 134                 assert( ppSeg != instances.end() );
 135                 ppSeg->second->Expand(instances, expanded);
 136                 ++ppSeg;
 137             }
 138             return true;
 139         }
 140     };
 141
 142     template <typename EntryType>
 143     void ExpandPalette(const EntryType* raw_values, uint32_t length,
 144         std::vector<EntryType>& palette)
 145     {
 146         typedef std::deque<Segment<EntryType>*> SegmentList;
 147         SegmentList segments;
 148         const EntryType* raw_seg = raw_values;
 149         while ( (std::distance(raw_values, raw_seg) * sizeof(EntryType)) <length ) {
 150             Segment<EntryType>* segment = NULL;
 151             if ( *raw_seg == 0 ) {
 152                 segment = new DiscreteSegment<EntryType>(raw_seg);
 153             } else if ( *raw_seg == 1 ) {
 154                 segment = new LinearSegment<EntryType>(raw_seg);
 155             } else if ( *raw_seg == 2 ) {
 156                 segment = new IndirectSegment<EntryType>(raw_seg);
 157             }
 158             if ( segment ) {
 159                 segments.push_back(segment);
 160                 raw_seg = segment->Last();
 161             } else {
 162                 // invalid opcode
 163                 break;
 164             }
 165         }
 166         typename Segment<EntryType>::SegmentMap instances;
 167         std::transform(segments.begin(), segments.end(),
 168             std::inserter(instances, instances.end()), typename Segment<EntryType>::ToMap());
 169         typename SegmentList::iterator ppSeg = segments.begin();
 170         typename SegmentList::iterator endOfSegments = segments.end();
 171         for ( ; ppSeg != endOfSegments; ++ppSeg ) {
 172             (*ppSeg)->Expand(instances, palette);
 173         }
 174         ppSeg = segments.begin();
 175         for ( ; ppSeg != endOfSegments; ++ppSeg ) {
 176             delete *ppSeg;
 177         }
 178     }
 179
 180     void ReadPalette(GDCM_NAME_SPACE::File* pds, const GDCM_NAME_SPACE::TagKey& descriptor,
 181       const GDCM_NAME_SPACE::TagKey& segment)
 182       {
 183       int desc_values[3] = {};
 184       unsigned long count = 0;
 185       //if ( pds->findAndGetUint16Array(descriptor, desc_values, &count).good() )
 186       std::string desc_values_str = pds->GetEntryString(descriptor.GetGroup(), descriptor.GetElement() );
 187       count = sscanf( desc_values_str.c_str(), "%d\\%d\\%d", desc_values, desc_values+1, desc_values+2 );
 188         {
 189         assert( count == 3 );
 190         unsigned int num_entries = desc_values[0];
 191         if ( num_entries == 0 ) {
 192           num_entries = 0x10000;
 193         }
 194         int min_pixel_value = desc_values[1];
 195         unsigned int entry_size = desc_values[2];
 196         assert( entry_size == 8 || entry_size == 16 );
 197         //DcmElement* pe = NULL;
 198         GDCM_NAME_SPACE::DataEntry* pe = NULL;
 199
 200         pe = pds->GetDataEntry(segment.GetGroup(), segment.GetElement() ); {
 201           //if ( pds->findAndGetElement(segment, pe).good() )
 202           unsigned long length = pe->GetLength();
 203           if ( entry_size == 8 ) {
 204             uint8_t* segment_values = NULL;
 205             //if ( pe->getUint8Array(segment_values).good() )
 206             segment_values = (uint8_t*)pe->GetBinArea(); {
 207               std::vector<uint8_t> palette;
 208               palette.reserve(num_entries);
 209               ExpandPalette(segment_values, length, palette);
 210             }
 211           } else if ( entry_size == 16 ) {
 212             uint16_t* segment_values = NULL;
 213             segment_values = (uint16_t*)pe->GetBinArea(); {
 214               //if ( pe->getUint16Array(segment_values).good() )
 215               std::vector<uint16_t> palette;
 216               palette.reserve(num_entries);
 217               ExpandPalette(segment_values, length, palette);
 218               std::copy(palette.begin(), palette.end(),
 219                 std::ostream_iterator<uint16_t>(std::cout, "\n"));
 220
 221             }
 222           }
 223         }
 224         }
 225       }
 226 } // end namespace
 227
 228 int main(int argc, char* argv[])
 229 {
 230 //    if ( argc < 2 ) {
 231 //        return 1;
 232 //    }
 233 //    DcmFileFormat ff;
 234 //    OFString filename(argv[1]);
 235 //    if ( ff.loadFile(filename.c_str()).good() ) {
 236 //        DcmDataset* pDataset = ff.getDataset();
 237 //        assert( pDataset );
 238 //        OFString pi;
 239 //        if ( pDataset->findAndGetOFString(DCM_PhotometricInterpretation, pi).good()
 240 //            && pi == OFString("PALETTE COLOR") ) {
 241 //            ReadPalette(pDataset, DCM_RedPaletteColorLookupTableDescriptor,
 242 //                DCM_SegmentedRedPaletteColorLookupTableData);
 243 //            ReadPalette(pDataset, DCM_GreenPaletteColorLookupTableDescriptor,
 244 //                DCM_SegmentedGreenPaletteColorLookupTableData);
 245 //            ReadPalette(pDataset, DCM_BluePaletteColorLookupTableDescriptor,
 246 //                DCM_SegmentedBluePaletteColorLookupTableData);
 247 //        }
 248 //    }
 249
 250   GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
 251   f->SetFileName( argv[1] );
 252   bool res = f->Load();
 253   f->Print( std::cout );
 254   GDCM_NAME_SPACE::TagKey DCM_RedPaletteColorLookupTableDescriptor (0x0028, 0x1101);
 255   GDCM_NAME_SPACE::TagKey DCM_GreenPaletteColorLookupTableDescriptor (0x0028, 0x1102);
 256   GDCM_NAME_SPACE::TagKey DCM_BluePaletteColorLookupTableDescriptor (0x0028, 0x1103);
 257
 258   GDCM_NAME_SPACE::TagKey DCM_SegmentedRedPaletteColorLookupTableData (0x0028, 0x1221);
 259   GDCM_NAME_SPACE::TagKey DCM_SegmentedGreenPaletteColorLookupTableData (0x0028, 0x1222);
 260   GDCM_NAME_SPACE::TagKey DCM_SegmentedBluePaletteColorLookupTableData (0x0028, 0x1223);
 261
 262
 263   // TODO need to check file is indeed PALETTE COLOR:
 264   ReadPalette(f, DCM_RedPaletteColorLookupTableDescriptor,
 265     DCM_SegmentedRedPaletteColorLookupTableData);
 266   ReadPalette(f, DCM_GreenPaletteColorLookupTableDescriptor,
 267     DCM_SegmentedGreenPaletteColorLookupTableData);
 268   ReadPalette(f, DCM_BluePaletteColorLookupTableDescriptor,
 269     DCM_SegmentedBluePaletteColorLookupTableData);
 270
 271     return 0;
 272 }
 273