1 /*=========================================================================
4 Module: $RCSfile: gdcmSegmentedPalette.h,v $
6 Date: $Date: 2007/10/24 07:15:32 $
7 Version: $Revision: 1.11 $
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.
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.
17 =========================================================================*/
19 #ifndef _GDCMSEGMENTEDPALETTE_H_
20 #define _GDCMSEGMENTEDPALETTE_H_
23 #include "gdcmTagKey.h"
24 #include "gdcmDataEntry.h"
26 // Notepad from Satomi Takeo:
27 // http://blog.goo.ne.jp/satomi_takeo/e/3643e5249b2a9650f9e10ef1c830e8b8
28 // I bet the code was compiled on VS6. Make it compile on other platform:
29 // * typedef are not inherited
30 // * need to explicitely add typename keyword
31 // * Uint8 / Uint16 are neither C nor C++
32 // * replace all dcmtk code with equivalent gdcm code
33 // * Add extra parameter to ReadPaletteInto to save extracted info
35 // MM: Over 50000 DICOM files I only found two that had a Segmented Palette LUT
36 // And both were coming from a ALOKA SSD-4000 station
39 // It compiles fine under gcc 4.1.2 and msvc 7
40 // It doesn't compile on msvc 6, borland and SunOS
51 #if defined(_MSC_VER) && (_MSC_VER < 1310)
54 #define GDCM_TYPENAME typename
57 namespace GDCM_NAME_SPACE
59 // abstract class for segment.
60 template <typename EntryType>
63 typedef std::map<const EntryType*, const Segment*> SegmentMap;
64 virtual bool Expand(const SegmentMap& instances,
65 std::vector<EntryType>& expanded) const = 0;
66 const EntryType* First() const { return _first; }
67 const EntryType* Last() const { return _last; }
70 typename SegmentMap::key_type,
71 typename SegmentMap::mapped_type
73 operator()(const Segment* segment) const
74 { return std::make_pair(segment->First(), segment); }
77 Segment(const EntryType* first, const EntryType* last) {
78 _first = first; _last = last;
80 const EntryType* _first;
81 const EntryType* _last;
84 // discrete segment (opcode = 0)
85 template <typename EntryType>
86 class DiscreteSegment : public Segment<EntryType> {
88 typedef typename Segment<EntryType>::SegmentMap SegmentMap;
89 DiscreteSegment(const EntryType* first)
90 : Segment<EntryType>(first, first+2+*(first+1)) {}
91 virtual bool Expand(const SegmentMap&,
92 std::vector<EntryType>& expanded) const
94 std::copy(this->_first + 2, this->_last, std::back_inserter(expanded));
99 // linear segment (opcode = 1)
100 template <typename EntryType>
101 class LinearSegment : public Segment<EntryType> {
103 typedef typename Segment<EntryType>::SegmentMap SegmentMap;
104 LinearSegment(const EntryType* first)
105 : Segment<EntryType>(first, first+3) {}
106 virtual bool Expand(const SegmentMap&,
107 std::vector<EntryType>& expanded) const
109 if ( expanded.empty() ) {
110 // linear segment can't be the first segment.
113 EntryType length = *(this->_first + 1);
114 EntryType y0 = expanded.back();
115 EntryType y1 = *(this->_first + 2);
116 double y01 = y1 - y0;
117 for ( EntryType i = 0; i <length; ++i ) {
119 = static_cast<double>(y0)
120 + (static_cast<double>(i)/static_cast<double>(length)) * y01;
121 EntryType value_int = static_cast<EntryType>(value_float + 0.5);
122 expanded.push_back(value_int);
128 // indirect segment (opcode = 2)
129 template <typename EntryType>
130 class IndirectSegment : public Segment<EntryType> {
132 typedef typename Segment<EntryType>::SegmentMap SegmentMap;
133 IndirectSegment(const EntryType* first)
134 : Segment<EntryType>(first, first+2+4/sizeof(EntryType)) {}
135 virtual bool Expand(const SegmentMap& instances,
136 std::vector<EntryType>& expanded) const
138 if ( instances.empty() ) {
139 // some other segments are required as references.
142 const EntryType* first_segment = instances.begin()->first;
143 const unsigned short* pOffset
144 = reinterpret_cast<const unsigned short*>(this->_first + 2);
145 unsigned long offsetBytes
146 = (*pOffset) | (static_cast<unsigned long>(*(pOffset + 1)) << 16);
147 const EntryType* copied_part_head
148 = first_segment + offsetBytes / sizeof(EntryType);
149 GDCM_TYPENAME SegmentMap::const_iterator ppHeadSeg = instances.find(copied_part_head);
150 if ( ppHeadSeg == instances.end() ) {
151 // referred segment not found
154 EntryType nNumCopies = *(this->_first + 1);
155 GDCM_TYPENAME SegmentMap::const_iterator ppSeg = ppHeadSeg;
156 while ( std::distance(ppHeadSeg, ppSeg) < nNumCopies ) {
157 assert( ppSeg != instances.end() );
158 ppSeg->second->Expand(instances, expanded);
165 template <typename EntryType>
166 void ExpandPalette(const EntryType* raw_values, uint32_t length,
167 std::vector<EntryType>& palette)
169 typedef std::deque<Segment<EntryType>*> SegmentList;
170 SegmentList segments;
171 const EntryType* raw_seg = raw_values;
172 while ( (std::distance(raw_values, raw_seg) * sizeof(EntryType)) <length ) {
173 Segment<EntryType>* segment = NULL;
174 if ( *raw_seg == 0 ) {
175 segment = new DiscreteSegment<EntryType>(raw_seg);
176 } else if ( *raw_seg == 1 ) {
177 segment = new LinearSegment<EntryType>(raw_seg);
178 } else if ( *raw_seg == 2 ) {
179 segment = new IndirectSegment<EntryType>(raw_seg);
182 segments.push_back(segment);
183 raw_seg = segment->Last();
189 GDCM_TYPENAME Segment<EntryType>::SegmentMap instances;
190 std::transform(segments.begin(), segments.end(),
191 std::inserter(instances, instances.end()), GDCM_TYPENAME Segment<EntryType>::ToMap());
192 GDCM_TYPENAME SegmentList::iterator ppSeg = segments.begin();
193 GDCM_TYPENAME SegmentList::iterator endOfSegments = segments.end();
194 for ( ; ppSeg != endOfSegments; ++ppSeg ) {
195 (*ppSeg)->Expand(instances, palette);
197 ppSeg = segments.begin();
198 for ( ; ppSeg != endOfSegments; ++ppSeg ) {
203 void ReadPaletteInto(GDCM_NAME_SPACE::File* pds, const GDCM_NAME_SPACE::TagKey& descriptor,
204 const GDCM_NAME_SPACE::TagKey& segment, uint8_t* lut)
206 unsigned int desc_values[3] = {0,0,0};
207 unsigned long count = 0;
208 //if ( pds->findAndGetUint16Array(descriptor, desc_values, &count).good() )
209 std::string desc_values_str = pds->GetEntryString(descriptor.GetGroup(), descriptor.GetElement() );
210 count = sscanf( desc_values_str.c_str(), "%u\\%u\\%u", desc_values, desc_values+1, desc_values+2 );
212 assert( count == 3 );
213 unsigned int num_entries = desc_values[0];
214 if ( num_entries == 0 ) {
215 num_entries = 0x10000;
217 unsigned int min_pixel_value = desc_values[1];
218 assert( min_pixel_value == 0 ); // FIXME
219 unsigned int entry_size = desc_values[2];
220 assert( entry_size == 8 || entry_size == 16 );
221 //DcmElement* pe = NULL;
222 GDCM_NAME_SPACE::DataEntry* pe = NULL;
224 pe = pds->GetDataEntry(segment.GetGroup(), segment.GetElement() );
226 //if ( pds->findAndGetElement(segment, pe).good() )
227 unsigned long length = pe->GetLength();
228 if ( entry_size == 8 )
230 uint8_t* segment_values = NULL;
231 //if ( pe->getUint8Array(segment_values).good() )
232 segment_values = (uint8_t*)pe->GetBinArea();
234 std::vector<uint8_t> palette;
235 palette.reserve(num_entries);
236 ExpandPalette(segment_values, length, palette);
237 memcpy(lut, &palette[0], palette.size() );
240 else if ( entry_size == 16 )
242 uint16_t* segment_values = NULL;
243 segment_values = (uint16_t*)pe->GetBinArea();
245 //if ( pe->getUint16Array(segment_values).good() )
246 std::vector<uint16_t> palette;
247 palette.reserve(num_entries);
248 ExpandPalette(segment_values, length, palette);
249 memcpy(lut, &palette[0], palette.size()*2 );
256 } // end namespace gdcm
259 // do not pollute namespace: