1 /*=========================================================================
4 Module: $RCSfile: gdcmSegmentedPalette.h,v $
6 Date: $Date: 2007/10/26 09:00:31 $
7 Version: $Revision: 1.13 $
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 // Long stody short: Sun compiler only provide the second interface of std::distance, since the implemenation
60 // is so trivial, I'd rather redo it myself.
62 // http://www.sgi.com/tech/stl/distance.html#2
63 // The second version of distance was the one defined in the original STL, and the first version is the one defined in the draft C++ standard; the definition was changed because the older interface was clumsy and error-prone. The older interface required the use of a temporary variable, and it has semantics that are somewhat nonintuitive: it increments n by the distance from first to last, rather than storing that distance in n
64 template<typename InputIterator>
66 mydistance(InputIterator first, InputIterator last)
77 // abstract class for segment.
78 template <typename EntryType>
81 typedef std::map<const EntryType*, const Segment*> SegmentMap;
82 virtual bool Expand(const SegmentMap& instances,
83 std::vector<EntryType>& expanded) const = 0;
84 const EntryType* First() const { return _first; }
85 const EntryType* Last() const { return _last; }
87 typename SegmentMap::value_type
88 operator()(const Segment* segment) const
89 { return std::make_pair(segment->First(), segment); }
92 Segment(const EntryType* first, const EntryType* last) {
93 _first = first; _last = last;
95 const EntryType* _first;
96 const EntryType* _last;
99 // discrete segment (opcode = 0)
100 template <typename EntryType>
101 class DiscreteSegment : public Segment<EntryType> {
103 typedef typename Segment<EntryType>::SegmentMap SegmentMap;
104 DiscreteSegment(const EntryType* first)
105 : Segment<EntryType>(first, first+2+*(first+1)) {}
106 virtual bool Expand(const SegmentMap&,
107 std::vector<EntryType>& expanded) const
109 std::copy(this->_first + 2, this->_last, std::back_inserter(expanded));
114 // linear segment (opcode = 1)
115 template <typename EntryType>
116 class LinearSegment : public Segment<EntryType> {
118 typedef typename Segment<EntryType>::SegmentMap SegmentMap;
119 LinearSegment(const EntryType* first)
120 : Segment<EntryType>(first, first+3) {}
121 virtual bool Expand(const SegmentMap&,
122 std::vector<EntryType>& expanded) const
124 if ( expanded.empty() ) {
125 // linear segment can't be the first segment.
128 EntryType length = *(this->_first + 1);
129 EntryType y0 = expanded.back();
130 EntryType y1 = *(this->_first + 2);
131 double y01 = y1 - y0;
132 for ( EntryType i = 0; i <length; ++i ) {
134 = static_cast<double>(y0)
135 + (static_cast<double>(i)/static_cast<double>(length)) * y01;
136 EntryType value_int = static_cast<EntryType>(value_float + 0.5);
137 expanded.push_back(value_int);
143 // indirect segment (opcode = 2)
144 template <typename EntryType>
145 class IndirectSegment : public Segment<EntryType> {
147 typedef typename Segment<EntryType>::SegmentMap SegmentMap;
148 IndirectSegment(const EntryType* first)
149 : Segment<EntryType>(first, first+2+4/sizeof(EntryType)) {}
150 virtual bool Expand(const SegmentMap& instances,
151 std::vector<EntryType>& expanded) const
153 if ( instances.empty() ) {
154 // some other segments are required as references.
157 const EntryType* first_segment = instances.begin()->first;
158 const unsigned short* pOffset
159 = reinterpret_cast<const unsigned short*>(this->_first + 2);
160 unsigned long offsetBytes
161 = (*pOffset) | (static_cast<unsigned long>(*(pOffset + 1)) << 16);
162 const EntryType* copied_part_head
163 = first_segment + offsetBytes / sizeof(EntryType);
164 GDCM_TYPENAME SegmentMap::const_iterator ppHeadSeg = instances.find(copied_part_head);
165 if ( ppHeadSeg == instances.end() ) {
166 // referred segment not found
169 EntryType nNumCopies = *(this->_first + 1);
170 GDCM_TYPENAME SegmentMap::const_iterator ppSeg = ppHeadSeg;
171 while ( mydistance(ppHeadSeg, ppSeg) < nNumCopies ) {
172 // assert( mydistance(ppHeadSeg, ppSeg) == std::distance(ppHeadSeg, ppSeg) );
173 assert( ppSeg != instances.end() );
174 ppSeg->second->Expand(instances, expanded);
181 template <typename EntryType>
182 void ExpandPalette(const EntryType* raw_values, uint32_t length,
183 std::vector<EntryType>& palette)
185 typedef std::deque<Segment<EntryType>*> SegmentList;
186 SegmentList segments;
187 const EntryType* raw_seg = raw_values;
188 while ( (mydistance(raw_values, raw_seg) * sizeof(EntryType)) < length ) {
189 // assert( mydistance(raw_values, raw_seg) == std::distance(raw_values, raw_seg) );
190 Segment<EntryType>* segment = NULL;
191 if ( *raw_seg == 0 ) {
192 segment = new DiscreteSegment<EntryType>(raw_seg);
193 } else if ( *raw_seg == 1 ) {
194 segment = new LinearSegment<EntryType>(raw_seg);
195 } else if ( *raw_seg == 2 ) {
196 segment = new IndirectSegment<EntryType>(raw_seg);
199 segments.push_back(segment);
200 raw_seg = segment->Last();
207 GDCM_TYPENAME Segment<EntryType>::SegmentMap instances;
208 std::transform(segments.begin(), segments.end(),
209 std::inserter(instances, instances.end()), GDCM_TYPENAME Segment<EntryType>::ToMap());
210 GDCM_TYPENAME SegmentList::iterator ppSeg = segments.begin();
211 GDCM_TYPENAME SegmentList::iterator endOfSegments = segments.end();
212 for ( ; ppSeg != endOfSegments; ++ppSeg ) {
213 (*ppSeg)->Expand(instances, palette);
215 ppSeg = segments.begin();
216 for ( ; ppSeg != endOfSegments; ++ppSeg ) {
221 void ReadPaletteInto(GDCM_NAME_SPACE::File* pds, const GDCM_NAME_SPACE::TagKey& descriptor,
222 const GDCM_NAME_SPACE::TagKey& segment, uint8_t* lut)
224 unsigned int desc_values[3] = {0,0,0};
225 unsigned long count = 0;
226 //if ( pds->findAndGetUint16Array(descriptor, desc_values, &count).good() )
227 std::string desc_values_str = pds->GetEntryString(descriptor.GetGroup(), descriptor.GetElement() );
228 count = sscanf( desc_values_str.c_str(), "%u\\%u\\%u", desc_values, desc_values+1, desc_values+2 );
230 assert( count == 3 );
231 unsigned int num_entries = desc_values[0];
232 if ( num_entries == 0 ) {
233 num_entries = 0x10000;
235 unsigned int min_pixel_value = desc_values[1];
236 assert( min_pixel_value == 0 ); // FIXME
237 unsigned int entry_size = desc_values[2];
238 assert( entry_size == 8 || entry_size == 16 );
239 //DcmElement* pe = NULL;
240 GDCM_NAME_SPACE::DataEntry* pe = NULL;
242 pe = pds->GetDataEntry(segment.GetGroup(), segment.GetElement() );
244 //if ( pds->findAndGetElement(segment, pe).good() )
245 unsigned long length = pe->GetLength();
246 if ( entry_size == 8 )
248 uint8_t* segment_values = NULL;
249 //if ( pe->getUint8Array(segment_values).good() )
250 segment_values = (uint8_t*)pe->GetBinArea();
252 std::vector<uint8_t> palette;
253 palette.reserve(num_entries);
254 ExpandPalette(segment_values, length, palette);
255 memcpy(lut, &palette[0], palette.size() );
258 else if ( entry_size == 16 )
260 uint16_t* segment_values = NULL;
261 segment_values = (uint16_t*)pe->GetBinArea();
263 //if ( pe->getUint16Array(segment_values).good() )
264 std::vector<uint16_t> palette;
265 palette.reserve(num_entries);
266 ExpandPalette(segment_values, length, palette);
267 memcpy(lut, &palette[0], palette.size()*2 );
274 } // end namespace gdcm
277 // do not pollute namespace: