Mercurial > hg > orthanc-stone
comparison Framework/Loaders/SeriesOrderedFrames.cpp @ 1228:c471a0aa137b broker
adding the next generation of loaders
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 09 Dec 2019 13:58:37 +0100 |
parents | |
children | 0ca50d275b9a |
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1227:a1c0c9c9f9af | 1228:c471a0aa137b |
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1 /** | |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
5 * Copyright (C) 2017-2019 Osimis S.A., Belgium | |
6 * | |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
22 #include "../Toolbox/SlicesSorter.h" | |
23 #include "SeriesOrderedFrames.h" | |
24 | |
25 #include <Core/OrthancException.h> | |
26 | |
27 namespace OrthancStone | |
28 { | |
29 class SeriesOrderedFrames::Instance : public boost::noncopyable | |
30 { | |
31 private: | |
32 std::auto_ptr<Orthanc::DicomMap> dicom_; | |
33 DicomInstanceParameters parameters_; | |
34 | |
35 public: | |
36 Instance(const Orthanc::DicomMap& dicom) : | |
37 dicom_(dicom.Clone()), | |
38 parameters_(dicom) | |
39 { | |
40 } | |
41 | |
42 const Orthanc::DicomMap& GetInstance() const | |
43 { | |
44 return *dicom_; | |
45 } | |
46 | |
47 const DicomInstanceParameters& GetInstanceParameters() const | |
48 { | |
49 return parameters_; | |
50 } | |
51 | |
52 bool Lookup3DGeometry(CoordinateSystem3D& target) const | |
53 { | |
54 try | |
55 { | |
56 std::string imagePositionPatient, imageOrientationPatient; | |
57 if (dicom_->LookupStringValue(imagePositionPatient, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && | |
58 dicom_->LookupStringValue(imageOrientationPatient, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) | |
59 { | |
60 target = CoordinateSystem3D(imagePositionPatient, imageOrientationPatient); | |
61 return true; | |
62 } | |
63 } | |
64 catch (Orthanc::OrthancException&) | |
65 { | |
66 } | |
67 | |
68 return false; | |
69 } | |
70 | |
71 bool LookupIndexInSeries(int& target) const | |
72 { | |
73 std::string value; | |
74 | |
75 if (dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_INSTANCE_NUMBER, false) || | |
76 dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_IMAGE_INDEX, false)) | |
77 { | |
78 try | |
79 { | |
80 target = boost::lexical_cast<int>(value); | |
81 return true; | |
82 } | |
83 catch (boost::bad_lexical_cast&) | |
84 { | |
85 } | |
86 } | |
87 | |
88 return false; | |
89 } | |
90 }; | |
91 | |
92 | |
93 class SeriesOrderedFrames::Frame : public boost::noncopyable | |
94 { | |
95 private: | |
96 const Instance* instance_; | |
97 unsigned int frameIndex_; | |
98 | |
99 public: | |
100 Frame(const Instance& instance, | |
101 unsigned int frameIndex) : | |
102 instance_(&instance), | |
103 frameIndex_(frameIndex) | |
104 { | |
105 if (frameIndex_ >= instance.GetInstanceParameters().GetImageInformation().GetNumberOfFrames()) | |
106 { | |
107 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
108 } | |
109 } | |
110 | |
111 const Orthanc::DicomMap& GetInstance() const | |
112 { | |
113 assert(instance_ != NULL); | |
114 return instance_->GetInstance(); | |
115 } | |
116 | |
117 const DicomInstanceParameters& GetInstanceParameters() const | |
118 { | |
119 assert(instance_ != NULL); | |
120 return instance_->GetInstanceParameters(); | |
121 } | |
122 | |
123 unsigned int GetFrameIndex() const | |
124 { | |
125 return frameIndex_; | |
126 } | |
127 }; | |
128 | |
129 | |
130 class SeriesOrderedFrames::InstanceWithIndexInSeries | |
131 { | |
132 private: | |
133 const Instance* instance_; // Don't use a reference to make "std::sort()" happy | |
134 int index_; | |
135 | |
136 public: | |
137 InstanceWithIndexInSeries(const Instance& instance) : | |
138 instance_(&instance) | |
139 { | |
140 if (!instance_->LookupIndexInSeries(index_)) | |
141 { | |
142 index_ = std::numeric_limits<int>::max(); | |
143 } | |
144 } | |
145 | |
146 const Instance& GetInstance() const | |
147 { | |
148 return *instance_; | |
149 } | |
150 | |
151 int GetIndexInSeries() const | |
152 { | |
153 return index_; | |
154 } | |
155 | |
156 bool operator< (const InstanceWithIndexInSeries& other) const | |
157 { | |
158 return (index_ < other.index_); | |
159 } | |
160 }; | |
161 | |
162 | |
163 void SeriesOrderedFrames::Clear() | |
164 { | |
165 for (size_t i = 0; i < instances_.size(); i++) | |
166 { | |
167 assert(instances_[i] != NULL); | |
168 delete instances_[i]; | |
169 } | |
170 | |
171 for (size_t i = 0; i < orderedFrames_.size(); i++) | |
172 { | |
173 assert(orderedFrames_[i] != NULL); | |
174 delete orderedFrames_[i]; | |
175 } | |
176 | |
177 instances_.clear(); | |
178 orderedFrames_.clear(); | |
179 } | |
180 | |
181 | |
182 bool SeriesOrderedFrames::Sort3DVolume() | |
183 { | |
184 SlicesSorter sorter; | |
185 sorter.Reserve(instances_.size()); | |
186 | |
187 for (size_t i = 0; i < instances_.size(); i++) | |
188 { | |
189 CoordinateSystem3D geometry; | |
190 if (instances_[i]->Lookup3DGeometry(geometry)) | |
191 { | |
192 sorter.AddSlice(geometry, new Orthanc::SingleValueObject<Instance*>(instances_[i])); | |
193 } | |
194 else | |
195 { | |
196 return false; // Not a 3D volume | |
197 } | |
198 } | |
199 | |
200 if (!sorter.Sort() || | |
201 sorter.GetSlicesCount() != instances_.size() || | |
202 !sorter.AreAllSlicesDistinct()) | |
203 { | |
204 return false; | |
205 } | |
206 else | |
207 { | |
208 for (size_t i = 0; i < sorter.GetSlicesCount(); i++) | |
209 { | |
210 assert(sorter.HasSlicePayload(i)); | |
211 | |
212 const Orthanc::SingleValueObject<Instance*>& payload = | |
213 dynamic_cast<const Orthanc::SingleValueObject<Instance*>&>(sorter.GetSlicePayload(i)); | |
214 | |
215 assert(payload.GetValue() != NULL); | |
216 | |
217 for (size_t j = 0; j < payload.GetValue()->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++) | |
218 { | |
219 orderedFrames_.push_back(new Frame(*payload.GetValue(), j)); | |
220 } | |
221 } | |
222 | |
223 isRegular_ = sorter.ComputeSpacingBetweenSlices(spacingBetweenSlices_); | |
224 return true; | |
225 } | |
226 } | |
227 | |
228 | |
229 void SeriesOrderedFrames::SortIndexInSeries() | |
230 { | |
231 std::vector<InstanceWithIndexInSeries> tmp; | |
232 tmp.reserve(instances_.size()); | |
233 | |
234 for (size_t i = 0; i < instances_.size(); i++) | |
235 { | |
236 assert(instances_[i] != NULL); | |
237 tmp.push_back(InstanceWithIndexInSeries(*instances_[i])); | |
238 } | |
239 | |
240 std::sort(tmp.begin(), tmp.end()); | |
241 | |
242 for (size_t i = 0; i < tmp.size(); i++) | |
243 { | |
244 for (size_t j = 0; j < tmp[i].GetInstance().GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++) | |
245 { | |
246 orderedFrames_.push_back(new Frame(tmp[i].GetInstance(), j)); | |
247 } | |
248 } | |
249 } | |
250 | |
251 | |
252 const SeriesOrderedFrames::Frame& SeriesOrderedFrames::GetFrame(size_t seriesIndex) const | |
253 { | |
254 if (seriesIndex >= orderedFrames_.size()) | |
255 { | |
256 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
257 } | |
258 else | |
259 { | |
260 assert(orderedFrames_[seriesIndex] != NULL); | |
261 return *(orderedFrames_[seriesIndex]); | |
262 } | |
263 } | |
264 | |
265 | |
266 SeriesOrderedFrames::SeriesOrderedFrames(LoadedDicomResources& instances) : | |
267 isVolume_(false), | |
268 isRegular_(false), | |
269 spacingBetweenSlices_(0) | |
270 { | |
271 instances_.reserve(instances.GetSize()); | |
272 | |
273 size_t numberOfFrames = 0; | |
274 | |
275 for (size_t i = 0; i < instances.GetSize(); i++) | |
276 { | |
277 try | |
278 { | |
279 std::auto_ptr<Instance> instance(new Instance(instances.GetResource(i))); | |
280 numberOfFrames += instance->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); | |
281 instances_.push_back(instance.release()); | |
282 } | |
283 catch (Orthanc::OrthancException&) | |
284 { | |
285 // The instance has not all the required DICOM tags, skip it | |
286 } | |
287 } | |
288 | |
289 orderedFrames_.reserve(numberOfFrames); | |
290 | |
291 if (Sort3DVolume()) | |
292 { | |
293 isVolume_ = true; | |
294 | |
295 if (isRegular_) | |
296 { | |
297 LOG(INFO) << "Regular 3D volume detected"; | |
298 } | |
299 else | |
300 { | |
301 LOG(INFO) << "Non-regular 3D volume detected"; | |
302 } | |
303 } | |
304 else | |
305 { | |
306 LOG(INFO) << "Series is not a 3D volume, sorting by index"; | |
307 SortIndexInSeries(); | |
308 } | |
309 | |
310 LOG(INFO) << "Number of frames: " << orderedFrames_.size(); | |
311 } | |
312 | |
313 | |
314 unsigned int SeriesOrderedFrames::GetFrameIndex(size_t seriesIndex) const | |
315 { | |
316 return GetFrame(seriesIndex).GetFrameIndex(); | |
317 } | |
318 | |
319 | |
320 const Orthanc::DicomMap& SeriesOrderedFrames::GetInstance(size_t seriesIndex) const | |
321 { | |
322 return GetFrame(seriesIndex).GetInstance(); | |
323 } | |
324 | |
325 | |
326 const DicomInstanceParameters& SeriesOrderedFrames::GetInstanceParameters(size_t seriesIndex) const | |
327 { | |
328 return GetFrame(seriesIndex).GetInstanceParameters(); | |
329 } | |
330 | |
331 | |
332 double SeriesOrderedFrames::GetSpacingBetweenSlices() const | |
333 { | |
334 if (IsRegular3DVolume()) | |
335 { | |
336 return spacingBetweenSlices_; | |
337 } | |
338 else | |
339 { | |
340 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
341 } | |
342 } | |
343 } |