Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/OrthancSeriesLoader.cpp @ 32:517c46f527cd
sync
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 19 Dec 2016 11:00:23 +0100 |
parents | 9aace933cb64 |
children | 6465fbd23bce |
rev | line source |
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0 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
5 * | |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU General Public License as | |
8 * published by the Free Software Foundation, either version 3 of the | |
9 * License, or (at your option) any later version. | |
10 * | |
11 * In addition, as a special exception, the copyright holders of this | |
12 * program give permission to link the code of its release with the | |
13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
14 * that use the same license as the "OpenSSL" library), and distribute | |
15 * the linked executables. You must obey the GNU General Public License | |
16 * in all respects for all of the code used other than "OpenSSL". If you | |
17 * modify file(s) with this exception, you may extend this exception to | |
18 * your version of the file(s), but you are not obligated to do so. If | |
19 * you do not wish to do so, delete this exception statement from your | |
20 * version. If you delete this exception statement from all source files | |
21 * in the program, then also delete it here. | |
22 * | |
23 * This program is distributed in the hope that it will be useful, but | |
24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
26 * General Public License for more details. | |
27 * | |
28 * You should have received a copy of the GNU General Public License | |
29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
30 **/ | |
31 | |
32 | |
33 #include "OrthancSeriesLoader.h" | |
34 | |
35 #include "../Messaging/MessagingToolbox.h" | |
16 | 36 #include "../../Resources/Orthanc/Core/Images/Image.h" |
37 #include "../../Resources/Orthanc/Core/Images/ImageProcessing.h" | |
38 #include "../../Resources/Orthanc/Core/Logging.h" | |
39 #include "../../Resources/Orthanc/Core/OrthancException.h" | |
32 | 40 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h" |
0 | 41 #include "DicomFrameConverter.h" |
42 | |
43 namespace OrthancStone | |
44 { | |
45 class OrthancSeriesLoader::Slice : public boost::noncopyable | |
46 { | |
47 private: | |
48 std::string instanceId_; | |
49 SliceGeometry geometry_; | |
50 double projectionAlongNormal_; | |
51 | |
52 public: | |
53 Slice(const std::string& instanceId, | |
54 const std::string& imagePositionPatient, | |
55 const std::string& imageOrientationPatient) : | |
56 instanceId_(instanceId), | |
57 geometry_(imagePositionPatient, imageOrientationPatient) | |
58 { | |
59 } | |
60 | |
61 const std::string GetInstanceId() const | |
62 { | |
63 return instanceId_; | |
64 } | |
65 | |
66 const SliceGeometry& GetGeometry() const | |
67 { | |
68 return geometry_; | |
69 } | |
70 | |
71 void SetNormal(const Vector& normal) | |
72 { | |
73 projectionAlongNormal_ = boost::numeric::ublas::inner_prod(geometry_.GetOrigin(), normal); | |
74 } | |
75 | |
76 double GetProjectionAlongNormal() const | |
77 { | |
78 return projectionAlongNormal_; | |
79 } | |
80 }; | |
81 | |
82 | |
83 class OrthancSeriesLoader::SetOfSlices : public boost::noncopyable | |
84 { | |
85 private: | |
86 std::vector<Slice*> slices_; | |
87 | |
88 struct Comparator | |
89 { | |
90 bool operator() (const Slice* const a, | |
91 const Slice* const b) const | |
92 { | |
93 return a->GetProjectionAlongNormal() < b->GetProjectionAlongNormal(); | |
94 } | |
95 }; | |
96 | |
97 public: | |
98 ~SetOfSlices() | |
99 { | |
100 for (size_t i = 0; i < slices_.size(); i++) | |
101 { | |
102 assert(slices_[i] != NULL); | |
103 delete slices_[i]; | |
104 } | |
105 } | |
106 | |
107 void Reserve(size_t size) | |
108 { | |
109 slices_.reserve(size); | |
110 } | |
111 | |
112 void AddSlice(const std::string& instanceId, | |
113 const std::string& imagePositionPatient, | |
114 const std::string& imageOrientationPatient) | |
115 { | |
116 slices_.push_back(new Slice(instanceId, imagePositionPatient, imageOrientationPatient)); | |
117 } | |
118 | |
119 size_t GetSliceCount() const | |
120 { | |
121 return slices_.size(); | |
122 } | |
123 | |
124 const Slice& GetSlice(size_t index) const | |
125 { | |
126 assert(slices_[index] != NULL); | |
127 return *slices_[index]; | |
128 } | |
129 | |
130 void Sort(const Vector& normal) | |
131 { | |
132 for (size_t i = 0; i < slices_.size(); i++) | |
133 { | |
134 slices_[i]->SetNormal(normal); | |
135 } | |
136 | |
137 Comparator comparator; | |
138 std::sort(slices_.begin(), slices_.end(), comparator); | |
139 } | |
140 | |
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
141 void LoadSeriesFast(OrthancPlugins::IOrthancConnection& orthanc, |
0 | 142 const std::string& series) |
143 { | |
144 // Retrieve the orientation of this series | |
145 Json::Value info; | |
146 MessagingToolbox::RestApiGet(info, orthanc, "/series/" + series); | |
147 | |
148 if (info.type() != Json::objectValue || | |
149 !info.isMember("MainDicomTags") || | |
150 info["MainDicomTags"].type() != Json::objectValue || | |
151 !info["MainDicomTags"].isMember("ImageOrientationPatient") || | |
152 info["MainDicomTags"]["ImageOrientationPatient"].type() != Json::stringValue) | |
153 { | |
154 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
155 } | |
156 | |
157 std::string imageOrientationPatient = info["MainDicomTags"]["ImageOrientationPatient"].asString(); | |
158 | |
159 | |
160 // Retrieve the Orthanc ID of all the instances of this series | |
161 Json::Value instances; | |
162 MessagingToolbox::RestApiGet(instances, orthanc, "/series/" + series + "/instances"); | |
163 | |
164 if (instances.type() != Json::arrayValue) | |
165 { | |
166 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
167 } | |
168 | |
169 if (instances.size() == 0) | |
170 { | |
171 LOG(ERROR) << "This series is empty"; | |
172 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
173 } | |
174 | |
175 | |
176 // Retrieve the DICOM tags of all the instances | |
177 std::vector<std::string> instancesId; | |
178 | |
179 instancesId.resize(instances.size()); | |
180 Reserve(instances.size()); | |
181 | |
182 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
183 { | |
184 if (instances[i].type() != Json::objectValue || | |
185 !instances[i].isMember("ID") || | |
186 !instances[i].isMember("MainDicomTags") || | |
187 instances[i]["ID"].type() != Json::stringValue || | |
188 instances[i]["MainDicomTags"].type() != Json::objectValue || | |
189 !instances[i]["MainDicomTags"].isMember("ImagePositionPatient") || | |
190 instances[i]["MainDicomTags"]["ImagePositionPatient"].type() != Json::stringValue) | |
191 { | |
192 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
193 } | |
194 else | |
195 { | |
196 instancesId[i] = instances[i]["ID"].asString(); | |
197 AddSlice(instancesId[i], | |
198 instances[i]["MainDicomTags"]["ImagePositionPatient"].asString(), | |
199 imageOrientationPatient); | |
200 } | |
201 } | |
202 | |
203 assert(GetSliceCount() == instances.size()); | |
204 } | |
205 | |
206 | |
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
207 void LoadSeriesSafe(OrthancPlugins::IOrthancConnection& orthanc, |
0 | 208 const std::string& seriesId) |
209 { | |
210 Json::Value series; | |
211 MessagingToolbox::RestApiGet(series, orthanc, "/series/" + seriesId + "/instances-tags?simplify"); | |
212 | |
213 if (series.type() != Json::objectValue) | |
214 { | |
215 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
216 } | |
217 | |
218 if (series.size() == 0) | |
219 { | |
220 LOG(ERROR) << "This series is empty"; | |
221 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
222 } | |
223 | |
224 Json::Value::Members instances = series.getMemberNames(); | |
225 | |
226 Reserve(instances.size()); | |
227 | |
228 for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) | |
229 { | |
230 const Json::Value& tags = series[instances[i]]; | |
231 | |
232 if (tags.type() != Json::objectValue || | |
233 !tags.isMember("ImagePositionPatient") || | |
234 !tags.isMember("ImageOrientationPatient") || | |
235 tags["ImagePositionPatient"].type() != Json::stringValue || | |
236 tags["ImageOrientationPatient"].type() != Json::stringValue) | |
237 { | |
238 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
239 } | |
240 else | |
241 { | |
242 AddSlice(instances[i], | |
243 tags["ImagePositionPatient"].asString(), | |
244 tags["ImageOrientationPatient"].asString()); | |
245 } | |
246 } | |
247 | |
248 assert(GetSliceCount() == instances.size()); | |
249 } | |
250 | |
251 | |
252 void SelectNormal(Vector& normal) const | |
253 { | |
254 std::vector<Vector> normalCandidates; | |
255 std::vector<unsigned int> normalCount; | |
256 | |
257 bool found = false; | |
258 | |
259 for (size_t i = 0; !found && i < GetSliceCount(); i++) | |
260 { | |
261 const Vector& normal = GetSlice(i).GetGeometry().GetNormal(); | |
262 | |
263 bool add = true; | |
264 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*) | |
265 { | |
266 if (GeometryToolbox::IsParallel(normal, normalCandidates[j])) | |
267 { | |
268 normalCount[j] += 1; | |
269 add = false; | |
270 } | |
271 } | |
272 | |
273 if (add) | |
274 { | |
275 if (normalCount.size() > 2) | |
276 { | |
277 // To get linear-time complexity in (*). This heuristics | |
278 // allows the series to have one single frame that is | |
279 // not parallel to the others (such a frame could be a | |
280 // generated preview) | |
281 found = false; | |
282 } | |
283 else | |
284 { | |
285 normalCandidates.push_back(normal); | |
286 normalCount.push_back(1); | |
287 } | |
288 } | |
289 } | |
290 | |
291 for (size_t i = 0; !found && i < normalCandidates.size(); i++) | |
292 { | |
293 unsigned int count = normalCount[i]; | |
294 if (count == GetSliceCount() || | |
295 count + 1 == GetSliceCount()) | |
296 { | |
297 normal = normalCandidates[i]; | |
298 found = true; | |
299 } | |
300 } | |
301 | |
302 if (!found) | |
303 { | |
304 LOG(ERROR) << "Cannot select a normal that is shared by most of the slices of this series"; | |
305 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
306 } | |
307 } | |
308 | |
309 | |
310 void FilterNormal(const Vector& normal) | |
311 { | |
312 size_t pos = 0; | |
313 | |
314 for (size_t i = 0; i < slices_.size(); i++) | |
315 { | |
316 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal())) | |
317 { | |
318 // This slice is compatible with the selected normal | |
319 slices_[pos] = slices_[i]; | |
320 pos += 1; | |
321 } | |
322 else | |
323 { | |
324 delete slices_[i]; | |
325 slices_[i] = NULL; | |
326 } | |
327 } | |
328 | |
329 slices_.resize(pos); | |
330 } | |
331 }; | |
332 | |
333 | |
334 | |
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
335 OrthancSeriesLoader::OrthancSeriesLoader(OrthancPlugins::IOrthancConnection& orthanc, |
0 | 336 const std::string& series) : |
337 orthanc_(orthanc), | |
338 slices_(new SetOfSlices) | |
339 { | |
340 /** | |
341 * The function "LoadSeriesFast()" might now behave properly if | |
342 * some slice has some outsider value for its normal, which | |
343 * happens sometimes on reprojected series (e.g. coronal and | |
344 * sagittal of Delphine). Don't use it. | |
345 **/ | |
346 | |
347 slices_->LoadSeriesSafe(orthanc, series); | |
348 | |
349 Vector normal; | |
350 slices_->SelectNormal(normal); | |
351 slices_->FilterNormal(normal); | |
352 slices_->Sort(normal); | |
353 | |
354 if (slices_->GetSliceCount() == 0) // Sanity check | |
355 { | |
356 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
357 } | |
358 | |
359 for (size_t i = 0; i < slices_->GetSliceCount(); i++) | |
360 { | |
361 assert(GeometryToolbox::IsParallel(normal, slices_->GetSlice(i).GetGeometry().GetNormal())); | |
362 geometry_.AddSlice(slices_->GetSlice(i).GetGeometry()); | |
363 } | |
364 | |
32 | 365 std::string uri = "/instances/" + slices_->GetSlice(0).GetInstanceId() + "/tags"; |
366 | |
367 OrthancPlugins::FullOrthancDataset dataset(orthanc_, uri); | |
368 OrthancPlugins::DicomDatasetReader reader(dataset); | |
369 | |
370 if (!reader.GetUnsignedIntegerValue(width_, OrthancPlugins::DICOM_TAG_COLUMNS) || | |
371 !reader.GetUnsignedIntegerValue(height_, OrthancPlugins::DICOM_TAG_ROWS)) | |
0 | 372 { |
373 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
374 } | |
375 | |
376 DicomFrameConverter converter; | |
32 | 377 converter.ReadParameters(dataset); |
0 | 378 format_ = converter.GetExpectedPixelFormat(); |
379 } | |
380 | |
381 | |
32 | 382 OrthancPlugins::IDicomDataset* OrthancSeriesLoader::DownloadDicom(size_t index) |
0 | 383 { |
32 | 384 std::string uri = "/instances/" + slices_->GetSlice(index).GetInstanceId() + "/tags"; |
0 | 385 |
32 | 386 std::auto_ptr<OrthancPlugins::IDicomDataset> dataset(new OrthancPlugins::FullOrthancDataset(orthanc_, uri)); |
387 OrthancPlugins::DicomDatasetReader reader(*dataset); | |
388 | |
389 unsigned int frames; | |
390 if (reader.GetUnsignedIntegerValue(frames, OrthancPlugins::DICOM_TAG_NUMBER_OF_FRAMES) && | |
391 frames != 1) | |
0 | 392 { |
393 LOG(ERROR) << "One instance in this series has more than 1 frame"; | |
394 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
395 } | |
396 | |
397 return dataset.release(); | |
398 } | |
399 | |
400 | |
401 void OrthancSeriesLoader::CheckFrame(const Orthanc::ImageAccessor& frame) const | |
402 { | |
403 if (frame.GetFormat() != format_ || | |
404 frame.GetWidth() != width_ || | |
405 frame.GetHeight() != height_) | |
406 { | |
407 LOG(ERROR) << "The parameters of this series vary accross its slices"; | |
408 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
409 } | |
410 } | |
411 | |
412 | |
413 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadFrame(size_t index) | |
414 { | |
415 const Slice& slice = slices_->GetSlice(index); | |
416 | |
417 std::auto_ptr<Orthanc::ImageAccessor> frame | |
418 (MessagingToolbox::DecodeFrame(orthanc_, slice.GetInstanceId(), 0, format_)); | |
419 | |
420 if (frame.get() != NULL) | |
421 { | |
422 CheckFrame(*frame); | |
423 } | |
424 | |
425 return frame.release(); | |
426 } | |
427 | |
428 | |
429 Orthanc::ImageAccessor* OrthancSeriesLoader::DownloadJpegFrame(size_t index, | |
430 unsigned int quality) | |
431 { | |
432 const Slice& slice = slices_->GetSlice(index); | |
433 | |
434 std::auto_ptr<Orthanc::ImageAccessor> frame | |
435 (MessagingToolbox::DecodeJpegFrame(orthanc_, slice.GetInstanceId(), 0, quality, format_)); | |
436 | |
437 if (frame.get() != NULL) | |
438 { | |
439 CheckFrame(*frame); | |
440 } | |
441 | |
442 return frame.release(); | |
443 } | |
444 | |
445 | |
446 bool OrthancSeriesLoader::IsJpegAvailable() | |
447 { | |
448 return MessagingToolbox::HasWebViewerInstalled(orthanc_); | |
449 } | |
450 } |