Mercurial > hg > orthanc-stone
comparison Framework/Toolbox/DicomStructureSet.cpp @ 0:351ab0da0150
initial commit
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 14 Oct 2016 15:34:11 +0200 |
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children | ff1e935768e7 |
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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 * | |
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 "DicomStructureSet.h" | |
34 | |
35 #include "../Orthanc/Core/Logging.h" | |
36 #include "../Orthanc/Core/OrthancException.h" | |
37 #include "../Messaging/MessagingToolbox.h" | |
38 | |
39 #include <stdio.h> | |
40 #include <boost/lexical_cast.hpp> | |
41 | |
42 namespace OrthancStone | |
43 { | |
44 static const Json::Value& GetSequence(const Json::Value& instance, | |
45 uint16_t group, | |
46 uint16_t element) | |
47 { | |
48 char buf[16]; | |
49 sprintf(buf, "%04x,%04x", group, element); | |
50 | |
51 if (instance.type() != Json::objectValue || | |
52 !instance.isMember(buf) || | |
53 instance[buf].type() != Json::objectValue || | |
54 !instance[buf].isMember("Type") || | |
55 !instance[buf].isMember("Value") || | |
56 instance[buf]["Type"].type() != Json::stringValue || | |
57 instance[buf]["Value"].type() != Json::arrayValue || | |
58 instance[buf]["Type"].asString() != "Sequence") | |
59 { | |
60 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
61 } | |
62 | |
63 return instance[buf]["Value"]; | |
64 } | |
65 | |
66 | |
67 static uint8_t ConvertColor(double v) | |
68 { | |
69 if (v < 0) | |
70 { | |
71 return 0; | |
72 } | |
73 else if (v >= 255) | |
74 { | |
75 return 255; | |
76 } | |
77 else | |
78 { | |
79 return static_cast<uint8_t>(v); | |
80 } | |
81 } | |
82 | |
83 | |
84 SliceGeometry DicomStructureSet::ExtractSliceGeometry(double& sliceThickness, | |
85 IOrthancConnection& orthanc, | |
86 const Json::Value& contour) | |
87 { | |
88 const Json::Value& sequence = GetSequence(contour, 0x3006, 0x0016); | |
89 | |
90 if (sequence.size() != 1) | |
91 { | |
92 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
93 } | |
94 | |
95 DicomDataset contourImageSequence(sequence[0]); | |
96 std::string parentUid = contourImageSequence.GetStringValue(std::make_pair(0x0008, 0x1155)); | |
97 | |
98 std::string post; | |
99 orthanc.RestApiPost(post, "/tools/lookup", parentUid); | |
100 | |
101 Json::Value tmp; | |
102 MessagingToolbox::ParseJson(tmp, post); | |
103 | |
104 if (tmp.type() != Json::arrayValue || | |
105 tmp.size() != 1 || | |
106 !tmp[0].isMember("Type") || | |
107 !tmp[0].isMember("Path") || | |
108 tmp[0]["Type"].type() != Json::stringValue || | |
109 tmp[0]["ID"].type() != Json::stringValue || | |
110 tmp[0]["Type"].asString() != "Instance") | |
111 { | |
112 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
113 } | |
114 | |
115 Json::Value parentInstance; | |
116 MessagingToolbox::RestApiGet(parentInstance, orthanc, "/instances/" + tmp[0]["ID"].asString()); | |
117 | |
118 if (parentInstance.type() != Json::objectValue || | |
119 !parentInstance.isMember("ParentSeries") || | |
120 parentInstance["ParentSeries"].type() != Json::stringValue) | |
121 { | |
122 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); | |
123 } | |
124 | |
125 std::string parentSeriesId = parentInstance["ParentSeries"].asString(); | |
126 bool isFirst = parentSeriesId_.empty(); | |
127 | |
128 if (isFirst) | |
129 { | |
130 parentSeriesId_ = parentSeriesId; | |
131 } | |
132 else if (parentSeriesId_ != parentSeriesId) | |
133 { | |
134 LOG(ERROR) << "This RT-STRUCT refers to several different series"; | |
135 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
136 } | |
137 | |
138 Json::Value parentTags; | |
139 MessagingToolbox::RestApiGet(parentTags, orthanc, "/instances/" + tmp[0]["ID"].asString() + "/tags?simplify"); | |
140 | |
141 if (parentTags.type() != Json::objectValue || | |
142 !parentTags.isMember("ImageOrientationPatient") || | |
143 !parentTags.isMember("ImagePositionPatient") || | |
144 parentTags["ImageOrientationPatient"].type() != Json::stringValue || | |
145 parentTags["ImagePositionPatient"].type() != Json::stringValue) | |
146 { | |
147 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); | |
148 } | |
149 | |
150 SliceGeometry slice(parentTags["ImagePositionPatient"].asString(), | |
151 parentTags["ImageOrientationPatient"].asString()); | |
152 | |
153 sliceThickness = 1; // 1 mm by default | |
154 | |
155 if (parentTags.isMember("SliceThickness") && | |
156 parentTags["SliceThickness"].type() == Json::stringValue) | |
157 { | |
158 Vector tmp; | |
159 GeometryToolbox::ParseVector(tmp, parentTags["SliceThickness"].asString()); | |
160 if (tmp.size() > 0) | |
161 { | |
162 sliceThickness = tmp[0]; | |
163 } | |
164 } | |
165 | |
166 if (isFirst) | |
167 { | |
168 normal_ = slice.GetNormal(); | |
169 } | |
170 else if (!GeometryToolbox::IsParallel(normal_, slice.GetNormal())) | |
171 { | |
172 LOG(ERROR) << "Incompatible orientation of slices in this RT-STRUCT"; | |
173 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
174 } | |
175 | |
176 return slice; | |
177 } | |
178 | |
179 | |
180 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const | |
181 { | |
182 if (index >= structures_.size()) | |
183 { | |
184 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
185 } | |
186 | |
187 return structures_[index]; | |
188 } | |
189 | |
190 | |
191 bool DicomStructureSet::IsPolygonOnSlice(const Polygon& polygon, | |
192 const SliceGeometry& geometry) const | |
193 { | |
194 double d = boost::numeric::ublas::inner_prod(geometry.GetOrigin(), normal_); | |
195 | |
196 return (GeometryToolbox::IsNear(d, polygon.projectionAlongNormal_, polygon.sliceThickness_ / 2.0) && | |
197 !polygon.points_.empty()); | |
198 } | |
199 | |
200 | |
201 DicomStructureSet::DicomStructureSet(IOrthancConnection& orthanc, | |
202 const std::string& instanceId) | |
203 { | |
204 Json::Value instance; | |
205 MessagingToolbox::RestApiGet(instance, orthanc, "/instances/" + instanceId + "/tags"); | |
206 | |
207 Json::Value rtRoiObservationSequence = GetSequence(instance, 0x3006, 0x0080); | |
208 Json::Value roiContourSequence = GetSequence(instance, 0x3006, 0x0039); | |
209 Json::Value structureSetRoiSequence = GetSequence(instance, 0x3006, 0x0020); | |
210 | |
211 Json::Value::ArrayIndex count = rtRoiObservationSequence.size(); | |
212 if (count != roiContourSequence.size() || | |
213 count != structureSetRoiSequence.size()) | |
214 { | |
215 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
216 } | |
217 | |
218 structures_.resize(count); | |
219 for (Json::Value::ArrayIndex i = 0; i < count; i++) | |
220 { | |
221 DicomDataset observation(rtRoiObservationSequence[i]); | |
222 DicomDataset roi(structureSetRoiSequence[i]); | |
223 DicomDataset content(roiContourSequence[i]); | |
224 | |
225 structures_[i].interpretation_ = observation.GetStringValue(std::make_pair(0x3006, 0x00a4), "No interpretation"); | |
226 structures_[i].name_ = roi.GetStringValue(std::make_pair(0x3006, 0x0026), "No name"); | |
227 structures_[i].red_ = 255; | |
228 structures_[i].green_ = 0; | |
229 structures_[i].blue_ = 0; | |
230 | |
231 DicomDataset::Tag tag(0x3006, 0x002a); | |
232 | |
233 Vector color; | |
234 if (content.HasTag(tag)) | |
235 { | |
236 content.GetVectorValue(color, tag); | |
237 if (color.size() == 3) | |
238 { | |
239 structures_[i].red_ = ConvertColor(color[0]); | |
240 structures_[i].green_ = ConvertColor(color[1]); | |
241 structures_[i].blue_ = ConvertColor(color[2]); | |
242 } | |
243 } | |
244 | |
245 const Json::Value& slices = GetSequence(roiContourSequence[i], 0x3006, 0x0040); | |
246 | |
247 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
248 << "\" with interpretation \"" << structures_[i].interpretation_ | |
249 << "\" containing " << slices.size() << " slices (color: " | |
250 << static_cast<int>(structures_[i].red_) << "," | |
251 << static_cast<int>(structures_[i].green_) << "," | |
252 << static_cast<int>(structures_[i].blue_) << ")"; | |
253 | |
254 for (Json::Value::ArrayIndex j = 0; j < slices.size(); j++) | |
255 { | |
256 DicomDataset slice(slices[j]); | |
257 | |
258 unsigned int npoints = slice.GetUnsignedIntegerValue(std::make_pair(0x3006, 0x0046)); | |
259 LOG(INFO) << "Parsing slice containing " << npoints << " vertices"; | |
260 | |
261 if (slice.GetStringValue(std::make_pair(0x3006, 0x0042)) != "CLOSED_PLANAR") | |
262 { | |
263 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
264 } | |
265 | |
266 std::string slicesData; | |
267 orthanc.RestApiGet(slicesData, "/instances/" + instanceId + "/content/3006-0039/" + | |
268 boost::lexical_cast<std::string>(i) + "/3006-0040/" + | |
269 boost::lexical_cast<std::string>(j) + "/3006-0050"); | |
270 | |
271 Vector points; | |
272 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
273 points.size() != 3 * npoints) | |
274 { | |
275 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
276 } | |
277 | |
278 Polygon polygon; | |
279 SliceGeometry geometry = ExtractSliceGeometry(polygon.sliceThickness_, orthanc, slices[j]); | |
280 polygon.projectionAlongNormal_ = geometry.ProjectAlongNormal(geometry.GetOrigin()); | |
281 | |
282 for (size_t k = 0; k < npoints; k++) | |
283 { | |
284 Vector v(3); | |
285 v[0] = points[3 * k]; | |
286 v[1] = points[3 * k + 1]; | |
287 v[2] = points[3 * k + 2]; | |
288 | |
289 if (!GeometryToolbox::IsNear(geometry.ProjectAlongNormal(v), | |
290 polygon.projectionAlongNormal_, | |
291 polygon.sliceThickness_ / 2.0 /* in mm */)) | |
292 { | |
293 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; | |
294 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
295 } | |
296 | |
297 polygon.points_.push_back(v); | |
298 } | |
299 | |
300 structures_[i].polygons_.push_back(polygon); | |
301 } | |
302 } | |
303 | |
304 if (parentSeriesId_.empty() || | |
305 normal_.size() != 3) | |
306 { | |
307 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
308 } | |
309 } | |
310 | |
311 | |
312 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
313 { | |
314 const Structure& structure = GetStructure(index); | |
315 | |
316 Vector center; | |
317 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
318 if (structure.polygons_.empty()) | |
319 { | |
320 return center; | |
321 } | |
322 | |
323 double n = static_cast<double>(structure.polygons_.size()); | |
324 | |
325 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
326 polygon != structure.polygons_.end(); ++polygon) | |
327 { | |
328 if (!polygon->points_.empty()) | |
329 { | |
330 center += polygon->points_.front() / n; | |
331 } | |
332 } | |
333 | |
334 return center; | |
335 } | |
336 | |
337 | |
338 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
339 { | |
340 return GetStructure(index).name_; | |
341 } | |
342 | |
343 | |
344 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
345 { | |
346 return GetStructure(index).interpretation_; | |
347 } | |
348 | |
349 | |
350 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
351 uint8_t& green, | |
352 uint8_t& blue, | |
353 size_t index) const | |
354 { | |
355 const Structure& s = GetStructure(index); | |
356 red = s.red_; | |
357 green = s.green_; | |
358 blue = s.blue_; | |
359 } | |
360 | |
361 | |
362 void DicomStructureSet::Render(CairoContext& context, | |
363 const SliceGeometry& slice) const | |
364 { | |
365 cairo_t* cr = context.GetObject(); | |
366 | |
367 for (Structures::const_iterator structure = structures_.begin(); | |
368 structure != structures_.end(); ++structure) | |
369 { | |
370 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
371 polygon != structure->polygons_.end(); ++polygon) | |
372 { | |
373 if (IsPolygonOnSlice(*polygon, slice)) | |
374 { | |
375 context.SetSourceColor(structure->red_, structure->green_, structure->blue_); | |
376 | |
377 Points::const_iterator p = polygon->points_.begin(); | |
378 | |
379 double x, y; | |
380 slice.ProjectPoint(x, y, *p); | |
381 cairo_move_to(cr, x, y); | |
382 ++p; | |
383 | |
384 while (p != polygon->points_.end()) | |
385 { | |
386 slice.ProjectPoint(x, y, *p); | |
387 cairo_line_to(cr, x, y); | |
388 ++p; | |
389 } | |
390 | |
391 slice.ProjectPoint(x, y, *polygon->points_.begin()); | |
392 cairo_line_to(cr, x, y); | |
393 } | |
394 } | |
395 } | |
396 | |
397 cairo_stroke(cr); | |
398 } | |
399 } |