Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.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 | a865c7992a87 |
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 "DicomStructureSet.h" | |
34 | |
16 | 35 #include "../../Resources/Orthanc/Core/Logging.h" |
36 #include "../../Resources/Orthanc/Core/OrthancException.h" | |
32 | 37 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h" |
0 | 38 #include "../Messaging/MessagingToolbox.h" |
39 | |
40 #include <stdio.h> | |
41 #include <boost/lexical_cast.hpp> | |
42 | |
43 namespace OrthancStone | |
44 { | |
32 | 45 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
46 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
47 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
48 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
49 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
50 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
51 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
52 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
53 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
54 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
55 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 56 |
57 | |
58 static uint8_t ConvertColor(double v) | |
59 { | |
60 if (v < 0) | |
61 { | |
62 return 0; | |
63 } | |
64 else if (v >= 255) | |
65 { | |
66 return 255; | |
67 } | |
68 else | |
69 { | |
70 return static_cast<uint8_t>(v); | |
71 } | |
72 } | |
73 | |
74 | |
75 SliceGeometry DicomStructureSet::ExtractSliceGeometry(double& sliceThickness, | |
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
76 OrthancPlugins::IOrthancConnection& orthanc, |
32 | 77 const OrthancPlugins::IDicomDataset& tags, |
78 size_t contourIndex, | |
79 size_t sliceIndex) | |
0 | 80 { |
32 | 81 using namespace OrthancPlugins; |
0 | 82 |
32 | 83 size_t size; |
84 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
85 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
86 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || | |
87 size != 1) | |
0 | 88 { |
89 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
90 } | |
91 | |
32 | 92 DicomDatasetReader reader(tags); |
93 std::string parentUid = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
94 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
95 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, | |
96 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); | |
0 | 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 | |
32 | 138 FullOrthancDataset parentTags(orthanc, "/instances/" + tmp[0]["ID"].asString() + "/tags"); |
139 SliceGeometry slice(parentTags); | |
0 | 140 |
32 | 141 Vector v; |
142 if (GeometryToolbox::ParseVector(v, parentTags, DICOM_TAG_SLICE_THICKNESS) && | |
143 v.size() > 0) | |
0 | 144 { |
32 | 145 sliceThickness = v[0]; |
146 } | |
147 else | |
148 { | |
149 sliceThickness = 1; // 1 mm by default | |
0 | 150 } |
151 | |
152 if (isFirst) | |
153 { | |
154 normal_ = slice.GetNormal(); | |
155 } | |
156 else if (!GeometryToolbox::IsParallel(normal_, slice.GetNormal())) | |
157 { | |
158 LOG(ERROR) << "Incompatible orientation of slices in this RT-STRUCT"; | |
159 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
160 } | |
161 | |
162 return slice; | |
163 } | |
164 | |
165 | |
166 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const | |
167 { | |
168 if (index >= structures_.size()) | |
169 { | |
170 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
171 } | |
172 | |
173 return structures_[index]; | |
174 } | |
175 | |
176 | |
177 bool DicomStructureSet::IsPolygonOnSlice(const Polygon& polygon, | |
178 const SliceGeometry& geometry) const | |
179 { | |
180 double d = boost::numeric::ublas::inner_prod(geometry.GetOrigin(), normal_); | |
181 | |
182 return (GeometryToolbox::IsNear(d, polygon.projectionAlongNormal_, polygon.sliceThickness_ / 2.0) && | |
183 !polygon.points_.empty()); | |
184 } | |
185 | |
186 | |
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
187 DicomStructureSet::DicomStructureSet(OrthancPlugins::IOrthancConnection& orthanc, |
0 | 188 const std::string& instanceId) |
189 { | |
32 | 190 using namespace OrthancPlugins; |
0 | 191 |
32 | 192 FullOrthancDataset tags(orthanc, "/instances/" + instanceId + "/tags"); |
193 DicomDatasetReader reader(tags); | |
194 | |
195 size_t count, tmp; | |
196 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
197 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
198 tmp != count || | |
199 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
200 tmp != count) | |
0 | 201 { |
202 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
203 } | |
204 | |
32 | 205 structures_.resize(count); |
206 for (size_t i = 0; i < count; i++) | |
207 { | |
208 structures_[i].interpretation_ = reader.GetStringValue(DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, | |
209 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), | |
210 "No interpretation"); | |
0 | 211 |
32 | 212 structures_[i].name_ = reader.GetStringValue(DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
213 DICOM_TAG_ROI_NAME), | |
214 "No interpretation"); | |
0 | 215 |
216 Vector color; | |
32 | 217 if (GeometryToolbox::ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
218 DICOM_TAG_ROI_DISPLAY_COLOR)) && | |
219 color.size() == 3) | |
0 | 220 { |
32 | 221 structures_[i].red_ = ConvertColor(color[0]); |
222 structures_[i].green_ = ConvertColor(color[1]); | |
223 structures_[i].blue_ = ConvertColor(color[2]); | |
224 } | |
225 else | |
226 { | |
227 structures_[i].red_ = 255; | |
228 structures_[i].green_ = 0; | |
229 structures_[i].blue_ = 0; | |
0 | 230 } |
231 | |
32 | 232 size_t countSlices; |
233 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
234 DICOM_TAG_CONTOUR_SEQUENCE))) | |
235 { | |
236 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
237 } | |
0 | 238 |
239 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
240 << "\" with interpretation \"" << structures_[i].interpretation_ | |
32 | 241 << "\" containing " << countSlices << " slices (color: " |
0 | 242 << static_cast<int>(structures_[i].red_) << "," |
243 << static_cast<int>(structures_[i].green_) << "," | |
244 << static_cast<int>(structures_[i].blue_) << ")"; | |
245 | |
32 | 246 for (size_t j = 0; j < countSlices; j++) |
0 | 247 { |
32 | 248 unsigned int countPoints; |
0 | 249 |
32 | 250 if (!reader.GetUnsignedIntegerValue(countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
251 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
252 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) | |
253 { | |
254 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
255 } | |
256 | |
257 LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; | |
0 | 258 |
32 | 259 std::string type = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
260 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
261 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); | |
262 if (type != "CLOSED_PLANAR") | |
0 | 263 { |
32 | 264 LOG(ERROR) << "Cannot handle contour with geometry type: " << type; |
0 | 265 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
266 } | |
267 | |
32 | 268 // The "CountourData" tag (3006,0050) is too large to be |
269 // returned by the "/instances/{id}/tags" URI: Access it using | |
270 // the raw "/instances/{id}/content/{...}" endpoint | |
0 | 271 std::string slicesData; |
272 orthanc.RestApiGet(slicesData, "/instances/" + instanceId + "/content/3006-0039/" + | |
273 boost::lexical_cast<std::string>(i) + "/3006-0040/" + | |
274 boost::lexical_cast<std::string>(j) + "/3006-0050"); | |
275 | |
276 Vector points; | |
277 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
32 | 278 points.size() != 3 * countPoints) |
0 | 279 { |
280 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
281 } | |
282 | |
283 Polygon polygon; | |
32 | 284 SliceGeometry geometry = ExtractSliceGeometry(polygon.sliceThickness_, orthanc, tags, i, j); |
0 | 285 polygon.projectionAlongNormal_ = geometry.ProjectAlongNormal(geometry.GetOrigin()); |
286 | |
32 | 287 for (size_t k = 0; k < countPoints; k++) |
0 | 288 { |
289 Vector v(3); | |
290 v[0] = points[3 * k]; | |
291 v[1] = points[3 * k + 1]; | |
292 v[2] = points[3 * k + 2]; | |
293 | |
294 if (!GeometryToolbox::IsNear(geometry.ProjectAlongNormal(v), | |
295 polygon.projectionAlongNormal_, | |
296 polygon.sliceThickness_ / 2.0 /* in mm */)) | |
297 { | |
298 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; | |
299 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
300 } | |
301 | |
302 polygon.points_.push_back(v); | |
303 } | |
304 | |
305 structures_[i].polygons_.push_back(polygon); | |
306 } | |
307 } | |
308 | |
309 if (parentSeriesId_.empty() || | |
310 normal_.size() != 3) | |
311 { | |
312 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
313 } | |
314 } | |
315 | |
316 | |
317 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
318 { | |
319 const Structure& structure = GetStructure(index); | |
320 | |
321 Vector center; | |
322 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
323 if (structure.polygons_.empty()) | |
324 { | |
325 return center; | |
326 } | |
327 | |
328 double n = static_cast<double>(structure.polygons_.size()); | |
329 | |
330 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
331 polygon != structure.polygons_.end(); ++polygon) | |
332 { | |
333 if (!polygon->points_.empty()) | |
334 { | |
335 center += polygon->points_.front() / n; | |
336 } | |
337 } | |
338 | |
339 return center; | |
340 } | |
341 | |
342 | |
343 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
344 { | |
345 return GetStructure(index).name_; | |
346 } | |
347 | |
348 | |
349 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
350 { | |
351 return GetStructure(index).interpretation_; | |
352 } | |
353 | |
354 | |
355 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
356 uint8_t& green, | |
357 uint8_t& blue, | |
358 size_t index) const | |
359 { | |
360 const Structure& s = GetStructure(index); | |
361 red = s.red_; | |
362 green = s.green_; | |
363 blue = s.blue_; | |
364 } | |
365 | |
366 | |
367 void DicomStructureSet::Render(CairoContext& context, | |
368 const SliceGeometry& slice) const | |
369 { | |
370 cairo_t* cr = context.GetObject(); | |
371 | |
372 for (Structures::const_iterator structure = structures_.begin(); | |
373 structure != structures_.end(); ++structure) | |
374 { | |
375 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
376 polygon != structure->polygons_.end(); ++polygon) | |
377 { | |
378 if (IsPolygonOnSlice(*polygon, slice)) | |
379 { | |
380 context.SetSourceColor(structure->red_, structure->green_, structure->blue_); | |
381 | |
382 Points::const_iterator p = polygon->points_.begin(); | |
383 | |
384 double x, y; | |
385 slice.ProjectPoint(x, y, *p); | |
386 cairo_move_to(cr, x, y); | |
387 ++p; | |
388 | |
389 while (p != polygon->points_.end()) | |
390 { | |
391 slice.ProjectPoint(x, y, *p); | |
392 cairo_line_to(cr, x, y); | |
393 ++p; | |
394 } | |
395 | |
396 slice.ProjectPoint(x, y, *polygon->points_.begin()); | |
397 cairo_line_to(cr, x, y); | |
398 } | |
399 } | |
400 } | |
401 | |
402 cairo_stroke(cr); | |
403 } | |
404 } |