Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 110:53025eecbc95 wasm
renamed SliceGeometry as CoordinateSystem3D
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 14 Jun 2017 15:50:38 +0200 |
parents | 28956ed68280 |
children | 2eca030792aa |
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 | |
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5 * Copyright (C) 2017 Osimis, Belgium |
0 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
47 | 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. | |
0 | 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 | |
47 | 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 | |
0 | 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
19 **/ | |
20 | |
21 | |
22 #include "DicomStructureSet.h" | |
23 | |
16 | 24 #include "../../Resources/Orthanc/Core/Logging.h" |
25 #include "../../Resources/Orthanc/Core/OrthancException.h" | |
32 | 26 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h" |
35 | 27 #include "../Toolbox/MessagingToolbox.h" |
0 | 28 |
29 #include <stdio.h> | |
30 #include <boost/lexical_cast.hpp> | |
31 | |
32 namespace OrthancStone | |
33 { | |
32 | 34 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
35 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
36 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
37 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
38 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
39 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
40 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
41 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
42 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
43 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
44 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 45 |
46 | |
47 static uint8_t ConvertColor(double v) | |
48 { | |
49 if (v < 0) | |
50 { | |
51 return 0; | |
52 } | |
53 else if (v >= 255) | |
54 { | |
55 return 255; | |
56 } | |
57 else | |
58 { | |
59 return static_cast<uint8_t>(v); | |
60 } | |
61 } | |
62 | |
63 | |
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64 CoordinateSystem3D DicomStructureSet::ExtractSliceGeometry(double& sliceThickness, |
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65 OrthancPlugins::IOrthancConnection& orthanc, |
32 | 66 const OrthancPlugins::IDicomDataset& tags, |
67 size_t contourIndex, | |
68 size_t sliceIndex) | |
0 | 69 { |
32 | 70 using namespace OrthancPlugins; |
0 | 71 |
32 | 72 size_t size; |
73 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
74 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
75 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || | |
76 size != 1) | |
0 | 77 { |
78 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
79 } | |
80 | |
32 | 81 DicomDatasetReader reader(tags); |
82 std::string parentUid = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
83 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
84 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, | |
85 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); | |
0 | 86 |
34 | 87 Json::Value parentLookup; |
88 MessagingToolbox::RestApiPost(parentLookup, orthanc, "/tools/lookup", parentUid); | |
0 | 89 |
34 | 90 if (parentLookup.type() != Json::arrayValue || |
91 parentLookup.size() != 1 || | |
92 !parentLookup[0].isMember("Type") || | |
93 !parentLookup[0].isMember("Path") || | |
94 parentLookup[0]["Type"].type() != Json::stringValue || | |
95 parentLookup[0]["ID"].type() != Json::stringValue || | |
96 parentLookup[0]["Type"].asString() != "Instance") | |
0 | 97 { |
98 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
99 } | |
100 | |
101 Json::Value parentInstance; | |
34 | 102 MessagingToolbox::RestApiGet(parentInstance, orthanc, "/instances/" + parentLookup[0]["ID"].asString()); |
0 | 103 |
104 if (parentInstance.type() != Json::objectValue || | |
105 !parentInstance.isMember("ParentSeries") || | |
106 parentInstance["ParentSeries"].type() != Json::stringValue) | |
107 { | |
108 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); | |
109 } | |
110 | |
111 std::string parentSeriesId = parentInstance["ParentSeries"].asString(); | |
112 bool isFirst = parentSeriesId_.empty(); | |
113 | |
114 if (isFirst) | |
115 { | |
116 parentSeriesId_ = parentSeriesId; | |
117 } | |
118 else if (parentSeriesId_ != parentSeriesId) | |
119 { | |
120 LOG(ERROR) << "This RT-STRUCT refers to several different series"; | |
121 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
122 } | |
123 | |
34 | 124 FullOrthancDataset parentTags(orthanc, "/instances/" + parentLookup[0]["ID"].asString() + "/tags"); |
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125 CoordinateSystem3D slice(parentTags); |
0 | 126 |
32 | 127 Vector v; |
128 if (GeometryToolbox::ParseVector(v, parentTags, DICOM_TAG_SLICE_THICKNESS) && | |
129 v.size() > 0) | |
0 | 130 { |
32 | 131 sliceThickness = v[0]; |
132 } | |
133 else | |
134 { | |
135 sliceThickness = 1; // 1 mm by default | |
0 | 136 } |
137 | |
138 if (isFirst) | |
139 { | |
140 normal_ = slice.GetNormal(); | |
141 } | |
142 else if (!GeometryToolbox::IsParallel(normal_, slice.GetNormal())) | |
143 { | |
144 LOG(ERROR) << "Incompatible orientation of slices in this RT-STRUCT"; | |
145 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
146 } | |
147 | |
148 return slice; | |
149 } | |
150 | |
151 | |
152 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const | |
153 { | |
154 if (index >= structures_.size()) | |
155 { | |
156 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
157 } | |
158 | |
159 return structures_[index]; | |
160 } | |
161 | |
162 | |
163 bool DicomStructureSet::IsPolygonOnSlice(const Polygon& polygon, | |
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164 const CoordinateSystem3D& geometry) const |
0 | 165 { |
166 double d = boost::numeric::ublas::inner_prod(geometry.GetOrigin(), normal_); | |
167 | |
168 return (GeometryToolbox::IsNear(d, polygon.projectionAlongNormal_, polygon.sliceThickness_ / 2.0) && | |
169 !polygon.points_.empty()); | |
170 } | |
171 | |
172 | |
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173 DicomStructureSet::DicomStructureSet(OrthancPlugins::IOrthancConnection& orthanc, |
0 | 174 const std::string& instanceId) |
175 { | |
32 | 176 using namespace OrthancPlugins; |
0 | 177 |
32 | 178 FullOrthancDataset tags(orthanc, "/instances/" + instanceId + "/tags"); |
179 DicomDatasetReader reader(tags); | |
180 | |
181 size_t count, tmp; | |
182 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
183 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
184 tmp != count || | |
185 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
186 tmp != count) | |
0 | 187 { |
188 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
189 } | |
190 | |
32 | 191 structures_.resize(count); |
192 for (size_t i = 0; i < count; i++) | |
193 { | |
194 structures_[i].interpretation_ = reader.GetStringValue(DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, | |
195 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), | |
196 "No interpretation"); | |
0 | 197 |
32 | 198 structures_[i].name_ = reader.GetStringValue(DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
199 DICOM_TAG_ROI_NAME), | |
200 "No interpretation"); | |
0 | 201 |
202 Vector color; | |
32 | 203 if (GeometryToolbox::ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
204 DICOM_TAG_ROI_DISPLAY_COLOR)) && | |
205 color.size() == 3) | |
0 | 206 { |
32 | 207 structures_[i].red_ = ConvertColor(color[0]); |
208 structures_[i].green_ = ConvertColor(color[1]); | |
209 structures_[i].blue_ = ConvertColor(color[2]); | |
210 } | |
211 else | |
212 { | |
213 structures_[i].red_ = 255; | |
214 structures_[i].green_ = 0; | |
215 structures_[i].blue_ = 0; | |
0 | 216 } |
217 | |
32 | 218 size_t countSlices; |
219 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
220 DICOM_TAG_CONTOUR_SEQUENCE))) | |
221 { | |
222 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
223 } | |
0 | 224 |
225 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
226 << "\" with interpretation \"" << structures_[i].interpretation_ | |
32 | 227 << "\" containing " << countSlices << " slices (color: " |
0 | 228 << static_cast<int>(structures_[i].red_) << "," |
229 << static_cast<int>(structures_[i].green_) << "," | |
230 << static_cast<int>(structures_[i].blue_) << ")"; | |
231 | |
32 | 232 for (size_t j = 0; j < countSlices; j++) |
0 | 233 { |
32 | 234 unsigned int countPoints; |
0 | 235 |
32 | 236 if (!reader.GetUnsignedIntegerValue(countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
237 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
238 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) | |
239 { | |
240 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
241 } | |
242 | |
243 LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; | |
0 | 244 |
32 | 245 std::string type = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
246 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
247 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); | |
248 if (type != "CLOSED_PLANAR") | |
0 | 249 { |
32 | 250 LOG(ERROR) << "Cannot handle contour with geometry type: " << type; |
0 | 251 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
252 } | |
253 | |
32 | 254 // The "CountourData" tag (3006,0050) is too large to be |
255 // returned by the "/instances/{id}/tags" URI: Access it using | |
256 // the raw "/instances/{id}/content/{...}" endpoint | |
0 | 257 std::string slicesData; |
258 orthanc.RestApiGet(slicesData, "/instances/" + instanceId + "/content/3006-0039/" + | |
259 boost::lexical_cast<std::string>(i) + "/3006-0040/" + | |
260 boost::lexical_cast<std::string>(j) + "/3006-0050"); | |
261 | |
262 Vector points; | |
263 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
32 | 264 points.size() != 3 * countPoints) |
0 | 265 { |
266 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
267 } | |
268 | |
269 Polygon polygon; | |
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270 CoordinateSystem3D geometry = ExtractSliceGeometry(polygon.sliceThickness_, orthanc, tags, i, j); |
0 | 271 polygon.projectionAlongNormal_ = geometry.ProjectAlongNormal(geometry.GetOrigin()); |
272 | |
32 | 273 for (size_t k = 0; k < countPoints; k++) |
0 | 274 { |
275 Vector v(3); | |
276 v[0] = points[3 * k]; | |
277 v[1] = points[3 * k + 1]; | |
278 v[2] = points[3 * k + 2]; | |
279 | |
280 if (!GeometryToolbox::IsNear(geometry.ProjectAlongNormal(v), | |
281 polygon.projectionAlongNormal_, | |
282 polygon.sliceThickness_ / 2.0 /* in mm */)) | |
283 { | |
284 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; | |
285 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
286 } | |
287 | |
288 polygon.points_.push_back(v); | |
289 } | |
290 | |
291 structures_[i].polygons_.push_back(polygon); | |
292 } | |
293 } | |
294 | |
295 if (parentSeriesId_.empty() || | |
296 normal_.size() != 3) | |
297 { | |
298 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
299 } | |
300 } | |
301 | |
302 | |
303 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
304 { | |
305 const Structure& structure = GetStructure(index); | |
306 | |
307 Vector center; | |
308 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
309 if (structure.polygons_.empty()) | |
310 { | |
311 return center; | |
312 } | |
313 | |
314 double n = static_cast<double>(structure.polygons_.size()); | |
315 | |
316 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
317 polygon != structure.polygons_.end(); ++polygon) | |
318 { | |
319 if (!polygon->points_.empty()) | |
320 { | |
321 center += polygon->points_.front() / n; | |
322 } | |
323 } | |
324 | |
325 return center; | |
326 } | |
327 | |
328 | |
329 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
330 { | |
331 return GetStructure(index).name_; | |
332 } | |
333 | |
334 | |
335 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
336 { | |
337 return GetStructure(index).interpretation_; | |
338 } | |
339 | |
340 | |
341 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
342 uint8_t& green, | |
343 uint8_t& blue, | |
344 size_t index) const | |
345 { | |
346 const Structure& s = GetStructure(index); | |
347 red = s.red_; | |
348 green = s.green_; | |
349 blue = s.blue_; | |
350 } | |
351 | |
352 | |
353 void DicomStructureSet::Render(CairoContext& context, | |
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354 const CoordinateSystem3D& slice) const |
0 | 355 { |
356 cairo_t* cr = context.GetObject(); | |
357 | |
358 for (Structures::const_iterator structure = structures_.begin(); | |
359 structure != structures_.end(); ++structure) | |
360 { | |
361 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
362 polygon != structure->polygons_.end(); ++polygon) | |
363 { | |
364 if (IsPolygonOnSlice(*polygon, slice)) | |
365 { | |
366 context.SetSourceColor(structure->red_, structure->green_, structure->blue_); | |
367 | |
368 Points::const_iterator p = polygon->points_.begin(); | |
369 | |
370 double x, y; | |
371 slice.ProjectPoint(x, y, *p); | |
372 cairo_move_to(cr, x, y); | |
373 ++p; | |
374 | |
375 while (p != polygon->points_.end()) | |
376 { | |
377 slice.ProjectPoint(x, y, *p); | |
378 cairo_line_to(cr, x, y); | |
379 ++p; | |
380 } | |
381 | |
382 slice.ProjectPoint(x, y, *polygon->points_.begin()); | |
383 cairo_line_to(cr, x, y); | |
384 } | |
385 } | |
386 } | |
387 | |
388 cairo_stroke(cr); | |
389 } | |
390 } |