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comparison Framework/Toolbox/DicomStructureSet2.cpp @ 998:38b6bb0bdd72

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added a new set of classes that correctly handle non-convex polygons (not used yet because of limitations in coordinates computing): DicomStructure2, DicomStructureSet2, DicomStructurePolygon2, DicomStructureSetSlicer2. Too many shortcuts have been taken when computing the actual position.
author Benjamin Golinvaux <bgo@osimis.io>
date Fri, 20 Sep 2019 11:58:00 +0200
parents 1f74bc3459ba
children 4f28d9459e31
comparison
equal deleted inserted replaced
995:9893fa8cd7a6 998:38b6bb0bdd72
16 * 16 *
17 * You should have received a copy of the GNU Affero General Public License 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/>. 18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
19 **/ 19 **/
20 20
21
22 #include "DicomStructureSet2.h" 21 #include "DicomStructureSet2.h"
23 22
24 #include "../Toolbox/GeometryToolbox.h" 23 #include "../Toolbox/LinearAlgebra.h"
24 #include "../StoneException.h"
25 25
26 #include <Core/Logging.h> 26 #include <Core/Logging.h>
27 #include <Core/OrthancException.h> 27 #include <Core/OrthancException.h>
28 #include <Core/Toolbox.h> 28 #include <Core/Toolbox.h>
29 #include <Core/DicomFormat/DicomTag.h>
30
29 #include <Plugins/Samples/Common/FullOrthancDataset.h> 31 #include <Plugins/Samples/Common/FullOrthancDataset.h>
30 #include <Plugins/Samples/Common/DicomDatasetReader.h> 32 #include <Plugins/Samples/Common/DicomDatasetReader.h>
31
32 #include <limits>
33 #include <stdio.h>
34 #include <boost/geometry.hpp>
35 #include <boost/geometry/geometries/point_xy.hpp>
36 #include <boost/geometry/geometries/polygon.hpp>
37 #include <boost/geometry/multi/geometries/multi_polygon.hpp>
38
39 typedef boost::geometry::model::d2::point_xy<double> BoostPoint;
40 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon;
41 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon;
42
43
44 static void Union(BoostMultiPolygon& output,
45 std::vector<BoostPolygon>& input)
46 {
47 for (size_t i = 0; i < input.size(); i++)
48 {
49 boost::geometry::correct(input[i]);
50 }
51
52 if (input.size() == 0)
53 {
54 output.clear();
55 }
56 else if (input.size() == 1)
57 {
58 output.resize(1);
59 output[0] = input[0];
60 }
61 else
62 {
63 boost::geometry::union_(input[0], input[1], output);
64
65 for (size_t i = 0; i < input.size(); i++)
66 {
67 BoostMultiPolygon tmp;
68 boost::geometry::union_(output, input[i], tmp);
69 output = tmp;
70 }
71 }
72 }
73
74
75 static BoostPolygon CreateRectangle(float x1, float y1,
76 float x2, float y2)
77 {
78 BoostPolygon r;
79 boost::geometry::append(r, BoostPoint(x1, y1));
80 boost::geometry::append(r, BoostPoint(x1, y2));
81 boost::geometry::append(r, BoostPoint(x2, y2));
82 boost::geometry::append(r, BoostPoint(x2, y1));
83 return r;
84 }
85
86
87 33
88 namespace OrthancStone 34 namespace OrthancStone
89 { 35 {
90 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); 36 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042);
91 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); 37 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016);
98 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); 44 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026);
99 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); 45 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4);
100 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); 46 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080);
101 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); 47 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020);
102 48
103 49 static inline uint8_t ConvertAndClipToByte(double v)
104 static uint8_t ConvertColor(double v)
105 { 50 {
106 if (v < 0) 51 if (v < 0)
107 { 52 {
108 return 0; 53 return 0;
109 } 54 }
115 { 60 {
116 return static_cast<uint8_t>(v); 61 return static_cast<uint8_t>(v);
117 } 62 }
118 } 63 }
119 64
120 65 static bool ReadDicomToVector(Vector& target,
121 static bool ParseVector(Vector& target, 66 const OrthancPlugins::IDicomDataset& dataset,
122 const OrthancPlugins::IDicomDataset& dataset, 67 const OrthancPlugins::DicomPath& tag)
123 const OrthancPlugins::DicomPath& tag)
124 { 68 {
125 std::string value; 69 std::string value;
126 return (dataset.GetStringValue(value, tag) && 70 return (dataset.GetStringValue(value, tag) &&
127 LinearAlgebra::ParseVector(target, value)); 71 LinearAlgebra::ParseVector(target, value));
128 } 72 }
129 73
130 void DicomStructureSet2::Polygon::CheckPointIsOnSlice(const Vector& v) const 74 std::ostream& operator<<(std::ostream& s, const OrthancPlugins::DicomPath& dicomPath)
131 { 75 {
132 if (hasSlice_) 76 std::stringstream tmp;
133 { 77 for (size_t i = 0; i < dicomPath.GetPrefixLength(); ++i)
134 double magnitude = 78 {
135 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); 79 OrthancPlugins::DicomTag tag = dicomPath.GetPrefixTag(i);
136 if(!LinearAlgebra::IsNear(
137 magnitude,
138 projectionAlongNormal_,
139 sliceThickness_ / 2.0 /* in mm */ ))
140 {
141 LOG(ERROR) << "This RT-STRUCT contains a point that is off the "
142 << "slice of its instance | "
143 << "magnitude = " << magnitude << " | "
144 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | "
145 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0);
146
147 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
148 }
149 }
150 }
151
152 bool DicomStructureSet2::Polygon::IsPointOnSliceIfAny(const Vector& v) const
153 {
154 if (hasSlice_)
155 {
156 double magnitude =
157 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal());
158 bool onSlice = LinearAlgebra::IsNear(
159 magnitude,
160 projectionAlongNormal_,
161 sliceThickness_ / 2.0 /* in mm */);
162 if (!onSlice)
163 {
164 LOG(WARNING) << "This RT-STRUCT contains a point that is off the "
165 << "slice of its instance | "
166 << "magnitude = " << magnitude << " | "
167 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | "
168 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0);
169 }
170 return onSlice;
171 }
172 else
173 {
174 return false;
175 }
176 }
177
178 void DicomStructureSet2::Polygon::AddPoint(const Vector& v)
179 {
180 #if 1
181 // BGO 2019-09-03
182 if (IsPointOnSliceIfAny(v))
183 {
184 points_.push_back(v);
185 }
186 #else
187 CheckPoint(v);
188 points_.push_back(v);
189 #endif
190 }
191
192
193 bool DicomStructureSet2::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices)
194 {
195 if (hasSlice_)
196 {
197 return true;
198 }
199 else
200 {
201 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_);
202 80
203 if (it == slices.end()) 81 // We use this other object to be able to use GetMainTagsName
204 { 82 // and Format
205 return false; 83 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
206 } 84 size_t index = dicomPath.GetPrefixIndex(i);
207 else 85 tmp << tag2.GetMainTagsName() << " (" << tag2.Format() << ") [" << index << "] / ";
208 { 86 }
209 const CoordinateSystem3D& geometry = it->second.geometry_; 87 const OrthancPlugins::DicomTag& tag = dicomPath.GetFinalTag();
210 88 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
211 hasSlice_ = true; 89 tmp << tag2.GetMainTagsName() << " (" << tag2.Format() << ")";
212 geometry_ = geometry; 90 s << tmp.str();
213 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); 91 return s;
214 sliceThickness_ = it->second.thickness_; 92 }
215 93
216 extent_.Reset(); 94
217 95 void DicomStructureSet2::SetContents(const OrthancPlugins::FullOrthancDataset& tags)
218 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it) 96 {
219 { 97 FillStructuresFromDataset(tags);
220 if (IsPointOnSliceIfAny(*it)) 98 ComputeDependentProperties();
221 { 99 }
222 double x, y; 100
223 geometry.ProjectPoint(x, y, *it); 101 void DicomStructureSet2::ComputeDependentProperties()
224 extent_.AddPoint(x, y); 102 {
225 } 103 for (size_t i = 0; i < structures_.size(); ++i)
226 } 104 {
227 return true; 105 structures_[i].ComputeDependentProperties();
228 } 106 }
229 } 107 }
230 } 108
231 109 void DicomStructureSet2::FillStructuresFromDataset(const OrthancPlugins::FullOrthancDataset& tags)
232 bool DicomStructureSet2::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const
233 {
234 bool isOpposite = false;
235
236 if (points_.empty() ||
237 !hasSlice_ ||
238 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal()))
239 {
240 return false;
241 }
242
243 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal());
244
245 return (LinearAlgebra::IsNear(d, projectionAlongNormal_,
246 sliceThickness_ / 2.0));
247 }
248
249 bool DicomStructureSet2::Polygon::Project(double& x1,
250 double& y1,
251 double& x2,
252 double& y2,
253 const CoordinateSystem3D& slice) const
254 {
255 // TODO: optimize this method using a sweep-line algorithm for polygons
256
257 if (!hasSlice_ ||
258 points_.size() <= 1)
259 {
260 return false;
261 }
262
263 double x, y;
264 geometry_.ProjectPoint(x, y, slice.GetOrigin());
265
266 bool isOpposite;
267 if (GeometryToolbox::IsParallelOrOpposite
268 (isOpposite, slice.GetNormal(), geometry_.GetAxisY()))
269 {
270 if (y < extent_.GetY1() ||
271 y > extent_.GetY2())
272 {
273 // The polygon does not intersect the input slice
274 return false;
275 }
276
277 bool isFirst = true;
278 double xmin = std::numeric_limits<double>::infinity();
279 double xmax = -std::numeric_limits<double>::infinity();
280
281 double prevX, prevY;
282 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]);
283
284 for (size_t i = 0; i < points_.size(); i++)
285 {
286 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py
287 double curX, curY;
288 geometry_.ProjectPoint(curX, curY, points_[i]);
289
290 if ((prevY < y && curY > y) ||
291 (prevY > y && curY < y))
292 {
293 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY);
294 xmin = std::min(xmin, p);
295 xmax = std::max(xmax, p);
296 isFirst = false;
297 }
298
299 prevX = curX;
300 prevY = curY;
301 }
302
303 if (isFirst)
304 {
305 return false;
306 }
307 else
308 {
309 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) +
310 sliceThickness_ / 2.0 * geometry_.GetNormal());
311 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) -
312 sliceThickness_ / 2.0 * geometry_.GetNormal());
313
314 slice.ProjectPoint(x1, y1, p1);
315 slice.ProjectPoint(x2, y2, p2);
316 return true;
317 }
318 }
319 else if (GeometryToolbox::IsParallelOrOpposite
320 (isOpposite, slice.GetNormal(), geometry_.GetAxisX()))
321 {
322 if (x < extent_.GetX1() ||
323 x > extent_.GetX2())
324 {
325 return false;
326 }
327
328 bool isFirst = true;
329 double ymin = std::numeric_limits<double>::infinity();
330 double ymax = -std::numeric_limits<double>::infinity();
331
332 double prevX, prevY;
333 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]);
334
335 for (size_t i = 0; i < points_.size(); i++)
336 {
337 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py
338 double curX, curY;
339 geometry_.ProjectPoint(curX, curY, points_[i]);
340
341 if ((prevX < x && curX > x) ||
342 (prevX > x && curX < x))
343 {
344 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX);
345 ymin = std::min(ymin, p);
346 ymax = std::max(ymax, p);
347 isFirst = false;
348 }
349
350 prevX = curX;
351 prevY = curY;
352 }
353
354 if (isFirst)
355 {
356 return false;
357 }
358 else
359 {
360 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) +
361 sliceThickness_ / 2.0 * geometry_.GetNormal());
362 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) -
363 sliceThickness_ / 2.0 * geometry_.GetNormal());
364
365 slice.ProjectPoint(x1, y1, p1);
366 slice.ProjectPoint(x2, y2, p2);
367
368 // TODO WHY THIS???
369 y1 = -y1;
370 y2 = -y2;
371
372 return true;
373 }
374 }
375 else
376 {
377 // Should not happen
378 return false;
379 }
380 }
381
382
383 const DicomStructureSet2::Structure& DicomStructureSet2::GetStructure(size_t index) const
384 {
385 if (index >= structures_.size())
386 {
387 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
388 }
389
390 return structures_[index];
391 }
392
393
394 DicomStructureSet2::Structure& DicomStructureSet2::GetStructure(size_t index)
395 {
396 if (index >= structures_.size())
397 {
398 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
399 }
400
401 return structures_[index];
402 }
403
404 DicomStructureSet2::DicomStructureSet2(const OrthancPlugins::FullOrthancDataset& tags)
405 { 110 {
406 OrthancPlugins::DicomDatasetReader reader(tags); 111 OrthancPlugins::DicomDatasetReader reader(tags);
407 112
408 size_t count, tmp; 113 // a few sanity checks
114 size_t count = 0, tmp = 0;
115
116 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080);
117 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
118 // DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE (0x3006, 0x0020);
409 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || 119 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) ||
410 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || 120 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) ||
411 tmp != count || 121 tmp != count ||
412 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || 122 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) ||
413 tmp != count) 123 tmp != count)
414 { 124 {
415 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); 125 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
416 } 126 }
417 127
128 // let's now parse the structures stored in the dicom file
129 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080)
130 // DICOM_TAG_RT_ROI_INTERPRETED_TYPE (0x3006, 0x00a4)
131 // DICOM_TAG_ROI_DISPLAY_COLOR (0x3006, 0x002a)
132 // DICOM_TAG_ROI_NAME (0x3006, 0x0026)
418 structures_.resize(count); 133 structures_.resize(count);
419 for (size_t i = 0; i < count; i++) 134 for (size_t i = 0; i < count; i++)
420 { 135 {
136 // (0x3006, 0x0080)[i]/(0x3006, 0x00a4)
421 structures_[i].interpretation_ = reader.GetStringValue 137 structures_[i].interpretation_ = reader.GetStringValue
422 (OrthancPlugins::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, 138 (OrthancPlugins::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
423 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), 139 DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
424 "No interpretation"); 140 "No interpretation");
425 141
142 // (0x3006, 0x0020)[i]/(0x3006, 0x0026)
426 structures_[i].name_ = reader.GetStringValue 143 structures_[i].name_ = reader.GetStringValue
427 (OrthancPlugins::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, 144 (OrthancPlugins::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
428 DICOM_TAG_ROI_NAME), 145 DICOM_TAG_ROI_NAME),
429 "No name"); 146 "No name");
430 147
431 Vector color; 148 Vector color;
432 if (ParseVector(color, tags, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, 149 // (0x3006, 0x0039)[i]/(0x3006, 0x002a)
433 DICOM_TAG_ROI_DISPLAY_COLOR)) && 150 if (ReadDicomToVector(color, tags, OrthancPlugins::DicomPath(
434 color.size() == 3) 151 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_ROI_DISPLAY_COLOR))
435 { 152 && color.size() == 3)
436 structures_[i].red_ = ConvertColor(color[0]); 153 {
437 structures_[i].green_ = ConvertColor(color[1]); 154 structures_[i].red_ = ConvertAndClipToByte(color[0]);
438 structures_[i].blue_ = ConvertColor(color[2]); 155 structures_[i].green_ = ConvertAndClipToByte(color[1]);
156 structures_[i].blue_ = ConvertAndClipToByte(color[2]);
439 } 157 }
440 else 158 else
441 { 159 {
442 structures_[i].red_ = 255; 160 structures_[i].red_ = 255;
443 structures_[i].green_ = 0; 161 structures_[i].green_ = 0;
444 structures_[i].blue_ = 0; 162 structures_[i].blue_ = 0;
445 } 163 }
446 164
447 size_t countSlices; 165 size_t countSlices;
448 if (!tags.GetSequenceSize(countSlices, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, 166 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
449 DICOM_TAG_CONTOUR_SEQUENCE))) 167 // DICOM_TAG_CONTOUR_SEQUENCE (0x3006, 0x0040);
450 { 168 if (!tags.GetSequenceSize(countSlices, OrthancPlugins::DicomPath(
169 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE)))
170 {
171 LOG(WARNING) << "DicomStructureSet2::SetContents | structure \"" << structures_[i].name_ << "\" has no slices!";
451 countSlices = 0; 172 countSlices = 0;
452 } 173 }
453 174
454 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ 175 LOG(INFO) << "New RT structure: \"" << structures_[i].name_
455 << "\" with interpretation \"" << structures_[i].interpretation_ 176 << "\" with interpretation \"" << structures_[i].interpretation_
456 << "\" containing " << countSlices << " slices (color: " 177 << "\" containing " << countSlices << " slices (color: "
457 << static_cast<int>(structures_[i].red_) << "," 178 << static_cast<int>(structures_[i].red_) << ","
458 << static_cast<int>(structures_[i].green_) << "," 179 << static_cast<int>(structures_[i].green_) << ","
459 << static_cast<int>(structures_[i].blue_) << ")"; 180 << static_cast<int>(structures_[i].blue_) << ")";
460 181
461 // These temporary variables avoid allocating many vectors in the loop below 182 // These temporary variables avoid allocating many vectors in the loop below
462 OrthancPlugins::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
463 DICOM_TAG_CONTOUR_SEQUENCE, 0,
464 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS);
465
466 OrthancPlugins::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
467 DICOM_TAG_CONTOUR_SEQUENCE, 0,
468 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE);
469 183
470 OrthancPlugins::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, 184 // (0x3006, 0x0039)[i]/(0x3006, 0x0040)[0]/(0x3006, 0x0046)
471 DICOM_TAG_CONTOUR_SEQUENCE, 0, 185 OrthancPlugins::DicomPath countPointsPath(
472 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); 186 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
187 DICOM_TAG_CONTOUR_SEQUENCE, 0,
188 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS);
189
190 OrthancPlugins::DicomPath geometricTypePath(
191 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
192 DICOM_TAG_CONTOUR_SEQUENCE, 0,
193 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE);
194
195 OrthancPlugins::DicomPath imageSequencePath(
196 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
197 DICOM_TAG_CONTOUR_SEQUENCE, 0,
198 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE);
473 199
474 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) 200 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)
475 OrthancPlugins::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, 201 OrthancPlugins::DicomPath referencedInstancePath(
476 DICOM_TAG_CONTOUR_SEQUENCE, 0, 202 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
477 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, 203 DICOM_TAG_CONTOUR_SEQUENCE, 0,
478 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); 204 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
479 205 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID);
480 OrthancPlugins::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, 206
481 DICOM_TAG_CONTOUR_SEQUENCE, 0, 207 OrthancPlugins::DicomPath contourDataPath(
482 DICOM_TAG_CONTOUR_DATA); 208 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
209 DICOM_TAG_CONTOUR_SEQUENCE, 0,
210 DICOM_TAG_CONTOUR_DATA);
483 211
484 for (size_t j = 0; j < countSlices; j++) 212 for (size_t j = 0; j < countSlices; j++)
485 { 213 {
486 unsigned int countPoints; 214 unsigned int countPoints = 0;
487 215
488 countPointsPath.SetPrefixIndex(1, j); 216 countPointsPath.SetPrefixIndex(1, j);
489 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) 217 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath))
490 { 218 {
219 LOG(ERROR) << "Dicom path " << countPointsPath << " is not valid (should contain an unsigned integer)";
491 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); 220 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
492 } 221 }
493 222
494 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; 223 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
495 224
496 geometricTypePath.SetPrefixIndex(1, j); 225 geometricTypePath.SetPrefixIndex(1, j);
497 std::string type = reader.GetMandatoryStringValue(geometricTypePath); 226 std::string type = reader.GetMandatoryStringValue(geometricTypePath);
498 if (type != "CLOSED_PLANAR") 227 if (type != "CLOSED_PLANAR")
499 { 228 {
229 // TODO: support points!!
500 LOG(WARNING) << "Ignoring contour with geometry type: " << type; 230 LOG(WARNING) << "Ignoring contour with geometry type: " << type;
501 continue; 231 continue;
502 } 232 }
503 233
504 size_t size; 234 size_t size = 0;
505 235
506 imageSequencePath.SetPrefixIndex(1, j); 236 imageSequencePath.SetPrefixIndex(1, j);
507 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) 237 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1)
508 { 238 {
509 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; 239 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry.";
510 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); 240 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
511 } 241 }
512 242
513 referencedInstancePath.SetPrefixIndex(1, j); 243 referencedInstancePath.SetPrefixIndex(1, j);
514 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); 244 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath);
515 245
516 contourDataPath.SetPrefixIndex(1, j); 246 contourDataPath.SetPrefixIndex(1, j);
517 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); 247 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath);
518 248
519 Vector points; 249 Vector points;
520 if (!LinearAlgebra::ParseVector(points, slicesData) || 250 if (!LinearAlgebra::ParseVector(points, slicesData) ||
521 points.size() != 3 * countPoints) 251 points.size() != 3 * countPoints)
522 { 252 {
523 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); 253 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
524 } 254 }
525 255
526 // seen in real world 256 // seen in real world
527 if(Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") 257 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "")
528 { 258 {
529 LOG(ERROR) << "WARNING. The following Dicom tag (Referenced SOP Instance UID) contains an empty value : // (3006,0039)[" << i << "] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)"; 259 LOG(ERROR) << "WARNING. The following Dicom tag (Referenced SOP Instance UID) contains an empty value : // (3006,0039)[" << i << "] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)";
530 } 260 }
531 261
532 Polygon polygon(sopInstanceUid); 262 DicomStructurePolygon2 polygon(sopInstanceUid,type);
533 polygon.Reserve(countPoints); 263 polygon.Reserve(countPoints);
534 264
535 for (size_t k = 0; k < countPoints; k++) 265 for (size_t k = 0; k < countPoints; k++)
536 { 266 {
537 Vector v(3); 267 Vector v(3);
538 v[0] = points[3 * k]; 268 v[0] = points[3 * k];
539 v[1] = points[3 * k + 1]; 269 v[1] = points[3 * k + 1];
540 v[2] = points[3 * k + 2]; 270 v[2] = points[3 * k + 2];
541 polygon.AddPoint(v); 271 polygon.AddPoint(v);
542 } 272 }
543 273 structures_[i].AddPolygon(polygon);
544 structures_[i].polygons_.push_back(polygon); 274 }
545 } 275 }
546 } 276 }
547 } 277
548 278
549 279 void DicomStructureSet2::Clear()
550 Vector DicomStructureSet2::GetStructureCenter(size_t index) const 280 {
551 { 281 structures_.clear();
552 const Structure& structure = GetStructure(index); 282 }
553 283
554 Vector center;
555 LinearAlgebra::AssignVector(center, 0, 0, 0);
556 if (structure.polygons_.empty())
557 {
558 return center;
559 }
560
561 double n = static_cast<double>(structure.polygons_.size());
562
563 for (Polygons::const_iterator polygon = structure.polygons_.begin();
564 polygon != structure.polygons_.end(); ++polygon)
565 {
566 if (!polygon->GetPoints().empty())
567 {
568 center += polygon->GetPoints().front() / n;
569 }
570 }
571
572 return center;
573 }
574
575
576 const std::string& DicomStructureSet2::GetStructureName(size_t index) const
577 {
578 return GetStructure(index).name_;
579 }
580
581
582 const std::string& DicomStructureSet2::GetStructureInterpretation(size_t index) const
583 {
584 return GetStructure(index).interpretation_;
585 }
586
587
588 Color DicomStructureSet2::GetStructureColor(size_t index) const
589 {
590 const Structure& s = GetStructure(index);
591 return Color(s.red_, s.green_, s.blue_);
592 }
593
594
595 void DicomStructureSet2::GetStructureColor(uint8_t& red,
596 uint8_t& green,
597 uint8_t& blue,
598 size_t index) const
599 {
600 const Structure& s = GetStructure(index);
601 red = s.red_;
602 green = s.green_;
603 blue = s.blue_;
604 }
605
606
607 void DicomStructureSet2::GetReferencedInstances(std::set<std::string>& instances)
608 {
609 for (Structures::const_iterator structure = structures_.begin();
610 structure != structures_.end(); ++structure)
611 {
612 for (Polygons::const_iterator polygon = structure->polygons_.begin();
613 polygon != structure->polygons_.end(); ++polygon)
614 {
615 instances.insert(polygon->GetSopInstanceUid());
616 }
617 }
618 }
619
620
621 void DicomStructureSet2::AddReferencedSlice(const std::string& sopInstanceUid,
622 const std::string& seriesInstanceUid,
623 const CoordinateSystem3D& geometry,
624 double thickness)
625 {
626 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end())
627 {
628 // This geometry is already known
629 LOG(ERROR) << "DicomStructureSet2::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid;
630
631 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
632 }
633 else
634 {
635 if (thickness < 0)
636 {
637 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
638 }
639
640 if (!referencedSlices_.empty())
641 {
642 const ReferencedSlice& reference = referencedSlices_.begin()->second;
643
644 if (reference.seriesInstanceUid_ != seriesInstanceUid)
645 {
646 LOG(ERROR) << "This RT-STRUCT refers to several different series";
647 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
648 }
649
650 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal()))
651 {
652 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel";
653 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
654 }
655 }
656
657 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness);
658
659 for (Structures::iterator structure = structures_.begin();
660 structure != structures_.end(); ++structure)
661 {
662 for (Polygons::iterator polygon = structure->polygons_.begin();
663 polygon != structure->polygons_.end(); ++polygon)
664 {
665 polygon->UpdateReferencedSlice(referencedSlices_);
666 }
667 }
668 }
669 }
670
671
672 void DicomStructureSet2::AddReferencedSlice(const Orthanc::DicomMap& dataset)
673 {
674 CoordinateSystem3D slice(dataset);
675
676 double thickness = 1; // 1 mm by default
677
678 std::string s;
679 Vector v;
680 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) &&
681 LinearAlgebra::ParseVector(v, s) &&
682 v.size() > 0)
683 {
684 thickness = v[0];
685 }
686
687 std::string instance, series;
688 if (dataset.LookupStringValue(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) &&
689 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false))
690 {
691 AddReferencedSlice(instance, series, slice, thickness);
692 }
693 else
694 {
695 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
696 }
697 }
698
699
700 void DicomStructureSet2::CheckReferencedSlices()
701 {
702 for (Structures::iterator structure = structures_.begin();
703 structure != structures_.end(); ++structure)
704 {
705 for (Polygons::iterator polygon = structure->polygons_.begin();
706 polygon != structure->polygons_.end(); ++polygon)
707 {
708 if (!polygon->UpdateReferencedSlice(referencedSlices_))
709 {
710 std::string sopInstanceUid = polygon->GetSopInstanceUid();
711 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "")
712 {
713 LOG(ERROR) << "DicomStructureSet2::CheckReferencedSlices(): "
714 << " missing information about referenced instance "
715 << "(sopInstanceUid is empty!)";
716 }
717 else
718 {
719 LOG(ERROR) << "DicomStructureSet2::CheckReferencedSlices(): "
720 << " missing information about referenced instance "
721 << "(sopInstanceUid = " << sopInstanceUid << ")";
722 }
723 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
724 }
725 }
726 }
727 }
728
729
730 Vector DicomStructureSet2::GetNormal() const
731 {
732 if (referencedSlices_.empty())
733 {
734 Vector v;
735 LinearAlgebra::AssignVector(v, 0, 0, 1);
736 return v;
737 }
738 else
739 {
740 return referencedSlices_.begin()->second.geometry_.GetNormal();
741 }
742 }
743
744
745 bool DicomStructureSet2::ProjectStructure(std::vector< std::vector<PolygonPoint2D> >& polygons,
746 const Structure& structure,
747 const CoordinateSystem3D& slice) const
748 {
749 polygons.clear();
750
751 Vector normal = GetNormal();
752
753 bool isOpposite;
754 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal()))
755 {
756 // This is an axial projection
757
758 for (Polygons::const_iterator polygon = structure.polygons_.begin();
759 polygon != structure.polygons_.end(); ++polygon)
760 {
761 if (polygon->IsOnSlice(slice))
762 {
763 polygons.push_back(std::vector<PolygonPoint2D>());
764
765 for (Points::const_iterator p = polygon->GetPoints().begin();
766 p != polygon->GetPoints().end(); ++p)
767 {
768 double x, y;
769 slice.ProjectPoint(x, y, *p);
770 polygons.back().push_back(std::make_pair(x, y));
771 }
772 }
773 }
774
775 return true;
776 }
777 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) ||
778 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY()))
779 {
780 #if 1
781 // Sagittal or coronal projection
782 std::vector<BoostPolygon> projected;
783
784 for (Polygons::const_iterator polygon = structure.polygons_.begin();
785 polygon != structure.polygons_.end(); ++polygon)
786 {
787 double x1, y1, x2, y2;
788 if (polygon->Project(x1, y1, x2, y2, slice))
789 {
790 projected.push_back(CreateRectangle(
791 static_cast<float>(x1),
792 static_cast<float>(y1),
793 static_cast<float>(x2),
794 static_cast<float>(y2)));
795 }
796 }
797
798 BoostMultiPolygon merged;
799 Union(merged, projected);
800
801 polygons.resize(merged.size());
802 for (size_t i = 0; i < merged.size(); i++)
803 {
804 const std::vector<BoostPoint>& outer = merged[i].outer();
805
806 polygons[i].resize(outer.size());
807 for (size_t j = 0; j < outer.size(); j++)
808 {
809 polygons[i][j] = std::make_pair(outer[j].x(), outer[j].y());
810 }
811 }
812 #else
813 for (Polygons::iterator polygon = structure.polygons_.begin();
814 polygon != structure.polygons_.end(); ++polygon)
815 {
816 double x1, y1, x2, y2;
817 if (polygon->Project(x1, y1, x2, y2, slice))
818 {
819 std::vector<PolygonPoint2D> p(4);
820 p[0] = std::make_pair(x1, y1);
821 p[1] = std::make_pair(x2, y1);
822 p[2] = std::make_pair(x2, y2);
823 p[3] = std::make_pair(x1, y2);
824 polygons.push_back(p);
825 }
826 }
827 #endif
828
829 return true;
830 }
831 else
832 {
833 return false;
834 }
835 }
836 } 284 }