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comparison OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 1512:244ad1e4e76a

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reorganization of folders
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 07 Jul 2020 16:21:02 +0200
parents Framework/Toolbox/DicomStructureSet.cpp@d8af188ab545
children 85e117739eca
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1511:9dfeee74c1e6 1512:244ad1e4e76a
1 /**
2 * Stone of Orthanc
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
4 * Department, University Hospital of Liege, Belgium
5 * Copyright (C) 2017-2020 Osimis S.A., Belgium
6 *
7 * This program is free software: you can redistribute it and/or
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.
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
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
18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
19 **/
20
21
22 #include "DicomStructureSet.h"
23 #include "DicomStructureSetUtils.h"
24
25 #include "../Toolbox/GeometryToolbox.h"
26 #include "OrthancDatasets/DicomDatasetReader.h"
27
28 #include <Logging.h>
29 #include <OrthancException.h>
30 #include <Toolbox.h>
31
32 #if defined(_MSC_VER)
33 # pragma warning(push)
34 # pragma warning(disable:4244)
35 #endif
36
37 #include <limits>
38 #include <stdio.h>
39 #include <boost/geometry.hpp>
40 #include <boost/geometry/geometries/point_xy.hpp>
41 #include <boost/geometry/geometries/polygon.hpp>
42 #include <boost/geometry/multi/geometries/multi_polygon.hpp>
43
44 #if defined(_MSC_VER)
45 # pragma warning(pop)
46 #endif
47
48 #if ORTHANC_ENABLE_DCMTK == 1
49 # include "ParsedDicomDataset.h"
50 #endif
51
52
53 typedef boost::geometry::model::d2::point_xy<double> BoostPoint;
54 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon;
55 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon;
56
57
58 static void Union(BoostMultiPolygon& output,
59 std::vector<BoostPolygon>& input)
60 {
61 for (size_t i = 0; i < input.size(); i++)
62 {
63 boost::geometry::correct(input[i]);
64 }
65
66 if (input.size() == 0)
67 {
68 output.clear();
69 }
70 else if (input.size() == 1)
71 {
72 output.resize(1);
73 output[0] = input[0];
74 }
75 else
76 {
77 boost::geometry::union_(input[0], input[1], output);
78
79 for (size_t i = 0; i < input.size(); i++)
80 {
81 BoostMultiPolygon tmp;
82 boost::geometry::union_(output, input[i], tmp);
83 output = tmp;
84 }
85 }
86 }
87
88 #if USE_BOOST_UNION_FOR_POLYGONS == 1
89
90 static BoostPolygon CreateRectangle(float x1, float y1,
91 float x2, float y2)
92 {
93 BoostPolygon r;
94 boost::geometry::append(r, BoostPoint(x1, y1));
95 boost::geometry::append(r, BoostPoint(x1, y2));
96 boost::geometry::append(r, BoostPoint(x2, y2));
97 boost::geometry::append(r, BoostPoint(x2, y1));
98 return r;
99 }
100
101 #else
102
103 namespace OrthancStone
104 {
105 static RtStructRectangleInSlab CreateRectangle(float x1, float y1,
106 float x2, float y2)
107 {
108 RtStructRectangleInSlab rect;
109 rect.xmin = std::min(x1, x2);
110 rect.xmax = std::max(x1, x2);
111 rect.ymin = std::min(y1, y2);
112 rect.ymax = std::max(y1, y2);
113 return rect;
114 }
115
116 bool CompareRectanglesForProjection(const std::pair<RtStructRectangleInSlab,double>& r1, const std::pair<RtStructRectangleInSlab, double>& r2)
117 {
118 return r1.second < r2.second;
119 }
120
121 bool CompareSlabsY(const RtStructRectanglesInSlab& r1, const RtStructRectanglesInSlab& r2)
122 {
123 if ((r1.size() == 0) || (r2.size() == 0))
124 return false;
125
126 return r1[0].ymax < r2[0].ymax;
127 }
128 }
129
130 #endif
131
132 namespace OrthancStone
133 {
134 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042);
135 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016);
136 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040);
137 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050);
138 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046);
139 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155);
140 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039);
141 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a);
142 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026);
143 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4);
144 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080);
145 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020);
146
147
148 static uint8_t ConvertColor(double v)
149 {
150 if (v < 0)
151 {
152 return 0;
153 }
154 else if (v >= 255)
155 {
156 return 255;
157 }
158 else
159 {
160 return static_cast<uint8_t>(v);
161 }
162 }
163
164
165 static bool ParseVector(Vector& target,
166 const IDicomDataset& dataset,
167 const DicomPath& tag)
168 {
169 std::string value;
170 return (dataset.GetStringValue(value, tag) &&
171 LinearAlgebra::ParseVector(target, value));
172 }
173
174 void DicomStructureSet::Polygon::CheckPointIsOnSlice(const Vector& v) const
175 {
176 if (hasSlice_)
177 {
178 double magnitude =
179 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal());
180 if(!LinearAlgebra::IsNear(
181 magnitude,
182 projectionAlongNormal_,
183 sliceThickness_ / 2.0 /* in mm */ ))
184 {
185 LOG(ERROR) << "This RT-STRUCT contains a point that is off the "
186 << "slice of its instance | "
187 << "magnitude = " << magnitude << " | "
188 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | "
189 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0);
190
191 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
192 }
193 }
194 }
195
196 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const
197 {
198 if (hasSlice_)
199 {
200 double magnitude =
201 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal());
202 bool onSlice = LinearAlgebra::IsNear(
203 magnitude,
204 projectionAlongNormal_,
205 sliceThickness_ / 2.0 /* in mm */);
206 if (!onSlice)
207 {
208 LOG(WARNING) << "This RT-STRUCT contains a point that is off the "
209 << "slice of its instance | "
210 << "magnitude = " << magnitude << " | "
211 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | "
212 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0);
213 }
214 return onSlice;
215 }
216 else
217 {
218 return true;
219 }
220 }
221
222 void DicomStructureSet::Polygon::AddPoint(const Vector& v)
223 {
224 #if 1
225 // BGO 2019-09-03
226 if (IsPointOnSliceIfAny(v))
227 {
228 points_.push_back(v);
229 }
230 #else
231 CheckPoint(v);
232 points_.push_back(v);
233 #endif
234 }
235
236
237 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices)
238 {
239 if (hasSlice_)
240 {
241 return true;
242 }
243 else
244 {
245 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_);
246
247 if (it == slices.end())
248 {
249 return false;
250 }
251 else
252 {
253 const CoordinateSystem3D& geometry = it->second.geometry_;
254
255 hasSlice_ = true;
256 geometry_ = geometry;
257 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal());
258 sliceThickness_ = it->second.thickness_;
259
260 extent_.Reset();
261
262 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it)
263 {
264 if (IsPointOnSliceIfAny(*it))
265 {
266 double x, y;
267 geometry.ProjectPoint2(x, y, *it);
268 extent_.AddPoint(x, y);
269 }
270 }
271 return true;
272 }
273 }
274 }
275
276 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const
277 {
278 bool isOpposite = false;
279
280 if (points_.empty() ||
281 !hasSlice_ ||
282 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal()))
283 {
284 return false;
285 }
286
287 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal());
288
289 return (LinearAlgebra::IsNear(d, projectionAlongNormal_,
290 sliceThickness_ / 2.0));
291 }
292
293 bool DicomStructureSet::Polygon::Project(double& x1,
294 double& y1,
295 double& x2,
296 double& y2,
297 const CoordinateSystem3D& slice) const
298 {
299 // TODO: optimize this method using a sweep-line algorithm for polygons
300
301 if (!hasSlice_ ||
302 points_.size() <= 1)
303 {
304 return false;
305 }
306
307 double x, y;
308 geometry_.ProjectPoint2(x, y, slice.GetOrigin());
309
310 bool isOpposite;
311 if (GeometryToolbox::IsParallelOrOpposite
312 (isOpposite, slice.GetNormal(), geometry_.GetAxisY()))
313 {
314 // plane is constant Y
315
316 if (y < extent_.GetY1() ||
317 y > extent_.GetY2())
318 {
319 // The polygon does not intersect the input slice
320 return false;
321 }
322
323 bool isFirst = true;
324 double xmin = std::numeric_limits<double>::infinity();
325 double xmax = -std::numeric_limits<double>::infinity();
326
327 double prevX, prevY;
328 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]);
329
330 for (size_t i = 0; i < points_.size(); i++)
331 {
332 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py
333 double curX, curY;
334 geometry_.ProjectPoint2(curX, curY, points_[i]);
335
336 // if prev* and cur* are on opposite sides of y, this means that the
337 // segment intersects the plane.
338 if ((prevY < y && curY > y) ||
339 (prevY > y && curY < y))
340 {
341 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY);
342 xmin = std::min(xmin, p);
343 xmax = std::max(xmax, p);
344 isFirst = false;
345
346 // xmin and xmax represent the extent of the rectangle along the
347 // intersection between the plane and the polygon geometry
348
349 }
350
351 prevX = curX;
352 prevY = curY;
353 }
354
355 // if NO segment intersects the plane
356 if (isFirst)
357 {
358 return false;
359 }
360 else
361 {
362 // y is the plane y coord in the polygon geometry
363 // xmin and xmax are ALSO expressed in the polygon geometry
364
365 // let's convert them to 3D world geometry...
366 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) +
367 sliceThickness_ / 2.0 * geometry_.GetNormal());
368 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) -
369 sliceThickness_ / 2.0 * geometry_.GetNormal());
370
371 // then to the cutting plane geometry...
372 slice.ProjectPoint2(x1, y1, p1);
373 slice.ProjectPoint2(x2, y2, p2);
374 return true;
375 }
376 }
377 else if (GeometryToolbox::IsParallelOrOpposite
378 (isOpposite, slice.GetNormal(), geometry_.GetAxisX()))
379 {
380 // plane is constant X => Sagittal view (remember that in the
381 // sagittal projection, the normal must be swapped)
382
383
384 /*
385 Please read the comments in the section above, by taking into account
386 the fact that, in this case, the plane has a constant X, not Y (in
387 polygon geometry_ coordinates)
388 */
389
390 if (x < extent_.GetX1() ||
391 x > extent_.GetX2())
392 {
393 return false;
394 }
395
396 bool isFirst = true;
397 double ymin = std::numeric_limits<double>::infinity();
398 double ymax = -std::numeric_limits<double>::infinity();
399
400 double prevX, prevY;
401 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]);
402
403 for (size_t i = 0; i < points_.size(); i++)
404 {
405 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py
406 double curX, curY;
407 geometry_.ProjectPoint2(curX, curY, points_[i]);
408
409 if ((prevX < x && curX > x) ||
410 (prevX > x && curX < x))
411 {
412 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX);
413 ymin = std::min(ymin, p);
414 ymax = std::max(ymax, p);
415 isFirst = false;
416 }
417
418 prevX = curX;
419 prevY = curY;
420 }
421
422 if (isFirst)
423 {
424 return false;
425 }
426 else
427 {
428 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) +
429 sliceThickness_ / 2.0 * geometry_.GetNormal());
430 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) -
431 sliceThickness_ / 2.0 * geometry_.GetNormal());
432
433 slice.ProjectPoint2(x1, y1, p1);
434 slice.ProjectPoint2(x2, y2, p2);
435
436 return true;
437 }
438 }
439 else
440 {
441 // Should not happen
442 return false;
443 }
444 }
445
446
447 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const
448 {
449 if (index >= structures_.size())
450 {
451 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
452 }
453
454 return structures_[index];
455 }
456
457
458 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index)
459 {
460 if (index >= structures_.size())
461 {
462 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
463 }
464
465 return structures_[index];
466 }
467
468 void DicomStructureSet::Setup(const IDicomDataset& tags)
469 {
470 DicomDatasetReader reader(tags);
471
472 size_t count, tmp;
473 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) ||
474 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) ||
475 tmp != count ||
476 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) ||
477 tmp != count)
478 {
479 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
480 }
481
482 structures_.resize(count);
483 for (size_t i = 0; i < count; i++)
484 {
485 structures_[i].interpretation_ = reader.GetStringValue
486 (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
487 DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
488 "No interpretation");
489
490 structures_[i].name_ = reader.GetStringValue
491 (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
492 DICOM_TAG_ROI_NAME),
493 "No name");
494
495 Vector color;
496 if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
497 DICOM_TAG_ROI_DISPLAY_COLOR)) &&
498 color.size() == 3)
499 {
500 structures_[i].red_ = ConvertColor(color[0]);
501 structures_[i].green_ = ConvertColor(color[1]);
502 structures_[i].blue_ = ConvertColor(color[2]);
503 }
504 else
505 {
506 structures_[i].red_ = 255;
507 structures_[i].green_ = 0;
508 structures_[i].blue_ = 0;
509 }
510
511 size_t countSlices;
512 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
513 DICOM_TAG_CONTOUR_SEQUENCE)))
514 {
515 countSlices = 0;
516 }
517
518 LOG(INFO) << "New RT structure: \"" << structures_[i].name_
519 << "\" with interpretation \"" << structures_[i].interpretation_
520 << "\" containing " << countSlices << " slices (color: "
521 << static_cast<int>(structures_[i].red_) << ","
522 << static_cast<int>(structures_[i].green_) << ","
523 << static_cast<int>(structures_[i].blue_) << ")";
524
525 // These temporary variables avoid allocating many vectors in the loop below
526 DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
527 DICOM_TAG_CONTOUR_SEQUENCE, 0,
528 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS);
529
530 DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
531 DICOM_TAG_CONTOUR_SEQUENCE, 0,
532 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE);
533
534 DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
535 DICOM_TAG_CONTOUR_SEQUENCE, 0,
536 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE);
537
538 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)
539 DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
540 DICOM_TAG_CONTOUR_SEQUENCE, 0,
541 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
542 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID);
543
544 DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
545 DICOM_TAG_CONTOUR_SEQUENCE, 0,
546 DICOM_TAG_CONTOUR_DATA);
547
548 for (size_t j = 0; j < countSlices; j++)
549 {
550 unsigned int countPoints;
551
552 countPointsPath.SetPrefixIndex(1, j);
553 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath))
554 {
555 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
556 }
557
558 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
559
560 geometricTypePath.SetPrefixIndex(1, j);
561 std::string type = reader.GetMandatoryStringValue(geometricTypePath);
562 if (type != "CLOSED_PLANAR")
563 {
564 LOG(WARNING) << "Ignoring contour with geometry type: " << type;
565 continue;
566 }
567
568 size_t size;
569
570 imageSequencePath.SetPrefixIndex(1, j);
571 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1)
572 {
573 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry.";
574 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
575 }
576
577 referencedInstancePath.SetPrefixIndex(1, j);
578 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath);
579
580 contourDataPath.SetPrefixIndex(1, j);
581 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath);
582
583 Vector points;
584 if (!LinearAlgebra::ParseVector(points, slicesData) ||
585 points.size() != 3 * countPoints)
586 {
587 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
588 }
589
590 // seen in real world
591 if(Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "")
592 {
593 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)";
594 }
595
596 Polygon polygon(sopInstanceUid);
597 polygon.Reserve(countPoints);
598
599 for (size_t k = 0; k < countPoints; k++)
600 {
601 Vector v(3);
602 v[0] = points[3 * k];
603 v[1] = points[3 * k + 1];
604 v[2] = points[3 * k + 2];
605 polygon.AddPoint(v);
606 }
607
608 structures_[i].polygons_.push_back(polygon);
609 }
610 }
611 }
612
613
614 #if ORTHANC_ENABLE_DCMTK == 1
615 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance)
616 {
617 ParsedDicomDataset dataset(instance);
618 Setup(dataset);
619 }
620 #endif
621
622
623 Vector DicomStructureSet::GetStructureCenter(size_t index) const
624 {
625 const Structure& structure = GetStructure(index);
626
627 Vector center;
628 LinearAlgebra::AssignVector(center, 0, 0, 0);
629 if (structure.polygons_.empty())
630 {
631 return center;
632 }
633
634 double n = static_cast<double>(structure.polygons_.size());
635
636 for (Polygons::const_iterator polygon = structure.polygons_.begin();
637 polygon != structure.polygons_.end(); ++polygon)
638 {
639 if (!polygon->GetPoints().empty())
640 {
641 center += polygon->GetPoints().front() / n;
642 }
643 }
644
645 return center;
646 }
647
648
649 const std::string& DicomStructureSet::GetStructureName(size_t index) const
650 {
651 return GetStructure(index).name_;
652 }
653
654
655 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const
656 {
657 return GetStructure(index).interpretation_;
658 }
659
660
661 Color DicomStructureSet::GetStructureColor(size_t index) const
662 {
663 const Structure& s = GetStructure(index);
664 return Color(s.red_, s.green_, s.blue_);
665 }
666
667
668 void DicomStructureSet::GetStructureColor(uint8_t& red,
669 uint8_t& green,
670 uint8_t& blue,
671 size_t index) const
672 {
673 const Structure& s = GetStructure(index);
674 red = s.red_;
675 green = s.green_;
676 blue = s.blue_;
677 }
678
679
680 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances)
681 {
682 for (Structures::const_iterator structure = structures_.begin();
683 structure != structures_.end(); ++structure)
684 {
685 for (Polygons::const_iterator polygon = structure->polygons_.begin();
686 polygon != structure->polygons_.end(); ++polygon)
687 {
688 instances.insert(polygon->GetSopInstanceUid());
689 }
690 }
691 }
692
693
694 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid,
695 const std::string& seriesInstanceUid,
696 const CoordinateSystem3D& geometry,
697 double thickness)
698 {
699 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end())
700 {
701 // This geometry is already known
702 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid;
703
704 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
705 }
706 else
707 {
708 if (thickness < 0)
709 {
710 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
711 }
712
713 if (!referencedSlices_.empty())
714 {
715 const ReferencedSlice& reference = referencedSlices_.begin()->second;
716
717 if (reference.seriesInstanceUid_ != seriesInstanceUid)
718 {
719 LOG(ERROR) << "This RT-STRUCT refers to several different series";
720 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
721 }
722
723 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal()))
724 {
725 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel";
726 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
727 }
728 }
729
730 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness);
731
732 for (Structures::iterator structure = structures_.begin();
733 structure != structures_.end(); ++structure)
734 {
735 for (Polygons::iterator polygon = structure->polygons_.begin();
736 polygon != structure->polygons_.end(); ++polygon)
737 {
738 polygon->UpdateReferencedSlice(referencedSlices_);
739 }
740 }
741 }
742 }
743
744
745 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset)
746 {
747 CoordinateSystem3D slice(dataset);
748
749 double thickness = 1; // 1 mm by default
750
751 std::string s;
752 Vector v;
753 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) &&
754 LinearAlgebra::ParseVector(v, s) &&
755 v.size() > 0)
756 {
757 thickness = v[0];
758 }
759
760 std::string instance, series;
761 if (dataset.LookupStringValue(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) &&
762 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false))
763 {
764 AddReferencedSlice(instance, series, slice, thickness);
765 }
766 else
767 {
768 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
769 }
770 }
771
772
773 void DicomStructureSet::CheckReferencedSlices()
774 {
775 for (Structures::iterator structure = structures_.begin();
776 structure != structures_.end(); ++structure)
777 {
778 for (Polygons::iterator polygon = structure->polygons_.begin();
779 polygon != structure->polygons_.end(); ++polygon)
780 {
781 if (!polygon->UpdateReferencedSlice(referencedSlices_))
782 {
783 std::string sopInstanceUid = polygon->GetSopInstanceUid();
784 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "")
785 {
786 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): "
787 << " missing information about referenced instance "
788 << "(sopInstanceUid is empty!)";
789 }
790 else
791 {
792 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): "
793 << " missing information about referenced instance "
794 << "(sopInstanceUid = " << sopInstanceUid << ")";
795 }
796 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
797 }
798 }
799 }
800 }
801
802
803 Vector DicomStructureSet::GetNormal() const
804 {
805 if (referencedSlices_.empty())
806 {
807 Vector v;
808 LinearAlgebra::AssignVector(v, 0, 0, 1);
809 return v;
810 }
811 else
812 {
813 return referencedSlices_.begin()->second.geometry_.GetNormal();
814 }
815 }
816
817 bool DicomStructureSet::ProjectStructure(
818 #if USE_BOOST_UNION_FOR_POLYGONS == 1
819 std::vector< std::vector<Point2D> >& polygons,
820 #else
821 std::vector< std::pair<Point2D, Point2D> >& segments,
822 #endif
823 const Structure& structure,
824 const CoordinateSystem3D& sourceSlice) const
825 {
826 const CoordinateSystem3D slice = CoordinateSystem3D::NormalizeCuttingPlane(sourceSlice);
827
828 #if USE_BOOST_UNION_FOR_POLYGONS == 1
829 polygons.clear();
830 #else
831 segments.clear();
832 #endif
833
834 Vector normal = GetNormal();
835
836 bool isOpposite;
837 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal()))
838 {
839 // This is an axial projection
840
841 for (Polygons::const_iterator polygon = structure.polygons_.begin();
842 polygon != structure.polygons_.end(); ++polygon)
843 {
844 if (polygon->IsOnSlice(slice))
845 {
846 #if USE_BOOST_UNION_FOR_POLYGONS == 1
847 polygons.push_back(std::vector<Point2D>());
848
849 for (Points::const_iterator p = polygon->GetPoints().begin();
850 p != polygon->GetPoints().end(); ++p)
851 {
852 double x, y;
853 slice.ProjectPoint2(x, y, *p);
854 polygons.back().push_back(Point2D(x, y));
855 }
856 #else
857 // we need to add all the segments corresponding to this polygon
858 const std::vector<Vector>& points3D = polygon->GetPoints();
859 if (points3D.size() >= 3)
860 {
861 Point2D prev2D;
862 {
863 Vector prev = points3D[0];
864 double prevX, prevY;
865 slice.ProjectPoint2(prevX, prevY, prev);
866 prev2D = Point2D(prevX, prevY);
867 }
868
869 size_t pointCount = points3D.size();
870 for (size_t ipt = 1; ipt < pointCount; ++ipt)
871 {
872 Vector next = points3D[ipt];
873 double nextX, nextY;
874 slice.ProjectPoint2(nextX, nextY, next);
875 Point2D next2D(nextX, nextY);
876 segments.push_back(std::pair<Point2D, Point2D>(prev2D, next2D));
877 prev2D = next2D;
878 }
879 }
880 else
881 {
882 LOG(ERROR) << "Contour with less than 3 points!";
883 // !!!
884 }
885 #endif
886 }
887 }
888
889 return true;
890 }
891 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) ||
892 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY()))
893 {
894 #if 1
895 // Sagittal or coronal projection
896
897 #if USE_BOOST_UNION_FOR_POLYGONS == 1
898 std::vector<BoostPolygon> projected;
899
900 for (Polygons::const_iterator polygon = structure.polygons_.begin();
901 polygon != structure.polygons_.end(); ++polygon)
902 {
903 double x1, y1, x2, y2;
904
905 if (polygon->Project(x1, y1, x2, y2, slice))
906 {
907 projected.push_back(CreateRectangle(x1, y1, x2, y2));
908 }
909 }
910 #else
911 // this will contain the intersection of the polygon slab with
912 // the cutting plane, projected on the cutting plane coord system
913 // (that yields a rectangle) + the Z coordinate of the polygon
914 // (this is required to group polygons with the same Z later)
915 std::vector<std::pair<RtStructRectangleInSlab, double> > projected;
916
917 for (Polygons::const_iterator polygon = structure.polygons_.begin();
918 polygon != structure.polygons_.end(); ++polygon)
919 {
920 double x1, y1, x2, y2;
921
922 if (polygon->Project(x1, y1, x2, y2, slice))
923 {
924 double curZ = polygon->GetGeometryOrigin()[2];
925
926 // x1,y1 and x2,y2 are in "slice" coordinates (the cutting plane
927 // geometry)
928 projected.push_back(std::make_pair(CreateRectangle(
929 static_cast<float>(x1),
930 static_cast<float>(y1),
931 static_cast<float>(x2),
932 static_cast<float>(y2)),curZ));
933 }
934 }
935 #endif
936
937 #if USE_BOOST_UNION_FOR_POLYGONS != 1
938 // projected contains a set of rectangles specified by two opposite
939 // corners (x1,y1,x2,y2)
940 // we need to merge them
941 // each slab yields ONE polygon!
942
943 // we need to sorted all the rectangles that originate from the same Z
944 // into lanes. To make sure they are grouped together in the array, we
945 // sort it.
946 std::sort(projected.begin(), projected.end(), CompareRectanglesForProjection);
947
948 std::vector<RtStructRectanglesInSlab> rectanglesForEachSlab;
949 rectanglesForEachSlab.reserve(projected.size());
950
951 double curZ = 0;
952 for (size_t i = 0; i < projected.size(); ++i)
953 {
954 #if 0
955 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab());
956 #else
957 if (i == 0)
958 {
959 curZ = projected[i].second;
960 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab());
961 }
962 else
963 {
964 // this check is needed to prevent creating a new slab if
965 // the new polygon is at the same Z coord than last one
966 if (!LinearAlgebra::IsNear(curZ, projected[i].second))
967 {
968 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab());
969 curZ = projected[i].second;
970 }
971 }
972 #endif
973
974 rectanglesForEachSlab.back().push_back(projected[i].first);
975
976 // as long as they have the same y, we should put them into the same lane
977 // BUT in Sebastien's code, there is only one polygon per lane.
978
979 //std::cout << "rect: xmin = " << rect.xmin << " xmax = " << rect.xmax << " ymin = " << rect.ymin << " ymax = " << rect.ymax << std::endl;
980 }
981
982 // now we need to sort the slabs in increasing Y order (see ConvertListOfSlabsToSegments)
983 std::sort(rectanglesForEachSlab.begin(), rectanglesForEachSlab.end(), CompareSlabsY);
984
985 ConvertListOfSlabsToSegments(segments, rectanglesForEachSlab, projected.size());
986 #else
987 BoostMultiPolygon merged;
988 Union(merged, projected);
989
990 polygons.resize(merged.size());
991 for (size_t i = 0; i < merged.size(); i++)
992 {
993 const std::vector<BoostPoint>& outer = merged[i].outer();
994
995 polygons[i].resize(outer.size());
996 for (size_t j = 0; j < outer.size(); j++)
997 {
998 polygons[i][j] = Point2D(outer[j].x(), outer[j].y());
999 }
1000 }
1001 #endif
1002
1003 #else
1004 for (Polygons::iterator polygon = structure.polygons_.begin();
1005 polygon != structure.polygons_.end(); ++polygon)
1006 {
1007 double x1, y1, x2, y2;
1008 if (polygon->Project(x1, y1, x2, y2, slice))
1009 {
1010 std::vector<Point2D> p(4);
1011 p[0] = std::make_pair(x1, y1);
1012 p[1] = std::make_pair(x2, y1);
1013 p[2] = std::make_pair(x2, y2);
1014 p[3] = std::make_pair(x1, y2);
1015 polygons.push_back(p);
1016 }
1017 }
1018 #endif
1019
1020 return true;
1021 }
1022 else
1023 {
1024 return false;
1025 }
1026 }
1027
1028
1029 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer,
1030 const CoordinateSystem3D& plane,
1031 size_t structureIndex,
1032 const Color& color) const
1033 {
1034 #if USE_BOOST_UNION_FOR_POLYGONS == 1
1035 std::vector< std::vector<Point2D> > polygons;
1036 if (ProjectStructure(polygons, structureIndex, plane))
1037 {
1038 for (size_t j = 0; j < polygons.size(); j++)
1039 {
1040 std::vector<ScenePoint2D> chain;
1041 chain.reserve(polygons[j].size());
1042
1043 for (size_t k = 0; k < polygons[j].size(); k++)
1044 {
1045 chain.push_back(ScenePoint2D(polygons[j][k].x, polygons[j][k].y));
1046 }
1047
1048 layer.AddChain(chain, true, color.GetRed(), color.GetGreen(), color.GetBlue());
1049 }
1050 }
1051
1052 #else
1053 std::vector< std::pair<Point2D, Point2D> > segments;
1054
1055 if (ProjectStructure(segments, structureIndex, plane))
1056 {
1057 for (size_t j = 0; j < segments.size(); j++)
1058 {
1059 std::vector<ScenePoint2D> chain(2);
1060 chain[0] = ScenePoint2D(segments[j].first.x, segments[j].first.y);
1061 chain[1] = ScenePoint2D(segments[j].second.x, segments[j].second.y);
1062 layer.AddChain(chain, false, color.GetRed(), color.GetGreen(), color.GetBlue());
1063 }
1064 }
1065 #endif
1066 }
1067 }