Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 121:e66b2c757790 wasm
displaying rt-struct
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 04 Oct 2017 17:53:47 +0200 |
| parents | a4d0b6c82b29 |
| children | e3433dabfb8d |
| rev | line source |
|---|---|
| 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 | |
| 35 | 24 #include "../Toolbox/MessagingToolbox.h" |
| 0 | 25 |
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26 #include <Core/Logging.h> |
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27 #include <Core/OrthancException.h> |
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28 #include <Plugins/Samples/Common/FullOrthancDataset.h> |
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29 #include <Plugins/Samples/Common/DicomDatasetReader.h> |
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30 |
| 0 | 31 #include <stdio.h> |
| 32 #include <boost/lexical_cast.hpp> | |
| 33 | |
| 34 namespace OrthancStone | |
| 35 { | |
| 32 | 36 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 37 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 38 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
| 39 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
| 40 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 41 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 42 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 43 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 44 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 45 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 46 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 47 |
| 48 | |
| 49 static uint8_t ConvertColor(double v) | |
| 50 { | |
| 51 if (v < 0) | |
| 52 { | |
| 53 return 0; | |
| 54 } | |
| 55 else if (v >= 255) | |
| 56 { | |
| 57 return 255; | |
| 58 } | |
| 59 else | |
| 60 { | |
| 61 return static_cast<uint8_t>(v); | |
| 62 } | |
| 63 } | |
| 64 | |
| 65 | |
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66 static bool ParseVector(Vector& target, |
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67 const OrthancPlugins::IDicomDataset& dataset, |
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68 const OrthancPlugins::DicomPath& tag) |
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69 { |
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70 std::string value; |
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71 return (dataset.GetStringValue(value, tag) && |
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72 GeometryToolbox::ParseVector(target, value)); |
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73 } |
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74 |
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75 CoordinateSystem3D DicomStructureSet:: |
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76 ExtractSliceGeometry(double& sliceThickness, |
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77 OrthancPlugins::IOrthancConnection& orthanc, |
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78 const OrthancPlugins::IDicomDataset& tags, |
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79 size_t contourIndex, |
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80 size_t sliceIndex) |
| 0 | 81 { |
| 32 | 82 using namespace OrthancPlugins; |
| 0 | 83 |
| 32 | 84 size_t size; |
| 85 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
| 86 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
| 87 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || | |
| 88 size != 1) | |
| 0 | 89 { |
| 90 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 91 } | |
| 92 | |
| 32 | 93 DicomDatasetReader reader(tags); |
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94 std::string parentUid = reader.GetMandatoryStringValue |
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95 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, |
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96 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, |
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97 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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98 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); |
| 0 | 99 |
| 34 | 100 Json::Value parentLookup; |
| 101 MessagingToolbox::RestApiPost(parentLookup, orthanc, "/tools/lookup", parentUid); | |
| 0 | 102 |
| 34 | 103 if (parentLookup.type() != Json::arrayValue || |
| 104 parentLookup.size() != 1 || | |
| 105 !parentLookup[0].isMember("Type") || | |
| 106 !parentLookup[0].isMember("Path") || | |
| 107 parentLookup[0]["Type"].type() != Json::stringValue || | |
| 108 parentLookup[0]["ID"].type() != Json::stringValue || | |
| 109 parentLookup[0]["Type"].asString() != "Instance") | |
| 0 | 110 { |
| 111 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 112 } | |
| 113 | |
| 114 Json::Value parentInstance; | |
| 34 | 115 MessagingToolbox::RestApiGet(parentInstance, orthanc, "/instances/" + parentLookup[0]["ID"].asString()); |
| 0 | 116 |
| 117 if (parentInstance.type() != Json::objectValue || | |
| 118 !parentInstance.isMember("ParentSeries") || | |
| 119 parentInstance["ParentSeries"].type() != Json::stringValue) | |
| 120 { | |
| 121 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); | |
| 122 } | |
| 123 | |
| 124 std::string parentSeriesId = parentInstance["ParentSeries"].asString(); | |
| 125 bool isFirst = parentSeriesId_.empty(); | |
| 126 | |
| 127 if (isFirst) | |
| 128 { | |
| 129 parentSeriesId_ = parentSeriesId; | |
| 130 } | |
| 131 else if (parentSeriesId_ != parentSeriesId) | |
| 132 { | |
| 133 LOG(ERROR) << "This RT-STRUCT refers to several different series"; | |
| 134 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 135 } | |
| 136 | |
| 34 | 137 FullOrthancDataset parentTags(orthanc, "/instances/" + parentLookup[0]["ID"].asString() + "/tags"); |
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138 CoordinateSystem3D slice(parentTags); |
| 0 | 139 |
| 32 | 140 Vector v; |
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141 if (ParseVector(v, parentTags, DICOM_TAG_SLICE_THICKNESS) && |
| 32 | 142 v.size() > 0) |
| 0 | 143 { |
| 32 | 144 sliceThickness = v[0]; |
| 145 } | |
| 146 else | |
| 147 { | |
| 148 sliceThickness = 1; // 1 mm by default | |
| 0 | 149 } |
| 150 | |
| 151 if (isFirst) | |
| 152 { | |
| 153 normal_ = slice.GetNormal(); | |
| 154 } | |
| 155 else if (!GeometryToolbox::IsParallel(normal_, slice.GetNormal())) | |
| 156 { | |
| 157 LOG(ERROR) << "Incompatible orientation of slices in this RT-STRUCT"; | |
| 158 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 159 } | |
| 160 | |
| 161 return slice; | |
| 162 } | |
| 163 | |
| 164 | |
| 165 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const | |
| 166 { | |
| 167 if (index >= structures_.size()) | |
| 168 { | |
| 169 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 170 } | |
| 171 | |
| 172 return structures_[index]; | |
| 173 } | |
| 174 | |
| 175 | |
| 176 bool DicomStructureSet::IsPolygonOnSlice(const Polygon& polygon, | |
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177 const CoordinateSystem3D& geometry) const |
| 0 | 178 { |
| 179 double d = boost::numeric::ublas::inner_prod(geometry.GetOrigin(), normal_); | |
| 180 | |
| 181 return (GeometryToolbox::IsNear(d, polygon.projectionAlongNormal_, polygon.sliceThickness_ / 2.0) && | |
| 182 !polygon.points_.empty()); | |
| 183 } | |
| 184 | |
| 185 | |
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186 DicomStructureSet::DicomStructureSet(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 187 const std::string& instanceId) |
| 188 { | |
| 32 | 189 using namespace OrthancPlugins; |
| 0 | 190 |
| 32 | 191 FullOrthancDataset tags(orthanc, "/instances/" + instanceId + "/tags"); |
| 192 DicomDatasetReader reader(tags); | |
| 193 | |
| 194 size_t count, tmp; | |
| 195 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
| 196 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
| 197 tmp != count || | |
| 198 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
| 199 tmp != count) | |
| 0 | 200 { |
| 201 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 202 } | |
| 203 | |
| 32 | 204 structures_.resize(count); |
| 205 for (size_t i = 0; i < count; i++) | |
| 206 { | |
| 207 structures_[i].interpretation_ = reader.GetStringValue(DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, | |
| 208 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), | |
| 209 "No interpretation"); | |
| 0 | 210 |
| 32 | 211 structures_[i].name_ = reader.GetStringValue(DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
| 212 DICOM_TAG_ROI_NAME), | |
| 213 "No interpretation"); | |
| 0 | 214 |
| 215 Vector color; | |
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216 if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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217 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 218 color.size() == 3) |
| 0 | 219 { |
| 32 | 220 structures_[i].red_ = ConvertColor(color[0]); |
| 221 structures_[i].green_ = ConvertColor(color[1]); | |
| 222 structures_[i].blue_ = ConvertColor(color[2]); | |
| 223 } | |
| 224 else | |
| 225 { | |
| 226 structures_[i].red_ = 255; | |
| 227 structures_[i].green_ = 0; | |
| 228 structures_[i].blue_ = 0; | |
| 0 | 229 } |
| 230 | |
| 32 | 231 size_t countSlices; |
| 232 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
| 233 DICOM_TAG_CONTOUR_SEQUENCE))) | |
| 234 { | |
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235 countSlices = 0; |
| 32 | 236 } |
| 0 | 237 |
| 238 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
| 239 << "\" with interpretation \"" << structures_[i].interpretation_ | |
| 32 | 240 << "\" containing " << countSlices << " slices (color: " |
| 0 | 241 << static_cast<int>(structures_[i].red_) << "," |
| 242 << static_cast<int>(structures_[i].green_) << "," | |
| 243 << static_cast<int>(structures_[i].blue_) << ")"; | |
| 244 | |
| 32 | 245 for (size_t j = 0; j < countSlices; j++) |
| 0 | 246 { |
| 32 | 247 unsigned int countPoints; |
| 0 | 248 |
| 32 | 249 if (!reader.GetUnsignedIntegerValue(countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
| 250 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
| 251 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) | |
| 252 { | |
| 253 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 254 } | |
| 255 | |
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256 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 257 |
| 32 | 258 std::string type = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
| 259 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
| 260 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); | |
| 261 if (type != "CLOSED_PLANAR") | |
| 0 | 262 { |
| 32 | 263 LOG(ERROR) << "Cannot handle contour with geometry type: " << type; |
| 0 | 264 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 265 } | |
| 266 | |
| 32 | 267 // The "CountourData" tag (3006,0050) is too large to be |
| 268 // returned by the "/instances/{id}/tags" URI: Access it using | |
| 269 // the raw "/instances/{id}/content/{...}" endpoint | |
| 0 | 270 std::string slicesData; |
| 271 orthanc.RestApiGet(slicesData, "/instances/" + instanceId + "/content/3006-0039/" + | |
| 272 boost::lexical_cast<std::string>(i) + "/3006-0040/" + | |
| 273 boost::lexical_cast<std::string>(j) + "/3006-0050"); | |
| 274 | |
| 275 Vector points; | |
| 276 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
| 32 | 277 points.size() != 3 * countPoints) |
| 0 | 278 { |
| 279 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 280 } | |
| 281 | |
| 282 Polygon polygon; | |
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283 CoordinateSystem3D geometry = ExtractSliceGeometry(polygon.sliceThickness_, orthanc, tags, i, j); |
| 0 | 284 polygon.projectionAlongNormal_ = geometry.ProjectAlongNormal(geometry.GetOrigin()); |
| 285 | |
| 32 | 286 for (size_t k = 0; k < countPoints; k++) |
| 0 | 287 { |
| 288 Vector v(3); | |
| 289 v[0] = points[3 * k]; | |
| 290 v[1] = points[3 * k + 1]; | |
| 291 v[2] = points[3 * k + 2]; | |
| 292 | |
| 293 if (!GeometryToolbox::IsNear(geometry.ProjectAlongNormal(v), | |
| 294 polygon.projectionAlongNormal_, | |
| 295 polygon.sliceThickness_ / 2.0 /* in mm */)) | |
| 296 { | |
| 297 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; | |
| 298 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 299 } | |
| 300 | |
| 301 polygon.points_.push_back(v); | |
| 302 } | |
| 303 | |
| 304 structures_[i].polygons_.push_back(polygon); | |
| 305 } | |
| 306 } | |
| 307 | |
| 308 if (parentSeriesId_.empty() || | |
| 309 normal_.size() != 3) | |
| 310 { | |
| 311 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 312 } | |
| 313 } | |
| 314 | |
| 315 | |
| 316 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
| 317 { | |
| 318 const Structure& structure = GetStructure(index); | |
| 319 | |
| 320 Vector center; | |
| 321 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
| 322 if (structure.polygons_.empty()) | |
| 323 { | |
| 324 return center; | |
| 325 } | |
| 326 | |
| 327 double n = static_cast<double>(structure.polygons_.size()); | |
| 328 | |
| 329 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 330 polygon != structure.polygons_.end(); ++polygon) | |
| 331 { | |
| 332 if (!polygon->points_.empty()) | |
| 333 { | |
| 334 center += polygon->points_.front() / n; | |
| 335 } | |
| 336 } | |
| 337 | |
| 338 return center; | |
| 339 } | |
| 340 | |
| 341 | |
| 342 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 343 { | |
| 344 return GetStructure(index).name_; | |
| 345 } | |
| 346 | |
| 347 | |
| 348 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 349 { | |
| 350 return GetStructure(index).interpretation_; | |
| 351 } | |
| 352 | |
| 353 | |
| 354 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
| 355 uint8_t& green, | |
| 356 uint8_t& blue, | |
| 357 size_t index) const | |
| 358 { | |
| 359 const Structure& s = GetStructure(index); | |
| 360 red = s.red_; | |
| 361 green = s.green_; | |
| 362 blue = s.blue_; | |
| 363 } | |
| 364 | |
| 365 | |
| 366 void DicomStructureSet::Render(CairoContext& context, | |
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367 const CoordinateSystem3D& slice) const |
| 0 | 368 { |
| 369 cairo_t* cr = context.GetObject(); | |
| 370 | |
| 371 for (Structures::const_iterator structure = structures_.begin(); | |
| 372 structure != structures_.end(); ++structure) | |
| 373 { | |
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374 if (structure->name_ != "SKIN" && |
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375 structure->name_ != "HEART" && |
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376 //structure->name_ != "CORD" && |
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377 structure->name_ != "ESOPHAGUS" && |
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378 structure->name_ != "LUNG_LT" && |
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379 structure->name_ != "LUNG_RT" && |
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380 structure->name_ != "GTV_EXH_PRIMARY" && |
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381 structure->name_ != "GTV_INH_PRIMARY" && |
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382 structure->name_ != "GTV_PRIMARY") |
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383 { |
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384 continue; |
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385 } |
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386 |
| 0 | 387 for (Polygons::const_iterator polygon = structure->polygons_.begin(); |
| 388 polygon != structure->polygons_.end(); ++polygon) | |
| 389 { | |
| 390 if (IsPolygonOnSlice(*polygon, slice)) | |
| 391 { | |
| 392 context.SetSourceColor(structure->red_, structure->green_, structure->blue_); | |
| 393 | |
| 394 Points::const_iterator p = polygon->points_.begin(); | |
| 395 | |
| 396 double x, y; | |
| 397 slice.ProjectPoint(x, y, *p); | |
| 398 cairo_move_to(cr, x, y); | |
| 399 ++p; | |
| 400 | |
| 401 while (p != polygon->points_.end()) | |
| 402 { | |
| 403 slice.ProjectPoint(x, y, *p); | |
| 404 cairo_line_to(cr, x, y); | |
| 405 ++p; | |
| 406 } | |
| 407 | |
| 408 slice.ProjectPoint(x, y, *polygon->points_.begin()); | |
| 409 cairo_line_to(cr, x, y); | |
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410 |
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411 cairo_stroke(cr); |
| 0 | 412 } |
| 413 } | |
| 414 } | |
| 415 } | |
| 416 } |