Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 32:517c46f527cd
sync
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 19 Dec 2016 11:00:23 +0100 |
| parents | 9aace933cb64 |
| children | a865c7992a87 |
| 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 | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 10 * | |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 22 * | |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
| 33 #include "DicomStructureSet.h" | |
| 34 | |
| 16 | 35 #include "../../Resources/Orthanc/Core/Logging.h" |
| 36 #include "../../Resources/Orthanc/Core/OrthancException.h" | |
| 32 | 37 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h" |
| 0 | 38 #include "../Messaging/MessagingToolbox.h" |
| 39 | |
| 40 #include <stdio.h> | |
| 41 #include <boost/lexical_cast.hpp> | |
| 42 | |
| 43 namespace OrthancStone | |
| 44 { | |
| 32 | 45 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 46 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 47 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
| 48 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
| 49 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 50 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 51 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 52 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 53 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 54 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 55 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 56 |
| 57 | |
| 58 static uint8_t ConvertColor(double v) | |
| 59 { | |
| 60 if (v < 0) | |
| 61 { | |
| 62 return 0; | |
| 63 } | |
| 64 else if (v >= 255) | |
| 65 { | |
| 66 return 255; | |
| 67 } | |
| 68 else | |
| 69 { | |
| 70 return static_cast<uint8_t>(v); | |
| 71 } | |
| 72 } | |
| 73 | |
| 74 | |
| 75 SliceGeometry DicomStructureSet::ExtractSliceGeometry(double& sliceThickness, | |
|
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
76 OrthancPlugins::IOrthancConnection& orthanc, |
| 32 | 77 const OrthancPlugins::IDicomDataset& tags, |
| 78 size_t contourIndex, | |
| 79 size_t sliceIndex) | |
| 0 | 80 { |
| 32 | 81 using namespace OrthancPlugins; |
| 0 | 82 |
| 32 | 83 size_t size; |
| 84 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
| 85 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
| 86 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || | |
| 87 size != 1) | |
| 0 | 88 { |
| 89 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 90 } | |
| 91 | |
| 32 | 92 DicomDatasetReader reader(tags); |
| 93 std::string parentUid = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
| 94 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
| 95 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, | |
| 96 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); | |
| 0 | 97 |
| 98 std::string post; | |
| 99 orthanc.RestApiPost(post, "/tools/lookup", parentUid); | |
| 100 | |
| 101 Json::Value tmp; | |
| 102 MessagingToolbox::ParseJson(tmp, post); | |
| 103 | |
| 104 if (tmp.type() != Json::arrayValue || | |
| 105 tmp.size() != 1 || | |
| 106 !tmp[0].isMember("Type") || | |
| 107 !tmp[0].isMember("Path") || | |
| 108 tmp[0]["Type"].type() != Json::stringValue || | |
| 109 tmp[0]["ID"].type() != Json::stringValue || | |
| 110 tmp[0]["Type"].asString() != "Instance") | |
| 111 { | |
| 112 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 113 } | |
| 114 | |
| 115 Json::Value parentInstance; | |
| 116 MessagingToolbox::RestApiGet(parentInstance, orthanc, "/instances/" + tmp[0]["ID"].asString()); | |
| 117 | |
| 118 if (parentInstance.type() != Json::objectValue || | |
| 119 !parentInstance.isMember("ParentSeries") || | |
| 120 parentInstance["ParentSeries"].type() != Json::stringValue) | |
| 121 { | |
| 122 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); | |
| 123 } | |
| 124 | |
| 125 std::string parentSeriesId = parentInstance["ParentSeries"].asString(); | |
| 126 bool isFirst = parentSeriesId_.empty(); | |
| 127 | |
| 128 if (isFirst) | |
| 129 { | |
| 130 parentSeriesId_ = parentSeriesId; | |
| 131 } | |
| 132 else if (parentSeriesId_ != parentSeriesId) | |
| 133 { | |
| 134 LOG(ERROR) << "This RT-STRUCT refers to several different series"; | |
| 135 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 136 } | |
| 137 | |
| 32 | 138 FullOrthancDataset parentTags(orthanc, "/instances/" + tmp[0]["ID"].asString() + "/tags"); |
| 139 SliceGeometry slice(parentTags); | |
| 0 | 140 |
| 32 | 141 Vector v; |
| 142 if (GeometryToolbox::ParseVector(v, parentTags, DICOM_TAG_SLICE_THICKNESS) && | |
| 143 v.size() > 0) | |
| 0 | 144 { |
| 32 | 145 sliceThickness = v[0]; |
| 146 } | |
| 147 else | |
| 148 { | |
| 149 sliceThickness = 1; // 1 mm by default | |
| 0 | 150 } |
| 151 | |
| 152 if (isFirst) | |
| 153 { | |
| 154 normal_ = slice.GetNormal(); | |
| 155 } | |
| 156 else if (!GeometryToolbox::IsParallel(normal_, slice.GetNormal())) | |
| 157 { | |
| 158 LOG(ERROR) << "Incompatible orientation of slices in this RT-STRUCT"; | |
| 159 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 160 } | |
| 161 | |
| 162 return slice; | |
| 163 } | |
| 164 | |
| 165 | |
| 166 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const | |
| 167 { | |
| 168 if (index >= structures_.size()) | |
| 169 { | |
| 170 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 171 } | |
| 172 | |
| 173 return structures_[index]; | |
| 174 } | |
| 175 | |
| 176 | |
| 177 bool DicomStructureSet::IsPolygonOnSlice(const Polygon& polygon, | |
| 178 const SliceGeometry& geometry) const | |
| 179 { | |
| 180 double d = boost::numeric::ublas::inner_prod(geometry.GetOrigin(), normal_); | |
| 181 | |
| 182 return (GeometryToolbox::IsNear(d, polygon.projectionAlongNormal_, polygon.sliceThickness_ / 2.0) && | |
| 183 !polygon.points_.empty()); | |
| 184 } | |
| 185 | |
| 186 | |
|
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
187 DicomStructureSet::DicomStructureSet(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 188 const std::string& instanceId) |
| 189 { | |
| 32 | 190 using namespace OrthancPlugins; |
| 0 | 191 |
| 32 | 192 FullOrthancDataset tags(orthanc, "/instances/" + instanceId + "/tags"); |
| 193 DicomDatasetReader reader(tags); | |
| 194 | |
| 195 size_t count, tmp; | |
| 196 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
| 197 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
| 198 tmp != count || | |
| 199 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
| 200 tmp != count) | |
| 0 | 201 { |
| 202 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 203 } | |
| 204 | |
| 32 | 205 structures_.resize(count); |
| 206 for (size_t i = 0; i < count; i++) | |
| 207 { | |
| 208 structures_[i].interpretation_ = reader.GetStringValue(DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, | |
| 209 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), | |
| 210 "No interpretation"); | |
| 0 | 211 |
| 32 | 212 structures_[i].name_ = reader.GetStringValue(DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
| 213 DICOM_TAG_ROI_NAME), | |
| 214 "No interpretation"); | |
| 0 | 215 |
| 216 Vector color; | |
| 32 | 217 if (GeometryToolbox::ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
| 218 DICOM_TAG_ROI_DISPLAY_COLOR)) && | |
| 219 color.size() == 3) | |
| 0 | 220 { |
| 32 | 221 structures_[i].red_ = ConvertColor(color[0]); |
| 222 structures_[i].green_ = ConvertColor(color[1]); | |
| 223 structures_[i].blue_ = ConvertColor(color[2]); | |
| 224 } | |
| 225 else | |
| 226 { | |
| 227 structures_[i].red_ = 255; | |
| 228 structures_[i].green_ = 0; | |
| 229 structures_[i].blue_ = 0; | |
| 0 | 230 } |
| 231 | |
| 32 | 232 size_t countSlices; |
| 233 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
| 234 DICOM_TAG_CONTOUR_SEQUENCE))) | |
| 235 { | |
| 236 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 237 } | |
| 0 | 238 |
| 239 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
| 240 << "\" with interpretation \"" << structures_[i].interpretation_ | |
| 32 | 241 << "\" containing " << countSlices << " slices (color: " |
| 0 | 242 << static_cast<int>(structures_[i].red_) << "," |
| 243 << static_cast<int>(structures_[i].green_) << "," | |
| 244 << static_cast<int>(structures_[i].blue_) << ")"; | |
| 245 | |
| 32 | 246 for (size_t j = 0; j < countSlices; j++) |
| 0 | 247 { |
| 32 | 248 unsigned int countPoints; |
| 0 | 249 |
| 32 | 250 if (!reader.GetUnsignedIntegerValue(countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
| 251 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
| 252 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) | |
| 253 { | |
| 254 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 255 } | |
| 256 | |
| 257 LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; | |
| 0 | 258 |
| 32 | 259 std::string type = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
| 260 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
| 261 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); | |
| 262 if (type != "CLOSED_PLANAR") | |
| 0 | 263 { |
| 32 | 264 LOG(ERROR) << "Cannot handle contour with geometry type: " << type; |
| 0 | 265 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 266 } | |
| 267 | |
| 32 | 268 // The "CountourData" tag (3006,0050) is too large to be |
| 269 // returned by the "/instances/{id}/tags" URI: Access it using | |
| 270 // the raw "/instances/{id}/content/{...}" endpoint | |
| 0 | 271 std::string slicesData; |
| 272 orthanc.RestApiGet(slicesData, "/instances/" + instanceId + "/content/3006-0039/" + | |
| 273 boost::lexical_cast<std::string>(i) + "/3006-0040/" + | |
| 274 boost::lexical_cast<std::string>(j) + "/3006-0050"); | |
| 275 | |
| 276 Vector points; | |
| 277 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
| 32 | 278 points.size() != 3 * countPoints) |
| 0 | 279 { |
| 280 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 281 } | |
| 282 | |
| 283 Polygon polygon; | |
| 32 | 284 SliceGeometry geometry = ExtractSliceGeometry(polygon.sliceThickness_, orthanc, tags, i, j); |
| 0 | 285 polygon.projectionAlongNormal_ = geometry.ProjectAlongNormal(geometry.GetOrigin()); |
| 286 | |
| 32 | 287 for (size_t k = 0; k < countPoints; k++) |
| 0 | 288 { |
| 289 Vector v(3); | |
| 290 v[0] = points[3 * k]; | |
| 291 v[1] = points[3 * k + 1]; | |
| 292 v[2] = points[3 * k + 2]; | |
| 293 | |
| 294 if (!GeometryToolbox::IsNear(geometry.ProjectAlongNormal(v), | |
| 295 polygon.projectionAlongNormal_, | |
| 296 polygon.sliceThickness_ / 2.0 /* in mm */)) | |
| 297 { | |
| 298 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; | |
| 299 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 300 } | |
| 301 | |
| 302 polygon.points_.push_back(v); | |
| 303 } | |
| 304 | |
| 305 structures_[i].polygons_.push_back(polygon); | |
| 306 } | |
| 307 } | |
| 308 | |
| 309 if (parentSeriesId_.empty() || | |
| 310 normal_.size() != 3) | |
| 311 { | |
| 312 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 313 } | |
| 314 } | |
| 315 | |
| 316 | |
| 317 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
| 318 { | |
| 319 const Structure& structure = GetStructure(index); | |
| 320 | |
| 321 Vector center; | |
| 322 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
| 323 if (structure.polygons_.empty()) | |
| 324 { | |
| 325 return center; | |
| 326 } | |
| 327 | |
| 328 double n = static_cast<double>(structure.polygons_.size()); | |
| 329 | |
| 330 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 331 polygon != structure.polygons_.end(); ++polygon) | |
| 332 { | |
| 333 if (!polygon->points_.empty()) | |
| 334 { | |
| 335 center += polygon->points_.front() / n; | |
| 336 } | |
| 337 } | |
| 338 | |
| 339 return center; | |
| 340 } | |
| 341 | |
| 342 | |
| 343 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 344 { | |
| 345 return GetStructure(index).name_; | |
| 346 } | |
| 347 | |
| 348 | |
| 349 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 350 { | |
| 351 return GetStructure(index).interpretation_; | |
| 352 } | |
| 353 | |
| 354 | |
| 355 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
| 356 uint8_t& green, | |
| 357 uint8_t& blue, | |
| 358 size_t index) const | |
| 359 { | |
| 360 const Structure& s = GetStructure(index); | |
| 361 red = s.red_; | |
| 362 green = s.green_; | |
| 363 blue = s.blue_; | |
| 364 } | |
| 365 | |
| 366 | |
| 367 void DicomStructureSet::Render(CairoContext& context, | |
| 368 const SliceGeometry& slice) const | |
| 369 { | |
| 370 cairo_t* cr = context.GetObject(); | |
| 371 | |
| 372 for (Structures::const_iterator structure = structures_.begin(); | |
| 373 structure != structures_.end(); ++structure) | |
| 374 { | |
| 375 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 376 polygon != structure->polygons_.end(); ++polygon) | |
| 377 { | |
| 378 if (IsPolygonOnSlice(*polygon, slice)) | |
| 379 { | |
| 380 context.SetSourceColor(structure->red_, structure->green_, structure->blue_); | |
| 381 | |
| 382 Points::const_iterator p = polygon->points_.begin(); | |
| 383 | |
| 384 double x, y; | |
| 385 slice.ProjectPoint(x, y, *p); | |
| 386 cairo_move_to(cr, x, y); | |
| 387 ++p; | |
| 388 | |
| 389 while (p != polygon->points_.end()) | |
| 390 { | |
| 391 slice.ProjectPoint(x, y, *p); | |
| 392 cairo_line_to(cr, x, y); | |
| 393 ++p; | |
| 394 } | |
| 395 | |
| 396 slice.ProjectPoint(x, y, *polygon->points_.begin()); | |
| 397 cairo_line_to(cr, x, y); | |
| 398 } | |
| 399 } | |
| 400 } | |
| 401 | |
| 402 cairo_stroke(cr); | |
| 403 } | |
| 404 } |