Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 40:7207a407bcd8
shared copyright with osimis
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 04 Jan 2017 16:37:42 +0100 |
| parents | 6465fbd23bce |
| children | 28956ed68280 |
| 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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7207a407bcd8
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changeset
|
5 * Copyright (C) 2017 Osimis, Belgium |
| 0 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU General Public License as | |
| 9 * published by the Free Software Foundation, either version 3 of the | |
| 10 * License, or (at your option) any later version. | |
| 11 * | |
| 12 * In addition, as a special exception, the copyright holders of this | |
| 13 * program give permission to link the code of its release with the | |
| 14 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 15 * that use the same license as the "OpenSSL" library), and distribute | |
| 16 * the linked executables. You must obey the GNU General Public License | |
| 17 * in all respects for all of the code used other than "OpenSSL". If you | |
| 18 * modify file(s) with this exception, you may extend this exception to | |
| 19 * your version of the file(s), but you are not obligated to do so. If | |
| 20 * you do not wish to do so, delete this exception statement from your | |
| 21 * version. If you delete this exception statement from all source files | |
| 22 * in the program, then also delete it here. | |
| 23 * | |
| 24 * This program is distributed in the hope that it will be useful, but | |
| 25 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 27 * General Public License for more details. | |
| 28 * | |
| 29 * You should have received a copy of the GNU General Public License | |
| 30 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 31 **/ | |
| 32 | |
| 33 | |
| 34 #include "DicomStructureSet.h" | |
| 35 | |
| 16 | 36 #include "../../Resources/Orthanc/Core/Logging.h" |
| 37 #include "../../Resources/Orthanc/Core/OrthancException.h" | |
| 32 | 38 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h" |
| 35 | 39 #include "../Toolbox/MessagingToolbox.h" |
| 0 | 40 |
| 41 #include <stdio.h> | |
| 42 #include <boost/lexical_cast.hpp> | |
| 43 | |
| 44 namespace OrthancStone | |
| 45 { | |
| 32 | 46 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 47 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 48 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
| 49 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
| 50 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 51 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 52 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 53 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 54 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 55 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 56 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 57 |
| 58 | |
| 59 static uint8_t ConvertColor(double v) | |
| 60 { | |
| 61 if (v < 0) | |
| 62 { | |
| 63 return 0; | |
| 64 } | |
| 65 else if (v >= 255) | |
| 66 { | |
| 67 return 255; | |
| 68 } | |
| 69 else | |
| 70 { | |
| 71 return static_cast<uint8_t>(v); | |
| 72 } | |
| 73 } | |
| 74 | |
| 75 | |
| 76 SliceGeometry DicomStructureSet::ExtractSliceGeometry(double& sliceThickness, | |
|
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77 OrthancPlugins::IOrthancConnection& orthanc, |
| 32 | 78 const OrthancPlugins::IDicomDataset& tags, |
| 79 size_t contourIndex, | |
| 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); |
| 94 std::string parentUid = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
| 95 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
| 96 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, | |
| 97 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); | |
| 0 | 98 |
| 34 | 99 Json::Value parentLookup; |
| 100 MessagingToolbox::RestApiPost(parentLookup, orthanc, "/tools/lookup", parentUid); | |
| 0 | 101 |
| 34 | 102 if (parentLookup.type() != Json::arrayValue || |
| 103 parentLookup.size() != 1 || | |
| 104 !parentLookup[0].isMember("Type") || | |
| 105 !parentLookup[0].isMember("Path") || | |
| 106 parentLookup[0]["Type"].type() != Json::stringValue || | |
| 107 parentLookup[0]["ID"].type() != Json::stringValue || | |
| 108 parentLookup[0]["Type"].asString() != "Instance") | |
| 0 | 109 { |
| 110 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 111 } | |
| 112 | |
| 113 Json::Value parentInstance; | |
| 34 | 114 MessagingToolbox::RestApiGet(parentInstance, orthanc, "/instances/" + parentLookup[0]["ID"].asString()); |
| 0 | 115 |
| 116 if (parentInstance.type() != Json::objectValue || | |
| 117 !parentInstance.isMember("ParentSeries") || | |
| 118 parentInstance["ParentSeries"].type() != Json::stringValue) | |
| 119 { | |
| 120 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); | |
| 121 } | |
| 122 | |
| 123 std::string parentSeriesId = parentInstance["ParentSeries"].asString(); | |
| 124 bool isFirst = parentSeriesId_.empty(); | |
| 125 | |
| 126 if (isFirst) | |
| 127 { | |
| 128 parentSeriesId_ = parentSeriesId; | |
| 129 } | |
| 130 else if (parentSeriesId_ != parentSeriesId) | |
| 131 { | |
| 132 LOG(ERROR) << "This RT-STRUCT refers to several different series"; | |
| 133 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 134 } | |
| 135 | |
| 34 | 136 FullOrthancDataset parentTags(orthanc, "/instances/" + parentLookup[0]["ID"].asString() + "/tags"); |
| 32 | 137 SliceGeometry slice(parentTags); |
| 0 | 138 |
| 32 | 139 Vector v; |
| 140 if (GeometryToolbox::ParseVector(v, parentTags, DICOM_TAG_SLICE_THICKNESS) && | |
| 141 v.size() > 0) | |
| 0 | 142 { |
| 32 | 143 sliceThickness = v[0]; |
| 144 } | |
| 145 else | |
| 146 { | |
| 147 sliceThickness = 1; // 1 mm by default | |
| 0 | 148 } |
| 149 | |
| 150 if (isFirst) | |
| 151 { | |
| 152 normal_ = slice.GetNormal(); | |
| 153 } | |
| 154 else if (!GeometryToolbox::IsParallel(normal_, slice.GetNormal())) | |
| 155 { | |
| 156 LOG(ERROR) << "Incompatible orientation of slices in this RT-STRUCT"; | |
| 157 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 158 } | |
| 159 | |
| 160 return slice; | |
| 161 } | |
| 162 | |
| 163 | |
| 164 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const | |
| 165 { | |
| 166 if (index >= structures_.size()) | |
| 167 { | |
| 168 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 169 } | |
| 170 | |
| 171 return structures_[index]; | |
| 172 } | |
| 173 | |
| 174 | |
| 175 bool DicomStructureSet::IsPolygonOnSlice(const Polygon& polygon, | |
| 176 const SliceGeometry& geometry) const | |
| 177 { | |
| 178 double d = boost::numeric::ublas::inner_prod(geometry.GetOrigin(), normal_); | |
| 179 | |
| 180 return (GeometryToolbox::IsNear(d, polygon.projectionAlongNormal_, polygon.sliceThickness_ / 2.0) && | |
| 181 !polygon.points_.empty()); | |
| 182 } | |
| 183 | |
| 184 | |
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parents:
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185 DicomStructureSet::DicomStructureSet(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 186 const std::string& instanceId) |
| 187 { | |
| 32 | 188 using namespace OrthancPlugins; |
| 0 | 189 |
| 32 | 190 FullOrthancDataset tags(orthanc, "/instances/" + instanceId + "/tags"); |
| 191 DicomDatasetReader reader(tags); | |
| 192 | |
| 193 size_t count, tmp; | |
| 194 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
| 195 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
| 196 tmp != count || | |
| 197 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
| 198 tmp != count) | |
| 0 | 199 { |
| 200 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 201 } | |
| 202 | |
| 32 | 203 structures_.resize(count); |
| 204 for (size_t i = 0; i < count; i++) | |
| 205 { | |
| 206 structures_[i].interpretation_ = reader.GetStringValue(DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, | |
| 207 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), | |
| 208 "No interpretation"); | |
| 0 | 209 |
| 32 | 210 structures_[i].name_ = reader.GetStringValue(DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
| 211 DICOM_TAG_ROI_NAME), | |
| 212 "No interpretation"); | |
| 0 | 213 |
| 214 Vector color; | |
| 32 | 215 if (GeometryToolbox::ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
| 216 DICOM_TAG_ROI_DISPLAY_COLOR)) && | |
| 217 color.size() == 3) | |
| 0 | 218 { |
| 32 | 219 structures_[i].red_ = ConvertColor(color[0]); |
| 220 structures_[i].green_ = ConvertColor(color[1]); | |
| 221 structures_[i].blue_ = ConvertColor(color[2]); | |
| 222 } | |
| 223 else | |
| 224 { | |
| 225 structures_[i].red_ = 255; | |
| 226 structures_[i].green_ = 0; | |
| 227 structures_[i].blue_ = 0; | |
| 0 | 228 } |
| 229 | |
| 32 | 230 size_t countSlices; |
| 231 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
| 232 DICOM_TAG_CONTOUR_SEQUENCE))) | |
| 233 { | |
| 234 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 235 } | |
| 0 | 236 |
| 237 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
| 238 << "\" with interpretation \"" << structures_[i].interpretation_ | |
| 32 | 239 << "\" containing " << countSlices << " slices (color: " |
| 0 | 240 << static_cast<int>(structures_[i].red_) << "," |
| 241 << static_cast<int>(structures_[i].green_) << "," | |
| 242 << static_cast<int>(structures_[i].blue_) << ")"; | |
| 243 | |
| 32 | 244 for (size_t j = 0; j < countSlices; j++) |
| 0 | 245 { |
| 32 | 246 unsigned int countPoints; |
| 0 | 247 |
| 32 | 248 if (!reader.GetUnsignedIntegerValue(countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
| 249 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
| 250 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) | |
| 251 { | |
| 252 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 253 } | |
| 254 | |
| 255 LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; | |
| 0 | 256 |
| 32 | 257 std::string type = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
| 258 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
| 259 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); | |
| 260 if (type != "CLOSED_PLANAR") | |
| 0 | 261 { |
| 32 | 262 LOG(ERROR) << "Cannot handle contour with geometry type: " << type; |
| 0 | 263 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 264 } | |
| 265 | |
| 32 | 266 // The "CountourData" tag (3006,0050) is too large to be |
| 267 // returned by the "/instances/{id}/tags" URI: Access it using | |
| 268 // the raw "/instances/{id}/content/{...}" endpoint | |
| 0 | 269 std::string slicesData; |
| 270 orthanc.RestApiGet(slicesData, "/instances/" + instanceId + "/content/3006-0039/" + | |
| 271 boost::lexical_cast<std::string>(i) + "/3006-0040/" + | |
| 272 boost::lexical_cast<std::string>(j) + "/3006-0050"); | |
| 273 | |
| 274 Vector points; | |
| 275 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
| 32 | 276 points.size() != 3 * countPoints) |
| 0 | 277 { |
| 278 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 279 } | |
| 280 | |
| 281 Polygon polygon; | |
| 32 | 282 SliceGeometry geometry = ExtractSliceGeometry(polygon.sliceThickness_, orthanc, tags, i, j); |
| 0 | 283 polygon.projectionAlongNormal_ = geometry.ProjectAlongNormal(geometry.GetOrigin()); |
| 284 | |
| 32 | 285 for (size_t k = 0; k < countPoints; k++) |
| 0 | 286 { |
| 287 Vector v(3); | |
| 288 v[0] = points[3 * k]; | |
| 289 v[1] = points[3 * k + 1]; | |
| 290 v[2] = points[3 * k + 2]; | |
| 291 | |
| 292 if (!GeometryToolbox::IsNear(geometry.ProjectAlongNormal(v), | |
| 293 polygon.projectionAlongNormal_, | |
| 294 polygon.sliceThickness_ / 2.0 /* in mm */)) | |
| 295 { | |
| 296 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; | |
| 297 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 298 } | |
| 299 | |
| 300 polygon.points_.push_back(v); | |
| 301 } | |
| 302 | |
| 303 structures_[i].polygons_.push_back(polygon); | |
| 304 } | |
| 305 } | |
| 306 | |
| 307 if (parentSeriesId_.empty() || | |
| 308 normal_.size() != 3) | |
| 309 { | |
| 310 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 311 } | |
| 312 } | |
| 313 | |
| 314 | |
| 315 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
| 316 { | |
| 317 const Structure& structure = GetStructure(index); | |
| 318 | |
| 319 Vector center; | |
| 320 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
| 321 if (structure.polygons_.empty()) | |
| 322 { | |
| 323 return center; | |
| 324 } | |
| 325 | |
| 326 double n = static_cast<double>(structure.polygons_.size()); | |
| 327 | |
| 328 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 329 polygon != structure.polygons_.end(); ++polygon) | |
| 330 { | |
| 331 if (!polygon->points_.empty()) | |
| 332 { | |
| 333 center += polygon->points_.front() / n; | |
| 334 } | |
| 335 } | |
| 336 | |
| 337 return center; | |
| 338 } | |
| 339 | |
| 340 | |
| 341 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 342 { | |
| 343 return GetStructure(index).name_; | |
| 344 } | |
| 345 | |
| 346 | |
| 347 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 348 { | |
| 349 return GetStructure(index).interpretation_; | |
| 350 } | |
| 351 | |
| 352 | |
| 353 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
| 354 uint8_t& green, | |
| 355 uint8_t& blue, | |
| 356 size_t index) const | |
| 357 { | |
| 358 const Structure& s = GetStructure(index); | |
| 359 red = s.red_; | |
| 360 green = s.green_; | |
| 361 blue = s.blue_; | |
| 362 } | |
| 363 | |
| 364 | |
| 365 void DicomStructureSet::Render(CairoContext& context, | |
| 366 const SliceGeometry& slice) const | |
| 367 { | |
| 368 cairo_t* cr = context.GetObject(); | |
| 369 | |
| 370 for (Structures::const_iterator structure = structures_.begin(); | |
| 371 structure != structures_.end(); ++structure) | |
| 372 { | |
| 373 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 374 polygon != structure->polygons_.end(); ++polygon) | |
| 375 { | |
| 376 if (IsPolygonOnSlice(*polygon, slice)) | |
| 377 { | |
| 378 context.SetSourceColor(structure->red_, structure->green_, structure->blue_); | |
| 379 | |
| 380 Points::const_iterator p = polygon->points_.begin(); | |
| 381 | |
| 382 double x, y; | |
| 383 slice.ProjectPoint(x, y, *p); | |
| 384 cairo_move_to(cr, x, y); | |
| 385 ++p; | |
| 386 | |
| 387 while (p != polygon->points_.end()) | |
| 388 { | |
| 389 slice.ProjectPoint(x, y, *p); | |
| 390 cairo_line_to(cr, x, y); | |
| 391 ++p; | |
| 392 } | |
| 393 | |
| 394 slice.ProjectPoint(x, y, *polygon->points_.begin()); | |
| 395 cairo_line_to(cr, x, y); | |
| 396 } | |
| 397 } | |
| 398 } | |
| 399 | |
| 400 cairo_stroke(cr); | |
| 401 } | |
| 402 } |