Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 1013:53cc787bd7bc toa2019092301
- Added an optimized ProjectPoint2 to CoordinateSystem3D. It has *not* replaced
the ProjectPoint method because more tests need to be written.
- ProjectPointOntoPlane2 is a faster version of
GeometryToolbox::ProjectPointOntoPlane. Same remark as above.
- DicomStructureSet.cpp now uses this optimized call.
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Mon, 23 Sep 2019 15:18:33 +0200 |
| parents | 4f28d9459e31 |
| children | 709aa65aca17 2d8ab34c8c91 |
| 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 | |
| 439 | 5 * Copyright (C) 2017-2019 Osimis S.A., 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" | |
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23 #include "DicomStructureSetUtils.h" |
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25 #include "../Toolbox/GeometryToolbox.h" |
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27 #include <Core/Logging.h> |
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28 #include <Core/OrthancException.h> |
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29 #include <Core/Toolbox.h> |
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30 #include <Plugins/Samples/Common/FullOrthancDataset.h> |
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31 #include <Plugins/Samples/Common/DicomDatasetReader.h> |
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32 |
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33 #if defined(_MSC_VER) |
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34 #pragma warning(push) |
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35 #pragma warning(disable:4244) |
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36 #endif |
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37 |
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38 #include <limits> |
| 0 | 39 #include <stdio.h> |
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40 #include <boost/geometry.hpp> |
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41 #include <boost/geometry/geometries/point_xy.hpp> |
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42 #include <boost/geometry/geometries/polygon.hpp> |
| 137 | 43 #include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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44 |
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45 #if defined(_MSC_VER) |
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46 #pragma warning(pop) |
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47 #endif |
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48 |
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49 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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50 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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51 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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52 |
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53 |
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54 static void Union(BoostMultiPolygon& output, |
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55 std::vector<BoostPolygon>& input) |
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56 { |
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57 for (size_t i = 0; i < input.size(); i++) |
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58 { |
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59 boost::geometry::correct(input[i]); |
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60 } |
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61 |
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62 if (input.size() == 0) |
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63 { |
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64 output.clear(); |
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65 } |
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66 else if (input.size() == 1) |
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67 { |
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68 output.resize(1); |
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69 output[0] = input[0]; |
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70 } |
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71 else |
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72 { |
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73 boost::geometry::union_(input[0], input[1], output); |
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74 |
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75 for (size_t i = 0; i < input.size(); i++) |
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76 { |
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77 BoostMultiPolygon tmp; |
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78 boost::geometry::union_(output, input[i], tmp); |
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79 output = tmp; |
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80 } |
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81 } |
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82 } |
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83 |
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84 #ifdef USE_BOOST_UNION_FOR_POLYGONS |
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85 |
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86 static BoostPolygon CreateRectangle(float x1, float y1, |
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87 float x2, float y2) |
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88 { |
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89 BoostPolygon r; |
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90 boost::geometry::append(r, BoostPoint(x1, y1)); |
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91 boost::geometry::append(r, BoostPoint(x1, y2)); |
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92 boost::geometry::append(r, BoostPoint(x2, y2)); |
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93 boost::geometry::append(r, BoostPoint(x2, y1)); |
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94 return r; |
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95 } |
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96 |
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97 #else |
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98 |
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99 namespace OrthancStone |
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100 { |
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101 static RtStructRectangleInSlab CreateRectangle(float x1, float y1, |
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102 float x2, float y2) |
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103 { |
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104 RtStructRectangleInSlab rect; |
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105 rect.xmin = std::min(x1, x2); |
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106 rect.xmax = std::max(x1, x2); |
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107 rect.ymin = std::min(y1, y2); |
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108 rect.ymax = std::max(y1, y2); |
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109 return rect; |
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110 } |
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111 |
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112 bool CompareRectanglesForProjection(const std::pair<RtStructRectangleInSlab,double>& r1, const std::pair<RtStructRectangleInSlab, double>& r2) |
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113 { |
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114 return r1.second < r2.second; |
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115 } |
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116 |
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117 bool CompareSlabsY(const RtStructRectanglesInSlab& r1, const RtStructRectanglesInSlab& r2) |
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118 { |
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119 if ((r1.size() == 0) || (r2.size() == 0)) |
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120 return false; |
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121 |
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122 return r1[0].ymax < r2[0].ymax; |
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123 } |
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124 } |
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125 |
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126 #endif |
| 0 | 127 |
| 128 namespace OrthancStone | |
| 129 { | |
| 32 | 130 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 131 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 132 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
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133 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); |
| 32 | 134 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); |
| 135 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 136 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 137 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 138 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 139 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 140 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 141 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 142 |
| 143 | |
| 144 static uint8_t ConvertColor(double v) | |
| 145 { | |
| 146 if (v < 0) | |
| 147 { | |
| 148 return 0; | |
| 149 } | |
| 150 else if (v >= 255) | |
| 151 { | |
| 152 return 255; | |
| 153 } | |
| 154 else | |
| 155 { | |
| 156 return static_cast<uint8_t>(v); | |
| 157 } | |
| 158 } | |
| 159 | |
| 160 | |
|
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161 static bool ParseVector(Vector& target, |
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162 const OrthancPlugins::IDicomDataset& dataset, |
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163 const OrthancPlugins::DicomPath& tag) |
| 0 | 164 { |
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165 std::string value; |
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166 return (dataset.GetStringValue(value, tag) && |
|
158
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167 LinearAlgebra::ParseVector(target, value)); |
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168 } |
| 0 | 169 |
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170 void DicomStructureSet::Polygon::CheckPointIsOnSlice(const Vector& v) const |
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171 { |
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172 if (hasSlice_) |
| 0 | 173 { |
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174 double magnitude = |
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175 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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176 if(!LinearAlgebra::IsNear( |
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177 magnitude, |
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178 projectionAlongNormal_, |
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179 sliceThickness_ / 2.0 /* in mm */ )) |
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180 { |
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181 LOG(ERROR) << "This RT-STRUCT contains a point that is off the " |
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182 << "slice of its instance | " |
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183 << "magnitude = " << magnitude << " | " |
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184 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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185 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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186 |
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187 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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188 } |
| 0 | 189 } |
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190 } |
| 0 | 191 |
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192 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const |
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193 { |
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194 if (hasSlice_) |
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195 { |
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196 double magnitude = |
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197 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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198 bool onSlice = LinearAlgebra::IsNear( |
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199 magnitude, |
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200 projectionAlongNormal_, |
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201 sliceThickness_ / 2.0 /* in mm */); |
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202 if (!onSlice) |
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203 { |
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204 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
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205 << "slice of its instance | " |
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206 << "magnitude = " << magnitude << " | " |
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207 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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208 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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209 } |
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210 return onSlice; |
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211 } |
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212 else |
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213 { |
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214 return true; |
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215 } |
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216 } |
| 0 | 217 |
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218 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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219 { |
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220 #if 1 |
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221 // BGO 2019-09-03 |
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222 if (IsPointOnSliceIfAny(v)) |
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223 { |
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224 points_.push_back(v); |
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225 } |
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226 #else |
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227 CheckPoint(v); |
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228 points_.push_back(v); |
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229 #endif |
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230 } |
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231 |
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232 |
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233 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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234 { |
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235 if (hasSlice_) |
| 0 | 236 { |
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237 return true; |
| 32 | 238 } |
| 239 else | |
| 240 { | |
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241 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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242 |
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243 if (it == slices.end()) |
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244 { |
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245 return false; |
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246 } |
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247 else |
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248 { |
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249 const CoordinateSystem3D& geometry = it->second.geometry_; |
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250 |
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251 hasSlice_ = true; |
| 131 | 252 geometry_ = geometry; |
| 253 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
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254 sliceThickness_ = it->second.thickness_; |
| 0 | 255 |
| 131 | 256 extent_.Reset(); |
| 257 | |
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258 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it) |
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259 { |
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260 if (IsPointOnSliceIfAny(*it)) |
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261 { |
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262 double x, y; |
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263 geometry.ProjectPoint2(x, y, *it); |
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264 extent_.AddPoint(x, y); |
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265 } |
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266 } |
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267 return true; |
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268 } |
| 0 | 269 } |
| 270 } | |
| 271 | |
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272 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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273 { |
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274 bool isOpposite = false; |
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275 |
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276 if (points_.empty() || |
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277 !hasSlice_ || |
| 131 | 278 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
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279 { |
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280 return false; |
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281 } |
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282 |
| 131 | 283 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
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284 |
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285 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, |
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286 sliceThickness_ / 2.0)); |
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287 } |
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288 |
| 131 | 289 bool DicomStructureSet::Polygon::Project(double& x1, |
| 290 double& y1, | |
| 291 double& x2, | |
| 292 double& y2, | |
| 293 const CoordinateSystem3D& slice) const | |
| 294 { | |
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295 // TODO: optimize this method using a sweep-line algorithm for polygons |
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296 |
| 131 | 297 if (!hasSlice_ || |
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298 points_.size() <= 1) |
| 131 | 299 { |
| 300 return false; | |
| 301 } | |
| 302 | |
| 303 double x, y; | |
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304 geometry_.ProjectPoint2(x, y, slice.GetOrigin()); |
| 131 | 305 |
| 306 bool isOpposite; | |
| 307 if (GeometryToolbox::IsParallelOrOpposite | |
| 308 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
| 309 { | |
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310 // plane is constant Y |
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311 |
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312 if (y < extent_.GetY1() || |
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313 y > extent_.GetY2()) |
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314 { |
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315 // The polygon does not intersect the input slice |
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316 return false; |
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317 } |
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318 |
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319 bool isFirst = true; |
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320 double xmin = std::numeric_limits<double>::infinity(); |
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321 double xmax = -std::numeric_limits<double>::infinity(); |
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322 |
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323 double prevX, prevY; |
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324 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
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325 |
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326 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 327 { |
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328 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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329 double curX, curY; |
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330 geometry_.ProjectPoint2(curX, curY, points_[i]); |
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331 |
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332 // if prev* and cur* are on opposite sides of y, this means that the |
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333 // segment intersects the plane. |
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334 if ((prevY < y && curY > y) || |
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335 (prevY > y && curY < y)) |
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336 { |
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337 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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338 xmin = std::min(xmin, p); |
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339 xmax = std::max(xmax, p); |
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340 isFirst = false; |
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341 |
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342 // xmin and xmax represent the extent of the rectangle along the |
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343 // intersection between the plane and the polygon geometry |
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344 |
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345 } |
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346 |
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347 prevX = curX; |
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348 prevY = curY; |
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349 } |
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350 |
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351 // if NO segment intersects the plane |
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352 if (isFirst) |
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353 { |
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354 return false; |
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355 } |
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356 else |
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357 { |
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358 // y is the plane y coord in the polygon geometry |
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359 // xmin and xmax are ALSO expressed in the polygon geometry |
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360 |
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361 // let's convert them to 3D world geometry... |
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362 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
| 131 | 363 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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364 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
| 131 | 365 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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366 |
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367 // then to the cutting plane geometry... |
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368 slice.ProjectPoint2(x1, y1, p1); |
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369 slice.ProjectPoint2(x2, y2, p2); |
| 131 | 370 return true; |
| 371 } | |
| 372 } | |
| 373 else if (GeometryToolbox::IsParallelOrOpposite | |
| 374 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
| 375 { | |
|
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376 // plane is constant X |
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377 |
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378 /* |
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379 Please read the comments in the section above, by taking into account |
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380 the fact that, in this case, the plane has a constant X, not Y (in |
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381 polygon geometry_ coordinates) |
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382 */ |
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383 |
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384 if (x < extent_.GetX1() || |
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385 x > extent_.GetX2()) |
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386 { |
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387 return false; |
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388 } |
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389 |
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390 bool isFirst = true; |
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391 double ymin = std::numeric_limits<double>::infinity(); |
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392 double ymax = -std::numeric_limits<double>::infinity(); |
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393 |
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394 double prevX, prevY; |
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395 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
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396 |
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397 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 398 { |
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399 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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400 double curX, curY; |
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401 geometry_.ProjectPoint2(curX, curY, points_[i]); |
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402 |
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403 if ((prevX < x && curX > x) || |
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404 (prevX > x && curX < x)) |
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405 { |
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406 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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407 ymin = std::min(ymin, p); |
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408 ymax = std::max(ymax, p); |
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409 isFirst = false; |
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410 } |
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411 |
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412 prevX = curX; |
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413 prevY = curY; |
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414 } |
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415 |
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416 if (isFirst) |
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417 { |
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418 return false; |
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419 } |
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420 else |
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421 { |
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422 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
| 131 | 423 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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424 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
| 131 | 425 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
| 426 | |
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427 slice.ProjectPoint2(x1, y1, p1); |
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428 slice.ProjectPoint2(x2, y2, p2); |
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429 |
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430 // TODO WHY THIS??? |
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431 y1 = -y1; |
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432 y2 = -y2; |
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433 |
| 131 | 434 return true; |
| 435 } | |
| 436 } | |
| 437 else | |
| 438 { | |
| 439 // Should not happen | |
| 440 return false; | |
| 441 } | |
| 442 } | |
| 443 | |
| 444 | |
| 0 | 445 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
| 446 { | |
| 447 if (index >= structures_.size()) | |
| 448 { | |
| 125 | 449 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
| 0 | 450 } |
| 451 | |
| 452 return structures_[index]; | |
| 453 } | |
| 454 | |
| 455 | |
| 125 | 456 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
| 0 | 457 { |
| 125 | 458 if (index >= structures_.size()) |
| 459 { | |
| 460 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 0 | 461 } |
| 462 | |
| 463 return structures_[index]; | |
| 464 } | |
| 465 | |
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466 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags) |
| 0 | 467 { |
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468 OrthancPlugins::DicomDatasetReader reader(tags); |
| 32 | 469 |
| 470 size_t count, tmp; | |
| 471 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
| 472 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
| 473 tmp != count || | |
| 474 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
| 475 tmp != count) | |
| 0 | 476 { |
| 477 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 478 } | |
| 479 | |
| 32 | 480 structures_.resize(count); |
| 481 for (size_t i = 0; i < count; i++) | |
| 482 { | |
|
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483 structures_[i].interpretation_ = reader.GetStringValue |
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484 (OrthancPlugins::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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485 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
|
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486 "No interpretation"); |
| 0 | 487 |
|
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488 structures_[i].name_ = reader.GetStringValue |
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489 (OrthancPlugins::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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490 DICOM_TAG_ROI_NAME), |
|
949
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OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
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491 "No name"); |
| 0 | 492 |
| 493 Vector color; | |
|
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494 if (ParseVector(color, tags, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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495 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 496 color.size() == 3) |
| 0 | 497 { |
| 32 | 498 structures_[i].red_ = ConvertColor(color[0]); |
| 499 structures_[i].green_ = ConvertColor(color[1]); | |
| 500 structures_[i].blue_ = ConvertColor(color[2]); | |
| 501 } | |
| 502 else | |
| 503 { | |
| 504 structures_[i].red_ = 255; | |
| 505 structures_[i].green_ = 0; | |
| 506 structures_[i].blue_ = 0; | |
| 0 | 507 } |
| 508 | |
| 32 | 509 size_t countSlices; |
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510 if (!tags.GetSequenceSize(countSlices, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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511 DICOM_TAG_CONTOUR_SEQUENCE))) |
| 32 | 512 { |
|
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513 countSlices = 0; |
| 32 | 514 } |
| 0 | 515 |
|
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|
516 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
| 0 | 517 << "\" with interpretation \"" << structures_[i].interpretation_ |
| 32 | 518 << "\" containing " << countSlices << " slices (color: " |
| 0 | 519 << static_cast<int>(structures_[i].red_) << "," |
| 520 << static_cast<int>(structures_[i].green_) << "," | |
| 521 << static_cast<int>(structures_[i].blue_) << ")"; | |
| 522 | |
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523 // These temporary variables avoid allocating many vectors in the loop below |
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524 OrthancPlugins::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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525 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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526 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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527 |
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528 OrthancPlugins::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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529 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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530 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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531 |
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532 OrthancPlugins::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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533 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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534 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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535 |
|
981
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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536 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
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537 OrthancPlugins::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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538 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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539 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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540 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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541 |
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542 OrthancPlugins::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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543 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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544 DICOM_TAG_CONTOUR_DATA); |
|
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|
545 |
| 32 | 546 for (size_t j = 0; j < countSlices; j++) |
| 0 | 547 { |
| 32 | 548 unsigned int countPoints; |
| 0 | 549 |
|
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550 countPointsPath.SetPrefixIndex(1, j); |
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551 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
| 32 | 552 { |
| 553 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 554 } | |
| 555 | |
|
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556 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 557 |
|
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558 geometricTypePath.SetPrefixIndex(1, j); |
|
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559 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
| 32 | 560 if (type != "CLOSED_PLANAR") |
| 0 | 561 { |
|
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562 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
|
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563 continue; |
| 0 | 564 } |
| 565 | |
|
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566 size_t size; |
|
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567 |
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568 imageSequencePath.SetPrefixIndex(1, j); |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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569 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
|
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570 { |
|
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571 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
| 0 | 572 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 573 } | |
| 574 | |
|
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575 referencedInstancePath.SetPrefixIndex(1, j); |
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576 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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577 |
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578 contourDataPath.SetPrefixIndex(1, j); |
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579 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
| 0 | 580 |
| 581 Vector points; | |
|
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582 if (!LinearAlgebra::ParseVector(points, slicesData) || |
| 32 | 583 points.size() != 3 * countPoints) |
| 0 | 584 { |
| 585 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 586 } | |
| 587 | |
|
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588 // seen in real world |
|
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589 if(Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") |
|
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590 { |
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591 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)"; |
|
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592 } |
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593 |
|
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594 Polygon polygon(sopInstanceUid); |
|
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595 polygon.Reserve(countPoints); |
| 0 | 596 |
| 32 | 597 for (size_t k = 0; k < countPoints; k++) |
| 0 | 598 { |
| 599 Vector v(3); | |
| 600 v[0] = points[3 * k]; | |
| 601 v[1] = points[3 * k + 1]; | |
| 602 v[2] = points[3 * k + 2]; | |
|
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603 polygon.AddPoint(v); |
| 0 | 604 } |
| 605 | |
| 606 structures_[i].polygons_.push_back(polygon); | |
| 607 } | |
| 608 } | |
| 609 } | |
| 610 | |
| 611 | |
| 612 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
| 613 { | |
| 614 const Structure& structure = GetStructure(index); | |
| 615 | |
| 616 Vector center; | |
|
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617 LinearAlgebra::AssignVector(center, 0, 0, 0); |
| 0 | 618 if (structure.polygons_.empty()) |
| 619 { | |
| 620 return center; | |
| 621 } | |
| 622 | |
| 623 double n = static_cast<double>(structure.polygons_.size()); | |
| 624 | |
| 625 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 626 polygon != structure.polygons_.end(); ++polygon) | |
| 627 { | |
|
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628 if (!polygon->GetPoints().empty()) |
| 0 | 629 { |
|
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630 center += polygon->GetPoints().front() / n; |
| 0 | 631 } |
| 632 } | |
| 633 | |
| 634 return center; | |
| 635 } | |
| 636 | |
| 637 | |
| 638 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 639 { | |
| 640 return GetStructure(index).name_; | |
| 641 } | |
| 642 | |
| 643 | |
| 644 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 645 { | |
| 646 return GetStructure(index).interpretation_; | |
| 647 } | |
| 648 | |
| 649 | |
|
804
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650 Color DicomStructureSet::GetStructureColor(size_t index) const |
|
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651 { |
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652 const Structure& s = GetStructure(index); |
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653 return Color(s.red_, s.green_, s.blue_); |
|
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|
654 } |
|
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|
655 |
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|
656 |
| 0 | 657 void DicomStructureSet::GetStructureColor(uint8_t& red, |
| 658 uint8_t& green, | |
| 659 uint8_t& blue, | |
| 660 size_t index) const | |
| 661 { | |
| 662 const Structure& s = GetStructure(index); | |
| 663 red = s.red_; | |
| 664 green = s.green_; | |
| 665 blue = s.blue_; | |
| 666 } | |
| 667 | |
| 668 | |
|
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669 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) |
| 0 | 670 { |
| 671 for (Structures::const_iterator structure = structures_.begin(); | |
| 672 structure != structures_.end(); ++structure) | |
| 673 { | |
| 674 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 675 polygon != structure->polygons_.end(); ++polygon) | |
| 676 { | |
|
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677 instances.insert(polygon->GetSopInstanceUid()); |
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678 } |
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679 } |
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680 } |
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|
681 |
|
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|
682 |
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683 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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684 const std::string& seriesInstanceUid, |
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685 const CoordinateSystem3D& geometry, |
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686 double thickness) |
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687 { |
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688 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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689 { |
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690 // This geometry is already known |
|
956
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|
691 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid; |
|
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|
692 |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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|
693 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
|
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694 } |
|
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695 else |
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696 { |
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697 if (thickness < 0) |
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698 { |
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699 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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700 } |
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701 |
|
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702 if (!referencedSlices_.empty()) |
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703 { |
|
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704 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
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705 |
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706 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
| 0 | 707 { |
|
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708 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
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709 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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|
710 } |
| 0 | 711 |
|
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712 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
|
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|
713 { |
|
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714 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
|
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715 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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|
716 } |
|
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717 } |
|
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|
718 |
|
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|
719 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
| 0 | 720 |
| 131 | 721 for (Structures::iterator structure = structures_.begin(); |
| 722 structure != structures_.end(); ++structure) | |
| 723 { | |
| 724 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
| 725 polygon != structure->polygons_.end(); ++polygon) | |
| 726 { | |
| 727 polygon->UpdateReferencedSlice(referencedSlices_); | |
| 728 } | |
| 729 } | |
|
122
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|
730 } |
|
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|
731 } |
|
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refactoring DicomStructureSet
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diff
changeset
|
732 |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
733 |
|
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diff
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|
734 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
|
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|
735 { |
|
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|
736 CoordinateSystem3D slice(dataset); |
|
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|
737 |
|
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refactoring DicomStructureSet
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|
738 double thickness = 1; // 1 mm by default |
| 0 | 739 |
|
122
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|
740 std::string s; |
|
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|
741 Vector v; |
|
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
742 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
|
158
a053ca7fa5c6
LinearAlgebra toolbox
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|
743 LinearAlgebra::ParseVector(v, s) && |
|
122
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|
744 v.size() > 0) |
|
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|
745 { |
|
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|
746 thickness = v[0]; |
|
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|
747 } |
|
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refactoring DicomStructureSet
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diff
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|
748 |
|
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refactoring DicomStructureSet
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diff
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|
749 std::string instance, series; |
|
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
750 if (dataset.LookupStringValue(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
|
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
751 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
|
122
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
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|
752 { |
|
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|
753 AddReferencedSlice(instance, series, slice, thickness); |
|
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|
754 } |
|
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refactoring DicomStructureSet
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diff
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|
755 else |
|
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refactoring DicomStructureSet
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parents:
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diff
changeset
|
756 { |
|
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|
757 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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|
758 } |
|
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refactoring DicomStructureSet
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parents:
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diff
changeset
|
759 } |
|
e3433dabfb8d
refactoring DicomStructureSet
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diff
changeset
|
760 |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
761 |
|
e3433dabfb8d
refactoring DicomStructureSet
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|
762 void DicomStructureSet::CheckReferencedSlices() |
|
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|
763 { |
|
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|
764 for (Structures::iterator structure = structures_.begin(); |
|
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|
765 structure != structures_.end(); ++structure) |
|
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|
766 { |
|
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|
767 for (Polygons::iterator polygon = structure->polygons_.begin(); |
|
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|
768 polygon != structure->polygons_.end(); ++polygon) |
|
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|
769 { |
|
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|
770 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
|
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|
771 { |
|
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
772 std::string sopInstanceUid = polygon->GetSopInstanceUid(); |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
773 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
774 { |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
775 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
776 << " missing information about referenced instance " |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
777 << "(sopInstanceUid is empty!)"; |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
778 } |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
779 else |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
780 { |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
781 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
782 << " missing information about referenced instance " |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
783 << "(sopInstanceUid = " << sopInstanceUid << ")"; |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
784 } |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
785 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 0 | 786 } |
| 787 } | |
| 788 } | |
|
122
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diff
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|
789 } |
| 0 | 790 |
|
122
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refactoring DicomStructureSet
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diff
changeset
|
791 |
|
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refactoring DicomStructureSet
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|
792 Vector DicomStructureSet::GetNormal() const |
|
e3433dabfb8d
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|
793 { |
|
126
c9e88e7935a4
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parents:
125
diff
changeset
|
794 if (referencedSlices_.empty()) |
|
122
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|
795 { |
|
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refactoring DicomStructureSet
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|
796 Vector v; |
|
158
a053ca7fa5c6
LinearAlgebra toolbox
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diff
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|
797 LinearAlgebra::AssignVector(v, 0, 0, 1); |
|
122
e3433dabfb8d
refactoring DicomStructureSet
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|
798 return v; |
|
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|
799 } |
|
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refactoring DicomStructureSet
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|
800 else |
|
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refactoring DicomStructureSet
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|
801 { |
|
e3433dabfb8d
refactoring DicomStructureSet
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802 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
|
e3433dabfb8d
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diff
changeset
|
803 } |
|
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parents:
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diff
changeset
|
804 } |
|
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parents:
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diff
changeset
|
805 |
|
1006
4f28d9459e31
Fixed unit tests and deprecated classes according to last API changes. UT all run ok.
Benjamin Golinvaux <bgo@osimis.io>
parents:
1000
diff
changeset
|
806 #ifdef USE_BOOST_UNION_FOR_POLYGONS |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
807 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<Point2D> >& polygons, |
| 794 | 808 const Structure& structure, |
| 809 const CoordinateSystem3D& slice) const | |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
994
diff
changeset
|
810 #else |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
994
diff
changeset
|
811 bool DicomStructureSet::ProjectStructure(std::vector< std::pair<Point2D, Point2D> >& segments, |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
812 const Structure& structure, |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
813 const CoordinateSystem3D& slice) const |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
994
diff
changeset
|
814 #endif |
| 125 | 815 { |
|
1006
4f28d9459e31
Fixed unit tests and deprecated classes according to last API changes. UT all run ok.
Benjamin Golinvaux <bgo@osimis.io>
parents:
1000
diff
changeset
|
816 #ifdef USE_BOOST_UNION_FOR_POLYGONS |
| 125 | 817 polygons.clear(); |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
994
diff
changeset
|
818 #else |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
819 segments.clear(); |
|
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changed RTSTRUCT rendering from polygons to segments
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parents:
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diff
changeset
|
820 #endif |
| 125 | 821 |
| 822 Vector normal = GetNormal(); | |
| 823 | |
| 824 bool isOpposite; | |
| 825 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
| 826 { | |
| 827 // This is an axial projection | |
| 828 | |
| 794 | 829 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
| 125 | 830 polygon != structure.polygons_.end(); ++polygon) |
| 831 { | |
| 832 if (polygon->IsOnSlice(slice)) | |
| 833 { | |
|
1006
4f28d9459e31
Fixed unit tests and deprecated classes according to last API changes. UT all run ok.
Benjamin Golinvaux <bgo@osimis.io>
parents:
1000
diff
changeset
|
834 #ifdef USE_BOOST_UNION_FOR_POLYGONS |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
994
diff
changeset
|
835 polygons.push_back(std::vector<Point2D>()); |
| 125 | 836 |
| 837 for (Points::const_iterator p = polygon->GetPoints().begin(); | |
| 838 p != polygon->GetPoints().end(); ++p) | |
| 839 { | |
| 840 double x, y; | |
|
1013
53cc787bd7bc
- Added an optimized ProjectPoint2 to CoordinateSystem3D. It has *not* replaced
Benjamin Golinvaux <bgo@osimis.io>
parents:
1006
diff
changeset
|
841 slice.ProjectPoint2(x, y, *p); |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
842 polygons.back().push_back(Point2D(x, y)); |
| 125 | 843 } |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
844 #else |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
845 // we need to add all the segments corresponding to this polygon |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
846 const std::vector<Vector>& points3D = polygon->GetPoints(); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
847 if (points3D.size() >= 3) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
848 { |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
849 Point2D prev2D; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
994
diff
changeset
|
850 { |
|
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changed RTSTRUCT rendering from polygons to segments
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851 Vector prev = points3D[0]; |
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852 double prevX, prevY; |
|
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- Added an optimized ProjectPoint2 to CoordinateSystem3D. It has *not* replaced
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853 slice.ProjectPoint2(prevX, prevY, prev); |
|
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854 prev2D = Point2D(prevX, prevY); |
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|
855 } |
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|
856 |
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857 size_t pointCount = points3D.size(); |
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858 for (size_t ipt = 1; ipt < pointCount; ++ipt) |
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859 { |
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860 Vector next = points3D[ipt]; |
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861 double nextX, nextY; |
|
1013
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|
862 slice.ProjectPoint2(nextX, nextY, next); |
|
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863 Point2D next2D(nextX, nextY); |
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864 segments.push_back(std::pair<Point2D, Point2D>(prev2D, next2D)); |
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865 prev2D = next2D; |
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866 } |
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867 } |
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868 else |
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869 { |
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870 LOG(ERROR) << "Contour with less than 3 points!"; |
|
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871 // !!! |
|
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872 } |
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873 #endif |
| 125 | 874 } |
| 875 } | |
| 876 | |
| 877 return true; | |
| 878 } | |
| 879 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
| 880 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
| 881 { | |
|
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882 #if 1 |
|
126
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883 // Sagittal or coronal projection |
|
1000
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changed RTSTRUCT rendering from polygons to segments
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884 |
|
1006
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Benjamin Golinvaux <bgo@osimis.io>
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|
885 #ifdef USE_BOOST_UNION_FOR_POLYGONS |
|
126
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|
886 std::vector<BoostPolygon> projected; |
|
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887 #else |
|
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888 // this will contain the intersection of the polygon slab with |
|
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|
889 // the cutting plane, projected on the cutting plane coord system |
|
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890 // (that yields a rectangle) + the Z coordinate of the polygon |
|
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891 // (this is required to group polygons with the same Z later) |
|
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892 std::vector<std::pair<RtStructRectangleInSlab, double> > projected; |
|
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|
893 #endif |
| 794 | 894 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
|
126
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|
895 polygon != structure.polygons_.end(); ++polygon) |
|
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896 { |
| 131 | 897 double x1, y1, x2, y2; |
|
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|
898 |
| 131 | 899 if (polygon->Project(x1, y1, x2, y2, slice)) |
|
126
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900 { |
|
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901 double curZ = polygon->GetGeometryOrigin()[2]; |
|
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|
902 |
|
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|
903 // x1,y1 and x2,y2 are in "slice" coordinates (the cutting plane |
|
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904 // geometry) |
|
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|
905 projected.push_back(std::make_pair(CreateRectangle( |
|
516
11fa6f00e33c
Dummy changes (warnings, dummy dtor to check proper deletion, line wrapping) +
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
906 static_cast<float>(x1), |
|
11fa6f00e33c
Dummy changes (warnings, dummy dtor to check proper deletion, line wrapping) +
Benjamin Golinvaux <bgo@osimis.io>
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|
907 static_cast<float>(y1), |
|
11fa6f00e33c
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Benjamin Golinvaux <bgo@osimis.io>
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|
908 static_cast<float>(x2), |
|
1000
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|
909 static_cast<float>(y2)),curZ)); |
|
126
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diff
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|
910 } |
|
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diff
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|
911 } |
|
1006
4f28d9459e31
Fixed unit tests and deprecated classes according to last API changes. UT all run ok.
Benjamin Golinvaux <bgo@osimis.io>
parents:
1000
diff
changeset
|
912 #ifndef USE_BOOST_UNION_FOR_POLYGONS |
|
1000
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
913 // projected contains a set of rectangles specified by two opposite |
|
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changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
914 // corners (x1,y1,x2,y2) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
915 // we need to merge them |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
916 // each slab yields ONE polygon! |
|
126
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|
917 |
|
1000
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
918 // we need to sorted all the rectangles that originate from the same Z |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
919 // into lanes. To make sure they are grouped together in the array, we |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
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diff
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|
920 // sort it. |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
921 std::sort(projected.begin(), projected.end(), CompareRectanglesForProjection); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
922 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
923 std::vector<RtStructRectanglesInSlab> rectanglesForEachSlab; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
924 rectanglesForEachSlab.reserve(projected.size()); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
925 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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994
diff
changeset
|
926 double curZ = 0; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
927 for (size_t i = 0; i < projected.size(); ++i) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
928 { |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
929 #if 0 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
930 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
931 #else |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
932 if (i == 0) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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994
diff
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|
933 { |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
934 curZ = projected[i].second; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
935 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
936 } |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
937 else |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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994
diff
changeset
|
938 { |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
939 // this check is needed to prevent creating a new slab if |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
940 // the new polygon is at the same Z coord than last one |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
941 if (!LinearAlgebra::IsNear(curZ, projected[i].second)) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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|
942 { |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
943 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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|
944 curZ = projected[i].second; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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|
945 } |
|
50e5acf5553b
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|
946 } |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
947 #endif |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
948 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
949 rectanglesForEachSlab.back().push_back(projected[i].first); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
950 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
951 // as long as they have the same y, we should put them into the same lane |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
952 // BUT in Sebastien's code, there is only one polygon per lane. |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
953 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
954 //std::cout << "rect: xmin = " << rect.xmin << " xmax = " << rect.xmax << " ymin = " << rect.ymin << " ymax = " << rect.ymax << std::endl; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
955 } |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
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diff
changeset
|
956 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
957 // now we need to sort the slabs in increasing Y order (see ConvertListOfSlabsToSegments) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
958 std::sort(rectanglesForEachSlab.begin(), rectanglesForEachSlab.end(), CompareSlabsY); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
959 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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994
diff
changeset
|
960 ConvertListOfSlabsToSegments(segments, rectanglesForEachSlab, projected.size()); |
|
50e5acf5553b
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diff
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|
961 #else |
|
126
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|
962 BoostMultiPolygon merged; |
|
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diff
changeset
|
963 Union(merged, projected); |
|
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125
diff
changeset
|
964 |
|
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125
diff
changeset
|
965 polygons.resize(merged.size()); |
|
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125
diff
changeset
|
966 for (size_t i = 0; i < merged.size(); i++) |
|
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125
diff
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|
967 { |
|
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125
diff
changeset
|
968 const std::vector<BoostPoint>& outer = merged[i].outer(); |
|
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125
diff
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|
969 |
|
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diff
changeset
|
970 polygons[i].resize(outer.size()); |
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971 for (size_t j = 0; j < outer.size(); j++) |
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972 { |
|
1000
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changed RTSTRUCT rendering from polygons to segments
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973 polygons[i][j] = Point2D(outer[j].x(), outer[j].y()); |
|
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974 } |
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975 } |
|
1000
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976 #endif |
|
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|
977 |
|
132
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978 #else |
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979 for (Polygons::iterator polygon = structure.polygons_.begin(); |
|
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980 polygon != structure.polygons_.end(); ++polygon) |
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981 { |
|
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|
982 double x1, y1, x2, y2; |
|
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983 if (polygon->Project(x1, y1, x2, y2, slice)) |
|
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|
984 { |
|
1000
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diff
changeset
|
985 std::vector<Point2D> p(4); |
|
132
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986 p[0] = std::make_pair(x1, y1); |
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987 p[1] = std::make_pair(x2, y1); |
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988 p[2] = std::make_pair(x2, y2); |
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989 p[3] = std::make_pair(x1, y2); |
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990 polygons.push_back(p); |
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991 } |
|
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|
992 } |
|
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|
993 #endif |
| 125 | 994 |
|
126
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995 return true; |
| 125 | 996 } |
| 997 else | |
| 998 { | |
| 999 return false; | |
| 1000 } | |
| 0 | 1001 } |
| 1002 } |