Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 1897:144f8f82c15a
added ctrl key in RtViewerWasm
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 26 Jan 2022 17:28:47 +0100 |
| parents | b3c08e607d9f |
| children | a5e54bd87b25 |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Stone of Orthanc | |
| 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 0 | 7 * |
| 8 * This program is free software: you can redistribute it and/or | |
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9 * modify it under the terms of the GNU Lesser General Public License |
| 47 | 10 * as published by the Free Software Foundation, either version 3 of |
| 11 * the License, or (at your option) any later version. | |
| 0 | 12 * |
| 13 * This program is distributed in the hope that it will be useful, but | |
| 14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * Lesser General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU Lesser General Public |
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19 * License along with this program. If not, see |
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20 * <http://www.gnu.org/licenses/>. |
| 0 | 21 **/ |
| 22 | |
| 23 | |
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24 #define USE_BOOST_UNION_FOR_POLYGONS 1 |
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| 0 | 26 #include "DicomStructureSet.h" |
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27 #include "DicomStructureSetUtils.h" // TODO REMOVE |
| 0 | 28 |
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29 #include "BucketAccumulator2D.h" |
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30 #include "GenericToolbox.h" |
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31 #include "GeometryToolbox.h" |
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32 #include "OrthancDatasets/DicomDatasetReader.h" |
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33 |
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34 #include <Logging.h> |
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35 #include <OrthancException.h> |
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36 #include <Toolbox.h> |
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37 |
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38 #if defined(_MSC_VER) |
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39 # pragma warning(push) |
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40 # pragma warning(disable:4244) |
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41 #endif |
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42 |
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43 #if STONE_TIME_BLOCKING_OPS |
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44 # include <boost/date_time/posix_time/posix_time.hpp> |
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45 #endif |
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46 |
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47 #if !defined(USE_BOOST_UNION_FOR_POLYGONS) |
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48 # error Macro USE_BOOST_UNION_FOR_POLYGONS must be defined |
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49 #endif |
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50 |
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51 #include <limits> |
| 0 | 52 #include <stdio.h> |
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53 #include <boost/math/constants/constants.hpp> |
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54 |
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55 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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56 # include <boost/geometry.hpp> |
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57 # include <boost/geometry/geometries/point_xy.hpp> |
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58 # include <boost/geometry/geometries/polygon.hpp> |
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59 # include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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60 #endif |
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61 |
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62 #if defined(_MSC_VER) |
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63 # pragma warning(pop) |
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64 #endif |
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65 |
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66 #if ORTHANC_ENABLE_DCMTK == 1 |
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67 # include "ParsedDicomDataset.h" |
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68 #endif |
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69 |
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70 |
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71 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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72 |
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73 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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74 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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75 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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76 |
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77 static void Union(BoostMultiPolygon& output, |
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78 std::vector<BoostPolygon>& input) |
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79 { |
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80 for (size_t i = 0; i < input.size(); i++) |
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81 { |
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82 boost::geometry::correct(input[i]); |
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83 } |
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84 |
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85 if (input.size() == 0) |
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86 { |
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87 output.clear(); |
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88 } |
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89 else if (input.size() == 1) |
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90 { |
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91 output.resize(1); |
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92 output[0] = input[0]; |
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93 } |
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94 else |
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95 { |
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96 boost::geometry::union_(input[0], input[1], output); |
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97 |
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98 for (size_t i = 0; i < input.size(); i++) |
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99 { |
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100 BoostMultiPolygon tmp; |
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101 boost::geometry::union_(output, input[i], tmp); |
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102 output = tmp; |
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103 } |
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104 } |
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105 } |
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106 |
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107 static BoostPolygon CreateRectangle(float x1, float y1, |
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108 float x2, float y2) |
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109 { |
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110 BoostPolygon r; |
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111 boost::geometry::append(r, BoostPoint(x1, y1)); |
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112 boost::geometry::append(r, BoostPoint(x1, y2)); |
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113 boost::geometry::append(r, BoostPoint(x2, y2)); |
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114 boost::geometry::append(r, BoostPoint(x2, y1)); |
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115 return r; |
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116 } |
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117 |
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118 #else |
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126
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119 |
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120 namespace OrthancStone |
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121 { |
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122 static RtStructRectangleInSlab CreateRectangle(float x1, float y1, |
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123 float x2, float y2) |
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124 { |
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125 RtStructRectangleInSlab rect; |
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126 rect.xmin = std::min(x1, x2); |
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127 rect.xmax = std::max(x1, x2); |
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128 rect.ymin = std::min(y1, y2); |
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129 rect.ymax = std::max(y1, y2); |
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130 return rect; |
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131 } |
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132 |
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133 bool CompareRectanglesForProjection(const std::pair<RtStructRectangleInSlab,double>& r1, |
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134 const std::pair<RtStructRectangleInSlab, double>& r2) |
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135 { |
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136 return r1.second < r2.second; |
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137 } |
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138 |
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139 bool CompareSlabsY(const RtStructRectanglesInSlab& r1, |
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140 const RtStructRectanglesInSlab& r2) |
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141 { |
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142 if ((r1.size() == 0) || (r2.size() == 0)) |
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143 return false; |
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144 |
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145 return r1[0].ymax < r2[0].ymax; |
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146 } |
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147 } |
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148 |
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149 #endif |
| 0 | 150 |
| 151 namespace OrthancStone | |
| 152 { | |
| 1504 | 153 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 154 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 155 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
| 156 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); | |
| 157 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
| 158 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 159 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 160 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 161 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 162 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 163 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 164 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 165 |
| 166 | |
| 167 static uint8_t ConvertColor(double v) | |
| 168 { | |
| 169 if (v < 0) | |
| 170 { | |
| 171 return 0; | |
| 172 } | |
| 173 else if (v >= 255) | |
| 174 { | |
| 175 return 255; | |
| 176 } | |
| 177 else | |
| 178 { | |
| 179 return static_cast<uint8_t>(v); | |
| 180 } | |
| 181 } | |
| 182 | |
| 183 | |
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184 static bool FastParseVector(Vector& target, |
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185 const IDicomDataset& dataset, |
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186 const Orthanc::DicomPath& tag) |
| 0 | 187 { |
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188 std::string value; |
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189 return (dataset.GetStringValue(value, tag) && |
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190 GenericToolbox::FastParseVector(target, value)); |
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191 } |
| 0 | 192 |
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193 void DicomStructureSet::Polygon::CheckPointIsOnSlice(const Vector& v) const |
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194 { |
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195 if (hasSlice_) |
| 0 | 196 { |
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197 double magnitude = |
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198 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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199 if(!LinearAlgebra::IsNear( |
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200 magnitude, |
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201 projectionAlongNormal_, |
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202 sliceThickness_ / 2.0 /* in mm */ )) |
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203 { |
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204 LOG(ERROR) << "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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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211 } |
| 0 | 212 } |
|
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213 } |
| 0 | 214 |
|
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215 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const |
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216 { |
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217 if (hasSlice_) |
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218 { |
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219 double magnitude = |
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220 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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221 bool onSlice = LinearAlgebra::IsNear( |
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222 magnitude, |
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223 projectionAlongNormal_, |
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224 sliceThickness_ / 2.0 /* in mm */); |
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225 if (!onSlice) |
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226 { |
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227 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
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228 << "slice of its instance | " |
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229 << "magnitude = " << magnitude << " | " |
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230 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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231 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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232 } |
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233 return onSlice; |
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234 } |
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235 else |
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236 { |
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237 return true; |
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238 } |
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239 } |
| 0 | 240 |
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241 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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242 { |
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243 #if 1 |
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244 // BGO 2019-09-03 |
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245 if (IsPointOnSliceIfAny(v)) |
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246 { |
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247 points_.push_back(v); |
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248 } |
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249 #else |
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250 CheckPoint(v); |
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251 points_.push_back(v); |
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252 #endif |
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253 } |
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254 |
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255 |
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256 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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257 { |
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258 if (hasSlice_) |
| 0 | 259 { |
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260 return true; |
| 32 | 261 } |
| 262 else | |
| 263 { | |
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264 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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265 |
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266 if (it == slices.end()) |
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267 { |
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268 return false; |
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269 } |
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270 else |
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271 { |
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272 const CoordinateSystem3D& geometry = it->second.geometry_; |
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273 |
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274 hasSlice_ = true; |
| 131 | 275 geometry_ = geometry; |
| 276 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
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277 sliceThickness_ = it->second.thickness_; |
| 0 | 278 |
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279 extent_.Clear(); |
| 131 | 280 |
| 1571 | 281 for (Points::const_iterator it2 = points_.begin(); it2 != points_.end(); ++it2) |
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282 { |
| 1571 | 283 if (IsPointOnSliceIfAny(*it2)) |
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284 { |
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285 double x, y; |
| 1571 | 286 geometry.ProjectPoint2(x, y, *it2); |
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287 extent_.AddPoint(x, y); |
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288 } |
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289 } |
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290 return true; |
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291 } |
| 0 | 292 } |
| 293 } | |
| 294 | |
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295 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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296 { |
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297 bool isOpposite = false; |
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298 |
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299 if (points_.empty() || |
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300 !hasSlice_ || |
| 131 | 301 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
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302 { |
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303 return false; |
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304 } |
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305 |
| 131 | 306 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
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307 |
|
158
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308 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, |
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309 sliceThickness_ / 2.0)); |
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310 } |
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311 |
| 131 | 312 bool DicomStructureSet::Polygon::Project(double& x1, |
| 313 double& y1, | |
| 314 double& x2, | |
| 315 double& y2, | |
| 316 const CoordinateSystem3D& slice) const | |
| 317 { | |
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318 // TODO: optimize this method using a sweep-line algorithm for polygons |
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319 |
| 131 | 320 if (!hasSlice_ || |
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321 points_.size() <= 1) |
| 131 | 322 { |
| 323 return false; | |
| 324 } | |
| 325 | |
| 326 double x, y; | |
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327 geometry_.ProjectPoint2(x, y, slice.GetOrigin()); |
| 131 | 328 |
| 329 bool isOpposite; | |
| 330 if (GeometryToolbox::IsParallelOrOpposite | |
| 331 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
| 332 { | |
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333 // plane is constant Y |
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334 |
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335 if (y < extent_.GetY1() || |
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336 y > extent_.GetY2()) |
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337 { |
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338 // The polygon does not intersect the input slice |
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339 return false; |
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340 } |
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341 |
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342 bool isFirst = true; |
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343 double xmin = std::numeric_limits<double>::infinity(); |
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344 double xmax = -std::numeric_limits<double>::infinity(); |
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345 |
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346 double prevX, prevY; |
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347 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
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348 |
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349 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 350 { |
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351 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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352 double curX, curY; |
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353 geometry_.ProjectPoint2(curX, curY, points_[i]); |
|
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354 |
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355 // if prev* and cur* are on opposite sides of y, this means that the |
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356 // segment intersects the plane. |
|
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357 if ((prevY <= y && curY >= y) || |
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358 (prevY >= y && curY <= y)) |
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359 { |
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360 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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361 xmin = std::min(xmin, p); |
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362 xmax = std::max(xmax, p); |
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363 isFirst = false; |
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364 |
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365 // xmin and xmax represent the extent of the rectangle along the |
|
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366 // intersection between the plane and the polygon geometry |
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367 |
|
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368 } |
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369 |
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370 prevX = curX; |
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371 prevY = curY; |
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372 } |
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373 |
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374 // if NO segment intersects the plane |
|
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375 if (isFirst) |
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376 { |
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377 return false; |
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378 } |
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379 else |
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380 { |
|
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381 // y is the plane y coord in the polygon geometry |
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382 // xmin and xmax are ALSO expressed in the polygon geometry |
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383 |
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384 // let's convert them to 3D world geometry... |
|
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385 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
| 131 | 386 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
|
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387 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
| 131 | 388 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
|
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389 |
|
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390 // then to the cutting plane geometry... |
|
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391 slice.ProjectPoint2(x1, y1, p1); |
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392 slice.ProjectPoint2(x2, y2, p2); |
| 131 | 393 return true; |
| 394 } | |
| 395 } | |
| 396 else if (GeometryToolbox::IsParallelOrOpposite | |
| 397 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
| 398 { | |
|
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399 // plane is constant X => Sagittal view (remember that in the |
|
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400 // sagittal projection, the normal must be swapped) |
|
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401 |
|
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402 |
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403 /* |
|
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DicomStructureSet::ProjectOntoLayer()
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404 Please read the comments in the section above, by taking into account |
|
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DicomStructureSet::ProjectOntoLayer()
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405 the fact that, in this case, the plane has a constant X, not Y (in |
|
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DicomStructureSet::ProjectOntoLayer()
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406 polygon geometry_ coordinates) |
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407 */ |
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408 |
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409 if (x < extent_.GetX1() || |
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410 x > extent_.GetX2()) |
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411 { |
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412 return false; |
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413 } |
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414 |
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415 bool isFirst = true; |
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416 double ymin = std::numeric_limits<double>::infinity(); |
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417 double ymax = -std::numeric_limits<double>::infinity(); |
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418 |
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419 double prevX, prevY; |
|
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420 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
|
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421 |
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422 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 423 { |
|
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424 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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425 double curX, curY; |
|
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|
426 geometry_.ProjectPoint2(curX, curY, points_[i]); |
|
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427 |
|
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fix wrong display of RTStruct when an RTStruct point has exactly the same X or Y coordinates as the origin
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|
428 if ((prevX <= x && curX >= x) || |
|
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|
429 (prevX >= x && curX <= x)) |
|
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430 { |
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431 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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432 ymin = std::min(ymin, p); |
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433 ymax = std::max(ymax, p); |
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434 isFirst = false; |
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435 } |
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436 |
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437 prevX = curX; |
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438 prevY = curY; |
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439 } |
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440 |
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441 if (isFirst) |
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442 { |
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443 return false; |
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444 } |
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445 else |
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446 { |
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447 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
| 131 | 448 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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449 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
| 131 | 450 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
| 451 | |
|
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diff
changeset
|
452 slice.ProjectPoint2(x1, y1, p1); |
|
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changeset
|
453 slice.ProjectPoint2(x2, y2, p2); |
|
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454 |
| 131 | 455 return true; |
| 456 } | |
| 457 } | |
| 458 else | |
| 459 { | |
| 460 // Should not happen | |
| 461 return false; | |
| 462 } | |
| 463 } | |
| 464 | |
| 465 | |
| 0 | 466 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
| 467 { | |
| 468 if (index >= structures_.size()) | |
| 469 { | |
| 125 | 470 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
| 0 | 471 } |
| 472 | |
| 473 return structures_[index]; | |
| 474 } | |
| 475 | |
| 476 | |
| 125 | 477 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
| 0 | 478 { |
| 125 | 479 if (index >= structures_.size()) |
| 480 { | |
| 481 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 0 | 482 } |
| 483 | |
| 484 return structures_[index]; | |
| 485 } | |
| 486 | |
| 1504 | 487 void DicomStructureSet::Setup(const IDicomDataset& tags) |
| 0 | 488 { |
|
1751
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FastParseVector usage + timing instrumentation guarded by STONE_TIME_BLOCKING_OPS
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|
489 #if STONE_TIME_BLOCKING_OPS |
|
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changeset
|
490 boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); |
|
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|
491 #endif |
|
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|
492 |
| 1504 | 493 DicomDatasetReader reader(tags); |
| 32 | 494 |
| 495 size_t count, tmp; | |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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diff
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|
496 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) || |
|
126522623e20
replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
497 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) || |
| 32 | 498 tmp != count || |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
499 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) || |
| 32 | 500 tmp != count) |
| 0 | 501 { |
| 502 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 503 } | |
| 504 | |
| 32 | 505 structures_.resize(count); |
| 506 for (size_t i = 0; i < count; i++) | |
| 507 { | |
|
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|
508 structures_[i].interpretation_ = reader.GetStringValue |
|
1834
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|
509 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
|
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|
510 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
|
122
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|
511 "No interpretation"); |
| 0 | 512 |
|
122
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|
513 structures_[i].name_ = reader.GetStringValue |
|
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|
514 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
515 DICOM_TAG_ROI_NAME), |
|
949
32eaf4929b08
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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841
diff
changeset
|
516 "No name"); |
| 0 | 517 |
| 518 Vector color; | |
|
1834
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|
519 if (FastParseVector(color, tags, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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|
520 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 521 color.size() == 3) |
| 0 | 522 { |
| 32 | 523 structures_[i].red_ = ConvertColor(color[0]); |
| 524 structures_[i].green_ = ConvertColor(color[1]); | |
| 525 structures_[i].blue_ = ConvertColor(color[2]); | |
| 526 } | |
| 527 else | |
| 528 { | |
| 529 structures_[i].red_ = 255; | |
| 530 structures_[i].green_ = 0; | |
| 531 structures_[i].blue_ = 0; | |
| 0 | 532 } |
| 533 | |
| 32 | 534 size_t countSlices; |
|
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535 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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|
536 DICOM_TAG_CONTOUR_SEQUENCE))) |
| 32 | 537 { |
|
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538 countSlices = 0; |
| 32 | 539 } |
| 0 | 540 |
|
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better error reporting in DicomStructureSetLoader + fixed POST request logic
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diff
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|
541 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
|
1178
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DicomStructureSet::ProjectOntoLayer()
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|
542 << "\" with interpretation \"" << structures_[i].interpretation_ |
|
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DicomStructureSet::ProjectOntoLayer()
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543 << "\" containing " << countSlices << " slices (color: " |
|
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544 << static_cast<int>(structures_[i].red_) << "," |
|
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545 << static_cast<int>(structures_[i].green_) << "," |
|
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DicomStructureSet::ProjectOntoLayer()
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|
546 << static_cast<int>(structures_[i].blue_) << ")"; |
| 0 | 547 |
|
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|
548 /** |
|
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|
549 * These temporary variables avoid allocating many vectors in |
|
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550 * the loop below (indeed, "Orthanc::DicomPath" handles a |
|
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|
551 * "std::vector<PrefixItem>") |
|
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552 **/ |
|
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|
553 Orthanc::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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changeset
|
554 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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555 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
|
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optimizing constructor of DicomStructureSet
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|
556 |
|
1834
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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557 Orthanc::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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|
558 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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559 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
|
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560 |
|
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|
561 Orthanc::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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|
562 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
563 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
|
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optimizing constructor of DicomStructureSet
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564 |
|
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:
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diff
changeset
|
565 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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diff
changeset
|
566 Orthanc::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
126522623e20
replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
567 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
568 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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changeset
|
569 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
|
786
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optimizing constructor of DicomStructureSet
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diff
changeset
|
570 |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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571 Orthanc::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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changeset
|
572 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
573 DICOM_TAG_CONTOUR_DATA); |
|
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optimizing constructor of DicomStructureSet
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diff
changeset
|
574 |
| 32 | 575 for (size_t j = 0; j < countSlices; j++) |
| 0 | 576 { |
| 32 | 577 unsigned int countPoints; |
| 0 | 578 |
|
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|
579 countPointsPath.SetPrefixIndex(1, j); |
|
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optimizing constructor of DicomStructureSet
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changeset
|
580 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
| 32 | 581 { |
| 582 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 583 } | |
| 584 | |
|
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|
585 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 586 |
|
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optimizing constructor of DicomStructureSet
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changeset
|
587 geometricTypePath.SetPrefixIndex(1, j); |
|
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optimizing constructor of DicomStructureSet
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changeset
|
588 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
| 32 | 589 if (type != "CLOSED_PLANAR") |
| 0 | 590 { |
|
173
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diff
changeset
|
591 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
|
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changeset
|
592 continue; |
| 0 | 593 } |
| 594 | |
|
122
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refactoring DicomStructureSet
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diff
changeset
|
595 size_t size; |
|
786
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optimizing constructor of DicomStructureSet
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diff
changeset
|
596 |
|
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optimizing constructor of DicomStructureSet
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changeset
|
597 imageSequencePath.SetPrefixIndex(1, j); |
|
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
|
598 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
|
122
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refactoring DicomStructureSet
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changeset
|
599 { |
|
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
|
600 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
| 0 | 601 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 602 } | |
| 603 | |
|
786
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optimizing constructor of DicomStructureSet
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diff
changeset
|
604 referencedInstancePath.SetPrefixIndex(1, j); |
|
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optimizing constructor of DicomStructureSet
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diff
changeset
|
605 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
|
5aa728500586
optimizing constructor of DicomStructureSet
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diff
changeset
|
606 |
|
5aa728500586
optimizing constructor of DicomStructureSet
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diff
changeset
|
607 contourDataPath.SetPrefixIndex(1, j); |
|
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optimizing constructor of DicomStructureSet
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diff
changeset
|
608 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
| 0 | 609 |
| 610 Vector points; | |
|
1751
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parents:
1739
diff
changeset
|
611 |
|
946eb7200b82
FastParseVector usage + timing instrumentation guarded by STONE_TIME_BLOCKING_OPS
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parents:
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diff
changeset
|
612 if (!GenericToolbox::FastParseVector(points, slicesData) || |
| 32 | 613 points.size() != 3 * countPoints) |
| 0 | 614 { |
| 615 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 616 } | |
| 617 | |
|
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:
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diff
changeset
|
618 // seen in real world |
|
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
|
619 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
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diff
changeset
|
620 { |
|
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
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parents:
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diff
changeset
|
621 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)"; |
|
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
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parents:
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diff
changeset
|
622 } |
|
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
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diff
changeset
|
623 |
|
122
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refactoring DicomStructureSet
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changeset
|
624 Polygon polygon(sopInstanceUid); |
|
132
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diff
changeset
|
625 polygon.Reserve(countPoints); |
| 0 | 626 |
| 32 | 627 for (size_t k = 0; k < countPoints; k++) |
| 0 | 628 { |
| 629 Vector v(3); | |
| 630 v[0] = points[3 * k]; | |
| 631 v[1] = points[3 * k + 1]; | |
| 632 v[2] = points[3 * k + 2]; | |
|
122
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changeset
|
633 polygon.AddPoint(v); |
| 0 | 634 } |
| 635 | |
| 636 structures_[i].polygons_.push_back(polygon); | |
| 637 } | |
| 638 } | |
|
1892
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estimated geometry of rt-struct
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diff
changeset
|
639 |
|
cdf91ad891a5
estimated geometry of rt-struct
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diff
changeset
|
640 EstimateGeometry(); |
|
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estimated geometry of rt-struct
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changeset
|
641 |
|
1751
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changeset
|
642 #if STONE_TIME_BLOCKING_OPS |
|
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changeset
|
643 boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); |
|
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changeset
|
644 boost::posix_time::time_duration duration = timerEnd - timerStart; |
|
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diff
changeset
|
645 int64_t durationMs = duration.total_milliseconds(); |
|
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changeset
|
646 LOG(WARNING) << "DicomStructureSet::Setup took " << durationMs << " ms"; |
|
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changeset
|
647 #endif |
| 0 | 648 } |
| 649 | |
| 650 | |
|
1180
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changeset
|
651 #if ORTHANC_ENABLE_DCMTK == 1 |
|
9c8f557ea799
ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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changeset
|
652 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance) |
|
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diff
changeset
|
653 { |
|
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changeset
|
654 ParsedDicomDataset dataset(instance); |
|
9c8f557ea799
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diff
changeset
|
655 Setup(dataset); |
|
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changeset
|
656 } |
|
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657 #endif |
|
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|
658 |
|
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659 |
| 0 | 660 Vector DicomStructureSet::GetStructureCenter(size_t index) const |
| 661 { | |
| 662 const Structure& structure = GetStructure(index); | |
| 663 | |
| 664 Vector center; | |
|
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665 LinearAlgebra::AssignVector(center, 0, 0, 0); |
| 0 | 666 if (structure.polygons_.empty()) |
| 667 { | |
| 668 return center; | |
| 669 } | |
| 670 | |
| 671 double n = static_cast<double>(structure.polygons_.size()); | |
| 672 | |
| 673 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 674 polygon != structure.polygons_.end(); ++polygon) | |
| 675 { | |
|
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676 if (!polygon->GetPoints().empty()) |
| 0 | 677 { |
|
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678 center += polygon->GetPoints().front() / n; |
| 0 | 679 } |
| 680 } | |
| 681 | |
| 682 return center; | |
| 683 } | |
| 684 | |
| 685 | |
| 686 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 687 { | |
| 688 return GetStructure(index).name_; | |
| 689 } | |
| 690 | |
| 691 | |
| 692 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 693 { | |
| 694 return GetStructure(index).interpretation_; | |
| 695 } | |
| 696 | |
| 697 | |
|
804
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698 Color DicomStructureSet::GetStructureColor(size_t index) const |
|
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|
699 { |
|
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700 const Structure& s = GetStructure(index); |
|
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701 return Color(s.red_, s.green_, s.blue_); |
|
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702 } |
|
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|
703 |
|
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|
704 |
|
1885
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|
705 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) const |
| 0 | 706 { |
| 707 for (Structures::const_iterator structure = structures_.begin(); | |
| 708 structure != structures_.end(); ++structure) | |
| 709 { | |
| 710 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 711 polygon != structure->polygons_.end(); ++polygon) | |
| 712 { | |
|
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713 instances.insert(polygon->GetSopInstanceUid()); |
|
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714 } |
|
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715 } |
|
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716 } |
|
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717 |
|
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|
718 |
|
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|
719 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
|
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720 const std::string& seriesInstanceUid, |
|
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721 const CoordinateSystem3D& geometry, |
|
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722 double thickness) |
|
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723 { |
|
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724 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
|
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|
725 { |
|
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|
726 // This geometry is already known |
|
956
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Made IsContextLost automatically set the flag by checking with the emscripten
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parents:
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diff
changeset
|
727 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid; |
|
981
c20dbaab360c
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Benjamin Golinvaux <bgo@osimis.io>
parents:
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changeset
|
728 |
|
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
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|
729 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
|
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730 } |
|
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731 else |
|
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732 { |
|
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|
733 if (thickness < 0) |
|
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734 { |
|
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|
735 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
|
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736 } |
|
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737 |
|
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|
738 if (!referencedSlices_.empty()) |
|
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|
739 { |
|
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|
740 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
|
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|
741 |
|
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742 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
| 0 | 743 { |
|
122
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744 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
|
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745 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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|
746 } |
| 0 | 747 |
|
122
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|
748 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
|
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|
749 { |
|
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|
750 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
|
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751 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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|
752 } |
|
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|
753 } |
|
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|
754 |
|
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refactoring DicomStructureSet
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|
755 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
| 0 | 756 |
| 131 | 757 for (Structures::iterator structure = structures_.begin(); |
| 758 structure != structures_.end(); ++structure) | |
| 759 { | |
| 760 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
| 761 polygon != structure->polygons_.end(); ++polygon) | |
| 762 { | |
| 763 polygon->UpdateReferencedSlice(referencedSlices_); | |
| 764 } | |
| 765 } | |
|
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|
766 } |
|
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|
767 } |
|
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refactoring DicomStructureSet
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diff
changeset
|
768 |
|
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refactoring DicomStructureSet
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changeset
|
769 |
|
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|
770 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
|
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|
771 { |
|
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|
772 CoordinateSystem3D slice(dataset); |
|
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|
773 |
|
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refactoring DicomStructureSet
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diff
changeset
|
774 double thickness = 1; // 1 mm by default |
| 0 | 775 |
|
122
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|
776 std::string s; |
|
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|
777 Vector v; |
|
994
1f74bc3459ba
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
778 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
|
158
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|
779 LinearAlgebra::ParseVector(v, s) && |
|
122
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780 v.size() > 0) |
|
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|
781 { |
|
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782 thickness = v[0]; |
|
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|
783 } |
|
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|
784 |
|
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|
785 std::string instance, series; |
|
994
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parents:
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changeset
|
786 if (dataset.LookupStringValue(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
|
1f74bc3459ba
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changeset
|
787 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
|
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|
788 { |
|
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|
789 AddReferencedSlice(instance, series, slice, thickness); |
|
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|
790 } |
|
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|
791 else |
|
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|
792 { |
|
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793 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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|
794 } |
|
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|
795 } |
|
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diff
changeset
|
796 |
|
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refactoring DicomStructureSet
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changeset
|
797 |
|
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|
798 void DicomStructureSet::CheckReferencedSlices() |
|
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|
799 { |
|
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|
800 for (Structures::iterator structure = structures_.begin(); |
|
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801 structure != structures_.end(); ++structure) |
|
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|
802 { |
|
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|
803 for (Polygons::iterator polygon = structure->polygons_.begin(); |
|
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804 polygon != structure->polygons_.end(); ++polygon) |
|
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805 { |
|
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806 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
|
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|
807 { |
|
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:
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diff
changeset
|
808 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
|
809 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
|
810 { |
|
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
|
811 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
812 << " missing information about referenced instance " |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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1170
diff
changeset
|
813 << "(sopInstanceUid is empty!)"; |
|
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
|
814 } |
|
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
|
815 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
|
816 { |
|
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
|
817 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
818 << " missing information about referenced instance " |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
819 << "(sopInstanceUid = " << sopInstanceUid << ")"; |
|
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
|
820 } |
|
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
|
821 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 0 | 822 } |
| 823 } | |
| 824 } | |
|
122
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refactoring DicomStructureSet
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diff
changeset
|
825 } |
| 0 | 826 |
|
122
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refactoring DicomStructureSet
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diff
changeset
|
827 |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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|
828 Vector DicomStructureSet::GetNormal() const |
|
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refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
829 { |
|
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
830 if (referencedSlices_.empty()) |
|
122
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refactoring DicomStructureSet
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diff
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|
831 { |
|
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refactoring DicomStructureSet
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diff
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|
832 Vector v; |
|
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
833 LinearAlgebra::AssignVector(v, 0, 0, 1); |
|
122
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refactoring DicomStructureSet
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|
834 return v; |
|
e3433dabfb8d
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diff
changeset
|
835 } |
|
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refactoring DicomStructureSet
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diff
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|
836 else |
|
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refactoring DicomStructureSet
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diff
changeset
|
837 { |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
838 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
|
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refactoring DicomStructureSet
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parents:
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diff
changeset
|
839 } |
|
e3433dabfb8d
refactoring DicomStructureSet
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diff
changeset
|
840 } |
|
e3433dabfb8d
refactoring DicomStructureSet
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diff
changeset
|
841 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
842 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<ScenePoint2D> >& chains, |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
843 const Structure& structure, |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
844 const CoordinateSystem3D& sourceSlice) const |
| 125 | 845 { |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
846 const CoordinateSystem3D slice = CoordinateSystem3D::NormalizeCuttingPlane(sourceSlice); |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
847 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
848 chains.clear(); |
| 125 | 849 |
| 850 Vector normal = GetNormal(); | |
| 851 | |
| 852 bool isOpposite; | |
| 853 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
| 854 { | |
| 855 // This is an axial projection | |
| 856 | |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
857 chains.reserve(structure.polygons_.size()); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
858 |
| 794 | 859 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
| 125 | 860 polygon != structure.polygons_.end(); ++polygon) |
| 861 { | |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
862 const Points& points = polygon->GetPoints(); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
863 |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
864 if (polygon->IsOnSlice(slice) && |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
865 !points.empty()) |
| 125 | 866 { |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
867 chains.push_back(std::vector<ScenePoint2D>()); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
868 chains.back().reserve(points.size() + 1); |
| 125 | 869 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
870 for (Points::const_iterator p = points.begin(); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
871 p != points.end(); ++p) |
| 125 | 872 { |
| 873 double x, y; | |
|
1013
53cc787bd7bc
- Added an optimized ProjectPoint2 to CoordinateSystem3D. It has *not* replaced
Benjamin Golinvaux <bgo@osimis.io>
parents:
1006
diff
changeset
|
874 slice.ProjectPoint2(x, y, *p); |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
875 chains.back().push_back(ScenePoint2D(x, y)); |
| 125 | 876 } |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
877 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
878 double x0, y0; |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
879 slice.ProjectPoint2(x0, y0, points.front()); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
880 chains.back().push_back(ScenePoint2D(x0, y0)); |
| 125 | 881 } |
| 882 } | |
| 883 | |
| 884 return true; | |
| 885 } | |
| 886 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
| 887 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
| 888 { | |
|
126
c9e88e7935a4
rt-struct projection
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parents:
125
diff
changeset
|
889 // Sagittal or coronal projection |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
890 |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
891 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
|
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
892 std::vector<BoostPolygon> projected; |
|
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
893 |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
894 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
895 polygon != structure.polygons_.end(); ++polygon) |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
896 { |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
897 double x1, y1, x2, y2; |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
898 |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
899 if (polygon->Project(x1, y1, x2, y2, slice)) |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
900 { |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
901 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
902 } |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
903 } |
|
1897
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
904 |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
905 BoostMultiPolygon merged; |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
906 Union(merged, projected); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
907 |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
908 chains.resize(merged.size()); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
909 for (size_t i = 0; i < merged.size(); i++) |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
910 { |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
911 const std::vector<BoostPoint>& outer = merged[i].outer(); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
912 |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
913 chains[i].resize(outer.size()); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
914 for (size_t j = 0; j < outer.size(); j++) |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
915 { |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
916 chains[i][j] = ScenePoint2D(outer[j].x(), outer[j].y()); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
917 } |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
918 } |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
919 #else |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
920 // this will contain the intersection of the polygon slab with |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
921 // the cutting plane, projected on the cutting plane coord system |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
922 // (that yields a rectangle) + the Z coordinate of the polygon |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
923 // (this is required to group polygons with the same Z later) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
924 std::vector<std::pair<RtStructRectangleInSlab, double> > projected; |
|
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
925 |
| 794 | 926 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
|
126
c9e88e7935a4
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diff
changeset
|
927 polygon != structure.polygons_.end(); ++polygon) |
|
c9e88e7935a4
rt-struct projection
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parents:
125
diff
changeset
|
928 { |
| 131 | 929 double x1, y1, x2, y2; |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
930 |
| 131 | 931 if (polygon->Project(x1, y1, x2, y2, slice)) |
|
126
c9e88e7935a4
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Sebastien Jodogne <s.jodogne@gmail.com>
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125
diff
changeset
|
932 { |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
933 double curZ = polygon->GetGeometryOrigin()[2]; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
934 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
935 // x1,y1 and x2,y2 are in "slice" coordinates (the cutting plane |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
936 // geometry) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
937 projected.push_back(std::make_pair(CreateRectangle( |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
938 static_cast<float>(x1), |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
939 static_cast<float>(y1), |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
940 static_cast<float>(x2), |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
941 static_cast<float>(y2)),curZ)); |
|
126
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Sebastien Jodogne <s.jodogne@gmail.com>
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125
diff
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|
942 } |
|
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125
diff
changeset
|
943 } |
|
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
944 |
|
1000
50e5acf5553b
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Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
945 // projected contains a set of rectangles specified by two opposite |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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994
diff
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|
946 // corners (x1,y1,x2,y2) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
947 // we need to merge them |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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994
diff
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|
948 // each slab yields ONE polygon! |
|
126
c9e88e7935a4
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diff
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|
949 |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
950 // 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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|
951 // into lanes. To make sure they are grouped together in the array, we |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
952 // sort it. |
|
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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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|
953 std::sort(projected.begin(), projected.end(), CompareRectanglesForProjection); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
954 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
955 std::vector<RtStructRectanglesInSlab> rectanglesForEachSlab; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
956 rectanglesForEachSlab.reserve(projected.size()); |
|
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diff
changeset
|
957 |
|
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diff
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|
958 double curZ = 0; |
|
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|
959 for (size_t i = 0; i < projected.size(); ++i) |
|
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|
960 { |
|
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diff
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|
961 #if 0 |
|
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|
962 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
|
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|
963 #else |
|
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|
964 if (i == 0) |
|
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diff
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|
965 { |
|
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
966 curZ = projected[i].second; |
|
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|
967 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
|
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diff
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|
968 } |
|
50e5acf5553b
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diff
changeset
|
969 else |
|
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diff
changeset
|
970 { |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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994
diff
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|
971 // this check is needed to prevent creating a new slab if |
|
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
972 // the new polygon is at the same Z coord than last one |
|
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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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|
973 if (!LinearAlgebra::IsNear(curZ, projected[i].second)) |
|
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
974 { |
|
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changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
975 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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|
976 curZ = projected[i].second; |
|
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
977 } |
|
50e5acf5553b
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diff
changeset
|
978 } |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
979 #endif |
|
50e5acf5553b
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diff
changeset
|
980 |
|
50e5acf5553b
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diff
changeset
|
981 rectanglesForEachSlab.back().push_back(projected[i].first); |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
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diff
changeset
|
982 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
983 // 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
|
984 // BUT in Sebastien's code, there is only one polygon per lane. |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
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diff
changeset
|
985 |
|
50e5acf5553b
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Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
986 //std::cout << "rect: xmin = " << rect.xmin << " xmax = " << rect.xmax << " ymin = " << rect.ymin << " ymax = " << rect.ymax << std::endl; |
|
50e5acf5553b
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parents:
994
diff
changeset
|
987 } |
|
50e5acf5553b
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parents:
994
diff
changeset
|
988 |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
989 // now we need to sort the slabs in increasing Y order (see ConvertListOfSlabsToSegments) |
|
50e5acf5553b
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parents:
994
diff
changeset
|
990 std::sort(rectanglesForEachSlab.begin(), rectanglesForEachSlab.end(), CompareSlabsY); |
|
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changed RTSTRUCT rendering from polygons to segments
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994
diff
changeset
|
991 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
992 std::vector< std::pair<ScenePoint2D, ScenePoint2D> > segments; |
|
1000
50e5acf5553b
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parents:
994
diff
changeset
|
993 ConvertListOfSlabsToSegments(segments, rectanglesForEachSlab, projected.size()); |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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parents:
1895
diff
changeset
|
994 |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
995 chains.resize(segments.size()); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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parents:
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diff
changeset
|
996 for (size_t i = 0; i < segments.size(); i++) |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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parents:
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diff
changeset
|
997 { |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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parents:
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diff
changeset
|
998 chains[i].resize(2); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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parents:
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diff
changeset
|
999 chains[i][0] = segments[i].first; |
|
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simplified signature of DicomStructureSet::ProjectStructure()
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diff
changeset
|
1000 chains[i][1] = segments[i].second; |
|
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simplified signature of DicomStructureSet::ProjectStructure()
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diff
changeset
|
1001 } |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
1002 #endif |
| 125 | 1003 |
|
126
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diff
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|
1004 return true; |
| 125 | 1005 } |
| 1006 else | |
| 1007 { | |
| 1008 return false; | |
| 1009 } | |
| 0 | 1010 } |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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1170
diff
changeset
|
1011 |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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diff
changeset
|
1012 |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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diff
changeset
|
1013 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer, |
|
3c7cdbf32e2a
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changeset
|
1014 const CoordinateSystem3D& plane, |
|
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changeset
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1015 size_t structureIndex, |
|
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1016 const Color& color) const |
|
3c7cdbf32e2a
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diff
changeset
|
1017 { |
|
1896
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|
1018 std::vector< std::vector<ScenePoint2D> > chains; |
|
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changeset
|
1019 |
|
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diff
changeset
|
1020 if (ProjectStructure(chains, structureIndex, plane)) |
|
1178
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DicomStructureSet::ProjectOntoLayer()
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changeset
|
1021 { |
|
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simplified signature of DicomStructureSet::ProjectStructure()
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diff
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|
1022 for (size_t j = 0; j < chains.size(); j++) |
|
1178
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DicomStructureSet::ProjectOntoLayer()
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changeset
|
1023 { |
|
1896
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simplified signature of DicomStructureSet::ProjectStructure()
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diff
changeset
|
1024 layer.AddChain(chains[j], false, color.GetRed(), color.GetGreen(), color.GetBlue()); |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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1170
diff
changeset
|
1025 } |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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diff
changeset
|
1026 } |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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diff
changeset
|
1027 } |
|
1885
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|
1028 |
|
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|
1029 |
|
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|
1030 void DicomStructureSet::GetStructurePoints(std::list< std::vector<Vector> >& target, |
|
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1031 size_t structureIndex, |
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1032 const std::string& sopInstanceUid) const |
|
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1033 { |
|
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changeset
|
1034 target.clear(); |
|
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|
1035 |
|
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changeset
|
1036 const Structure& structure = GetStructure(structureIndex); |
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|
1037 |
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1038 // TODO - Could be optimized by adding a multimap on "Structure", mapping |
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1039 // from SOP Instance UID to polygons |
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|
1040 |
|
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1041 for (Polygons::const_iterator it = structure.polygons_.begin(); |
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1042 it != structure.polygons_.end(); ++it) |
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1043 { |
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1044 if (it->GetSopInstanceUid() == sopInstanceUid) |
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1045 { |
|
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1046 target.push_back(it->GetPoints()); |
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1047 } |
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1048 } |
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1049 } |
|
1890
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1050 |
|
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|
1051 |
|
1892
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1052 void DicomStructureSet::EstimateGeometry() |
|
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|
1053 { |
|
1892
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1054 static const double PI = boost::math::constants::pi<double>(); |
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|
1055 |
|
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1056 BucketAccumulator2D accumulator(0, PI, 9, /* for acos() */ |
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1057 -PI, PI, 9, /* for atan() */ |
|
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1058 true /* store values */); |
|
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1059 |
|
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1060 unsigned int countPolygons = 0; |
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1061 for (size_t i = 0; i < structures_.size(); i++) |
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|
1062 { |
|
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1063 const Polygons& polygons = structures_[i].polygons_; |
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1064 |
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1065 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1066 { |
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1067 countPolygons++; |
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1068 |
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1069 const Points& points = it->GetPoints(); |
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1070 |
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1071 if (points.size() >= 3) |
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1072 { |
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1073 // Compute the normal of the polygon using 3 successive points |
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1074 Vector normal; |
|
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1075 bool valid = false; |
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1076 |
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1077 for (size_t i = 0; i + 2 < points.size(); i++) |
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1078 { |
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1079 const Vector& a = points[i]; |
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1080 const Vector& b = points[i + 1]; |
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1081 const Vector& c = points[i + 2]; |
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1082 LinearAlgebra::CrossProduct(normal, b - a, c - a); // (*) |
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1083 LinearAlgebra::NormalizeVector(normal); |
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1084 |
|
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1085 if (LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal), 1.0)) // (**) |
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|
1086 { |
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1087 valid = true; |
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|
1088 break; |
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1089 } |
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1090 } |
|
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|
1091 |
|
1892
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|
1092 if (valid) |
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|
1093 { |
|
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1094 // Check that all the points of the polygon lie in the plane defined by the normal |
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1095 double d1 = GeometryToolbox::ProjectAlongNormal(points[0], normal); |
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|
1096 |
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changeset
|
1097 for (size_t i = 1; i < points.size(); i++) |
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|
1098 { |
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1099 double d2 = GeometryToolbox::ProjectAlongNormal(points[i], normal); |
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1100 |
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1101 if (!LinearAlgebra::IsNear(d1, d2)) |
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1102 { |
|
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1103 valid = false; |
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|
1104 break; |
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1105 } |
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1106 } |
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1107 } |
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|
1108 |
|
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1109 if (valid) |
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|
1110 { |
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1111 if (normal[2] < 0) |
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|
1112 { |
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1113 normal = -normal; |
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|
1114 } |
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changeset
|
1115 |
|
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|
1116 // The normal is a non-zero unit vector because of (*) and (**), so "r == 1" |
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|
1117 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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|
1118 |
|
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1119 const double theta = acos(normal[2]); |
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1120 const double phi = atan(normal[1]); |
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|
1121 accumulator.AddValue(theta, phi); |
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|
1122 } |
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|
1123 } |
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|
1124 } |
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|
1125 } |
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|
1126 |
|
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|
1127 size_t bestX, bestY; |
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|
1128 accumulator.FindBestBucket(bestX, bestY); |
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|
1129 |
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|
1130 if (accumulator.GetBucketContentSize(bestX, bestY) > 0) |
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|
1131 { |
|
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|
1132 double normalTheta, normalPhi; |
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|
1133 accumulator.ComputeBestMedian(normalTheta, normalPhi); |
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|
1134 |
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|
1135 // Back to (x,y,z) normal, taking "r == 1" |
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|
1136 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1137 double sinTheta = sin(normalTheta); |
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1138 estimatedNormal_ = LinearAlgebra::CreateVector(sinTheta * cos(normalPhi), sinTheta * sin(normalPhi), cos(normalTheta)); |
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|
1139 } |
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|
1140 |
|
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|
1141 std::vector<double> polygonsProjection; |
|
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|
1142 polygonsProjection.reserve(countPolygons); |
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|
1143 |
|
1890
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|
1144 for (size_t i = 0; i < structures_.size(); i++) |
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|
1145 { |
|
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|
1146 const Polygons& polygons = structures_[i].polygons_; |
|
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changeset
|
1147 |
|
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|
1148 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
|
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|
1149 { |
|
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|
1150 const Points& points = it->GetPoints(); |
|
1892
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1151 polygonsProjection.push_back(GeometryToolbox::ProjectAlongNormal(points[0], estimatedNormal_)); |
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|
1152 } |
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|
1153 } |
|
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|
1154 |
|
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changeset
|
1155 std::sort(polygonsProjection.begin(), polygonsProjection.end()); |
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1156 |
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1157 std::vector<double> deltas; |
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1158 deltas.reserve(polygonsProjection.size()); |
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6ce81914f7e4
added classes BucketAccumulator1D/2D
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parents:
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1159 |
|
1892
cdf91ad891a5
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parents:
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1160 for (size_t i = 0; i + 1 < polygonsProjection.size(); i++) |
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parents:
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1161 { |
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parents:
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1162 if (!LinearAlgebra::IsNear(polygonsProjection[i], polygonsProjection[i + 1])) |
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parents:
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1163 { |
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cdf91ad891a5
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parents:
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1164 assert(polygonsProjection[i + 1] > polygonsProjection[i]); |
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parents:
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1165 deltas.push_back(polygonsProjection[i + 1] - polygonsProjection[i]); |
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1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
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parents:
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1166 } |
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6ce81914f7e4
added classes BucketAccumulator1D/2D
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parents:
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1167 } |
|
1892
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1168 |
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parents:
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1169 if (deltas.empty()) |
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1170 { |
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parents:
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1171 estimatedSliceThickness_ = 1; |
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parents:
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1172 } |
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parents:
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1173 else |
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parents:
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1174 { |
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cdf91ad891a5
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parents:
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1175 estimatedSliceThickness_ = LinearAlgebra::ComputeMedian(deltas); |
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parents:
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|
1176 } |
|
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
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parents:
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1177 } |
| 0 | 1178 } |