Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 1890:6ce81914f7e4
added classes BucketAccumulator1D/2D
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 18 Jan 2022 22:08:55 +0100 |
| parents | ddaee6b96501 |
| children | cdf91ad891a5 |
| 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 | |
| 24 #include "DicomStructureSet.h" | |
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25 #include "DicomStructureSetUtils.h" |
| 0 | 26 |
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27 #include "GeometryToolbox.h" |
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28 #include "GenericToolbox.h" |
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29 |
| 1504 | 30 #include "OrthancDatasets/DicomDatasetReader.h" |
| 0 | 31 |
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32 #include <Logging.h> |
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33 #include <OrthancException.h> |
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34 #include <Toolbox.h> |
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35 |
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36 #if defined(_MSC_VER) |
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37 # pragma warning(push) |
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38 # pragma warning(disable:4244) |
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39 #endif |
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40 |
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41 #if STONE_TIME_BLOCKING_OPS |
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42 # include <boost/date_time/posix_time/posix_time.hpp> |
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43 #endif |
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44 |
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45 #include <limits> |
| 0 | 46 #include <stdio.h> |
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47 #include <boost/geometry.hpp> |
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48 #include <boost/geometry/geometries/point_xy.hpp> |
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49 #include <boost/geometry/geometries/polygon.hpp> |
| 137 | 50 #include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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51 |
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52 #if defined(_MSC_VER) |
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53 # pragma warning(pop) |
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54 #endif |
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55 |
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56 #if ORTHANC_ENABLE_DCMTK == 1 |
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57 # include "ParsedDicomDataset.h" |
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58 #endif |
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59 |
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60 |
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61 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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62 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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63 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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64 |
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65 |
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66 static void Union(BoostMultiPolygon& output, |
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67 std::vector<BoostPolygon>& input) |
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68 { |
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69 for (size_t i = 0; i < input.size(); i++) |
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70 { |
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71 boost::geometry::correct(input[i]); |
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72 } |
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73 |
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74 if (input.size() == 0) |
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75 { |
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76 output.clear(); |
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77 } |
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78 else if (input.size() == 1) |
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79 { |
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80 output.resize(1); |
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81 output[0] = input[0]; |
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82 } |
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83 else |
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84 { |
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85 boost::geometry::union_(input[0], input[1], output); |
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86 |
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87 for (size_t i = 0; i < input.size(); i++) |
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88 { |
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89 BoostMultiPolygon tmp; |
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90 boost::geometry::union_(output, input[i], tmp); |
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91 output = tmp; |
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92 } |
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93 } |
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94 } |
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95 |
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96 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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97 |
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98 static BoostPolygon CreateRectangle(float x1, float y1, |
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99 float x2, float y2) |
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100 { |
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101 BoostPolygon r; |
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102 boost::geometry::append(r, BoostPoint(x1, y1)); |
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103 boost::geometry::append(r, BoostPoint(x1, y2)); |
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104 boost::geometry::append(r, BoostPoint(x2, y2)); |
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105 boost::geometry::append(r, BoostPoint(x2, y1)); |
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106 return r; |
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107 } |
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108 |
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109 #else |
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110 |
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111 namespace OrthancStone |
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112 { |
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113 static RtStructRectangleInSlab CreateRectangle(float x1, float y1, |
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114 float x2, float y2) |
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115 { |
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116 RtStructRectangleInSlab rect; |
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117 rect.xmin = std::min(x1, x2); |
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118 rect.xmax = std::max(x1, x2); |
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119 rect.ymin = std::min(y1, y2); |
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120 rect.ymax = std::max(y1, y2); |
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121 return rect; |
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122 } |
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123 |
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124 bool CompareRectanglesForProjection(const std::pair<RtStructRectangleInSlab,double>& r1, const std::pair<RtStructRectangleInSlab, double>& r2) |
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125 { |
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126 return r1.second < r2.second; |
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127 } |
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128 |
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129 bool CompareSlabsY(const RtStructRectanglesInSlab& r1, const RtStructRectanglesInSlab& r2) |
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130 { |
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131 if ((r1.size() == 0) || (r2.size() == 0)) |
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132 return false; |
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133 |
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134 return r1[0].ymax < r2[0].ymax; |
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135 } |
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136 } |
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137 |
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138 #endif |
| 0 | 139 |
| 140 namespace OrthancStone | |
| 141 { | |
| 1504 | 142 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 143 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 144 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
| 145 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); | |
| 146 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
| 147 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 148 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 149 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 150 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 151 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 152 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 153 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 154 |
| 155 | |
| 156 static uint8_t ConvertColor(double v) | |
| 157 { | |
| 158 if (v < 0) | |
| 159 { | |
| 160 return 0; | |
| 161 } | |
| 162 else if (v >= 255) | |
| 163 { | |
| 164 return 255; | |
| 165 } | |
| 166 else | |
| 167 { | |
| 168 return static_cast<uint8_t>(v); | |
| 169 } | |
| 170 } | |
| 171 | |
| 172 | |
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173 static bool FastParseVector(Vector& target, |
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174 const IDicomDataset& dataset, |
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175 const Orthanc::DicomPath& tag) |
| 0 | 176 { |
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177 std::string value; |
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178 return (dataset.GetStringValue(value, tag) && |
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179 GenericToolbox::FastParseVector(target, value)); |
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180 } |
| 0 | 181 |
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182 void DicomStructureSet::Polygon::CheckPointIsOnSlice(const Vector& v) const |
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183 { |
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184 if (hasSlice_) |
| 0 | 185 { |
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186 double magnitude = |
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187 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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188 if(!LinearAlgebra::IsNear( |
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189 magnitude, |
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190 projectionAlongNormal_, |
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191 sliceThickness_ / 2.0 /* in mm */ )) |
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192 { |
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193 LOG(ERROR) << "This RT-STRUCT contains a point that is off the " |
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194 << "slice of its instance | " |
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195 << "magnitude = " << magnitude << " | " |
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196 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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197 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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198 |
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199 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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200 } |
| 0 | 201 } |
|
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202 } |
| 0 | 203 |
|
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204 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const |
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205 { |
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206 if (hasSlice_) |
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207 { |
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208 double magnitude = |
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209 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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210 bool onSlice = LinearAlgebra::IsNear( |
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211 magnitude, |
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212 projectionAlongNormal_, |
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213 sliceThickness_ / 2.0 /* in mm */); |
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214 if (!onSlice) |
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215 { |
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216 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
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217 << "slice of its instance | " |
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218 << "magnitude = " << magnitude << " | " |
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219 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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220 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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221 } |
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222 return onSlice; |
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223 } |
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224 else |
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225 { |
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226 return true; |
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227 } |
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228 } |
| 0 | 229 |
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230 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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231 { |
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232 #if 1 |
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233 // BGO 2019-09-03 |
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234 if (IsPointOnSliceIfAny(v)) |
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235 { |
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236 points_.push_back(v); |
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237 } |
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238 #else |
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239 CheckPoint(v); |
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240 points_.push_back(v); |
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241 #endif |
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242 } |
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243 |
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244 |
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245 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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246 { |
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247 if (hasSlice_) |
| 0 | 248 { |
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249 return true; |
| 32 | 250 } |
| 251 else | |
| 252 { | |
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253 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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254 |
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255 if (it == slices.end()) |
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256 { |
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257 return false; |
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258 } |
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259 else |
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260 { |
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261 const CoordinateSystem3D& geometry = it->second.geometry_; |
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262 |
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263 hasSlice_ = true; |
| 131 | 264 geometry_ = geometry; |
| 265 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
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266 sliceThickness_ = it->second.thickness_; |
| 0 | 267 |
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268 extent_.Clear(); |
| 131 | 269 |
| 1571 | 270 for (Points::const_iterator it2 = points_.begin(); it2 != points_.end(); ++it2) |
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271 { |
| 1571 | 272 if (IsPointOnSliceIfAny(*it2)) |
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273 { |
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274 double x, y; |
| 1571 | 275 geometry.ProjectPoint2(x, y, *it2); |
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276 extent_.AddPoint(x, y); |
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277 } |
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278 } |
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279 return true; |
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280 } |
| 0 | 281 } |
| 282 } | |
| 283 | |
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284 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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285 { |
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286 bool isOpposite = false; |
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287 |
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288 if (points_.empty() || |
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289 !hasSlice_ || |
| 131 | 290 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
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291 { |
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292 return false; |
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293 } |
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294 |
| 131 | 295 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
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296 |
|
158
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297 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, |
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298 sliceThickness_ / 2.0)); |
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299 } |
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300 |
| 131 | 301 bool DicomStructureSet::Polygon::Project(double& x1, |
| 302 double& y1, | |
| 303 double& x2, | |
| 304 double& y2, | |
| 305 const CoordinateSystem3D& slice) const | |
| 306 { | |
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307 // TODO: optimize this method using a sweep-line algorithm for polygons |
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308 |
| 131 | 309 if (!hasSlice_ || |
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310 points_.size() <= 1) |
| 131 | 311 { |
| 312 return false; | |
| 313 } | |
| 314 | |
| 315 double x, y; | |
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316 geometry_.ProjectPoint2(x, y, slice.GetOrigin()); |
| 131 | 317 |
| 318 bool isOpposite; | |
| 319 if (GeometryToolbox::IsParallelOrOpposite | |
| 320 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
| 321 { | |
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322 // plane is constant Y |
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323 |
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324 if (y < extent_.GetY1() || |
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325 y > extent_.GetY2()) |
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326 { |
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327 // The polygon does not intersect the input slice |
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328 return false; |
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329 } |
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330 |
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331 bool isFirst = true; |
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332 double xmin = std::numeric_limits<double>::infinity(); |
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333 double xmax = -std::numeric_limits<double>::infinity(); |
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334 |
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335 double prevX, prevY; |
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336 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
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337 |
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338 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 339 { |
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340 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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341 double curX, curY; |
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342 geometry_.ProjectPoint2(curX, curY, points_[i]); |
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343 |
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344 // if prev* and cur* are on opposite sides of y, this means that the |
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345 // segment intersects the plane. |
|
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346 if ((prevY <= y && curY >= y) || |
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347 (prevY >= y && curY <= y)) |
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348 { |
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349 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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350 xmin = std::min(xmin, p); |
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351 xmax = std::max(xmax, p); |
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352 isFirst = false; |
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353 |
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354 // xmin and xmax represent the extent of the rectangle along the |
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355 // intersection between the plane and the polygon geometry |
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356 |
|
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357 } |
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358 |
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359 prevX = curX; |
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360 prevY = curY; |
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361 } |
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362 |
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363 // if NO segment intersects the plane |
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364 if (isFirst) |
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365 { |
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366 return false; |
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367 } |
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368 else |
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369 { |
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370 // y is the plane y coord in the polygon geometry |
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371 // xmin and xmax are ALSO expressed in the polygon geometry |
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372 |
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373 // let's convert them to 3D world geometry... |
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374 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
| 131 | 375 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
|
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376 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
| 131 | 377 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
|
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378 |
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379 // then to the cutting plane geometry... |
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380 slice.ProjectPoint2(x1, y1, p1); |
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381 slice.ProjectPoint2(x2, y2, p2); |
| 131 | 382 return true; |
| 383 } | |
| 384 } | |
| 385 else if (GeometryToolbox::IsParallelOrOpposite | |
| 386 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
| 387 { | |
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388 // plane is constant X => Sagittal view (remember that in the |
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389 // sagittal projection, the normal must be swapped) |
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390 |
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391 |
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392 /* |
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393 Please read the comments in the section above, by taking into account |
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394 the fact that, in this case, the plane has a constant X, not Y (in |
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395 polygon geometry_ coordinates) |
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396 */ |
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397 |
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398 if (x < extent_.GetX1() || |
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399 x > extent_.GetX2()) |
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400 { |
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401 return false; |
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402 } |
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403 |
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404 bool isFirst = true; |
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405 double ymin = std::numeric_limits<double>::infinity(); |
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406 double ymax = -std::numeric_limits<double>::infinity(); |
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407 |
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408 double prevX, prevY; |
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409 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
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410 |
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411 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 412 { |
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413 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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414 double curX, curY; |
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415 geometry_.ProjectPoint2(curX, curY, points_[i]); |
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416 |
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417 if ((prevX <= x && curX >= x) || |
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418 (prevX >= x && curX <= x)) |
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419 { |
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420 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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421 ymin = std::min(ymin, p); |
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422 ymax = std::max(ymax, p); |
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423 isFirst = false; |
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424 } |
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425 |
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426 prevX = curX; |
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427 prevY = curY; |
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428 } |
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429 |
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430 if (isFirst) |
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431 { |
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432 return false; |
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433 } |
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434 else |
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435 { |
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436 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
| 131 | 437 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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438 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
| 131 | 439 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
| 440 | |
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441 slice.ProjectPoint2(x1, y1, p1); |
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442 slice.ProjectPoint2(x2, y2, p2); |
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443 |
| 131 | 444 return true; |
| 445 } | |
| 446 } | |
| 447 else | |
| 448 { | |
| 449 // Should not happen | |
| 450 return false; | |
| 451 } | |
| 452 } | |
| 453 | |
| 454 | |
| 0 | 455 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
| 456 { | |
| 457 if (index >= structures_.size()) | |
| 458 { | |
| 125 | 459 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
| 0 | 460 } |
| 461 | |
| 462 return structures_[index]; | |
| 463 } | |
| 464 | |
| 465 | |
| 125 | 466 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
| 0 | 467 { |
| 125 | 468 if (index >= structures_.size()) |
| 469 { | |
| 470 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 0 | 471 } |
| 472 | |
| 473 return structures_[index]; | |
| 474 } | |
| 475 | |
| 1504 | 476 void DicomStructureSet::Setup(const IDicomDataset& tags) |
| 0 | 477 { |
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478 #if STONE_TIME_BLOCKING_OPS |
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479 boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); |
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480 #endif |
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481 |
| 1504 | 482 DicomDatasetReader reader(tags); |
| 32 | 483 |
| 484 size_t count, tmp; | |
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485 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) || |
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486 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) || |
| 32 | 487 tmp != count || |
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488 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) || |
| 32 | 489 tmp != count) |
| 0 | 490 { |
| 491 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 492 } | |
| 493 | |
| 32 | 494 structures_.resize(count); |
| 495 for (size_t i = 0; i < count; i++) | |
| 496 { | |
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497 structures_[i].interpretation_ = reader.GetStringValue |
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498 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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499 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
|
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500 "No interpretation"); |
| 0 | 501 |
|
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502 structures_[i].name_ = reader.GetStringValue |
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503 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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504 DICOM_TAG_ROI_NAME), |
|
949
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OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
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505 "No name"); |
| 0 | 506 |
| 507 Vector color; | |
|
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508 if (FastParseVector(color, tags, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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509 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 510 color.size() == 3) |
| 0 | 511 { |
| 32 | 512 structures_[i].red_ = ConvertColor(color[0]); |
| 513 structures_[i].green_ = ConvertColor(color[1]); | |
| 514 structures_[i].blue_ = ConvertColor(color[2]); | |
| 515 } | |
| 516 else | |
| 517 { | |
| 518 structures_[i].red_ = 255; | |
| 519 structures_[i].green_ = 0; | |
| 520 structures_[i].blue_ = 0; | |
| 0 | 521 } |
| 522 | |
| 32 | 523 size_t countSlices; |
|
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524 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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525 DICOM_TAG_CONTOUR_SEQUENCE))) |
| 32 | 526 { |
|
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527 countSlices = 0; |
| 32 | 528 } |
| 0 | 529 |
|
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|
530 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
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531 << "\" with interpretation \"" << structures_[i].interpretation_ |
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532 << "\" containing " << countSlices << " slices (color: " |
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533 << static_cast<int>(structures_[i].red_) << "," |
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534 << static_cast<int>(structures_[i].green_) << "," |
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535 << static_cast<int>(structures_[i].blue_) << ")"; |
| 0 | 536 |
|
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537 /** |
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538 * These temporary variables avoid allocating many vectors in |
|
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539 * the loop below (indeed, "Orthanc::DicomPath" handles a |
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|
540 * "std::vector<PrefixItem>") |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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541 **/ |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
542 Orthanc::DicomPath countPointsPath(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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543 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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|
544 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
|
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optimizing constructor of DicomStructureSet
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|
545 |
|
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|
546 Orthanc::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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547 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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548 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
|
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549 |
|
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|
550 Orthanc::DicomPath imageSequencePath(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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551 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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|
552 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
|
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553 |
|
981
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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parents:
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554 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
|
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555 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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556 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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557 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
|
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558 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
|
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559 |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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560 Orthanc::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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561 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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562 DICOM_TAG_CONTOUR_DATA); |
|
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563 |
| 32 | 564 for (size_t j = 0; j < countSlices; j++) |
| 0 | 565 { |
| 32 | 566 unsigned int countPoints; |
| 0 | 567 |
|
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568 countPointsPath.SetPrefixIndex(1, j); |
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optimizing constructor of DicomStructureSet
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569 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
| 32 | 570 { |
| 571 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 572 } | |
| 573 | |
|
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574 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 575 |
|
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576 geometricTypePath.SetPrefixIndex(1, j); |
|
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optimizing constructor of DicomStructureSet
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|
577 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
| 32 | 578 if (type != "CLOSED_PLANAR") |
| 0 | 579 { |
|
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580 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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581 continue; |
| 0 | 582 } |
| 583 | |
|
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refactoring DicomStructureSet
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584 size_t size; |
|
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585 |
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586 imageSequencePath.SetPrefixIndex(1, j); |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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|
587 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
|
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588 { |
|
981
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changeset
|
589 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
| 0 | 590 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 591 } | |
| 592 | |
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593 referencedInstancePath.SetPrefixIndex(1, j); |
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594 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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|
595 |
|
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596 contourDataPath.SetPrefixIndex(1, j); |
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597 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
| 0 | 598 |
| 599 Vector points; | |
|
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|
600 |
|
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changeset
|
601 if (!GenericToolbox::FastParseVector(points, slicesData) || |
| 32 | 602 points.size() != 3 * countPoints) |
| 0 | 603 { |
| 604 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 605 } | |
| 606 | |
|
981
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changeset
|
607 // seen in real world |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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changeset
|
608 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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changeset
|
609 { |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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parents:
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diff
changeset
|
610 LOG(ERROR) << "WARNING. The following Dicom tag (Referenced SOP Instance UID) contains an empty value : // (3006,0039)[" << i << "] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)"; |
|
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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
|
611 } |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
612 |
|
122
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refactoring DicomStructureSet
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|
613 Polygon polygon(sopInstanceUid); |
|
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diff
changeset
|
614 polygon.Reserve(countPoints); |
| 0 | 615 |
| 32 | 616 for (size_t k = 0; k < countPoints; k++) |
| 0 | 617 { |
| 618 Vector v(3); | |
| 619 v[0] = points[3 * k]; | |
| 620 v[1] = points[3 * k + 1]; | |
| 621 v[2] = points[3 * k + 2]; | |
|
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|
622 polygon.AddPoint(v); |
| 0 | 623 } |
| 624 | |
| 625 structures_[i].polygons_.push_back(polygon); | |
| 626 } | |
| 627 } | |
|
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parents:
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changeset
|
628 #if STONE_TIME_BLOCKING_OPS |
|
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changeset
|
629 boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); |
|
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|
630 boost::posix_time::time_duration duration = timerEnd - timerStart; |
|
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|
631 int64_t durationMs = duration.total_milliseconds(); |
|
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|
632 LOG(WARNING) << "DicomStructureSet::Setup took " << durationMs << " ms"; |
|
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|
633 #endif |
| 0 | 634 } |
| 635 | |
| 636 | |
|
1180
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changeset
|
637 #if ORTHANC_ENABLE_DCMTK == 1 |
|
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changeset
|
638 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance) |
|
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639 { |
|
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changeset
|
640 ParsedDicomDataset dataset(instance); |
|
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changeset
|
641 Setup(dataset); |
|
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|
642 } |
|
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|
643 #endif |
|
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|
644 |
|
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changeset
|
645 |
| 0 | 646 Vector DicomStructureSet::GetStructureCenter(size_t index) const |
| 647 { | |
| 648 const Structure& structure = GetStructure(index); | |
| 649 | |
| 650 Vector center; | |
|
158
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LinearAlgebra toolbox
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changeset
|
651 LinearAlgebra::AssignVector(center, 0, 0, 0); |
| 0 | 652 if (structure.polygons_.empty()) |
| 653 { | |
| 654 return center; | |
| 655 } | |
| 656 | |
| 657 double n = static_cast<double>(structure.polygons_.size()); | |
| 658 | |
| 659 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 660 polygon != structure.polygons_.end(); ++polygon) | |
| 661 { | |
|
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662 if (!polygon->GetPoints().empty()) |
| 0 | 663 { |
|
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|
664 center += polygon->GetPoints().front() / n; |
| 0 | 665 } |
| 666 } | |
| 667 | |
| 668 return center; | |
| 669 } | |
| 670 | |
| 671 | |
| 672 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 673 { | |
| 674 return GetStructure(index).name_; | |
| 675 } | |
| 676 | |
| 677 | |
| 678 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 679 { | |
| 680 return GetStructure(index).interpretation_; | |
| 681 } | |
| 682 | |
| 683 | |
|
804
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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changeset
|
684 Color DicomStructureSet::GetStructureColor(size_t index) const |
|
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diff
changeset
|
685 { |
|
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changeset
|
686 const Structure& s = GetStructure(index); |
|
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changeset
|
687 return Color(s.red_, s.green_, s.blue_); |
|
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changeset
|
688 } |
|
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changeset
|
689 |
|
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PolylineSceneLayer now has one color per chain
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diff
changeset
|
690 |
| 0 | 691 void DicomStructureSet::GetStructureColor(uint8_t& red, |
| 692 uint8_t& green, | |
| 693 uint8_t& blue, | |
| 694 size_t index) const | |
| 695 { | |
| 696 const Structure& s = GetStructure(index); | |
| 697 red = s.red_; | |
| 698 green = s.green_; | |
| 699 blue = s.blue_; | |
| 700 } | |
| 701 | |
| 702 | |
|
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diff
changeset
|
703 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) const |
| 0 | 704 { |
| 705 for (Structures::const_iterator structure = structures_.begin(); | |
| 706 structure != structures_.end(); ++structure) | |
| 707 { | |
| 708 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 709 polygon != structure->polygons_.end(); ++polygon) | |
| 710 { | |
|
122
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parents:
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diff
changeset
|
711 instances.insert(polygon->GetSopInstanceUid()); |
|
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parents:
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diff
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|
712 } |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
713 } |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
714 } |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
715 |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
716 |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
717 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
|
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parents:
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|
718 const std::string& seriesInstanceUid, |
|
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parents:
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diff
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|
719 const CoordinateSystem3D& geometry, |
|
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|
720 double thickness) |
|
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refactoring DicomStructureSet
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|
721 { |
|
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parents:
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diff
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|
722 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
|
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refactoring DicomStructureSet
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parents:
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diff
changeset
|
723 { |
|
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parents:
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diff
changeset
|
724 // This geometry is already known |
|
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
Benjamin Golinvaux <bgo@osimis.io>
parents:
949
diff
changeset
|
725 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). 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
|
726 |
|
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
|
727 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
|
122
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
728 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
729 else |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
730 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
731 if (thickness < 0) |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
732 { |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
733 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
734 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
735 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
736 if (!referencedSlices_.empty()) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
737 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
738 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
739 |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
740 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
| 0 | 741 { |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
742 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
743 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
744 } |
| 0 | 745 |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
746 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
747 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
748 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
749 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
750 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
751 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
752 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
753 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
| 0 | 754 |
| 131 | 755 for (Structures::iterator structure = structures_.begin(); |
| 756 structure != structures_.end(); ++structure) | |
| 757 { | |
| 758 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
| 759 polygon != structure->polygons_.end(); ++polygon) | |
| 760 { | |
| 761 polygon->UpdateReferencedSlice(referencedSlices_); | |
| 762 } | |
| 763 } | |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
764 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
765 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
766 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
767 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
768 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
769 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
770 CoordinateSystem3D slice(dataset); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
771 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
772 double thickness = 1; // 1 mm by default |
| 0 | 773 |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
774 std::string s; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
775 Vector v; |
|
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
776 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
|
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
777 LinearAlgebra::ParseVector(v, s) && |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
778 v.size() > 0) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
779 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
780 thickness = v[0]; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
781 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
782 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
783 std::string instance, series; |
|
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
784 if (dataset.LookupStringValue(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
|
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
785 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
786 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
787 AddReferencedSlice(instance, series, slice, thickness); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
788 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
789 else |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
790 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
791 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
792 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
793 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
794 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
795 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
796 void DicomStructureSet::CheckReferencedSlices() |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
797 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
798 for (Structures::iterator structure = structures_.begin(); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
799 structure != structures_.end(); ++structure) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
800 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
801 for (Polygons::iterator polygon = structure->polygons_.begin(); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
802 polygon != structure->polygons_.end(); ++polygon) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
803 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
804 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
805 { |
|
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
|
806 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
|
807 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
|
808 { |
|
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 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
810 << " missing information about referenced instance " |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
811 << "(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
|
812 } |
|
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
|
813 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
|
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 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
816 << " missing information about referenced instance " |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
817 << "(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
|
818 } |
|
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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819 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 0 | 820 } |
| 821 } | |
| 822 } | |
|
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823 } |
| 0 | 824 |
|
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825 |
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826 Vector DicomStructureSet::GetNormal() const |
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827 { |
|
126
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828 if (referencedSlices_.empty()) |
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829 { |
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830 Vector v; |
|
158
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LinearAlgebra toolbox
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831 LinearAlgebra::AssignVector(v, 0, 0, 1); |
|
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832 return v; |
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833 } |
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834 else |
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835 { |
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836 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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837 } |
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838 } |
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839 |
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840 bool DicomStructureSet::ProjectStructure( |
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841 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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842 std::vector< std::vector<Point2D> >& polygons, |
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|
843 #else |
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844 std::vector< std::pair<Point2D, Point2D> >& segments, |
|
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845 #endif |
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846 const Structure& structure, |
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847 const CoordinateSystem3D& sourceSlice) const |
| 125 | 848 { |
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849 const CoordinateSystem3D slice = CoordinateSystem3D::NormalizeCuttingPlane(sourceSlice); |
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850 |
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851 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
| 125 | 852 polygons.clear(); |
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853 #else |
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854 segments.clear(); |
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855 #endif |
| 125 | 856 |
| 857 Vector normal = GetNormal(); | |
| 858 | |
| 859 bool isOpposite; | |
| 860 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
| 861 { | |
| 862 // This is an axial projection | |
| 863 | |
| 794 | 864 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
| 125 | 865 polygon != structure.polygons_.end(); ++polygon) |
| 866 { | |
| 867 if (polygon->IsOnSlice(slice)) | |
| 868 { | |
|
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869 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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870 polygons.push_back(std::vector<Point2D>()); |
| 125 | 871 |
| 872 for (Points::const_iterator p = polygon->GetPoints().begin(); | |
| 873 p != polygon->GetPoints().end(); ++p) | |
| 874 { | |
| 875 double x, y; | |
|
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876 slice.ProjectPoint2(x, y, *p); |
|
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877 polygons.back().push_back(Point2D(x, y)); |
| 125 | 878 } |
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879 #else |
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|
880 // we need to add all the segments corresponding to this polygon |
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881 const std::vector<Vector>& points3D = polygon->GetPoints(); |
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882 if (points3D.size() >= 3) |
|
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883 { |
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884 Point2D prev2D; |
|
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885 { |
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|
886 Vector prev = points3D[0]; |
|
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parents:
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|
887 double prevX, prevY; |
|
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Benjamin Golinvaux <bgo@osimis.io>
parents:
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|
888 slice.ProjectPoint2(prevX, prevY, prev); |
|
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889 prev2D = Point2D(prevX, prevY); |
|
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|
890 } |
|
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|
891 |
|
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|
892 size_t pointCount = points3D.size(); |
|
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893 for (size_t ipt = 1; ipt < pointCount; ++ipt) |
|
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|
894 { |
|
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|
895 Vector next = points3D[ipt]; |
|
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diff
changeset
|
896 double nextX, nextY; |
|
1013
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Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
897 slice.ProjectPoint2(nextX, nextY, next); |
|
1000
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diff
changeset
|
898 Point2D next2D(nextX, nextY); |
|
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parents:
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diff
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|
899 segments.push_back(std::pair<Point2D, Point2D>(prev2D, next2D)); |
|
50e5acf5553b
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|
900 prev2D = next2D; |
|
50e5acf5553b
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|
901 } |
|
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|
902 } |
|
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diff
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|
903 else |
|
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|
904 { |
|
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|
905 LOG(ERROR) << "Contour with less than 3 points!"; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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|
906 // !!! |
|
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|
907 } |
|
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diff
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|
908 #endif |
| 125 | 909 } |
| 910 } | |
| 911 | |
| 912 return true; | |
| 913 } | |
| 914 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
| 915 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
| 916 { | |
|
132
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diff
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|
917 #if 1 |
|
126
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changeset
|
918 // Sagittal or coronal projection |
|
1000
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diff
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|
919 |
|
1178
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DicomStructureSet::ProjectOntoLayer()
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|
920 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
|
126
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diff
changeset
|
921 std::vector<BoostPolygon> projected; |
|
1162
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diff
changeset
|
922 |
|
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diff
changeset
|
923 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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|
924 polygon != structure.polygons_.end(); ++polygon) |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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|
925 { |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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diff
changeset
|
926 double x1, y1, x2, y2; |
|
709aa65aca17
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|
927 |
|
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diff
changeset
|
928 if (polygon->Project(x1, y1, x2, y2, slice)) |
|
709aa65aca17
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changeset
|
929 { |
|
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|
930 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
|
709aa65aca17
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|
931 } |
|
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|
932 } |
|
1000
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|
933 #else |
|
50e5acf5553b
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|
934 // this will contain the intersection of the polygon slab with |
|
50e5acf5553b
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diff
changeset
|
935 // the cutting plane, projected on the cutting plane coord system |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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changeset
|
936 // (that yields a rectangle) + the Z coordinate of the polygon |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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changeset
|
937 // (this is required to group polygons with the same Z later) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
938 std::vector<std::pair<RtStructRectangleInSlab, double> > projected; |
|
1162
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diff
changeset
|
939 |
| 794 | 940 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
|
126
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|
941 polygon != structure.polygons_.end(); ++polygon) |
|
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|
942 { |
| 131 | 943 double x1, y1, x2, y2; |
|
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changed RTSTRUCT rendering from polygons to segments
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|
944 |
| 131 | 945 if (polygon->Project(x1, y1, x2, y2, slice)) |
|
126
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rt-struct projection
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|
946 { |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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|
947 double curZ = polygon->GetGeometryOrigin()[2]; |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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994
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changeset
|
948 |
|
50e5acf5553b
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994
diff
changeset
|
949 // x1,y1 and x2,y2 are in "slice" coordinates (the cutting plane |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
950 // geometry) |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
951 projected.push_back(std::make_pair(CreateRectangle( |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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parents:
1170
diff
changeset
|
952 static_cast<float>(x1), |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
953 static_cast<float>(y1), |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
954 static_cast<float>(x2), |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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955 static_cast<float>(y2)),curZ)); |
|
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956 } |
|
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957 } |
|
1162
709aa65aca17
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|
958 #endif |
|
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959 |
|
1178
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960 #if USE_BOOST_UNION_FOR_POLYGONS != 1 |
|
1000
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961 // projected contains a set of rectangles specified by two opposite |
|
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962 // corners (x1,y1,x2,y2) |
|
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963 // we need to merge them |
|
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964 // each slab yields ONE polygon! |
|
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965 |
|
1000
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966 // we need to sorted all the rectangles that originate from the same Z |
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967 // into lanes. To make sure they are grouped together in the array, we |
|
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968 // sort it. |
|
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969 std::sort(projected.begin(), projected.end(), CompareRectanglesForProjection); |
|
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970 |
|
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971 std::vector<RtStructRectanglesInSlab> rectanglesForEachSlab; |
|
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972 rectanglesForEachSlab.reserve(projected.size()); |
|
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973 |
|
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974 double curZ = 0; |
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975 for (size_t i = 0; i < projected.size(); ++i) |
|
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976 { |
|
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977 #if 0 |
|
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978 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
|
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979 #else |
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980 if (i == 0) |
|
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981 { |
|
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982 curZ = projected[i].second; |
|
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983 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
|
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984 } |
|
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|
985 else |
|
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|
986 { |
|
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987 // this check is needed to prevent creating a new slab if |
|
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988 // the new polygon is at the same Z coord than last one |
|
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989 if (!LinearAlgebra::IsNear(curZ, projected[i].second)) |
|
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|
990 { |
|
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991 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
|
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|
992 curZ = projected[i].second; |
|
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|
993 } |
|
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|
994 } |
|
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|
995 #endif |
|
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|
996 |
|
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|
997 rectanglesForEachSlab.back().push_back(projected[i].first); |
|
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|
998 |
|
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|
999 // as long as they have the same y, we should put them into the same lane |
|
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1000 // BUT in Sebastien's code, there is only one polygon per lane. |
|
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|
1001 |
|
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|
1002 //std::cout << "rect: xmin = " << rect.xmin << " xmax = " << rect.xmax << " ymin = " << rect.ymin << " ymax = " << rect.ymax << std::endl; |
|
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1003 } |
|
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1004 |
|
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|
1005 // now we need to sort the slabs in increasing Y order (see ConvertListOfSlabsToSegments) |
|
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1006 std::sort(rectanglesForEachSlab.begin(), rectanglesForEachSlab.end(), CompareSlabsY); |
|
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diff
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|
1007 |
|
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diff
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|
1008 ConvertListOfSlabsToSegments(segments, rectanglesForEachSlab, projected.size()); |
|
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|
1009 #else |
|
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1010 BoostMultiPolygon merged; |
|
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1011 Union(merged, projected); |
|
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1012 |
|
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1013 polygons.resize(merged.size()); |
|
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1014 for (size_t i = 0; i < merged.size(); i++) |
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1015 { |
|
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1016 const std::vector<BoostPoint>& outer = merged[i].outer(); |
|
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1017 |
|
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1018 polygons[i].resize(outer.size()); |
|
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1019 for (size_t j = 0; j < outer.size(); j++) |
|
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1020 { |
|
1000
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1021 polygons[i][j] = Point2D(outer[j].x(), outer[j].y()); |
|
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1022 } |
|
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1023 } |
|
1000
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1024 #endif |
|
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1025 |
|
132
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1026 #else |
|
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1027 for (Polygons::iterator polygon = structure.polygons_.begin(); |
|
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1028 polygon != structure.polygons_.end(); ++polygon) |
|
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1029 { |
|
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1030 double x1, y1, x2, y2; |
|
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1031 if (polygon->Project(x1, y1, x2, y2, slice)) |
|
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1032 { |
|
1000
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1033 std::vector<Point2D> p(4); |
|
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1034 p[0] = std::make_pair(x1, y1); |
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1035 p[1] = std::make_pair(x2, y1); |
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1036 p[2] = std::make_pair(x2, y2); |
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1037 p[3] = std::make_pair(x1, y2); |
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1038 polygons.push_back(p); |
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1039 } |
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1040 } |
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1041 #endif |
| 125 | 1042 |
|
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1043 return true; |
| 125 | 1044 } |
| 1045 else | |
| 1046 { | |
| 1047 return false; | |
| 1048 } | |
| 0 | 1049 } |
|
1178
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1050 |
|
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1051 |
|
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1052 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer, |
|
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1053 const CoordinateSystem3D& plane, |
|
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1054 size_t structureIndex, |
|
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1055 const Color& color) const |
|
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1056 { |
|
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|
1057 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
|
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1058 std::vector< std::vector<Point2D> > polygons; |
|
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1059 if (ProjectStructure(polygons, structureIndex, plane)) |
|
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|
1060 { |
|
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1061 for (size_t j = 0; j < polygons.size(); j++) |
|
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|
1062 { |
|
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1063 std::vector<ScenePoint2D> chain; |
|
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|
1064 chain.reserve(polygons[j].size()); |
|
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|
1065 |
|
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changeset
|
1066 for (size_t k = 0; k < polygons[j].size(); k++) |
|
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|
1067 { |
|
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|
1068 chain.push_back(ScenePoint2D(polygons[j][k].x, polygons[j][k].y)); |
|
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|
1069 } |
|
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|
1070 |
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1071 layer.AddChain(chain, true, color.GetRed(), color.GetGreen(), color.GetBlue()); |
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1072 } |
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1073 } |
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1074 |
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1075 #else |
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1076 std::vector< std::pair<Point2D, Point2D> > segments; |
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1077 |
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1078 if (ProjectStructure(segments, structureIndex, plane)) |
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1079 { |
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1080 for (size_t j = 0; j < segments.size(); j++) |
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1081 { |
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1082 std::vector<ScenePoint2D> chain(2); |
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1083 chain[0] = ScenePoint2D(segments[j].first.x, segments[j].first.y); |
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1084 chain[1] = ScenePoint2D(segments[j].second.x, segments[j].second.y); |
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1085 layer.AddChain(chain, false, color.GetRed(), color.GetGreen(), color.GetBlue()); |
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1086 } |
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1087 } |
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1088 #endif |
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1089 } |
|
1885
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1090 |
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1091 |
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1092 void DicomStructureSet::GetStructurePoints(std::list< std::vector<Vector> >& target, |
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1093 size_t structureIndex, |
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1094 const std::string& sopInstanceUid) const |
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1095 { |
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1096 target.clear(); |
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1097 |
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1098 const Structure& structure = GetStructure(structureIndex); |
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1099 |
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1100 // TODO - Could be optimized by adding a multimap on "Structure", mapping |
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1101 // from SOP Instance UID to polygons |
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1102 |
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1103 for (Polygons::const_iterator it = structure.polygons_.begin(); |
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1104 it != structure.polygons_.end(); ++it) |
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1105 { |
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1106 if (it->GetSopInstanceUid() == sopInstanceUid) |
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1107 { |
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1108 target.push_back(it->GetPoints()); |
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1109 } |
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1110 } |
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1111 } |
|
1890
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1112 |
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1113 |
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1114 void DicomStructureSet::Test() |
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1115 { |
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1116 printf("OK\n"); |
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1117 |
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1118 for (size_t i = 0; i < structures_.size(); i++) |
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1119 { |
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1120 const Polygons& polygons = structures_[i].polygons_; |
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1121 |
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1122 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1123 { |
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1124 const Points& points = it->GetPoints(); |
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1125 |
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1126 if (points.size() >= 3) |
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1127 { |
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1128 const Vector& a = points[0]; |
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1129 const Vector& b = points[1]; |
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1130 const Vector& c = points[2]; |
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1131 Vector n; |
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1132 LinearAlgebra::CrossProduct(n, b - a, c - a); |
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1133 LinearAlgebra::NormalizeVector(n); |
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1134 if (n[2] < 0) |
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1135 n = -n; |
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1136 //LinearAlgebra::Print(n); |
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1137 |
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1138 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1139 double r = 1.0; |
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1140 double theta = acos(n[2]); |
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1141 double phi = atan(n[1]); |
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1142 printf("%.02f %.02f %.02f => ", n[0], n[1], n[2]); |
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1143 printf("%.02f %.02f =>", theta, phi); |
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1144 printf("%.02f %.02f %.02f\n", r * sin(theta) * cos(phi), r * sin(theta) * sin(phi), r * cos(theta)); |
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1145 } |
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1146 } |
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1147 } |
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1148 } |
| 0 | 1149 } |