Mercurial > hg > orthanc-stone
annotate Framework/Deprecated/Toolbox/Slice.cpp @ 819:a68cd7ae8838
fix
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 29 May 2019 13:39:31 +0200 |
parents | c35e98d22764 |
children | 1f74bc3459ba |
rev | line source |
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73 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
439 | 5 * Copyright (C) 2017-2019 Osimis S.A., Belgium |
73 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
22 #include "Slice.h" | |
23 | |
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24 #include "../../StoneEnumerations.h" |
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25 #include "../../Toolbox/GeometryToolbox.h" |
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26 |
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27 #include <Core/Logging.h> |
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28 #include <Core/OrthancException.h> |
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29 #include <Core/Toolbox.h> |
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30 |
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31 #include <boost/lexical_cast.hpp> |
73 | 32 |
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33 namespace Deprecated |
73 | 34 { |
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35 static bool ParseDouble(double& target, |
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36 const std::string& source) |
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37 { |
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38 try |
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39 { |
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40 target = boost::lexical_cast<double>(source); |
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41 return true; |
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42 } |
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43 catch (boost::bad_lexical_cast&) |
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44 { |
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45 return false; |
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46 } |
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47 } |
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48 |
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49 Slice* Slice::Clone() const |
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50 { |
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51 std::auto_ptr<Slice> target(new Slice()); |
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52 |
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53 target->type_ = type_; |
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54 target->orthancInstanceId_ = orthancInstanceId_; |
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55 target->sopClassUid_ = sopClassUid_; |
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56 target->frame_ = frame_; |
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57 target->frameCount_ = frameCount_; |
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58 target->geometry_ = geometry_; |
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59 target->pixelSpacingX_ = pixelSpacingX_; |
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60 target->pixelSpacingY_ = pixelSpacingY_; |
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61 target->thickness_ = thickness_; |
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62 target->width_ = width_; |
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63 target->height_ = height_; |
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64 target->converter_ = converter_; |
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65 if (imageInformation_.get() != NULL) |
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66 target->imageInformation_.reset(imageInformation_->Clone()); |
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67 |
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68 return target.release(); |
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69 } |
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70 |
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71 bool Slice::ComputeRTDoseGeometry(const Orthanc::DicomMap& dataset, |
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72 unsigned int frame) |
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73 { |
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74 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html |
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75 |
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76 { |
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77 std::string increment; |
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78 |
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79 if (dataset.CopyToString(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false)) |
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80 { |
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81 Orthanc::Toolbox::ToUpperCase(increment); |
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82 if (increment != "3004,000C") // This is the "Grid Frame Offset Vector" tag |
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83 { |
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84 LOG(ERROR) << "Bad value for the \"FrameIncrementPointer\" tag"; |
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85 return false; |
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86 } |
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87 } |
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88 } |
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89 |
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90 std::string offsetTag; |
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91 |
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92 if (!dataset.CopyToString(offsetTag, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, false) || |
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93 offsetTag.empty()) |
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94 { |
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95 LOG(ERROR) << "Cannot read the \"GridFrameOffsetVector\" tag, check you are using Orthanc >= 1.3.1"; |
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96 return false; |
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97 } |
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98 |
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99 std::vector<std::string> offsets; |
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100 Orthanc::Toolbox::TokenizeString(offsets, offsetTag, '\\'); |
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101 |
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102 if (frameCount_ <= 1 || |
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103 offsets.size() < frameCount_ || |
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104 offsets.size() < 2 || |
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105 frame >= frameCount_) |
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106 { |
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107 LOG(ERROR) << "No information about the 3D location of some slice(s) in a RT DOSE"; |
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108 return false; |
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109 } |
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110 |
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111 double offset0, offset1, z; |
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112 |
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113 if (!ParseDouble(offset0, offsets[0]) || |
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114 !ParseDouble(offset1, offsets[1]) || |
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115 !ParseDouble(z, offsets[frame])) |
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116 { |
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117 LOG(ERROR) << "Invalid syntax"; |
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118 return false; |
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119 } |
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120 |
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121 if (!OrthancStone::LinearAlgebra::IsCloseToZero(offset0)) |
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122 { |
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123 LOG(ERROR) << "Invalid syntax"; |
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124 return false; |
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125 } |
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126 |
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127 geometry_ = OrthancStone::CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(), |
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128 //+ 650 * geometry_.GetAxisX(), |
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129 geometry_.GetAxisX(), |
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130 geometry_.GetAxisY()); |
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131 |
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132 thickness_ = offset1 - offset0; |
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133 if (thickness_ < 0) |
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134 { |
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135 thickness_ = -thickness_; |
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136 } |
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137 |
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138 return true; |
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139 } |
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140 |
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141 |
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142 bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset, |
73 | 143 const std::string& instanceId, |
144 unsigned int frame) | |
145 { | |
117
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146 orthancInstanceId_ = instanceId; |
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147 frame_ = frame; |
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148 type_ = Type_OrthancDecodableFrame; |
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149 imageInformation_.reset(new Orthanc::DicomImageInformation(dataset)); |
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150 |
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151 if (!dataset.CopyToString(sopClassUid_, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) || |
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152 sopClassUid_.empty()) |
73 | 153 { |
117
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154 LOG(ERROR) << "Instance without a SOP class UID"; |
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155 return false; |
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156 } |
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157 |
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158 if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)) |
117
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159 { |
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160 frameCount_ = 1; // Assume instance with one frame |
73 | 161 } |
162 | |
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163 if (frame >= frameCount_) |
73 | 164 { |
165 return false; | |
166 } | |
167 | |
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168 if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) || |
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169 !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS)) |
73 | 170 { |
117
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171 return false; |
73 | 172 } |
173 | |
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174 thickness_ = 100.0 * std::numeric_limits<double>::epsilon(); |
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175 |
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176 std::string tmp; |
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177 if (dataset.CopyToString(tmp, Orthanc::DICOM_TAG_SLICE_THICKNESS, false)) |
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178 { |
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179 if (!tmp.empty() && |
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180 !ParseDouble(thickness_, tmp)) |
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181 { |
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182 return false; // Syntax error |
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183 } |
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184 } |
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185 |
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186 converter_.ReadParameters(dataset); |
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187 |
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188 OrthancStone::GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset); |
73 | 189 |
190 std::string position, orientation; | |
118
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191 if (dataset.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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192 dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
73 | 193 { |
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194 geometry_ = OrthancStone::CoordinateSystem3D(position, orientation); |
117
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195 |
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196 bool ok = true; |
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197 |
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198 switch (OrthancStone::StringToSopClassUid(sopClassUid_)) |
117
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199 { |
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200 case OrthancStone::SopClassUid_RTDose: |
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201 type_ = Type_OrthancRawFrame; |
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202 ok = ComputeRTDoseGeometry(dataset, frame); |
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203 break; |
117
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204 |
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205 default: |
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206 break; |
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207 } |
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208 |
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209 if (!ok) |
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210 { |
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211 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame |
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212 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_; |
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213 return false; |
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214 } |
73 | 215 } |
216 | |
117
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217 return true; |
73 | 218 } |
219 | |
220 | |
221 const std::string Slice::GetOrthancInstanceId() const | |
222 { | |
117
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223 if (type_ == Type_OrthancDecodableFrame || |
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224 type_ == Type_OrthancRawFrame) |
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225 { |
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226 return orthancInstanceId_; |
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227 } |
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228 else |
73 | 229 { |
230 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
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231 } |
73 | 232 } |
233 | |
234 | |
235 unsigned int Slice::GetFrame() const | |
236 { | |
237 if (type_ == Type_Invalid) | |
238 { | |
239 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
240 } | |
241 | |
242 return frame_; | |
243 } | |
244 | |
245 | |
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246 const OrthancStone::CoordinateSystem3D& Slice::GetGeometry() const |
73 | 247 { |
248 if (type_ == Type_Invalid) | |
249 { | |
250 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
251 } | |
252 | |
253 return geometry_; | |
254 } | |
255 | |
256 | |
257 double Slice::GetThickness() const | |
258 { | |
259 if (type_ == Type_Invalid) | |
260 { | |
261 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
262 } | |
263 | |
264 return thickness_; | |
265 } | |
266 | |
267 | |
268 double Slice::GetPixelSpacingX() const | |
269 { | |
270 if (type_ == Type_Invalid) | |
271 { | |
272 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
273 } | |
274 | |
275 return pixelSpacingX_; | |
276 } | |
277 | |
278 | |
279 double Slice::GetPixelSpacingY() const | |
280 { | |
281 if (type_ == Type_Invalid) | |
282 { | |
283 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
284 } | |
285 | |
286 return pixelSpacingY_; | |
287 } | |
288 | |
289 | |
290 unsigned int Slice::GetWidth() const | |
291 { | |
292 if (type_ == Type_Invalid) | |
293 { | |
294 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
295 } | |
296 | |
297 return width_; | |
298 } | |
299 | |
300 | |
301 unsigned int Slice::GetHeight() const | |
302 { | |
303 if (type_ == Type_Invalid) | |
304 { | |
305 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
306 } | |
307 | |
308 return height_; | |
309 } | |
310 | |
311 | |
312 const DicomFrameConverter& Slice::GetConverter() const | |
313 { | |
314 if (type_ == Type_Invalid) | |
315 { | |
316 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
317 } | |
318 | |
319 return converter_; | |
320 } | |
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321 |
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322 |
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323 bool Slice::ContainsPlane(const OrthancStone::CoordinateSystem3D& plane) const |
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324 { |
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325 if (type_ == Type_Invalid) |
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326 { |
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327 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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328 } |
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329 |
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330 bool opposite; |
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331 return (OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, |
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332 GetGeometry().GetNormal(), |
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333 plane.GetNormal()) && |
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334 OrthancStone::LinearAlgebra::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()), |
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335 GetGeometry().ProjectAlongNormal(plane.GetOrigin()), |
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336 thickness_ / 2.0)); |
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337 } |
102 | 338 |
339 | |
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340 void Slice::GetExtent(std::vector<OrthancStone::Vector>& points) const |
102 | 341 { |
342 double sx = GetPixelSpacingX(); | |
343 double sy = GetPixelSpacingY(); | |
344 double w = static_cast<double>(GetWidth()); | |
345 double h = static_cast<double>(GetHeight()); | |
346 | |
347 points.clear(); | |
348 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy)); | |
349 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy)); | |
350 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy)); | |
351 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy)); | |
352 } | |
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353 |
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354 |
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355 const Orthanc::DicomImageInformation& Slice::GetImageInformation() const |
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356 { |
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357 if (imageInformation_.get() == NULL) |
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358 { |
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359 // Only available if constructing the "Slice" object with a DICOM map |
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360 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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361 } |
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362 else |
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363 { |
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364 return *imageInformation_; |
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365 } |
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366 } |
73 | 367 } |