Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/Slice.cpp @ 370:8ac7161d5fea
integration captain->default
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 05 Nov 2018 10:04:19 +0100 |
parents | 5412adf19980 |
children | 3a4ca166fafa |
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 | |
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5 * Copyright (C) 2017-2018 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 "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 |
33 namespace OrthancStone | |
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 bool Slice::ComputeRTDoseGeometry(const Orthanc::DicomMap& dataset, |
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50 unsigned int frame) |
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51 { |
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52 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html |
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53 |
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54 { |
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55 std::string increment; |
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56 |
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57 if (dataset.CopyToString(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false)) |
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58 { |
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59 Orthanc::Toolbox::ToUpperCase(increment); |
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60 if (increment != "3004,000C") // This is the "Grid Frame Offset Vector" tag |
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61 { |
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62 LOG(ERROR) << "Bad value for the \"FrameIncrementPointer\" tag"; |
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63 return false; |
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64 } |
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65 } |
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66 } |
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67 |
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68 std::string offsetTag; |
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69 |
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70 if (!dataset.CopyToString(offsetTag, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, false) || |
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71 offsetTag.empty()) |
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72 { |
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73 LOG(ERROR) << "Cannot read the \"GridFrameOffsetVector\" tag, check you are using Orthanc >= 1.3.1"; |
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74 return false; |
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75 } |
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76 |
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77 std::vector<std::string> offsets; |
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78 Orthanc::Toolbox::TokenizeString(offsets, offsetTag, '\\'); |
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79 |
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80 if (frameCount_ <= 1 || |
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81 offsets.size() < frameCount_ || |
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82 offsets.size() < 2 || |
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83 frame >= frameCount_) |
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84 { |
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85 LOG(ERROR) << "No information about the 3D location of some slice(s) in a RT DOSE"; |
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86 return false; |
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87 } |
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88 |
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89 double offset0, offset1, z; |
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90 |
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91 if (!ParseDouble(offset0, offsets[0]) || |
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92 !ParseDouble(offset1, offsets[1]) || |
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93 !ParseDouble(z, offsets[frame])) |
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94 { |
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95 LOG(ERROR) << "Invalid syntax"; |
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96 return false; |
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97 } |
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98 |
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99 if (!LinearAlgebra::IsCloseToZero(offset0)) |
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100 { |
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101 LOG(ERROR) << "Invalid syntax"; |
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102 return false; |
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103 } |
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104 |
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105 geometry_ = CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(), |
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106 //+ 650 * geometry_.GetAxisX(), |
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107 geometry_.GetAxisX(), |
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108 geometry_.GetAxisY()); |
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109 |
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110 thickness_ = offset1 - offset0; |
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111 if (thickness_ < 0) |
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112 { |
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113 thickness_ = -thickness_; |
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114 } |
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115 |
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116 return true; |
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117 } |
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118 |
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119 |
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120 bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset, |
73 | 121 const std::string& instanceId, |
122 unsigned int frame) | |
123 { | |
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124 orthancInstanceId_ = instanceId; |
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125 frame_ = frame; |
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126 type_ = Type_OrthancDecodableFrame; |
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127 imageInformation_.reset(new Orthanc::DicomImageInformation(dataset)); |
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128 |
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129 if (!dataset.CopyToString(sopClassUid_, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) || |
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130 sopClassUid_.empty()) |
73 | 131 { |
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132 LOG(ERROR) << "Instance without a SOP class UID"; |
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133 return false; |
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134 } |
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135 |
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136 if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)) |
117
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137 { |
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138 frameCount_ = 1; // Assume instance with one frame |
73 | 139 } |
140 | |
117
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141 if (frame >= frameCount_) |
73 | 142 { |
143 return false; | |
144 } | |
145 | |
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146 if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) || |
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147 !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS)) |
73 | 148 { |
117
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149 return false; |
73 | 150 } |
151 | |
117
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152 thickness_ = 100.0 * std::numeric_limits<double>::epsilon(); |
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153 |
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154 std::string tmp; |
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155 if (dataset.CopyToString(tmp, Orthanc::DICOM_TAG_SLICE_THICKNESS, false)) |
117
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156 { |
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157 if (!tmp.empty() && |
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158 !ParseDouble(thickness_, tmp)) |
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159 { |
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160 return false; // Syntax error |
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161 } |
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162 } |
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163 |
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164 converter_.ReadParameters(dataset); |
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165 |
73 | 166 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset); |
167 | |
168 std::string position, orientation; | |
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169 if (dataset.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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170 dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
73 | 171 { |
110
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172 geometry_ = CoordinateSystem3D(position, orientation); |
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173 |
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174 bool ok = true; |
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175 SopClassUid tmp; |
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176 |
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177 if (StringToSopClassUid(tmp, sopClassUid_)) |
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178 { |
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179 switch (tmp) |
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180 { |
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181 case SopClassUid_RTDose: |
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182 type_ = Type_OrthancRawFrame; |
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183 ok = ComputeRTDoseGeometry(dataset, frame); |
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184 break; |
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185 |
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186 default: |
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187 break; |
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188 } |
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189 } |
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190 |
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191 if (!ok) |
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192 { |
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193 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame |
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194 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_; |
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195 return false; |
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196 } |
73 | 197 } |
198 | |
117
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199 return true; |
73 | 200 } |
201 | |
202 | |
203 const std::string Slice::GetOrthancInstanceId() const | |
204 { | |
117
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205 if (type_ == Type_OrthancDecodableFrame || |
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206 type_ == Type_OrthancRawFrame) |
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207 { |
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208 return orthancInstanceId_; |
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209 } |
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210 else |
73 | 211 { |
212 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
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213 } |
73 | 214 } |
215 | |
216 | |
217 unsigned int Slice::GetFrame() const | |
218 { | |
219 if (type_ == Type_Invalid) | |
220 { | |
221 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
222 } | |
223 | |
224 return frame_; | |
225 } | |
226 | |
227 | |
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228 const CoordinateSystem3D& Slice::GetGeometry() const |
73 | 229 { |
230 if (type_ == Type_Invalid) | |
231 { | |
232 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
233 } | |
234 | |
235 return geometry_; | |
236 } | |
237 | |
238 | |
239 double Slice::GetThickness() const | |
240 { | |
241 if (type_ == Type_Invalid) | |
242 { | |
243 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
244 } | |
245 | |
246 return thickness_; | |
247 } | |
248 | |
249 | |
250 double Slice::GetPixelSpacingX() const | |
251 { | |
252 if (type_ == Type_Invalid) | |
253 { | |
254 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
255 } | |
256 | |
257 return pixelSpacingX_; | |
258 } | |
259 | |
260 | |
261 double Slice::GetPixelSpacingY() const | |
262 { | |
263 if (type_ == Type_Invalid) | |
264 { | |
265 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
266 } | |
267 | |
268 return pixelSpacingY_; | |
269 } | |
270 | |
271 | |
272 unsigned int Slice::GetWidth() const | |
273 { | |
274 if (type_ == Type_Invalid) | |
275 { | |
276 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
277 } | |
278 | |
279 return width_; | |
280 } | |
281 | |
282 | |
283 unsigned int Slice::GetHeight() const | |
284 { | |
285 if (type_ == Type_Invalid) | |
286 { | |
287 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
288 } | |
289 | |
290 return height_; | |
291 } | |
292 | |
293 | |
294 const DicomFrameConverter& Slice::GetConverter() const | |
295 { | |
296 if (type_ == Type_Invalid) | |
297 { | |
298 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
299 } | |
300 | |
301 return converter_; | |
302 } | |
89
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303 |
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304 |
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305 bool Slice::ContainsPlane(const CoordinateSystem3D& plane) const |
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306 { |
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307 if (type_ == Type_Invalid) |
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308 { |
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309 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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310 } |
101
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311 |
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312 bool opposite; |
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313 return (GeometryToolbox::IsParallelOrOpposite(opposite, |
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314 GetGeometry().GetNormal(), |
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315 plane.GetNormal()) && |
158
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316 LinearAlgebra::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()), |
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317 GetGeometry().ProjectAlongNormal(plane.GetOrigin()), |
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318 thickness_ / 2.0)); |
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319 } |
102 | 320 |
321 | |
322 void Slice::GetExtent(std::vector<Vector>& points) const | |
323 { | |
324 double sx = GetPixelSpacingX(); | |
325 double sy = GetPixelSpacingY(); | |
326 double w = static_cast<double>(GetWidth()); | |
327 double h = static_cast<double>(GetHeight()); | |
328 | |
329 points.clear(); | |
330 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy)); | |
331 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy)); | |
332 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy)); | |
333 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy)); | |
334 } | |
119
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335 |
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336 |
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337 const Orthanc::DicomImageInformation& Slice::GetImageInformation() const |
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338 { |
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339 if (imageInformation_.get() == NULL) |
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340 { |
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341 // Only available if constructing the "Slice" object with a DICOM map |
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342 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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343 } |
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344 else |
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345 { |
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346 return *imageInformation_; |
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347 } |
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348 } |
73 | 349 } |