Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/Slice.cpp @ 118:a4d0b6c82b29 wasm
using Orthanc::DicomMap instead of OrthancPlugins::DicomDatasetReader
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 02 Oct 2017 14:31:26 +0200 |
parents | 42c05a3baee3 |
children | ba83e38cf3ff |
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 | |
5 * Copyright (C) 2017 Osimis, Belgium | |
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 "../Enumerations.h" |
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25 |
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26 #include <Core/Logging.h> |
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27 #include <Core/OrthancException.h> |
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28 #include <Core/Toolbox.h> |
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29 |
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30 #include <boost/lexical_cast.hpp> |
73 | 31 |
32 namespace OrthancStone | |
33 { | |
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34 static bool ParseDouble(double& target, |
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35 const std::string& source) |
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36 { |
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37 try |
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38 { |
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39 target = boost::lexical_cast<double>(source); |
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40 return true; |
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41 } |
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42 catch (boost::bad_lexical_cast&) |
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43 { |
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44 return false; |
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45 } |
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46 } |
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47 |
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48 bool Slice::ComputeRTDoseGeometry(const Orthanc::DicomMap& dataset, |
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49 unsigned int frame) |
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50 { |
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51 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html |
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52 |
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53 std::string increment, offsetTag; |
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54 |
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55 if (!dataset.CopyToString(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false) || |
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56 !dataset.CopyToString(offsetTag, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, false)) |
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57 { |
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58 LOG(ERROR) << "Cannot read the \"GridFrameOffsetVector\" tag, check you are using Orthanc >= 1.3.1"; |
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59 return false; |
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60 } |
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61 |
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62 Orthanc::Toolbox::ToUpperCase(increment); |
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63 if (increment != "3004,000C" || |
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64 offsetTag.empty()) |
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65 { |
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66 return false; |
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67 } |
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68 |
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69 std::vector<std::string> offsets; |
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70 Orthanc::Toolbox::TokenizeString(offsets, offsetTag, '\\'); |
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71 |
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72 if (frameCount_ == 0 || |
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73 offsets.size() != frameCount_ || |
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74 frame >= frameCount_) |
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75 { |
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76 LOG(ERROR) << "No information about the 3D location of some slice(s) in a RT DOSE"; |
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77 return false; |
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78 } |
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79 |
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80 double offset0, z; |
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81 |
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82 if (!ParseDouble(offset0, offsets[0]) || |
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83 !ParseDouble(z, offsets[frame])) |
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84 { |
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85 LOG(ERROR) << "Invalid syntax"; |
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86 return false; |
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87 } |
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88 |
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89 if (!GeometryToolbox::IsCloseToZero(offset0)) |
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90 { |
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91 LOG(ERROR) << "Invalid syntax"; |
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92 return false; |
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93 } |
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94 |
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95 geometry_ = CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(), |
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96 geometry_.GetAxisX(), |
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97 geometry_.GetAxisY()); |
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98 |
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99 return true; |
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100 } |
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101 |
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102 |
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103 bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset, |
73 | 104 const std::string& instanceId, |
105 unsigned int frame) | |
106 { | |
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107 orthancInstanceId_ = instanceId; |
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108 frame_ = frame; |
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109 type_ = Type_OrthancDecodableFrame; |
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110 |
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111 if (!dataset.CopyToString(sopClassUid_, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) || |
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112 sopClassUid_.empty()) |
73 | 113 { |
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114 LOG(ERROR) << "Instance without a SOP class UID"; |
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115 return false; |
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116 } |
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117 |
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118 if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)) |
117
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119 { |
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120 frameCount_ = 1; // Assume instance with one frame |
73 | 121 } |
122 | |
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123 if (frame >= frameCount_) |
73 | 124 { |
125 return false; | |
126 } | |
127 | |
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128 if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) || |
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129 !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS)) |
73 | 130 { |
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131 return false; |
73 | 132 } |
133 | |
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134 thickness_ = 100.0 * std::numeric_limits<double>::epsilon(); |
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135 |
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136 std::string tmp; |
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137 if (dataset.CopyToString(tmp, Orthanc::DICOM_TAG_SLICE_THICKNESS, false)) |
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138 { |
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139 if (!tmp.empty() && |
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140 !ParseDouble(thickness_, tmp)) |
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141 { |
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142 return false; // Syntax error |
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143 } |
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144 } |
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145 |
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146 converter_.ReadParameters(dataset); |
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147 |
73 | 148 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset); |
149 | |
150 std::string position, orientation; | |
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151 if (dataset.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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152 dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
73 | 153 { |
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154 geometry_ = CoordinateSystem3D(position, orientation); |
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155 |
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156 bool ok = true; |
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157 SopClassUid tmp; |
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158 |
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159 if (StringToSopClassUid(tmp, sopClassUid_)) |
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160 { |
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161 switch (tmp) |
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162 { |
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163 case SopClassUid_RTDose: |
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164 type_ = Type_OrthancRawFrame; |
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165 ok = ComputeRTDoseGeometry(dataset, frame); |
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166 break; |
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167 |
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168 default: |
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169 break; |
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170 } |
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171 } |
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172 |
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173 if (!ok) |
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174 { |
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175 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame |
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176 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_; |
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177 return false; |
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178 } |
73 | 179 } |
180 | |
117
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181 return true; |
73 | 182 } |
183 | |
184 | |
185 const std::string Slice::GetOrthancInstanceId() const | |
186 { | |
117
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187 if (type_ == Type_OrthancDecodableFrame || |
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188 type_ == Type_OrthancRawFrame) |
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189 { |
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190 return orthancInstanceId_; |
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191 } |
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192 else |
73 | 193 { |
194 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
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195 } |
73 | 196 } |
197 | |
198 | |
199 unsigned int Slice::GetFrame() const | |
200 { | |
201 if (type_ == Type_Invalid) | |
202 { | |
203 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
204 } | |
205 | |
206 return frame_; | |
207 } | |
208 | |
209 | |
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210 const CoordinateSystem3D& Slice::GetGeometry() const |
73 | 211 { |
212 if (type_ == Type_Invalid) | |
213 { | |
214 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
215 } | |
216 | |
217 return geometry_; | |
218 } | |
219 | |
220 | |
221 double Slice::GetThickness() const | |
222 { | |
223 if (type_ == Type_Invalid) | |
224 { | |
225 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
226 } | |
227 | |
228 return thickness_; | |
229 } | |
230 | |
231 | |
232 double Slice::GetPixelSpacingX() const | |
233 { | |
234 if (type_ == Type_Invalid) | |
235 { | |
236 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
237 } | |
238 | |
239 return pixelSpacingX_; | |
240 } | |
241 | |
242 | |
243 double Slice::GetPixelSpacingY() const | |
244 { | |
245 if (type_ == Type_Invalid) | |
246 { | |
247 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
248 } | |
249 | |
250 return pixelSpacingY_; | |
251 } | |
252 | |
253 | |
254 unsigned int Slice::GetWidth() const | |
255 { | |
256 if (type_ == Type_Invalid) | |
257 { | |
258 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
259 } | |
260 | |
261 return width_; | |
262 } | |
263 | |
264 | |
265 unsigned int Slice::GetHeight() const | |
266 { | |
267 if (type_ == Type_Invalid) | |
268 { | |
269 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
270 } | |
271 | |
272 return height_; | |
273 } | |
274 | |
275 | |
276 const DicomFrameConverter& Slice::GetConverter() const | |
277 { | |
278 if (type_ == Type_Invalid) | |
279 { | |
280 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
281 } | |
282 | |
283 return converter_; | |
284 } | |
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285 |
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286 |
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287 bool Slice::ContainsPlane(const CoordinateSystem3D& plane) const |
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288 { |
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289 if (type_ == Type_Invalid) |
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290 { |
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291 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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292 } |
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293 |
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294 bool opposite; |
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295 return (GeometryToolbox::IsParallelOrOpposite(opposite, |
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296 GetGeometry().GetNormal(), |
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297 plane.GetNormal()) && |
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298 GeometryToolbox::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()), |
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299 GetGeometry().ProjectAlongNormal(plane.GetOrigin()), |
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300 thickness_ / 2.0)); |
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301 } |
102 | 302 |
303 | |
304 void Slice::GetExtent(std::vector<Vector>& points) const | |
305 { | |
306 double sx = GetPixelSpacingX(); | |
307 double sy = GetPixelSpacingY(); | |
308 double w = static_cast<double>(GetWidth()); | |
309 double h = static_cast<double>(GetHeight()); | |
310 | |
311 points.clear(); | |
312 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy)); | |
313 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy)); | |
314 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy)); | |
315 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy)); | |
316 } | |
73 | 317 } |