Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/Slice.cpp @ 117:42c05a3baee3 wasm
loading multi-frame instances as 3D volumes
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 28 Sep 2017 16:55:51 +0200 |
parents | 2eca030792aa |
children | a4d0b6c82b29 |
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 OrthancPlugins::DicomDatasetReader& reader, |
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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 static const OrthancPlugins::DicomTag DICOM_TAG_GRID_FRAME_OFFSET_VECTOR(0x3004, 0x000c); |
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53 static const OrthancPlugins::DicomTag DICOM_TAG_FRAME_INCREMENT_POINTER(0x0028, 0x0009); |
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54 |
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55 std::string increment = reader.GetStringValue(DICOM_TAG_FRAME_INCREMENT_POINTER, ""); |
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56 std::string offsetTag; |
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57 |
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58 bool ok = reader.GetDataset().GetStringValue(offsetTag, DICOM_TAG_GRID_FRAME_OFFSET_VECTOR); |
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59 if (!ok) |
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60 { |
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61 LOG(ERROR) << "Cannot read the \"GridFrameOffsetVector\" tag, check you are using Orthanc >= 1.3.1"; |
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62 return false; |
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63 } |
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64 |
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65 Orthanc::Toolbox::ToUpperCase(increment); |
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66 if (increment != "3004,000C" || |
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67 offsetTag.empty()) |
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68 { |
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69 return false; |
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70 } |
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71 |
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72 std::vector<std::string> offsets; |
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73 Orthanc::Toolbox::TokenizeString(offsets, offsetTag, '\\'); |
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74 |
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75 if (frameCount_ == 0 || |
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76 offsets.size() != frameCount_ || |
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77 frame >= frameCount_) |
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78 { |
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79 LOG(ERROR) << "No information about the 3D location of some slice(s) in a RT DOSE"; |
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80 return false; |
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81 } |
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82 |
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83 double offset0, z; |
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84 |
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85 if (!ParseDouble(offset0, offsets[0]) || |
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86 !ParseDouble(z, offsets[frame])) |
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87 { |
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88 LOG(ERROR) << "Invalid syntax"; |
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89 return false; |
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90 } |
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91 |
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92 if (!GeometryToolbox::IsCloseToZero(offset0)) |
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93 { |
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94 LOG(ERROR) << "Invalid syntax"; |
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95 return false; |
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96 } |
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97 |
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98 geometry_ = CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(), |
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99 geometry_.GetAxisX(), |
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100 geometry_.GetAxisY()); |
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101 |
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102 return true; |
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103 } |
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104 |
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105 |
73 | 106 bool Slice::ParseOrthancFrame(const OrthancPlugins::IDicomDataset& dataset, |
107 const std::string& instanceId, | |
108 unsigned int frame) | |
109 { | |
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110 orthancInstanceId_ = instanceId; |
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111 frame_ = frame; |
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112 type_ = Type_OrthancDecodableFrame; |
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113 |
73 | 114 OrthancPlugins::DicomDatasetReader reader(dataset); |
115 | |
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116 sopClassUid_ = reader.GetStringValue(OrthancPlugins::DICOM_TAG_SOP_CLASS_UID, ""); |
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117 if (sopClassUid_.empty()) |
73 | 118 { |
117
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119 LOG(ERROR) << "Instance without a SOP class UID"; |
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120 return false; |
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121 } |
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122 |
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123 if (!reader.GetUnsignedIntegerValue(frameCount_, OrthancPlugins::DICOM_TAG_NUMBER_OF_FRAMES)) |
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124 { |
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125 frameCount_ = 1; // Assume instance with one frame |
73 | 126 } |
127 | |
117
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128 if (frame >= frameCount_) |
73 | 129 { |
130 return false; | |
131 } | |
132 | |
117
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133 if (!reader.GetUnsignedIntegerValue(width_, OrthancPlugins::DICOM_TAG_COLUMNS) || |
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134 !reader.GetUnsignedIntegerValue(height_, OrthancPlugins::DICOM_TAG_ROWS)) |
73 | 135 { |
117
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136 return false; |
73 | 137 } |
138 | |
117
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139 thickness_ = 100.0 * std::numeric_limits<double>::epsilon(); |
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140 |
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141 std::string tmp; |
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142 if (dataset.GetStringValue(tmp, OrthancPlugins::DICOM_TAG_SLICE_THICKNESS)) |
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143 { |
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144 if (!tmp.empty() && |
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145 !ParseDouble(thickness_, tmp)) |
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146 { |
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147 return false; // Syntax error |
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148 } |
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149 } |
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150 |
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151 converter_.ReadParameters(dataset); |
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152 |
73 | 153 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset); |
154 | |
155 std::string position, orientation; | |
156 if (dataset.GetStringValue(position, OrthancPlugins::DICOM_TAG_IMAGE_POSITION_PATIENT) && | |
157 dataset.GetStringValue(orientation, OrthancPlugins::DICOM_TAG_IMAGE_ORIENTATION_PATIENT)) | |
158 { | |
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159 geometry_ = CoordinateSystem3D(position, orientation); |
117
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160 |
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161 bool ok = true; |
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162 SopClassUid tmp; |
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163 |
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164 if (StringToSopClassUid(tmp, sopClassUid_)) |
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165 { |
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166 switch (tmp) |
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167 { |
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168 case SopClassUid_RTDose: |
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169 type_ = Type_OrthancRawFrame; |
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170 ok = ComputeRTDoseGeometry(reader, frame); |
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171 break; |
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172 |
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173 default: |
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174 break; |
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175 } |
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176 } |
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177 |
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178 if (!ok) |
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179 { |
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180 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame |
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181 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_; |
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182 return false; |
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183 } |
73 | 184 } |
185 | |
117
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186 return true; |
73 | 187 } |
188 | |
189 | |
190 const std::string Slice::GetOrthancInstanceId() const | |
191 { | |
117
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192 if (type_ == Type_OrthancDecodableFrame || |
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193 type_ == Type_OrthancRawFrame) |
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194 { |
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195 return orthancInstanceId_; |
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196 } |
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197 else |
73 | 198 { |
199 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
117
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200 } |
73 | 201 } |
202 | |
203 | |
204 unsigned int Slice::GetFrame() const | |
205 { | |
206 if (type_ == Type_Invalid) | |
207 { | |
208 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
209 } | |
210 | |
211 return frame_; | |
212 } | |
213 | |
214 | |
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215 const CoordinateSystem3D& Slice::GetGeometry() const |
73 | 216 { |
217 if (type_ == Type_Invalid) | |
218 { | |
219 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
220 } | |
221 | |
222 return geometry_; | |
223 } | |
224 | |
225 | |
226 double Slice::GetThickness() const | |
227 { | |
228 if (type_ == Type_Invalid) | |
229 { | |
230 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
231 } | |
232 | |
233 return thickness_; | |
234 } | |
235 | |
236 | |
237 double Slice::GetPixelSpacingX() const | |
238 { | |
239 if (type_ == Type_Invalid) | |
240 { | |
241 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
242 } | |
243 | |
244 return pixelSpacingX_; | |
245 } | |
246 | |
247 | |
248 double Slice::GetPixelSpacingY() const | |
249 { | |
250 if (type_ == Type_Invalid) | |
251 { | |
252 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
253 } | |
254 | |
255 return pixelSpacingY_; | |
256 } | |
257 | |
258 | |
259 unsigned int Slice::GetWidth() const | |
260 { | |
261 if (type_ == Type_Invalid) | |
262 { | |
263 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
264 } | |
265 | |
266 return width_; | |
267 } | |
268 | |
269 | |
270 unsigned int Slice::GetHeight() const | |
271 { | |
272 if (type_ == Type_Invalid) | |
273 { | |
274 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
275 } | |
276 | |
277 return height_; | |
278 } | |
279 | |
280 | |
281 const DicomFrameConverter& Slice::GetConverter() const | |
282 { | |
283 if (type_ == Type_Invalid) | |
284 { | |
285 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
286 } | |
287 | |
288 return converter_; | |
289 } | |
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290 |
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291 |
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292 bool Slice::ContainsPlane(const CoordinateSystem3D& plane) const |
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293 { |
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294 if (type_ == Type_Invalid) |
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295 { |
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296 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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297 } |
101
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298 |
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299 bool opposite; |
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300 return (GeometryToolbox::IsParallelOrOpposite(opposite, |
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301 GetGeometry().GetNormal(), |
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302 plane.GetNormal()) && |
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303 GeometryToolbox::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()), |
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304 GetGeometry().ProjectAlongNormal(plane.GetOrigin()), |
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305 thickness_ / 2.0)); |
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306 } |
102 | 307 |
308 | |
309 void Slice::GetExtent(std::vector<Vector>& points) const | |
310 { | |
311 double sx = GetPixelSpacingX(); | |
312 double sy = GetPixelSpacingY(); | |
313 double w = static_cast<double>(GetWidth()); | |
314 double h = static_cast<double>(GetHeight()); | |
315 | |
316 points.clear(); | |
317 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy)); | |
318 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy)); | |
319 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy)); | |
320 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy)); | |
321 } | |
73 | 322 } |