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annotate Framework/Toolbox/Slice.cpp @ 158:a053ca7fa5c6 wasm

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LinearAlgebra toolbox
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 14 Feb 2018 08:58:31 +0100
parents e2fe9352f240
children 0a73d76333db
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1 /**
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2 * Stone of Orthanc
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2018 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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20
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21
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22 #include "Slice.h"
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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>
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31
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32 namespace OrthancStone
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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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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_ <= 1 ||
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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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80 double offset0, offset1, z;
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81
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82 if (!ParseDouble(offset0, offsets[0]) ||
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83 !ParseDouble(offset1, offsets[1]) ||
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84 !ParseDouble(z, offsets[frame]))
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85 {
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86 LOG(ERROR) << "Invalid syntax";
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87 return false;
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88 }
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89
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90 if (!LinearAlgebra::IsCloseToZero(offset0))
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91 {
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92 LOG(ERROR) << "Invalid syntax";
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93 return false;
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94 }
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96 geometry_ = CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(),
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97 //+ 650 * geometry_.GetAxisX(),
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98 geometry_.GetAxisX(),
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99 geometry_.GetAxisY());
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100
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101 thickness_ = offset1 - offset0;
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102 if (thickness_ < 0)
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103 {
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104 thickness_ = -thickness_;
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105 }
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106
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107 return true;
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108 }
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111 bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset,
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112 const std::string& instanceId,
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113 unsigned int frame)
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114 {
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115 orthancInstanceId_ = instanceId;
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116 frame_ = frame;
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117 type_ = Type_OrthancDecodableFrame;
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118 imageInformation_.reset(new Orthanc::DicomImageInformation(dataset));
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120 if (!dataset.CopyToString(sopClassUid_, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) ||
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121 sopClassUid_.empty())
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122 {
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123 LOG(ERROR) << "Instance without a SOP class UID";
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124 return false;
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125 }
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126
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127 if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
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128 {
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129 frameCount_ = 1; // Assume instance with one frame
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130 }
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131
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132 if (frame >= frameCount_)
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133 {
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134 return false;
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135 }
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136
118
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137 if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) ||
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138 !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS))
73
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139 {
117
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140 return false;
73
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141 }
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142
117
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143 thickness_ = 100.0 * std::numeric_limits<double>::epsilon();
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144
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145 std::string tmp;
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146 if (dataset.CopyToString(tmp, Orthanc::DICOM_TAG_SLICE_THICKNESS, false))
117
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147 {
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148 if (!tmp.empty() &&
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149 !ParseDouble(thickness_, tmp))
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150 {
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151 return false; // Syntax error
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152 }
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153 }
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154
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155 converter_.ReadParameters(dataset);
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156
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157 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset);
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158
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159 std::string position, orientation;
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160 if (dataset.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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161 dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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162 {
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163 geometry_ = CoordinateSystem3D(position, orientation);
117
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164
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165 bool ok = true;
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166 SopClassUid tmp;
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167
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168 if (StringToSopClassUid(tmp, sopClassUid_))
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169 {
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170 switch (tmp)
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171 {
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172 case SopClassUid_RTDose:
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173 type_ = Type_OrthancRawFrame;
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174 ok = ComputeRTDoseGeometry(dataset, frame);
117
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175 break;
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176
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177 default:
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178 break;
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179 }
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180 }
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181
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182 if (!ok)
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183 {
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184 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame
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185 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_;
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186 return false;
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187 }
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188 }
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189
117
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190 return true;
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191 }
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192
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193
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194 const std::string Slice::GetOrthancInstanceId() const
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195 {
117
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196 if (type_ == Type_OrthancDecodableFrame ||
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197 type_ == Type_OrthancRawFrame)
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198 {
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199 return orthancInstanceId_;
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200 }
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201 else
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202 {
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203 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
117
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204 }
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205 }
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206
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207
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208 unsigned int Slice::GetFrame() const
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209 {
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210 if (type_ == Type_Invalid)
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211 {
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212 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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213 }
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214
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215 return frame_;
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216 }
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217
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218
110
53025eecbc95 renamed SliceGeometry as CoordinateSystem3D
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diff changeset
219 const CoordinateSystem3D& Slice::GetGeometry() const
73
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220 {
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221 if (type_ == Type_Invalid)
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222 {
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223 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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224 }
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225
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226 return geometry_;
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227 }
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228
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229
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230 double Slice::GetThickness() const
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231 {
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232 if (type_ == Type_Invalid)
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233 {
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234 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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235 }
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236
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237 return thickness_;
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238 }
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239
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240
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241 double Slice::GetPixelSpacingX() const
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242 {
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243 if (type_ == Type_Invalid)
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244 {
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245 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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246 }
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247
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248 return pixelSpacingX_;
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249 }
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250
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251
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252 double Slice::GetPixelSpacingY() const
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253 {
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254 if (type_ == Type_Invalid)
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255 {
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256 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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257 }
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diff changeset
258
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259 return pixelSpacingY_;
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260 }
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261
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262
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263 unsigned int Slice::GetWidth() const
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264 {
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265 if (type_ == Type_Invalid)
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266 {
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267 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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268 }
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269
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270 return width_;
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271 }
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272
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273
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274 unsigned int Slice::GetHeight() const
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275 {
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276 if (type_ == Type_Invalid)
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277 {
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278 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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279 }
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280
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281 return height_;
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282 }
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283
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284
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285 const DicomFrameConverter& Slice::GetConverter() const
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286 {
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287 if (type_ == Type_Invalid)
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288 {
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289 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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290 }
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291
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292 return converter_;
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293 }
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294
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295
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296 bool Slice::ContainsPlane(const CoordinateSystem3D& plane) const
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297 {
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298 if (type_ == Type_Invalid)
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299 {
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300 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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301 }
101
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302
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303 bool opposite;
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304 return (GeometryToolbox::IsParallelOrOpposite(opposite,
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305 GetGeometry().GetNormal(),
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306 plane.GetNormal()) &&
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307 LinearAlgebra::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()),
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308 GetGeometry().ProjectAlongNormal(plane.GetOrigin()),
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309 thickness_ / 2.0));
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310 }
102
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311
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312
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313 void Slice::GetExtent(std::vector<Vector>& points) const
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314 {
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315 double sx = GetPixelSpacingX();
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316 double sy = GetPixelSpacingY();
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317 double w = static_cast<double>(GetWidth());
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318 double h = static_cast<double>(GetHeight());
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319
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320 points.clear();
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321 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy));
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322 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy));
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323 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy));
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324 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy));
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325 }
119
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326
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327
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328 const Orthanc::DicomImageInformation& Slice::GetImageInformation() const
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329 {
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330 if (imageInformation_.get() == NULL)
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331 {
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332 // Only available if constructing the "Slice" object with a DICOM map
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333 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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334 }
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335 else
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336 {
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337 return *imageInformation_;
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338 }
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339 }
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340 }