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annotate Framework/Toolbox/Slice.cpp @ 174:a7674c0ae4ac wasm

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fix captain rt-dose
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 08 Mar 2018 20:22:47 +0100
parents 0a73d76333db
children 7a031ac16b2d
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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 #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>
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32
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33 namespace OrthancStone
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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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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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120 bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset,
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121 const std::string& instanceId,
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122 unsigned int frame)
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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())
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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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diff changeset
136 if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
117
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diff changeset
137 {
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138 frameCount_ = 1; // Assume instance with one frame
73
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139 }
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140
117
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diff changeset
141 if (frame >= frameCount_)
73
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142 {
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143 return false;
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144 }
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145
118
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diff changeset
146 if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) ||
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147 !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS))
73
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148 {
117
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diff changeset
149 return false;
73
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150 }
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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
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166 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset);
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167
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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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diff changeset
170 dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
73
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171 {
110
53025eecbc95 renamed SliceGeometry as CoordinateSystem3D
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172 geometry_ = CoordinateSystem3D(position, orientation);
117
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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);
117
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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 }
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197 }
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198
117
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199 return true;
73
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200 }
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201
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202
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203 const std::string Slice::GetOrthancInstanceId() const
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204 {
117
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205 if (type_ == Type_OrthancDecodableFrame ||
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diff changeset
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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diff changeset
210 else
73
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211 {
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212 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
117
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213 }
73
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214 }
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215
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216
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217 unsigned int Slice::GetFrame() const
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218 {
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219 if (type_ == Type_Invalid)
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220 {
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221 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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222 }
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223
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224 return frame_;
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225 }
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226
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227
110
53025eecbc95 renamed SliceGeometry as CoordinateSystem3D
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diff changeset
228 const CoordinateSystem3D& Slice::GetGeometry() const
73
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229 {
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230 if (type_ == Type_Invalid)
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231 {
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diff changeset
232 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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233 }
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234
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diff changeset
235 return geometry_;
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parents:
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236 }
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parents:
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237
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238
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diff changeset
239 double Slice::GetThickness() const
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240 {
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diff changeset
241 if (type_ == Type_Invalid)
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diff changeset
242 {
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diff changeset
243 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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244 }
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parents:
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245
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246 return thickness_;
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247 }
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parents:
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248
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249
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250 double Slice::GetPixelSpacingX() const
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251 {
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diff changeset
252 if (type_ == Type_Invalid)
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253 {
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254 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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255 }
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diff changeset
256
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diff changeset
257 return pixelSpacingX_;
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parents:
diff changeset
258 }
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parents:
diff changeset
259
ffa6dded91bd reorganization
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parents:
diff changeset
260
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parents:
diff changeset
261 double Slice::GetPixelSpacingY() const
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parents:
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262 {
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parents:
diff changeset
263 if (type_ == Type_Invalid)
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parents:
diff changeset
264 {
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diff changeset
265 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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266 }
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parents:
diff changeset
267
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diff changeset
268 return pixelSpacingY_;
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parents:
diff changeset
269 }
ffa6dded91bd reorganization
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parents:
diff changeset
270
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parents:
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271
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272 unsigned int Slice::GetWidth() const
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273 {
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parents:
diff changeset
274 if (type_ == Type_Invalid)
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parents:
diff changeset
275 {
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diff changeset
276 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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277 }
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parents:
diff changeset
278
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diff changeset
279 return width_;
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parents:
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280 }
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parents:
diff changeset
281
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282
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diff changeset
283 unsigned int Slice::GetHeight() const
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284 {
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diff changeset
285 if (type_ == Type_Invalid)
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286 {
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287 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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288 }
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289
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290 return height_;
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291 }
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292
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293
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294 const DicomFrameConverter& Slice::GetConverter() const
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295 {
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296 if (type_ == Type_Invalid)
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297 {
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298 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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299 }
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300
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301 return converter_;
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302 }
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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()) &&
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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
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320
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321
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322 void Slice::GetExtent(std::vector<Vector>& points) const
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323 {
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324 double sx = GetPixelSpacingX();
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325 double sy = GetPixelSpacingY();
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326 double w = static_cast<double>(GetWidth());
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327 double h = static_cast<double>(GetHeight());
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328
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329 points.clear();
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330 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy));
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331 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy));
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332 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy));
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333 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy));
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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
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349 }