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annotate Framework/Toolbox/Slice.cpp @ 159:0a73d76333db wasm

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populating LinearAlgebra
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 14 Feb 2018 09:15:08 +0100
parents a053ca7fa5c6
children a7674c0ae4ac
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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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e2fe9352f240 upgrade to year 2018
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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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54 std::string increment, offsetTag;
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56 if (!dataset.CopyToString(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false) ||
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57 !dataset.CopyToString(offsetTag, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, false))
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58 {
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59 LOG(ERROR) << "Cannot read the \"GridFrameOffsetVector\" tag, check you are using Orthanc >= 1.3.1";
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60 return false;
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61 }
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62
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63 Orthanc::Toolbox::ToUpperCase(increment);
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64 if (increment != "3004,000C" ||
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65 offsetTag.empty())
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66 {
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67 return false;
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68 }
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70 std::vector<std::string> offsets;
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71 Orthanc::Toolbox::TokenizeString(offsets, offsetTag, '\\');
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73 if (frameCount_ <= 1 ||
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74 offsets.size() != frameCount_ ||
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75 frame >= frameCount_)
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76 {
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77 LOG(ERROR) << "No information about the 3D location of some slice(s) in a RT DOSE";
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78 return false;
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79 }
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80
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81 double offset0, offset1, z;
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82
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83 if (!ParseDouble(offset0, offsets[0]) ||
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84 !ParseDouble(offset1, offsets[1]) ||
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85 !ParseDouble(z, offsets[frame]))
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86 {
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87 LOG(ERROR) << "Invalid syntax";
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88 return false;
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89 }
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91 if (!LinearAlgebra::IsCloseToZero(offset0))
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92 {
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93 LOG(ERROR) << "Invalid syntax";
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94 return false;
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95 }
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96
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97 geometry_ = CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(),
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98 //+ 650 * geometry_.GetAxisX(),
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99 geometry_.GetAxisX(),
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100 geometry_.GetAxisY());
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101
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102 thickness_ = offset1 - offset0;
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103 if (thickness_ < 0)
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104 {
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105 thickness_ = -thickness_;
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106 }
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107
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108 return true;
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109 }
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112 bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset,
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113 const std::string& instanceId,
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114 unsigned int frame)
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115 {
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116 orthancInstanceId_ = instanceId;
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117 frame_ = frame;
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118 type_ = Type_OrthancDecodableFrame;
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119 imageInformation_.reset(new Orthanc::DicomImageInformation(dataset));
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121 if (!dataset.CopyToString(sopClassUid_, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) ||
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122 sopClassUid_.empty())
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123 {
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124 LOG(ERROR) << "Instance without a SOP class UID";
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125 return false;
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126 }
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128 if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
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129 {
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130 frameCount_ = 1; // Assume instance with one frame
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131 }
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132
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diff changeset
133 if (frame >= frameCount_)
73
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134 {
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135 return false;
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136 }
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137
118
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diff changeset
138 if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) ||
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diff changeset
139 !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS))
73
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140 {
117
42c05a3baee3 loading multi-frame instances as 3D volumes
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diff changeset
141 return false;
73
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142 }
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143
117
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diff changeset
144 thickness_ = 100.0 * std::numeric_limits<double>::epsilon();
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diff changeset
145
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diff changeset
146 std::string tmp;
118
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diff changeset
147 if (dataset.CopyToString(tmp, Orthanc::DICOM_TAG_SLICE_THICKNESS, false))
117
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148 {
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149 if (!tmp.empty() &&
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150 !ParseDouble(thickness_, tmp))
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151 {
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152 return false; // Syntax error
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153 }
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154 }
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155
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156 converter_.ReadParameters(dataset);
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157
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158 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset);
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159
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160 std::string position, orientation;
118
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diff changeset
161 if (dataset.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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diff changeset
162 dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
73
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163 {
110
53025eecbc95 renamed SliceGeometry as CoordinateSystem3D
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164 geometry_ = CoordinateSystem3D(position, orientation);
117
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165
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166 bool ok = true;
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167 SopClassUid tmp;
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168
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169 if (StringToSopClassUid(tmp, sopClassUid_))
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170 {
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171 switch (tmp)
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172 {
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173 case SopClassUid_RTDose:
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174 type_ = Type_OrthancRawFrame;
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175 ok = ComputeRTDoseGeometry(dataset, frame);
117
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176 break;
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177
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178 default:
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179 break;
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180 }
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181 }
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182
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183 if (!ok)
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184 {
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185 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame
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186 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_;
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187 return false;
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188 }
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189 }
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190
117
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191 return true;
73
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192 }
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193
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194
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195 const std::string Slice::GetOrthancInstanceId() const
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196 {
117
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197 if (type_ == Type_OrthancDecodableFrame ||
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diff changeset
198 type_ == Type_OrthancRawFrame)
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199 {
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200 return orthancInstanceId_;
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201 }
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diff changeset
202 else
73
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203 {
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204 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
117
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205 }
73
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206 }
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parents:
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207
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208
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209 unsigned int Slice::GetFrame() const
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210 {
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211 if (type_ == Type_Invalid)
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212 {
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213 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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214 }
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215
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216 return frame_;
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217 }
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diff changeset
218
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219
110
53025eecbc95 renamed SliceGeometry as CoordinateSystem3D
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diff changeset
220 const CoordinateSystem3D& Slice::GetGeometry() const
73
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221 {
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222 if (type_ == Type_Invalid)
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diff changeset
223 {
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diff changeset
224 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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225 }
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parents:
diff changeset
226
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diff changeset
227 return geometry_;
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parents:
diff changeset
228 }
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
229
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parents:
diff changeset
230
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parents:
diff changeset
231 double Slice::GetThickness() const
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232 {
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diff changeset
233 if (type_ == Type_Invalid)
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parents:
diff changeset
234 {
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diff changeset
235 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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236 }
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parents:
diff changeset
237
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diff changeset
238 return thickness_;
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parents:
diff changeset
239 }
ffa6dded91bd reorganization
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parents:
diff changeset
240
ffa6dded91bd reorganization
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parents:
diff changeset
241
ffa6dded91bd reorganization
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parents:
diff changeset
242 double Slice::GetPixelSpacingX() const
ffa6dded91bd reorganization
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parents:
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243 {
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parents:
diff changeset
244 if (type_ == Type_Invalid)
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parents:
diff changeset
245 {
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diff changeset
246 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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247 }
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parents:
diff changeset
248
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diff changeset
249 return pixelSpacingX_;
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parents:
diff changeset
250 }
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
252
ffa6dded91bd reorganization
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parents:
diff changeset
253 double Slice::GetPixelSpacingY() const
ffa6dded91bd reorganization
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parents:
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254 {
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parents:
diff changeset
255 if (type_ == Type_Invalid)
ffa6dded91bd reorganization
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parents:
diff changeset
256 {
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diff changeset
257 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents:
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258 }
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parents:
diff changeset
259
ffa6dded91bd reorganization
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parents:
diff changeset
260 return pixelSpacingY_;
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parents:
diff changeset
261 }
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
262
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
263
ffa6dded91bd reorganization
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parents:
diff changeset
264 unsigned int Slice::GetWidth() const
ffa6dded91bd reorganization
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parents:
diff changeset
265 {
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parents:
diff changeset
266 if (type_ == Type_Invalid)
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parents:
diff changeset
267 {
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parents:
diff changeset
268 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents:
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269 }
ffa6dded91bd reorganization
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parents:
diff changeset
270
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parents:
diff changeset
271 return width_;
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parents:
diff changeset
272 }
ffa6dded91bd reorganization
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parents:
diff changeset
273
ffa6dded91bd reorganization
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parents:
diff changeset
274
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parents:
diff changeset
275 unsigned int Slice::GetHeight() const
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parents:
diff changeset
276 {
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parents:
diff changeset
277 if (type_ == Type_Invalid)
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parents:
diff changeset
278 {
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diff changeset
279 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents:
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280 }
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parents:
diff changeset
281
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parents:
diff changeset
282 return height_;
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parents:
diff changeset
283 }
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parents:
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284
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285
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286 const DicomFrameConverter& Slice::GetConverter() const
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287 {
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288 if (type_ == Type_Invalid)
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289 {
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290 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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291 }
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292
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293 return converter_;
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294 }
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295
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296
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297 bool Slice::ContainsPlane(const CoordinateSystem3D& plane) const
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298 {
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299 if (type_ == Type_Invalid)
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300 {
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301 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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302 }
101
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303
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304 bool opposite;
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305 return (GeometryToolbox::IsParallelOrOpposite(opposite,
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306 GetGeometry().GetNormal(),
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307 plane.GetNormal()) &&
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308 LinearAlgebra::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()),
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309 GetGeometry().ProjectAlongNormal(plane.GetOrigin()),
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310 thickness_ / 2.0));
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311 }
102
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312
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313
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314 void Slice::GetExtent(std::vector<Vector>& points) const
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315 {
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316 double sx = GetPixelSpacingX();
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317 double sy = GetPixelSpacingY();
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318 double w = static_cast<double>(GetWidth());
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319 double h = static_cast<double>(GetHeight());
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320
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321 points.clear();
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322 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy));
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323 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy));
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324 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy));
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325 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy));
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326 }
119
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327
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328
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329 const Orthanc::DicomImageInformation& Slice::GetImageInformation() const
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330 {
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331 if (imageInformation_.get() == NULL)
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332 {
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333 // Only available if constructing the "Slice" object with a DICOM map
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334 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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335 }
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336 else
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337 {
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338 return *imageInformation_;
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339 }
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340 }
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341 }