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annotate Framework/Toolbox/Slice.cpp @ 418:c23df8b3433b

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refactoring
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 15 Nov 2018 18:32:48 +0100
parents 3a4ca166fafa
children b70e9be013e4
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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 "../StoneEnumerations.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 Slice* Slice::Clone() const
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50 {
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51 std::auto_ptr<Slice> target(new Slice());
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52
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53 target->type_ = type_;
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54 target->orthancInstanceId_ = orthancInstanceId_;
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55 target->sopClassUid_ = sopClassUid_;
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56 target->frame_ = frame_;
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57 target->frameCount_ = frameCount_;
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58 target->geometry_ = geometry_;
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59 target->pixelSpacingX_ = pixelSpacingX_;
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60 target->pixelSpacingY_ = pixelSpacingY_;
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61 target->thickness_ = thickness_;
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62 target->width_ = width_;
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63 target->height_ = height_;
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64 target->converter_ = converter_;
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65 if (imageInformation_.get() != NULL)
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66 target->imageInformation_.reset(imageInformation_->Clone());
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67
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68 return target.release();
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69 }
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71 bool Slice::ComputeRTDoseGeometry(const Orthanc::DicomMap& dataset,
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72 unsigned int frame)
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73 {
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74 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html
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76 {
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77 std::string increment;
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78
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79 if (dataset.CopyToString(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false))
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80 {
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81 Orthanc::Toolbox::ToUpperCase(increment);
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82 if (increment != "3004,000C") // This is the "Grid Frame Offset Vector" tag
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83 {
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84 LOG(ERROR) << "Bad value for the \"FrameIncrementPointer\" tag";
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85 return false;
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86 }
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87 }
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88 }
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89
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90 std::string offsetTag;
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91
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92 if (!dataset.CopyToString(offsetTag, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, false) ||
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93 offsetTag.empty())
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94 {
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95 LOG(ERROR) << "Cannot read the \"GridFrameOffsetVector\" tag, check you are using Orthanc >= 1.3.1";
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96 return false;
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97 }
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99 std::vector<std::string> offsets;
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100 Orthanc::Toolbox::TokenizeString(offsets, offsetTag, '\\');
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101
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102 if (frameCount_ <= 1 ||
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103 offsets.size() < frameCount_ ||
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104 offsets.size() < 2 ||
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105 frame >= frameCount_)
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106 {
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107 LOG(ERROR) << "No information about the 3D location of some slice(s) in a RT DOSE";
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108 return false;
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109 }
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110
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111 double offset0, offset1, z;
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112
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113 if (!ParseDouble(offset0, offsets[0]) ||
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114 !ParseDouble(offset1, offsets[1]) ||
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115 !ParseDouble(z, offsets[frame]))
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116 {
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117 LOG(ERROR) << "Invalid syntax";
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118 return false;
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119 }
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121 if (!LinearAlgebra::IsCloseToZero(offset0))
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122 {
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123 LOG(ERROR) << "Invalid syntax";
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124 return false;
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125 }
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126
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127 geometry_ = CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(),
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128 //+ 650 * geometry_.GetAxisX(),
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129 geometry_.GetAxisX(),
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130 geometry_.GetAxisY());
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131
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132 thickness_ = offset1 - offset0;
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133 if (thickness_ < 0)
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134 {
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135 thickness_ = -thickness_;
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136 }
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137
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138 return true;
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139 }
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140
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141
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142 bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset,
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143 const std::string& instanceId,
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144 unsigned int frame)
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145 {
117
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146 orthancInstanceId_ = instanceId;
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147 frame_ = frame;
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148 type_ = Type_OrthancDecodableFrame;
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149 imageInformation_.reset(new Orthanc::DicomImageInformation(dataset));
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150
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151 if (!dataset.CopyToString(sopClassUid_, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) ||
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152 sopClassUid_.empty())
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153 {
117
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154 LOG(ERROR) << "Instance without a SOP class UID";
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155 return false;
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156 }
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157
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158 if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
117
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159 {
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160 frameCount_ = 1; // Assume instance with one frame
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161 }
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162
117
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163 if (frame >= frameCount_)
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164 {
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165 return false;
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166 }
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167
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168 if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) ||
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169 !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS))
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170 {
117
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171 return false;
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172 }
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173
117
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174 thickness_ = 100.0 * std::numeric_limits<double>::epsilon();
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175
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176 std::string tmp;
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177 if (dataset.CopyToString(tmp, Orthanc::DICOM_TAG_SLICE_THICKNESS, false))
117
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178 {
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179 if (!tmp.empty() &&
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180 !ParseDouble(thickness_, tmp))
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181 {
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182 return false; // Syntax error
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183 }
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184 }
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185
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186 converter_.ReadParameters(dataset);
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187
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188 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset);
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189
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190 std::string position, orientation;
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191 if (dataset.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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192 dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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193 {
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194 geometry_ = CoordinateSystem3D(position, orientation);
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195
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196 bool ok = true;
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197 SopClassUid tmp;
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198
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199 if (StringToSopClassUid(tmp, sopClassUid_))
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200 {
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201 switch (tmp)
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202 {
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203 case SopClassUid_RTDose:
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204 type_ = Type_OrthancRawFrame;
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205 ok = ComputeRTDoseGeometry(dataset, frame);
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206 break;
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207
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208 default:
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209 break;
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210 }
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211 }
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212
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213 if (!ok)
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214 {
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215 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame
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216 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_;
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217 return false;
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218 }
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219 }
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220
117
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221 return true;
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222 }
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223
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224
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225 const std::string Slice::GetOrthancInstanceId() const
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226 {
117
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227 if (type_ == Type_OrthancDecodableFrame ||
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228 type_ == Type_OrthancRawFrame)
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229 {
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230 return orthancInstanceId_;
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231 }
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232 else
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233 {
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234 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
117
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235 }
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236 }
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237
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238
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239 unsigned int Slice::GetFrame() const
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240 {
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241 if (type_ == Type_Invalid)
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242 {
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243 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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244 }
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245
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246 return frame_;
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247 }
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248
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249
110
53025eecbc95 renamed SliceGeometry as CoordinateSystem3D
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250 const CoordinateSystem3D& Slice::GetGeometry() const
73
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251 {
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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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256
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257 return geometry_;
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258 }
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259
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260
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261 double Slice::GetThickness() const
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262 {
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263 if (type_ == Type_Invalid)
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264 {
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265 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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266 }
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267
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268 return thickness_;
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269 }
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270
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271
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272 double Slice::GetPixelSpacingX() const
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273 {
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274 if (type_ == Type_Invalid)
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275 {
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276 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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277 }
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278
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279 return pixelSpacingX_;
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280 }
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281
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282
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283 double Slice::GetPixelSpacingY() const
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284 {
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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 pixelSpacingY_;
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291 }
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292
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293
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294 unsigned int Slice::GetWidth() 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 width_;
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302 }
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303
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304
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305 unsigned int Slice::GetHeight() 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 }
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311
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312 return height_;
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313 }
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314
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315
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316 const DicomFrameConverter& Slice::GetConverter() const
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317 {
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318 if (type_ == Type_Invalid)
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319 {
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320 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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321 }
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322
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323 return converter_;
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324 }
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325
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326
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327 bool Slice::ContainsPlane(const CoordinateSystem3D& plane) const
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328 {
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329 if (type_ == Type_Invalid)
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330 {
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331 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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332 }
101
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333
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334 bool opposite;
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335 return (GeometryToolbox::IsParallelOrOpposite(opposite,
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336 GetGeometry().GetNormal(),
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337 plane.GetNormal()) &&
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338 LinearAlgebra::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()),
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339 GetGeometry().ProjectAlongNormal(plane.GetOrigin()),
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340 thickness_ / 2.0));
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341 }
102
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342
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343
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344 void Slice::GetExtent(std::vector<Vector>& points) const
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345 {
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346 double sx = GetPixelSpacingX();
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347 double sy = GetPixelSpacingY();
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348 double w = static_cast<double>(GetWidth());
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349 double h = static_cast<double>(GetHeight());
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350
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351 points.clear();
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352 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy));
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353 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy));
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354 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy));
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355 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy));
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356 }
119
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357
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358
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359 const Orthanc::DicomImageInformation& Slice::GetImageInformation() const
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360 {
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361 if (imageInformation_.get() == NULL)
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362 {
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363 // Only available if constructing the "Slice" object with a DICOM map
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364 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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365 }
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366 else
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367 {
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368 return *imageInformation_;
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369 }
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370 }
73
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371 }