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annotate Framework/Toolbox/Slice.cpp @ 118:a4d0b6c82b29 wasm

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using Orthanc::DicomMap instead of OrthancPlugins::DicomDatasetReader
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 02 Oct 2017 14:31:26 +0200
parents 42c05a3baee3
children ba83e38cf3ff
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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 Osimis, 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_ == 0 ||
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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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79
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80 double offset0, z;
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81
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82 if (!ParseDouble(offset0, offsets[0]) ||
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83 !ParseDouble(z, offsets[frame]))
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84 {
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85 LOG(ERROR) << "Invalid syntax";
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86 return false;
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87 }
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88
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89 if (!GeometryToolbox::IsCloseToZero(offset0))
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90 {
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91 LOG(ERROR) << "Invalid syntax";
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92 return false;
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93 }
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94
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95 geometry_ = CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(),
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96 geometry_.GetAxisX(),
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97 geometry_.GetAxisY());
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98
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99 return true;
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100 }
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101
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102
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103 bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset,
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104 const std::string& instanceId,
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105 unsigned int frame)
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106 {
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107 orthancInstanceId_ = instanceId;
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108 frame_ = frame;
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109 type_ = Type_OrthancDecodableFrame;
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110
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111 if (!dataset.CopyToString(sopClassUid_, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) ||
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112 sopClassUid_.empty())
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113 {
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114 LOG(ERROR) << "Instance without a SOP class UID";
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115 return false;
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116 }
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118 if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
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119 {
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120 frameCount_ = 1; // Assume instance with one frame
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121 }
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122
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123 if (frame >= frameCount_)
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124 {
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125 return false;
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126 }
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127
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128 if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) ||
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129 !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS))
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130 {
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131 return false;
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132 }
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133
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134 thickness_ = 100.0 * std::numeric_limits<double>::epsilon();
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135
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136 std::string tmp;
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137 if (dataset.CopyToString(tmp, Orthanc::DICOM_TAG_SLICE_THICKNESS, false))
117
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138 {
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139 if (!tmp.empty() &&
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140 !ParseDouble(thickness_, tmp))
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141 {
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142 return false; // Syntax error
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143 }
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144 }
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145
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146 converter_.ReadParameters(dataset);
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147
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148 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset);
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149
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150 std::string position, orientation;
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151 if (dataset.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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152 dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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153 {
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154 geometry_ = CoordinateSystem3D(position, orientation);
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155
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156 bool ok = true;
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157 SopClassUid tmp;
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158
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159 if (StringToSopClassUid(tmp, sopClassUid_))
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160 {
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161 switch (tmp)
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162 {
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163 case SopClassUid_RTDose:
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164 type_ = Type_OrthancRawFrame;
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165 ok = ComputeRTDoseGeometry(dataset, frame);
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166 break;
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167
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168 default:
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169 break;
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170 }
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171 }
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172
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173 if (!ok)
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174 {
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175 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame
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176 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_;
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177 return false;
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178 }
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179 }
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180
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181 return true;
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182 }
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183
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184
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185 const std::string Slice::GetOrthancInstanceId() const
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186 {
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187 if (type_ == Type_OrthancDecodableFrame ||
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188 type_ == Type_OrthancRawFrame)
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189 {
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190 return orthancInstanceId_;
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191 }
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192 else
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193 {
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194 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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195 }
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196 }
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197
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198
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199 unsigned int Slice::GetFrame() const
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200 {
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201 if (type_ == Type_Invalid)
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202 {
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203 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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204 }
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205
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206 return frame_;
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207 }
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208
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209
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210 const CoordinateSystem3D& Slice::GetGeometry() const
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211 {
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212 if (type_ == Type_Invalid)
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213 {
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214 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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215 }
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216
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217 return geometry_;
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218 }
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219
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220
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221 double Slice::GetThickness() const
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222 {
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223 if (type_ == Type_Invalid)
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224 {
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225 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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226 }
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227
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228 return thickness_;
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229 }
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230
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231
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232 double Slice::GetPixelSpacingX() const
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233 {
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234 if (type_ == Type_Invalid)
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235 {
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236 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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237 }
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238
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239 return pixelSpacingX_;
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240 }
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241
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242
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243 double Slice::GetPixelSpacingY() const
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244 {
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245 if (type_ == Type_Invalid)
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246 {
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247 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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248 }
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249
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250 return pixelSpacingY_;
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251 }
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252
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253
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254 unsigned int Slice::GetWidth() const
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255 {
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256 if (type_ == Type_Invalid)
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257 {
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258 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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259 }
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260
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261 return width_;
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262 }
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263
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264
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265 unsigned int Slice::GetHeight() const
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266 {
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267 if (type_ == Type_Invalid)
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268 {
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269 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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270 }
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271
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272 return height_;
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273 }
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274
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275
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276 const DicomFrameConverter& Slice::GetConverter() const
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277 {
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278 if (type_ == Type_Invalid)
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279 {
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280 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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281 }
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282
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283 return converter_;
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284 }
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f244018a4e4b BUGGY- trying to remove IVolumeSlicesObserver
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285
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286
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287 bool Slice::ContainsPlane(const CoordinateSystem3D& plane) const
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288 {
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289 if (type_ == Type_Invalid)
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290 {
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291 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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292 }
101
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293
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294 bool opposite;
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295 return (GeometryToolbox::IsParallelOrOpposite(opposite,
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296 GetGeometry().GetNormal(),
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297 plane.GetNormal()) &&
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298 GeometryToolbox::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()),
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299 GetGeometry().ProjectAlongNormal(plane.GetOrigin()),
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300 thickness_ / 2.0));
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301 }
102
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302
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303
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304 void Slice::GetExtent(std::vector<Vector>& points) const
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305 {
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306 double sx = GetPixelSpacingX();
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307 double sy = GetPixelSpacingY();
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308 double w = static_cast<double>(GetWidth());
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309 double h = static_cast<double>(GetHeight());
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310
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311 points.clear();
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312 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy));
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313 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy));
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314 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy));
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315 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy));
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316 }
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ffa6dded91bd reorganization
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317 }