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annotate Framework/Toolbox/Slice.cpp @ 117:42c05a3baee3 wasm

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loading multi-frame instances as 3D volumes
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 28 Sep 2017 16:55:51 +0200
parents 2eca030792aa
children a4d0b6c82b29
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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
117
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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 OrthancPlugins::DicomDatasetReader& reader,
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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 static const OrthancPlugins::DicomTag DICOM_TAG_GRID_FRAME_OFFSET_VECTOR(0x3004, 0x000c);
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53 static const OrthancPlugins::DicomTag DICOM_TAG_FRAME_INCREMENT_POINTER(0x0028, 0x0009);
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54
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55 std::string increment = reader.GetStringValue(DICOM_TAG_FRAME_INCREMENT_POINTER, "");
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56 std::string offsetTag;
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57
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58 bool ok = reader.GetDataset().GetStringValue(offsetTag, DICOM_TAG_GRID_FRAME_OFFSET_VECTOR);
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59 if (!ok)
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60 {
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61 LOG(ERROR) << "Cannot read the \"GridFrameOffsetVector\" tag, check you are using Orthanc >= 1.3.1";
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62 return false;
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63 }
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64
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65 Orthanc::Toolbox::ToUpperCase(increment);
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66 if (increment != "3004,000C" ||
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67 offsetTag.empty())
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68 {
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69 return false;
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70 }
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71
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72 std::vector<std::string> offsets;
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73 Orthanc::Toolbox::TokenizeString(offsets, offsetTag, '\\');
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74
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75 if (frameCount_ == 0 ||
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76 offsets.size() != frameCount_ ||
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77 frame >= frameCount_)
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78 {
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79 LOG(ERROR) << "No information about the 3D location of some slice(s) in a RT DOSE";
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80 return false;
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81 }
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82
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83 double offset0, z;
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84
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85 if (!ParseDouble(offset0, offsets[0]) ||
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86 !ParseDouble(z, offsets[frame]))
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87 {
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88 LOG(ERROR) << "Invalid syntax";
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89 return false;
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90 }
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91
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92 if (!GeometryToolbox::IsCloseToZero(offset0))
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93 {
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94 LOG(ERROR) << "Invalid syntax";
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95 return false;
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96 }
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97
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98 geometry_ = CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(),
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99 geometry_.GetAxisX(),
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100 geometry_.GetAxisY());
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101
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102 return true;
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103 }
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104
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105
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106 bool Slice::ParseOrthancFrame(const OrthancPlugins::IDicomDataset& dataset,
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107 const std::string& instanceId,
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108 unsigned int frame)
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109 {
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110 orthancInstanceId_ = instanceId;
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111 frame_ = frame;
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112 type_ = Type_OrthancDecodableFrame;
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113
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114 OrthancPlugins::DicomDatasetReader reader(dataset);
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115
117
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116 sopClassUid_ = reader.GetStringValue(OrthancPlugins::DICOM_TAG_SOP_CLASS_UID, "");
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117 if (sopClassUid_.empty())
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118 {
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119 LOG(ERROR) << "Instance without a SOP class UID";
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120 return false;
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121 }
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122
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123 if (!reader.GetUnsignedIntegerValue(frameCount_, OrthancPlugins::DICOM_TAG_NUMBER_OF_FRAMES))
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124 {
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125 frameCount_ = 1; // Assume instance with one frame
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126 }
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127
117
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128 if (frame >= frameCount_)
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129 {
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130 return false;
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131 }
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132
117
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133 if (!reader.GetUnsignedIntegerValue(width_, OrthancPlugins::DICOM_TAG_COLUMNS) ||
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134 !reader.GetUnsignedIntegerValue(height_, OrthancPlugins::DICOM_TAG_ROWS))
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135 {
117
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136 return false;
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137 }
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138
117
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139 thickness_ = 100.0 * std::numeric_limits<double>::epsilon();
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140
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141 std::string tmp;
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142 if (dataset.GetStringValue(tmp, OrthancPlugins::DICOM_TAG_SLICE_THICKNESS))
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143 {
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144 if (!tmp.empty() &&
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145 !ParseDouble(thickness_, tmp))
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146 {
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147 return false; // Syntax error
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148 }
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149 }
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150
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151 converter_.ReadParameters(dataset);
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152
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153 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset);
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154
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155 std::string position, orientation;
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156 if (dataset.GetStringValue(position, OrthancPlugins::DICOM_TAG_IMAGE_POSITION_PATIENT) &&
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157 dataset.GetStringValue(orientation, OrthancPlugins::DICOM_TAG_IMAGE_ORIENTATION_PATIENT))
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158 {
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159 geometry_ = CoordinateSystem3D(position, orientation);
117
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160
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161 bool ok = true;
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162 SopClassUid tmp;
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163
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164 if (StringToSopClassUid(tmp, sopClassUid_))
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165 {
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166 switch (tmp)
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167 {
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168 case SopClassUid_RTDose:
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169 type_ = Type_OrthancRawFrame;
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170 ok = ComputeRTDoseGeometry(reader, frame);
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171 break;
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172
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173 default:
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174 break;
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175 }
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176 }
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177
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178 if (!ok)
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179 {
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180 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame
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181 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_;
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182 return false;
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183 }
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184 }
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185
117
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186 return true;
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187 }
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188
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189
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190 const std::string Slice::GetOrthancInstanceId() const
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191 {
117
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192 if (type_ == Type_OrthancDecodableFrame ||
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193 type_ == Type_OrthancRawFrame)
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194 {
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195 return orthancInstanceId_;
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196 }
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197 else
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198 {
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199 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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200 }
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201 }
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202
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203
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204 unsigned int Slice::GetFrame() const
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205 {
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206 if (type_ == Type_Invalid)
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207 {
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208 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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209 }
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210
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211 return frame_;
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212 }
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213
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214
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215 const CoordinateSystem3D& Slice::GetGeometry() const
73
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216 {
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217 if (type_ == Type_Invalid)
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218 {
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219 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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220 }
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221
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222 return geometry_;
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223 }
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224
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225
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226 double Slice::GetThickness() const
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227 {
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228 if (type_ == Type_Invalid)
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229 {
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230 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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231 }
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232
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233 return thickness_;
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234 }
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235
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236
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237 double Slice::GetPixelSpacingX() const
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238 {
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239 if (type_ == Type_Invalid)
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240 {
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241 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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242 }
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243
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244 return pixelSpacingX_;
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245 }
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246
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247
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248 double Slice::GetPixelSpacingY() const
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249 {
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250 if (type_ == Type_Invalid)
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251 {
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252 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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253 }
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254
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255 return pixelSpacingY_;
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256 }
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257
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258
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259 unsigned int Slice::GetWidth() const
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260 {
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261 if (type_ == Type_Invalid)
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262 {
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263 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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264 }
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265
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266 return width_;
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267 }
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268
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269
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270 unsigned int Slice::GetHeight() const
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271 {
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272 if (type_ == Type_Invalid)
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273 {
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274 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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275 }
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276
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277 return height_;
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278 }
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279
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280
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281 const DicomFrameConverter& Slice::GetConverter() const
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282 {
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283 if (type_ == Type_Invalid)
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284 {
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285 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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286 }
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287
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288 return converter_;
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289 }
89
f244018a4e4b BUGGY- trying to remove IVolumeSlicesObserver
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290
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291
110
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292 bool Slice::ContainsPlane(const CoordinateSystem3D& plane) const
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293 {
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294 if (type_ == Type_Invalid)
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295 {
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296 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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297 }
101
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298
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299 bool opposite;
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300 return (GeometryToolbox::IsParallelOrOpposite(opposite,
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301 GetGeometry().GetNormal(),
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302 plane.GetNormal()) &&
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303 GeometryToolbox::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()),
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304 GetGeometry().ProjectAlongNormal(plane.GetOrigin()),
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305 thickness_ / 2.0));
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306 }
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307
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308
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309 void Slice::GetExtent(std::vector<Vector>& points) const
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310 {
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311 double sx = GetPixelSpacingX();
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312 double sy = GetPixelSpacingY();
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313 double w = static_cast<double>(GetWidth());
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314 double h = static_cast<double>(GetHeight());
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315
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316 points.clear();
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317 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy));
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318 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy));
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319 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy));
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320 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy));
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321 }
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322 }