Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Loaders/SeriesOrderedFrames.cpp @ 1871:7053b8a0aaec

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 11 Jan 2022 11:18:48 +0100
parents 3889ae96d2e9
children 07964689cb0b
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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
1871
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5 * Copyright (C) 2017-2022 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Lesser General Public License
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Lesser General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Lesser General Public
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19 * License along with this program. If not, see
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20 * <http://www.gnu.org/licenses/>.
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21 **/
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22
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23
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24 #include "../Toolbox/SlicesSorter.h"
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25 #include "SeriesOrderedFrames.h"
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27 #include <Logging.h>
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28 #include <OrthancException.h>
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29
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30 namespace OrthancStone
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31 {
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32 class SeriesOrderedFrames::Instance : public boost::noncopyable
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33 {
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34 private:
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35 std::unique_ptr<Orthanc::DicomMap> dicom_;
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36 DicomInstanceParameters parameters_;
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37
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38 public:
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39 explicit Instance(const Orthanc::DicomMap& dicom) :
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40 dicom_(dicom.Clone()),
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41 parameters_(dicom)
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42 {
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43 }
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44
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45 const Orthanc::DicomMap& GetInstance() const
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46 {
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47 return *dicom_;
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48 }
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49
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50 const DicomInstanceParameters& GetInstanceParameters() const
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51 {
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52 return parameters_;
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53 }
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54
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55 bool Lookup3DGeometry(CoordinateSystem3D& target) const
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56 {
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57 try
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58 {
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59 std::string imagePositionPatient, imageOrientationPatient;
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60 if (dicom_->LookupStringValue(imagePositionPatient, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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61 dicom_->LookupStringValue(imageOrientationPatient, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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62 {
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63 target = CoordinateSystem3D(imagePositionPatient, imageOrientationPatient);
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64 return true;
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65 }
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66 }
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67 catch (Orthanc::OrthancException&)
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68 {
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69 }
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70
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71 return false;
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72 }
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73
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74 bool LookupIndexInSeries(int& target) const
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75 {
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76 std::string value;
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77
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78 if (dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_INSTANCE_NUMBER, false) ||
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79 dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_IMAGE_INDEX, false))
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80 {
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81 try
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82 {
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83 target = boost::lexical_cast<int>(value);
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84 return true;
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85 }
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86 catch (boost::bad_lexical_cast&)
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87 {
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88 }
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89 }
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90
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91 return false;
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92 }
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93 };
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94
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95
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96 class SeriesOrderedFrames::Frame : public boost::noncopyable
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97 {
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98 private:
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99 const Instance* instance_;
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100 unsigned int frameIndex_;
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101
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102 public:
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103 Frame(const Instance& instance,
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104 unsigned int frameIndex) :
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105 instance_(&instance),
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106 frameIndex_(frameIndex)
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107 {
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108 if (frameIndex_ >= instance.GetInstanceParameters().GetImageInformation().GetNumberOfFrames())
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109 {
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110 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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111 }
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112 }
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113
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114 const Orthanc::DicomMap& GetInstance() const
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115 {
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116 assert(instance_ != NULL);
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117 return instance_->GetInstance();
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118 }
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119
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120 const DicomInstanceParameters& GetInstanceParameters() const
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121 {
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122 assert(instance_ != NULL);
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123 return instance_->GetInstanceParameters();
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124 }
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125
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126 unsigned int GetFrameIndex() const
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127 {
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128 return frameIndex_;
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129 }
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130 };
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131
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132
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133 class SeriesOrderedFrames::InstanceWithIndexInSeries
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134 {
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135 private:
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136 const Instance* instance_; // Don't use a reference to make "std::sort()" happy
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137 int index_;
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138
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139 public:
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140 explicit InstanceWithIndexInSeries(const Instance& instance) :
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141 instance_(&instance)
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142 {
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143 if (!instance_->LookupIndexInSeries(index_))
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144 {
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145 index_ = std::numeric_limits<int>::max();
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146 }
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147 }
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148
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149 const Instance& GetInstance() const
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150 {
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151 return *instance_;
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152 }
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153
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154 int GetIndexInSeries() const
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155 {
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156 return index_;
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157 }
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158
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159 bool operator< (const InstanceWithIndexInSeries& other) const
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160 {
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161 return (index_ < other.index_);
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162 }
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163 };
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164
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165
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166 void SeriesOrderedFrames::Clear()
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167 {
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168 for (size_t i = 0; i < instances_.size(); i++)
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169 {
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170 assert(instances_[i] != NULL);
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171 delete instances_[i];
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172 }
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173
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174 for (size_t i = 0; i < orderedFrames_.size(); i++)
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175 {
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176 assert(orderedFrames_[i] != NULL);
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177 delete orderedFrames_[i];
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178 }
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179
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180 instances_.clear();
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181 orderedFrames_.clear();
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182 }
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183
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184
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185 bool SeriesOrderedFrames::Sort3DVolume()
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186 {
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187 SlicesSorter sorter;
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188 sorter.Reserve(instances_.size());
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189
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190 for (size_t i = 0; i < instances_.size(); i++)
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191 {
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192 CoordinateSystem3D geometry;
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193 if (instances_[i]->Lookup3DGeometry(geometry))
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194 {
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195 sorter.AddSlice(geometry, new Orthanc::SingleValueObject<Instance*>(instances_[i]));
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196 }
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197 else
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198 {
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199 return false; // Not a 3D volume
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200 }
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201 }
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202
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203 if (!sorter.Sort() ||
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204 sorter.GetSlicesCount() != instances_.size() ||
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205 !sorter.AreAllSlicesDistinct())
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206 {
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207 return false;
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208 }
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209 else
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210 {
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211 for (size_t i = 0; i < sorter.GetSlicesCount(); i++)
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212 {
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213 assert(sorter.HasSlicePayload(i));
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214
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215 const Orthanc::SingleValueObject<Instance*>& payload =
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216 dynamic_cast<const Orthanc::SingleValueObject<Instance*>&>(sorter.GetSlicePayload(i));
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217
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218 assert(payload.GetValue() != NULL);
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219
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220 for (size_t j = 0; j < payload.GetValue()->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
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221 {
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222 orderedFrames_.push_back(new Frame(*payload.GetValue(),
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223 static_cast<unsigned int>(j)));
1228
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224 }
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225 }
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226
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227 isRegular_ = sorter.ComputeSpacingBetweenSlices(spacingBetweenSlices_);
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228 return true;
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229 }
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230 }
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231
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232
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233 void SeriesOrderedFrames::SortIndexInSeries()
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234 {
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235 std::vector<InstanceWithIndexInSeries> tmp;
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236 tmp.reserve(instances_.size());
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237
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238 for (size_t i = 0; i < instances_.size(); i++)
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239 {
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240 assert(instances_[i] != NULL);
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diff changeset
241 tmp.push_back(InstanceWithIndexInSeries(*instances_[i]));
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242 }
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243
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244 std::sort(tmp.begin(), tmp.end());
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245
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246 for (size_t i = 0; i < tmp.size(); i++)
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247 {
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248 for (size_t j = 0; j < tmp[i].GetInstance().GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
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diff changeset
249 {
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250 orderedFrames_.push_back(new Frame(tmp[i].GetInstance(),
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diff changeset
251 static_cast<unsigned int>(j)));
1228
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252 }
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253 }
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254 }
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255
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diff changeset
256
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257 const SeriesOrderedFrames::Frame& SeriesOrderedFrames::GetFrame(size_t seriesIndex) const
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258 {
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diff changeset
259 if (seriesIndex >= orderedFrames_.size())
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260 {
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diff changeset
261 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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262 }
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263 else
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diff changeset
264 {
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265 assert(orderedFrames_[seriesIndex] != NULL);
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266 return *(orderedFrames_[seriesIndex]);
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267 }
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268 }
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269
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diff changeset
270
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271 SeriesOrderedFrames::SeriesOrderedFrames(LoadedDicomResources& instances) :
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272 isVolume_(false),
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273 isRegular_(false),
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274 spacingBetweenSlices_(0)
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275 {
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276 instances_.reserve(instances.GetSize());
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277
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278 size_t numberOfFrames = 0;
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279
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280 for (size_t i = 0; i < instances.GetSize(); i++)
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281 {
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282 try
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diff changeset
283 {
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c38c89684d83 replacing std::auto_ptr by std::unique_ptr
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diff changeset
284 std::unique_ptr<Instance> instance(new Instance(instances.GetResource(i)));
1228
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diff changeset
285 numberOfFrames += instance->GetInstanceParameters().GetImageInformation().GetNumberOfFrames();
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286 instances_.push_back(instance.release());
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287 }
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288 catch (Orthanc::OrthancException&)
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289 {
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290 // The instance has not all the required DICOM tags, skip it
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291 }
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292 }
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293
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294 orderedFrames_.reserve(numberOfFrames);
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295
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296 if (Sort3DVolume())
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297 {
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298 isVolume_ = true;
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299
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300 if (isRegular_)
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301 {
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302 LOG(INFO) << "Regular 3D volume detected";
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303 }
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304 else
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305 {
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306 LOG(INFO) << "Non-regular 3D volume detected";
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307 }
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308 }
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309 else
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310 {
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311 LOG(INFO) << "Series is not a 3D volume, sorting by index";
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312 SortIndexInSeries();
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313 }
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314
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315 LOG(INFO) << "Number of frames: " << orderedFrames_.size();
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316 }
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317
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318
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319 unsigned int SeriesOrderedFrames::GetFrameIndex(size_t seriesIndex) const
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320 {
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321 return GetFrame(seriesIndex).GetFrameIndex();
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322 }
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323
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324
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325 const Orthanc::DicomMap& SeriesOrderedFrames::GetInstance(size_t seriesIndex) const
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326 {
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327 return GetFrame(seriesIndex).GetInstance();
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328 }
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329
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330
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331 const DicomInstanceParameters& SeriesOrderedFrames::GetInstanceParameters(size_t seriesIndex) const
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332 {
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333 return GetFrame(seriesIndex).GetInstanceParameters();
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334 }
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335
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336
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337 double SeriesOrderedFrames::GetSpacingBetweenSlices() const
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338 {
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339 if (IsRegular3DVolume())
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340 {
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341 return spacingBetweenSlices_;
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342 }
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343 else
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344 {
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345 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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346 }
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347 }
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348 }