Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Loaders/SeriesOrderedFrames.cpp @ 1689:fad38c4525f9
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 25 Nov 2020 17:07:32 +0100 |
parents | 59f95b9ea858 |
children | 9ac2a65d4172 |
rev | line source |
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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) 2017-2020 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 Lesser 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 * Lesser 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 Lesser General Public |
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18 * License along with this program. If not, see |
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19 * <http://www.gnu.org/licenses/>. |
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20 **/ |
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21 |
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22 |
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23 #include "../Toolbox/SlicesSorter.h" |
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24 #include "SeriesOrderedFrames.h" |
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25 |
1624 | 26 #include <Logging.h> |
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27 #include <OrthancException.h> |
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29 namespace OrthancStone |
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30 { |
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31 class SeriesOrderedFrames::Instance : public boost::noncopyable |
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32 { |
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33 private: |
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34 std::unique_ptr<Orthanc::DicomMap> dicom_; |
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35 DicomInstanceParameters parameters_; |
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36 |
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37 public: |
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39 dicom_(dicom.Clone()), |
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40 parameters_(dicom) |
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41 { |
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42 } |
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43 |
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44 const Orthanc::DicomMap& GetInstance() const |
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45 { |
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46 return *dicom_; |
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47 } |
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48 |
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49 const DicomInstanceParameters& GetInstanceParameters() const |
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50 { |
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51 return parameters_; |
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52 } |
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53 |
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54 bool Lookup3DGeometry(CoordinateSystem3D& target) const |
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55 { |
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56 try |
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57 { |
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58 std::string imagePositionPatient, imageOrientationPatient; |
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59 if (dicom_->LookupStringValue(imagePositionPatient, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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60 dicom_->LookupStringValue(imageOrientationPatient, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
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61 { |
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62 target = CoordinateSystem3D(imagePositionPatient, imageOrientationPatient); |
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63 return true; |
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64 } |
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65 } |
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66 catch (Orthanc::OrthancException&) |
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67 { |
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68 } |
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69 |
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70 return false; |
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71 } |
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72 |
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73 bool LookupIndexInSeries(int& target) const |
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74 { |
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75 std::string value; |
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76 |
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77 if (dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_INSTANCE_NUMBER, false) || |
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78 dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_IMAGE_INDEX, false)) |
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79 { |
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80 try |
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81 { |
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82 target = boost::lexical_cast<int>(value); |
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83 return true; |
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84 } |
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85 catch (boost::bad_lexical_cast&) |
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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 return false; |
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91 } |
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92 }; |
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93 |
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94 |
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95 class SeriesOrderedFrames::Frame : public boost::noncopyable |
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96 { |
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97 private: |
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98 const Instance* instance_; |
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99 unsigned int frameIndex_; |
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100 |
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101 public: |
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102 Frame(const Instance& instance, |
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103 unsigned int frameIndex) : |
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104 instance_(&instance), |
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105 frameIndex_(frameIndex) |
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106 { |
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107 if (frameIndex_ >= instance.GetInstanceParameters().GetImageInformation().GetNumberOfFrames()) |
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108 { |
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109 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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110 } |
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111 } |
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112 |
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113 const Orthanc::DicomMap& GetInstance() const |
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114 { |
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115 assert(instance_ != NULL); |
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116 return instance_->GetInstance(); |
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117 } |
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118 |
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119 const DicomInstanceParameters& GetInstanceParameters() const |
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120 { |
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121 assert(instance_ != NULL); |
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122 return instance_->GetInstanceParameters(); |
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123 } |
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124 |
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125 unsigned int GetFrameIndex() const |
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126 { |
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127 return frameIndex_; |
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128 } |
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129 }; |
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130 |
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131 |
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132 class SeriesOrderedFrames::InstanceWithIndexInSeries |
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133 { |
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134 private: |
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135 const Instance* instance_; // Don't use a reference to make "std::sort()" happy |
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136 int index_; |
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137 |
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138 public: |
1571 | 139 explicit InstanceWithIndexInSeries(const Instance& instance) : |
140 instance_(&instance) | |
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141 { |
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142 if (!instance_->LookupIndexInSeries(index_)) |
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143 { |
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144 index_ = std::numeric_limits<int>::max(); |
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145 } |
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146 } |
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147 |
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148 const Instance& GetInstance() const |
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149 { |
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150 return *instance_; |
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151 } |
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152 |
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153 int GetIndexInSeries() const |
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154 { |
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155 return index_; |
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156 } |
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157 |
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158 bool operator< (const InstanceWithIndexInSeries& other) const |
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159 { |
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160 return (index_ < other.index_); |
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161 } |
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162 }; |
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163 |
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164 |
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165 void SeriesOrderedFrames::Clear() |
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166 { |
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167 for (size_t i = 0; i < instances_.size(); i++) |
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168 { |
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169 assert(instances_[i] != NULL); |
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170 delete instances_[i]; |
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171 } |
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172 |
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173 for (size_t i = 0; i < orderedFrames_.size(); i++) |
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174 { |
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175 assert(orderedFrames_[i] != NULL); |
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176 delete orderedFrames_[i]; |
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177 } |
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178 |
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179 instances_.clear(); |
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180 orderedFrames_.clear(); |
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181 } |
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182 |
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183 |
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184 bool SeriesOrderedFrames::Sort3DVolume() |
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185 { |
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186 SlicesSorter sorter; |
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187 sorter.Reserve(instances_.size()); |
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188 |
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189 for (size_t i = 0; i < instances_.size(); i++) |
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190 { |
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191 CoordinateSystem3D geometry; |
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192 if (instances_[i]->Lookup3DGeometry(geometry)) |
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193 { |
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194 sorter.AddSlice(geometry, new Orthanc::SingleValueObject<Instance*>(instances_[i])); |
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195 } |
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196 else |
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197 { |
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198 return false; // Not a 3D volume |
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199 } |
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200 } |
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201 |
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202 if (!sorter.Sort() || |
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203 sorter.GetSlicesCount() != instances_.size() || |
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204 !sorter.AreAllSlicesDistinct()) |
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205 { |
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206 return false; |
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207 } |
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208 else |
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209 { |
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210 for (size_t i = 0; i < sorter.GetSlicesCount(); i++) |
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211 { |
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212 assert(sorter.HasSlicePayload(i)); |
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213 |
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214 const Orthanc::SingleValueObject<Instance*>& payload = |
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215 dynamic_cast<const Orthanc::SingleValueObject<Instance*>&>(sorter.GetSlicePayload(i)); |
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216 |
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217 assert(payload.GetValue() != NULL); |
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218 |
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219 for (size_t j = 0; j < payload.GetValue()->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++) |
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220 { |
1323 | 221 orderedFrames_.push_back(new Frame(*payload.GetValue(), |
222 static_cast<unsigned int>(j))); | |
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223 } |
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224 } |
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225 |
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226 isRegular_ = sorter.ComputeSpacingBetweenSlices(spacingBetweenSlices_); |
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227 return true; |
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228 } |
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229 } |
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230 |
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231 |
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232 void SeriesOrderedFrames::SortIndexInSeries() |
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233 { |
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234 std::vector<InstanceWithIndexInSeries> tmp; |
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235 tmp.reserve(instances_.size()); |
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236 |
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237 for (size_t i = 0; i < instances_.size(); i++) |
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238 { |
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239 assert(instances_[i] != NULL); |
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240 tmp.push_back(InstanceWithIndexInSeries(*instances_[i])); |
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241 } |
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242 |
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243 std::sort(tmp.begin(), tmp.end()); |
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244 |
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245 for (size_t i = 0; i < tmp.size(); i++) |
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246 { |
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247 for (size_t j = 0; j < tmp[i].GetInstance().GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++) |
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248 { |
1323 | 249 orderedFrames_.push_back(new Frame(tmp[i].GetInstance(), |
250 static_cast<unsigned int>(j))); | |
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251 } |
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252 } |
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253 } |
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254 |
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255 |
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256 const SeriesOrderedFrames::Frame& SeriesOrderedFrames::GetFrame(size_t seriesIndex) const |
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257 { |
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258 if (seriesIndex >= orderedFrames_.size()) |
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259 { |
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260 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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261 } |
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262 else |
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263 { |
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264 assert(orderedFrames_[seriesIndex] != NULL); |
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265 return *(orderedFrames_[seriesIndex]); |
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266 } |
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267 } |
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268 |
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269 |
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270 SeriesOrderedFrames::SeriesOrderedFrames(LoadedDicomResources& instances) : |
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271 isVolume_(false), |
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272 isRegular_(false), |
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273 spacingBetweenSlices_(0) |
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274 { |
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275 instances_.reserve(instances.GetSize()); |
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276 |
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277 size_t numberOfFrames = 0; |
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278 |
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279 for (size_t i = 0; i < instances.GetSize(); i++) |
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280 { |
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281 try |
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282 { |
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283 std::unique_ptr<Instance> instance(new Instance(instances.GetResource(i))); |
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284 numberOfFrames += instance->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); |
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285 instances_.push_back(instance.release()); |
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286 } |
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287 catch (Orthanc::OrthancException&) |
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288 { |
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289 // The instance has not all the required DICOM tags, skip it |
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290 } |
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291 } |
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292 |
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293 orderedFrames_.reserve(numberOfFrames); |
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294 |
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295 if (Sort3DVolume()) |
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296 { |
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297 isVolume_ = true; |
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298 |
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299 if (isRegular_) |
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300 { |
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301 LOG(INFO) << "Regular 3D volume detected"; |
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302 } |
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303 else |
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304 { |
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305 LOG(INFO) << "Non-regular 3D volume detected"; |
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306 } |
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307 } |
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308 else |
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309 { |
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310 LOG(INFO) << "Series is not a 3D volume, sorting by index"; |
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311 SortIndexInSeries(); |
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312 } |
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313 |
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314 LOG(INFO) << "Number of frames: " << orderedFrames_.size(); |
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315 } |
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316 |
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317 |
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318 unsigned int SeriesOrderedFrames::GetFrameIndex(size_t seriesIndex) const |
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319 { |
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320 return GetFrame(seriesIndex).GetFrameIndex(); |
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321 } |
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322 |
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323 |
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324 const Orthanc::DicomMap& SeriesOrderedFrames::GetInstance(size_t seriesIndex) const |
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325 { |
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326 return GetFrame(seriesIndex).GetInstance(); |
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327 } |
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328 |
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329 |
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330 const DicomInstanceParameters& SeriesOrderedFrames::GetInstanceParameters(size_t seriesIndex) const |
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331 { |
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332 return GetFrame(seriesIndex).GetInstanceParameters(); |
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333 } |
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334 |
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335 |
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336 double SeriesOrderedFrames::GetSpacingBetweenSlices() const |
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337 { |
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338 if (IsRegular3DVolume()) |
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339 { |
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340 return spacingBetweenSlices_; |
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341 } |
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342 else |
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343 { |
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344 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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345 } |
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346 } |
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347 } |