Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Loaders/SeriesOrderedFrames.cpp @ 1777:d9c5474c5588

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 14 May 2021 07:35:13 +0200
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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) 2017-2021 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
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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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38 explicit Instance(const Orthanc::DicomMap& dicom) :
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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:
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139 explicit InstanceWithIndexInSeries(const Instance& instance) :
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140 instance_(&instance)
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parents:
diff changeset
141 {
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parents:
diff changeset
142 if (!instance_->LookupIndexInSeries(index_))
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parents:
diff changeset
143 {
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diff changeset
144 index_ = std::numeric_limits<int>::max();
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diff changeset
145 }
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parents:
diff changeset
146 }
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diff changeset
147
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diff changeset
148 const Instance& GetInstance() const
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149 {
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diff changeset
150 return *instance_;
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parents:
diff changeset
151 }
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152
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diff changeset
153 int GetIndexInSeries() const
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154 {
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diff changeset
155 return index_;
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156 }
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diff changeset
157
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parents:
diff changeset
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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diff changeset
162 };
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diff changeset
163
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diff changeset
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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diff changeset
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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diff changeset
191 CoordinateSystem3D geometry;
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diff changeset
192 if (instances_[i]->Lookup3DGeometry(geometry))
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diff changeset
193 {
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diff changeset
194 sorter.AddSlice(geometry, new Orthanc::SingleValueObject<Instance*>(instances_[i]));
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195 }
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diff changeset
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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parents:
diff changeset
201
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parents:
diff changeset
202 if (!sorter.Sort() ||
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parents:
diff changeset
203 sorter.GetSlicesCount() != instances_.size() ||
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diff changeset
204 !sorter.AreAllSlicesDistinct())
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parents:
diff changeset
205 {
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diff changeset
206 return false;
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parents:
diff changeset
207 }
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diff changeset
208 else
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parents:
diff changeset
209 {
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parents:
diff changeset
210 for (size_t i = 0; i < sorter.GetSlicesCount(); i++)
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parents:
diff changeset
211 {
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parents:
diff changeset
212 assert(sorter.HasSlicePayload(i));
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parents:
diff changeset
213
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parents:
diff changeset
214 const Orthanc::SingleValueObject<Instance*>& payload =
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parents:
diff changeset
215 dynamic_cast<const Orthanc::SingleValueObject<Instance*>&>(sorter.GetSlicePayload(i));
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parents:
diff changeset
216
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parents:
diff changeset
217 assert(payload.GetValue() != NULL);
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
218
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diff changeset
219 for (size_t j = 0; j < payload.GetValue()->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
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parents:
diff changeset
220 {
1323
c0af7657d398 Fixed warnings
Benjamin Golinvaux <bgo@osimis.io>
parents: 1299
diff changeset
221 orderedFrames_.push_back(new Frame(*payload.GetValue(),
c0af7657d398 Fixed warnings
Benjamin Golinvaux <bgo@osimis.io>
parents: 1299
diff changeset
222 static_cast<unsigned int>(j)));
1228
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parents:
diff changeset
223 }
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parents:
diff changeset
224 }
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parents:
diff changeset
225
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parents:
diff changeset
226 isRegular_ = sorter.ComputeSpacingBetweenSlices(spacingBetweenSlices_);
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parents:
diff changeset
227 return true;
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parents:
diff changeset
228 }
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parents:
diff changeset
229 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
231
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
232 void SeriesOrderedFrames::SortIndexInSeries()
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parents:
diff changeset
233 {
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parents:
diff changeset
234 std::vector<InstanceWithIndexInSeries> tmp;
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parents:
diff changeset
235 tmp.reserve(instances_.size());
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
236
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
237 for (size_t i = 0; i < instances_.size(); i++)
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parents:
diff changeset
238 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239 assert(instances_[i] != NULL);
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
240 tmp.push_back(InstanceWithIndexInSeries(*instances_[i]));
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
241 }
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
242
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
243 std::sort(tmp.begin(), tmp.end());
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parents:
diff changeset
244
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parents:
diff changeset
245 for (size_t i = 0; i < tmp.size(); i++)
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parents:
diff changeset
246 {
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parents:
diff changeset
247 for (size_t j = 0; j < tmp[i].GetInstance().GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
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parents:
diff changeset
248 {
1323
c0af7657d398 Fixed warnings
Benjamin Golinvaux <bgo@osimis.io>
parents: 1299
diff changeset
249 orderedFrames_.push_back(new Frame(tmp[i].GetInstance(),
c0af7657d398 Fixed warnings
Benjamin Golinvaux <bgo@osimis.io>
parents: 1299
diff changeset
250 static_cast<unsigned int>(j)));
1228
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
251 }
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
252 }
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
253 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
254
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
255
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
256 const SeriesOrderedFrames::Frame& SeriesOrderedFrames::GetFrame(size_t seriesIndex) const
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parents:
diff changeset
257 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
258 if (seriesIndex >= orderedFrames_.size())
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parents:
diff changeset
259 {
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parents:
diff changeset
260 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
261 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
262 else
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
263 {
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
264 assert(orderedFrames_[seriesIndex] != NULL);
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
265 return *(orderedFrames_[seriesIndex]);
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
266 }
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
267 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
268
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
269
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
270 SeriesOrderedFrames::SeriesOrderedFrames(LoadedDicomResources& instances) :
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parents:
diff changeset
271 isVolume_(false),
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parents:
diff changeset
272 isRegular_(false),
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
273 spacingBetweenSlices_(0)
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parents:
diff changeset
274 {
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parents:
diff changeset
275 instances_.reserve(instances.GetSize());
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parents:
diff changeset
276
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parents:
diff changeset
277 size_t numberOfFrames = 0;
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
278
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
279 for (size_t i = 0; i < instances.GetSize(); i++)
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parents:
diff changeset
280 {
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parents:
diff changeset
281 try
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
282 {
1299
c38c89684d83 replacing std::auto_ptr by std::unique_ptr
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parents: 1271
diff changeset
283 std::unique_ptr<Instance> instance(new Instance(instances.GetResource(i)));
1228
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
284 numberOfFrames += instance->GetInstanceParameters().GetImageInformation().GetNumberOfFrames();
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parents:
diff changeset
285 instances_.push_back(instance.release());
c471a0aa137b adding the next generation of loaders
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parents:
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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 }