Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Loaders/SeriesOrderedFrames.cpp @ 1598:8563ea5d8ae4

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 26 Oct 2020 20:49:28 +0100
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children 59f95b9ea858
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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
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26 #include <OrthancException.h>
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27
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28 namespace OrthancStone
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29 {
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30 class SeriesOrderedFrames::Instance : public boost::noncopyable
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31 {
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32 private:
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33 std::unique_ptr<Orthanc::DicomMap> dicom_;
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34 DicomInstanceParameters parameters_;
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35
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36 public:
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37 explicit Instance(const Orthanc::DicomMap& dicom) :
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38 dicom_(dicom.Clone()),
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39 parameters_(dicom)
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40 {
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41 }
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42
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43 const Orthanc::DicomMap& GetInstance() const
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44 {
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45 return *dicom_;
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46 }
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47
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48 const DicomInstanceParameters& GetInstanceParameters() const
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49 {
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50 return parameters_;
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51 }
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52
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53 bool Lookup3DGeometry(CoordinateSystem3D& target) const
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54 {
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55 try
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56 {
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57 std::string imagePositionPatient, imageOrientationPatient;
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58 if (dicom_->LookupStringValue(imagePositionPatient, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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59 dicom_->LookupStringValue(imageOrientationPatient, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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60 {
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61 target = CoordinateSystem3D(imagePositionPatient, imageOrientationPatient);
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62 return true;
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63 }
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64 }
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65 catch (Orthanc::OrthancException&)
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66 {
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67 }
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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 bool LookupIndexInSeries(int& target) const
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73 {
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74 std::string value;
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75
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76 if (dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_INSTANCE_NUMBER, false) ||
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77 dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_IMAGE_INDEX, false))
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78 {
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79 try
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80 {
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81 target = boost::lexical_cast<int>(value);
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82 return true;
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83 }
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84 catch (boost::bad_lexical_cast&)
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85 {
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86 }
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87 }
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88
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89 return false;
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90 }
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91 };
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92
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93
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94 class SeriesOrderedFrames::Frame : public boost::noncopyable
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95 {
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96 private:
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97 const Instance* instance_;
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98 unsigned int frameIndex_;
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99
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100 public:
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101 Frame(const Instance& instance,
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102 unsigned int frameIndex) :
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103 instance_(&instance),
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104 frameIndex_(frameIndex)
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105 {
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106 if (frameIndex_ >= instance.GetInstanceParameters().GetImageInformation().GetNumberOfFrames())
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107 {
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108 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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109 }
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110 }
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111
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112 const Orthanc::DicomMap& GetInstance() const
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113 {
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114 assert(instance_ != NULL);
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115 return instance_->GetInstance();
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116 }
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117
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118 const DicomInstanceParameters& GetInstanceParameters() const
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119 {
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120 assert(instance_ != NULL);
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121 return instance_->GetInstanceParameters();
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122 }
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123
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124 unsigned int GetFrameIndex() const
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125 {
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126 return frameIndex_;
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127 }
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128 };
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129
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130
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131 class SeriesOrderedFrames::InstanceWithIndexInSeries
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132 {
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133 private:
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134 const Instance* instance_; // Don't use a reference to make "std::sort()" happy
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135 int index_;
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136
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137 public:
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138 explicit InstanceWithIndexInSeries(const Instance& instance) :
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139 instance_(&instance)
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140 {
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parents:
diff changeset
141 if (!instance_->LookupIndexInSeries(index_))
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parents:
diff changeset
142 {
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parents:
diff changeset
143 index_ = std::numeric_limits<int>::max();
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diff changeset
144 }
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parents:
diff changeset
145 }
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parents:
diff changeset
146
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diff changeset
147 const Instance& GetInstance() const
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148 {
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diff changeset
149 return *instance_;
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diff changeset
150 }
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parents:
diff changeset
151
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diff changeset
152 int GetIndexInSeries() const
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153 {
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parents:
diff changeset
154 return index_;
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parents:
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155 }
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diff changeset
156
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parents:
diff changeset
157 bool operator< (const InstanceWithIndexInSeries& other) const
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158 {
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parents:
diff changeset
159 return (index_ < other.index_);
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160 }
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parents:
diff changeset
161 };
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diff changeset
162
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diff changeset
163
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diff changeset
164 void SeriesOrderedFrames::Clear()
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165 {
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166 for (size_t i = 0; i < instances_.size(); i++)
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167 {
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diff changeset
168 assert(instances_[i] != NULL);
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169 delete instances_[i];
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170 }
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diff changeset
171
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172 for (size_t i = 0; i < orderedFrames_.size(); i++)
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173 {
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174 assert(orderedFrames_[i] != NULL);
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175 delete orderedFrames_[i];
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176 }
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177
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178 instances_.clear();
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179 orderedFrames_.clear();
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180 }
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181
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182
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183 bool SeriesOrderedFrames::Sort3DVolume()
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184 {
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185 SlicesSorter sorter;
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186 sorter.Reserve(instances_.size());
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187
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188 for (size_t i = 0; i < instances_.size(); i++)
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189 {
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parents:
diff changeset
190 CoordinateSystem3D geometry;
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parents:
diff changeset
191 if (instances_[i]->Lookup3DGeometry(geometry))
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diff changeset
192 {
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diff changeset
193 sorter.AddSlice(geometry, new Orthanc::SingleValueObject<Instance*>(instances_[i]));
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194 }
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parents:
diff changeset
195 else
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parents:
diff changeset
196 {
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diff changeset
197 return false; // Not a 3D volume
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198 }
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199 }
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parents:
diff changeset
200
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
201 if (!sorter.Sort() ||
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parents:
diff changeset
202 sorter.GetSlicesCount() != instances_.size() ||
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parents:
diff changeset
203 !sorter.AreAllSlicesDistinct())
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parents:
diff changeset
204 {
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parents:
diff changeset
205 return false;
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parents:
diff changeset
206 }
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parents:
diff changeset
207 else
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parents:
diff changeset
208 {
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parents:
diff changeset
209 for (size_t i = 0; i < sorter.GetSlicesCount(); i++)
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parents:
diff changeset
210 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 assert(sorter.HasSlicePayload(i));
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212
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parents:
diff changeset
213 const Orthanc::SingleValueObject<Instance*>& payload =
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parents:
diff changeset
214 dynamic_cast<const Orthanc::SingleValueObject<Instance*>&>(sorter.GetSlicePayload(i));
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parents:
diff changeset
215
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parents:
diff changeset
216 assert(payload.GetValue() != NULL);
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
217
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parents:
diff changeset
218 for (size_t j = 0; j < payload.GetValue()->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
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parents:
diff changeset
219 {
1323
c0af7657d398 Fixed warnings
Benjamin Golinvaux <bgo@osimis.io>
parents: 1299
diff changeset
220 orderedFrames_.push_back(new Frame(*payload.GetValue(),
c0af7657d398 Fixed warnings
Benjamin Golinvaux <bgo@osimis.io>
parents: 1299
diff changeset
221 static_cast<unsigned int>(j)));
1228
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parents:
diff changeset
222 }
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parents:
diff changeset
223 }
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parents:
diff changeset
224
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parents:
diff changeset
225 isRegular_ = sorter.ComputeSpacingBetweenSlices(spacingBetweenSlices_);
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parents:
diff changeset
226 return true;
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parents:
diff changeset
227 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
228 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
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
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231 void SeriesOrderedFrames::SortIndexInSeries()
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
232 {
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parents:
diff changeset
233 std::vector<InstanceWithIndexInSeries> tmp;
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parents:
diff changeset
234 tmp.reserve(instances_.size());
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
235
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
236 for (size_t i = 0; i < instances_.size(); i++)
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parents:
diff changeset
237 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
238 assert(instances_[i] != NULL);
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239 tmp.push_back(InstanceWithIndexInSeries(*instances_[i]));
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
240 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
242 std::sort(tmp.begin(), tmp.end());
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parents:
diff changeset
243
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parents:
diff changeset
244 for (size_t i = 0; i < tmp.size(); i++)
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parents:
diff changeset
245 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
246 for (size_t j = 0; j < tmp[i].GetInstance().GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
247 {
1323
c0af7657d398 Fixed warnings
Benjamin Golinvaux <bgo@osimis.io>
parents: 1299
diff changeset
248 orderedFrames_.push_back(new Frame(tmp[i].GetInstance(),
c0af7657d398 Fixed warnings
Benjamin Golinvaux <bgo@osimis.io>
parents: 1299
diff changeset
249 static_cast<unsigned int>(j)));
1228
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
250 }
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
Sebastien Jodogne <s.jodogne@gmail.com>
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 const SeriesOrderedFrames::Frame& SeriesOrderedFrames::GetFrame(size_t seriesIndex) const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
256 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
257 if (seriesIndex >= orderedFrames_.size())
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parents:
diff changeset
258 {
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parents:
diff changeset
259 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents:
diff changeset
260 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
261 else
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
262 {
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
263 assert(orderedFrames_[seriesIndex] != NULL);
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
264 return *(orderedFrames_[seriesIndex]);
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
265 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
266 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
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 SeriesOrderedFrames::SeriesOrderedFrames(LoadedDicomResources& instances) :
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parents:
diff changeset
270 isVolume_(false),
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parents:
diff changeset
271 isRegular_(false),
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
272 spacingBetweenSlices_(0)
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parents:
diff changeset
273 {
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parents:
diff changeset
274 instances_.reserve(instances.GetSize());
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parents:
diff changeset
275
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parents:
diff changeset
276 size_t numberOfFrames = 0;
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
277
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
278 for (size_t i = 0; i < instances.GetSize(); i++)
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parents:
diff changeset
279 {
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
280 try
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
281 {
1299
c38c89684d83 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1271
diff changeset
282 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
283 numberOfFrames += instance->GetInstanceParameters().GetImageInformation().GetNumberOfFrames();
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parents:
diff changeset
284 instances_.push_back(instance.release());
c471a0aa137b adding the next generation of loaders
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parents:
diff changeset
285 }
c471a0aa137b adding the next generation of loaders
Sebastien Jodogne <s.jodogne@gmail.com>
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286 catch (Orthanc::OrthancException&)
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287 {
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288 // The instance has not all the required DICOM tags, skip it
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289 }
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290 }
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291
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292 orderedFrames_.reserve(numberOfFrames);
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293
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294 if (Sort3DVolume())
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295 {
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296 isVolume_ = true;
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297
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298 if (isRegular_)
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299 {
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300 LOG(INFO) << "Regular 3D volume detected";
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301 }
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302 else
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303 {
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304 LOG(INFO) << "Non-regular 3D volume detected";
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305 }
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306 }
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307 else
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308 {
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309 LOG(INFO) << "Series is not a 3D volume, sorting by index";
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310 SortIndexInSeries();
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311 }
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312
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313 LOG(INFO) << "Number of frames: " << orderedFrames_.size();
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314 }
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315
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316
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317 unsigned int SeriesOrderedFrames::GetFrameIndex(size_t seriesIndex) const
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318 {
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319 return GetFrame(seriesIndex).GetFrameIndex();
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320 }
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321
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322
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323 const Orthanc::DicomMap& SeriesOrderedFrames::GetInstance(size_t seriesIndex) const
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324 {
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325 return GetFrame(seriesIndex).GetInstance();
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326 }
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327
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328
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329 const DicomInstanceParameters& SeriesOrderedFrames::GetInstanceParameters(size_t seriesIndex) const
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330 {
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331 return GetFrame(seriesIndex).GetInstanceParameters();
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332 }
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333
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334
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335 double SeriesOrderedFrames::GetSpacingBetweenSlices() const
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336 {
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337 if (IsRegular3DVolume())
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338 {
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339 return spacingBetweenSlices_;
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340 }
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341 else
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342 {
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343 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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344 }
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345 }
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346 }