Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Toolbox/SlicesSorter.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 "SlicesSorter.h"
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24
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25 #include "GeometryToolbox.h"
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26
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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 SlicesSorter::SliceWithDepth : public boost::noncopyable
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32 {
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33 private:
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34 CoordinateSystem3D geometry_;
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35 double depth_;
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36
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37 std::unique_ptr<Orthanc::IDynamicObject> payload_;
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38
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39 public:
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40 SliceWithDepth(const CoordinateSystem3D& geometry,
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41 Orthanc::IDynamicObject* payload) :
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42 geometry_(geometry),
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43 depth_(0),
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44 payload_(payload)
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45 {
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46 }
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47
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48 void SetNormal(const Vector& normal)
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49 {
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50 depth_ = boost::numeric::ublas::inner_prod(geometry_.GetOrigin(), normal);
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51 }
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52
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53 double GetDepth() const
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54 {
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55 return depth_;
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56 }
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57
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58 const CoordinateSystem3D& GetGeometry() const
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59 {
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60 return geometry_;
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61 }
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62
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63 bool HasPayload() const
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64 {
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65 return (payload_.get() != NULL);
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66 }
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67
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68 const Orthanc::IDynamicObject& GetPayload() const
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69 {
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70 if (HasPayload())
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71 {
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72 return *payload_;
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73 }
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74 else
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75 {
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76 LOG(ERROR) << "SlicesSorter::SliceWithDepth::GetPayload(): (!HasPayload())";
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77 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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78 }
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79 }
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80 };
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81
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82
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83 struct SlicesSorter::Comparator
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84 {
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85 bool operator() (const SliceWithDepth* const& a,
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86 const SliceWithDepth* const& b) const
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87 {
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88 return a->GetDepth() < b->GetDepth();
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89 }
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90 };
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91
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92
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93 SlicesSorter::~SlicesSorter()
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94 {
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95 for (size_t i = 0; i < slices_.size(); i++)
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96 {
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97 assert(slices_[i] != NULL);
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98 delete slices_[i];
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99 }
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100 }
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101
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102
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103 void SlicesSorter::AddSlice(const CoordinateSystem3D& slice,
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104 Orthanc::IDynamicObject* payload)
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105 {
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106 slices_.push_back(new SliceWithDepth(slice, payload));
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107 }
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108
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109
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110 const SlicesSorter::SliceWithDepth& SlicesSorter::GetSlice(size_t i) const
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111 {
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112 if (i >= slices_.size())
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113 {
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114 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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115 }
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116 else
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117 {
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118 assert(slices_[i] != NULL);
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119 return *slices_[i];
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120 }
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121 }
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123
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124 const CoordinateSystem3D& SlicesSorter::GetSliceGeometry(size_t i) const
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125 {
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126 return GetSlice(i).GetGeometry();
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127 }
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128
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129
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130 bool SlicesSorter::HasSlicePayload(size_t i) const
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131 {
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132 return GetSlice(i).HasPayload();
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133 }
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136 const Orthanc::IDynamicObject& SlicesSorter::GetSlicePayload(size_t i) const
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137 {
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138 return GetSlice(i).GetPayload();
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139 }
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140
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141
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142 void SlicesSorter::SetNormal(const Vector& normal)
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143 {
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144 for (size_t i = 0; i < slices_.size(); i++)
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145 {
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146 slices_[i]->SetNormal(normal);
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147 }
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148
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149 hasNormal_ = true;
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150 }
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151
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152
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153 void SlicesSorter::SortInternal()
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154 {
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155 if (!hasNormal_)
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156 {
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157 LOG(ERROR) << "SlicesSorter::SortInternal(): (!hasNormal_)";
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158 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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159 }
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160
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161 Comparator comparator;
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162 std::sort(slices_.begin(), slices_.end(), comparator);
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163 }
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164
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165
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166 void SlicesSorter::FilterNormal(const Vector& normal)
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167 {
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168 size_t pos = 0;
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169
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170 for (size_t i = 0; i < slices_.size(); i++)
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171 {
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172 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal()))
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173 {
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174 // This slice is compatible with the selected normal
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175 slices_[pos] = slices_[i];
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176 pos += 1;
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177 }
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178 else
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179 {
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180 delete slices_[i];
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181 slices_[i] = NULL;
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182 }
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183 }
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184
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185 slices_.resize(pos);
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186 }
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187
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188
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189 bool SlicesSorter::SelectNormal(Vector& normal) const
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190 {
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191 std::vector<Vector> normalCandidates;
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192 std::vector<unsigned int> normalCount;
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193
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194 bool found = false;
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195
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196 for (size_t i = 0; !found && i < GetSlicesCount(); i++)
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197 {
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198 const Vector& normal = GetSlice(i).GetGeometry().GetNormal();
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199
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200 bool add = true;
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201 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*)
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202 {
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203 if (GeometryToolbox::IsParallel(normal, normalCandidates[j]))
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204 {
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205 normalCount[j] += 1;
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206 add = false;
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207 }
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208 }
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209
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210 if (add)
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211 {
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212 if (normalCount.size() > 2)
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213 {
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214 // To get linear-time complexity in (*). This heuristics
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215 // allows the series to have one single frame that is
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216 // not parallel to the others (such a frame could be a
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217 // generated preview)
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218 found = false;
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219 }
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220 else
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221 {
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222 normalCandidates.push_back(normal);
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223 normalCount.push_back(1);
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224 }
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225 }
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226 }
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227
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228 for (size_t i = 0; !found && i < normalCandidates.size(); i++)
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229 {
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230 unsigned int count = normalCount[i];
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231 if (count == GetSlicesCount() ||
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diff changeset
232 count + 1 == GetSlicesCount())
73
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233 {
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234 normal = normalCandidates[i];
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235 found = true;
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236 }
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237 }
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238
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239 return found;
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240 }
77
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241
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242
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243 bool SlicesSorter::Sort()
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244 {
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245 if (GetSlicesCount() > 0)
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246 {
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247 Vector normal;
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248 if (SelectNormal(normal))
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249 {
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250 FilterNormal(normal);
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251 SetNormal(normal);
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252 SortInternal();
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253 return true;
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254 }
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255 }
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256
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257 return false;
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258 }
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259
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260
647
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diff changeset
261 bool SlicesSorter::LookupClosestSlice(size_t& index,
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diff changeset
262 double& distance,
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
263 const CoordinateSystem3D& slice) const
77
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264 {
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265 // TODO Turn this linear-time lookup into a log-time lookup,
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266 // keeping track of whether the slices are sorted along the normal
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267
647
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diff changeset
268 bool found = false;
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
269
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diff changeset
270 distance = std::numeric_limits<double>::infinity();
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diff changeset
271
77
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272 for (size_t i = 0; i < slices_.size(); i++)
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273 {
647
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
274 assert(slices_[i] != NULL);
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diff changeset
275
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diff changeset
276 double tmp;
757
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diff changeset
277 if (CoordinateSystem3D::ComputeDistance(tmp, slices_[i]->GetGeometry(), slice))
77
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diff changeset
278 {
647
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diff changeset
279 if (!found ||
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
280 tmp < distance)
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diff changeset
281 {
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diff changeset
282 index = i;
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diff changeset
283 distance = tmp;
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diff changeset
284 found = true;
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diff changeset
285 }
77
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286 }
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diff changeset
287 }
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288
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6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
289 return found;
77
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diff changeset
290 }
667
e9339f2b5de7 refactoring of VolumeImage
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291
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diff changeset
292
1156
34ee7204fde3 removing IGeometryProvider
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diff changeset
293 bool SlicesSorter::ComputeSpacingBetweenSlices(double& spacing /* out */) const
667
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294 {
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295 if (GetSlicesCount() <= 1)
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296 {
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297 // This is a volume that is empty or that contains one single
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298 // slice: Choose a dummy z-dimension for voxels
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299 spacing = 1.0;
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300 return true;
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301 }
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302
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303 const OrthancStone::CoordinateSystem3D& reference = GetSliceGeometry(0);
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304
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305 double referencePosition = reference.ProjectAlongNormal(reference.GetOrigin());
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306
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307 double p = reference.ProjectAlongNormal(GetSliceGeometry(1).GetOrigin());
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308 spacing = p - referencePosition;
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309
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310 if (spacing <= 0)
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311 {
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312 LOG(ERROR) << "SlicesSorter::ComputeSpacingBetweenSlices(): (spacing <= 0)";
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313 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls,
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314 "Please call the Sort() method before");
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315 }
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316
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317 for (size_t i = 1; i < GetSlicesCount(); i++)
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318 {
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319 OrthancStone::Vector q = reference.GetOrigin() + spacing * static_cast<double>(i) * reference.GetNormal();
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320 double d = boost::numeric::ublas::norm_2(q - GetSliceGeometry(i).GetOrigin());
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321
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322 if (!OrthancStone::LinearAlgebra::IsNear(d, 0, 0.001 /* tolerance expressed in mm */))
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323 {
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324 return false;
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325 }
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326 }
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327
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328 return true;
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329 }
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330
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331
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332 bool SlicesSorter::AreAllSlicesDistinct() const
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333 {
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334 if (GetSlicesCount() <= 1)
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335 {
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336 return true;
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337 }
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338 else
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339 {
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340 const OrthancStone::CoordinateSystem3D& reference = GetSliceGeometry(0);
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341 double previousPosition = reference.ProjectAlongNormal(GetSliceGeometry(0).GetOrigin());
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342
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343 for (size_t i = 1; i < GetSlicesCount(); i++)
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344 {
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345 double position = reference.ProjectAlongNormal(GetSliceGeometry(i).GetOrigin());
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346
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347 if (OrthancStone::LinearAlgebra::IsNear(position, previousPosition, 0.001 /* tolerance expressed in mm */))
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348 {
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349 return false;
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350 }
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351
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352 previousPosition = position;
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353 }
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354
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355 return true;
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356 }
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357 }
73
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358 }