Mercurial > hg > orthanc-stone

annotate Framework/Toolbox/SlicesSorter.cpp @ 667:e9339f2b5de7

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refactoring of VolumeImage
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 15 May 2019 17:30:58 +0200
parents 1088d4c4d78c
children f7c236894c1a
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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) 2017-2019 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 Affero 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 * Affero 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 Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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20
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21
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22 #include "SlicesSorter.h"
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23
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24 #include "GeometryToolbox.h"
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25
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26 #include <Core/OrthancException.h>
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28 namespace OrthancStone
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29 {
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30 class SlicesSorter::SliceWithDepth : public boost::noncopyable
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31 {
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32 private:
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33 CoordinateSystem3D geometry_;
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34 double depth_;
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35
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36 std::auto_ptr<Orthanc::IDynamicObject> payload_;
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37
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38 public:
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39 SliceWithDepth(const CoordinateSystem3D& geometry,
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40 Orthanc::IDynamicObject* payload) :
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41 geometry_(geometry),
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42 depth_(0),
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43 payload_(payload)
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44 {
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45 }
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46
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47 void SetNormal(const Vector& normal)
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48 {
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49 depth_ = boost::numeric::ublas::inner_prod(geometry_.GetOrigin(), normal);
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50 }
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51
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52 double GetDepth() const
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53 {
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54 return depth_;
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55 }
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56
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57 const CoordinateSystem3D& GetGeometry() const
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58 {
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59 return geometry_;
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60 }
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61
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62 bool HasPayload() const
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63 {
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64 return (payload_.get() != NULL);
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65 }
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66
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67 const Orthanc::IDynamicObject& GetPayload() const
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68 {
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69 if (HasPayload())
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70 {
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71 return *payload_;
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72 }
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73 else
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74 {
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75 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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76 }
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77 }
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78 };
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79
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80
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81 struct SlicesSorter::Comparator
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82 {
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83 bool operator() (const SliceWithDepth* const& a,
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84 const SliceWithDepth* const& b) const
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85 {
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86 return a->GetDepth() < b->GetDepth();
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87 }
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88 };
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89
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90
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91 SlicesSorter::~SlicesSorter()
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92 {
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93 for (size_t i = 0; i < slices_.size(); i++)
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94 {
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95 assert(slices_[i] != NULL);
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96 delete slices_[i];
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97 }
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98 }
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99
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100
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101 void SlicesSorter::AddSlice(const CoordinateSystem3D& slice,
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102 Orthanc::IDynamicObject* payload)
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103 {
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104 slices_.push_back(new SliceWithDepth(slice, payload));
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105 }
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106
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107
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108 const SlicesSorter::SliceWithDepth& SlicesSorter::GetSlice(size_t i) const
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109 {
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110 if (i >= slices_.size())
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111 {
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112 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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113 }
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114 else
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115 {
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116 assert(slices_[i] != NULL);
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117 return *slices_[i];
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118 }
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119 }
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120
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121
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122 const CoordinateSystem3D& SlicesSorter::GetSliceGeometry(size_t i) const
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123 {
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124 return GetSlice(i).GetGeometry();
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125 }
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126
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127
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128 bool SlicesSorter::HasSlicePayload(size_t i) const
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129 {
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130 return GetSlice(i).HasPayload();
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131 }
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132
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133
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134 const Orthanc::IDynamicObject& SlicesSorter::GetSlicePayload(size_t i) const
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135 {
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136 return GetSlice(i).GetPayload();
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137 }
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138
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139
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140 void SlicesSorter::SetNormal(const Vector& normal)
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141 {
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142 for (size_t i = 0; i < slices_.size(); i++)
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143 {
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144 slices_[i]->SetNormal(normal);
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145 }
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146
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147 hasNormal_ = true;
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148 }
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149
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150
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151 void SlicesSorter::SortInternal()
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152 {
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153 if (!hasNormal_)
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154 {
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155 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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156 }
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157
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158 Comparator comparator;
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159 std::sort(slices_.begin(), slices_.end(), comparator);
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160 }
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161
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162
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163 void SlicesSorter::FilterNormal(const Vector& normal)
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164 {
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165 size_t pos = 0;
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166
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167 for (size_t i = 0; i < slices_.size(); i++)
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168 {
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169 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal()))
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170 {
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171 // This slice is compatible with the selected normal
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172 slices_[pos] = slices_[i];
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173 pos += 1;
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174 }
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175 else
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176 {
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177 delete slices_[i];
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178 slices_[i] = NULL;
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179 }
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180 }
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181
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182 slices_.resize(pos);
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183 }
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184
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185
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186 bool SlicesSorter::SelectNormal(Vector& normal) const
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187 {
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188 std::vector<Vector> normalCandidates;
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189 std::vector<unsigned int> normalCount;
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190
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191 bool found = false;
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192
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193 for (size_t i = 0; !found && i < GetSlicesCount(); i++)
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194 {
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195 const Vector& normal = GetSlice(i).GetGeometry().GetNormal();
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196
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197 bool add = true;
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198 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*)
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199 {
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200 if (GeometryToolbox::IsParallel(normal, normalCandidates[j]))
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201 {
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202 normalCount[j] += 1;
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203 add = false;
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204 }
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205 }
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206
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207 if (add)
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208 {
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209 if (normalCount.size() > 2)
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210 {
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211 // To get linear-time complexity in (*). This heuristics
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212 // allows the series to have one single frame that is
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213 // not parallel to the others (such a frame could be a
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214 // generated preview)
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215 found = false;
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216 }
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217 else
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218 {
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219 normalCandidates.push_back(normal);
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220 normalCount.push_back(1);
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221 }
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222 }
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223 }
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224
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225 for (size_t i = 0; !found && i < normalCandidates.size(); i++)
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226 {
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227 unsigned int count = normalCount[i];
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228 if (count == GetSlicesCount() ||
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229 count + 1 == GetSlicesCount())
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230 {
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231 normal = normalCandidates[i];
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232 found = true;
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233 }
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234 }
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235
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236 return found;
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237 }
77
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238
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239
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240 bool SlicesSorter::Sort()
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241 {
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242 if (GetSlicesCount() > 0)
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243 {
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244 Vector normal;
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245 if (SelectNormal(normal))
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246 {
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247 FilterNormal(normal);
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248 SetNormal(normal);
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249 SortInternal();
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250 return true;
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251 }
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252 }
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253
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254 return false;
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255 }
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256
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257
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258 bool SlicesSorter::LookupClosestSlice(size_t& index,
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259 double& distance,
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260 const CoordinateSystem3D& slice) const
77
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261 {
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262 // TODO Turn this linear-time lookup into a log-time lookup,
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263 // keeping track of whether the slices are sorted along the normal
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264
647
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diff changeset
265 bool found = false;
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266
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diff changeset
267 distance = std::numeric_limits<double>::infinity();
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diff changeset
268
77
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diff changeset
269 for (size_t i = 0; i < slices_.size(); i++)
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270 {
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diff changeset
271 assert(slices_[i] != NULL);
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272
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diff changeset
273 double tmp;
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
274 if (CoordinateSystem3D::GetDistance(tmp, slices_[i]->GetGeometry(), slice))
77
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275 {
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diff changeset
276 if (!found ||
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diff changeset
277 tmp < distance)
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diff changeset
278 {
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diff changeset
279 index = i;
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diff changeset
280 distance = tmp;
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diff changeset
281 found = true;
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diff changeset
282 }
77
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283 }
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284 }
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285
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6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
286 return found;
77
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diff changeset
287 }
667
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diff changeset
288
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diff changeset
289
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diff changeset
290 double SlicesSorter::ComputeSpacingBetweenSlices() const
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diff changeset
291 {
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diff changeset
292 if (GetSlicesCount() <= 1)
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diff changeset
293 {
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294 // This is a volume that is empty or that contains one single
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diff changeset
295 // slice: Choose a dummy z-dimension for voxels
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diff changeset
296 return 1.0;
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diff changeset
297 }
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298
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299 const OrthancStone::CoordinateSystem3D& reference = GetSliceGeometry(0);
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300
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301 double referencePosition = reference.ProjectAlongNormal(reference.GetOrigin());
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302
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303 double p = reference.ProjectAlongNormal(GetSliceGeometry(1).GetOrigin());
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304 double spacingZ = p - referencePosition;
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305
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306 if (spacingZ <= 0)
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307 {
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308 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls,
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309 "Please call the Sort() method before");
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310 }
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311
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312 for (size_t i = 1; i < GetSlicesCount(); i++)
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313 {
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314 OrthancStone::Vector p = reference.GetOrigin() + spacingZ * static_cast<double>(i) * reference.GetNormal();
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315 double d = boost::numeric::ublas::norm_2(p - GetSliceGeometry(i).GetOrigin());
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316
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317 if (!OrthancStone::LinearAlgebra::IsNear(d, 0, 0.001 /* tolerance expressed in mm */))
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318 {
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319 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadGeometry,
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320 "The origins of the slices of a volume image are not regularly spaced");
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321 }
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322 }
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323
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324 return spacingZ;
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325 }
73
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326 }