Mercurial > hg > orthanc-stone

annotate Framework/Toolbox/SlicesSorter.cpp @ 976:3abc47e051c8

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Added tag toa2019083101 for changeset e75fd08d6c75
author Benjamin Golinvaux <bgo@osimis.io>
date Sat, 31 Aug 2019 13:50:11 +0200
parents a7351ad54960
children 24fecc02bfb1
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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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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 LOG(ERROR) << "SlicesSorter::SliceWithDepth::GetPayload(): (!HasPayload())";
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76 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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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
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82 struct SlicesSorter::Comparator
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83 {
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84 bool operator() (const SliceWithDepth* const& a,
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85 const SliceWithDepth* const& b) const
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86 {
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87 return a->GetDepth() < b->GetDepth();
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88 }
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89 };
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90
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91
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92 SlicesSorter::~SlicesSorter()
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93 {
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94 for (size_t i = 0; i < slices_.size(); i++)
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95 {
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96 assert(slices_[i] != NULL);
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97 delete slices_[i];
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98 }
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99 }
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100
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101
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102 void SlicesSorter::AddSlice(const CoordinateSystem3D& slice,
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103 Orthanc::IDynamicObject* payload)
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104 {
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105 slices_.push_back(new SliceWithDepth(slice, payload));
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106 }
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107
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108
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109 const SlicesSorter::SliceWithDepth& SlicesSorter::GetSlice(size_t i) const
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110 {
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111 if (i >= slices_.size())
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112 {
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113 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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114 }
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115 else
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116 {
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117 assert(slices_[i] != NULL);
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118 return *slices_[i];
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119 }
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120 }
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121
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122
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123 const CoordinateSystem3D& SlicesSorter::GetSliceGeometry(size_t i) const
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124 {
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125 return GetSlice(i).GetGeometry();
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126 }
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127
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128
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129 bool SlicesSorter::HasSlicePayload(size_t i) const
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130 {
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131 return GetSlice(i).HasPayload();
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132 }
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133
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134
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135 const Orthanc::IDynamicObject& SlicesSorter::GetSlicePayload(size_t i) const
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136 {
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137 return GetSlice(i).GetPayload();
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138 }
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139
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140
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141 void SlicesSorter::SetNormal(const Vector& normal)
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142 {
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143 for (size_t i = 0; i < slices_.size(); i++)
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144 {
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145 slices_[i]->SetNormal(normal);
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146 }
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147
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148 hasNormal_ = true;
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149 }
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150
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151
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152 void SlicesSorter::SortInternal()
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153 {
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154 if (!hasNormal_)
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155 {
956
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156 LOG(ERROR) << "SlicesSorter::SortInternal(): (!hasNormal_)";
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157 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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158 }
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159
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160 Comparator comparator;
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161 std::sort(slices_.begin(), slices_.end(), comparator);
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162 }
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163
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164
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165 void SlicesSorter::FilterNormal(const Vector& normal)
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166 {
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167 size_t pos = 0;
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168
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169 for (size_t i = 0; i < slices_.size(); i++)
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170 {
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171 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal()))
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172 {
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173 // This slice is compatible with the selected normal
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174 slices_[pos] = slices_[i];
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175 pos += 1;
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176 }
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177 else
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178 {
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179 delete slices_[i];
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180 slices_[i] = NULL;
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181 }
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182 }
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183
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184 slices_.resize(pos);
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185 }
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186
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187
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188 bool SlicesSorter::SelectNormal(Vector& normal) const
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189 {
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190 std::vector<Vector> normalCandidates;
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191 std::vector<unsigned int> normalCount;
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192
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193 bool found = false;
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194
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195 for (size_t i = 0; !found && i < GetSlicesCount(); i++)
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196 {
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197 const Vector& normal = GetSlice(i).GetGeometry().GetNormal();
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198
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199 bool add = true;
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200 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*)
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201 {
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202 if (GeometryToolbox::IsParallel(normal, normalCandidates[j]))
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203 {
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204 normalCount[j] += 1;
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205 add = false;
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206 }
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207 }
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208
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209 if (add)
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210 {
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211 if (normalCount.size() > 2)
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212 {
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213 // To get linear-time complexity in (*). This heuristics
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214 // allows the series to have one single frame that is
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215 // not parallel to the others (such a frame could be a
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216 // generated preview)
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217 found = false;
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218 }
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219 else
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220 {
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221 normalCandidates.push_back(normal);
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222 normalCount.push_back(1);
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223 }
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224 }
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225 }
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226
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227 for (size_t i = 0; !found && i < normalCandidates.size(); i++)
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228 {
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229 unsigned int count = normalCount[i];
647
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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230 if (count == GetSlicesCount() ||
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diff changeset
231 count + 1 == GetSlicesCount())
73
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232 {
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233 normal = normalCandidates[i];
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234 found = true;
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235 }
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236 }
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237
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238 return found;
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239 }
77
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240
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241
648
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242 bool SlicesSorter::Sort()
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243 {
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244 if (GetSlicesCount() > 0)
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245 {
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246 Vector normal;
Sebastien Jodogne <s.jodogne@gmail.com>
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247 if (SelectNormal(normal))
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248 {
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249 FilterNormal(normal);
Sebastien Jodogne <s.jodogne@gmail.com>
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250 SetNormal(normal);
Sebastien Jodogne <s.jodogne@gmail.com>
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251 SortInternal();
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252 return true;
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parents: 647
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253 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 647
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254 }
Sebastien Jodogne <s.jodogne@gmail.com>
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255
Sebastien Jodogne <s.jodogne@gmail.com>
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256 return false;
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
257 }
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diff changeset
258
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
259
647
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parents: 439
diff changeset
260 bool SlicesSorter::LookupClosestSlice(size_t& index,
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diff changeset
261 double& distance,
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
262 const CoordinateSystem3D& slice) const
77
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diff changeset
263 {
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diff changeset
264 // TODO Turn this linear-time lookup into a log-time lookup,
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parents: 73
diff changeset
265 // keeping track of whether the slices are sorted along the normal
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diff changeset
266
647
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
267 bool found = false;
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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parents: 439
diff changeset
268
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
269 distance = std::numeric_limits<double>::infinity();
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
270
77
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diff changeset
271 for (size_t i = 0; i < slices_.size(); i++)
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272 {
647
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
273 assert(slices_[i] != NULL);
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parents: 439
diff changeset
274
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diff changeset
275 double tmp;
757
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diff changeset
276 if (CoordinateSystem3D::ComputeDistance(tmp, slices_[i]->GetGeometry(), slice))
77
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277 {
647
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
278 if (!found ||
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
279 tmp < distance)
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diff changeset
280 {
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diff changeset
281 index = i;
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
282 distance = tmp;
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
283 found = true;
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
284 }
77
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diff changeset
285 }
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diff changeset
286 }
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diff changeset
287
647
6af3099ed8da uncoupling OrthancStone::SlicesSorter from OrthancStone::Slice
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diff changeset
288 return found;
77
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diff changeset
289 }
667
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290
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diff changeset
291
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diff changeset
292 double SlicesSorter::ComputeSpacingBetweenSlices() const
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parents: 648
diff changeset
293 {
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diff changeset
294 if (GetSlicesCount() <= 1)
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diff changeset
295 {
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diff changeset
296 // This is a volume that is empty or that contains one single
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297 // slice: Choose a dummy z-dimension for voxels
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298 return 1.0;
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299 }
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300
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301 const OrthancStone::CoordinateSystem3D& reference = GetSliceGeometry(0);
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302
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303 double referencePosition = reference.ProjectAlongNormal(reference.GetOrigin());
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304
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305 double p = reference.ProjectAlongNormal(GetSliceGeometry(1).GetOrigin());
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306 double spacingZ = p - referencePosition;
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307
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308 if (spacingZ <= 0)
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309 {
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310 LOG(ERROR) << "SlicesSorter::ComputeSpacingBetweenSlices(): (spacingZ <= 0)";
667
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311 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls,
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312 "Please call the Sort() method before");
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313 }
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314
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315 for (size_t i = 1; i < GetSlicesCount(); i++)
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316 {
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317 OrthancStone::Vector p = reference.GetOrigin() + spacingZ * static_cast<double>(i) * reference.GetNormal();
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318 double d = boost::numeric::ublas::norm_2(p - GetSliceGeometry(i).GetOrigin());
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319
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320 if (!OrthancStone::LinearAlgebra::IsNear(d, 0, 0.001 /* tolerance expressed in mm */))
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321 {
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322 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadGeometry,
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323 "The origins of the slices of a volume image are not regularly spaced");
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324 }
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325 }
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326
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327 return spacingZ;
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328 }
73
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329 }