Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/SlicesSorter.cpp @ 844:84cd55245e2d
Merge
author | Benjamin Golinvaux <bgo@osimis.io> |
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date | Fri, 14 Jun 2019 12:16:38 +0200 |
parents | f7c236894c1a |
children | a7351ad54960 |
rev | line source |
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73 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
439 | 5 * Copyright (C) 2017-2019 Osimis S.A., Belgium |
73 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
22 #include "SlicesSorter.h" | |
23 | |
159
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24 #include "GeometryToolbox.h" |
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25 |
212
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26 #include <Core/OrthancException.h> |
73 | 27 |
28 namespace OrthancStone | |
29 { | |
30 class SlicesSorter::SliceWithDepth : public boost::noncopyable | |
31 { | |
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_; |
73 | 37 |
38 public: | |
647
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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) |
73 | 44 { |
45 } | |
46 | |
47 void SetNormal(const Vector& normal) | |
48 { | |
647
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49 depth_ = boost::numeric::ublas::inner_prod(geometry_.GetOrigin(), normal); |
73 | 50 } |
51 | |
52 double GetDepth() const | |
53 { | |
54 return depth_; | |
55 } | |
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 |
73 | 63 { |
647
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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 } |
73 | 77 } |
78 }; | |
79 | |
80 | |
81 struct SlicesSorter::Comparator | |
82 { | |
83 bool operator() (const SliceWithDepth* const& a, | |
84 const SliceWithDepth* const& b) const | |
85 { | |
86 return a->GetDepth() < b->GetDepth(); | |
87 } | |
88 }; | |
89 | |
90 | |
91 SlicesSorter::~SlicesSorter() | |
92 { | |
93 for (size_t i = 0; i < slices_.size(); i++) | |
94 { | |
95 assert(slices_[i] != NULL); | |
96 delete slices_[i]; | |
97 } | |
98 } | |
99 | |
100 | |
647
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101 void SlicesSorter::AddSlice(const CoordinateSystem3D& slice, |
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102 Orthanc::IDynamicObject* payload) |
73 | 103 { |
647
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104 slices_.push_back(new SliceWithDepth(slice, payload)); |
73 | 105 } |
106 | |
107 | |
647
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108 const SlicesSorter::SliceWithDepth& SlicesSorter::GetSlice(size_t i) const |
73 | 109 { |
110 if (i >= slices_.size()) | |
111 { | |
112 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
113 } | |
647
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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 } |
73 | 120 |
647
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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(); |
73 | 137 } |
138 | |
139 | |
140 void SlicesSorter::SetNormal(const Vector& normal) | |
141 { | |
142 for (size_t i = 0; i < slices_.size(); i++) | |
143 { | |
144 slices_[i]->SetNormal(normal); | |
145 } | |
146 | |
147 hasNormal_ = true; | |
148 } | |
149 | |
150 | |
648 | 151 void SlicesSorter::SortInternal() |
73 | 152 { |
153 if (!hasNormal_) | |
154 { | |
155 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
156 } | |
157 | |
158 Comparator comparator; | |
159 std::sort(slices_.begin(), slices_.end(), comparator); | |
160 } | |
161 | |
162 | |
163 void SlicesSorter::FilterNormal(const Vector& normal) | |
164 { | |
165 size_t pos = 0; | |
166 | |
167 for (size_t i = 0; i < slices_.size(); i++) | |
168 { | |
647
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169 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal())) |
73 | 170 { |
171 // This slice is compatible with the selected normal | |
172 slices_[pos] = slices_[i]; | |
173 pos += 1; | |
174 } | |
175 else | |
176 { | |
177 delete slices_[i]; | |
178 slices_[i] = NULL; | |
179 } | |
180 } | |
181 | |
182 slices_.resize(pos); | |
183 } | |
184 | |
185 | |
186 bool SlicesSorter::SelectNormal(Vector& normal) const | |
187 { | |
188 std::vector<Vector> normalCandidates; | |
189 std::vector<unsigned int> normalCount; | |
190 | |
191 bool found = false; | |
192 | |
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193 for (size_t i = 0; !found && i < GetSlicesCount(); i++) |
73 | 194 { |
195 const Vector& normal = GetSlice(i).GetGeometry().GetNormal(); | |
196 | |
197 bool add = true; | |
198 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*) | |
199 { | |
200 if (GeometryToolbox::IsParallel(normal, normalCandidates[j])) | |
201 { | |
202 normalCount[j] += 1; | |
203 add = false; | |
204 } | |
205 } | |
206 | |
207 if (add) | |
208 { | |
209 if (normalCount.size() > 2) | |
210 { | |
211 // To get linear-time complexity in (*). This heuristics | |
212 // allows the series to have one single frame that is | |
213 // not parallel to the others (such a frame could be a | |
214 // generated preview) | |
215 found = false; | |
216 } | |
217 else | |
218 { | |
219 normalCandidates.push_back(normal); | |
220 normalCount.push_back(1); | |
221 } | |
222 } | |
223 } | |
224 | |
225 for (size_t i = 0; !found && i < normalCandidates.size(); i++) | |
226 { | |
227 unsigned int count = normalCount[i]; | |
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228 if (count == GetSlicesCount() || |
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229 count + 1 == GetSlicesCount()) |
73 | 230 { |
231 normal = normalCandidates[i]; | |
232 found = true; | |
233 } | |
234 } | |
235 | |
236 return found; | |
237 } | |
77 | 238 |
239 | |
648 | 240 bool SlicesSorter::Sort() |
241 { | |
242 if (GetSlicesCount() > 0) | |
243 { | |
244 Vector normal; | |
245 if (SelectNormal(normal)) | |
246 { | |
247 FilterNormal(normal); | |
248 SetNormal(normal); | |
249 SortInternal(); | |
250 return true; | |
251 } | |
252 } | |
253 | |
254 return false; | |
255 } | |
256 | |
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 | 261 { |
262 // TODO Turn this linear-time lookup into a log-time lookup, | |
263 // keeping track of whether the slices are sorted along the normal | |
264 | |
647
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265 bool found = false; |
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266 |
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267 distance = std::numeric_limits<double>::infinity(); |
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268 |
77 | 269 for (size_t i = 0; i < slices_.size(); i++) |
270 { | |
647
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271 assert(slices_[i] != NULL); |
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272 |
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273 double tmp; |
757 | 274 if (CoordinateSystem3D::ComputeDistance(tmp, slices_[i]->GetGeometry(), slice)) |
77 | 275 { |
647
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276 if (!found || |
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277 tmp < distance) |
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278 { |
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279 index = i; |
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280 distance = tmp; |
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281 found = true; |
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282 } |
77 | 283 } |
284 } | |
285 | |
647
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286 return found; |
77 | 287 } |
667
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288 |
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289 |
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290 double SlicesSorter::ComputeSpacingBetweenSlices() const |
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291 { |
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292 if (GetSlicesCount() <= 1) |
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293 { |
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294 // This is a volume that is empty or that contains one single |
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295 // slice: Choose a dummy z-dimension for voxels |
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296 return 1.0; |
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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 | 326 } |