Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/SlicesSorter.cpp @ 1584:bd180f97c734
parsing osirix annotations
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 21 Oct 2020 17:33:17 +0200 |
parents | 85e117739eca |
children | 4fb8fdf03314 |
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 | |
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5 * Copyright (C) 2017-2020 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 | |
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24 #include "GeometryToolbox.h" |
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25 |
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26 #include <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::unique_ptr<Orthanc::IDynamicObject> payload_; |
73 | 37 |
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) |
73 | 44 { |
45 } | |
46 | |
47 void SetNormal(const Vector& normal) | |
48 { | |
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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 { |
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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 LOG(ERROR) << "SlicesSorter::SliceWithDepth::GetPayload(): (!HasPayload())"; |
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76 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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77 } |
73 | 78 } |
79 }; | |
80 | |
81 | |
82 struct SlicesSorter::Comparator | |
83 { | |
84 bool operator() (const SliceWithDepth* const& a, | |
85 const SliceWithDepth* const& b) const | |
86 { | |
87 return a->GetDepth() < b->GetDepth(); | |
88 } | |
89 }; | |
90 | |
91 | |
92 SlicesSorter::~SlicesSorter() | |
93 { | |
94 for (size_t i = 0; i < slices_.size(); i++) | |
95 { | |
96 assert(slices_[i] != NULL); | |
97 delete slices_[i]; | |
98 } | |
99 } | |
100 | |
101 | |
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102 void SlicesSorter::AddSlice(const CoordinateSystem3D& slice, |
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103 Orthanc::IDynamicObject* payload) |
73 | 104 { |
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105 slices_.push_back(new SliceWithDepth(slice, payload)); |
73 | 106 } |
107 | |
108 | |
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109 const SlicesSorter::SliceWithDepth& SlicesSorter::GetSlice(size_t i) const |
73 | 110 { |
111 if (i >= slices_.size()) | |
112 { | |
113 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
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 } |
73 | 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(); |
73 | 138 } |
139 | |
140 | |
141 void SlicesSorter::SetNormal(const Vector& normal) | |
142 { | |
143 for (size_t i = 0; i < slices_.size(); i++) | |
144 { | |
145 slices_[i]->SetNormal(normal); | |
146 } | |
147 | |
148 hasNormal_ = true; | |
149 } | |
150 | |
151 | |
648 | 152 void SlicesSorter::SortInternal() |
73 | 153 { |
154 if (!hasNormal_) | |
155 { | |
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156 LOG(ERROR) << "SlicesSorter::SortInternal(): (!hasNormal_)"; |
73 | 157 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
158 } | |
159 | |
160 Comparator comparator; | |
161 std::sort(slices_.begin(), slices_.end(), comparator); | |
162 } | |
163 | |
164 | |
165 void SlicesSorter::FilterNormal(const Vector& normal) | |
166 { | |
167 size_t pos = 0; | |
168 | |
169 for (size_t i = 0; i < slices_.size(); i++) | |
170 { | |
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171 if (GeometryToolbox::IsParallel(normal, slices_[i]->GetGeometry().GetNormal())) |
73 | 172 { |
173 // This slice is compatible with the selected normal | |
174 slices_[pos] = slices_[i]; | |
175 pos += 1; | |
176 } | |
177 else | |
178 { | |
179 delete slices_[i]; | |
180 slices_[i] = NULL; | |
181 } | |
182 } | |
183 | |
184 slices_.resize(pos); | |
185 } | |
186 | |
187 | |
188 bool SlicesSorter::SelectNormal(Vector& normal) const | |
189 { | |
190 std::vector<Vector> normalCandidates; | |
191 std::vector<unsigned int> normalCount; | |
192 | |
193 bool found = false; | |
194 | |
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195 for (size_t i = 0; !found && i < GetSlicesCount(); i++) |
73 | 196 { |
197 const Vector& normal = GetSlice(i).GetGeometry().GetNormal(); | |
198 | |
199 bool add = true; | |
200 for (size_t j = 0; add && j < normalCandidates.size(); j++) // (*) | |
201 { | |
202 if (GeometryToolbox::IsParallel(normal, normalCandidates[j])) | |
203 { | |
204 normalCount[j] += 1; | |
205 add = false; | |
206 } | |
207 } | |
208 | |
209 if (add) | |
210 { | |
211 if (normalCount.size() > 2) | |
212 { | |
213 // To get linear-time complexity in (*). This heuristics | |
214 // allows the series to have one single frame that is | |
215 // not parallel to the others (such a frame could be a | |
216 // generated preview) | |
217 found = false; | |
218 } | |
219 else | |
220 { | |
221 normalCandidates.push_back(normal); | |
222 normalCount.push_back(1); | |
223 } | |
224 } | |
225 } | |
226 | |
227 for (size_t i = 0; !found && i < normalCandidates.size(); i++) | |
228 { | |
229 unsigned int count = normalCount[i]; | |
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230 if (count == GetSlicesCount() || |
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231 count + 1 == GetSlicesCount()) |
73 | 232 { |
233 normal = normalCandidates[i]; | |
234 found = true; | |
235 } | |
236 } | |
237 | |
238 return found; | |
239 } | |
77 | 240 |
241 | |
648 | 242 bool SlicesSorter::Sort() |
243 { | |
244 if (GetSlicesCount() > 0) | |
245 { | |
246 Vector normal; | |
247 if (SelectNormal(normal)) | |
248 { | |
249 FilterNormal(normal); | |
250 SetNormal(normal); | |
251 SortInternal(); | |
252 return true; | |
253 } | |
254 } | |
255 | |
256 return false; | |
257 } | |
258 | |
259 | |
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260 bool SlicesSorter::LookupClosestSlice(size_t& index, |
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261 double& distance, |
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262 const CoordinateSystem3D& slice) const |
77 | 263 { |
264 // TODO Turn this linear-time lookup into a log-time lookup, | |
265 // keeping track of whether the slices are sorted along the normal | |
266 | |
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267 bool found = false; |
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268 |
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269 distance = std::numeric_limits<double>::infinity(); |
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270 |
77 | 271 for (size_t i = 0; i < slices_.size(); i++) |
272 { | |
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273 assert(slices_[i] != NULL); |
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274 |
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275 double tmp; |
757 | 276 if (CoordinateSystem3D::ComputeDistance(tmp, slices_[i]->GetGeometry(), slice)) |
77 | 277 { |
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278 if (!found || |
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279 tmp < distance) |
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280 { |
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281 index = i; |
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282 distance = tmp; |
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283 found = true; |
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284 } |
77 | 285 } |
286 } | |
287 | |
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288 return found; |
77 | 289 } |
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290 |
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291 |
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292 bool SlicesSorter::ComputeSpacingBetweenSlices(double& spacing /* out */) const |
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293 { |
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294 if (GetSlicesCount() <= 1) |
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295 { |
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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 spacing = 1.0; |
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299 return true; |
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300 } |
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301 |
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302 const OrthancStone::CoordinateSystem3D& reference = GetSliceGeometry(0); |
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303 |
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304 double referencePosition = reference.ProjectAlongNormal(reference.GetOrigin()); |
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305 |
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306 double p = reference.ProjectAlongNormal(GetSliceGeometry(1).GetOrigin()); |
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307 spacing = p - referencePosition; |
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308 |
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309 if (spacing <= 0) |
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310 { |
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311 LOG(ERROR) << "SlicesSorter::ComputeSpacingBetweenSlices(): (spacing <= 0)"; |
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312 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls, |
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313 "Please call the Sort() method before"); |
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314 } |
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315 |
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316 for (size_t i = 1; i < GetSlicesCount(); i++) |
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317 { |
1571 | 318 OrthancStone::Vector q = reference.GetOrigin() + spacing * static_cast<double>(i) * reference.GetNormal(); |
319 double d = boost::numeric::ublas::norm_2(q - GetSliceGeometry(i).GetOrigin()); | |
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320 |
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321 if (!OrthancStone::LinearAlgebra::IsNear(d, 0, 0.001 /* tolerance expressed in mm */)) |
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322 { |
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323 return false; |
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324 } |
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325 } |
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326 |
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327 return true; |
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328 } |
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329 |
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330 |
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331 bool SlicesSorter::AreAllSlicesDistinct() const |
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332 { |
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333 if (GetSlicesCount() <= 1) |
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334 { |
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335 return true; |
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336 } |
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337 else |
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338 { |
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339 const OrthancStone::CoordinateSystem3D& reference = GetSliceGeometry(0); |
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340 double previousPosition = reference.ProjectAlongNormal(GetSliceGeometry(0).GetOrigin()); |
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341 |
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342 for (size_t i = 1; i < GetSlicesCount(); i++) |
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343 { |
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344 double position = reference.ProjectAlongNormal(GetSliceGeometry(i).GetOrigin()); |
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345 |
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346 if (OrthancStone::LinearAlgebra::IsNear(position, previousPosition, 0.001 /* tolerance expressed in mm */)) |
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347 { |
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348 return false; |
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349 } |
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350 |
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351 previousPosition = position; |
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352 } |
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353 |
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354 return true; |
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355 } |
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356 } |
73 | 357 } |