Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/OpenSlideLibrary.cpp @ 279:77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 12 Jul 2023 18:06:34 +0200 |
parents | 169f168ba07a |
children | 7020852a8fa9 |
rev | line source |
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0 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
254 | 5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
6 * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium | |
0 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
9 * modify it under the terms of the GNU Affero General Public License | |
10 * as published by the Free Software Foundation, either version 3 of | |
11 * the License, or (at your option) any later version. | |
12 * | |
13 * This program is distributed in the hope that it will be useful, but | |
14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
16 * Affero General Public License for more details. | |
17 * | |
18 * You should have received a copy of the GNU Affero General Public License | |
19 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
20 **/ | |
21 | |
22 | |
16
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23 #include "../PrecompiledHeadersWSI.h" |
0 | 24 #include "OpenSlideLibrary.h" |
25 | |
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26 #include <Compatibility.h> // For std::unique_ptr |
192 | 27 #include <Logging.h> |
28 #include <Images/Image.h> | |
29 #include <OrthancException.h> | |
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30 |
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31 #include <memory> |
0 | 32 |
33 namespace OrthancWSI | |
34 { | |
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35 static std::unique_ptr<OpenSlideLibrary> globalLibrary_; |
0 | 36 |
37 | |
38 OpenSlideLibrary::OpenSlideLibrary(const std::string& path) : | |
39 library_(path) | |
40 { | |
41 close_ = (FunctionClose) library_.GetFunction("openslide_close"); | |
42 getLevelCount_ = (FunctionGetLevelCount) library_.GetFunction("openslide_get_level_count"); | |
43 getLevelDimensions_ = (FunctionGetLevelDimensions) library_.GetFunction("openslide_get_level_dimensions"); | |
44 getLevelDownsample_ = (FunctionGetLevelDownsample) library_.GetFunction("openslide_get_level_downsample"); | |
45 open_ = (FunctionOpen) library_.GetFunction("openslide_open"); | |
46 readRegion_ = (FunctionReadRegion) library_.GetFunction("openslide_read_region"); | |
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47 getPropertyNames_ = (FunctionGetPropertyNames) library_.GetFunction("openslide_get_property_names"); |
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48 getPropertyValue_ = (FunctionGetPropertyValue) library_.GetFunction("openslide_get_property_value"); |
0 | 49 } |
50 | |
51 | |
52 OpenSlideLibrary::Image::Level::Level() : | |
53 width_(0), | |
54 height_(0), | |
55 downsample_(1) | |
56 { | |
57 } | |
58 | |
59 | |
60 OpenSlideLibrary::Image::Level::Level(int64_t width, | |
61 int64_t height, | |
62 double downsample) : | |
63 width_(static_cast<unsigned int>(width)), | |
64 height_(static_cast<unsigned int>(height)), | |
65 downsample_(downsample) | |
66 { | |
67 if (width < 0 || | |
68 height < 0 || | |
69 downsample <= 0) | |
70 { | |
71 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
72 } | |
73 | |
74 if (static_cast<int64_t>(width_) != width || | |
75 static_cast<int64_t>(height_) != height) | |
76 { | |
77 LOG(ERROR) << "The whole-slide image is too large"; | |
78 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
79 } | |
80 } | |
81 | |
82 | |
83 void OpenSlideLibrary::Image::Initialize(const std::string& path) | |
84 { | |
85 handle_ = that_.open_(path.c_str()); | |
86 if (handle_ == NULL) | |
87 { | |
88 LOG(ERROR) << "Cannot open an image with OpenSlide: " << path; | |
89 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
90 } | |
91 | |
92 try | |
93 { | |
94 LOG(INFO) << "Opening an image with OpenSlide: " << path; | |
95 | |
96 int32_t tmp = that_.getLevelCount_(handle_); | |
97 if (tmp <= 0) | |
98 { | |
99 LOG(ERROR) << "Image with no pyramid level"; | |
100 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
101 } | |
102 | |
103 levels_.resize(tmp); | |
104 | |
105 for (int32_t level = 0; level < tmp; level++) | |
106 { | |
107 int64_t width, height; | |
108 that_.getLevelDimensions_(handle_, level, &width, &height); | |
109 | |
110 double downsample = that_.getLevelDownsample_(handle_, level); | |
111 | |
112 levels_[level] = Level(width, height, downsample); | |
113 } | |
114 | |
115 for (size_t i = 1; i < levels_.size(); i++) | |
116 { | |
117 if (levels_[i].width_ >= levels_[i - 1].width_ || | |
118 levels_[i].height_ >= levels_[i - 1].height_) | |
119 { | |
120 // This is not a pyramid with levels of decreasing sizes | |
121 // (level "0" must be the finest level) | |
122 LOG(ERROR) << "The pyramid does not have levels of strictly decreasing sizes"; | |
123 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
124 } | |
125 } | |
126 } | |
127 catch (Orthanc::OrthancException&) | |
128 { | |
129 Close(); | |
130 throw; | |
131 } | |
132 } | |
133 | |
134 | |
135 OpenSlideLibrary::Image::Image(OpenSlideLibrary& that, | |
136 const std::string& path) : | |
137 that_(that), | |
138 handle_(NULL) | |
139 { | |
140 Initialize(path); | |
141 } | |
142 | |
143 | |
144 OpenSlideLibrary::Image::Image(const std::string& path) : | |
145 that_(OpenSlideLibrary::GetInstance()), | |
146 handle_(NULL) | |
147 { | |
148 Initialize(path); | |
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149 |
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150 const char* const* properties = that_.getPropertyNames_(handle_); |
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151 if (properties == NULL) |
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152 { |
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153 that_.close_(handle_); |
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154 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); |
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155 } |
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156 |
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157 for (size_t i = 0; properties[i] != NULL; i++) |
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158 { |
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159 const char* value = that_.getPropertyValue_(handle_, properties[i]); |
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160 if (value == NULL) |
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161 { |
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162 that_.close_(handle_); |
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163 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); |
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164 } |
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165 else |
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166 { |
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167 properties_[properties[i]] = value; |
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168 } |
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169 } |
0 | 170 } |
171 | |
172 | |
173 void OpenSlideLibrary::Image::Close() | |
174 { | |
175 if (handle_ != NULL) | |
176 { | |
177 that_.close_(handle_); | |
178 handle_ = NULL; | |
179 } | |
180 } | |
181 | |
182 | |
183 void OpenSlideLibrary::Image::CheckLevel(unsigned int level) const | |
184 { | |
185 if (level >= levels_.size()) | |
186 { | |
187 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
188 } | |
189 } | |
190 | |
191 | |
192 double OpenSlideLibrary::Image::GetLevelDownsample(unsigned int level) const | |
193 { | |
194 CheckLevel(level); | |
195 return levels_[level].downsample_; | |
196 } | |
197 | |
198 | |
199 unsigned int OpenSlideLibrary::Image::GetLevelWidth(unsigned int level) const | |
200 { | |
201 CheckLevel(level); | |
202 return levels_[level].width_; | |
203 } | |
204 | |
205 | |
206 unsigned int OpenSlideLibrary::Image::GetLevelHeight(unsigned int level) const | |
207 { | |
208 CheckLevel(level); | |
209 return levels_[level].height_; | |
210 } | |
211 | |
212 | |
213 Orthanc::ImageAccessor* OpenSlideLibrary::Image::ReadRegion(unsigned int level, | |
214 uint64_t x, | |
215 uint64_t y, | |
216 unsigned int width, | |
217 unsigned int height) | |
218 { | |
219 CheckLevel(level); | |
220 | |
221 // Create a new image, with minimal pitch so as to be compatible with OpenSlide API | |
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222 std::unique_ptr<Orthanc::ImageAccessor> region(new Orthanc::Image(Orthanc::PixelFormat_BGRA32, width, height, true)); |
0 | 223 |
224 if (region->GetWidth() != 0 && | |
225 region->GetHeight() != 0) | |
226 { | |
227 double zoom = levels_[level].downsample_; | |
228 x = static_cast<uint64_t>(zoom * static_cast<double>(x)); | |
229 y = static_cast<uint64_t>(zoom * static_cast<double>(y)); | |
230 | |
231 that_.readRegion_(handle_, reinterpret_cast<uint32_t*>(region->GetBuffer()), | |
232 x, y, level, region->GetWidth(), region->GetHeight()); | |
233 } | |
234 | |
235 return region.release(); | |
236 } | |
237 | |
238 | |
239 OpenSlideLibrary& OpenSlideLibrary::GetInstance() | |
240 { | |
241 if (globalLibrary_.get() == NULL) | |
242 { | |
32 | 243 LOG(ERROR) << "OpenSlide has not been initialized, use the \"--openslide\" command-line option"; |
0 | 244 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
245 } | |
246 else | |
247 { | |
248 return *globalLibrary_; | |
249 } | |
250 } | |
251 | |
252 | |
253 void OpenSlideLibrary::Initialize(const std::string& path) | |
254 { | |
255 globalLibrary_.reset(new OpenSlideLibrary(path)); | |
256 } | |
257 | |
258 | |
259 void OpenSlideLibrary::Finalize() | |
260 { | |
261 globalLibrary_.reset(NULL); | |
262 } | |
278
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263 |
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264 |
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265 bool OpenSlideLibrary::Image::LookupProperty(std::string& value, |
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266 const std::string& property) const |
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267 { |
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268 std::map<std::string, std::string>::const_iterator found = properties_.find(property); |
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269 |
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270 if (found == properties_.end()) |
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271 { |
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272 return false; |
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273 } |
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274 else |
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275 { |
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276 value = found->second; |
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277 return true; |
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278 } |
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279 } |
0 | 280 } |