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annotate Framework/Inputs/OpenSlideLibrary.cpp @ 334:f011fc199b6a default tip
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 18 Oct 2024 15:44:18 +0200 |
parents | 0683312e21ba |
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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 | |
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5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 8 * |
9 * This program is free software: you can redistribute it and/or | |
10 * modify it under the terms of the GNU Affero General Public License | |
11 * as published by the Free Software Foundation, either version 3 of | |
12 * the License, or (at your option) any later version. | |
13 * | |
14 * This program is distributed in the hope that it will be useful, but | |
15 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
17 * Affero General Public License for more details. | |
18 * | |
19 * You should have received a copy of the GNU Affero General Public License | |
20 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
21 **/ | |
22 | |
23 | |
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24 #include "../PrecompiledHeadersWSI.h" |
0 | 25 #include "OpenSlideLibrary.h" |
26 | |
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27 #include <Compatibility.h> // For std::unique_ptr |
192 | 28 #include <Logging.h> |
29 #include <Images/Image.h> | |
30 #include <OrthancException.h> | |
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31 |
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32 #include <memory> |
0 | 33 |
34 namespace OrthancWSI | |
35 { | |
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36 static std::unique_ptr<OpenSlideLibrary> globalLibrary_; |
0 | 37 |
38 | |
39 OpenSlideLibrary::OpenSlideLibrary(const std::string& path) : | |
40 library_(path) | |
41 { | |
42 close_ = (FunctionClose) library_.GetFunction("openslide_close"); | |
43 getLevelCount_ = (FunctionGetLevelCount) library_.GetFunction("openslide_get_level_count"); | |
44 getLevelDimensions_ = (FunctionGetLevelDimensions) library_.GetFunction("openslide_get_level_dimensions"); | |
45 getLevelDownsample_ = (FunctionGetLevelDownsample) library_.GetFunction("openslide_get_level_downsample"); | |
46 open_ = (FunctionOpen) library_.GetFunction("openslide_open"); | |
47 readRegion_ = (FunctionReadRegion) library_.GetFunction("openslide_read_region"); | |
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48 getPropertyNames_ = (FunctionGetPropertyNames) library_.GetFunction("openslide_get_property_names"); |
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49 getPropertyValue_ = (FunctionGetPropertyValue) library_.GetFunction("openslide_get_property_value"); |
0 | 50 } |
51 | |
52 | |
53 OpenSlideLibrary::Image::Level::Level() : | |
54 width_(0), | |
55 height_(0), | |
56 downsample_(1) | |
57 { | |
58 } | |
59 | |
60 | |
61 OpenSlideLibrary::Image::Level::Level(int64_t width, | |
62 int64_t height, | |
63 double downsample) : | |
64 width_(static_cast<unsigned int>(width)), | |
65 height_(static_cast<unsigned int>(height)), | |
66 downsample_(downsample) | |
67 { | |
68 if (width < 0 || | |
69 height < 0 || | |
70 downsample <= 0) | |
71 { | |
72 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
73 } | |
74 | |
75 if (static_cast<int64_t>(width_) != width || | |
76 static_cast<int64_t>(height_) != height) | |
77 { | |
78 LOG(ERROR) << "The whole-slide image is too large"; | |
79 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
80 } | |
81 } | |
82 | |
83 | |
84 void OpenSlideLibrary::Image::Initialize(const std::string& path) | |
85 { | |
86 handle_ = that_.open_(path.c_str()); | |
87 if (handle_ == NULL) | |
88 { | |
89 LOG(ERROR) << "Cannot open an image with OpenSlide: " << path; | |
90 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
91 } | |
92 | |
93 try | |
94 { | |
95 LOG(INFO) << "Opening an image with OpenSlide: " << path; | |
96 | |
97 int32_t tmp = that_.getLevelCount_(handle_); | |
98 if (tmp <= 0) | |
99 { | |
100 LOG(ERROR) << "Image with no pyramid level"; | |
101 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
102 } | |
103 | |
104 levels_.resize(tmp); | |
105 | |
106 for (int32_t level = 0; level < tmp; level++) | |
107 { | |
108 int64_t width, height; | |
109 that_.getLevelDimensions_(handle_, level, &width, &height); | |
110 | |
111 double downsample = that_.getLevelDownsample_(handle_, level); | |
112 | |
113 levels_[level] = Level(width, height, downsample); | |
114 } | |
115 | |
116 for (size_t i = 1; i < levels_.size(); i++) | |
117 { | |
118 if (levels_[i].width_ >= levels_[i - 1].width_ || | |
119 levels_[i].height_ >= levels_[i - 1].height_) | |
120 { | |
121 // This is not a pyramid with levels of decreasing sizes | |
122 // (level "0" must be the finest level) | |
123 LOG(ERROR) << "The pyramid does not have levels of strictly decreasing sizes"; | |
124 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
125 } | |
126 } | |
127 } | |
128 catch (Orthanc::OrthancException&) | |
129 { | |
130 Close(); | |
131 throw; | |
132 } | |
133 } | |
134 | |
135 | |
136 OpenSlideLibrary::Image::Image(OpenSlideLibrary& that, | |
137 const std::string& path) : | |
138 that_(that), | |
139 handle_(NULL) | |
140 { | |
141 Initialize(path); | |
142 } | |
143 | |
144 | |
145 OpenSlideLibrary::Image::Image(const std::string& path) : | |
146 that_(OpenSlideLibrary::GetInstance()), | |
147 handle_(NULL) | |
148 { | |
149 Initialize(path); | |
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150 |
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151 const char* const* properties = that_.getPropertyNames_(handle_); |
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152 if (properties == NULL) |
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153 { |
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154 that_.close_(handle_); |
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155 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); |
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156 } |
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157 |
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158 for (size_t i = 0; properties[i] != NULL; i++) |
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159 { |
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160 const char* value = that_.getPropertyValue_(handle_, properties[i]); |
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161 if (value == NULL) |
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162 { |
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163 that_.close_(handle_); |
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164 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); |
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165 } |
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166 else |
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167 { |
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168 properties_[properties[i]] = value; |
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169 } |
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170 } |
0 | 171 } |
172 | |
173 | |
174 void OpenSlideLibrary::Image::Close() | |
175 { | |
176 if (handle_ != NULL) | |
177 { | |
178 that_.close_(handle_); | |
179 handle_ = NULL; | |
180 } | |
181 } | |
182 | |
183 | |
184 void OpenSlideLibrary::Image::CheckLevel(unsigned int level) const | |
185 { | |
186 if (level >= levels_.size()) | |
187 { | |
188 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
189 } | |
190 } | |
191 | |
192 | |
193 double OpenSlideLibrary::Image::GetLevelDownsample(unsigned int level) const | |
194 { | |
195 CheckLevel(level); | |
196 return levels_[level].downsample_; | |
197 } | |
198 | |
199 | |
200 unsigned int OpenSlideLibrary::Image::GetLevelWidth(unsigned int level) const | |
201 { | |
202 CheckLevel(level); | |
203 return levels_[level].width_; | |
204 } | |
205 | |
206 | |
207 unsigned int OpenSlideLibrary::Image::GetLevelHeight(unsigned int level) const | |
208 { | |
209 CheckLevel(level); | |
210 return levels_[level].height_; | |
211 } | |
212 | |
213 | |
214 Orthanc::ImageAccessor* OpenSlideLibrary::Image::ReadRegion(unsigned int level, | |
215 uint64_t x, | |
216 uint64_t y, | |
217 unsigned int width, | |
218 unsigned int height) | |
219 { | |
220 CheckLevel(level); | |
221 | |
222 // Create a new image, with minimal pitch so as to be compatible with OpenSlide API | |
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223 std::unique_ptr<Orthanc::ImageAccessor> region(new Orthanc::Image(Orthanc::PixelFormat_BGRA32, width, height, true)); |
0 | 224 |
225 if (region->GetWidth() != 0 && | |
226 region->GetHeight() != 0) | |
227 { | |
228 double zoom = levels_[level].downsample_; | |
229 x = static_cast<uint64_t>(zoom * static_cast<double>(x)); | |
230 y = static_cast<uint64_t>(zoom * static_cast<double>(y)); | |
231 | |
232 that_.readRegion_(handle_, reinterpret_cast<uint32_t*>(region->GetBuffer()), | |
233 x, y, level, region->GetWidth(), region->GetHeight()); | |
234 } | |
235 | |
236 return region.release(); | |
237 } | |
238 | |
239 | |
240 OpenSlideLibrary& OpenSlideLibrary::GetInstance() | |
241 { | |
242 if (globalLibrary_.get() == NULL) | |
243 { | |
32 | 244 LOG(ERROR) << "OpenSlide has not been initialized, use the \"--openslide\" command-line option"; |
0 | 245 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
246 } | |
247 else | |
248 { | |
249 return *globalLibrary_; | |
250 } | |
251 } | |
252 | |
253 | |
254 void OpenSlideLibrary::Initialize(const std::string& path) | |
255 { | |
256 globalLibrary_.reset(new OpenSlideLibrary(path)); | |
257 } | |
258 | |
259 | |
260 void OpenSlideLibrary::Finalize() | |
261 { | |
262 globalLibrary_.reset(NULL); | |
263 } | |
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264 |
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265 |
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266 bool OpenSlideLibrary::Image::LookupProperty(std::string& value, |
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267 const std::string& property) const |
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268 { |
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269 std::map<std::string, std::string>::const_iterator found = properties_.find(property); |
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270 |
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271 if (found == properties_.end()) |
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272 { |
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273 return false; |
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274 } |
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275 else |
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276 { |
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277 value = found->second; |
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278 return true; |
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279 } |
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280 } |
0 | 281 } |