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> |
|---|---|
| date | Wed, 12 Jul 2023 18:06:34 +0200 |
| parents | 169f168ba07a |
| children | 7020852a8fa9 |
| rev | line source |
|---|---|
| 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 | |
|
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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 } | |
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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 } |