Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/OpenSlideLibrary.cpp @ 137:90b392cb1aba
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 11 Apr 2018 15:45:26 +0200 |
| parents | e8fe7c9a7d6c |
| children | a0f9a3df1110 |
| 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 | |
|
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5 * Copyright (C) 2017-2018 Osimis S.A., Belgium |
| 0 | 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 | |
|
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preparing for precompiled headers
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22 #include "../PrecompiledHeadersWSI.h" |
| 0 | 23 #include "OpenSlideLibrary.h" |
| 24 | |
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25 #include "../../Resources/Orthanc/Core/Logging.h" |
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26 #include "../../Resources/Orthanc/Core/Images/Image.h" |
| 123 | 27 #include "../../Resources/Orthanc/Core/OrthancException.h" |
| 0 | 28 |
| 29 namespace OrthancWSI | |
| 30 { | |
| 31 static std::auto_ptr<OpenSlideLibrary> globalLibrary_; | |
| 32 | |
| 33 | |
| 34 OpenSlideLibrary::OpenSlideLibrary(const std::string& path) : | |
| 35 library_(path) | |
| 36 { | |
| 37 close_ = (FunctionClose) library_.GetFunction("openslide_close"); | |
| 38 getLevelCount_ = (FunctionGetLevelCount) library_.GetFunction("openslide_get_level_count"); | |
| 39 getLevelDimensions_ = (FunctionGetLevelDimensions) library_.GetFunction("openslide_get_level_dimensions"); | |
| 40 getLevelDownsample_ = (FunctionGetLevelDownsample) library_.GetFunction("openslide_get_level_downsample"); | |
| 41 open_ = (FunctionOpen) library_.GetFunction("openslide_open"); | |
| 42 readRegion_ = (FunctionReadRegion) library_.GetFunction("openslide_read_region"); | |
| 43 } | |
| 44 | |
| 45 | |
| 46 OpenSlideLibrary::Image::Level::Level() : | |
| 47 width_(0), | |
| 48 height_(0), | |
| 49 downsample_(1) | |
| 50 { | |
| 51 } | |
| 52 | |
| 53 | |
| 54 OpenSlideLibrary::Image::Level::Level(int64_t width, | |
| 55 int64_t height, | |
| 56 double downsample) : | |
| 57 width_(static_cast<unsigned int>(width)), | |
| 58 height_(static_cast<unsigned int>(height)), | |
| 59 downsample_(downsample) | |
| 60 { | |
| 61 if (width < 0 || | |
| 62 height < 0 || | |
| 63 downsample <= 0) | |
| 64 { | |
| 65 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 66 } | |
| 67 | |
| 68 if (static_cast<int64_t>(width_) != width || | |
| 69 static_cast<int64_t>(height_) != height) | |
| 70 { | |
| 71 LOG(ERROR) << "The whole-slide image is too large"; | |
| 72 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 73 } | |
| 74 } | |
| 75 | |
| 76 | |
| 77 void OpenSlideLibrary::Image::Initialize(const std::string& path) | |
| 78 { | |
| 79 handle_ = that_.open_(path.c_str()); | |
| 80 if (handle_ == NULL) | |
| 81 { | |
| 82 LOG(ERROR) << "Cannot open an image with OpenSlide: " << path; | |
| 83 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 84 } | |
| 85 | |
| 86 try | |
| 87 { | |
| 88 LOG(INFO) << "Opening an image with OpenSlide: " << path; | |
| 89 | |
| 90 int32_t tmp = that_.getLevelCount_(handle_); | |
| 91 if (tmp <= 0) | |
| 92 { | |
| 93 LOG(ERROR) << "Image with no pyramid level"; | |
| 94 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 95 } | |
| 96 | |
| 97 levels_.resize(tmp); | |
| 98 | |
| 99 for (int32_t level = 0; level < tmp; level++) | |
| 100 { | |
| 101 int64_t width, height; | |
| 102 that_.getLevelDimensions_(handle_, level, &width, &height); | |
| 103 | |
| 104 double downsample = that_.getLevelDownsample_(handle_, level); | |
| 105 | |
| 106 levels_[level] = Level(width, height, downsample); | |
| 107 } | |
| 108 | |
| 109 for (size_t i = 1; i < levels_.size(); i++) | |
| 110 { | |
| 111 if (levels_[i].width_ >= levels_[i - 1].width_ || | |
| 112 levels_[i].height_ >= levels_[i - 1].height_) | |
| 113 { | |
| 114 // This is not a pyramid with levels of decreasing sizes | |
| 115 // (level "0" must be the finest level) | |
| 116 LOG(ERROR) << "The pyramid does not have levels of strictly decreasing sizes"; | |
| 117 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 118 } | |
| 119 } | |
| 120 } | |
| 121 catch (Orthanc::OrthancException&) | |
| 122 { | |
| 123 Close(); | |
| 124 throw; | |
| 125 } | |
| 126 } | |
| 127 | |
| 128 | |
| 129 OpenSlideLibrary::Image::Image(OpenSlideLibrary& that, | |
| 130 const std::string& path) : | |
| 131 that_(that), | |
| 132 handle_(NULL) | |
| 133 { | |
| 134 Initialize(path); | |
| 135 } | |
| 136 | |
| 137 | |
| 138 OpenSlideLibrary::Image::Image(const std::string& path) : | |
| 139 that_(OpenSlideLibrary::GetInstance()), | |
| 140 handle_(NULL) | |
| 141 { | |
| 142 Initialize(path); | |
| 143 } | |
| 144 | |
| 145 | |
| 146 void OpenSlideLibrary::Image::Close() | |
| 147 { | |
| 148 if (handle_ != NULL) | |
| 149 { | |
| 150 that_.close_(handle_); | |
| 151 handle_ = NULL; | |
| 152 } | |
| 153 } | |
| 154 | |
| 155 | |
| 156 void OpenSlideLibrary::Image::CheckLevel(unsigned int level) const | |
| 157 { | |
| 158 if (level >= levels_.size()) | |
| 159 { | |
| 160 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 161 } | |
| 162 } | |
| 163 | |
| 164 | |
| 165 double OpenSlideLibrary::Image::GetLevelDownsample(unsigned int level) const | |
| 166 { | |
| 167 CheckLevel(level); | |
| 168 return levels_[level].downsample_; | |
| 169 } | |
| 170 | |
| 171 | |
| 172 unsigned int OpenSlideLibrary::Image::GetLevelWidth(unsigned int level) const | |
| 173 { | |
| 174 CheckLevel(level); | |
| 175 return levels_[level].width_; | |
| 176 } | |
| 177 | |
| 178 | |
| 179 unsigned int OpenSlideLibrary::Image::GetLevelHeight(unsigned int level) const | |
| 180 { | |
| 181 CheckLevel(level); | |
| 182 return levels_[level].height_; | |
| 183 } | |
| 184 | |
| 185 | |
| 186 Orthanc::ImageAccessor* OpenSlideLibrary::Image::ReadRegion(unsigned int level, | |
| 187 uint64_t x, | |
| 188 uint64_t y, | |
| 189 unsigned int width, | |
| 190 unsigned int height) | |
| 191 { | |
| 192 CheckLevel(level); | |
| 193 | |
| 194 // Create a new image, with minimal pitch so as to be compatible with OpenSlide API | |
|
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Fix issue #30: Bad colorspace if using OpenSlide
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195 std::auto_ptr<Orthanc::ImageAccessor> region(new Orthanc::Image(Orthanc::PixelFormat_BGRA32, width, height, true)); |
| 0 | 196 |
| 197 if (region->GetWidth() != 0 && | |
| 198 region->GetHeight() != 0) | |
| 199 { | |
| 200 double zoom = levels_[level].downsample_; | |
| 201 x = static_cast<uint64_t>(zoom * static_cast<double>(x)); | |
| 202 y = static_cast<uint64_t>(zoom * static_cast<double>(y)); | |
| 203 | |
| 204 that_.readRegion_(handle_, reinterpret_cast<uint32_t*>(region->GetBuffer()), | |
| 205 x, y, level, region->GetWidth(), region->GetHeight()); | |
| 206 } | |
| 207 | |
| 208 return region.release(); | |
| 209 } | |
| 210 | |
| 211 | |
| 212 OpenSlideLibrary& OpenSlideLibrary::GetInstance() | |
| 213 { | |
| 214 if (globalLibrary_.get() == NULL) | |
| 215 { | |
| 32 | 216 LOG(ERROR) << "OpenSlide has not been initialized, use the \"--openslide\" command-line option"; |
| 0 | 217 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 218 } | |
| 219 else | |
| 220 { | |
| 221 return *globalLibrary_; | |
| 222 } | |
| 223 } | |
| 224 | |
| 225 | |
| 226 void OpenSlideLibrary::Initialize(const std::string& path) | |
| 227 { | |
| 228 globalLibrary_.reset(new OpenSlideLibrary(path)); | |
| 229 } | |
| 230 | |
| 231 | |
| 232 void OpenSlideLibrary::Finalize() | |
| 233 { | |
| 234 globalLibrary_.reset(NULL); | |
| 235 } | |
| 236 } |