Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/OpenSlideLibrary.cpp @ 64:63d0a5c74460
DicomPyramidInstance::Serialize
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 25 Nov 2016 18:34:17 +0100 |
| parents | 7a3853d51c45 |
| children | ff0ef01c332c |
| 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 | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU Affero General Public License | |
| 8 * as published by the Free Software Foundation, either version 3 of | |
| 9 * the License, or (at your option) any later version. | |
| 10 * | |
| 11 * This program is distributed in the hope that it will be useful, but | |
| 12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 14 * Affero General Public License for more details. | |
| 15 * | |
| 16 * You should have received a copy of the GNU Affero General Public License | |
| 17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 **/ | |
| 19 | |
| 20 | |
|
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7a88c614be04
preparing for precompiled headers
Sebastien Jodogne <s.jodogne@gmail.com>
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21 #include "../PrecompiledHeadersWSI.h" |
| 0 | 22 #include "OpenSlideLibrary.h" |
| 23 | |
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7a3853d51c45
Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
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24 #include "../../Resources/Orthanc/Core/Logging.h" |
|
7a3853d51c45
Move "Framework/Orthanc/" as "Resources/Orthanc/"
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25 #include "../../Resources/Orthanc/Core/Images/Image.h" |
| 0 | 26 |
| 27 namespace OrthancWSI | |
| 28 { | |
| 29 static std::auto_ptr<OpenSlideLibrary> globalLibrary_; | |
| 30 | |
| 31 | |
| 32 OpenSlideLibrary::OpenSlideLibrary(const std::string& path) : | |
| 33 library_(path) | |
| 34 { | |
| 35 close_ = (FunctionClose) library_.GetFunction("openslide_close"); | |
| 36 getLevelCount_ = (FunctionGetLevelCount) library_.GetFunction("openslide_get_level_count"); | |
| 37 getLevelDimensions_ = (FunctionGetLevelDimensions) library_.GetFunction("openslide_get_level_dimensions"); | |
| 38 getLevelDownsample_ = (FunctionGetLevelDownsample) library_.GetFunction("openslide_get_level_downsample"); | |
| 39 open_ = (FunctionOpen) library_.GetFunction("openslide_open"); | |
| 40 readRegion_ = (FunctionReadRegion) library_.GetFunction("openslide_read_region"); | |
| 41 } | |
| 42 | |
| 43 | |
| 44 OpenSlideLibrary::Image::Level::Level() : | |
| 45 width_(0), | |
| 46 height_(0), | |
| 47 downsample_(1) | |
| 48 { | |
| 49 } | |
| 50 | |
| 51 | |
| 52 OpenSlideLibrary::Image::Level::Level(int64_t width, | |
| 53 int64_t height, | |
| 54 double downsample) : | |
| 55 width_(static_cast<unsigned int>(width)), | |
| 56 height_(static_cast<unsigned int>(height)), | |
| 57 downsample_(downsample) | |
| 58 { | |
| 59 if (width < 0 || | |
| 60 height < 0 || | |
| 61 downsample <= 0) | |
| 62 { | |
| 63 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 64 } | |
| 65 | |
| 66 if (static_cast<int64_t>(width_) != width || | |
| 67 static_cast<int64_t>(height_) != height) | |
| 68 { | |
| 69 LOG(ERROR) << "The whole-slide image is too large"; | |
| 70 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 71 } | |
| 72 } | |
| 73 | |
| 74 | |
| 75 void OpenSlideLibrary::Image::Initialize(const std::string& path) | |
| 76 { | |
| 77 handle_ = that_.open_(path.c_str()); | |
| 78 if (handle_ == NULL) | |
| 79 { | |
| 80 LOG(ERROR) << "Cannot open an image with OpenSlide: " << path; | |
| 81 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 82 } | |
| 83 | |
| 84 try | |
| 85 { | |
| 86 LOG(INFO) << "Opening an image with OpenSlide: " << path; | |
| 87 | |
| 88 int32_t tmp = that_.getLevelCount_(handle_); | |
| 89 if (tmp <= 0) | |
| 90 { | |
| 91 LOG(ERROR) << "Image with no pyramid level"; | |
| 92 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 93 } | |
| 94 | |
| 95 levels_.resize(tmp); | |
| 96 | |
| 97 for (int32_t level = 0; level < tmp; level++) | |
| 98 { | |
| 99 int64_t width, height; | |
| 100 that_.getLevelDimensions_(handle_, level, &width, &height); | |
| 101 | |
| 102 double downsample = that_.getLevelDownsample_(handle_, level); | |
| 103 | |
| 104 levels_[level] = Level(width, height, downsample); | |
| 105 } | |
| 106 | |
| 107 for (size_t i = 1; i < levels_.size(); i++) | |
| 108 { | |
| 109 if (levels_[i].width_ >= levels_[i - 1].width_ || | |
| 110 levels_[i].height_ >= levels_[i - 1].height_) | |
| 111 { | |
| 112 // This is not a pyramid with levels of decreasing sizes | |
| 113 // (level "0" must be the finest level) | |
| 114 LOG(ERROR) << "The pyramid does not have levels of strictly decreasing sizes"; | |
| 115 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 116 } | |
| 117 } | |
| 118 } | |
| 119 catch (Orthanc::OrthancException&) | |
| 120 { | |
| 121 Close(); | |
| 122 throw; | |
| 123 } | |
| 124 } | |
| 125 | |
| 126 | |
| 127 OpenSlideLibrary::Image::Image(OpenSlideLibrary& that, | |
| 128 const std::string& path) : | |
| 129 that_(that), | |
| 130 handle_(NULL) | |
| 131 { | |
| 132 Initialize(path); | |
| 133 } | |
| 134 | |
| 135 | |
| 136 OpenSlideLibrary::Image::Image(const std::string& path) : | |
| 137 that_(OpenSlideLibrary::GetInstance()), | |
| 138 handle_(NULL) | |
| 139 { | |
| 140 Initialize(path); | |
| 141 } | |
| 142 | |
| 143 | |
| 144 void OpenSlideLibrary::Image::Close() | |
| 145 { | |
| 146 if (handle_ != NULL) | |
| 147 { | |
| 148 that_.close_(handle_); | |
| 149 handle_ = NULL; | |
| 150 } | |
| 151 } | |
| 152 | |
| 153 | |
| 154 void OpenSlideLibrary::Image::CheckLevel(unsigned int level) const | |
| 155 { | |
| 156 if (level >= levels_.size()) | |
| 157 { | |
| 158 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 159 } | |
| 160 } | |
| 161 | |
| 162 | |
| 163 double OpenSlideLibrary::Image::GetLevelDownsample(unsigned int level) const | |
| 164 { | |
| 165 CheckLevel(level); | |
| 166 return levels_[level].downsample_; | |
| 167 } | |
| 168 | |
| 169 | |
| 170 unsigned int OpenSlideLibrary::Image::GetLevelWidth(unsigned int level) const | |
| 171 { | |
| 172 CheckLevel(level); | |
| 173 return levels_[level].width_; | |
| 174 } | |
| 175 | |
| 176 | |
| 177 unsigned int OpenSlideLibrary::Image::GetLevelHeight(unsigned int level) const | |
| 178 { | |
| 179 CheckLevel(level); | |
| 180 return levels_[level].height_; | |
| 181 } | |
| 182 | |
| 183 | |
| 184 Orthanc::ImageAccessor* OpenSlideLibrary::Image::ReadRegion(unsigned int level, | |
| 185 uint64_t x, | |
| 186 uint64_t y, | |
| 187 unsigned int width, | |
| 188 unsigned int height) | |
| 189 { | |
| 190 CheckLevel(level); | |
| 191 | |
| 192 // Create a new image, with minimal pitch so as to be compatible with OpenSlide API | |
| 193 std::auto_ptr<Orthanc::ImageAccessor> region(new Orthanc::Image(Orthanc::PixelFormat_RGBA32, width, height, true)); | |
| 194 | |
| 195 if (region->GetWidth() != 0 && | |
| 196 region->GetHeight() != 0) | |
| 197 { | |
| 198 double zoom = levels_[level].downsample_; | |
| 199 x = static_cast<uint64_t>(zoom * static_cast<double>(x)); | |
| 200 y = static_cast<uint64_t>(zoom * static_cast<double>(y)); | |
| 201 | |
| 202 that_.readRegion_(handle_, reinterpret_cast<uint32_t*>(region->GetBuffer()), | |
| 203 x, y, level, region->GetWidth(), region->GetHeight()); | |
| 204 } | |
| 205 | |
| 206 return region.release(); | |
| 207 } | |
| 208 | |
| 209 | |
| 210 OpenSlideLibrary& OpenSlideLibrary::GetInstance() | |
| 211 { | |
| 212 if (globalLibrary_.get() == NULL) | |
| 213 { | |
| 32 | 214 LOG(ERROR) << "OpenSlide has not been initialized, use the \"--openslide\" command-line option"; |
| 0 | 215 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 216 } | |
| 217 else | |
| 218 { | |
| 219 return *globalLibrary_; | |
| 220 } | |
| 221 } | |
| 222 | |
| 223 | |
| 224 void OpenSlideLibrary::Initialize(const std::string& path) | |
| 225 { | |
| 226 globalLibrary_.reset(new OpenSlideLibrary(path)); | |
| 227 } | |
| 228 | |
| 229 | |
| 230 void OpenSlideLibrary::Finalize() | |
| 231 { | |
| 232 globalLibrary_.reset(NULL); | |
| 233 } | |
| 234 } |