Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/OpenSlideLibrary.cpp @ 161:dd736430e3a4 OrthancWSI-0.6
OrthancWSI-0.6
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Sat, 26 Jan 2019 10:48:48 +0100 |
parents | 6b8ccfc02051 |
children | e3cbf890b588 |
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 | |
157 | 5 * Copyright (C) 2017-2019 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 | |
16
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22 #include "../PrecompiledHeadersWSI.h" |
0 | 23 #include "OpenSlideLibrary.h" |
24 | |
140
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25 #include <Core/Logging.h> |
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26 #include <Core/Images/Image.h> |
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27 #include <Core/OrthancException.h> |
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28 |
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29 #include <memory> |
0 | 30 |
31 namespace OrthancWSI | |
32 { | |
33 static std::auto_ptr<OpenSlideLibrary> globalLibrary_; | |
34 | |
35 | |
36 OpenSlideLibrary::OpenSlideLibrary(const std::string& path) : | |
37 library_(path) | |
38 { | |
39 close_ = (FunctionClose) library_.GetFunction("openslide_close"); | |
40 getLevelCount_ = (FunctionGetLevelCount) library_.GetFunction("openslide_get_level_count"); | |
41 getLevelDimensions_ = (FunctionGetLevelDimensions) library_.GetFunction("openslide_get_level_dimensions"); | |
42 getLevelDownsample_ = (FunctionGetLevelDownsample) library_.GetFunction("openslide_get_level_downsample"); | |
43 open_ = (FunctionOpen) library_.GetFunction("openslide_open"); | |
44 readRegion_ = (FunctionReadRegion) library_.GetFunction("openslide_read_region"); | |
45 } | |
46 | |
47 | |
48 OpenSlideLibrary::Image::Level::Level() : | |
49 width_(0), | |
50 height_(0), | |
51 downsample_(1) | |
52 { | |
53 } | |
54 | |
55 | |
56 OpenSlideLibrary::Image::Level::Level(int64_t width, | |
57 int64_t height, | |
58 double downsample) : | |
59 width_(static_cast<unsigned int>(width)), | |
60 height_(static_cast<unsigned int>(height)), | |
61 downsample_(downsample) | |
62 { | |
63 if (width < 0 || | |
64 height < 0 || | |
65 downsample <= 0) | |
66 { | |
67 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
68 } | |
69 | |
70 if (static_cast<int64_t>(width_) != width || | |
71 static_cast<int64_t>(height_) != height) | |
72 { | |
73 LOG(ERROR) << "The whole-slide image is too large"; | |
74 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
75 } | |
76 } | |
77 | |
78 | |
79 void OpenSlideLibrary::Image::Initialize(const std::string& path) | |
80 { | |
81 handle_ = that_.open_(path.c_str()); | |
82 if (handle_ == NULL) | |
83 { | |
84 LOG(ERROR) << "Cannot open an image with OpenSlide: " << path; | |
85 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
86 } | |
87 | |
88 try | |
89 { | |
90 LOG(INFO) << "Opening an image with OpenSlide: " << path; | |
91 | |
92 int32_t tmp = that_.getLevelCount_(handle_); | |
93 if (tmp <= 0) | |
94 { | |
95 LOG(ERROR) << "Image with no pyramid level"; | |
96 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
97 } | |
98 | |
99 levels_.resize(tmp); | |
100 | |
101 for (int32_t level = 0; level < tmp; level++) | |
102 { | |
103 int64_t width, height; | |
104 that_.getLevelDimensions_(handle_, level, &width, &height); | |
105 | |
106 double downsample = that_.getLevelDownsample_(handle_, level); | |
107 | |
108 levels_[level] = Level(width, height, downsample); | |
109 } | |
110 | |
111 for (size_t i = 1; i < levels_.size(); i++) | |
112 { | |
113 if (levels_[i].width_ >= levels_[i - 1].width_ || | |
114 levels_[i].height_ >= levels_[i - 1].height_) | |
115 { | |
116 // This is not a pyramid with levels of decreasing sizes | |
117 // (level "0" must be the finest level) | |
118 LOG(ERROR) << "The pyramid does not have levels of strictly decreasing sizes"; | |
119 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
120 } | |
121 } | |
122 } | |
123 catch (Orthanc::OrthancException&) | |
124 { | |
125 Close(); | |
126 throw; | |
127 } | |
128 } | |
129 | |
130 | |
131 OpenSlideLibrary::Image::Image(OpenSlideLibrary& that, | |
132 const std::string& path) : | |
133 that_(that), | |
134 handle_(NULL) | |
135 { | |
136 Initialize(path); | |
137 } | |
138 | |
139 | |
140 OpenSlideLibrary::Image::Image(const std::string& path) : | |
141 that_(OpenSlideLibrary::GetInstance()), | |
142 handle_(NULL) | |
143 { | |
144 Initialize(path); | |
145 } | |
146 | |
147 | |
148 void OpenSlideLibrary::Image::Close() | |
149 { | |
150 if (handle_ != NULL) | |
151 { | |
152 that_.close_(handle_); | |
153 handle_ = NULL; | |
154 } | |
155 } | |
156 | |
157 | |
158 void OpenSlideLibrary::Image::CheckLevel(unsigned int level) const | |
159 { | |
160 if (level >= levels_.size()) | |
161 { | |
162 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
163 } | |
164 } | |
165 | |
166 | |
167 double OpenSlideLibrary::Image::GetLevelDownsample(unsigned int level) const | |
168 { | |
169 CheckLevel(level); | |
170 return levels_[level].downsample_; | |
171 } | |
172 | |
173 | |
174 unsigned int OpenSlideLibrary::Image::GetLevelWidth(unsigned int level) const | |
175 { | |
176 CheckLevel(level); | |
177 return levels_[level].width_; | |
178 } | |
179 | |
180 | |
181 unsigned int OpenSlideLibrary::Image::GetLevelHeight(unsigned int level) const | |
182 { | |
183 CheckLevel(level); | |
184 return levels_[level].height_; | |
185 } | |
186 | |
187 | |
188 Orthanc::ImageAccessor* OpenSlideLibrary::Image::ReadRegion(unsigned int level, | |
189 uint64_t x, | |
190 uint64_t y, | |
191 unsigned int width, | |
192 unsigned int height) | |
193 { | |
194 CheckLevel(level); | |
195 | |
196 // Create a new image, with minimal pitch so as to be compatible with OpenSlide API | |
100
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197 std::auto_ptr<Orthanc::ImageAccessor> region(new Orthanc::Image(Orthanc::PixelFormat_BGRA32, width, height, true)); |
0 | 198 |
199 if (region->GetWidth() != 0 && | |
200 region->GetHeight() != 0) | |
201 { | |
202 double zoom = levels_[level].downsample_; | |
203 x = static_cast<uint64_t>(zoom * static_cast<double>(x)); | |
204 y = static_cast<uint64_t>(zoom * static_cast<double>(y)); | |
205 | |
206 that_.readRegion_(handle_, reinterpret_cast<uint32_t*>(region->GetBuffer()), | |
207 x, y, level, region->GetWidth(), region->GetHeight()); | |
208 } | |
209 | |
210 return region.release(); | |
211 } | |
212 | |
213 | |
214 OpenSlideLibrary& OpenSlideLibrary::GetInstance() | |
215 { | |
216 if (globalLibrary_.get() == NULL) | |
217 { | |
32 | 218 LOG(ERROR) << "OpenSlide has not been initialized, use the \"--openslide\" command-line option"; |
0 | 219 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
220 } | |
221 else | |
222 { | |
223 return *globalLibrary_; | |
224 } | |
225 } | |
226 | |
227 | |
228 void OpenSlideLibrary::Initialize(const std::string& path) | |
229 { | |
230 globalLibrary_.reset(new OpenSlideLibrary(path)); | |
231 } | |
232 | |
233 | |
234 void OpenSlideLibrary::Finalize() | |
235 { | |
236 globalLibrary_.reset(NULL); | |
237 } | |
238 } |