Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/OpenSlideLibrary.cpp @ 122:7bfcc8f04ef7
sync
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 04 Jan 2018 20:04:41 +0100 |
parents | a51dee6a1515 |
children | e8fe7c9a7d6c |
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) 2017-2018 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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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" |
0 | 27 |
28 namespace OrthancWSI | |
29 { | |
30 static std::auto_ptr<OpenSlideLibrary> globalLibrary_; | |
31 | |
32 | |
33 OpenSlideLibrary::OpenSlideLibrary(const std::string& path) : | |
34 library_(path) | |
35 { | |
36 close_ = (FunctionClose) library_.GetFunction("openslide_close"); | |
37 getLevelCount_ = (FunctionGetLevelCount) library_.GetFunction("openslide_get_level_count"); | |
38 getLevelDimensions_ = (FunctionGetLevelDimensions) library_.GetFunction("openslide_get_level_dimensions"); | |
39 getLevelDownsample_ = (FunctionGetLevelDownsample) library_.GetFunction("openslide_get_level_downsample"); | |
40 open_ = (FunctionOpen) library_.GetFunction("openslide_open"); | |
41 readRegion_ = (FunctionReadRegion) library_.GetFunction("openslide_read_region"); | |
42 } | |
43 | |
44 | |
45 OpenSlideLibrary::Image::Level::Level() : | |
46 width_(0), | |
47 height_(0), | |
48 downsample_(1) | |
49 { | |
50 } | |
51 | |
52 | |
53 OpenSlideLibrary::Image::Level::Level(int64_t width, | |
54 int64_t height, | |
55 double downsample) : | |
56 width_(static_cast<unsigned int>(width)), | |
57 height_(static_cast<unsigned int>(height)), | |
58 downsample_(downsample) | |
59 { | |
60 if (width < 0 || | |
61 height < 0 || | |
62 downsample <= 0) | |
63 { | |
64 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
65 } | |
66 | |
67 if (static_cast<int64_t>(width_) != width || | |
68 static_cast<int64_t>(height_) != height) | |
69 { | |
70 LOG(ERROR) << "The whole-slide image is too large"; | |
71 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
72 } | |
73 } | |
74 | |
75 | |
76 void OpenSlideLibrary::Image::Initialize(const std::string& path) | |
77 { | |
78 handle_ = that_.open_(path.c_str()); | |
79 if (handle_ == NULL) | |
80 { | |
81 LOG(ERROR) << "Cannot open an image with OpenSlide: " << path; | |
82 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
83 } | |
84 | |
85 try | |
86 { | |
87 LOG(INFO) << "Opening an image with OpenSlide: " << path; | |
88 | |
89 int32_t tmp = that_.getLevelCount_(handle_); | |
90 if (tmp <= 0) | |
91 { | |
92 LOG(ERROR) << "Image with no pyramid level"; | |
93 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
94 } | |
95 | |
96 levels_.resize(tmp); | |
97 | |
98 for (int32_t level = 0; level < tmp; level++) | |
99 { | |
100 int64_t width, height; | |
101 that_.getLevelDimensions_(handle_, level, &width, &height); | |
102 | |
103 double downsample = that_.getLevelDownsample_(handle_, level); | |
104 | |
105 levels_[level] = Level(width, height, downsample); | |
106 } | |
107 | |
108 for (size_t i = 1; i < levels_.size(); i++) | |
109 { | |
110 if (levels_[i].width_ >= levels_[i - 1].width_ || | |
111 levels_[i].height_ >= levels_[i - 1].height_) | |
112 { | |
113 // This is not a pyramid with levels of decreasing sizes | |
114 // (level "0" must be the finest level) | |
115 LOG(ERROR) << "The pyramid does not have levels of strictly decreasing sizes"; | |
116 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
117 } | |
118 } | |
119 } | |
120 catch (Orthanc::OrthancException&) | |
121 { | |
122 Close(); | |
123 throw; | |
124 } | |
125 } | |
126 | |
127 | |
128 OpenSlideLibrary::Image::Image(OpenSlideLibrary& that, | |
129 const std::string& path) : | |
130 that_(that), | |
131 handle_(NULL) | |
132 { | |
133 Initialize(path); | |
134 } | |
135 | |
136 | |
137 OpenSlideLibrary::Image::Image(const std::string& path) : | |
138 that_(OpenSlideLibrary::GetInstance()), | |
139 handle_(NULL) | |
140 { | |
141 Initialize(path); | |
142 } | |
143 | |
144 | |
145 void OpenSlideLibrary::Image::Close() | |
146 { | |
147 if (handle_ != NULL) | |
148 { | |
149 that_.close_(handle_); | |
150 handle_ = NULL; | |
151 } | |
152 } | |
153 | |
154 | |
155 void OpenSlideLibrary::Image::CheckLevel(unsigned int level) const | |
156 { | |
157 if (level >= levels_.size()) | |
158 { | |
159 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
160 } | |
161 } | |
162 | |
163 | |
164 double OpenSlideLibrary::Image::GetLevelDownsample(unsigned int level) const | |
165 { | |
166 CheckLevel(level); | |
167 return levels_[level].downsample_; | |
168 } | |
169 | |
170 | |
171 unsigned int OpenSlideLibrary::Image::GetLevelWidth(unsigned int level) const | |
172 { | |
173 CheckLevel(level); | |
174 return levels_[level].width_; | |
175 } | |
176 | |
177 | |
178 unsigned int OpenSlideLibrary::Image::GetLevelHeight(unsigned int level) const | |
179 { | |
180 CheckLevel(level); | |
181 return levels_[level].height_; | |
182 } | |
183 | |
184 | |
185 Orthanc::ImageAccessor* OpenSlideLibrary::Image::ReadRegion(unsigned int level, | |
186 uint64_t x, | |
187 uint64_t y, | |
188 unsigned int width, | |
189 unsigned int height) | |
190 { | |
191 CheckLevel(level); | |
192 | |
193 // Create a new image, with minimal pitch so as to be compatible with OpenSlide API | |
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194 std::auto_ptr<Orthanc::ImageAccessor> region(new Orthanc::Image(Orthanc::PixelFormat_BGRA32, width, height, true)); |
0 | 195 |
196 if (region->GetWidth() != 0 && | |
197 region->GetHeight() != 0) | |
198 { | |
199 double zoom = levels_[level].downsample_; | |
200 x = static_cast<uint64_t>(zoom * static_cast<double>(x)); | |
201 y = static_cast<uint64_t>(zoom * static_cast<double>(y)); | |
202 | |
203 that_.readRegion_(handle_, reinterpret_cast<uint32_t*>(region->GetBuffer()), | |
204 x, y, level, region->GetWidth(), region->GetHeight()); | |
205 } | |
206 | |
207 return region.release(); | |
208 } | |
209 | |
210 | |
211 OpenSlideLibrary& OpenSlideLibrary::GetInstance() | |
212 { | |
213 if (globalLibrary_.get() == NULL) | |
214 { | |
32 | 215 LOG(ERROR) << "OpenSlide has not been initialized, use the \"--openslide\" command-line option"; |
0 | 216 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
217 } | |
218 else | |
219 { | |
220 return *globalLibrary_; | |
221 } | |
222 } | |
223 | |
224 | |
225 void OpenSlideLibrary::Initialize(const std::string& path) | |
226 { | |
227 globalLibrary_.reset(new OpenSlideLibrary(path)); | |
228 } | |
229 | |
230 | |
231 void OpenSlideLibrary::Finalize() | |
232 { | |
233 globalLibrary_.reset(NULL); | |
234 } | |
235 } |