Mercurial > hg > orthanc-wsi
comparison Framework/Inputs/OpenSlideLibrary.cpp @ 0:4a7a53257c7d
initial commit
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Sat, 22 Oct 2016 21:48:33 +0200 |
parents | |
children | 7a88c614be04 |
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-1:000000000000 | 0:4a7a53257c7d |
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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 | |
21 #include "OpenSlideLibrary.h" | |
22 | |
23 #include "../Orthanc/Core/Logging.h" | |
24 #include "../Orthanc/Core/Images/Image.h" | |
25 | |
26 namespace OrthancWSI | |
27 { | |
28 static std::auto_ptr<OpenSlideLibrary> globalLibrary_; | |
29 | |
30 | |
31 OpenSlideLibrary::OpenSlideLibrary(const std::string& path) : | |
32 library_(path) | |
33 { | |
34 close_ = (FunctionClose) library_.GetFunction("openslide_close"); | |
35 getLevelCount_ = (FunctionGetLevelCount) library_.GetFunction("openslide_get_level_count"); | |
36 getLevelDimensions_ = (FunctionGetLevelDimensions) library_.GetFunction("openslide_get_level_dimensions"); | |
37 getLevelDownsample_ = (FunctionGetLevelDownsample) library_.GetFunction("openslide_get_level_downsample"); | |
38 open_ = (FunctionOpen) library_.GetFunction("openslide_open"); | |
39 readRegion_ = (FunctionReadRegion) library_.GetFunction("openslide_read_region"); | |
40 } | |
41 | |
42 | |
43 OpenSlideLibrary::Image::Level::Level() : | |
44 width_(0), | |
45 height_(0), | |
46 downsample_(1) | |
47 { | |
48 } | |
49 | |
50 | |
51 OpenSlideLibrary::Image::Level::Level(int64_t width, | |
52 int64_t height, | |
53 double downsample) : | |
54 width_(static_cast<unsigned int>(width)), | |
55 height_(static_cast<unsigned int>(height)), | |
56 downsample_(downsample) | |
57 { | |
58 if (width < 0 || | |
59 height < 0 || | |
60 downsample <= 0) | |
61 { | |
62 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
63 } | |
64 | |
65 if (static_cast<int64_t>(width_) != width || | |
66 static_cast<int64_t>(height_) != height) | |
67 { | |
68 LOG(ERROR) << "The whole-slide image is too large"; | |
69 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
70 } | |
71 } | |
72 | |
73 | |
74 void OpenSlideLibrary::Image::Initialize(const std::string& path) | |
75 { | |
76 handle_ = that_.open_(path.c_str()); | |
77 if (handle_ == NULL) | |
78 { | |
79 LOG(ERROR) << "Cannot open an image with OpenSlide: " << path; | |
80 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
81 } | |
82 | |
83 try | |
84 { | |
85 LOG(INFO) << "Opening an image with OpenSlide: " << path; | |
86 | |
87 int32_t tmp = that_.getLevelCount_(handle_); | |
88 if (tmp <= 0) | |
89 { | |
90 LOG(ERROR) << "Image with no pyramid level"; | |
91 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
92 } | |
93 | |
94 levels_.resize(tmp); | |
95 | |
96 for (int32_t level = 0; level < tmp; level++) | |
97 { | |
98 int64_t width, height; | |
99 that_.getLevelDimensions_(handle_, level, &width, &height); | |
100 | |
101 double downsample = that_.getLevelDownsample_(handle_, level); | |
102 | |
103 levels_[level] = Level(width, height, downsample); | |
104 } | |
105 | |
106 for (size_t i = 1; i < levels_.size(); i++) | |
107 { | |
108 if (levels_[i].width_ >= levels_[i - 1].width_ || | |
109 levels_[i].height_ >= levels_[i - 1].height_) | |
110 { | |
111 // This is not a pyramid with levels of decreasing sizes | |
112 // (level "0" must be the finest level) | |
113 LOG(ERROR) << "The pyramid does not have levels of strictly decreasing sizes"; | |
114 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
115 } | |
116 } | |
117 } | |
118 catch (Orthanc::OrthancException&) | |
119 { | |
120 Close(); | |
121 throw; | |
122 } | |
123 } | |
124 | |
125 | |
126 OpenSlideLibrary::Image::Image(OpenSlideLibrary& that, | |
127 const std::string& path) : | |
128 that_(that), | |
129 handle_(NULL) | |
130 { | |
131 Initialize(path); | |
132 } | |
133 | |
134 | |
135 OpenSlideLibrary::Image::Image(const std::string& path) : | |
136 that_(OpenSlideLibrary::GetInstance()), | |
137 handle_(NULL) | |
138 { | |
139 Initialize(path); | |
140 } | |
141 | |
142 | |
143 void OpenSlideLibrary::Image::Close() | |
144 { | |
145 if (handle_ != NULL) | |
146 { | |
147 that_.close_(handle_); | |
148 handle_ = NULL; | |
149 } | |
150 } | |
151 | |
152 | |
153 void OpenSlideLibrary::Image::CheckLevel(unsigned int level) const | |
154 { | |
155 if (level >= levels_.size()) | |
156 { | |
157 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
158 } | |
159 } | |
160 | |
161 | |
162 double OpenSlideLibrary::Image::GetLevelDownsample(unsigned int level) const | |
163 { | |
164 CheckLevel(level); | |
165 return levels_[level].downsample_; | |
166 } | |
167 | |
168 | |
169 unsigned int OpenSlideLibrary::Image::GetLevelWidth(unsigned int level) const | |
170 { | |
171 CheckLevel(level); | |
172 return levels_[level].width_; | |
173 } | |
174 | |
175 | |
176 unsigned int OpenSlideLibrary::Image::GetLevelHeight(unsigned int level) const | |
177 { | |
178 CheckLevel(level); | |
179 return levels_[level].height_; | |
180 } | |
181 | |
182 | |
183 Orthanc::ImageAccessor* OpenSlideLibrary::Image::ReadRegion(unsigned int level, | |
184 uint64_t x, | |
185 uint64_t y, | |
186 unsigned int width, | |
187 unsigned int height) | |
188 { | |
189 CheckLevel(level); | |
190 | |
191 // Create a new image, with minimal pitch so as to be compatible with OpenSlide API | |
192 std::auto_ptr<Orthanc::ImageAccessor> region(new Orthanc::Image(Orthanc::PixelFormat_RGBA32, width, height, true)); | |
193 | |
194 if (region->GetWidth() != 0 && | |
195 region->GetHeight() != 0) | |
196 { | |
197 double zoom = levels_[level].downsample_; | |
198 x = static_cast<uint64_t>(zoom * static_cast<double>(x)); | |
199 y = static_cast<uint64_t>(zoom * static_cast<double>(y)); | |
200 | |
201 that_.readRegion_(handle_, reinterpret_cast<uint32_t*>(region->GetBuffer()), | |
202 x, y, level, region->GetWidth(), region->GetHeight()); | |
203 } | |
204 | |
205 return region.release(); | |
206 } | |
207 | |
208 | |
209 OpenSlideLibrary& OpenSlideLibrary::GetInstance() | |
210 { | |
211 if (globalLibrary_.get() == NULL) | |
212 { | |
213 LOG(ERROR) << "OpenSlide has not been initialized"; | |
214 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
215 } | |
216 else | |
217 { | |
218 return *globalLibrary_; | |
219 } | |
220 } | |
221 | |
222 | |
223 void OpenSlideLibrary::Initialize(const std::string& path) | |
224 { | |
225 globalLibrary_.reset(new OpenSlideLibrary(path)); | |
226 } | |
227 | |
228 | |
229 void OpenSlideLibrary::Finalize() | |
230 { | |
231 globalLibrary_.reset(NULL); | |
232 } | |
233 } |