Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/OpenSlideLibrary.cpp @ 215:02cb86d07966
Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 11 Jan 2021 17:12:24 +0100 |
parents | 1e864138f0da |
children | 49f647ed1b4c |
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) 2017-2021 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 <Compatibility.h> // For std::unique_ptr |
192 | 26 #include <Logging.h> |
27 #include <Images/Image.h> | |
28 #include <OrthancException.h> | |
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30 #include <memory> |
0 | 31 |
32 namespace OrthancWSI | |
33 { | |
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34 static std::unique_ptr<OpenSlideLibrary> globalLibrary_; |
0 | 35 |
36 | |
37 OpenSlideLibrary::OpenSlideLibrary(const std::string& path) : | |
38 library_(path) | |
39 { | |
40 close_ = (FunctionClose) library_.GetFunction("openslide_close"); | |
41 getLevelCount_ = (FunctionGetLevelCount) library_.GetFunction("openslide_get_level_count"); | |
42 getLevelDimensions_ = (FunctionGetLevelDimensions) library_.GetFunction("openslide_get_level_dimensions"); | |
43 getLevelDownsample_ = (FunctionGetLevelDownsample) library_.GetFunction("openslide_get_level_downsample"); | |
44 open_ = (FunctionOpen) library_.GetFunction("openslide_open"); | |
45 readRegion_ = (FunctionReadRegion) library_.GetFunction("openslide_read_region"); | |
46 } | |
47 | |
48 | |
49 OpenSlideLibrary::Image::Level::Level() : | |
50 width_(0), | |
51 height_(0), | |
52 downsample_(1) | |
53 { | |
54 } | |
55 | |
56 | |
57 OpenSlideLibrary::Image::Level::Level(int64_t width, | |
58 int64_t height, | |
59 double downsample) : | |
60 width_(static_cast<unsigned int>(width)), | |
61 height_(static_cast<unsigned int>(height)), | |
62 downsample_(downsample) | |
63 { | |
64 if (width < 0 || | |
65 height < 0 || | |
66 downsample <= 0) | |
67 { | |
68 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
69 } | |
70 | |
71 if (static_cast<int64_t>(width_) != width || | |
72 static_cast<int64_t>(height_) != height) | |
73 { | |
74 LOG(ERROR) << "The whole-slide image is too large"; | |
75 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
76 } | |
77 } | |
78 | |
79 | |
80 void OpenSlideLibrary::Image::Initialize(const std::string& path) | |
81 { | |
82 handle_ = that_.open_(path.c_str()); | |
83 if (handle_ == NULL) | |
84 { | |
85 LOG(ERROR) << "Cannot open an image with OpenSlide: " << path; | |
86 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
87 } | |
88 | |
89 try | |
90 { | |
91 LOG(INFO) << "Opening an image with OpenSlide: " << path; | |
92 | |
93 int32_t tmp = that_.getLevelCount_(handle_); | |
94 if (tmp <= 0) | |
95 { | |
96 LOG(ERROR) << "Image with no pyramid level"; | |
97 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
98 } | |
99 | |
100 levels_.resize(tmp); | |
101 | |
102 for (int32_t level = 0; level < tmp; level++) | |
103 { | |
104 int64_t width, height; | |
105 that_.getLevelDimensions_(handle_, level, &width, &height); | |
106 | |
107 double downsample = that_.getLevelDownsample_(handle_, level); | |
108 | |
109 levels_[level] = Level(width, height, downsample); | |
110 } | |
111 | |
112 for (size_t i = 1; i < levels_.size(); i++) | |
113 { | |
114 if (levels_[i].width_ >= levels_[i - 1].width_ || | |
115 levels_[i].height_ >= levels_[i - 1].height_) | |
116 { | |
117 // This is not a pyramid with levels of decreasing sizes | |
118 // (level "0" must be the finest level) | |
119 LOG(ERROR) << "The pyramid does not have levels of strictly decreasing sizes"; | |
120 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
121 } | |
122 } | |
123 } | |
124 catch (Orthanc::OrthancException&) | |
125 { | |
126 Close(); | |
127 throw; | |
128 } | |
129 } | |
130 | |
131 | |
132 OpenSlideLibrary::Image::Image(OpenSlideLibrary& that, | |
133 const std::string& path) : | |
134 that_(that), | |
135 handle_(NULL) | |
136 { | |
137 Initialize(path); | |
138 } | |
139 | |
140 | |
141 OpenSlideLibrary::Image::Image(const std::string& path) : | |
142 that_(OpenSlideLibrary::GetInstance()), | |
143 handle_(NULL) | |
144 { | |
145 Initialize(path); | |
146 } | |
147 | |
148 | |
149 void OpenSlideLibrary::Image::Close() | |
150 { | |
151 if (handle_ != NULL) | |
152 { | |
153 that_.close_(handle_); | |
154 handle_ = NULL; | |
155 } | |
156 } | |
157 | |
158 | |
159 void OpenSlideLibrary::Image::CheckLevel(unsigned int level) const | |
160 { | |
161 if (level >= levels_.size()) | |
162 { | |
163 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
164 } | |
165 } | |
166 | |
167 | |
168 double OpenSlideLibrary::Image::GetLevelDownsample(unsigned int level) const | |
169 { | |
170 CheckLevel(level); | |
171 return levels_[level].downsample_; | |
172 } | |
173 | |
174 | |
175 unsigned int OpenSlideLibrary::Image::GetLevelWidth(unsigned int level) const | |
176 { | |
177 CheckLevel(level); | |
178 return levels_[level].width_; | |
179 } | |
180 | |
181 | |
182 unsigned int OpenSlideLibrary::Image::GetLevelHeight(unsigned int level) const | |
183 { | |
184 CheckLevel(level); | |
185 return levels_[level].height_; | |
186 } | |
187 | |
188 | |
189 Orthanc::ImageAccessor* OpenSlideLibrary::Image::ReadRegion(unsigned int level, | |
190 uint64_t x, | |
191 uint64_t y, | |
192 unsigned int width, | |
193 unsigned int height) | |
194 { | |
195 CheckLevel(level); | |
196 | |
197 // Create a new image, with minimal pitch so as to be compatible with OpenSlide API | |
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198 std::unique_ptr<Orthanc::ImageAccessor> region(new Orthanc::Image(Orthanc::PixelFormat_BGRA32, width, height, true)); |
0 | 199 |
200 if (region->GetWidth() != 0 && | |
201 region->GetHeight() != 0) | |
202 { | |
203 double zoom = levels_[level].downsample_; | |
204 x = static_cast<uint64_t>(zoom * static_cast<double>(x)); | |
205 y = static_cast<uint64_t>(zoom * static_cast<double>(y)); | |
206 | |
207 that_.readRegion_(handle_, reinterpret_cast<uint32_t*>(region->GetBuffer()), | |
208 x, y, level, region->GetWidth(), region->GetHeight()); | |
209 } | |
210 | |
211 return region.release(); | |
212 } | |
213 | |
214 | |
215 OpenSlideLibrary& OpenSlideLibrary::GetInstance() | |
216 { | |
217 if (globalLibrary_.get() == NULL) | |
218 { | |
32 | 219 LOG(ERROR) << "OpenSlide has not been initialized, use the \"--openslide\" command-line option"; |
0 | 220 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
221 } | |
222 else | |
223 { | |
224 return *globalLibrary_; | |
225 } | |
226 } | |
227 | |
228 | |
229 void OpenSlideLibrary::Initialize(const std::string& path) | |
230 { | |
231 globalLibrary_.reset(new OpenSlideLibrary(path)); | |
232 } | |
233 | |
234 | |
235 void OpenSlideLibrary::Finalize() | |
236 { | |
237 globalLibrary_.reset(NULL); | |
238 } | |
239 } |