Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/HierarchicalTiff.cpp @ 309:7020852a8fa9
updated year to 2024
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Fri, 22 Mar 2024 15:48:12 +0100 |
parents | c1687b8fc800 |
children | 0683312e21ba |
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 | |
309
7020852a8fa9
updated year to 2024
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
297
diff
changeset
|
5 * Copyright (C) 2017-2024 Osimis S.A., Belgium |
7020852a8fa9
updated year to 2024
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
297
diff
changeset
|
6 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
9 * modify it under the terms of the GNU Affero General Public License | |
10 * as published by the Free Software Foundation, either version 3 of | |
11 * the License, or (at your option) any later version. | |
12 * | |
13 * This program is distributed in the hope that it will be useful, but | |
14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
16 * Affero General Public License for more details. | |
17 * | |
18 * You should have received a copy of the GNU Affero General Public License | |
19 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
20 **/ | |
21 | |
22 | |
16
7a88c614be04
preparing for precompiled headers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
23 #include "../PrecompiledHeadersWSI.h" |
0 | 24 #include "HierarchicalTiff.h" |
25 | |
192 | 26 #include <Logging.h> |
27 #include <OrthancException.h> | |
0 | 28 |
29 #include <iostream> | |
30 #include <algorithm> | |
31 #include <cassert> | |
32 #include <string.h> | |
33 | |
34 namespace OrthancWSI | |
35 { | |
36 HierarchicalTiff::Level::Level(TIFF* tiff, | |
37 tdir_t directory, | |
38 unsigned int width, | |
39 unsigned int height) : | |
40 directory_(directory), | |
41 width_(width), | |
42 height_(height) | |
43 { | |
44 // Read the JPEG headers shared at that level, if any | |
45 uint8_t *tables = NULL; | |
46 uint32_t size; | |
47 if (TIFFGetField(tiff, TIFFTAG_JPEGTABLES, &size, &tables) && | |
48 size > 0 && | |
49 tables != NULL) | |
50 { | |
51 // Look for the EOI (end-of-image) tag == FF D9 | |
52 // https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format | |
53 | |
54 bool found = false; | |
55 | |
56 for (size_t i = 0; i + 1 < size; i++) | |
57 { | |
58 if (tables[i] == 0xff && | |
59 tables[i + 1] == 0xd9) | |
60 { | |
61 headers_.assign(reinterpret_cast<const char*>(tables), i); | |
62 found = true; | |
63 } | |
64 } | |
65 | |
66 if (!found) | |
67 { | |
68 headers_.assign(reinterpret_cast<const char*>(tables), size); | |
69 } | |
70 } | |
71 } | |
72 | |
73 struct HierarchicalTiff::Comparator | |
74 { | |
75 bool operator() (const HierarchicalTiff::Level& a, | |
76 const HierarchicalTiff::Level& b) const | |
77 { | |
78 return a.width_ > b.width_; | |
79 } | |
80 }; | |
81 | |
82 | |
83 void HierarchicalTiff::CheckLevel(unsigned int level) const | |
84 { | |
85 if (level >= levels_.size()) | |
86 { | |
87 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
88 } | |
89 } | |
90 | |
91 | |
297 | 92 HierarchicalTiff::HierarchicalTiff(const std::string& path) : |
93 reader_(path), | |
94 tileWidth_(0), | |
95 tileHeight_(0) | |
0 | 96 { |
97 bool first = true; | |
98 tdir_t pos = 0; | |
99 | |
100 do | |
101 { | |
102 uint32_t w, h, tw, th; | |
103 ImageCompression compression; | |
104 Orthanc::PixelFormat pixelFormat; | |
166
f0dac1e8f736
access to photometric interpretation of source pyramids
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
105 Orthanc::PhotometricInterpretation photometric; |
0 | 106 |
297 | 107 if (TIFFSetDirectory(reader_.GetTiff(), pos) && |
108 TIFFGetField(reader_.GetTiff(), TIFFTAG_IMAGEWIDTH, &w) && | |
109 TIFFGetField(reader_.GetTiff(), TIFFTAG_IMAGELENGTH, &h) && | |
110 TIFFGetField(reader_.GetTiff(), TIFFTAG_TILEWIDTH, &tw) && | |
111 TIFFGetField(reader_.GetTiff(), TIFFTAG_TILELENGTH, &th) && | |
0 | 112 w > 0 && |
113 h > 0 && | |
114 tw > 0 && | |
115 th > 0 && | |
297 | 116 reader_.GetCurrentDirectoryInformation(compression, pixelFormat, photometric)) |
0 | 117 { |
118 if (first) | |
119 { | |
120 tileWidth_ = tw; | |
121 tileHeight_ = th; | |
122 compression_ = compression; | |
123 pixelFormat_ = pixelFormat; | |
166
f0dac1e8f736
access to photometric interpretation of source pyramids
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
124 photometric_ = photometric; |
0 | 125 first = false; |
126 } | |
127 else if (tw != tileWidth_ || | |
128 th != tileHeight_ || | |
129 compression_ != compression || | |
166
f0dac1e8f736
access to photometric interpretation of source pyramids
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
130 pixelFormat_ != pixelFormat || |
f0dac1e8f736
access to photometric interpretation of source pyramids
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
131 photometric_ != photometric) |
0 | 132 { |
297 | 133 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
134 "The tile size or compression of the TIFF file varies along levels, this is not supported"); | |
0 | 135 } |
136 | |
297 | 137 levels_.push_back(Level(reader_.GetTiff(), pos, w, h)); |
0 | 138 } |
139 | |
140 pos++; | |
141 } | |
297 | 142 while (TIFFReadDirectory(reader_.GetTiff())); |
0 | 143 |
144 if (levels_.size() == 0) | |
145 { | |
297 | 146 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "This is not a tiled TIFF image"); |
0 | 147 } |
148 | |
149 std::sort(levels_.begin(), levels_.end(), Comparator()); | |
150 } | |
151 | |
152 | |
153 unsigned int HierarchicalTiff::GetLevelWidth(unsigned int level) const | |
154 { | |
155 CheckLevel(level); | |
156 return levels_[level].width_; | |
157 } | |
158 | |
159 | |
160 unsigned int HierarchicalTiff::GetLevelHeight(unsigned int level) const | |
161 { | |
162 CheckLevel(level); | |
163 return levels_[level].height_; | |
164 } | |
165 | |
166 | |
167 bool HierarchicalTiff::ReadRawTile(std::string& tile, | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
168 ImageCompression& compression, |
0 | 169 unsigned int level, |
170 unsigned int tileX, | |
171 unsigned int tileY) | |
172 { | |
173 boost::mutex::scoped_lock lock(mutex_); | |
174 | |
175 CheckLevel(level); | |
176 | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
177 compression = compression_; |
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
178 |
0 | 179 // Make the TIFF context point to the level of interest |
297 | 180 if (!TIFFSetDirectory(reader_.GetTiff(), levels_[level].directory_)) |
0 | 181 { |
182 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
183 } | |
184 | |
185 // Get the index of the tile | |
297 | 186 ttile_t index = TIFFComputeTile(reader_.GetTiff(), tileX * tileWidth_, tileY * tileHeight_, 0 /*z*/, 0 /*sample*/); |
0 | 187 |
188 // Read the raw tile | |
189 toff_t *sizes; | |
297 | 190 if (!TIFFGetField(reader_.GetTiff(), TIFFTAG_TILEBYTECOUNTS, &sizes)) |
0 | 191 { |
192 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
193 } | |
194 | |
195 std::string raw; | |
196 raw.resize(sizes[index]); | |
197 | |
297 | 198 tsize_t read = TIFFReadRawTile(reader_.GetTiff(), index, &raw[0], raw.size()); |
0 | 199 if (read != static_cast<tsize_t>(sizes[index])) |
200 { | |
201 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
202 } | |
203 | |
204 const std::string& headers = levels_[level].headers_; | |
205 | |
206 // Possibly prepend the raw tile with the shared JPEG headers | |
207 if (headers.empty() || | |
208 compression_ != ImageCompression_Jpeg) | |
209 { | |
210 tile.swap(raw); // Same as "tile.assign(raw)", but optimizes memory | |
211 } | |
212 else | |
213 { | |
214 assert(compression_ == ImageCompression_Jpeg); | |
215 | |
216 // Check that the raw JPEG tile starts with the SOI (start-of-image) tag == FF D8 | |
217 if (raw.size() < 2 || | |
218 static_cast<uint8_t>(raw[0]) != 0xff || | |
219 static_cast<uint8_t>(raw[1]) != 0xd8) | |
220 { | |
221 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
222 } | |
223 | |
218
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
224 if (photometric_ == Orthanc::PhotometricInterpretation_RGB && |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
225 pixelFormat_ == Orthanc::PixelFormat_RGB24) |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
226 { |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
227 /** |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
228 * Insert an Adobe APP14 marker with the "transform" flag set |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
229 * to value 0, which indicates to the JPEG decoder that |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
230 * "3-channel images are assumed to be RGB". Section 18 of |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
231 * "Supporting the DCT Filters in PostScript Level 2 - |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
232 * Technical Note #5116": |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
233 * https://stackoverflow.com/a/9658206/881731 |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
234 * https://docs.oracle.com/javase/6/docs/api/javax/imageio/metadata/doc-files/jpeg_metadata.html |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
235 * https://www.pdfa.org/wp-content/uploads/2020/07/5116.DCT_Filter.pdf |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
236 **/ |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
237 static const uint8_t APP14[] = { |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
238 0xff, 0xee, /* JPEG Marker for Adobe segment: http://www.ozhiker.com/electronics/pjmt/jpeg_info/app_segments.html */ |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
239 0x00, 0x0e, /* Length (without the JPEG marker) == 0x0e == 14 bytes */ |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
240 0x41, 0x64, 0x6f, 0x62, 0x65, /* "Adobe" string in ASCII */ |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
241 0x00, 0x64, /* Version == Two-byte DCTEncode/DCTDecode version number == 0x64 */ |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
242 0x80, 0x00, /* Two-byte "flags0" 0x8000 bit: Encoder used Blend=1 downsampling */ |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
243 0x00, 0x00, /* Two-byte "flags1": Set to zero */ |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
244 0x00 /* One-byte color transform code == 0 <== This is the important one */ |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
245 }; |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
246 assert(sizeof(APP14) == 16); |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
247 |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
248 tile.resize(headers.size() + sizeof(APP14) + raw.size() - 2); |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
249 memcpy(&tile[0], &headers[0], headers.size()); |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
250 memcpy(&tile[0] + headers.size(), APP14, sizeof(APP14)); |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
251 memcpy(&tile[0] + headers.size() + sizeof(APP14), &raw[2], raw.size() - 2); |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
252 } |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
253 else |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
254 { |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
255 tile.resize(headers.size() + raw.size() - 2); |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
256 memcpy(&tile[0], &headers[0], headers.size()); |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
257 memcpy(&tile[0] + headers.size(), &raw[2], raw.size() - 2); |
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
258 } |
0 | 259 } |
218
c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
260 |
0 | 261 return true; |
262 } | |
263 } |