Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 314:0a1ad7492050
update year to 2024
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 22 Mar 2024 15:45:07 +0100 |
parents | d959cf2a8d5c |
children | 591ca447ebf8 |
rev | line source |
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0 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
122 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
0 | 4 * Department, University Hospital of Liege, Belgium |
303 | 5 * Copyright (C) 2017-2022 Osimis S.A., Belgium |
314
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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 | |
23 #include "DecodedImageAdapter.h" | |
24 | |
25 #include "ViewerToolbox.h" | |
26 | |
266
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27 #include <Images/ImageBuffer.h> |
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28 #include <Images/ImageProcessing.h> |
287 | 29 #include <Logging.h> |
266
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30 #include <OrthancException.h> |
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31 #include <Toolbox.h> |
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32 |
0 | 33 #include <boost/lexical_cast.hpp> |
34 #include <boost/algorithm/string/predicate.hpp> | |
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35 #include <boost/regex.hpp> |
0 | 36 |
103 | 37 |
0 | 38 namespace OrthancPlugins |
39 { | |
160 | 40 static bool GetStringTag(std::string& value, |
41 const Json::Value& tags, | |
42 const std::string& tag) | |
43 { | |
44 if (tags.type() == Json::objectValue && | |
45 tags.isMember(tag) && | |
46 tags[tag].type() == Json::objectValue && | |
47 tags[tag].isMember("Type") && | |
48 tags[tag].isMember("Value") && | |
49 tags[tag]["Type"].type() == Json::stringValue && | |
50 tags[tag]["Value"].type() == Json::stringValue && | |
51 tags[tag]["Type"].asString() == "String") | |
52 { | |
53 value = tags[tag]["Value"].asString(); | |
54 return true; | |
55 } | |
56 else | |
57 { | |
58 return false; | |
59 } | |
60 } | |
61 | |
62 | |
63 static float GetFloatTag(const Json::Value& tags, | |
64 const std::string& tag, | |
65 float defaultValue) | |
66 { | |
67 std::string tmp; | |
68 if (GetStringTag(tmp, tags, tag)) | |
69 { | |
70 try | |
71 { | |
72 return boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tmp)); | |
73 } | |
74 catch (boost::bad_lexical_cast&) | |
75 { | |
76 } | |
77 } | |
78 | |
79 return defaultValue; | |
80 } | |
81 | |
82 | |
0 | 83 bool DecodedImageAdapter::ParseUri(CompressionType& type, |
84 uint8_t& compressionLevel, | |
85 std::string& instanceId, | |
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86 unsigned int& frameIndex, |
0 | 87 const std::string& uri) |
88 { | |
99
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89 boost::regex pattern("^([a-z0-9]+)-([a-z0-9-]+)_([0-9]+)$"); |
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90 |
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91 boost::cmatch what; |
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92 if (!regex_match(uri.c_str(), what, pattern)) |
0 | 93 { |
94 return false; | |
95 } | |
99
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96 |
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97 std::string compression(what[1]); |
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98 instanceId = what[2]; |
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99 frameIndex = boost::lexical_cast<unsigned int>(what[3]); |
0 | 100 |
101 if (compression == "deflate") | |
102 { | |
103 type = CompressionType_Deflate; | |
104 } | |
105 else if (boost::starts_with(compression, "jpeg")) | |
106 { | |
107 type = CompressionType_Jpeg; | |
108 int level = boost::lexical_cast<int>(compression.substr(4)); | |
109 if (level <= 0 || level > 100) | |
110 { | |
111 return false; | |
112 } | |
113 | |
114 compressionLevel = static_cast<uint8_t>(level); | |
115 } | |
116 else | |
117 { | |
118 return false; | |
119 } | |
120 | |
121 return true; | |
122 } | |
123 | |
124 | |
125 | |
126 bool DecodedImageAdapter::Create(std::string& content, | |
127 const std::string& uri) | |
128 { | |
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129 LOG(INFO) << "Decoding DICOM instance: " << uri; |
0 | 130 |
131 CompressionType type; | |
132 uint8_t level; | |
133 std::string instanceId; | |
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134 unsigned int frameIndex; |
0 | 135 |
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136 if (!ParseUri(type, level, instanceId, frameIndex, uri)) |
0 | 137 { |
138 return false; | |
139 } | |
140 | |
96 | 141 bool ok = false; |
142 | |
143 Json::Value tags; | |
144 std::string dicom; | |
145 if (!GetStringFromOrthanc(dicom, context_, "/instances/" + instanceId + "/file") || | |
146 !GetJsonFromOrthanc(tags, context_, "/instances/" + instanceId + "/tags")) | |
147 { | |
148 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
149 } | |
150 | |
230
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151 std::unique_ptr<OrthancImage> image( |
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152 new OrthancImage(OrthancPluginDecodeDicomImage( |
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153 context_, dicom.c_str(), dicom.size(), frameIndex))); |
96 | 154 |
155 Json::Value json; | |
156 if (GetCornerstoneMetadata(json, tags, *image)) | |
157 { | |
158 if (type == CompressionType_Deflate) | |
159 { | |
173
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160 ok = EncodeUsingDeflate(json, *image); |
96 | 161 } |
162 else if (type == CompressionType_Jpeg) | |
163 { | |
164 ok = EncodeUsingJpeg(json, *image, level); | |
165 } | |
166 } | |
167 | |
31 | 168 if (ok) |
169 { | |
160 | 170 std::string photometric; |
171 if (GetStringTag(photometric, tags, "0028,0004")) | |
172 { | |
173 json["Orthanc"]["PhotometricInterpretation"] = photometric; | |
174 } | |
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175 |
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176 Orthanc::Toolbox::WriteFastJson(content, json); |
31 | 177 return true; |
0 | 178 } |
179 else | |
180 { | |
234
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181 LOG(WARNING) << "Unable to decode the following instance: " << uri; |
0 | 182 return false; |
183 } | |
184 } | |
96 | 185 |
186 | |
187 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
188 const Json::Value& tags, | |
304 | 189 const OrthancImage& image) |
96 | 190 { |
191 float windowCenter, windowWidth; | |
192 | |
193 Orthanc::ImageAccessor accessor; | |
230
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194 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetPixelFormat()), image.GetWidth(), |
96 | 195 image.GetHeight(), image.GetPitch(), image.GetBuffer()); |
196 | |
197 switch (accessor.GetFormat()) | |
198 { | |
296
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199 case Orthanc::PixelFormat_Grayscale8: |
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200 case Orthanc::PixelFormat_Grayscale16: |
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201 case Orthanc::PixelFormat_SignedGrayscale16: |
96 | 202 { |
203 int64_t a, b; | |
172 | 204 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
96 | 205 result["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); |
206 result["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
207 result["color"] = false; | |
208 | |
209 windowCenter = static_cast<float>(a + b) / 2.0f; | |
210 | |
211 if (a == b) | |
212 { | |
213 windowWidth = 256.0f; // Arbitrary value | |
214 } | |
215 else | |
216 { | |
217 windowWidth = static_cast<float>(b - a) / 2.0f; | |
218 } | |
219 | |
220 break; | |
221 } | |
222 | |
296
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223 case Orthanc::PixelFormat_RGB24: |
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224 case Orthanc::PixelFormat_RGB48: |
96 | 225 result["minPixelValue"] = 0; |
226 result["maxPixelValue"] = 255; | |
227 result["color"] = true; | |
228 windowCenter = 127.5f; | |
229 windowWidth = 256.0f; | |
230 break; | |
231 | |
232 default: | |
233 return false; | |
234 } | |
235 | |
102 | 236 float slope = GetFloatTag(tags, "0028,1053", 1.0f); |
103 | 237 float intercept = GetFloatTag(tags, "0028,1052", 0.0f); |
102 | 238 |
239 result["slope"] = slope; | |
240 result["intercept"] = intercept; | |
96 | 241 result["rows"] = image.GetHeight(); |
242 result["columns"] = image.GetWidth(); | |
243 result["height"] = image.GetHeight(); | |
244 result["width"] = image.GetWidth(); | |
245 | |
102 | 246 bool ok = false; |
247 std::string pixelSpacing; | |
248 if (GetStringTag(pixelSpacing, tags, "0028,0030")) | |
96 | 249 { |
102 | 250 std::vector<std::string> tokens; |
251 Orthanc::Toolbox::TokenizeString(tokens, pixelSpacing, '\\'); | |
252 | |
253 if (tokens.size() >= 2) | |
96 | 254 { |
102 | 255 try |
256 { | |
103 | 257 result["columnPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[1])); |
258 result["rowPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[0])); | |
102 | 259 ok = true; |
260 } | |
261 catch (boost::bad_lexical_cast&) | |
262 { | |
263 } | |
96 | 264 } |
265 } | |
102 | 266 |
267 if (!ok) | |
96 | 268 { |
102 | 269 result["columnPixelSpacing"] = 1.0f; |
270 result["rowPixelSpacing"] = 1.0f; | |
96 | 271 } |
272 | |
102 | 273 result["windowCenter"] = GetFloatTag(tags, "0028,1050", windowCenter * slope + intercept); |
274 result["windowWidth"] = GetFloatTag(tags, "0028,1051", windowWidth * slope); | |
275 | |
96 | 276 return true; |
277 } | |
278 | |
279 | |
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280 static void ConvertRGB48ToRGB24(Orthanc::ImageAccessor& target, |
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281 const Orthanc::ImageAccessor& source) |
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282 { |
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283 if (source.GetWidth() != target.GetWidth() || |
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284 source.GetHeight() != target.GetHeight()) |
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285 { |
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286 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
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287 } |
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288 |
287 | 289 const unsigned int width = source.GetWidth(); |
290 const unsigned int height = source.GetHeight(); | |
291 | |
292 for (unsigned int y = 0; y < height; y++) | |
173
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293 { |
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294 const uint16_t* p = reinterpret_cast<const uint16_t*>(source.GetConstRow(y)); |
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295 uint8_t* q = reinterpret_cast<uint8_t*>(target.GetRow(y)); |
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296 |
287 | 297 for (unsigned int x = 0; x < width; x++) |
173
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298 { |
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299 q[0] = p[0] >> 8; |
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300 q[1] = p[1] >> 8; |
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301 q[2] = p[2] >> 8; |
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302 p += 3; |
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303 q += 3; |
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304 } |
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305 } |
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306 } |
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307 |
96 | 308 |
309 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
304 | 310 const OrthancImage& image) |
96 | 311 { |
312 Orthanc::ImageAccessor accessor; | |
230
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313 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetPixelFormat()), image.GetWidth(), |
96 | 314 image.GetHeight(), image.GetPitch(), image.GetBuffer()); |
315 | |
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316 std::unique_ptr<Orthanc::ImageBuffer> buffer; |
96 | 317 |
318 Orthanc::ImageAccessor converted; | |
319 | |
320 switch (accessor.GetFormat()) | |
321 { | |
322 case Orthanc::PixelFormat_RGB24: | |
207
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323 accessor.GetReadOnlyAccessor(converted); |
96 | 324 break; |
325 | |
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326 case Orthanc::PixelFormat_RGB48: |
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327 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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328 accessor.GetWidth(), |
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329 accessor.GetHeight(), false)); |
207
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330 buffer->GetWriteableAccessor(converted); |
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331 ConvertRGB48ToRGB24(converted, accessor); |
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332 break; |
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333 |
96 | 334 case Orthanc::PixelFormat_Grayscale8: |
335 case Orthanc::PixelFormat_Grayscale16: | |
145 | 336 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale16, |
337 accessor.GetWidth(), | |
338 accessor.GetHeight(), | |
339 true /* force minimal pitch */)); | |
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340 buffer->GetWriteableAccessor(converted); |
96 | 341 Orthanc::ImageProcessing::Convert(converted, accessor); |
342 break; | |
343 | |
344 case Orthanc::PixelFormat_SignedGrayscale16: | |
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345 accessor.GetReadOnlyAccessor(converted); |
96 | 346 break; |
347 | |
348 default: | |
349 // Unsupported pixel format | |
350 return false; | |
351 } | |
352 | |
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353 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
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354 |
96 | 355 // Sanity check: The pitch must be minimal |
356 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
357 GetBytesPerPixel(converted.GetFormat())); | |
358 result["Orthanc"]["Compression"] = "Deflate"; | |
359 result["sizeInBytes"] = converted.GetSize(); | |
360 | |
361 std::string z; | |
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362 CompressUsingDeflate(z, GetGlobalContext(), converted.GetConstBuffer(), converted.GetSize()); |
216 | 363 |
364 std::string s; | |
365 Orthanc::Toolbox::EncodeBase64(s, z); | |
366 result["Orthanc"]["PixelData"] = s; | |
96 | 367 |
368 return true; | |
369 } | |
370 | |
371 | |
372 | |
373 template <typename TargetType, typename SourceType> | |
374 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
375 const Orthanc::ImageAccessor& source, | |
376 SourceType source1, TargetType target1, | |
377 SourceType source2, TargetType target2) | |
378 { | |
379 if (source.GetWidth() != target.GetWidth() || | |
380 source.GetHeight() != target.GetHeight()) | |
381 { | |
382 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
383 } | |
384 | |
385 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
386 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
387 | |
388 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
389 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
390 | |
287 | 391 const unsigned int width = source.GetWidth(); |
392 const unsigned int height = source.GetHeight(); | |
393 | |
394 for (unsigned int y = 0; y < height; y++) | |
96 | 395 { |
396 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
397 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
398 | |
287 | 399 for (unsigned int x = 0; x < width; x++, p++, q++) |
96 | 400 { |
401 float v = (scale * static_cast<float>(*p)) + offset; | |
402 | |
403 if (v > maxValue) | |
404 { | |
405 *q = std::numeric_limits<TargetType>::max(); | |
406 } | |
407 else if (v < minValue) | |
408 { | |
409 *q = std::numeric_limits<TargetType>::min(); | |
410 } | |
411 else | |
412 { | |
101 | 413 //*q = static_cast<TargetType>(boost::math::iround(v)); |
414 | |
415 // http://stackoverflow.com/a/485546/881731 | |
416 *q = static_cast<TargetType>(floor(v + 0.5f)); | |
96 | 417 } |
418 } | |
419 } | |
420 } | |
421 | |
422 | |
423 bool DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result, | |
304 | 424 const OrthancImage& image, |
96 | 425 uint8_t quality /* between 0 and 100 */) |
426 { | |
427 Orthanc::ImageAccessor accessor; | |
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428 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetPixelFormat()), image.GetWidth(), |
96 | 429 image.GetHeight(), image.GetPitch(), image.GetBuffer()); |
430 | |
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431 std::unique_ptr<Orthanc::ImageBuffer> buffer; |
96 | 432 |
433 Orthanc::ImageAccessor converted; | |
434 | |
435 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
436 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
437 { | |
438 result["Orthanc"]["Stretched"] = false; | |
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439 accessor.GetReadOnlyAccessor(converted); |
96 | 440 } |
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441 else if (accessor.GetFormat() == Orthanc::PixelFormat_RGB48) |
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442 { |
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443 result["Orthanc"]["Stretched"] = false; |
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444 |
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445 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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446 accessor.GetWidth(), |
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447 accessor.GetHeight(), false)); |
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448 buffer->GetWriteableAccessor(converted); |
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449 |
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450 ConvertRGB48ToRGB24(converted, accessor); |
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451 } |
96 | 452 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || |
453 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
454 { | |
455 result["Orthanc"]["Stretched"] = true; | |
145 | 456 |
457 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale8, | |
458 accessor.GetWidth(), | |
459 accessor.GetHeight(), | |
460 true /* force minimal pitch */)); | |
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461 buffer->GetWriteableAccessor(converted); |
96 | 462 |
463 int64_t a, b; | |
172 | 464 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
96 | 465 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); |
466 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
467 | |
468 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
469 { | |
470 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
471 } | |
472 else | |
473 { | |
474 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
475 } | |
476 } | |
477 else | |
478 { | |
479 return false; | |
480 } | |
481 | |
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482 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
96 | 483 result["Orthanc"]["Compression"] = "Jpeg"; |
484 result["sizeInBytes"] = converted.GetSize(); | |
485 | |
486 std::string jpeg; | |
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487 WriteJpegToMemory(jpeg, GetGlobalContext(), converted, quality); |
96 | 488 |
216 | 489 std::string s; |
490 Orthanc::Toolbox::EncodeBase64(s, jpeg); | |
491 result["Orthanc"]["PixelData"] = s; | |
492 | |
96 | 493 return true; |
494 } | |
0 | 495 } |