Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 287:ec1af1fdcaca
fix build
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 06 Nov 2020 17:33:32 +0100 |
parents | 4e9d30c19b4b |
children | aadbffcee805 |
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 |
226
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5 * Copyright (C) 2017-2020 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 | |
22 #include "DecodedImageAdapter.h" | |
23 | |
24 #include "ViewerToolbox.h" | |
25 | |
266
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26 #include <Images/ImageBuffer.h> |
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27 #include <Images/ImageProcessing.h> |
287 | 28 #include <Logging.h> |
266
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29 #include <OrthancException.h> |
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30 #include <Toolbox.h> |
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31 |
0 | 32 #include <boost/lexical_cast.hpp> |
33 #include <boost/algorithm/string/predicate.hpp> | |
34 #include <json/writer.h> | |
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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 { | |
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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 } | |
175 | |
31 | 176 Json::FastWriter writer; |
177 content = writer.write(json); | |
178 return true; | |
0 | 179 } |
180 else | |
181 { | |
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182 LOG(WARNING) << "Unable to decode the following instance: " << uri; |
0 | 183 return false; |
184 } | |
185 } | |
96 | 186 |
187 | |
188 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
189 const Json::Value& tags, | |
230
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190 OrthancImage& image) |
96 | 191 { |
192 using namespace Orthanc; | |
193 | |
194 float windowCenter, windowWidth; | |
195 | |
196 Orthanc::ImageAccessor accessor; | |
230
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197 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetPixelFormat()), image.GetWidth(), |
96 | 198 image.GetHeight(), image.GetPitch(), image.GetBuffer()); |
199 | |
200 switch (accessor.GetFormat()) | |
201 { | |
202 case PixelFormat_Grayscale8: | |
203 case PixelFormat_Grayscale16: | |
204 case PixelFormat_SignedGrayscale16: | |
205 { | |
206 int64_t a, b; | |
172 | 207 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
96 | 208 result["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); |
209 result["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
210 result["color"] = false; | |
211 | |
212 windowCenter = static_cast<float>(a + b) / 2.0f; | |
213 | |
214 if (a == b) | |
215 { | |
216 windowWidth = 256.0f; // Arbitrary value | |
217 } | |
218 else | |
219 { | |
220 windowWidth = static_cast<float>(b - a) / 2.0f; | |
221 } | |
222 | |
223 break; | |
224 } | |
225 | |
226 case PixelFormat_RGB24: | |
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227 case PixelFormat_RGB48: |
96 | 228 result["minPixelValue"] = 0; |
229 result["maxPixelValue"] = 255; | |
230 result["color"] = true; | |
231 windowCenter = 127.5f; | |
232 windowWidth = 256.0f; | |
233 break; | |
234 | |
235 default: | |
236 return false; | |
237 } | |
238 | |
102 | 239 float slope = GetFloatTag(tags, "0028,1053", 1.0f); |
103 | 240 float intercept = GetFloatTag(tags, "0028,1052", 0.0f); |
102 | 241 |
242 result["slope"] = slope; | |
243 result["intercept"] = intercept; | |
96 | 244 result["rows"] = image.GetHeight(); |
245 result["columns"] = image.GetWidth(); | |
246 result["height"] = image.GetHeight(); | |
247 result["width"] = image.GetWidth(); | |
248 | |
102 | 249 bool ok = false; |
250 std::string pixelSpacing; | |
251 if (GetStringTag(pixelSpacing, tags, "0028,0030")) | |
96 | 252 { |
102 | 253 std::vector<std::string> tokens; |
254 Orthanc::Toolbox::TokenizeString(tokens, pixelSpacing, '\\'); | |
255 | |
256 if (tokens.size() >= 2) | |
96 | 257 { |
102 | 258 try |
259 { | |
103 | 260 result["columnPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[1])); |
261 result["rowPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[0])); | |
102 | 262 ok = true; |
263 } | |
264 catch (boost::bad_lexical_cast&) | |
265 { | |
266 } | |
96 | 267 } |
268 } | |
102 | 269 |
270 if (!ok) | |
96 | 271 { |
102 | 272 result["columnPixelSpacing"] = 1.0f; |
273 result["rowPixelSpacing"] = 1.0f; | |
96 | 274 } |
275 | |
102 | 276 result["windowCenter"] = GetFloatTag(tags, "0028,1050", windowCenter * slope + intercept); |
277 result["windowWidth"] = GetFloatTag(tags, "0028,1051", windowWidth * slope); | |
278 | |
96 | 279 return true; |
280 } | |
281 | |
282 | |
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283 static void ConvertRGB48ToRGB24(Orthanc::ImageAccessor& target, |
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284 const Orthanc::ImageAccessor& source) |
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285 { |
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286 if (source.GetWidth() != target.GetWidth() || |
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287 source.GetHeight() != target.GetHeight()) |
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288 { |
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289 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
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290 } |
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291 |
287 | 292 const unsigned int width = source.GetWidth(); |
293 const unsigned int height = source.GetHeight(); | |
294 | |
295 for (unsigned int y = 0; y < height; y++) | |
173
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296 { |
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297 const uint16_t* p = reinterpret_cast<const uint16_t*>(source.GetConstRow(y)); |
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298 uint8_t* q = reinterpret_cast<uint8_t*>(target.GetRow(y)); |
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299 |
287 | 300 for (unsigned int x = 0; x < width; x++) |
173
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301 { |
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302 q[0] = p[0] >> 8; |
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303 q[1] = p[1] >> 8; |
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304 q[2] = p[2] >> 8; |
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305 p += 3; |
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306 q += 3; |
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307 } |
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308 } |
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309 } |
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310 |
96 | 311 |
312 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
230
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313 OrthancImage& image) |
96 | 314 { |
315 Orthanc::ImageAccessor accessor; | |
230
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316 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetPixelFormat()), image.GetWidth(), |
96 | 317 image.GetHeight(), image.GetPitch(), image.GetBuffer()); |
318 | |
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319 std::unique_ptr<Orthanc::ImageBuffer> buffer; |
96 | 320 |
321 Orthanc::ImageAccessor converted; | |
322 | |
323 switch (accessor.GetFormat()) | |
324 { | |
325 case Orthanc::PixelFormat_RGB24: | |
207
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326 accessor.GetReadOnlyAccessor(converted); |
96 | 327 break; |
328 | |
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329 case Orthanc::PixelFormat_RGB48: |
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330 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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331 accessor.GetWidth(), |
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332 accessor.GetHeight(), false)); |
207
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333 buffer->GetWriteableAccessor(converted); |
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334 ConvertRGB48ToRGB24(converted, accessor); |
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335 break; |
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336 |
96 | 337 case Orthanc::PixelFormat_Grayscale8: |
338 case Orthanc::PixelFormat_Grayscale16: | |
145 | 339 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale16, |
340 accessor.GetWidth(), | |
341 accessor.GetHeight(), | |
342 true /* force minimal pitch */)); | |
207
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343 buffer->GetWriteableAccessor(converted); |
96 | 344 Orthanc::ImageProcessing::Convert(converted, accessor); |
345 break; | |
346 | |
347 case Orthanc::PixelFormat_SignedGrayscale16: | |
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348 accessor.GetReadOnlyAccessor(converted); |
96 | 349 break; |
350 | |
351 default: | |
352 // Unsupported pixel format | |
353 return false; | |
354 } | |
355 | |
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356 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
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357 |
96 | 358 // Sanity check: The pitch must be minimal |
359 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
360 GetBytesPerPixel(converted.GetFormat())); | |
361 result["Orthanc"]["Compression"] = "Deflate"; | |
362 result["sizeInBytes"] = converted.GetSize(); | |
363 | |
364 std::string z; | |
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365 CompressUsingDeflate(z, GetGlobalContext(), converted.GetConstBuffer(), converted.GetSize()); |
216 | 366 |
367 std::string s; | |
368 Orthanc::Toolbox::EncodeBase64(s, z); | |
369 result["Orthanc"]["PixelData"] = s; | |
96 | 370 |
371 return true; | |
372 } | |
373 | |
374 | |
375 | |
376 template <typename TargetType, typename SourceType> | |
377 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
378 const Orthanc::ImageAccessor& source, | |
379 SourceType source1, TargetType target1, | |
380 SourceType source2, TargetType target2) | |
381 { | |
382 if (source.GetWidth() != target.GetWidth() || | |
383 source.GetHeight() != target.GetHeight()) | |
384 { | |
385 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
386 } | |
387 | |
388 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
389 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
390 | |
391 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
392 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
393 | |
287 | 394 const unsigned int width = source.GetWidth(); |
395 const unsigned int height = source.GetHeight(); | |
396 | |
397 for (unsigned int y = 0; y < height; y++) | |
96 | 398 { |
399 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
400 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
401 | |
287 | 402 for (unsigned int x = 0; x < width; x++, p++, q++) |
96 | 403 { |
404 float v = (scale * static_cast<float>(*p)) + offset; | |
405 | |
406 if (v > maxValue) | |
407 { | |
408 *q = std::numeric_limits<TargetType>::max(); | |
409 } | |
410 else if (v < minValue) | |
411 { | |
412 *q = std::numeric_limits<TargetType>::min(); | |
413 } | |
414 else | |
415 { | |
101 | 416 //*q = static_cast<TargetType>(boost::math::iround(v)); |
417 | |
418 // http://stackoverflow.com/a/485546/881731 | |
419 *q = static_cast<TargetType>(floor(v + 0.5f)); | |
96 | 420 } |
421 } | |
422 } | |
423 } | |
424 | |
425 | |
426 bool DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result, | |
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427 OrthancImage& image, |
96 | 428 uint8_t quality /* between 0 and 100 */) |
429 { | |
430 Orthanc::ImageAccessor accessor; | |
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431 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetPixelFormat()), image.GetWidth(), |
96 | 432 image.GetHeight(), image.GetPitch(), image.GetBuffer()); |
433 | |
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434 std::unique_ptr<Orthanc::ImageBuffer> buffer; |
96 | 435 |
436 Orthanc::ImageAccessor converted; | |
437 | |
438 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
439 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
440 { | |
441 result["Orthanc"]["Stretched"] = false; | |
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442 accessor.GetReadOnlyAccessor(converted); |
96 | 443 } |
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444 else if (accessor.GetFormat() == Orthanc::PixelFormat_RGB48) |
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445 { |
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446 result["Orthanc"]["Stretched"] = false; |
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447 |
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448 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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449 accessor.GetWidth(), |
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450 accessor.GetHeight(), false)); |
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451 buffer->GetWriteableAccessor(converted); |
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452 |
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453 ConvertRGB48ToRGB24(converted, accessor); |
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454 } |
96 | 455 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || |
456 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
457 { | |
458 result["Orthanc"]["Stretched"] = true; | |
145 | 459 |
460 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale8, | |
461 accessor.GetWidth(), | |
462 accessor.GetHeight(), | |
463 true /* force minimal pitch */)); | |
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464 buffer->GetWriteableAccessor(converted); |
96 | 465 |
466 int64_t a, b; | |
172 | 467 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
96 | 468 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); |
469 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
470 | |
471 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
472 { | |
473 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
474 } | |
475 else | |
476 { | |
477 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
478 } | |
479 } | |
480 else | |
481 { | |
482 return false; | |
483 } | |
484 | |
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485 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
96 | 486 result["Orthanc"]["Compression"] = "Jpeg"; |
487 result["sizeInBytes"] = converted.GetSize(); | |
488 | |
489 std::string jpeg; | |
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490 WriteJpegToMemory(jpeg, GetGlobalContext(), converted, quality); |
96 | 491 |
216 | 492 std::string s; |
493 Orthanc::Toolbox::EncodeBase64(s, jpeg); | |
494 result["Orthanc"]["PixelData"] = s; | |
495 | |
96 | 496 return true; |
497 } | |
0 | 498 } |