Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 227:e4def26f0fd3
replacing std::auto_ptr by std::unique_ptr
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 13 Mar 2020 12:38:45 +0100 |
parents | aee499712ac4 |
children | cce89307af28 |
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 |
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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 | |
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26 #include <Core/Images/ImageBuffer.h> |
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27 #include <Core/Images/ImageProcessing.h> |
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28 #include <Core/OrthancException.h> |
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29 #include <Core/Toolbox.h> |
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30 #include <Plugins/Samples/GdcmDecoder/OrthancImageWrapper.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 } | |
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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 { | |
129 std::string message = "Decoding DICOM instance: " + uri; | |
130 OrthancPluginLogInfo(context_, message.c_str()); | |
131 | |
132 CompressionType type; | |
133 uint8_t level; | |
134 std::string instanceId; | |
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135 unsigned int frameIndex; |
0 | 136 |
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137 if (!ParseUri(type, level, instanceId, frameIndex, uri)) |
0 | 138 { |
139 return false; | |
140 } | |
141 | |
96 | 142 |
143 bool ok = false; | |
144 | |
145 Json::Value tags; | |
146 std::string dicom; | |
147 if (!GetStringFromOrthanc(dicom, context_, "/instances/" + instanceId + "/file") || | |
148 !GetJsonFromOrthanc(tags, context_, "/instances/" + instanceId + "/tags")) | |
149 { | |
150 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
151 } | |
152 | |
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153 std::unique_ptr<OrthancImageWrapper> image( |
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154 new OrthancImageWrapper(context_, OrthancPluginDecodeDicomImage( |
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155 context_, dicom.c_str(), dicom.size(), frameIndex))); |
96 | 156 |
157 Json::Value json; | |
158 if (GetCornerstoneMetadata(json, tags, *image)) | |
159 { | |
160 if (type == CompressionType_Deflate) | |
161 { | |
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162 ok = EncodeUsingDeflate(json, *image); |
96 | 163 } |
164 else if (type == CompressionType_Jpeg) | |
165 { | |
166 ok = EncodeUsingJpeg(json, *image, level); | |
167 } | |
168 } | |
169 | |
31 | 170 if (ok) |
171 { | |
160 | 172 std::string photometric; |
173 if (GetStringTag(photometric, tags, "0028,0004")) | |
174 { | |
175 json["Orthanc"]["PhotometricInterpretation"] = photometric; | |
176 } | |
177 | |
31 | 178 Json::FastWriter writer; |
179 content = writer.write(json); | |
180 return true; | |
0 | 181 } |
182 else | |
183 { | |
31 | 184 char msg[1024]; |
185 sprintf(msg, "Unable to decode the following instance: %s", uri.c_str()); | |
186 OrthancPluginLogWarning(context_, msg); | |
0 | 187 return false; |
188 } | |
189 } | |
96 | 190 |
191 | |
192 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
193 const Json::Value& tags, | |
194 OrthancImageWrapper& image) | |
195 { | |
196 using namespace Orthanc; | |
197 | |
198 float windowCenter, windowWidth; | |
199 | |
200 Orthanc::ImageAccessor accessor; | |
201 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
202 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
203 | |
204 switch (accessor.GetFormat()) | |
205 { | |
206 case PixelFormat_Grayscale8: | |
207 case PixelFormat_Grayscale16: | |
208 case PixelFormat_SignedGrayscale16: | |
209 { | |
210 int64_t a, b; | |
172 | 211 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
96 | 212 result["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); |
213 result["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
214 result["color"] = false; | |
215 | |
216 windowCenter = static_cast<float>(a + b) / 2.0f; | |
217 | |
218 if (a == b) | |
219 { | |
220 windowWidth = 256.0f; // Arbitrary value | |
221 } | |
222 else | |
223 { | |
224 windowWidth = static_cast<float>(b - a) / 2.0f; | |
225 } | |
226 | |
227 break; | |
228 } | |
229 | |
230 case PixelFormat_RGB24: | |
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231 case PixelFormat_RGB48: |
96 | 232 result["minPixelValue"] = 0; |
233 result["maxPixelValue"] = 255; | |
234 result["color"] = true; | |
235 windowCenter = 127.5f; | |
236 windowWidth = 256.0f; | |
237 break; | |
238 | |
239 default: | |
240 return false; | |
241 } | |
242 | |
102 | 243 float slope = GetFloatTag(tags, "0028,1053", 1.0f); |
103 | 244 float intercept = GetFloatTag(tags, "0028,1052", 0.0f); |
102 | 245 |
246 result["slope"] = slope; | |
247 result["intercept"] = intercept; | |
96 | 248 result["rows"] = image.GetHeight(); |
249 result["columns"] = image.GetWidth(); | |
250 result["height"] = image.GetHeight(); | |
251 result["width"] = image.GetWidth(); | |
252 | |
102 | 253 bool ok = false; |
254 std::string pixelSpacing; | |
255 if (GetStringTag(pixelSpacing, tags, "0028,0030")) | |
96 | 256 { |
102 | 257 std::vector<std::string> tokens; |
258 Orthanc::Toolbox::TokenizeString(tokens, pixelSpacing, '\\'); | |
259 | |
260 if (tokens.size() >= 2) | |
96 | 261 { |
102 | 262 try |
263 { | |
103 | 264 result["columnPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[1])); |
265 result["rowPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[0])); | |
102 | 266 ok = true; |
267 } | |
268 catch (boost::bad_lexical_cast&) | |
269 { | |
270 } | |
96 | 271 } |
272 } | |
102 | 273 |
274 if (!ok) | |
96 | 275 { |
102 | 276 result["columnPixelSpacing"] = 1.0f; |
277 result["rowPixelSpacing"] = 1.0f; | |
96 | 278 } |
279 | |
102 | 280 result["windowCenter"] = GetFloatTag(tags, "0028,1050", windowCenter * slope + intercept); |
281 result["windowWidth"] = GetFloatTag(tags, "0028,1051", windowWidth * slope); | |
282 | |
96 | 283 return true; |
284 } | |
285 | |
286 | |
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287 static void ConvertRGB48ToRGB24(Orthanc::ImageAccessor& target, |
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288 const Orthanc::ImageAccessor& source) |
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289 { |
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290 if (source.GetWidth() != target.GetWidth() || |
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291 source.GetHeight() != target.GetHeight()) |
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292 { |
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293 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
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294 } |
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295 |
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296 for (unsigned int y = 0; y < source.GetHeight(); y++) |
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297 { |
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298 const uint16_t* p = reinterpret_cast<const uint16_t*>(source.GetConstRow(y)); |
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299 uint8_t* q = reinterpret_cast<uint8_t*>(target.GetRow(y)); |
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300 |
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301 for (unsigned int x = 0; x < source.GetWidth(); x++) |
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302 { |
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303 q[0] = p[0] >> 8; |
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304 q[1] = p[1] >> 8; |
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305 q[2] = p[2] >> 8; |
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306 p += 3; |
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307 q += 3; |
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308 } |
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309 } |
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310 } |
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311 |
96 | 312 |
313 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
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314 OrthancImageWrapper& image) |
96 | 315 { |
316 Orthanc::ImageAccessor accessor; | |
317 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
318 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
319 | |
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320 std::unique_ptr<Orthanc::ImageBuffer> buffer; |
96 | 321 |
322 Orthanc::ImageAccessor converted; | |
323 | |
324 switch (accessor.GetFormat()) | |
325 { | |
326 case Orthanc::PixelFormat_RGB24: | |
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327 accessor.GetReadOnlyAccessor(converted); |
96 | 328 break; |
329 | |
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330 case Orthanc::PixelFormat_RGB48: |
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331 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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332 accessor.GetWidth(), |
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333 accessor.GetHeight(), false)); |
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334 buffer->GetWriteableAccessor(converted); |
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335 ConvertRGB48ToRGB24(converted, accessor); |
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336 break; |
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337 |
96 | 338 case Orthanc::PixelFormat_Grayscale8: |
339 case Orthanc::PixelFormat_Grayscale16: | |
145 | 340 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale16, |
341 accessor.GetWidth(), | |
342 accessor.GetHeight(), | |
343 true /* force minimal pitch */)); | |
207
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344 buffer->GetWriteableAccessor(converted); |
96 | 345 Orthanc::ImageProcessing::Convert(converted, accessor); |
346 break; | |
347 | |
348 case Orthanc::PixelFormat_SignedGrayscale16: | |
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349 accessor.GetReadOnlyAccessor(converted); |
96 | 350 break; |
351 | |
352 default: | |
353 // Unsupported pixel format | |
354 return false; | |
355 } | |
356 | |
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357 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
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358 |
96 | 359 // Sanity check: The pitch must be minimal |
360 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
361 GetBytesPerPixel(converted.GetFormat())); | |
362 result["Orthanc"]["Compression"] = "Deflate"; | |
363 result["sizeInBytes"] = converted.GetSize(); | |
364 | |
365 std::string z; | |
366 CompressUsingDeflate(z, image.GetContext(), converted.GetConstBuffer(), converted.GetSize()); | |
216 | 367 |
368 std::string s; | |
369 Orthanc::Toolbox::EncodeBase64(s, z); | |
370 result["Orthanc"]["PixelData"] = s; | |
96 | 371 |
372 return true; | |
373 } | |
374 | |
375 | |
376 | |
377 template <typename TargetType, typename SourceType> | |
378 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
379 const Orthanc::ImageAccessor& source, | |
380 SourceType source1, TargetType target1, | |
381 SourceType source2, TargetType target2) | |
382 { | |
383 if (source.GetWidth() != target.GetWidth() || | |
384 source.GetHeight() != target.GetHeight()) | |
385 { | |
386 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
387 } | |
388 | |
389 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
390 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
391 | |
392 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
393 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
394 | |
395 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
396 { | |
397 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
398 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
399 | |
400 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
401 { | |
402 float v = (scale * static_cast<float>(*p)) + offset; | |
403 | |
404 if (v > maxValue) | |
405 { | |
406 *q = std::numeric_limits<TargetType>::max(); | |
407 } | |
408 else if (v < minValue) | |
409 { | |
410 *q = std::numeric_limits<TargetType>::min(); | |
411 } | |
412 else | |
413 { | |
101 | 414 //*q = static_cast<TargetType>(boost::math::iround(v)); |
415 | |
416 // http://stackoverflow.com/a/485546/881731 | |
417 *q = static_cast<TargetType>(floor(v + 0.5f)); | |
96 | 418 } |
419 } | |
420 } | |
421 } | |
422 | |
423 | |
424 bool DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result, | |
425 OrthancImageWrapper& image, | |
426 uint8_t quality /* between 0 and 100 */) | |
427 { | |
428 Orthanc::ImageAccessor accessor; | |
429 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
430 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
431 | |
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432 std::unique_ptr<Orthanc::ImageBuffer> buffer; |
96 | 433 |
434 Orthanc::ImageAccessor converted; | |
435 | |
436 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
437 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
438 { | |
439 result["Orthanc"]["Stretched"] = false; | |
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440 accessor.GetReadOnlyAccessor(converted); |
96 | 441 } |
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442 else if (accessor.GetFormat() == Orthanc::PixelFormat_RGB48) |
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443 { |
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444 result["Orthanc"]["Stretched"] = false; |
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445 |
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446 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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447 accessor.GetWidth(), |
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448 accessor.GetHeight(), false)); |
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449 buffer->GetWriteableAccessor(converted); |
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450 |
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451 ConvertRGB48ToRGB24(converted, accessor); |
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452 } |
96 | 453 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || |
454 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
455 { | |
456 result["Orthanc"]["Stretched"] = true; | |
145 | 457 |
458 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale8, | |
459 accessor.GetWidth(), | |
460 accessor.GetHeight(), | |
461 true /* force minimal pitch */)); | |
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462 buffer->GetWriteableAccessor(converted); |
96 | 463 |
464 int64_t a, b; | |
172 | 465 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
96 | 466 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); |
467 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
468 | |
469 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
470 { | |
471 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
472 } | |
473 else | |
474 { | |
475 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
476 } | |
477 } | |
478 else | |
479 { | |
480 return false; | |
481 } | |
482 | |
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483 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
96 | 484 result["Orthanc"]["Compression"] = "Jpeg"; |
485 result["sizeInBytes"] = converted.GetSize(); | |
486 | |
487 std::string jpeg; | |
488 WriteJpegToMemory(jpeg, image.GetContext(), converted, quality); | |
489 | |
216 | 490 std::string s; |
491 Orthanc::Toolbox::EncodeBase64(s, jpeg); | |
492 result["Orthanc"]["PixelData"] = s; | |
493 | |
96 | 494 return true; |
495 } | |
0 | 496 } |