Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 216:47d52db10369
fix
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 22 Mar 2019 10:34:11 +0100 |
parents | 2f27287c047c |
children | aee499712ac4 |
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 |
209 | 5 * Copyright (C) 2017-2019 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 | |
191
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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 } | |
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 { | |
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 | |
102 | 153 std::auto_ptr<OrthancImageWrapper> image(new OrthancImageWrapper(context_, OrthancPluginDecodeDicomImage(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 { | |
31 | 182 char msg[1024]; |
183 sprintf(msg, "Unable to decode the following instance: %s", uri.c_str()); | |
184 OrthancPluginLogWarning(context_, msg); | |
0 | 185 return false; |
186 } | |
187 } | |
96 | 188 |
189 | |
190 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
191 const Json::Value& tags, | |
192 OrthancImageWrapper& image) | |
193 { | |
194 using namespace Orthanc; | |
195 | |
196 float windowCenter, windowWidth; | |
197 | |
198 Orthanc::ImageAccessor accessor; | |
199 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
200 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
201 | |
202 switch (accessor.GetFormat()) | |
203 { | |
204 case PixelFormat_Grayscale8: | |
205 case PixelFormat_Grayscale16: | |
206 case PixelFormat_SignedGrayscale16: | |
207 { | |
208 int64_t a, b; | |
172 | 209 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
96 | 210 result["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); |
211 result["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
212 result["color"] = false; | |
213 | |
214 windowCenter = static_cast<float>(a + b) / 2.0f; | |
215 | |
216 if (a == b) | |
217 { | |
218 windowWidth = 256.0f; // Arbitrary value | |
219 } | |
220 else | |
221 { | |
222 windowWidth = static_cast<float>(b - a) / 2.0f; | |
223 } | |
224 | |
225 break; | |
226 } | |
227 | |
228 case PixelFormat_RGB24: | |
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229 case PixelFormat_RGB48: |
96 | 230 result["minPixelValue"] = 0; |
231 result["maxPixelValue"] = 255; | |
232 result["color"] = true; | |
233 windowCenter = 127.5f; | |
234 windowWidth = 256.0f; | |
235 break; | |
236 | |
237 default: | |
238 return false; | |
239 } | |
240 | |
102 | 241 float slope = GetFloatTag(tags, "0028,1053", 1.0f); |
103 | 242 float intercept = GetFloatTag(tags, "0028,1052", 0.0f); |
102 | 243 |
244 result["slope"] = slope; | |
245 result["intercept"] = intercept; | |
96 | 246 result["rows"] = image.GetHeight(); |
247 result["columns"] = image.GetWidth(); | |
248 result["height"] = image.GetHeight(); | |
249 result["width"] = image.GetWidth(); | |
250 | |
102 | 251 bool ok = false; |
252 std::string pixelSpacing; | |
253 if (GetStringTag(pixelSpacing, tags, "0028,0030")) | |
96 | 254 { |
102 | 255 std::vector<std::string> tokens; |
256 Orthanc::Toolbox::TokenizeString(tokens, pixelSpacing, '\\'); | |
257 | |
258 if (tokens.size() >= 2) | |
96 | 259 { |
102 | 260 try |
261 { | |
103 | 262 result["columnPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[1])); |
263 result["rowPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[0])); | |
102 | 264 ok = true; |
265 } | |
266 catch (boost::bad_lexical_cast&) | |
267 { | |
268 } | |
96 | 269 } |
270 } | |
102 | 271 |
272 if (!ok) | |
96 | 273 { |
102 | 274 result["columnPixelSpacing"] = 1.0f; |
275 result["rowPixelSpacing"] = 1.0f; | |
96 | 276 } |
277 | |
102 | 278 result["windowCenter"] = GetFloatTag(tags, "0028,1050", windowCenter * slope + intercept); |
279 result["windowWidth"] = GetFloatTag(tags, "0028,1051", windowWidth * slope); | |
280 | |
96 | 281 return true; |
282 } | |
283 | |
284 | |
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285 static void ConvertRGB48ToRGB24(Orthanc::ImageAccessor& target, |
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286 const Orthanc::ImageAccessor& source) |
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287 { |
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288 if (source.GetWidth() != target.GetWidth() || |
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289 source.GetHeight() != target.GetHeight()) |
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290 { |
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291 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
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292 } |
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293 |
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294 for (unsigned int y = 0; y < source.GetHeight(); y++) |
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295 { |
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296 const uint16_t* p = reinterpret_cast<const uint16_t*>(source.GetConstRow(y)); |
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297 uint8_t* q = reinterpret_cast<uint8_t*>(target.GetRow(y)); |
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298 |
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299 for (unsigned int x = 0; x < source.GetWidth(); x++) |
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300 { |
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301 q[0] = p[0] >> 8; |
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302 q[1] = p[1] >> 8; |
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303 q[2] = p[2] >> 8; |
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304 p += 3; |
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305 q += 3; |
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306 } |
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307 } |
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308 } |
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309 |
96 | 310 |
311 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
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312 OrthancImageWrapper& image) |
96 | 313 { |
314 Orthanc::ImageAccessor accessor; | |
315 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
316 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
317 | |
145 | 318 std::auto_ptr<Orthanc::ImageBuffer> buffer; |
96 | 319 |
320 Orthanc::ImageAccessor converted; | |
321 | |
322 switch (accessor.GetFormat()) | |
323 { | |
324 case Orthanc::PixelFormat_RGB24: | |
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325 accessor.GetReadOnlyAccessor(converted); |
96 | 326 break; |
327 | |
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328 case Orthanc::PixelFormat_RGB48: |
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329 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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330 accessor.GetWidth(), |
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331 accessor.GetHeight(), false)); |
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332 buffer->GetWriteableAccessor(converted); |
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333 ConvertRGB48ToRGB24(converted, accessor); |
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334 break; |
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335 |
96 | 336 case Orthanc::PixelFormat_Grayscale8: |
337 case Orthanc::PixelFormat_Grayscale16: | |
145 | 338 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale16, |
339 accessor.GetWidth(), | |
340 accessor.GetHeight(), | |
341 true /* force minimal pitch */)); | |
207
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342 buffer->GetWriteableAccessor(converted); |
96 | 343 Orthanc::ImageProcessing::Convert(converted, accessor); |
344 break; | |
345 | |
346 case Orthanc::PixelFormat_SignedGrayscale16: | |
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347 accessor.GetReadOnlyAccessor(converted); |
96 | 348 break; |
349 | |
350 default: | |
351 // Unsupported pixel format | |
352 return false; | |
353 } | |
354 | |
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355 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
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356 |
96 | 357 // Sanity check: The pitch must be minimal |
358 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
359 GetBytesPerPixel(converted.GetFormat())); | |
360 result["Orthanc"]["Compression"] = "Deflate"; | |
361 result["sizeInBytes"] = converted.GetSize(); | |
362 | |
363 std::string z; | |
364 CompressUsingDeflate(z, image.GetContext(), converted.GetConstBuffer(), converted.GetSize()); | |
216 | 365 |
366 std::string s; | |
367 Orthanc::Toolbox::EncodeBase64(s, z); | |
368 result["Orthanc"]["PixelData"] = s; | |
96 | 369 |
370 return true; | |
371 } | |
372 | |
373 | |
374 | |
375 template <typename TargetType, typename SourceType> | |
376 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
377 const Orthanc::ImageAccessor& source, | |
378 SourceType source1, TargetType target1, | |
379 SourceType source2, TargetType target2) | |
380 { | |
381 if (source.GetWidth() != target.GetWidth() || | |
382 source.GetHeight() != target.GetHeight()) | |
383 { | |
384 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
385 } | |
386 | |
387 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
388 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
389 | |
390 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
391 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
392 | |
393 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
394 { | |
395 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
396 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
397 | |
398 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
399 { | |
400 float v = (scale * static_cast<float>(*p)) + offset; | |
401 | |
402 if (v > maxValue) | |
403 { | |
404 *q = std::numeric_limits<TargetType>::max(); | |
405 } | |
406 else if (v < minValue) | |
407 { | |
408 *q = std::numeric_limits<TargetType>::min(); | |
409 } | |
410 else | |
411 { | |
101 | 412 //*q = static_cast<TargetType>(boost::math::iround(v)); |
413 | |
414 // http://stackoverflow.com/a/485546/881731 | |
415 *q = static_cast<TargetType>(floor(v + 0.5f)); | |
96 | 416 } |
417 } | |
418 } | |
419 } | |
420 | |
421 | |
422 bool DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result, | |
423 OrthancImageWrapper& image, | |
424 uint8_t quality /* between 0 and 100 */) | |
425 { | |
426 Orthanc::ImageAccessor accessor; | |
427 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
428 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
429 | |
145 | 430 std::auto_ptr<Orthanc::ImageBuffer> buffer; |
96 | 431 |
432 Orthanc::ImageAccessor converted; | |
433 | |
434 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
435 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
436 { | |
437 result["Orthanc"]["Stretched"] = false; | |
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438 accessor.GetReadOnlyAccessor(converted); |
96 | 439 } |
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440 else if (accessor.GetFormat() == Orthanc::PixelFormat_RGB48) |
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441 { |
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442 result["Orthanc"]["Stretched"] = false; |
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443 |
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444 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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445 accessor.GetWidth(), |
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446 accessor.GetHeight(), false)); |
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447 buffer->GetWriteableAccessor(converted); |
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448 |
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449 ConvertRGB48ToRGB24(converted, accessor); |
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450 } |
96 | 451 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || |
452 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
453 { | |
454 result["Orthanc"]["Stretched"] = true; | |
145 | 455 |
456 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale8, | |
457 accessor.GetWidth(), | |
458 accessor.GetHeight(), | |
459 true /* force minimal pitch */)); | |
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460 buffer->GetWriteableAccessor(converted); |
96 | 461 |
462 int64_t a, b; | |
172 | 463 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
96 | 464 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); |
465 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
466 | |
467 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
468 { | |
469 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
470 } | |
471 else | |
472 { | |
473 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
474 } | |
475 } | |
476 else | |
477 { | |
478 return false; | |
479 } | |
480 | |
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481 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
96 | 482 result["Orthanc"]["Compression"] = "Jpeg"; |
483 result["sizeInBytes"] = converted.GetSize(); | |
484 | |
485 std::string jpeg; | |
486 WriteJpegToMemory(jpeg, image.GetContext(), converted, quality); | |
487 | |
216 | 488 std::string s; |
489 Orthanc::Toolbox::EncodeBase64(s, jpeg); | |
490 result["Orthanc"]["PixelData"] = s; | |
491 | |
96 | 492 return true; |
493 } | |
0 | 494 } |