Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 298:165723f96767
sync
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 25 Feb 2021 12:15:44 +0100 |
parents | d179f3928342 |
children | fb7d62e3235e |
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 |
293
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5 * Copyright (C) 2017-2021 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> | |
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34 #include <boost/regex.hpp> |
0 | 35 |
103 | 36 |
0 | 37 namespace OrthancPlugins |
38 { | |
160 | 39 static bool GetStringTag(std::string& value, |
40 const Json::Value& tags, | |
41 const std::string& tag) | |
42 { | |
43 if (tags.type() == Json::objectValue && | |
44 tags.isMember(tag) && | |
45 tags[tag].type() == Json::objectValue && | |
46 tags[tag].isMember("Type") && | |
47 tags[tag].isMember("Value") && | |
48 tags[tag]["Type"].type() == Json::stringValue && | |
49 tags[tag]["Value"].type() == Json::stringValue && | |
50 tags[tag]["Type"].asString() == "String") | |
51 { | |
52 value = tags[tag]["Value"].asString(); | |
53 return true; | |
54 } | |
55 else | |
56 { | |
57 return false; | |
58 } | |
59 } | |
60 | |
61 | |
62 static float GetFloatTag(const Json::Value& tags, | |
63 const std::string& tag, | |
64 float defaultValue) | |
65 { | |
66 std::string tmp; | |
67 if (GetStringTag(tmp, tags, tag)) | |
68 { | |
69 try | |
70 { | |
71 return boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tmp)); | |
72 } | |
73 catch (boost::bad_lexical_cast&) | |
74 { | |
75 } | |
76 } | |
77 | |
78 return defaultValue; | |
79 } | |
80 | |
81 | |
0 | 82 bool DecodedImageAdapter::ParseUri(CompressionType& type, |
83 uint8_t& compressionLevel, | |
84 std::string& instanceId, | |
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85 unsigned int& frameIndex, |
0 | 86 const std::string& uri) |
87 { | |
99
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88 boost::regex pattern("^([a-z0-9]+)-([a-z0-9-]+)_([0-9]+)$"); |
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89 |
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90 boost::cmatch what; |
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91 if (!regex_match(uri.c_str(), what, pattern)) |
0 | 92 { |
93 return false; | |
94 } | |
99
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95 |
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96 std::string compression(what[1]); |
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97 instanceId = what[2]; |
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98 frameIndex = boost::lexical_cast<unsigned int>(what[3]); |
0 | 99 |
100 if (compression == "deflate") | |
101 { | |
102 type = CompressionType_Deflate; | |
103 } | |
104 else if (boost::starts_with(compression, "jpeg")) | |
105 { | |
106 type = CompressionType_Jpeg; | |
107 int level = boost::lexical_cast<int>(compression.substr(4)); | |
108 if (level <= 0 || level > 100) | |
109 { | |
110 return false; | |
111 } | |
112 | |
113 compressionLevel = static_cast<uint8_t>(level); | |
114 } | |
115 else | |
116 { | |
117 return false; | |
118 } | |
119 | |
120 return true; | |
121 } | |
122 | |
123 | |
124 | |
125 bool DecodedImageAdapter::Create(std::string& content, | |
126 const std::string& uri) | |
127 { | |
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128 LOG(INFO) << "Decoding DICOM instance: " << uri; |
0 | 129 |
130 CompressionType type; | |
131 uint8_t level; | |
132 std::string instanceId; | |
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133 unsigned int frameIndex; |
0 | 134 |
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135 if (!ParseUri(type, level, instanceId, frameIndex, uri)) |
0 | 136 { |
137 return false; | |
138 } | |
139 | |
96 | 140 bool ok = false; |
141 | |
142 Json::Value tags; | |
143 std::string dicom; | |
144 if (!GetStringFromOrthanc(dicom, context_, "/instances/" + instanceId + "/file") || | |
145 !GetJsonFromOrthanc(tags, context_, "/instances/" + instanceId + "/tags")) | |
146 { | |
147 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
148 } | |
149 | |
230
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150 std::unique_ptr<OrthancImage> image( |
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151 new OrthancImage(OrthancPluginDecodeDicomImage( |
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152 context_, dicom.c_str(), dicom.size(), frameIndex))); |
96 | 153 |
154 Json::Value json; | |
155 if (GetCornerstoneMetadata(json, tags, *image)) | |
156 { | |
157 if (type == CompressionType_Deflate) | |
158 { | |
173
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159 ok = EncodeUsingDeflate(json, *image); |
96 | 160 } |
161 else if (type == CompressionType_Jpeg) | |
162 { | |
163 ok = EncodeUsingJpeg(json, *image, level); | |
164 } | |
165 } | |
166 | |
31 | 167 if (ok) |
168 { | |
160 | 169 std::string photometric; |
170 if (GetStringTag(photometric, tags, "0028,0004")) | |
171 { | |
172 json["Orthanc"]["PhotometricInterpretation"] = photometric; | |
173 } | |
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174 |
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175 Orthanc::Toolbox::WriteFastJson(content, json); |
31 | 176 return true; |
0 | 177 } |
178 else | |
179 { | |
234
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180 LOG(WARNING) << "Unable to decode the following instance: " << uri; |
0 | 181 return false; |
182 } | |
183 } | |
96 | 184 |
185 | |
186 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
187 const Json::Value& tags, | |
230
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188 OrthancImage& image) |
96 | 189 { |
190 float windowCenter, windowWidth; | |
191 | |
192 Orthanc::ImageAccessor accessor; | |
230
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193 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetPixelFormat()), image.GetWidth(), |
96 | 194 image.GetHeight(), image.GetPitch(), image.GetBuffer()); |
195 | |
196 switch (accessor.GetFormat()) | |
197 { | |
296
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198 case Orthanc::PixelFormat_Grayscale8: |
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199 case Orthanc::PixelFormat_Grayscale16: |
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200 case Orthanc::PixelFormat_SignedGrayscale16: |
96 | 201 { |
202 int64_t a, b; | |
172 | 203 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
96 | 204 result["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); |
205 result["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
206 result["color"] = false; | |
207 | |
208 windowCenter = static_cast<float>(a + b) / 2.0f; | |
209 | |
210 if (a == b) | |
211 { | |
212 windowWidth = 256.0f; // Arbitrary value | |
213 } | |
214 else | |
215 { | |
216 windowWidth = static_cast<float>(b - a) / 2.0f; | |
217 } | |
218 | |
219 break; | |
220 } | |
221 | |
296
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222 case Orthanc::PixelFormat_RGB24: |
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223 case Orthanc::PixelFormat_RGB48: |
96 | 224 result["minPixelValue"] = 0; |
225 result["maxPixelValue"] = 255; | |
226 result["color"] = true; | |
227 windowCenter = 127.5f; | |
228 windowWidth = 256.0f; | |
229 break; | |
230 | |
231 default: | |
232 return false; | |
233 } | |
234 | |
102 | 235 float slope = GetFloatTag(tags, "0028,1053", 1.0f); |
103 | 236 float intercept = GetFloatTag(tags, "0028,1052", 0.0f); |
102 | 237 |
238 result["slope"] = slope; | |
239 result["intercept"] = intercept; | |
96 | 240 result["rows"] = image.GetHeight(); |
241 result["columns"] = image.GetWidth(); | |
242 result["height"] = image.GetHeight(); | |
243 result["width"] = image.GetWidth(); | |
244 | |
102 | 245 bool ok = false; |
246 std::string pixelSpacing; | |
247 if (GetStringTag(pixelSpacing, tags, "0028,0030")) | |
96 | 248 { |
102 | 249 std::vector<std::string> tokens; |
250 Orthanc::Toolbox::TokenizeString(tokens, pixelSpacing, '\\'); | |
251 | |
252 if (tokens.size() >= 2) | |
96 | 253 { |
102 | 254 try |
255 { | |
103 | 256 result["columnPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[1])); |
257 result["rowPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[0])); | |
102 | 258 ok = true; |
259 } | |
260 catch (boost::bad_lexical_cast&) | |
261 { | |
262 } | |
96 | 263 } |
264 } | |
102 | 265 |
266 if (!ok) | |
96 | 267 { |
102 | 268 result["columnPixelSpacing"] = 1.0f; |
269 result["rowPixelSpacing"] = 1.0f; | |
96 | 270 } |
271 | |
102 | 272 result["windowCenter"] = GetFloatTag(tags, "0028,1050", windowCenter * slope + intercept); |
273 result["windowWidth"] = GetFloatTag(tags, "0028,1051", windowWidth * slope); | |
274 | |
96 | 275 return true; |
276 } | |
277 | |
278 | |
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279 static void ConvertRGB48ToRGB24(Orthanc::ImageAccessor& target, |
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280 const Orthanc::ImageAccessor& source) |
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281 { |
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282 if (source.GetWidth() != target.GetWidth() || |
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283 source.GetHeight() != target.GetHeight()) |
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284 { |
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285 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
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286 } |
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287 |
287 | 288 const unsigned int width = source.GetWidth(); |
289 const unsigned int height = source.GetHeight(); | |
290 | |
291 for (unsigned int y = 0; y < height; y++) | |
173
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292 { |
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293 const uint16_t* p = reinterpret_cast<const uint16_t*>(source.GetConstRow(y)); |
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294 uint8_t* q = reinterpret_cast<uint8_t*>(target.GetRow(y)); |
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295 |
287 | 296 for (unsigned int x = 0; x < width; x++) |
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297 { |
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298 q[0] = p[0] >> 8; |
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299 q[1] = p[1] >> 8; |
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300 q[2] = p[2] >> 8; |
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301 p += 3; |
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302 q += 3; |
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303 } |
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304 } |
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305 } |
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306 |
96 | 307 |
308 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
230
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309 OrthancImage& image) |
96 | 310 { |
311 Orthanc::ImageAccessor accessor; | |
230
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312 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetPixelFormat()), image.GetWidth(), |
96 | 313 image.GetHeight(), image.GetPitch(), image.GetBuffer()); |
314 | |
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315 std::unique_ptr<Orthanc::ImageBuffer> buffer; |
96 | 316 |
317 Orthanc::ImageAccessor converted; | |
318 | |
319 switch (accessor.GetFormat()) | |
320 { | |
321 case Orthanc::PixelFormat_RGB24: | |
207
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322 accessor.GetReadOnlyAccessor(converted); |
96 | 323 break; |
324 | |
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325 case Orthanc::PixelFormat_RGB48: |
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326 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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327 accessor.GetWidth(), |
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328 accessor.GetHeight(), false)); |
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329 buffer->GetWriteableAccessor(converted); |
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330 ConvertRGB48ToRGB24(converted, accessor); |
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331 break; |
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332 |
96 | 333 case Orthanc::PixelFormat_Grayscale8: |
334 case Orthanc::PixelFormat_Grayscale16: | |
145 | 335 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale16, |
336 accessor.GetWidth(), | |
337 accessor.GetHeight(), | |
338 true /* force minimal pitch */)); | |
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339 buffer->GetWriteableAccessor(converted); |
96 | 340 Orthanc::ImageProcessing::Convert(converted, accessor); |
341 break; | |
342 | |
343 case Orthanc::PixelFormat_SignedGrayscale16: | |
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344 accessor.GetReadOnlyAccessor(converted); |
96 | 345 break; |
346 | |
347 default: | |
348 // Unsupported pixel format | |
349 return false; | |
350 } | |
351 | |
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352 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
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353 |
96 | 354 // Sanity check: The pitch must be minimal |
355 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
356 GetBytesPerPixel(converted.GetFormat())); | |
357 result["Orthanc"]["Compression"] = "Deflate"; | |
358 result["sizeInBytes"] = converted.GetSize(); | |
359 | |
360 std::string z; | |
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361 CompressUsingDeflate(z, GetGlobalContext(), converted.GetConstBuffer(), converted.GetSize()); |
216 | 362 |
363 std::string s; | |
364 Orthanc::Toolbox::EncodeBase64(s, z); | |
365 result["Orthanc"]["PixelData"] = s; | |
96 | 366 |
367 return true; | |
368 } | |
369 | |
370 | |
371 | |
372 template <typename TargetType, typename SourceType> | |
373 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
374 const Orthanc::ImageAccessor& source, | |
375 SourceType source1, TargetType target1, | |
376 SourceType source2, TargetType target2) | |
377 { | |
378 if (source.GetWidth() != target.GetWidth() || | |
379 source.GetHeight() != target.GetHeight()) | |
380 { | |
381 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
382 } | |
383 | |
384 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
385 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
386 | |
387 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
388 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
389 | |
287 | 390 const unsigned int width = source.GetWidth(); |
391 const unsigned int height = source.GetHeight(); | |
392 | |
393 for (unsigned int y = 0; y < height; y++) | |
96 | 394 { |
395 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
396 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
397 | |
287 | 398 for (unsigned int x = 0; x < width; x++, p++, q++) |
96 | 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, | |
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423 OrthancImage& image, |
96 | 424 uint8_t quality /* between 0 and 100 */) |
425 { | |
426 Orthanc::ImageAccessor accessor; | |
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427 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetPixelFormat()), image.GetWidth(), |
96 | 428 image.GetHeight(), image.GetPitch(), image.GetBuffer()); |
429 | |
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430 std::unique_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 } |
173
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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; | |
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486 WriteJpegToMemory(jpeg, GetGlobalContext(), converted, quality); |
96 | 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 } |