Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 316:591ca447ebf8
Upgrade to Orthanc framework 1.12.3
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 26 Mar 2024 11:15:27 +0100 |
| parents | 0a1ad7492050 |
| children | 553fa466835a |
| rev | line source |
|---|---|
| 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) 2017-2024 Osimis S.A., Belgium |
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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 | |
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27 #include <Images/ImageBuffer.h> |
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28 #include <Images/ImageProcessing.h> |
| 287 | 29 #include <Logging.h> |
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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 { | |
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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 { | |
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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 | |
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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 { | |
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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 { | |
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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; | |
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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 { | |
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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 | |
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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++) | |
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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++) |
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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; | |
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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: | |
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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)); |
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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 } |