Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 300:7dc18c36dd3d
sync + no more need of "-DORTHANC_FRAMEWORK_ADDITIONAL_LIBRARIES" to dynamically link against system-wide orthanc framework
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Sat, 12 Jun 2021 08:35:27 +0200 |
| parents | d179f3928342 |
| children | fb7d62e3235e |
| 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) 2017-2021 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 | |
|
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26 #include <Images/ImageBuffer.h> |
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27 #include <Images/ImageProcessing.h> |
| 287 | 28 #include <Logging.h> |
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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 { | |
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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 } | |
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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 | |
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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 { | |
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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 { | |
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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, | |
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188 OrthancImage& image) |
| 96 | 189 { |
| 190 float windowCenter, windowWidth; | |
| 191 | |
| 192 Orthanc::ImageAccessor accessor; | |
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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 { | |
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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 | |
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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++) | |
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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, | |
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309 OrthancImage& image) |
| 96 | 310 { |
| 311 Orthanc::ImageAccessor accessor; | |
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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: | |
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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 } |
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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 } |