Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 226:aee499712ac4
upgrade to year 2020
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 31 Jan 2020 17:41:38 +0100 |
| parents | 47d52db10369 |
| children | e4def26f0fd3 |
| 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) 2017-2020 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 | |
| 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 { | |
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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 */)); | |
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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 } |