Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 199:21df474deeb1 OrthancWebViewer-2.4
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 23 Apr 2018 13:40:44 +0200 |
| parents | 993dd140bd30 |
| children | 3d3d00e3e715 |
| 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) 2017-2018 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 #include <Resources/ThirdParty/base64/base64.h> |
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32 |
| 0 | 33 #include <boost/lexical_cast.hpp> |
| 34 #include <boost/algorithm/string/predicate.hpp> | |
| 35 #include <json/writer.h> | |
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36 #include <boost/regex.hpp> |
| 0 | 37 |
| 103 | 38 |
| 0 | 39 namespace OrthancPlugins |
| 40 { | |
| 160 | 41 static bool GetStringTag(std::string& value, |
| 42 const Json::Value& tags, | |
| 43 const std::string& tag) | |
| 44 { | |
| 45 if (tags.type() == Json::objectValue && | |
| 46 tags.isMember(tag) && | |
| 47 tags[tag].type() == Json::objectValue && | |
| 48 tags[tag].isMember("Type") && | |
| 49 tags[tag].isMember("Value") && | |
| 50 tags[tag]["Type"].type() == Json::stringValue && | |
| 51 tags[tag]["Value"].type() == Json::stringValue && | |
| 52 tags[tag]["Type"].asString() == "String") | |
| 53 { | |
| 54 value = tags[tag]["Value"].asString(); | |
| 55 return true; | |
| 56 } | |
| 57 else | |
| 58 { | |
| 59 return false; | |
| 60 } | |
| 61 } | |
| 62 | |
| 63 | |
| 64 static float GetFloatTag(const Json::Value& tags, | |
| 65 const std::string& tag, | |
| 66 float defaultValue) | |
| 67 { | |
| 68 std::string tmp; | |
| 69 if (GetStringTag(tmp, tags, tag)) | |
| 70 { | |
| 71 try | |
| 72 { | |
| 73 return boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tmp)); | |
| 74 } | |
| 75 catch (boost::bad_lexical_cast&) | |
| 76 { | |
| 77 } | |
| 78 } | |
| 79 | |
| 80 return defaultValue; | |
| 81 } | |
| 82 | |
| 83 | |
| 0 | 84 bool DecodedImageAdapter::ParseUri(CompressionType& type, |
| 85 uint8_t& compressionLevel, | |
| 86 std::string& instanceId, | |
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87 unsigned int& frameIndex, |
| 0 | 88 const std::string& uri) |
| 89 { | |
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90 boost::regex pattern("^([a-z0-9]+)-([a-z0-9-]+)_([0-9]+)$"); |
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91 |
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92 boost::cmatch what; |
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93 if (!regex_match(uri.c_str(), what, pattern)) |
| 0 | 94 { |
| 95 return false; | |
| 96 } | |
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97 |
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98 std::string compression(what[1]); |
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99 instanceId = what[2]; |
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100 frameIndex = boost::lexical_cast<unsigned int>(what[3]); |
| 0 | 101 |
| 102 if (compression == "deflate") | |
| 103 { | |
| 104 type = CompressionType_Deflate; | |
| 105 } | |
| 106 else if (boost::starts_with(compression, "jpeg")) | |
| 107 { | |
| 108 type = CompressionType_Jpeg; | |
| 109 int level = boost::lexical_cast<int>(compression.substr(4)); | |
| 110 if (level <= 0 || level > 100) | |
| 111 { | |
| 112 return false; | |
| 113 } | |
| 114 | |
| 115 compressionLevel = static_cast<uint8_t>(level); | |
| 116 } | |
| 117 else | |
| 118 { | |
| 119 return false; | |
| 120 } | |
| 121 | |
| 122 return true; | |
| 123 } | |
| 124 | |
| 125 | |
| 126 | |
| 127 bool DecodedImageAdapter::Create(std::string& content, | |
| 128 const std::string& uri) | |
| 129 { | |
| 130 std::string message = "Decoding DICOM instance: " + uri; | |
| 131 OrthancPluginLogInfo(context_, message.c_str()); | |
| 132 | |
| 133 CompressionType type; | |
| 134 uint8_t level; | |
| 135 std::string instanceId; | |
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136 unsigned int frameIndex; |
| 0 | 137 |
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138 if (!ParseUri(type, level, instanceId, frameIndex, uri)) |
| 0 | 139 { |
| 140 return false; | |
| 141 } | |
| 142 | |
| 96 | 143 |
| 144 bool ok = false; | |
| 145 | |
| 146 Json::Value tags; | |
| 147 std::string dicom; | |
| 148 if (!GetStringFromOrthanc(dicom, context_, "/instances/" + instanceId + "/file") || | |
| 149 !GetJsonFromOrthanc(tags, context_, "/instances/" + instanceId + "/tags")) | |
| 150 { | |
| 151 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 152 } | |
| 153 | |
| 102 | 154 std::auto_ptr<OrthancImageWrapper> image(new OrthancImageWrapper(context_, OrthancPluginDecodeDicomImage(context_, dicom.c_str(), dicom.size(), frameIndex))); |
| 96 | 155 |
| 156 Json::Value json; | |
| 157 if (GetCornerstoneMetadata(json, tags, *image)) | |
| 158 { | |
| 159 if (type == CompressionType_Deflate) | |
| 160 { | |
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161 ok = EncodeUsingDeflate(json, *image); |
| 96 | 162 } |
| 163 else if (type == CompressionType_Jpeg) | |
| 164 { | |
| 165 ok = EncodeUsingJpeg(json, *image, level); | |
| 166 } | |
| 167 } | |
| 168 | |
| 31 | 169 if (ok) |
| 170 { | |
| 160 | 171 std::string photometric; |
| 172 if (GetStringTag(photometric, tags, "0028,0004")) | |
| 173 { | |
| 174 json["Orthanc"]["PhotometricInterpretation"] = photometric; | |
| 175 } | |
| 176 | |
| 31 | 177 Json::FastWriter writer; |
| 178 content = writer.write(json); | |
| 179 return true; | |
| 0 | 180 } |
| 181 else | |
| 182 { | |
| 31 | 183 char msg[1024]; |
| 184 sprintf(msg, "Unable to decode the following instance: %s", uri.c_str()); | |
| 185 OrthancPluginLogWarning(context_, msg); | |
| 0 | 186 return false; |
| 187 } | |
| 188 } | |
| 96 | 189 |
| 190 | |
| 191 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
| 192 const Json::Value& tags, | |
| 193 OrthancImageWrapper& image) | |
| 194 { | |
| 195 using namespace Orthanc; | |
| 196 | |
| 197 float windowCenter, windowWidth; | |
| 198 | |
| 199 Orthanc::ImageAccessor accessor; | |
| 200 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 201 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 202 | |
| 203 switch (accessor.GetFormat()) | |
| 204 { | |
| 205 case PixelFormat_Grayscale8: | |
| 206 case PixelFormat_Grayscale16: | |
| 207 case PixelFormat_SignedGrayscale16: | |
| 208 { | |
| 209 int64_t a, b; | |
| 172 | 210 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
| 96 | 211 result["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); |
| 212 result["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
| 213 result["color"] = false; | |
| 214 | |
| 215 windowCenter = static_cast<float>(a + b) / 2.0f; | |
| 216 | |
| 217 if (a == b) | |
| 218 { | |
| 219 windowWidth = 256.0f; // Arbitrary value | |
| 220 } | |
| 221 else | |
| 222 { | |
| 223 windowWidth = static_cast<float>(b - a) / 2.0f; | |
| 224 } | |
| 225 | |
| 226 break; | |
| 227 } | |
| 228 | |
| 229 case PixelFormat_RGB24: | |
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230 case PixelFormat_RGB48: |
| 96 | 231 result["minPixelValue"] = 0; |
| 232 result["maxPixelValue"] = 255; | |
| 233 result["color"] = true; | |
| 234 windowCenter = 127.5f; | |
| 235 windowWidth = 256.0f; | |
| 236 break; | |
| 237 | |
| 238 default: | |
| 239 return false; | |
| 240 } | |
| 241 | |
| 102 | 242 float slope = GetFloatTag(tags, "0028,1053", 1.0f); |
| 103 | 243 float intercept = GetFloatTag(tags, "0028,1052", 0.0f); |
| 102 | 244 |
| 245 result["slope"] = slope; | |
| 246 result["intercept"] = intercept; | |
| 96 | 247 result["rows"] = image.GetHeight(); |
| 248 result["columns"] = image.GetWidth(); | |
| 249 result["height"] = image.GetHeight(); | |
| 250 result["width"] = image.GetWidth(); | |
| 251 | |
| 102 | 252 bool ok = false; |
| 253 std::string pixelSpacing; | |
| 254 if (GetStringTag(pixelSpacing, tags, "0028,0030")) | |
| 96 | 255 { |
| 102 | 256 std::vector<std::string> tokens; |
| 257 Orthanc::Toolbox::TokenizeString(tokens, pixelSpacing, '\\'); | |
| 258 | |
| 259 if (tokens.size() >= 2) | |
| 96 | 260 { |
| 102 | 261 try |
| 262 { | |
| 103 | 263 result["columnPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[1])); |
| 264 result["rowPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[0])); | |
| 102 | 265 ok = true; |
| 266 } | |
| 267 catch (boost::bad_lexical_cast&) | |
| 268 { | |
| 269 } | |
| 96 | 270 } |
| 271 } | |
| 102 | 272 |
| 273 if (!ok) | |
| 96 | 274 { |
| 102 | 275 result["columnPixelSpacing"] = 1.0f; |
| 276 result["rowPixelSpacing"] = 1.0f; | |
| 96 | 277 } |
| 278 | |
| 102 | 279 result["windowCenter"] = GetFloatTag(tags, "0028,1050", windowCenter * slope + intercept); |
| 280 result["windowWidth"] = GetFloatTag(tags, "0028,1051", windowWidth * slope); | |
| 281 | |
| 96 | 282 return true; |
| 283 } | |
| 284 | |
| 285 | |
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286 static void ConvertRGB48ToRGB24(Orthanc::ImageAccessor& target, |
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287 const Orthanc::ImageAccessor& source) |
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288 { |
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289 if (source.GetWidth() != target.GetWidth() || |
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290 source.GetHeight() != target.GetHeight()) |
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291 { |
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292 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
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293 } |
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294 |
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295 for (unsigned int y = 0; y < source.GetHeight(); y++) |
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296 { |
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297 const uint16_t* p = reinterpret_cast<const uint16_t*>(source.GetConstRow(y)); |
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298 uint8_t* q = reinterpret_cast<uint8_t*>(target.GetRow(y)); |
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299 |
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300 for (unsigned int x = 0; x < source.GetWidth(); x++) |
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301 { |
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302 q[0] = p[0] >> 8; |
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303 q[1] = p[1] >> 8; |
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304 q[2] = p[2] >> 8; |
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305 p += 3; |
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306 q += 3; |
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307 } |
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308 } |
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309 } |
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310 |
| 96 | 311 |
| 312 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
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313 OrthancImageWrapper& image) |
| 96 | 314 { |
| 315 Orthanc::ImageAccessor accessor; | |
| 316 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 317 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 318 | |
| 145 | 319 std::auto_ptr<Orthanc::ImageBuffer> buffer; |
| 96 | 320 |
| 321 Orthanc::ImageAccessor converted; | |
| 322 | |
| 323 switch (accessor.GetFormat()) | |
| 324 { | |
| 325 case Orthanc::PixelFormat_RGB24: | |
| 326 converted = accessor; | |
| 327 break; | |
| 328 | |
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329 case Orthanc::PixelFormat_RGB48: |
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330 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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331 accessor.GetWidth(), |
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332 accessor.GetHeight(), false)); |
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333 converted = buffer->GetAccessor(); |
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334 ConvertRGB48ToRGB24(converted, accessor); |
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335 break; |
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336 |
| 96 | 337 case Orthanc::PixelFormat_Grayscale8: |
| 338 case Orthanc::PixelFormat_Grayscale16: | |
| 145 | 339 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale16, |
| 340 accessor.GetWidth(), | |
| 341 accessor.GetHeight(), | |
| 342 true /* force minimal pitch */)); | |
| 343 converted = buffer->GetAccessor(); | |
| 96 | 344 Orthanc::ImageProcessing::Convert(converted, accessor); |
| 345 break; | |
| 346 | |
| 347 case Orthanc::PixelFormat_SignedGrayscale16: | |
| 348 converted = accessor; | |
| 349 break; | |
| 350 | |
| 351 default: | |
| 352 // Unsupported pixel format | |
| 353 return false; | |
| 354 } | |
| 355 | |
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356 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
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357 |
| 96 | 358 // Sanity check: The pitch must be minimal |
| 359 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
| 360 GetBytesPerPixel(converted.GetFormat())); | |
| 361 result["Orthanc"]["Compression"] = "Deflate"; | |
| 362 result["sizeInBytes"] = converted.GetSize(); | |
| 363 | |
| 364 std::string z; | |
| 365 CompressUsingDeflate(z, image.GetContext(), converted.GetConstBuffer(), converted.GetSize()); | |
| 366 | |
| 367 result["Orthanc"]["PixelData"] = base64_encode(z); | |
| 368 | |
| 369 return true; | |
| 370 } | |
| 371 | |
| 372 | |
| 373 | |
| 374 template <typename TargetType, typename SourceType> | |
| 375 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
| 376 const Orthanc::ImageAccessor& source, | |
| 377 SourceType source1, TargetType target1, | |
| 378 SourceType source2, TargetType target2) | |
| 379 { | |
| 380 if (source.GetWidth() != target.GetWidth() || | |
| 381 source.GetHeight() != target.GetHeight()) | |
| 382 { | |
| 383 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 384 } | |
| 385 | |
| 386 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
| 387 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
| 388 | |
| 389 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
| 390 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
| 391 | |
| 392 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
| 393 { | |
| 394 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
| 395 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
| 396 | |
| 397 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
| 398 { | |
| 399 float v = (scale * static_cast<float>(*p)) + offset; | |
| 400 | |
| 401 if (v > maxValue) | |
| 402 { | |
| 403 *q = std::numeric_limits<TargetType>::max(); | |
| 404 } | |
| 405 else if (v < minValue) | |
| 406 { | |
| 407 *q = std::numeric_limits<TargetType>::min(); | |
| 408 } | |
| 409 else | |
| 410 { | |
| 101 | 411 //*q = static_cast<TargetType>(boost::math::iround(v)); |
| 412 | |
| 413 // http://stackoverflow.com/a/485546/881731 | |
| 414 *q = static_cast<TargetType>(floor(v + 0.5f)); | |
| 96 | 415 } |
| 416 } | |
| 417 } | |
| 418 } | |
| 419 | |
| 420 | |
| 421 bool DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result, | |
| 422 OrthancImageWrapper& image, | |
| 423 uint8_t quality /* between 0 and 100 */) | |
| 424 { | |
| 425 Orthanc::ImageAccessor accessor; | |
| 426 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 427 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 428 | |
| 145 | 429 std::auto_ptr<Orthanc::ImageBuffer> buffer; |
| 96 | 430 |
| 431 Orthanc::ImageAccessor converted; | |
| 432 | |
| 433 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
| 434 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
| 435 { | |
| 436 result["Orthanc"]["Stretched"] = false; | |
| 437 converted = accessor; | |
| 438 } | |
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439 else if (accessor.GetFormat() == Orthanc::PixelFormat_RGB48) |
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440 { |
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441 result["Orthanc"]["Stretched"] = false; |
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442 |
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443 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_RGB24, |
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444 accessor.GetWidth(), |
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445 accessor.GetHeight(), false)); |
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446 converted = buffer->GetAccessor(); |
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447 ConvertRGB48ToRGB24(converted, accessor); |
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448 } |
| 96 | 449 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || |
| 450 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
| 451 { | |
| 452 result["Orthanc"]["Stretched"] = true; | |
| 145 | 453 |
| 454 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale8, | |
| 455 accessor.GetWidth(), | |
| 456 accessor.GetHeight(), | |
| 457 true /* force minimal pitch */)); | |
| 458 converted = buffer->GetAccessor(); | |
| 96 | 459 |
| 460 int64_t a, b; | |
| 172 | 461 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, accessor); |
| 96 | 462 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); |
| 463 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
| 464 | |
| 465 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
| 466 { | |
| 467 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
| 468 } | |
| 469 else | |
| 470 { | |
| 471 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
| 472 } | |
| 473 } | |
| 474 else | |
| 475 { | |
| 476 return false; | |
| 477 } | |
| 478 | |
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479 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
| 96 | 480 result["Orthanc"]["Compression"] = "Jpeg"; |
| 481 result["sizeInBytes"] = converted.GetSize(); | |
| 482 | |
| 483 std::string jpeg; | |
| 484 WriteJpegToMemory(jpeg, image.GetContext(), converted, quality); | |
| 485 | |
| 486 result["Orthanc"]["PixelData"] = base64_encode(jpeg); | |
| 487 return true; | |
| 488 } | |
| 0 | 489 } |