Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 159:5dc54316d68b
shared copyright with osimis
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 04 Jan 2017 16:41:43 +0100 |
| parents | d850500b8ca6 |
| children | b0910ae2ace5 |
| 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 Osimis, 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 | |
| 96 | 24 #include "../Orthanc/Core/Images/ImageBuffer.h" |
| 25 #include "../Orthanc/Core/Images/ImageProcessing.h" | |
| 26 #include "../Orthanc/Core/OrthancException.h" | |
| 102 | 27 #include "../Orthanc/Core/Toolbox.h" |
| 96 | 28 #include "../Orthanc/Plugins/Samples/GdcmDecoder/OrthancImageWrapper.h" |
| 29 #include "../Orthanc/Resources/ThirdParty/base64/base64.h" | |
| 0 | 30 #include "ViewerToolbox.h" |
| 31 | |
| 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 { | |
| 40 bool DecodedImageAdapter::ParseUri(CompressionType& type, | |
| 41 uint8_t& compressionLevel, | |
| 42 std::string& instanceId, | |
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43 unsigned int& frameIndex, |
| 0 | 44 const std::string& uri) |
| 45 { | |
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46 boost::regex pattern("^([a-z0-9]+)-([a-z0-9-]+)_([0-9]+)$"); |
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47 |
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48 boost::cmatch what; |
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49 if (!regex_match(uri.c_str(), what, pattern)) |
| 0 | 50 { |
| 51 return false; | |
| 52 } | |
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53 |
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54 std::string compression(what[1]); |
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55 instanceId = what[2]; |
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56 frameIndex = boost::lexical_cast<unsigned int>(what[3]); |
| 0 | 57 |
| 58 if (compression == "deflate") | |
| 59 { | |
| 60 type = CompressionType_Deflate; | |
| 61 } | |
| 62 else if (boost::starts_with(compression, "jpeg")) | |
| 63 { | |
| 64 type = CompressionType_Jpeg; | |
| 65 int level = boost::lexical_cast<int>(compression.substr(4)); | |
| 66 if (level <= 0 || level > 100) | |
| 67 { | |
| 68 return false; | |
| 69 } | |
| 70 | |
| 71 compressionLevel = static_cast<uint8_t>(level); | |
| 72 } | |
| 73 else | |
| 74 { | |
| 75 return false; | |
| 76 } | |
| 77 | |
| 78 return true; | |
| 79 } | |
| 80 | |
| 81 | |
| 82 | |
| 83 bool DecodedImageAdapter::Create(std::string& content, | |
| 84 const std::string& uri) | |
| 85 { | |
| 86 std::string message = "Decoding DICOM instance: " + uri; | |
| 87 OrthancPluginLogInfo(context_, message.c_str()); | |
| 88 | |
| 89 CompressionType type; | |
| 90 uint8_t level; | |
| 91 std::string instanceId; | |
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92 unsigned int frameIndex; |
| 0 | 93 |
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94 if (!ParseUri(type, level, instanceId, frameIndex, uri)) |
| 0 | 95 { |
| 96 return false; | |
| 97 } | |
| 98 | |
| 96 | 99 |
| 100 bool ok = false; | |
| 101 | |
| 102 Json::Value tags; | |
| 103 std::string dicom; | |
| 104 if (!GetStringFromOrthanc(dicom, context_, "/instances/" + instanceId + "/file") || | |
| 105 !GetJsonFromOrthanc(tags, context_, "/instances/" + instanceId + "/tags")) | |
| 106 { | |
| 107 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 108 } | |
| 109 | |
| 102 | 110 std::auto_ptr<OrthancImageWrapper> image(new OrthancImageWrapper(context_, OrthancPluginDecodeDicomImage(context_, dicom.c_str(), dicom.size(), frameIndex))); |
| 96 | 111 |
| 112 Json::Value json; | |
| 113 if (GetCornerstoneMetadata(json, tags, *image)) | |
| 114 { | |
| 115 if (type == CompressionType_Deflate) | |
| 116 { | |
| 117 ok = EncodeUsingDeflate(json, *image, 9); | |
| 118 } | |
| 119 else if (type == CompressionType_Jpeg) | |
| 120 { | |
| 121 ok = EncodeUsingJpeg(json, *image, level); | |
| 122 } | |
| 123 } | |
| 124 | |
| 31 | 125 if (ok) |
| 126 { | |
| 127 Json::FastWriter writer; | |
| 128 content = writer.write(json); | |
| 129 return true; | |
| 0 | 130 } |
| 131 else | |
| 132 { | |
| 31 | 133 char msg[1024]; |
| 134 sprintf(msg, "Unable to decode the following instance: %s", uri.c_str()); | |
| 135 OrthancPluginLogWarning(context_, msg); | |
| 0 | 136 return false; |
| 137 } | |
| 138 } | |
| 96 | 139 |
| 140 | |
| 102 | 141 static bool GetStringTag(std::string& value, |
| 142 const Json::Value& tags, | |
| 143 const std::string& tag) | |
| 96 | 144 { |
| 145 if (tags.type() == Json::objectValue && | |
| 146 tags.isMember(tag) && | |
| 147 tags[tag].type() == Json::objectValue && | |
| 148 tags[tag].isMember("Type") && | |
| 149 tags[tag].isMember("Value") && | |
| 150 tags[tag]["Type"].type() == Json::stringValue && | |
| 151 tags[tag]["Value"].type() == Json::stringValue && | |
| 152 tags[tag]["Type"].asString() == "String") | |
| 153 { | |
| 154 value = tags[tag]["Value"].asString(); | |
| 155 return true; | |
| 156 } | |
| 157 else | |
| 158 { | |
| 159 return false; | |
| 160 } | |
| 161 } | |
| 162 | |
| 163 | |
| 102 | 164 static float GetFloatTag(const Json::Value& tags, |
| 165 const std::string& tag, | |
| 166 float defaultValue) | |
| 167 { | |
| 168 std::string tmp; | |
| 169 if (GetStringTag(tmp, tags, tag)) | |
| 170 { | |
| 171 try | |
| 172 { | |
| 103 | 173 return boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tmp)); |
| 102 | 174 } |
| 175 catch (boost::bad_lexical_cast&) | |
| 176 { | |
| 177 } | |
| 178 } | |
| 179 | |
| 180 return defaultValue; | |
| 181 } | |
| 182 | |
| 183 | |
| 96 | 184 |
| 185 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
| 186 const Json::Value& tags, | |
| 187 OrthancImageWrapper& image) | |
| 188 { | |
| 189 using namespace Orthanc; | |
| 190 | |
| 191 float windowCenter, windowWidth; | |
| 192 | |
| 193 Orthanc::ImageAccessor accessor; | |
| 194 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 195 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 196 | |
| 197 switch (accessor.GetFormat()) | |
| 198 { | |
| 199 case PixelFormat_Grayscale8: | |
| 200 case PixelFormat_Grayscale16: | |
| 201 case PixelFormat_SignedGrayscale16: | |
| 202 { | |
| 203 int64_t a, b; | |
| 204 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
| 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 | |
| 223 case PixelFormat_RGB24: | |
| 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 | |
| 279 | |
| 280 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
| 281 OrthancImageWrapper& image, | |
| 282 uint8_t compressionLevel /* between 0 and 9 */) | |
| 283 { | |
| 284 Orthanc::ImageAccessor accessor; | |
| 285 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 286 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 287 | |
| 145 | 288 std::auto_ptr<Orthanc::ImageBuffer> buffer; |
| 96 | 289 |
| 290 Orthanc::ImageAccessor converted; | |
| 291 | |
| 292 switch (accessor.GetFormat()) | |
| 293 { | |
| 294 case Orthanc::PixelFormat_RGB24: | |
| 295 converted = accessor; | |
| 296 break; | |
| 297 | |
| 298 case Orthanc::PixelFormat_Grayscale8: | |
| 299 case Orthanc::PixelFormat_Grayscale16: | |
| 145 | 300 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale16, |
| 301 accessor.GetWidth(), | |
| 302 accessor.GetHeight(), | |
| 303 true /* force minimal pitch */)); | |
| 304 converted = buffer->GetAccessor(); | |
| 96 | 305 Orthanc::ImageProcessing::Convert(converted, accessor); |
| 306 break; | |
| 307 | |
| 308 case Orthanc::PixelFormat_SignedGrayscale16: | |
| 309 converted = accessor; | |
| 310 break; | |
| 311 | |
| 312 default: | |
| 313 // Unsupported pixel format | |
| 314 return false; | |
| 315 } | |
| 316 | |
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317 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
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318 |
| 96 | 319 // Sanity check: The pitch must be minimal |
| 320 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
| 321 GetBytesPerPixel(converted.GetFormat())); | |
| 322 result["Orthanc"]["Compression"] = "Deflate"; | |
| 323 result["sizeInBytes"] = converted.GetSize(); | |
| 324 | |
| 325 std::string z; | |
| 326 CompressUsingDeflate(z, image.GetContext(), converted.GetConstBuffer(), converted.GetSize()); | |
| 327 | |
| 328 result["Orthanc"]["PixelData"] = base64_encode(z); | |
| 329 | |
| 330 return true; | |
| 331 } | |
| 332 | |
| 333 | |
| 334 | |
| 335 template <typename TargetType, typename SourceType> | |
| 336 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
| 337 const Orthanc::ImageAccessor& source, | |
| 338 SourceType source1, TargetType target1, | |
| 339 SourceType source2, TargetType target2) | |
| 340 { | |
| 341 if (source.GetWidth() != target.GetWidth() || | |
| 342 source.GetHeight() != target.GetHeight()) | |
| 343 { | |
| 344 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 345 } | |
| 346 | |
| 347 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
| 348 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
| 349 | |
| 350 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
| 351 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
| 352 | |
| 353 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
| 354 { | |
| 355 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
| 356 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
| 357 | |
| 358 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
| 359 { | |
| 360 float v = (scale * static_cast<float>(*p)) + offset; | |
| 361 | |
| 362 if (v > maxValue) | |
| 363 { | |
| 364 *q = std::numeric_limits<TargetType>::max(); | |
| 365 } | |
| 366 else if (v < minValue) | |
| 367 { | |
| 368 *q = std::numeric_limits<TargetType>::min(); | |
| 369 } | |
| 370 else | |
| 371 { | |
| 101 | 372 //*q = static_cast<TargetType>(boost::math::iround(v)); |
| 373 | |
| 374 // http://stackoverflow.com/a/485546/881731 | |
| 375 *q = static_cast<TargetType>(floor(v + 0.5f)); | |
| 96 | 376 } |
| 377 } | |
| 378 } | |
| 379 } | |
| 380 | |
| 381 | |
| 382 bool DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result, | |
| 383 OrthancImageWrapper& image, | |
| 384 uint8_t quality /* between 0 and 100 */) | |
| 385 { | |
| 386 Orthanc::ImageAccessor accessor; | |
| 387 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 388 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 389 | |
| 145 | 390 std::auto_ptr<Orthanc::ImageBuffer> buffer; |
| 96 | 391 |
| 392 Orthanc::ImageAccessor converted; | |
| 393 | |
| 394 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
| 395 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
| 396 { | |
| 397 result["Orthanc"]["Stretched"] = false; | |
| 398 converted = accessor; | |
| 399 } | |
| 400 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || | |
| 401 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
| 402 { | |
| 403 result["Orthanc"]["Stretched"] = true; | |
| 145 | 404 |
| 405 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale8, | |
| 406 accessor.GetWidth(), | |
| 407 accessor.GetHeight(), | |
| 408 true /* force minimal pitch */)); | |
| 409 converted = buffer->GetAccessor(); | |
| 96 | 410 |
| 411 int64_t a, b; | |
| 412 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
| 413 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); | |
| 414 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
| 415 | |
| 416 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
| 417 { | |
| 418 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
| 419 } | |
| 420 else | |
| 421 { | |
| 422 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
| 423 } | |
| 424 } | |
| 425 else | |
| 426 { | |
| 427 return false; | |
| 428 } | |
| 429 | |
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430 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
| 96 | 431 result["Orthanc"]["Compression"] = "Jpeg"; |
| 432 result["sizeInBytes"] = converted.GetSize(); | |
| 433 | |
| 434 std::string jpeg; | |
| 435 WriteJpegToMemory(jpeg, image.GetContext(), converted, quality); | |
| 436 | |
| 437 result["Orthanc"]["PixelData"] = base64_encode(jpeg); | |
| 438 return true; | |
| 439 } | |
| 0 | 440 } |