Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 142:d9e3f7bb9986
link to orthanc book
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 20 Jul 2016 13:01:30 +0200 |
| parents | f99adade8b77 |
| children | d850500b8ca6 |
| 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 |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU Affero General Public License | |
| 8 * as published by the Free Software Foundation, either version 3 of | |
| 9 * the License, or (at your option) any later version. | |
| 10 * | |
| 11 * This program is distributed in the hope that it will be useful, but | |
| 12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 14 * Affero General Public License for more details. | |
| 15 * | |
| 16 * You should have received a copy of the GNU Affero General Public License | |
| 17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 **/ | |
| 19 | |
| 20 | |
| 21 #include "DecodedImageAdapter.h" | |
| 22 | |
| 96 | 23 #include "../Orthanc/Core/Images/ImageBuffer.h" |
| 24 #include "../Orthanc/Core/Images/ImageProcessing.h" | |
| 25 #include "../Orthanc/Core/OrthancException.h" | |
| 102 | 26 #include "../Orthanc/Core/Toolbox.h" |
| 96 | 27 #include "../Orthanc/Plugins/Samples/GdcmDecoder/OrthancImageWrapper.h" |
| 28 #include "../Orthanc/Resources/ThirdParty/base64/base64.h" | |
| 0 | 29 #include "ViewerToolbox.h" |
| 30 | |
| 31 #include <boost/lexical_cast.hpp> | |
| 32 #include <boost/algorithm/string/predicate.hpp> | |
| 33 #include <json/writer.h> | |
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34 #include <boost/regex.hpp> |
| 0 | 35 |
| 103 | 36 |
| 0 | 37 namespace OrthancPlugins |
| 38 { | |
| 39 bool DecodedImageAdapter::ParseUri(CompressionType& type, | |
| 40 uint8_t& compressionLevel, | |
| 41 std::string& instanceId, | |
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42 unsigned int& frameIndex, |
| 0 | 43 const std::string& uri) |
| 44 { | |
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45 boost::regex pattern("^([a-z0-9]+)-([a-z0-9-]+)_([0-9]+)$"); |
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46 |
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47 boost::cmatch what; |
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48 if (!regex_match(uri.c_str(), what, pattern)) |
| 0 | 49 { |
| 50 return false; | |
| 51 } | |
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52 |
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53 std::string compression(what[1]); |
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54 instanceId = what[2]; |
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55 frameIndex = boost::lexical_cast<unsigned int>(what[3]); |
| 0 | 56 |
| 57 if (compression == "deflate") | |
| 58 { | |
| 59 type = CompressionType_Deflate; | |
| 60 } | |
| 61 else if (boost::starts_with(compression, "jpeg")) | |
| 62 { | |
| 63 type = CompressionType_Jpeg; | |
| 64 int level = boost::lexical_cast<int>(compression.substr(4)); | |
| 65 if (level <= 0 || level > 100) | |
| 66 { | |
| 67 return false; | |
| 68 } | |
| 69 | |
| 70 compressionLevel = static_cast<uint8_t>(level); | |
| 71 } | |
| 72 else | |
| 73 { | |
| 74 return false; | |
| 75 } | |
| 76 | |
| 77 return true; | |
| 78 } | |
| 79 | |
| 80 | |
| 81 | |
| 82 bool DecodedImageAdapter::Create(std::string& content, | |
| 83 const std::string& uri) | |
| 84 { | |
| 85 std::string message = "Decoding DICOM instance: " + uri; | |
| 86 OrthancPluginLogInfo(context_, message.c_str()); | |
| 87 | |
| 88 CompressionType type; | |
| 89 uint8_t level; | |
| 90 std::string instanceId; | |
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91 unsigned int frameIndex; |
| 0 | 92 |
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93 if (!ParseUri(type, level, instanceId, frameIndex, uri)) |
| 0 | 94 { |
| 95 return false; | |
| 96 } | |
| 97 | |
| 96 | 98 |
| 99 bool ok = false; | |
| 100 | |
| 101 Json::Value tags; | |
| 102 std::string dicom; | |
| 103 if (!GetStringFromOrthanc(dicom, context_, "/instances/" + instanceId + "/file") || | |
| 104 !GetJsonFromOrthanc(tags, context_, "/instances/" + instanceId + "/tags")) | |
| 105 { | |
| 106 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 107 } | |
| 108 | |
| 102 | 109 std::auto_ptr<OrthancImageWrapper> image(new OrthancImageWrapper(context_, OrthancPluginDecodeDicomImage(context_, dicom.c_str(), dicom.size(), frameIndex))); |
| 96 | 110 |
| 111 Json::Value json; | |
| 112 if (GetCornerstoneMetadata(json, tags, *image)) | |
| 113 { | |
| 114 if (type == CompressionType_Deflate) | |
| 115 { | |
| 116 ok = EncodeUsingDeflate(json, *image, 9); | |
| 117 } | |
| 118 else if (type == CompressionType_Jpeg) | |
| 119 { | |
| 120 ok = EncodeUsingJpeg(json, *image, level); | |
| 121 } | |
| 122 } | |
| 123 | |
| 31 | 124 if (ok) |
| 125 { | |
| 126 Json::FastWriter writer; | |
| 127 content = writer.write(json); | |
| 128 return true; | |
| 0 | 129 } |
| 130 else | |
| 131 { | |
| 31 | 132 char msg[1024]; |
| 133 sprintf(msg, "Unable to decode the following instance: %s", uri.c_str()); | |
| 134 OrthancPluginLogWarning(context_, msg); | |
| 0 | 135 return false; |
| 136 } | |
| 137 } | |
| 96 | 138 |
| 139 | |
| 102 | 140 static bool GetStringTag(std::string& value, |
| 141 const Json::Value& tags, | |
| 142 const std::string& tag) | |
| 96 | 143 { |
| 144 if (tags.type() == Json::objectValue && | |
| 145 tags.isMember(tag) && | |
| 146 tags[tag].type() == Json::objectValue && | |
| 147 tags[tag].isMember("Type") && | |
| 148 tags[tag].isMember("Value") && | |
| 149 tags[tag]["Type"].type() == Json::stringValue && | |
| 150 tags[tag]["Value"].type() == Json::stringValue && | |
| 151 tags[tag]["Type"].asString() == "String") | |
| 152 { | |
| 153 value = tags[tag]["Value"].asString(); | |
| 154 return true; | |
| 155 } | |
| 156 else | |
| 157 { | |
| 158 return false; | |
| 159 } | |
| 160 } | |
| 161 | |
| 162 | |
| 102 | 163 static float GetFloatTag(const Json::Value& tags, |
| 164 const std::string& tag, | |
| 165 float defaultValue) | |
| 166 { | |
| 167 std::string tmp; | |
| 168 if (GetStringTag(tmp, tags, tag)) | |
| 169 { | |
| 170 try | |
| 171 { | |
| 103 | 172 return boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tmp)); |
| 102 | 173 } |
| 174 catch (boost::bad_lexical_cast&) | |
| 175 { | |
| 176 } | |
| 177 } | |
| 178 | |
| 179 return defaultValue; | |
| 180 } | |
| 181 | |
| 182 | |
| 96 | 183 |
| 184 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
| 185 const Json::Value& tags, | |
| 186 OrthancImageWrapper& image) | |
| 187 { | |
| 188 using namespace Orthanc; | |
| 189 | |
| 190 float windowCenter, windowWidth; | |
| 191 | |
| 192 Orthanc::ImageAccessor accessor; | |
| 193 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 194 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 195 | |
| 196 switch (accessor.GetFormat()) | |
| 197 { | |
| 198 case PixelFormat_Grayscale8: | |
| 199 case PixelFormat_Grayscale16: | |
| 200 case PixelFormat_SignedGrayscale16: | |
| 201 { | |
| 202 int64_t a, b; | |
| 203 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
| 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 | |
| 222 case PixelFormat_RGB24: | |
| 223 result["minPixelValue"] = 0; | |
| 224 result["maxPixelValue"] = 255; | |
| 225 result["color"] = true; | |
| 226 windowCenter = 127.5f; | |
| 227 windowWidth = 256.0f; | |
| 228 break; | |
| 229 | |
| 230 default: | |
| 231 return false; | |
| 232 } | |
| 233 | |
| 102 | 234 float slope = GetFloatTag(tags, "0028,1053", 1.0f); |
| 103 | 235 float intercept = GetFloatTag(tags, "0028,1052", 0.0f); |
| 102 | 236 |
| 237 result["slope"] = slope; | |
| 238 result["intercept"] = intercept; | |
| 96 | 239 result["rows"] = image.GetHeight(); |
| 240 result["columns"] = image.GetWidth(); | |
| 241 result["height"] = image.GetHeight(); | |
| 242 result["width"] = image.GetWidth(); | |
| 243 | |
| 102 | 244 bool ok = false; |
| 245 std::string pixelSpacing; | |
| 246 if (GetStringTag(pixelSpacing, tags, "0028,0030")) | |
| 96 | 247 { |
| 102 | 248 std::vector<std::string> tokens; |
| 249 Orthanc::Toolbox::TokenizeString(tokens, pixelSpacing, '\\'); | |
| 250 | |
| 251 if (tokens.size() >= 2) | |
| 96 | 252 { |
| 102 | 253 try |
| 254 { | |
| 103 | 255 result["columnPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[1])); |
| 256 result["rowPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[0])); | |
| 102 | 257 ok = true; |
| 258 } | |
| 259 catch (boost::bad_lexical_cast&) | |
| 260 { | |
| 261 } | |
| 96 | 262 } |
| 263 } | |
| 102 | 264 |
| 265 if (!ok) | |
| 96 | 266 { |
| 102 | 267 result["columnPixelSpacing"] = 1.0f; |
| 268 result["rowPixelSpacing"] = 1.0f; | |
| 96 | 269 } |
| 270 | |
| 102 | 271 result["windowCenter"] = GetFloatTag(tags, "0028,1050", windowCenter * slope + intercept); |
| 272 result["windowWidth"] = GetFloatTag(tags, "0028,1051", windowWidth * slope); | |
| 273 | |
| 96 | 274 return true; |
| 275 } | |
| 276 | |
| 277 | |
| 278 | |
| 279 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
| 280 OrthancImageWrapper& image, | |
| 281 uint8_t compressionLevel /* between 0 and 9 */) | |
| 282 { | |
| 283 Orthanc::ImageAccessor accessor; | |
| 284 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 285 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 286 | |
| 287 Orthanc::ImageBuffer buffer; | |
| 288 buffer.SetMinimalPitchForced(true); | |
| 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: | |
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300 buffer.SetFormat(Orthanc::PixelFormat_Grayscale16); |
| 96 | 301 buffer.SetWidth(accessor.GetWidth()); |
| 302 buffer.SetHeight(accessor.GetHeight()); | |
| 303 converted = buffer.GetAccessor(); | |
| 304 Orthanc::ImageProcessing::Convert(converted, accessor); | |
| 305 break; | |
| 306 | |
| 307 case Orthanc::PixelFormat_SignedGrayscale16: | |
| 308 converted = accessor; | |
| 309 break; | |
| 310 | |
| 311 default: | |
| 312 // Unsupported pixel format | |
| 313 return false; | |
| 314 } | |
| 315 | |
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316 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
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317 |
| 96 | 318 // Sanity check: The pitch must be minimal |
| 319 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
| 320 GetBytesPerPixel(converted.GetFormat())); | |
| 321 result["Orthanc"]["Compression"] = "Deflate"; | |
| 322 result["sizeInBytes"] = converted.GetSize(); | |
| 323 | |
| 324 std::string z; | |
| 325 CompressUsingDeflate(z, image.GetContext(), converted.GetConstBuffer(), converted.GetSize()); | |
| 326 | |
| 327 result["Orthanc"]["PixelData"] = base64_encode(z); | |
| 328 | |
| 329 return true; | |
| 330 } | |
| 331 | |
| 332 | |
| 333 | |
| 334 template <typename TargetType, typename SourceType> | |
| 335 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
| 336 const Orthanc::ImageAccessor& source, | |
| 337 SourceType source1, TargetType target1, | |
| 338 SourceType source2, TargetType target2) | |
| 339 { | |
| 340 if (source.GetWidth() != target.GetWidth() || | |
| 341 source.GetHeight() != target.GetHeight()) | |
| 342 { | |
| 343 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 344 } | |
| 345 | |
| 346 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
| 347 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
| 348 | |
| 349 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
| 350 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
| 351 | |
| 352 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
| 353 { | |
| 354 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
| 355 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
| 356 | |
| 357 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
| 358 { | |
| 359 float v = (scale * static_cast<float>(*p)) + offset; | |
| 360 | |
| 361 if (v > maxValue) | |
| 362 { | |
| 363 *q = std::numeric_limits<TargetType>::max(); | |
| 364 } | |
| 365 else if (v < minValue) | |
| 366 { | |
| 367 *q = std::numeric_limits<TargetType>::min(); | |
| 368 } | |
| 369 else | |
| 370 { | |
| 101 | 371 //*q = static_cast<TargetType>(boost::math::iround(v)); |
| 372 | |
| 373 // http://stackoverflow.com/a/485546/881731 | |
| 374 *q = static_cast<TargetType>(floor(v + 0.5f)); | |
| 96 | 375 } |
| 376 } | |
| 377 } | |
| 378 } | |
| 379 | |
| 380 | |
| 381 bool DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result, | |
| 382 OrthancImageWrapper& image, | |
| 383 uint8_t quality /* between 0 and 100 */) | |
| 384 { | |
| 385 Orthanc::ImageAccessor accessor; | |
| 386 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 387 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 388 | |
| 389 Orthanc::ImageBuffer buffer; | |
| 390 buffer.SetMinimalPitchForced(true); | |
| 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; | |
| 404 buffer.SetFormat(Orthanc::PixelFormat_Grayscale8); | |
| 405 buffer.SetWidth(accessor.GetWidth()); | |
| 406 buffer.SetHeight(accessor.GetHeight()); | |
| 407 converted = buffer.GetAccessor(); | |
| 408 | |
| 409 int64_t a, b; | |
| 410 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
| 411 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); | |
| 412 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
| 413 | |
| 414 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
| 415 { | |
| 416 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
| 417 } | |
| 418 else | |
| 419 { | |
| 420 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
| 421 } | |
| 422 } | |
| 423 else | |
| 424 { | |
| 425 return false; | |
| 426 } | |
| 427 | |
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428 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
| 96 | 429 result["Orthanc"]["Compression"] = "Jpeg"; |
| 430 result["sizeInBytes"] = converted.GetSize(); | |
| 431 | |
| 432 std::string jpeg; | |
| 433 WriteJpegToMemory(jpeg, image.GetContext(), converted, quality); | |
| 434 | |
| 435 result["Orthanc"]["PixelData"] = base64_encode(jpeg); | |
| 436 return true; | |
| 437 } | |
| 0 | 438 } |