Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 99:46ec13a1177c refactoring
use of ordered-slices
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 27 Nov 2015 21:39:41 +0100 |
| parents | ef1b27ba7dfc |
| children | 2932473a9b19 |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics | |
| 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" | |
| 26 #include "../Orthanc/Plugins/Samples/GdcmDecoder/OrthancImageWrapper.h" | |
| 27 #include "../Orthanc/Resources/ThirdParty/base64/base64.h" | |
| 0 | 28 #include "ViewerToolbox.h" |
| 29 | |
| 30 #include <boost/lexical_cast.hpp> | |
| 31 #include <boost/algorithm/string/predicate.hpp> | |
| 32 #include <json/writer.h> | |
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33 #include <boost/regex.hpp> |
| 0 | 34 |
| 35 namespace OrthancPlugins | |
| 36 { | |
| 37 bool DecodedImageAdapter::ParseUri(CompressionType& type, | |
| 38 uint8_t& compressionLevel, | |
| 39 std::string& instanceId, | |
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40 unsigned int& frameIndex, |
| 0 | 41 const std::string& uri) |
| 42 { | |
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43 boost::regex pattern("^([a-z0-9]+)-([a-z0-9-]+)_([0-9]+)$"); |
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44 |
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45 boost::cmatch what; |
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46 if (!regex_match(uri.c_str(), what, pattern)) |
| 0 | 47 { |
| 48 return false; | |
| 49 } | |
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50 |
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51 printf("[%s] [%s] [%s]\n", what[1].str().c_str(), what[2].str().c_str(), what[3].str().c_str()); |
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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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parents:
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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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parents:
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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 | |
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parents:
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109 std::auto_ptr<OrthancImageWrapper> image(decoderCache_.Decode(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 | |
| 140 static bool GetTagValue(std::string& value, | |
| 141 const Json::Value& tags, | |
| 142 const std::string& tag) | |
| 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 | |
| 163 | |
| 164 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
| 165 const Json::Value& tags, | |
| 166 OrthancImageWrapper& image) | |
| 167 { | |
| 168 using namespace Orthanc; | |
| 169 | |
| 170 float windowCenter, windowWidth; | |
| 171 | |
| 172 Orthanc::ImageAccessor accessor; | |
| 173 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 174 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 175 | |
| 176 switch (accessor.GetFormat()) | |
| 177 { | |
| 178 case PixelFormat_Grayscale8: | |
| 179 case PixelFormat_Grayscale16: | |
| 180 case PixelFormat_SignedGrayscale16: | |
| 181 { | |
| 182 int64_t a, b; | |
| 183 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
| 184 result["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); | |
| 185 result["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
| 186 result["color"] = false; | |
| 187 | |
| 188 windowCenter = static_cast<float>(a + b) / 2.0f; | |
| 189 | |
| 190 if (a == b) | |
| 191 { | |
| 192 windowWidth = 256.0f; // Arbitrary value | |
| 193 } | |
| 194 else | |
| 195 { | |
| 196 windowWidth = static_cast<float>(b - a) / 2.0f; | |
| 197 } | |
| 198 | |
| 199 break; | |
| 200 } | |
| 201 | |
| 202 case PixelFormat_RGB24: | |
| 203 result["minPixelValue"] = 0; | |
| 204 result["maxPixelValue"] = 255; | |
| 205 result["color"] = true; | |
| 206 windowCenter = 127.5f; | |
| 207 windowWidth = 256.0f; | |
| 208 break; | |
| 209 | |
| 210 default: | |
| 211 return false; | |
| 212 } | |
| 213 | |
| 214 result["slope"] = image.GetSlope(); | |
| 215 result["intercept"] = image.GetIntercept(); | |
| 216 result["rows"] = image.GetHeight(); | |
| 217 result["columns"] = image.GetWidth(); | |
| 218 result["height"] = image.GetHeight(); | |
| 219 result["width"] = image.GetWidth(); | |
| 220 result["columnPixelSpacing"] = image.GetColumnPixelSpacing(); | |
| 221 result["rowPixelSpacing"] = image.GetRowPixelSpacing(); | |
| 222 | |
| 223 result["windowCenter"] = windowCenter * image.GetSlope() + image.GetIntercept(); | |
| 224 result["windowWidth"] = windowWidth * image.GetSlope(); | |
| 225 | |
| 226 try | |
| 227 { | |
| 228 std::string width, center; | |
| 229 if (GetTagValue(center, tags, "0028,1050" /*DICOM_TAG_WINDOW_CENTER*/) && | |
| 230 GetTagValue(width, tags, "0028,1051" /*DICOM_TAG_WINDOW_WIDTH*/)) | |
| 231 { | |
| 232 float a = boost::lexical_cast<float>(width); | |
| 233 float b = boost::lexical_cast<float>(center); | |
| 234 result["windowWidth"] = a; | |
| 235 result["windowCenter"] = b; | |
| 236 } | |
| 237 } | |
| 238 catch (boost::bad_lexical_cast&) | |
| 239 { | |
| 240 } | |
| 241 | |
| 242 return true; | |
| 243 } | |
| 244 | |
| 245 | |
| 246 | |
| 247 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
| 248 OrthancImageWrapper& image, | |
| 249 uint8_t compressionLevel /* between 0 and 9 */) | |
| 250 { | |
| 251 Orthanc::ImageAccessor accessor; | |
| 252 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 253 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 254 | |
| 255 Orthanc::ImageBuffer buffer; | |
| 256 buffer.SetMinimalPitchForced(true); | |
| 257 | |
| 258 Orthanc::ImageAccessor converted; | |
| 259 | |
| 260 switch (accessor.GetFormat()) | |
| 261 { | |
| 262 case Orthanc::PixelFormat_RGB24: | |
| 263 converted = accessor; | |
| 264 break; | |
| 265 | |
| 266 case Orthanc::PixelFormat_Grayscale8: | |
| 267 case Orthanc::PixelFormat_Grayscale16: | |
| 268 buffer.SetFormat(Orthanc::PixelFormat_SignedGrayscale16); | |
| 269 buffer.SetWidth(accessor.GetWidth()); | |
| 270 buffer.SetHeight(accessor.GetHeight()); | |
| 271 converted = buffer.GetAccessor(); | |
| 272 Orthanc::ImageProcessing::Convert(converted, accessor); | |
| 273 break; | |
| 274 | |
| 275 case Orthanc::PixelFormat_SignedGrayscale16: | |
| 276 converted = accessor; | |
| 277 break; | |
| 278 | |
| 279 default: | |
| 280 // Unsupported pixel format | |
| 281 return false; | |
| 282 } | |
| 283 | |
| 284 // Sanity check: The pitch must be minimal | |
| 285 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
| 286 GetBytesPerPixel(converted.GetFormat())); | |
| 287 result["Orthanc"]["Compression"] = "Deflate"; | |
| 288 result["sizeInBytes"] = converted.GetSize(); | |
| 289 | |
| 290 std::string z; | |
| 291 CompressUsingDeflate(z, image.GetContext(), converted.GetConstBuffer(), converted.GetSize()); | |
| 292 | |
| 293 result["Orthanc"]["PixelData"] = base64_encode(z); | |
| 294 | |
| 295 return true; | |
| 296 } | |
| 297 | |
| 298 | |
| 299 | |
| 300 template <typename TargetType, typename SourceType> | |
| 301 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
| 302 const Orthanc::ImageAccessor& source, | |
| 303 SourceType source1, TargetType target1, | |
| 304 SourceType source2, TargetType target2) | |
| 305 { | |
| 306 if (source.GetWidth() != target.GetWidth() || | |
| 307 source.GetHeight() != target.GetHeight()) | |
| 308 { | |
| 309 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 310 } | |
| 311 | |
| 312 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
| 313 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
| 314 | |
| 315 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
| 316 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
| 317 | |
| 318 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
| 319 { | |
| 320 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
| 321 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
| 322 | |
| 323 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
| 324 { | |
| 325 float v = (scale * static_cast<float>(*p)) + offset; | |
| 326 | |
| 327 if (v > maxValue) | |
| 328 { | |
| 329 *q = std::numeric_limits<TargetType>::max(); | |
| 330 } | |
| 331 else if (v < minValue) | |
| 332 { | |
| 333 *q = std::numeric_limits<TargetType>::min(); | |
| 334 } | |
| 335 else | |
| 336 { | |
| 337 *q = static_cast<TargetType>(boost::math::iround(v)); | |
| 338 } | |
| 339 } | |
| 340 } | |
| 341 } | |
| 342 | |
| 343 | |
| 344 bool DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result, | |
| 345 OrthancImageWrapper& image, | |
| 346 uint8_t quality /* between 0 and 100 */) | |
| 347 { | |
| 348 Orthanc::ImageAccessor accessor; | |
| 349 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
| 350 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
| 351 | |
| 352 Orthanc::ImageBuffer buffer; | |
| 353 buffer.SetMinimalPitchForced(true); | |
| 354 | |
| 355 Orthanc::ImageAccessor converted; | |
| 356 | |
| 357 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
| 358 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
| 359 { | |
| 360 result["Orthanc"]["Stretched"] = false; | |
| 361 converted = accessor; | |
| 362 } | |
| 363 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || | |
| 364 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
| 365 { | |
| 366 result["Orthanc"]["Stretched"] = true; | |
| 367 buffer.SetFormat(Orthanc::PixelFormat_Grayscale8); | |
| 368 buffer.SetWidth(accessor.GetWidth()); | |
| 369 buffer.SetHeight(accessor.GetHeight()); | |
| 370 converted = buffer.GetAccessor(); | |
| 371 | |
| 372 int64_t a, b; | |
| 373 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
| 374 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); | |
| 375 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
| 376 | |
| 377 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
| 378 { | |
| 379 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
| 380 } | |
| 381 else | |
| 382 { | |
| 383 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
| 384 } | |
| 385 } | |
| 386 else | |
| 387 { | |
| 388 return false; | |
| 389 } | |
| 390 | |
| 391 result["Orthanc"]["Compression"] = "Jpeg"; | |
| 392 result["sizeInBytes"] = converted.GetSize(); | |
| 393 | |
| 394 std::string jpeg; | |
| 395 WriteJpegToMemory(jpeg, image.GetContext(), converted, quality); | |
| 396 | |
| 397 result["Orthanc"]["PixelData"] = base64_encode(jpeg); | |
| 398 return true; | |
| 399 } | |
| 0 | 400 } |