Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/MultiframeDicomWriter.cpp @ 234:a464169306ce
integration 1.0->mainline
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 14 Jan 2021 08:50:27 +0100 |
| parents | 7ffcce8ec94c |
| children | 49f647ed1b4c |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 4 * Department, University Hospital of Liege, Belgium | |
|
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5 * Copyright (C) 2017-2021 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 | |
|
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22 #include "../PrecompiledHeadersWSI.h" |
| 0 | 23 #include "MultiframeDicomWriter.h" |
| 24 | |
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25 #include "../DicomToolbox.h" |
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26 |
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27 #include <Compatibility.h> // For std::unique_ptr |
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28 #include <DicomParsing/FromDcmtkBridge.h> |
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29 #include <Logging.h> |
| 192 | 30 #include <OrthancException.h> |
| 0 | 31 |
| 32 #include <dcmtk/dcmdata/dcuid.h> | |
| 33 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 34 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 35 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 36 #include <dcmtk/dcmdata/dcpixel.h> | |
| 37 #include <dcmtk/dcmdata/dcvrat.h> | |
| 38 | |
| 39 #include <boost/lexical_cast.hpp> | |
| 40 | |
| 14 | 41 #if DCMTK_VERSION_NUMBER <= 360 |
| 42 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax | |
| 43 #endif | |
| 44 | |
| 45 | |
| 0 | 46 namespace OrthancWSI |
| 47 { | |
| 48 static void SaveDicomToMemory(std::string& target, | |
| 49 DcmFileFormat& dicom, | |
| 50 E_TransferSyntax transferSyntax) | |
| 51 { | |
| 52 dicom.validateMetaInfo(transferSyntax); | |
| 53 dicom.removeInvalidGroups(); | |
| 54 | |
| 55 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
| 56 | |
| 57 // Create a memory buffer with the proper size | |
| 58 { | |
| 59 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*) | |
| 60 target.resize(estimatedSize); | |
| 61 } | |
| 62 | |
| 63 DcmOutputBufferStream ob(&target[0], target.size()); | |
| 64 | |
| 65 // Fill the memory buffer with the meta-header and the dataset | |
| 66 dicom.transferInit(); | |
| 67 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL, | |
| 68 /*opt_groupLength*/ EGL_recalcGL, | |
| 69 /*opt_paddingType*/ EPD_withoutPadding); | |
| 70 dicom.transferEnd(); | |
| 71 | |
| 72 if (!c.good()) | |
| 73 { | |
| 74 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 75 } | |
| 76 | |
| 77 // The DICOM file is successfully written, truncate the target | |
| 78 // buffer if its size was overestimated by (*) | |
| 79 ob.flush(); | |
| 80 | |
| 81 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
| 82 if (effectiveSize < target.size()) | |
| 83 { | |
| 84 target.resize(effectiveSize); | |
| 85 } | |
| 86 } | |
| 87 | |
| 88 | |
| 89 void MultiframeDicomWriter::ResetImage() | |
| 90 { | |
| 91 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence)); | |
| 92 | |
| 93 if (compression_ != ImageCompression_None) | |
| 94 { | |
| 95 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB))); | |
| 96 | |
| 97 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB); | |
| 98 compressedPixelSequence_->insert(offsetTable_); | |
| 99 offsetList_.reset(new DcmOffsetList); | |
| 100 } | |
| 101 | |
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102 firstFrameInInstance_ += framesCount_; |
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103 countInstances_ ++; |
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104 |
| 0 | 105 writtenSize_ = 0; |
| 106 framesCount_ = 0; | |
| 107 } | |
| 108 | |
| 109 | |
| 110 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom) | |
| 111 { | |
| 112 static const size_t GIGABYTE = 1024 * 1024 * 1024; | |
| 113 | |
| 114 std::string pixelData; | |
| 115 uncompressedPixelData_.Flatten(pixelData); | |
| 116 | |
| 117 // Prevent the creation of too large DICOM files | |
| 118 // (uncompressed DICOM files are limited to 2GB) | |
| 119 if (pixelData.size() > GIGABYTE) | |
| 120 { | |
| 121 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); | |
| 122 } | |
| 123 | |
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124 std::unique_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData)); |
| 0 | 125 |
| 126 uint8_t* target = NULL; | |
| 127 if (!pixels->createUint8Array(pixelData.size(), target).good()) | |
| 128 { | |
| 129 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 130 } | |
| 131 | |
| 132 if (pixelData.size() > 0) | |
| 133 { | |
| 134 if (target == NULL) | |
| 135 { | |
| 136 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 137 } | |
| 138 | |
| 139 // TODO Avoid this memcpy() | |
| 140 memcpy(target, pixelData.c_str(), pixelData.size()); | |
| 141 } | |
| 142 | |
| 143 if (!dicom.getDataset()->insert(pixels.release(), false, false).good()) | |
| 144 { | |
| 145 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 146 } | |
| 147 } | |
| 148 | |
| 149 | |
| 150 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset, | |
| 151 ImageCompression compression, | |
| 152 Orthanc::PixelFormat pixelFormat, | |
| 153 unsigned int width, | |
| 154 unsigned int height, | |
| 155 unsigned int tileWidth, | |
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156 unsigned int tileHeight, |
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157 Orthanc::PhotometricInterpretation photometric, |
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158 bool isConcatenation) : |
| 0 | 159 compression_(compression), |
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160 framesCount_(0), |
| 0 | 161 width_(width), |
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162 height_(height), |
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163 isConcatenation_(isConcatenation), |
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164 countInstances_(0), |
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165 firstFrameInInstance_(0) |
| 0 | 166 { |
| 167 switch (compression) | |
| 168 { | |
| 169 case ImageCompression_None: | |
| 170 transferSyntax_ = EXS_LittleEndianImplicit; | |
| 171 break; | |
| 172 | |
| 173 case ImageCompression_Jpeg: | |
| 174 // Default transfer syntax for lossy JPEG 8bit compression | |
| 14 | 175 transferSyntax_ = EXS_JPEGProcess1; |
| 0 | 176 break; |
| 177 | |
| 178 case ImageCompression_Jpeg2000: | |
| 179 // JPEG2000 compression (lossless only) | |
| 180 transferSyntax_ = EXS_JPEG2000LosslessOnly; | |
| 181 break; | |
| 182 | |
| 183 default: | |
| 184 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 185 } | |
| 186 | |
| 187 if (!sharedTags_.copyFrom(dataset).good()) | |
| 188 { | |
| 189 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 190 } | |
| 191 | |
| 192 // We only take care of grayscale or RGB images in 8bpp | |
| 193 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width); | |
| 194 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height); | |
| 195 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values | |
| 196 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth); | |
| 197 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight); | |
| 198 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8); | |
| 199 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8); | |
| 200 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7); | |
| 201 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values | |
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202 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, Orthanc::EnumerationToString(photometric)); |
| 0 | 203 |
| 204 switch (pixelFormat) | |
| 205 { | |
| 206 case Orthanc::PixelFormat_RGB24: | |
| 207 uncompressedFrameSize_ = 3 * tileWidth * tileHeight; | |
| 208 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3); | |
| 209 break; | |
| 210 | |
| 211 case Orthanc::PixelFormat_Grayscale8: | |
| 212 uncompressedFrameSize_ = tileWidth * tileHeight; | |
| 213 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1); | |
| 214 break; | |
| 215 | |
| 216 default: | |
| 217 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 218 } | |
| 219 | |
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220 if (isConcatenation) |
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221 { |
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222 /** |
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223 * Generate a shared SOP Instance UID that corresponds to the |
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224 * main instance containing all the instances. This main |
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225 * instance is purely "virtual", as it is never generated. |
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226 * https://bugs.orthanc-server.com/show_bug.cgi?id=145 |
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227 * http://dicom.nema.org/medical/dicom/2020d/output/chtml/part03/figures/PS3.3_C.7.6.16-1a.svg |
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228 **/ |
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229 DicomToolbox::SetStringTag(sharedTags_, DCM_SOPInstanceUIDOfConcatenationSource, |
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230 Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance)); |
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231 |
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232 /** |
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233 * Similarly, we generate one random UID to identify the |
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234 * concatenation. As we never generate two different |
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235 * concatenations of the "main" instance, this UID is shared by |
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236 * all the instances of the concatenation. |
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237 **/ |
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238 DicomToolbox::SetStringTag(sharedTags_, DCM_ConcatenationUID, |
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239 Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance)); |
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240 } |
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241 |
| 0 | 242 ResetImage(); |
| 243 } | |
| 244 | |
| 245 | |
| 246 void MultiframeDicomWriter::AddFrame(const std::string& frame, | |
| 247 DcmItem* functionalGroup) // This takes the ownership | |
| 248 { | |
| 249 // Free the functional group on error | |
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250 std::unique_ptr<DcmItem> functionalGroupRaii(functionalGroup); |
| 0 | 251 |
| 252 if (compression_ == ImageCompression_None) | |
| 253 { | |
| 254 if (frame.size() != uncompressedFrameSize_) | |
| 255 { | |
| 256 LOG(ERROR) << "An uncompressed frame has not the proper size: " | |
| 257 << frame.size() << " instead of " << uncompressedFrameSize_; | |
| 258 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 259 } | |
| 260 | |
| 261 uncompressedPixelData_.AddChunk(frame); | |
| 262 } | |
| 263 else | |
| 264 { | |
| 265 uint8_t* bytes = const_cast<uint8_t*>(reinterpret_cast<const uint8_t*>(frame.c_str())); | |
| 266 | |
| 267 compressedPixelSequence_->storeCompressedFrame(*offsetList_, bytes, frame.size(), | |
| 268 0 /* unlimited fragment size */); | |
| 269 } | |
| 270 | |
| 271 if (functionalGroup != NULL) | |
| 272 { | |
| 273 perFrameFunctionalGroups_->insert(functionalGroupRaii.release()); | |
| 274 } | |
| 275 else | |
| 276 { | |
| 277 perFrameFunctionalGroups_->insert(new DcmItem); | |
| 278 } | |
| 279 | |
| 280 writtenSize_ += frame.size(); | |
| 281 framesCount_ += 1; | |
| 282 } | |
| 283 | |
| 284 | |
| 285 void MultiframeDicomWriter::Flush(std::string& target, | |
| 286 unsigned int instanceNumber) | |
| 287 { | |
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288 if (instanceNumber == 0) |
| 0 | 289 { |
| 290 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 291 } | |
| 292 | |
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293 std::unique_ptr<DcmFileFormat> dicom(new DcmFileFormat); |
| 0 | 294 |
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295 const std::string uid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
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296 |
| 0 | 297 if (!dicom->getDataset()->copyFrom(sharedTags_).good() || |
| 298 !dicom->getDataset()->insert(perFrameFunctionalGroups_.release(), false, false).good() || | |
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299 !dicom->getDataset()->putAndInsertString(DCM_SOPInstanceUID, uid.c_str()).good()) |
| 0 | 300 { |
| 301 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 302 } | |
| 303 | |
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304 // The two tags below have "IS" (integer string) value representation |
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305 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_InstanceNumber, boost::lexical_cast<std::string>(instanceNumber)); |
| 0 | 306 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_NumberOfFrames, boost::lexical_cast<std::string>(framesCount_)); |
| 307 | |
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308 if (isConcatenation_) |
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309 { |
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7ffcce8ec94c
Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
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310 DicomToolbox::SetUint32Tag(*dicom->getDataset(), DCM_ConcatenationFrameOffsetNumber, firstFrameInInstance_); |
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7ffcce8ec94c
Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
311 DicomToolbox::SetUint16Tag(*dicom->getDataset(), DCM_InConcatenationNumber, countInstances_); |
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7ffcce8ec94c
Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
312 } |
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7ffcce8ec94c
Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
313 |
| 0 | 314 switch (compression_) |
| 315 { | |
| 316 case ImageCompression_None: | |
| 317 InjectUncompressedPixelData(*dicom); | |
| 318 break; | |
| 319 | |
| 320 case ImageCompression_Jpeg: | |
| 321 case ImageCompression_Jpeg2000: | |
| 322 offsetTable_->createOffsetTable(*offsetList_); | |
| 323 dicom->getDataset()->insert(compressedPixelSequence_.release()); | |
| 324 break; | |
| 325 | |
| 326 default: | |
| 327 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 328 } | |
| 329 | |
| 330 ResetImage(); | |
| 331 | |
| 332 SaveDicomToMemory(target, *dicom, transferSyntax_); | |
| 333 } | |
| 334 } |