Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/MultiframeDicomWriter.cpp @ 242:49f647ed1b4c
added copyright UCLouvain
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 06 Dec 2021 16:05:42 +0100 |
| parents | 7ffcce8ec94c |
| children | 20a730889ae2 |
| 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 |
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6 * Copyright (C) 2021-2021 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 0 | 7 * |
| 8 * This program is free software: you can redistribute it and/or | |
| 9 * modify it under the terms of the GNU Affero General Public License | |
| 10 * as published by the Free Software Foundation, either version 3 of | |
| 11 * the License, or (at your option) any later version. | |
| 12 * | |
| 13 * This program is distributed in the hope that it will be useful, but | |
| 14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 16 * Affero General Public License for more details. | |
| 17 * | |
| 18 * You should have received a copy of the GNU Affero General Public License | |
| 19 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 20 **/ | |
| 21 | |
| 22 | |
|
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23 #include "../PrecompiledHeadersWSI.h" |
| 0 | 24 #include "MultiframeDicomWriter.h" |
| 25 | |
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26 #include "../DicomToolbox.h" |
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27 |
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28 #include <Compatibility.h> // For std::unique_ptr |
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29 #include <DicomParsing/FromDcmtkBridge.h> |
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30 #include <Logging.h> |
| 192 | 31 #include <OrthancException.h> |
| 0 | 32 |
| 33 #include <dcmtk/dcmdata/dcuid.h> | |
| 34 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 35 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 36 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 37 #include <dcmtk/dcmdata/dcpixel.h> | |
| 38 #include <dcmtk/dcmdata/dcvrat.h> | |
| 39 | |
| 40 #include <boost/lexical_cast.hpp> | |
| 41 | |
| 14 | 42 #if DCMTK_VERSION_NUMBER <= 360 |
| 43 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax | |
| 44 #endif | |
| 45 | |
| 46 | |
| 0 | 47 namespace OrthancWSI |
| 48 { | |
| 49 static void SaveDicomToMemory(std::string& target, | |
| 50 DcmFileFormat& dicom, | |
| 51 E_TransferSyntax transferSyntax) | |
| 52 { | |
| 53 dicom.validateMetaInfo(transferSyntax); | |
| 54 dicom.removeInvalidGroups(); | |
| 55 | |
| 56 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
| 57 | |
| 58 // Create a memory buffer with the proper size | |
| 59 { | |
| 60 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*) | |
| 61 target.resize(estimatedSize); | |
| 62 } | |
| 63 | |
| 64 DcmOutputBufferStream ob(&target[0], target.size()); | |
| 65 | |
| 66 // Fill the memory buffer with the meta-header and the dataset | |
| 67 dicom.transferInit(); | |
| 68 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL, | |
| 69 /*opt_groupLength*/ EGL_recalcGL, | |
| 70 /*opt_paddingType*/ EPD_withoutPadding); | |
| 71 dicom.transferEnd(); | |
| 72 | |
| 73 if (!c.good()) | |
| 74 { | |
| 75 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 76 } | |
| 77 | |
| 78 // The DICOM file is successfully written, truncate the target | |
| 79 // buffer if its size was overestimated by (*) | |
| 80 ob.flush(); | |
| 81 | |
| 82 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
| 83 if (effectiveSize < target.size()) | |
| 84 { | |
| 85 target.resize(effectiveSize); | |
| 86 } | |
| 87 } | |
| 88 | |
| 89 | |
| 90 void MultiframeDicomWriter::ResetImage() | |
| 91 { | |
| 92 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence)); | |
| 93 | |
| 94 if (compression_ != ImageCompression_None) | |
| 95 { | |
| 96 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB))); | |
| 97 | |
| 98 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB); | |
| 99 compressedPixelSequence_->insert(offsetTable_); | |
| 100 offsetList_.reset(new DcmOffsetList); | |
| 101 } | |
| 102 | |
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103 firstFrameInInstance_ += framesCount_; |
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104 countInstances_ ++; |
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105 |
| 0 | 106 writtenSize_ = 0; |
| 107 framesCount_ = 0; | |
| 108 } | |
| 109 | |
| 110 | |
| 111 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom) | |
| 112 { | |
| 113 static const size_t GIGABYTE = 1024 * 1024 * 1024; | |
| 114 | |
| 115 std::string pixelData; | |
| 116 uncompressedPixelData_.Flatten(pixelData); | |
| 117 | |
| 118 // Prevent the creation of too large DICOM files | |
| 119 // (uncompressed DICOM files are limited to 2GB) | |
| 120 if (pixelData.size() > GIGABYTE) | |
| 121 { | |
| 122 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); | |
| 123 } | |
| 124 | |
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125 std::unique_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData)); |
| 0 | 126 |
| 127 uint8_t* target = NULL; | |
| 128 if (!pixels->createUint8Array(pixelData.size(), target).good()) | |
| 129 { | |
| 130 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 131 } | |
| 132 | |
| 133 if (pixelData.size() > 0) | |
| 134 { | |
| 135 if (target == NULL) | |
| 136 { | |
| 137 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 138 } | |
| 139 | |
| 140 // TODO Avoid this memcpy() | |
| 141 memcpy(target, pixelData.c_str(), pixelData.size()); | |
| 142 } | |
| 143 | |
| 144 if (!dicom.getDataset()->insert(pixels.release(), false, false).good()) | |
| 145 { | |
| 146 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 147 } | |
| 148 } | |
| 149 | |
| 150 | |
| 151 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset, | |
| 152 ImageCompression compression, | |
| 153 Orthanc::PixelFormat pixelFormat, | |
| 154 unsigned int width, | |
| 155 unsigned int height, | |
| 156 unsigned int tileWidth, | |
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157 unsigned int tileHeight, |
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158 Orthanc::PhotometricInterpretation photometric, |
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159 bool isConcatenation) : |
| 0 | 160 compression_(compression), |
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161 framesCount_(0), |
| 0 | 162 width_(width), |
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163 height_(height), |
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164 isConcatenation_(isConcatenation), |
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165 countInstances_(0), |
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166 firstFrameInInstance_(0) |
| 0 | 167 { |
| 168 switch (compression) | |
| 169 { | |
| 170 case ImageCompression_None: | |
| 171 transferSyntax_ = EXS_LittleEndianImplicit; | |
| 172 break; | |
| 173 | |
| 174 case ImageCompression_Jpeg: | |
| 175 // Default transfer syntax for lossy JPEG 8bit compression | |
| 14 | 176 transferSyntax_ = EXS_JPEGProcess1; |
| 0 | 177 break; |
| 178 | |
| 179 case ImageCompression_Jpeg2000: | |
| 180 // JPEG2000 compression (lossless only) | |
| 181 transferSyntax_ = EXS_JPEG2000LosslessOnly; | |
| 182 break; | |
| 183 | |
| 184 default: | |
| 185 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 186 } | |
| 187 | |
| 188 if (!sharedTags_.copyFrom(dataset).good()) | |
| 189 { | |
| 190 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 191 } | |
| 192 | |
| 193 // We only take care of grayscale or RGB images in 8bpp | |
| 194 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width); | |
| 195 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height); | |
| 196 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values | |
| 197 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth); | |
| 198 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight); | |
| 199 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8); | |
| 200 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8); | |
| 201 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7); | |
| 202 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values | |
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203 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, Orthanc::EnumerationToString(photometric)); |
| 0 | 204 |
| 205 switch (pixelFormat) | |
| 206 { | |
| 207 case Orthanc::PixelFormat_RGB24: | |
| 208 uncompressedFrameSize_ = 3 * tileWidth * tileHeight; | |
| 209 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3); | |
| 210 break; | |
| 211 | |
| 212 case Orthanc::PixelFormat_Grayscale8: | |
| 213 uncompressedFrameSize_ = tileWidth * tileHeight; | |
| 214 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1); | |
| 215 break; | |
| 216 | |
| 217 default: | |
| 218 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 219 } | |
| 220 | |
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221 if (isConcatenation) |
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222 { |
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223 /** |
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224 * Generate a shared SOP Instance UID that corresponds to the |
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225 * main instance containing all the instances. This main |
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226 * instance is purely "virtual", as it is never generated. |
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227 * https://bugs.orthanc-server.com/show_bug.cgi?id=145 |
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228 * http://dicom.nema.org/medical/dicom/2020d/output/chtml/part03/figures/PS3.3_C.7.6.16-1a.svg |
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229 **/ |
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230 DicomToolbox::SetStringTag(sharedTags_, DCM_SOPInstanceUIDOfConcatenationSource, |
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231 Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance)); |
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232 |
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233 /** |
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234 * Similarly, we generate one random UID to identify the |
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235 * concatenation. As we never generate two different |
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236 * concatenations of the "main" instance, this UID is shared by |
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237 * all the instances of the concatenation. |
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238 **/ |
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239 DicomToolbox::SetStringTag(sharedTags_, DCM_ConcatenationUID, |
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240 Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance)); |
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241 } |
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242 |
| 0 | 243 ResetImage(); |
| 244 } | |
| 245 | |
| 246 | |
| 247 void MultiframeDicomWriter::AddFrame(const std::string& frame, | |
| 248 DcmItem* functionalGroup) // This takes the ownership | |
| 249 { | |
| 250 // Free the functional group on error | |
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251 std::unique_ptr<DcmItem> functionalGroupRaii(functionalGroup); |
| 0 | 252 |
| 253 if (compression_ == ImageCompression_None) | |
| 254 { | |
| 255 if (frame.size() != uncompressedFrameSize_) | |
| 256 { | |
| 257 LOG(ERROR) << "An uncompressed frame has not the proper size: " | |
| 258 << frame.size() << " instead of " << uncompressedFrameSize_; | |
| 259 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 260 } | |
| 261 | |
| 262 uncompressedPixelData_.AddChunk(frame); | |
| 263 } | |
| 264 else | |
| 265 { | |
| 266 uint8_t* bytes = const_cast<uint8_t*>(reinterpret_cast<const uint8_t*>(frame.c_str())); | |
| 267 | |
| 268 compressedPixelSequence_->storeCompressedFrame(*offsetList_, bytes, frame.size(), | |
| 269 0 /* unlimited fragment size */); | |
| 270 } | |
| 271 | |
| 272 if (functionalGroup != NULL) | |
| 273 { | |
| 274 perFrameFunctionalGroups_->insert(functionalGroupRaii.release()); | |
| 275 } | |
| 276 else | |
| 277 { | |
| 278 perFrameFunctionalGroups_->insert(new DcmItem); | |
| 279 } | |
| 280 | |
| 281 writtenSize_ += frame.size(); | |
| 282 framesCount_ += 1; | |
| 283 } | |
| 284 | |
| 285 | |
| 286 void MultiframeDicomWriter::Flush(std::string& target, | |
| 287 unsigned int instanceNumber) | |
| 288 { | |
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289 if (instanceNumber == 0) |
| 0 | 290 { |
| 291 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 292 } | |
| 293 | |
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294 std::unique_ptr<DcmFileFormat> dicom(new DcmFileFormat); |
| 0 | 295 |
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296 const std::string uid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
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297 |
| 0 | 298 if (!dicom->getDataset()->copyFrom(sharedTags_).good() || |
| 299 !dicom->getDataset()->insert(perFrameFunctionalGroups_.release(), false, false).good() || | |
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300 !dicom->getDataset()->putAndInsertString(DCM_SOPInstanceUID, uid.c_str()).good()) |
| 0 | 301 { |
| 302 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 303 } | |
| 304 | |
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305 // The two tags below have "IS" (integer string) value representation |
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306 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_InstanceNumber, boost::lexical_cast<std::string>(instanceNumber)); |
| 0 | 307 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_NumberOfFrames, boost::lexical_cast<std::string>(framesCount_)); |
| 308 | |
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309 if (isConcatenation_) |
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Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
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310 { |
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7ffcce8ec94c
Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
311 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
|
312 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
|
313 } |
|
7ffcce8ec94c
Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
314 |
| 0 | 315 switch (compression_) |
| 316 { | |
| 317 case ImageCompression_None: | |
| 318 InjectUncompressedPixelData(*dicom); | |
| 319 break; | |
| 320 | |
| 321 case ImageCompression_Jpeg: | |
| 322 case ImageCompression_Jpeg2000: | |
| 323 offsetTable_->createOffsetTable(*offsetList_); | |
| 324 dicom->getDataset()->insert(compressedPixelSequence_.release()); | |
| 325 break; | |
| 326 | |
| 327 default: | |
| 328 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 329 } | |
| 330 | |
| 331 ResetImage(); | |
| 332 | |
| 333 SaveDicomToMemory(target, *dicom, transferSyntax_); | |
| 334 } | |
| 335 } |