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annotate Framework/Outputs/MultiframeDicomWriter.cpp @ 334:f011fc199b6a default tip
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 18 Oct 2024 15:44:18 +0200 |
| parents | 0683312e21ba |
| children |
| 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) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 0 | 8 * |
| 9 * This program is free software: you can redistribute it and/or | |
| 10 * modify it under the terms of the GNU Affero General Public License | |
| 11 * as published by the Free Software Foundation, either version 3 of | |
| 12 * the License, or (at your option) any later version. | |
| 13 * | |
| 14 * This program is distributed in the hope that it will be useful, but | |
| 15 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 17 * Affero General Public License for more details. | |
| 18 * | |
| 19 * You should have received a copy of the GNU Affero General Public License | |
| 20 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 21 **/ | |
| 22 | |
| 23 | |
|
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24 #include "../PrecompiledHeadersWSI.h" |
| 0 | 25 #include "MultiframeDicomWriter.h" |
| 26 | |
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27 #include "../DicomToolbox.h" |
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28 |
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29 #include <Compatibility.h> // For std::unique_ptr |
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30 #include <DicomParsing/FromDcmtkBridge.h> |
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31 #include <Logging.h> |
| 192 | 32 #include <OrthancException.h> |
| 0 | 33 |
| 34 #include <dcmtk/dcmdata/dcuid.h> | |
| 35 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 36 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 37 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 38 #include <dcmtk/dcmdata/dcpixel.h> | |
| 39 #include <dcmtk/dcmdata/dcvrat.h> | |
| 40 | |
| 41 #include <boost/lexical_cast.hpp> | |
| 42 | |
| 14 | 43 #if DCMTK_VERSION_NUMBER <= 360 |
| 44 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax | |
| 45 #endif | |
| 46 | |
| 47 | |
| 0 | 48 namespace OrthancWSI |
| 49 { | |
| 50 static void SaveDicomToMemory(std::string& target, | |
| 51 DcmFileFormat& dicom, | |
| 52 E_TransferSyntax transferSyntax) | |
| 53 { | |
| 54 dicom.validateMetaInfo(transferSyntax); | |
| 55 dicom.removeInvalidGroups(); | |
| 56 | |
| 57 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
| 58 | |
| 59 // Create a memory buffer with the proper size | |
| 60 { | |
| 61 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*) | |
| 62 target.resize(estimatedSize); | |
| 63 } | |
| 64 | |
| 65 DcmOutputBufferStream ob(&target[0], target.size()); | |
| 66 | |
| 67 // Fill the memory buffer with the meta-header and the dataset | |
| 68 dicom.transferInit(); | |
| 69 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL, | |
| 70 /*opt_groupLength*/ EGL_recalcGL, | |
| 71 /*opt_paddingType*/ EPD_withoutPadding); | |
| 72 dicom.transferEnd(); | |
| 73 | |
| 74 if (!c.good()) | |
| 75 { | |
| 76 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 77 } | |
| 78 | |
| 79 // The DICOM file is successfully written, truncate the target | |
| 80 // buffer if its size was overestimated by (*) | |
| 81 ob.flush(); | |
| 82 | |
| 83 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
| 84 if (effectiveSize < target.size()) | |
| 85 { | |
| 86 target.resize(effectiveSize); | |
| 87 } | |
| 88 } | |
| 89 | |
| 90 | |
| 91 void MultiframeDicomWriter::ResetImage() | |
| 92 { | |
| 93 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence)); | |
| 94 | |
| 95 if (compression_ != ImageCompression_None) | |
| 96 { | |
| 97 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB))); | |
| 98 | |
| 99 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB); | |
| 100 compressedPixelSequence_->insert(offsetTable_); | |
| 101 offsetList_.reset(new DcmOffsetList); | |
| 102 } | |
| 103 | |
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104 firstFrameInInstance_ += framesCount_; |
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105 countInstances_ ++; |
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106 |
| 0 | 107 writtenSize_ = 0; |
| 108 framesCount_ = 0; | |
| 109 } | |
| 110 | |
| 111 | |
| 112 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom) | |
| 113 { | |
| 114 static const size_t GIGABYTE = 1024 * 1024 * 1024; | |
| 115 | |
| 116 std::string pixelData; | |
| 117 uncompressedPixelData_.Flatten(pixelData); | |
| 118 | |
| 119 // Prevent the creation of too large DICOM files | |
| 120 // (uncompressed DICOM files are limited to 2GB) | |
| 121 if (pixelData.size() > GIGABYTE) | |
| 122 { | |
| 123 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); | |
| 124 } | |
| 125 | |
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126 std::unique_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData)); |
| 0 | 127 |
| 128 uint8_t* target = NULL; | |
| 129 if (!pixels->createUint8Array(pixelData.size(), target).good()) | |
| 130 { | |
| 131 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 132 } | |
| 133 | |
| 134 if (pixelData.size() > 0) | |
| 135 { | |
| 136 if (target == NULL) | |
| 137 { | |
| 138 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 139 } | |
| 140 | |
| 141 // TODO Avoid this memcpy() | |
| 142 memcpy(target, pixelData.c_str(), pixelData.size()); | |
| 143 } | |
| 144 | |
| 145 if (!dicom.getDataset()->insert(pixels.release(), false, false).good()) | |
| 146 { | |
| 147 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 148 } | |
| 149 } | |
| 150 | |
| 151 | |
| 152 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset, | |
| 153 ImageCompression compression, | |
| 154 Orthanc::PixelFormat pixelFormat, | |
| 155 unsigned int width, | |
| 156 unsigned int height, | |
| 157 unsigned int tileWidth, | |
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158 unsigned int tileHeight, |
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159 Orthanc::PhotometricInterpretation photometric, |
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160 bool isConcatenation) : |
| 0 | 161 compression_(compression), |
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162 framesCount_(0), |
| 0 | 163 width_(width), |
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164 height_(height), |
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165 isConcatenation_(isConcatenation), |
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166 countInstances_(0), |
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167 firstFrameInInstance_(0) |
| 0 | 168 { |
| 169 switch (compression) | |
| 170 { | |
| 171 case ImageCompression_None: | |
| 172 transferSyntax_ = EXS_LittleEndianImplicit; | |
| 173 break; | |
| 174 | |
| 175 case ImageCompression_Jpeg: | |
| 176 // Default transfer syntax for lossy JPEG 8bit compression | |
| 14 | 177 transferSyntax_ = EXS_JPEGProcess1; |
| 0 | 178 break; |
| 179 | |
| 180 case ImageCompression_Jpeg2000: | |
| 181 // JPEG2000 compression (lossless only) | |
| 182 transferSyntax_ = EXS_JPEG2000LosslessOnly; | |
| 183 break; | |
| 184 | |
| 185 default: | |
| 186 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 187 } | |
| 188 | |
| 189 if (!sharedTags_.copyFrom(dataset).good()) | |
| 190 { | |
| 191 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 192 } | |
| 193 | |
| 194 // We only take care of grayscale or RGB images in 8bpp | |
| 195 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width); | |
| 196 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height); | |
| 197 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values | |
| 198 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth); | |
| 199 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight); | |
| 200 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8); | |
| 201 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8); | |
| 202 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7); | |
| 203 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values | |
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204 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, Orthanc::EnumerationToString(photometric)); |
| 0 | 205 |
| 206 switch (pixelFormat) | |
| 207 { | |
| 208 case Orthanc::PixelFormat_RGB24: | |
| 209 uncompressedFrameSize_ = 3 * tileWidth * tileHeight; | |
| 210 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3); | |
| 211 break; | |
| 212 | |
| 213 case Orthanc::PixelFormat_Grayscale8: | |
| 214 uncompressedFrameSize_ = tileWidth * tileHeight; | |
| 215 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1); | |
| 216 break; | |
| 217 | |
| 218 default: | |
| 219 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 220 } | |
| 221 | |
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222 if (isConcatenation) |
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223 { |
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224 /** |
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225 * Generate a shared SOP Instance UID that corresponds to the |
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226 * main instance containing all the instances. This main |
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227 * instance is purely "virtual", as it is never generated. |
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228 * https://orthanc.uclouvain.be/bugs/show_bug.cgi?id=145 |
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229 * http://dicom.nema.org/medical/dicom/2020d/output/chtml/part03/figures/PS3.3_C.7.6.16-1a.svg |
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230 **/ |
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231 DicomToolbox::SetStringTag(sharedTags_, DCM_SOPInstanceUIDOfConcatenationSource, |
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232 Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance)); |
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233 |
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234 /** |
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235 * Similarly, we generate one random UID to identify the |
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236 * concatenation. As we never generate two different |
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237 * concatenations of the "main" instance, this UID is shared by |
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238 * all the instances of the concatenation. |
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239 **/ |
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240 DicomToolbox::SetStringTag(sharedTags_, DCM_ConcatenationUID, |
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241 Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance)); |
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242 } |
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243 |
| 0 | 244 ResetImage(); |
| 245 } | |
| 246 | |
| 247 | |
| 248 void MultiframeDicomWriter::AddFrame(const std::string& frame, | |
| 249 DcmItem* functionalGroup) // This takes the ownership | |
| 250 { | |
| 251 // Free the functional group on error | |
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252 std::unique_ptr<DcmItem> functionalGroupRaii(functionalGroup); |
| 0 | 253 |
| 254 if (compression_ == ImageCompression_None) | |
| 255 { | |
| 256 if (frame.size() != uncompressedFrameSize_) | |
| 257 { | |
| 258 LOG(ERROR) << "An uncompressed frame has not the proper size: " | |
| 259 << frame.size() << " instead of " << uncompressedFrameSize_; | |
| 260 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 261 } | |
| 262 | |
| 263 uncompressedPixelData_.AddChunk(frame); | |
| 264 } | |
| 265 else | |
| 266 { | |
| 267 uint8_t* bytes = const_cast<uint8_t*>(reinterpret_cast<const uint8_t*>(frame.c_str())); | |
| 268 | |
| 269 compressedPixelSequence_->storeCompressedFrame(*offsetList_, bytes, frame.size(), | |
| 270 0 /* unlimited fragment size */); | |
| 271 } | |
| 272 | |
| 273 if (functionalGroup != NULL) | |
| 274 { | |
| 275 perFrameFunctionalGroups_->insert(functionalGroupRaii.release()); | |
| 276 } | |
| 277 else | |
| 278 { | |
| 279 perFrameFunctionalGroups_->insert(new DcmItem); | |
| 280 } | |
| 281 | |
| 282 writtenSize_ += frame.size(); | |
| 283 framesCount_ += 1; | |
| 284 } | |
| 285 | |
| 286 | |
| 287 void MultiframeDicomWriter::Flush(std::string& target, | |
| 288 unsigned int instanceNumber) | |
| 289 { | |
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290 if (instanceNumber == 0) |
| 0 | 291 { |
| 292 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 293 } | |
| 294 | |
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295 std::unique_ptr<DcmFileFormat> dicom(new DcmFileFormat); |
| 0 | 296 |
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297 const std::string uid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
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298 |
| 0 | 299 if (!dicom->getDataset()->copyFrom(sharedTags_).good() || |
| 300 !dicom->getDataset()->insert(perFrameFunctionalGroups_.release(), false, false).good() || | |
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301 !dicom->getDataset()->putAndInsertString(DCM_SOPInstanceUID, uid.c_str()).good()) |
| 0 | 302 { |
| 303 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 304 } | |
| 305 | |
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306 // The two tags below have "IS" (integer string) value representation |
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307 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_InstanceNumber, boost::lexical_cast<std::string>(instanceNumber)); |
| 0 | 308 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_NumberOfFrames, boost::lexical_cast<std::string>(framesCount_)); |
| 309 | |
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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 if (isConcatenation_) |
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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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311 { |
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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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312 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
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313 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
|
314 } |
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7ffcce8ec94c
Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
315 |
| 0 | 316 switch (compression_) |
| 317 { | |
| 318 case ImageCompression_None: | |
| 319 InjectUncompressedPixelData(*dicom); | |
| 320 break; | |
| 321 | |
| 322 case ImageCompression_Jpeg: | |
| 323 case ImageCompression_Jpeg2000: | |
| 324 offsetTable_->createOffsetTable(*offsetList_); | |
| 325 dicom->getDataset()->insert(compressedPixelSequence_.release()); | |
| 326 break; | |
| 327 | |
| 328 default: | |
| 329 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 330 } | |
| 331 | |
| 332 ResetImage(); | |
| 333 | |
| 334 SaveDicomToMemory(target, *dicom, transferSyntax_); | |
| 335 } | |
| 336 } |