Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/MultiframeDicomWriter.cpp @ 214:1e864138f0da
upgrade to year 2021
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 06 Jan 2021 18:10:07 +0100 |
| parents | a1c265cb2174 |
| children | 7ffcce8ec94c |
| 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 |
| 192 | 28 #include <OrthancException.h> |
| 29 #include <Logging.h> | |
| 0 | 30 |
| 31 #include <dcmtk/dcmdata/dcuid.h> | |
| 32 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 33 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 34 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 35 #include <dcmtk/dcmdata/dcpixel.h> | |
| 36 #include <dcmtk/dcmdata/dcvrat.h> | |
| 37 | |
| 38 #include <boost/lexical_cast.hpp> | |
| 39 | |
| 14 | 40 #if DCMTK_VERSION_NUMBER <= 360 |
| 41 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax | |
| 42 #endif | |
| 43 | |
| 44 | |
| 0 | 45 namespace OrthancWSI |
| 46 { | |
| 47 static void SaveDicomToMemory(std::string& target, | |
| 48 DcmFileFormat& dicom, | |
| 49 E_TransferSyntax transferSyntax) | |
| 50 { | |
| 51 dicom.validateMetaInfo(transferSyntax); | |
| 52 dicom.removeInvalidGroups(); | |
| 53 | |
| 54 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
| 55 | |
| 56 // Create a memory buffer with the proper size | |
| 57 { | |
| 58 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*) | |
| 59 target.resize(estimatedSize); | |
| 60 } | |
| 61 | |
| 62 DcmOutputBufferStream ob(&target[0], target.size()); | |
| 63 | |
| 64 // Fill the memory buffer with the meta-header and the dataset | |
| 65 dicom.transferInit(); | |
| 66 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL, | |
| 67 /*opt_groupLength*/ EGL_recalcGL, | |
| 68 /*opt_paddingType*/ EPD_withoutPadding); | |
| 69 dicom.transferEnd(); | |
| 70 | |
| 71 if (!c.good()) | |
| 72 { | |
| 73 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 74 } | |
| 75 | |
| 76 // The DICOM file is successfully written, truncate the target | |
| 77 // buffer if its size was overestimated by (*) | |
| 78 ob.flush(); | |
| 79 | |
| 80 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
| 81 if (effectiveSize < target.size()) | |
| 82 { | |
| 83 target.resize(effectiveSize); | |
| 84 } | |
| 85 } | |
| 86 | |
| 87 | |
| 88 void MultiframeDicomWriter::ResetImage() | |
| 89 { | |
| 90 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence)); | |
| 91 | |
| 92 if (compression_ != ImageCompression_None) | |
| 93 { | |
| 94 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB))); | |
| 95 | |
| 96 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB); | |
| 97 compressedPixelSequence_->insert(offsetTable_); | |
| 98 offsetList_.reset(new DcmOffsetList); | |
| 99 } | |
| 100 | |
| 101 writtenSize_ = 0; | |
| 102 framesCount_ = 0; | |
| 103 } | |
| 104 | |
| 105 | |
| 106 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom) | |
| 107 { | |
| 108 static const size_t GIGABYTE = 1024 * 1024 * 1024; | |
| 109 | |
| 110 std::string pixelData; | |
| 111 uncompressedPixelData_.Flatten(pixelData); | |
| 112 | |
| 113 // Prevent the creation of too large DICOM files | |
| 114 // (uncompressed DICOM files are limited to 2GB) | |
| 115 if (pixelData.size() > GIGABYTE) | |
| 116 { | |
| 117 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); | |
| 118 } | |
| 119 | |
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120 std::unique_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData)); |
| 0 | 121 |
| 122 uint8_t* target = NULL; | |
| 123 if (!pixels->createUint8Array(pixelData.size(), target).good()) | |
| 124 { | |
| 125 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 126 } | |
| 127 | |
| 128 if (pixelData.size() > 0) | |
| 129 { | |
| 130 if (target == NULL) | |
| 131 { | |
| 132 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 133 } | |
| 134 | |
| 135 // TODO Avoid this memcpy() | |
| 136 memcpy(target, pixelData.c_str(), pixelData.size()); | |
| 137 } | |
| 138 | |
| 139 if (!dicom.getDataset()->insert(pixels.release(), false, false).good()) | |
| 140 { | |
| 141 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 142 } | |
| 143 } | |
| 144 | |
| 145 | |
| 146 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset, | |
| 147 ImageCompression compression, | |
| 148 Orthanc::PixelFormat pixelFormat, | |
| 149 unsigned int width, | |
| 150 unsigned int height, | |
| 151 unsigned int tileWidth, | |
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152 unsigned int tileHeight, |
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153 Orthanc::PhotometricInterpretation photometric) : |
| 0 | 154 compression_(compression), |
| 155 width_(width), | |
| 156 height_(height) | |
| 157 { | |
| 158 switch (compression) | |
| 159 { | |
| 160 case ImageCompression_None: | |
| 161 transferSyntax_ = EXS_LittleEndianImplicit; | |
| 162 break; | |
| 163 | |
| 164 case ImageCompression_Jpeg: | |
| 165 // Default transfer syntax for lossy JPEG 8bit compression | |
| 14 | 166 transferSyntax_ = EXS_JPEGProcess1; |
| 0 | 167 break; |
| 168 | |
| 169 case ImageCompression_Jpeg2000: | |
| 170 // JPEG2000 compression (lossless only) | |
| 171 transferSyntax_ = EXS_JPEG2000LosslessOnly; | |
| 172 break; | |
| 173 | |
| 174 default: | |
| 175 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 176 } | |
| 177 | |
| 178 if (!sharedTags_.copyFrom(dataset).good()) | |
| 179 { | |
| 180 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 181 } | |
| 182 | |
| 183 // We only take care of grayscale or RGB images in 8bpp | |
| 184 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width); | |
| 185 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height); | |
| 186 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values | |
| 187 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth); | |
| 188 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight); | |
| 189 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8); | |
| 190 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8); | |
| 191 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7); | |
| 192 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values | |
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193 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, Orthanc::EnumerationToString(photometric)); |
| 0 | 194 |
| 195 switch (pixelFormat) | |
| 196 { | |
| 197 case Orthanc::PixelFormat_RGB24: | |
| 198 uncompressedFrameSize_ = 3 * tileWidth * tileHeight; | |
| 199 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3); | |
| 200 break; | |
| 201 | |
| 202 case Orthanc::PixelFormat_Grayscale8: | |
| 203 uncompressedFrameSize_ = tileWidth * tileHeight; | |
| 204 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1); | |
| 205 break; | |
| 206 | |
| 207 default: | |
| 208 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 209 } | |
| 210 | |
| 211 ResetImage(); | |
| 212 } | |
| 213 | |
| 214 | |
| 215 void MultiframeDicomWriter::AddFrame(const std::string& frame, | |
| 216 DcmItem* functionalGroup) // This takes the ownership | |
| 217 { | |
| 218 // Free the functional group on error | |
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219 std::unique_ptr<DcmItem> functionalGroupRaii(functionalGroup); |
| 0 | 220 |
| 221 if (compression_ == ImageCompression_None) | |
| 222 { | |
| 223 if (frame.size() != uncompressedFrameSize_) | |
| 224 { | |
| 225 LOG(ERROR) << "An uncompressed frame has not the proper size: " | |
| 226 << frame.size() << " instead of " << uncompressedFrameSize_; | |
| 227 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 228 } | |
| 229 | |
| 230 uncompressedPixelData_.AddChunk(frame); | |
| 231 } | |
| 232 else | |
| 233 { | |
| 234 uint8_t* bytes = const_cast<uint8_t*>(reinterpret_cast<const uint8_t*>(frame.c_str())); | |
| 235 | |
| 236 compressedPixelSequence_->storeCompressedFrame(*offsetList_, bytes, frame.size(), | |
| 237 0 /* unlimited fragment size */); | |
| 238 } | |
| 239 | |
| 240 if (functionalGroup != NULL) | |
| 241 { | |
| 242 perFrameFunctionalGroups_->insert(functionalGroupRaii.release()); | |
| 243 } | |
| 244 else | |
| 245 { | |
| 246 perFrameFunctionalGroups_->insert(new DcmItem); | |
| 247 } | |
| 248 | |
| 249 writtenSize_ += frame.size(); | |
| 250 framesCount_ += 1; | |
| 251 } | |
| 252 | |
| 253 | |
| 254 void MultiframeDicomWriter::Flush(std::string& target, | |
| 255 unsigned int instanceNumber) | |
| 256 { | |
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257 if (instanceNumber == 0) |
| 0 | 258 { |
| 259 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 260 } | |
| 261 | |
| 262 std::string tmp = boost::lexical_cast<std::string>(instanceNumber); | |
| 263 | |
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264 std::unique_ptr<DcmFileFormat> dicom(new DcmFileFormat); |
| 0 | 265 |
| 266 char uid[100]; | |
| 267 dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); | |
| 268 | |
| 269 if (!dicom->getDataset()->copyFrom(sharedTags_).good() || | |
| 270 !dicom->getDataset()->insert(perFrameFunctionalGroups_.release(), false, false).good() || | |
| 271 !dicom->getDataset()->putAndInsertString(DCM_SOPInstanceUID, uid).good() || | |
| 272 !dicom->getDataset()->putAndInsertString(DCM_InstanceNumber, tmp.c_str()).good()) | |
| 273 { | |
| 274 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 275 } | |
| 276 | |
| 277 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_NumberOfFrames, boost::lexical_cast<std::string>(framesCount_)); | |
| 278 | |
| 279 switch (compression_) | |
| 280 { | |
| 281 case ImageCompression_None: | |
| 282 InjectUncompressedPixelData(*dicom); | |
| 283 break; | |
| 284 | |
| 285 case ImageCompression_Jpeg: | |
| 286 case ImageCompression_Jpeg2000: | |
| 287 offsetTable_->createOffsetTable(*offsetList_); | |
| 288 dicom->getDataset()->insert(compressedPixelSequence_.release()); | |
| 289 break; | |
| 290 | |
| 291 default: | |
| 292 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 293 } | |
| 294 | |
| 295 ResetImage(); | |
| 296 | |
| 297 SaveDicomToMemory(target, *dicom, transferSyntax_); | |
| 298 } | |
| 299 } |