Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/MultiframeDicomWriter.cpp @ 115:a51dee6a1515
upgrade to year 2018
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 02 Jan 2018 10:01:35 +0100 |
| parents | ff0ef01c332c |
| children | a0f9a3df1110 |
| 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) 2017-2018 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 "../../Resources/Orthanc/Core/OrthancException.h" |
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26 #include "../../Resources/Orthanc/Core/Logging.h" |
| 0 | 27 #include "../DicomToolbox.h" |
| 28 | |
| 29 #include <dcmtk/dcmdata/dcuid.h> | |
| 30 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 31 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 32 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 33 #include <dcmtk/dcmdata/dcpixel.h> | |
| 34 #include <dcmtk/dcmdata/dcvrat.h> | |
| 35 | |
| 36 #include <boost/lexical_cast.hpp> | |
| 37 | |
| 14 | 38 #if DCMTK_VERSION_NUMBER <= 360 |
| 39 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax | |
| 40 #endif | |
| 41 | |
| 42 | |
| 0 | 43 namespace OrthancWSI |
| 44 { | |
| 45 static void SaveDicomToMemory(std::string& target, | |
| 46 DcmFileFormat& dicom, | |
| 47 E_TransferSyntax transferSyntax) | |
| 48 { | |
| 49 dicom.validateMetaInfo(transferSyntax); | |
| 50 dicom.removeInvalidGroups(); | |
| 51 | |
| 52 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
| 53 | |
| 54 // Create a memory buffer with the proper size | |
| 55 { | |
| 56 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*) | |
| 57 target.resize(estimatedSize); | |
| 58 } | |
| 59 | |
| 60 DcmOutputBufferStream ob(&target[0], target.size()); | |
| 61 | |
| 62 // Fill the memory buffer with the meta-header and the dataset | |
| 63 dicom.transferInit(); | |
| 64 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL, | |
| 65 /*opt_groupLength*/ EGL_recalcGL, | |
| 66 /*opt_paddingType*/ EPD_withoutPadding); | |
| 67 dicom.transferEnd(); | |
| 68 | |
| 69 if (!c.good()) | |
| 70 { | |
| 71 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 72 } | |
| 73 | |
| 74 // The DICOM file is successfully written, truncate the target | |
| 75 // buffer if its size was overestimated by (*) | |
| 76 ob.flush(); | |
| 77 | |
| 78 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
| 79 if (effectiveSize < target.size()) | |
| 80 { | |
| 81 target.resize(effectiveSize); | |
| 82 } | |
| 83 } | |
| 84 | |
| 85 | |
| 86 void MultiframeDicomWriter::ResetImage() | |
| 87 { | |
| 88 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence)); | |
| 89 | |
| 90 if (compression_ != ImageCompression_None) | |
| 91 { | |
| 92 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB))); | |
| 93 | |
| 94 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB); | |
| 95 compressedPixelSequence_->insert(offsetTable_); | |
| 96 offsetList_.reset(new DcmOffsetList); | |
| 97 } | |
| 98 | |
| 99 writtenSize_ = 0; | |
| 100 framesCount_ = 0; | |
| 101 } | |
| 102 | |
| 103 | |
| 104 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom) | |
| 105 { | |
| 106 static const size_t GIGABYTE = 1024 * 1024 * 1024; | |
| 107 | |
| 108 std::string pixelData; | |
| 109 uncompressedPixelData_.Flatten(pixelData); | |
| 110 | |
| 111 // Prevent the creation of too large DICOM files | |
| 112 // (uncompressed DICOM files are limited to 2GB) | |
| 113 if (pixelData.size() > GIGABYTE) | |
| 114 { | |
| 115 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); | |
| 116 } | |
| 117 | |
| 118 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData)); | |
| 119 | |
| 120 uint8_t* target = NULL; | |
| 121 if (!pixels->createUint8Array(pixelData.size(), target).good()) | |
| 122 { | |
| 123 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 124 } | |
| 125 | |
| 126 if (pixelData.size() > 0) | |
| 127 { | |
| 128 if (target == NULL) | |
| 129 { | |
| 130 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 131 } | |
| 132 | |
| 133 // TODO Avoid this memcpy() | |
| 134 memcpy(target, pixelData.c_str(), pixelData.size()); | |
| 135 } | |
| 136 | |
| 137 if (!dicom.getDataset()->insert(pixels.release(), false, false).good()) | |
| 138 { | |
| 139 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 140 } | |
| 141 } | |
| 142 | |
| 143 | |
| 144 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset, | |
| 145 ImageCompression compression, | |
| 146 Orthanc::PixelFormat pixelFormat, | |
| 147 unsigned int width, | |
| 148 unsigned int height, | |
| 149 unsigned int tileWidth, | |
| 150 unsigned int tileHeight) : | |
| 151 compression_(compression), | |
| 152 width_(width), | |
| 153 height_(height) | |
| 154 { | |
| 155 switch (compression) | |
| 156 { | |
| 157 case ImageCompression_None: | |
| 158 transferSyntax_ = EXS_LittleEndianImplicit; | |
| 159 break; | |
| 160 | |
| 161 case ImageCompression_Jpeg: | |
| 162 // Default transfer syntax for lossy JPEG 8bit compression | |
| 14 | 163 transferSyntax_ = EXS_JPEGProcess1; |
| 0 | 164 break; |
| 165 | |
| 166 case ImageCompression_Jpeg2000: | |
| 167 // JPEG2000 compression (lossless only) | |
| 168 transferSyntax_ = EXS_JPEG2000LosslessOnly; | |
| 169 break; | |
| 170 | |
| 171 default: | |
| 172 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 173 } | |
| 174 | |
| 175 if (!sharedTags_.copyFrom(dataset).good()) | |
| 176 { | |
| 177 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 178 } | |
| 179 | |
| 180 // We only take care of grayscale or RGB images in 8bpp | |
| 181 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width); | |
| 182 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height); | |
| 183 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values | |
| 184 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth); | |
| 185 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight); | |
| 186 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8); | |
| 187 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8); | |
| 188 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7); | |
| 189 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values | |
| 190 | |
| 191 switch (pixelFormat) | |
| 192 { | |
| 193 case Orthanc::PixelFormat_RGB24: | |
| 194 uncompressedFrameSize_ = 3 * tileWidth * tileHeight; | |
| 195 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3); | |
| 196 | |
| 197 if (compression_ == ImageCompression_Jpeg) | |
| 198 { | |
| 199 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "YBR_FULL_422"); | |
| 200 } | |
| 201 else | |
| 202 { | |
| 203 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "RGB"); | |
| 204 } | |
| 205 | |
| 206 break; | |
| 207 | |
| 208 case Orthanc::PixelFormat_Grayscale8: | |
| 209 uncompressedFrameSize_ = tileWidth * tileHeight; | |
| 210 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1); | |
| 211 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "MONOCHROME2"); | |
| 212 break; | |
| 213 | |
| 214 default: | |
| 215 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 216 } | |
| 217 | |
| 218 ResetImage(); | |
| 219 } | |
| 220 | |
| 221 | |
| 222 void MultiframeDicomWriter::AddFrame(const std::string& frame, | |
| 223 DcmItem* functionalGroup) // This takes the ownership | |
| 224 { | |
| 225 // Free the functional group on error | |
| 226 std::auto_ptr<DcmItem> functionalGroupRaii(functionalGroup); | |
| 227 | |
| 228 if (compression_ == ImageCompression_None) | |
| 229 { | |
| 230 if (frame.size() != uncompressedFrameSize_) | |
| 231 { | |
| 232 LOG(ERROR) << "An uncompressed frame has not the proper size: " | |
| 233 << frame.size() << " instead of " << uncompressedFrameSize_; | |
| 234 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 235 } | |
| 236 | |
| 237 uncompressedPixelData_.AddChunk(frame); | |
| 238 } | |
| 239 else | |
| 240 { | |
| 241 uint8_t* bytes = const_cast<uint8_t*>(reinterpret_cast<const uint8_t*>(frame.c_str())); | |
| 242 | |
| 243 compressedPixelSequence_->storeCompressedFrame(*offsetList_, bytes, frame.size(), | |
| 244 0 /* unlimited fragment size */); | |
| 245 } | |
| 246 | |
| 247 if (functionalGroup != NULL) | |
| 248 { | |
| 249 perFrameFunctionalGroups_->insert(functionalGroupRaii.release()); | |
| 250 } | |
| 251 else | |
| 252 { | |
| 253 perFrameFunctionalGroups_->insert(new DcmItem); | |
| 254 } | |
| 255 | |
| 256 writtenSize_ += frame.size(); | |
| 257 framesCount_ += 1; | |
| 258 } | |
| 259 | |
| 260 | |
| 261 void MultiframeDicomWriter::Flush(std::string& target, | |
| 262 unsigned int instanceNumber) | |
| 263 { | |
| 264 if (instanceNumber <= 0) | |
| 265 { | |
| 266 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 267 } | |
| 268 | |
| 269 std::string tmp = boost::lexical_cast<std::string>(instanceNumber); | |
| 270 | |
| 271 std::auto_ptr<DcmFileFormat> dicom(new DcmFileFormat); | |
| 272 | |
| 273 char uid[100]; | |
| 274 dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); | |
| 275 | |
| 276 if (!dicom->getDataset()->copyFrom(sharedTags_).good() || | |
| 277 !dicom->getDataset()->insert(perFrameFunctionalGroups_.release(), false, false).good() || | |
| 278 !dicom->getDataset()->putAndInsertString(DCM_SOPInstanceUID, uid).good() || | |
| 279 !dicom->getDataset()->putAndInsertString(DCM_InstanceNumber, tmp.c_str()).good()) | |
| 280 { | |
| 281 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 282 } | |
| 283 | |
| 284 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_NumberOfFrames, boost::lexical_cast<std::string>(framesCount_)); | |
| 285 | |
| 286 switch (compression_) | |
| 287 { | |
| 288 case ImageCompression_None: | |
| 289 InjectUncompressedPixelData(*dicom); | |
| 290 break; | |
| 291 | |
| 292 case ImageCompression_Jpeg: | |
| 293 case ImageCompression_Jpeg2000: | |
| 294 offsetTable_->createOffsetTable(*offsetList_); | |
| 295 dicom->getDataset()->insert(compressedPixelSequence_.release()); | |
| 296 break; | |
| 297 | |
| 298 default: | |
| 299 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 300 } | |
| 301 | |
| 302 ResetImage(); | |
| 303 | |
| 304 SaveDicomToMemory(target, *dicom, transferSyntax_); | |
| 305 } | |
| 306 } |