Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/DicomPyramidWriter.cpp @ 309:7020852a8fa9
updated year to 2024
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 22 Mar 2024 15:48:12 +0100 |
| parents | 20a730889ae2 |
| children | 0683312e21ba |
| 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) 2017-2024 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2024 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 "DicomPyramidWriter.h" |
| 25 | |
| 26 #include "../DicomToolbox.h" | |
| 27 | |
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28 #include <Compatibility.h> // For std::unique_ptr |
| 192 | 29 #include <Logging.h> |
| 30 #include <OrthancException.h> | |
| 31 #include <DicomParsing/FromDcmtkBridge.h> | |
| 0 | 32 |
| 33 #include <boost/lexical_cast.hpp> | |
| 34 | |
| 35 namespace OrthancWSI | |
| 36 { | |
| 37 void DicomPyramidWriter::FlushInternal(MultiframeDicomWriter& writer, | |
| 38 bool force) | |
| 39 { | |
| 40 if (writer.GetFramesCount() > 0 && | |
| 41 writer.GetSize() > 0 && | |
| 42 (force || (maxSize_ != 0 && writer.GetSize() >= maxSize_))) | |
| 43 { | |
| 44 countInstances_ += 1; | |
| 45 | |
| 46 std::string dicom; | |
| 47 writer.Flush(dicom, countInstances_); | |
| 48 target_.Write(dicom); | |
| 49 } | |
| 50 } | |
| 51 | |
| 52 | |
| 53 DcmItem* DicomPyramidWriter::CreateFunctionalGroup(unsigned int frame, | |
| 54 unsigned int x, | |
| 55 unsigned int y, | |
| 56 unsigned int totalWidth, | |
| 57 unsigned int totalHeight, | |
| 58 float physicalZ) const | |
| 59 { | |
| 60 float physicalX, physicalY; | |
| 61 volume_.GetLocation(physicalX, physicalY, x, y, totalWidth, totalHeight); | |
| 62 | |
| 63 std::string tmpX = boost::lexical_cast<std::string>(physicalX); | |
| 64 std::string tmpY = boost::lexical_cast<std::string>(physicalY); | |
| 65 std::string tmpZ = boost::lexical_cast<std::string>(physicalZ); | |
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66 |
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67 // NB: Method DcmItem::putAndInsertUint32Array() should be used at |
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68 // this point, but it is missing in DCMTK 3.6.0 |
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69 std::string index = (boost::lexical_cast<std::string>(x / GetTileWidth() + 1) + "\\" + |
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70 boost::lexical_cast<std::string>(y / GetTileHeight() + 1)); |
| 0 | 71 |
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72 std::unique_ptr<DcmItem> dimension(new DcmItem); |
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73 if (!dimension->putAndInsertString(DCM_DimensionIndexValues, index.c_str()).good()) |
| 0 | 74 { |
| 75 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 76 } | |
| 77 | |
| 78 // From Supp 145: The column position of the top left pixel of the | |
| 79 // Total Pixel Matrix is 1. The row position of the top left pixel | |
| 80 // of the Total Pixel Matrix is 1. | |
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81 std::unique_ptr<DcmItem> position(new DcmItem); |
| 0 | 82 if (!position->putAndInsertSint32(DCM_ColumnPositionInTotalImagePixelMatrix, x + 1).good() || |
| 83 !position->putAndInsertSint32(DCM_RowPositionInTotalImagePixelMatrix, y + 1).good() || | |
| 84 !position->putAndInsertString(DCM_XOffsetInSlideCoordinateSystem, tmpX.c_str()).good() || | |
| 85 !position->putAndInsertString(DCM_YOffsetInSlideCoordinateSystem, tmpY.c_str()).good() || | |
| 86 !position->putAndInsertString(DCM_ZOffsetInSlideCoordinateSystem, tmpZ.c_str()).good()) | |
| 87 { | |
| 88 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 89 } | |
| 90 | |
| 91 | |
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92 std::unique_ptr<DcmSequenceOfItems> sequencePosition(new DcmSequenceOfItems(DCM_PlanePositionSlideSequence)); |
| 0 | 93 if (!sequencePosition->insert(position.release(), false, false).good()) |
| 94 { | |
| 95 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 96 } | |
| 97 | |
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98 std::unique_ptr<DcmSequenceOfItems> sequenceDimension(new DcmSequenceOfItems(DCM_FrameContentSequence)); |
| 0 | 99 if (!sequenceDimension->insert(dimension.release(), false, false).good()) |
| 100 { | |
| 101 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 102 } | |
| 103 | |
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104 std::unique_ptr<DcmItem> item(new DcmItem); |
| 0 | 105 if (!item->insert(sequencePosition.release(), false, false).good() || |
| 106 !item->insert(sequenceDimension.release(), false, false).good()) | |
| 107 { | |
| 108 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 109 } | |
| 110 | |
| 111 return item.release(); | |
| 112 } | |
| 113 | |
| 114 | |
| 115 void DicomPyramidWriter::WriteRawTileInternal(const std::string& tile, | |
| 116 const Level& level, | |
| 117 unsigned int x, | |
| 118 unsigned int y) | |
| 119 { | |
| 120 if (x >= level.countTilesX_ || | |
| 121 y >= level.countTilesY_) | |
| 122 { | |
| 123 LOG(ERROR) << "Tile index out of range: " << x << "," << y | |
| 124 << " (max: " << level.countTilesX_ << "," << level.countTilesY_ << ")"; | |
| 125 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 126 } | |
| 127 | |
| 128 const unsigned int z = level.z_; | |
| 129 | |
| 130 { | |
| 131 boost::mutex::scoped_lock lock(mutex_); | |
| 132 | |
| 133 if (z >= writers_.size()) | |
| 134 { | |
| 135 writers_.resize(z + 1); | |
| 136 } | |
| 137 | |
| 138 MultiframeDicomWriter* writer = writers_[z]; | |
| 139 | |
| 140 if (writer == NULL) | |
| 141 { | |
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142 const bool isConcatenation = (maxSize_ != 0); |
| 0 | 143 writer = new MultiframeDicomWriter |
| 144 (dataset_, GetImageCompression(), GetPixelFormat(), level.width_, level.height_, | |
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145 GetTileWidth(), GetTileHeight(), photometric_, isConcatenation); |
| 0 | 146 writers_[z] = writer; |
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147 |
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148 { |
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149 // Fix issue 139: The PixelSpacing information changes at each level |
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150 // https://bitbucket.org/sjodogne/orthanc/issues/139/orthancwsidicomizer-pixelspacing |
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151 |
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152 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
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153 float spacingX = volume_.GetWidth() / static_cast<float>(level.height_); |
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154 float spacingY = volume_.GetHeight() / static_cast<float>(level.width_); |
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155 |
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156 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' + |
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157 boost::lexical_cast<std::string>(spacingY)); |
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158 |
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159 std::unique_ptr<DcmItem> item(new DcmItem); |
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160 |
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161 std::unique_ptr<DcmItem> item2(new DcmItem); |
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162 DicomToolbox::SetStringTag(*item2, DCM_SliceThickness, |
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163 boost::lexical_cast<std::string>(volume_.GetDepth())); |
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164 DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing); |
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165 |
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166 std::unique_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence)); |
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167 if (!sequence2->insert(item2.release(), false, false).good()) |
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168 { |
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169 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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170 } |
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171 |
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172 DcmSequenceOfItems* sequence = NULL; |
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173 if (!writer->GetSharedTags().findAndGetSequence(DCM_SharedFunctionalGroupsSequence, sequence).good() || |
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174 sequence == NULL || |
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175 sequence->card() != 1 || |
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176 sequence->getItem(0) == NULL || |
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177 !sequence->getItem(0)->insert(sequence2.release(), false, false).good()) |
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178 { |
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179 // This sequence should have been created by "SetupDimension()" in Dicomizer.cpp |
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180 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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181 } |
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182 } |
| 0 | 183 } |
| 184 | |
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185 std::unique_ptr<DcmItem> functionalGroup(CreateFunctionalGroup(writer->GetFramesCount() + 1, |
| 0 | 186 x * GetTileWidth(), |
| 187 y * GetTileHeight(), | |
| 188 writer->GetTotalWidth(), | |
| 189 writer->GetTotalHeight(), | |
| 190 0.0f /* TODO Z-plane */)); | |
| 191 | |
| 192 writer->AddFrame(tile, functionalGroup.release()); | |
| 193 FlushInternal(*writer, false); | |
| 194 | |
| 195 countTiles_ ++; | |
| 196 } | |
| 197 } | |
| 198 | |
| 199 | |
| 200 DicomPyramidWriter::DicomPyramidWriter(IFileTarget& target, | |
| 201 const DcmDataset& dataset, | |
| 202 Orthanc::PixelFormat pixelFormat, | |
| 203 ImageCompression compression, | |
| 204 unsigned int tileWidth, | |
| 205 unsigned int tileHeight, | |
| 206 size_t maxSize, // If "0", no automatic flushing | |
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207 const ImagedVolumeParameters& volume, |
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208 Orthanc::PhotometricInterpretation photometric) : |
| 0 | 209 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), |
| 210 target_(target), | |
| 211 dataset_(dataset), | |
| 212 maxSize_(maxSize), | |
| 213 countTiles_(0), | |
| 214 countInstances_(0), | |
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215 volume_(volume), |
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216 photometric_(photometric) |
| 0 | 217 { |
| 218 } | |
| 219 | |
| 220 | |
| 221 DicomPyramidWriter::~DicomPyramidWriter() | |
| 222 { | |
| 223 LOG(WARNING) << "Closing the DICOM pyramid (" << countTiles_ << " tiles were written)"; | |
| 224 | |
| 225 for (size_t i = 0; i < writers_.size(); i++) | |
| 226 { | |
| 227 if (writers_[i] != NULL) | |
| 228 { | |
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229 try |
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230 { |
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231 FlushInternal(*writers_[i], true); |
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232 } |
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233 catch (Orthanc::OrthancException&) |
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234 { |
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235 LOG(ERROR) << "Cannot push the pending tiles to the DICOM pyramid while finalizing"; |
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236 } |
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237 |
| 0 | 238 delete writers_[i]; |
| 239 } | |
| 240 } | |
| 241 } | |
| 242 | |
| 243 | |
| 244 void DicomPyramidWriter::Flush() | |
| 245 { | |
| 246 boost::mutex::scoped_lock lock(mutex_); | |
| 247 | |
| 248 for (size_t i = 0; i < writers_.size(); i++) | |
| 249 { | |
| 250 FlushInternal(*writers_[i], true); | |
| 251 } | |
| 252 } | |
| 253 } |