Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/DicomPyramidWriter.cpp @ 205:a8f25caebc07
fix
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 04 Aug 2020 13:29:52 +0200 |
parents | a1c265cb2174 |
children | 1e864138f0da |
rev | line source |
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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) 2017-2020 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 "DicomPyramidWriter.h" |
24 | |
25 #include "../DicomToolbox.h" | |
26 | |
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27 #include <Compatibility.h> // For std::unique_ptr |
192 | 28 #include <Logging.h> |
29 #include <OrthancException.h> | |
30 #include <DicomParsing/FromDcmtkBridge.h> | |
0 | 31 |
32 #include <boost/lexical_cast.hpp> | |
33 | |
34 namespace OrthancWSI | |
35 { | |
36 void DicomPyramidWriter::FlushInternal(MultiframeDicomWriter& writer, | |
37 bool force) | |
38 { | |
39 if (writer.GetFramesCount() > 0 && | |
40 writer.GetSize() > 0 && | |
41 (force || (maxSize_ != 0 && writer.GetSize() >= maxSize_))) | |
42 { | |
43 countInstances_ += 1; | |
44 | |
45 std::string dicom; | |
46 writer.Flush(dicom, countInstances_); | |
47 target_.Write(dicom); | |
48 } | |
49 } | |
50 | |
51 | |
52 DcmItem* DicomPyramidWriter::CreateFunctionalGroup(unsigned int frame, | |
53 unsigned int x, | |
54 unsigned int y, | |
55 unsigned int totalWidth, | |
56 unsigned int totalHeight, | |
57 float physicalZ) const | |
58 { | |
59 float physicalX, physicalY; | |
60 volume_.GetLocation(physicalX, physicalY, x, y, totalWidth, totalHeight); | |
61 | |
62 std::string tmpX = boost::lexical_cast<std::string>(physicalX); | |
63 std::string tmpY = boost::lexical_cast<std::string>(physicalY); | |
64 std::string tmpZ = boost::lexical_cast<std::string>(physicalZ); | |
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65 |
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66 // NB: Method DcmItem::putAndInsertUint32Array() should be used at |
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67 // this point, but it is missing in DCMTK 3.6.0 |
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68 std::string index = (boost::lexical_cast<std::string>(x / GetTileWidth() + 1) + "\\" + |
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69 boost::lexical_cast<std::string>(y / GetTileHeight() + 1)); |
0 | 70 |
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71 std::unique_ptr<DcmItem> dimension(new DcmItem); |
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72 if (!dimension->putAndInsertString(DCM_DimensionIndexValues, index.c_str()).good()) |
0 | 73 { |
74 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
75 } | |
76 | |
77 // From Supp 145: The column position of the top left pixel of the | |
78 // Total Pixel Matrix is 1. The row position of the top left pixel | |
79 // of the Total Pixel Matrix is 1. | |
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80 std::unique_ptr<DcmItem> position(new DcmItem); |
0 | 81 if (!position->putAndInsertSint32(DCM_ColumnPositionInTotalImagePixelMatrix, x + 1).good() || |
82 !position->putAndInsertSint32(DCM_RowPositionInTotalImagePixelMatrix, y + 1).good() || | |
83 !position->putAndInsertString(DCM_XOffsetInSlideCoordinateSystem, tmpX.c_str()).good() || | |
84 !position->putAndInsertString(DCM_YOffsetInSlideCoordinateSystem, tmpY.c_str()).good() || | |
85 !position->putAndInsertString(DCM_ZOffsetInSlideCoordinateSystem, tmpZ.c_str()).good()) | |
86 { | |
87 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
88 } | |
89 | |
90 | |
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91 std::unique_ptr<DcmSequenceOfItems> sequencePosition(new DcmSequenceOfItems(DCM_PlanePositionSlideSequence)); |
0 | 92 if (!sequencePosition->insert(position.release(), false, false).good()) |
93 { | |
94 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
95 } | |
96 | |
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97 std::unique_ptr<DcmSequenceOfItems> sequenceDimension(new DcmSequenceOfItems(DCM_FrameContentSequence)); |
0 | 98 if (!sequenceDimension->insert(dimension.release(), false, false).good()) |
99 { | |
100 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
101 } | |
102 | |
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103 std::unique_ptr<DcmItem> item(new DcmItem); |
0 | 104 if (!item->insert(sequencePosition.release(), false, false).good() || |
105 !item->insert(sequenceDimension.release(), false, false).good()) | |
106 { | |
107 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
108 } | |
109 | |
110 return item.release(); | |
111 } | |
112 | |
113 | |
114 void DicomPyramidWriter::WriteRawTileInternal(const std::string& tile, | |
115 const Level& level, | |
116 unsigned int x, | |
117 unsigned int y) | |
118 { | |
119 if (x >= level.countTilesX_ || | |
120 y >= level.countTilesY_) | |
121 { | |
122 LOG(ERROR) << "Tile index out of range: " << x << "," << y | |
123 << " (max: " << level.countTilesX_ << "," << level.countTilesY_ << ")"; | |
124 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
125 } | |
126 | |
127 const unsigned int z = level.z_; | |
128 | |
129 { | |
130 boost::mutex::scoped_lock lock(mutex_); | |
131 | |
132 if (z >= writers_.size()) | |
133 { | |
134 writers_.resize(z + 1); | |
135 } | |
136 | |
137 MultiframeDicomWriter* writer = writers_[z]; | |
138 | |
139 if (writer == NULL) | |
140 { | |
141 writer = new MultiframeDicomWriter | |
142 (dataset_, GetImageCompression(), GetPixelFormat(), level.width_, level.height_, | |
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143 GetTileWidth(), GetTileHeight(), photometric_); |
0 | 144 writers_[z] = writer; |
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145 |
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146 { |
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147 // Fix issue 139: The PixelSpacing information changes at each level |
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148 // https://bitbucket.org/sjodogne/orthanc/issues/139/orthancwsidicomizer-pixelspacing |
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149 |
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150 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
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151 float spacingX = volume_.GetWidth() / static_cast<float>(level.height_); |
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152 float spacingY = volume_.GetHeight() / static_cast<float>(level.width_); |
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153 |
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154 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' + |
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155 boost::lexical_cast<std::string>(spacingY)); |
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156 |
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157 std::unique_ptr<DcmItem> item(new DcmItem); |
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158 |
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159 std::unique_ptr<DcmItem> item2(new DcmItem); |
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160 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_SliceThickness, |
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161 boost::lexical_cast<std::string>(volume_.GetDepth())); |
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162 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing); |
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163 |
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164 std::unique_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence)); |
168
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165 if (!sequence2->insert(item2.release(), false, false).good()) |
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166 { |
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167 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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168 } |
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169 |
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170 DcmSequenceOfItems* sequence = NULL; |
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171 if (!writer->GetSharedTags().findAndGetSequence(DCM_SharedFunctionalGroupsSequence, sequence).good() || |
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172 sequence == NULL || |
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173 sequence->card() != 1 || |
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174 sequence->getItem(0) == NULL || |
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175 !sequence->getItem(0)->insert(sequence2.release(), false, false).good()) |
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176 { |
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177 // This sequence should have been created by "SetupDimension()" in Dicomizer.cpp |
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178 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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179 } |
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180 } |
0 | 181 } |
182 | |
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183 std::unique_ptr<DcmItem> functionalGroup(CreateFunctionalGroup(writer->GetFramesCount() + 1, |
0 | 184 x * GetTileWidth(), |
185 y * GetTileHeight(), | |
186 writer->GetTotalWidth(), | |
187 writer->GetTotalHeight(), | |
188 0.0f /* TODO Z-plane */)); | |
189 | |
190 writer->AddFrame(tile, functionalGroup.release()); | |
191 FlushInternal(*writer, false); | |
192 | |
193 countTiles_ ++; | |
194 } | |
195 } | |
196 | |
197 | |
198 DicomPyramidWriter::DicomPyramidWriter(IFileTarget& target, | |
199 const DcmDataset& dataset, | |
200 Orthanc::PixelFormat pixelFormat, | |
201 ImageCompression compression, | |
202 unsigned int tileWidth, | |
203 unsigned int tileHeight, | |
204 size_t maxSize, // If "0", no automatic flushing | |
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205 const ImagedVolumeParameters& volume, |
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206 Orthanc::PhotometricInterpretation photometric) : |
0 | 207 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), |
208 target_(target), | |
209 dataset_(dataset), | |
210 maxSize_(maxSize), | |
211 countTiles_(0), | |
212 countInstances_(0), | |
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213 volume_(volume), |
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214 photometric_(photometric) |
0 | 215 { |
216 } | |
217 | |
218 | |
219 DicomPyramidWriter::~DicomPyramidWriter() | |
220 { | |
221 LOG(WARNING) << "Closing the DICOM pyramid (" << countTiles_ << " tiles were written)"; | |
222 | |
223 for (size_t i = 0; i < writers_.size(); i++) | |
224 { | |
225 if (writers_[i] != NULL) | |
226 { | |
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227 try |
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228 { |
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229 FlushInternal(*writers_[i], true); |
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230 } |
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231 catch (Orthanc::OrthancException&) |
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232 { |
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233 LOG(ERROR) << "Cannot push the pending tiles to the DICOM pyramid while finalizing"; |
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234 } |
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235 |
0 | 236 delete writers_[i]; |
237 } | |
238 } | |
239 } | |
240 | |
241 | |
242 void DicomPyramidWriter::Flush() | |
243 { | |
244 boost::mutex::scoped_lock lock(mutex_); | |
245 | |
246 for (size_t i = 0; i < writers_.size(); i++) | |
247 { | |
248 FlushInternal(*writers_[i], true); | |
249 } | |
250 } | |
251 } |