Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/DicomPyramidWriter.cpp @ 167:605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 12 Jul 2019 12:00:31 +0200 |
parents | 6b8ccfc02051 |
children | d3aea0af03e1 |
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 | |
157 | 5 * Copyright (C) 2017-2019 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 | |
16
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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 <Core/Logging.h> |
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28 #include <Core/OrthancException.h> |
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29 #include <Core/DicomParsing/FromDcmtkBridge.h> |
0 | 30 |
31 #include <dcmtk/dcmdata/dcdeftag.h> | |
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 |
71 std::auto_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. | |
80 std::auto_ptr<DcmItem> position(new DcmItem); | |
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 | |
91 std::auto_ptr<DcmSequenceOfItems> sequencePosition(new DcmSequenceOfItems(DCM_PlanePositionSlideSequence)); | |
92 if (!sequencePosition->insert(position.release(), false, false).good()) | |
93 { | |
94 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
95 } | |
96 | |
97 std::auto_ptr<DcmSequenceOfItems> sequenceDimension(new DcmSequenceOfItems(DCM_FrameContentSequence)); | |
98 if (!sequenceDimension->insert(dimension.release(), false, false).good()) | |
99 { | |
100 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
101 } | |
102 | |
103 std::auto_ptr<DcmItem> item(new DcmItem); | |
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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605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
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parents:
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143 GetTileWidth(), GetTileHeight(), photometric_); |
0 | 144 writers_[z] = writer; |
145 } | |
146 | |
147 std::auto_ptr<DcmItem> functionalGroup(CreateFunctionalGroup(writer->GetFramesCount() + 1, | |
148 x * GetTileWidth(), | |
149 y * GetTileHeight(), | |
150 writer->GetTotalWidth(), | |
151 writer->GetTotalHeight(), | |
152 0.0f /* TODO Z-plane */)); | |
153 | |
154 writer->AddFrame(tile, functionalGroup.release()); | |
155 FlushInternal(*writer, false); | |
156 | |
157 countTiles_ ++; | |
158 } | |
159 } | |
160 | |
161 | |
162 DicomPyramidWriter::DicomPyramidWriter(IFileTarget& target, | |
163 const DcmDataset& dataset, | |
164 Orthanc::PixelFormat pixelFormat, | |
165 ImageCompression compression, | |
166 unsigned int tileWidth, | |
167 unsigned int tileHeight, | |
168 size_t maxSize, // If "0", no automatic flushing | |
167
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Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
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169 const ImagedVolumeParameters& volume, |
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170 Orthanc::PhotometricInterpretation photometric) : |
0 | 171 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), |
172 target_(target), | |
173 dataset_(dataset), | |
174 maxSize_(maxSize), | |
175 countTiles_(0), | |
176 countInstances_(0), | |
167
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177 volume_(volume), |
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178 photometric_(photometric) |
0 | 179 { |
180 } | |
181 | |
182 | |
183 DicomPyramidWriter::~DicomPyramidWriter() | |
184 { | |
185 LOG(WARNING) << "Closing the DICOM pyramid (" << countTiles_ << " tiles were written)"; | |
186 | |
187 for (size_t i = 0; i < writers_.size(); i++) | |
188 { | |
189 if (writers_[i] != NULL) | |
190 { | |
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191 try |
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192 { |
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193 FlushInternal(*writers_[i], true); |
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194 } |
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195 catch (Orthanc::OrthancException&) |
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196 { |
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197 LOG(ERROR) << "Cannot push the pending tiles to the DICOM pyramid while finalizing"; |
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198 } |
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199 |
0 | 200 delete writers_[i]; |
201 } | |
202 } | |
203 } | |
204 | |
205 | |
206 void DicomPyramidWriter::Flush() | |
207 { | |
208 boost::mutex::scoped_lock lock(mutex_); | |
209 | |
210 for (size_t i = 0; i < writers_.size(); i++) | |
211 { | |
212 FlushInternal(*writers_[i], true); | |
213 } | |
214 } | |
215 } |