Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/DicomPyramidWriter.cpp @ 334:f011fc199b6a default tip
back to mainline
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 18 Oct 2024 15:44:18 +0200 |
| parents | 0683312e21ba |
| children |
| 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 | |
|
312
0683312e21ba
updated copyright, as Orthanc Team now replaces Osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
309
diff
changeset
|
5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
|
0683312e21ba
updated copyright, as Orthanc Team now replaces Osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
309
diff
changeset
|
6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
|
309
7020852a8fa9
updated year to 2024
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 0 | 8 * |
| 9 * This program is free software: you can redistribute it and/or | |
| 10 * modify it under the terms of the GNU Affero General Public License | |
| 11 * as published by the Free Software Foundation, either version 3 of | |
| 12 * the License, or (at your option) any later version. | |
| 13 * | |
| 14 * This program is distributed in the hope that it will be useful, but | |
| 15 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 17 * Affero General Public License for more details. | |
| 18 * | |
| 19 * You should have received a copy of the GNU Affero General Public License | |
| 20 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 21 **/ | |
| 22 | |
| 23 | |
|
16
7a88c614be04
preparing for precompiled headers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
24 #include "../PrecompiledHeadersWSI.h" |
| 0 | 25 #include "DicomPyramidWriter.h" |
| 26 | |
| 27 #include "../DicomToolbox.h" | |
| 28 | |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
29 #include <Compatibility.h> // For std::unique_ptr |
| 192 | 30 #include <Logging.h> |
| 31 #include <OrthancException.h> | |
| 32 #include <DicomParsing/FromDcmtkBridge.h> | |
| 0 | 33 |
| 34 #include <boost/lexical_cast.hpp> | |
| 35 | |
| 36 namespace OrthancWSI | |
| 37 { | |
| 38 void DicomPyramidWriter::FlushInternal(MultiframeDicomWriter& writer, | |
| 39 bool force) | |
| 40 { | |
| 41 if (writer.GetFramesCount() > 0 && | |
| 42 writer.GetSize() > 0 && | |
| 43 (force || (maxSize_ != 0 && writer.GetSize() >= maxSize_))) | |
| 44 { | |
| 45 countInstances_ += 1; | |
| 46 | |
| 47 std::string dicom; | |
| 48 writer.Flush(dicom, countInstances_); | |
| 49 target_.Write(dicom); | |
| 50 } | |
| 51 } | |
| 52 | |
| 53 | |
| 54 DcmItem* DicomPyramidWriter::CreateFunctionalGroup(unsigned int frame, | |
| 55 unsigned int x, | |
| 56 unsigned int y, | |
| 57 unsigned int totalWidth, | |
| 58 unsigned int totalHeight, | |
| 59 float physicalZ) const | |
| 60 { | |
| 61 float physicalX, physicalY; | |
| 62 volume_.GetLocation(physicalX, physicalY, x, y, totalWidth, totalHeight); | |
| 63 | |
| 64 std::string tmpX = boost::lexical_cast<std::string>(physicalX); | |
| 65 std::string tmpY = boost::lexical_cast<std::string>(physicalY); | |
| 66 std::string tmpZ = boost::lexical_cast<std::string>(physicalZ); | |
|
84
727670c5c125
fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
59
diff
changeset
|
67 |
|
727670c5c125
fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
59
diff
changeset
|
68 // NB: Method DcmItem::putAndInsertUint32Array() should be used at |
|
727670c5c125
fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
59
diff
changeset
|
69 // this point, but it is missing in DCMTK 3.6.0 |
|
727670c5c125
fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
59
diff
changeset
|
70 std::string index = (boost::lexical_cast<std::string>(x / GetTileWidth() + 1) + "\\" + |
|
727670c5c125
fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
59
diff
changeset
|
71 boost::lexical_cast<std::string>(y / GetTileHeight() + 1)); |
| 0 | 72 |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
73 std::unique_ptr<DcmItem> dimension(new DcmItem); |
|
84
727670c5c125
fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
59
diff
changeset
|
74 if (!dimension->putAndInsertString(DCM_DimensionIndexValues, index.c_str()).good()) |
| 0 | 75 { |
| 76 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 77 } | |
| 78 | |
| 79 // From Supp 145: The column position of the top left pixel of the | |
| 80 // Total Pixel Matrix is 1. The row position of the top left pixel | |
| 81 // of the Total Pixel Matrix is 1. | |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
82 std::unique_ptr<DcmItem> position(new DcmItem); |
| 0 | 83 if (!position->putAndInsertSint32(DCM_ColumnPositionInTotalImagePixelMatrix, x + 1).good() || |
| 84 !position->putAndInsertSint32(DCM_RowPositionInTotalImagePixelMatrix, y + 1).good() || | |
| 85 !position->putAndInsertString(DCM_XOffsetInSlideCoordinateSystem, tmpX.c_str()).good() || | |
| 86 !position->putAndInsertString(DCM_YOffsetInSlideCoordinateSystem, tmpY.c_str()).good() || | |
| 87 !position->putAndInsertString(DCM_ZOffsetInSlideCoordinateSystem, tmpZ.c_str()).good()) | |
| 88 { | |
| 89 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 90 } | |
| 91 | |
| 92 | |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
93 std::unique_ptr<DcmSequenceOfItems> sequencePosition(new DcmSequenceOfItems(DCM_PlanePositionSlideSequence)); |
| 0 | 94 if (!sequencePosition->insert(position.release(), false, false).good()) |
| 95 { | |
| 96 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 97 } | |
| 98 | |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
99 std::unique_ptr<DcmSequenceOfItems> sequenceDimension(new DcmSequenceOfItems(DCM_FrameContentSequence)); |
| 0 | 100 if (!sequenceDimension->insert(dimension.release(), false, false).good()) |
| 101 { | |
| 102 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 103 } | |
| 104 | |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
105 std::unique_ptr<DcmItem> item(new DcmItem); |
| 0 | 106 if (!item->insert(sequencePosition.release(), false, false).good() || |
| 107 !item->insert(sequenceDimension.release(), false, false).good()) | |
| 108 { | |
| 109 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 110 } | |
| 111 | |
| 112 return item.release(); | |
| 113 } | |
| 114 | |
| 115 | |
| 116 void DicomPyramidWriter::WriteRawTileInternal(const std::string& tile, | |
| 117 const Level& level, | |
| 118 unsigned int x, | |
| 119 unsigned int y) | |
| 120 { | |
| 121 if (x >= level.countTilesX_ || | |
| 122 y >= level.countTilesY_) | |
| 123 { | |
| 124 LOG(ERROR) << "Tile index out of range: " << x << "," << y | |
| 125 << " (max: " << level.countTilesX_ << "," << level.countTilesY_ << ")"; | |
| 126 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 127 } | |
| 128 | |
| 129 const unsigned int z = level.z_; | |
| 130 | |
| 131 { | |
| 132 boost::mutex::scoped_lock lock(mutex_); | |
| 133 | |
| 134 if (z >= writers_.size()) | |
| 135 { | |
| 136 writers_.resize(z + 1); | |
| 137 } | |
| 138 | |
| 139 MultiframeDicomWriter* writer = writers_[z]; | |
| 140 | |
| 141 if (writer == NULL) | |
| 142 { | |
|
220
7ffcce8ec94c
Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
143 const bool isConcatenation = (maxSize_ != 0); |
| 0 | 144 writer = new MultiframeDicomWriter |
| 145 (dataset_, GetImageCompression(), GetPixelFormat(), level.width_, level.height_, | |
|
220
7ffcce8ec94c
Fix issue #145 (support of Concatenation UID)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
146 GetTileWidth(), GetTileHeight(), photometric_, isConcatenation); |
| 0 | 147 writers_[z] = writer; |
|
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
148 |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
149 { |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
150 // Fix issue 139: The PixelSpacing information changes at each level |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
151 // https://bitbucket.org/sjodogne/orthanc/issues/139/orthancwsidicomizer-pixelspacing |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
152 |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
153 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
154 float spacingX = volume_.GetWidth() / static_cast<float>(level.height_); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
155 float spacingY = volume_.GetHeight() / static_cast<float>(level.width_); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
156 |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
157 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' + |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
158 boost::lexical_cast<std::string>(spacingY)); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
159 |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
160 std::unique_ptr<DcmItem> item(new DcmItem); |
|
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
161 |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
162 std::unique_ptr<DcmItem> item2(new DcmItem); |
|
236
b0ee417b667a
migrating new definitions in namespace Orthanc to namespace OrthancWSI
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
220
diff
changeset
|
163 DicomToolbox::SetStringTag(*item2, DCM_SliceThickness, |
|
b0ee417b667a
migrating new definitions in namespace Orthanc to namespace OrthancWSI
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
220
diff
changeset
|
164 boost::lexical_cast<std::string>(volume_.GetDepth())); |
|
b0ee417b667a
migrating new definitions in namespace Orthanc to namespace OrthancWSI
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
220
diff
changeset
|
165 DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing); |
|
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
166 |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
167 std::unique_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence)); |
|
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
168 if (!sequence2->insert(item2.release(), false, false).good()) |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
169 { |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
170 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
171 } |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
172 |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
173 DcmSequenceOfItems* sequence = NULL; |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
174 if (!writer->GetSharedTags().findAndGetSequence(DCM_SharedFunctionalGroupsSequence, sequence).good() || |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
175 sequence == NULL || |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
176 sequence->card() != 1 || |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
177 sequence->getItem(0) == NULL || |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
178 !sequence->getItem(0)->insert(sequence2.release(), false, false).good()) |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
179 { |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
180 // This sequence should have been created by "SetupDimension()" in Dicomizer.cpp |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
181 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
182 } |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
183 } |
| 0 | 184 } |
| 185 | |
|
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
186 std::unique_ptr<DcmItem> functionalGroup(CreateFunctionalGroup(writer->GetFramesCount() + 1, |
| 0 | 187 x * GetTileWidth(), |
| 188 y * GetTileHeight(), | |
| 189 writer->GetTotalWidth(), | |
| 190 writer->GetTotalHeight(), | |
| 191 0.0f /* TODO Z-plane */)); | |
| 192 | |
| 193 writer->AddFrame(tile, functionalGroup.release()); | |
| 194 FlushInternal(*writer, false); | |
| 195 | |
| 196 countTiles_ ++; | |
| 197 } | |
| 198 } | |
| 199 | |
| 200 | |
| 201 DicomPyramidWriter::DicomPyramidWriter(IFileTarget& target, | |
| 202 const DcmDataset& dataset, | |
| 203 Orthanc::PixelFormat pixelFormat, | |
| 204 ImageCompression compression, | |
| 205 unsigned int tileWidth, | |
| 206 unsigned int tileHeight, | |
| 207 size_t maxSize, // If "0", no automatic flushing | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
208 const ImagedVolumeParameters& volume, |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
209 Orthanc::PhotometricInterpretation photometric) : |
| 0 | 210 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), |
| 211 target_(target), | |
| 212 dataset_(dataset), | |
| 213 maxSize_(maxSize), | |
| 214 countTiles_(0), | |
| 215 countInstances_(0), | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
216 volume_(volume), |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
217 photometric_(photometric) |
| 0 | 218 { |
| 219 } | |
| 220 | |
| 221 | |
| 222 DicomPyramidWriter::~DicomPyramidWriter() | |
| 223 { | |
| 224 LOG(WARNING) << "Closing the DICOM pyramid (" << countTiles_ << " tiles were written)"; | |
| 225 | |
| 226 for (size_t i = 0; i < writers_.size(); i++) | |
| 227 { | |
| 228 if (writers_[i] != NULL) | |
| 229 { | |
|
7
bc3ca410b765
Fix freeze if the target Orthanc is not accepting images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
230 try |
|
bc3ca410b765
Fix freeze if the target Orthanc is not accepting images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
231 { |
|
bc3ca410b765
Fix freeze if the target Orthanc is not accepting images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
232 FlushInternal(*writers_[i], true); |
|
bc3ca410b765
Fix freeze if the target Orthanc is not accepting images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
233 } |
|
bc3ca410b765
Fix freeze if the target Orthanc is not accepting images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
234 catch (Orthanc::OrthancException&) |
|
bc3ca410b765
Fix freeze if the target Orthanc is not accepting images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
235 { |
|
bc3ca410b765
Fix freeze if the target Orthanc is not accepting images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
236 LOG(ERROR) << "Cannot push the pending tiles to the DICOM pyramid while finalizing"; |
|
bc3ca410b765
Fix freeze if the target Orthanc is not accepting images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
237 } |
|
bc3ca410b765
Fix freeze if the target Orthanc is not accepting images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
238 |
| 0 | 239 delete writers_[i]; |
| 240 } | |
| 241 } | |
| 242 } | |
| 243 | |
| 244 | |
| 245 void DicomPyramidWriter::Flush() | |
| 246 { | |
| 247 boost::mutex::scoped_lock lock(mutex_); | |
| 248 | |
| 249 for (size_t i = 0; i < writers_.size(); i++) | |
| 250 { | |
| 251 FlushInternal(*writers_[i], true); | |
| 252 } | |
| 253 } | |
| 254 } |