Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/MultiframeDicomWriter.cpp @ 218:c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 12 Jan 2021 16:20:57 +0100 |
parents | 1e864138f0da |
children | 7ffcce8ec94c |
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) 2017-2021 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 "../DicomToolbox.h" |
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26 |
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27 #include <Compatibility.h> // For std::unique_ptr |
192 | 28 #include <OrthancException.h> |
29 #include <Logging.h> | |
0 | 30 |
31 #include <dcmtk/dcmdata/dcuid.h> | |
32 #include <dcmtk/dcmdata/dcdeftag.h> | |
33 #include <dcmtk/dcmdata/dcostrmb.h> | |
34 #include <dcmtk/dcmdata/dcpxitem.h> | |
35 #include <dcmtk/dcmdata/dcpixel.h> | |
36 #include <dcmtk/dcmdata/dcvrat.h> | |
37 | |
38 #include <boost/lexical_cast.hpp> | |
39 | |
14 | 40 #if DCMTK_VERSION_NUMBER <= 360 |
41 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax | |
42 #endif | |
43 | |
44 | |
0 | 45 namespace OrthancWSI |
46 { | |
47 static void SaveDicomToMemory(std::string& target, | |
48 DcmFileFormat& dicom, | |
49 E_TransferSyntax transferSyntax) | |
50 { | |
51 dicom.validateMetaInfo(transferSyntax); | |
52 dicom.removeInvalidGroups(); | |
53 | |
54 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
55 | |
56 // Create a memory buffer with the proper size | |
57 { | |
58 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*) | |
59 target.resize(estimatedSize); | |
60 } | |
61 | |
62 DcmOutputBufferStream ob(&target[0], target.size()); | |
63 | |
64 // Fill the memory buffer with the meta-header and the dataset | |
65 dicom.transferInit(); | |
66 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL, | |
67 /*opt_groupLength*/ EGL_recalcGL, | |
68 /*opt_paddingType*/ EPD_withoutPadding); | |
69 dicom.transferEnd(); | |
70 | |
71 if (!c.good()) | |
72 { | |
73 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
74 } | |
75 | |
76 // The DICOM file is successfully written, truncate the target | |
77 // buffer if its size was overestimated by (*) | |
78 ob.flush(); | |
79 | |
80 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
81 if (effectiveSize < target.size()) | |
82 { | |
83 target.resize(effectiveSize); | |
84 } | |
85 } | |
86 | |
87 | |
88 void MultiframeDicomWriter::ResetImage() | |
89 { | |
90 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence)); | |
91 | |
92 if (compression_ != ImageCompression_None) | |
93 { | |
94 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB))); | |
95 | |
96 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB); | |
97 compressedPixelSequence_->insert(offsetTable_); | |
98 offsetList_.reset(new DcmOffsetList); | |
99 } | |
100 | |
101 writtenSize_ = 0; | |
102 framesCount_ = 0; | |
103 } | |
104 | |
105 | |
106 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom) | |
107 { | |
108 static const size_t GIGABYTE = 1024 * 1024 * 1024; | |
109 | |
110 std::string pixelData; | |
111 uncompressedPixelData_.Flatten(pixelData); | |
112 | |
113 // Prevent the creation of too large DICOM files | |
114 // (uncompressed DICOM files are limited to 2GB) | |
115 if (pixelData.size() > GIGABYTE) | |
116 { | |
117 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); | |
118 } | |
119 | |
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120 std::unique_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData)); |
0 | 121 |
122 uint8_t* target = NULL; | |
123 if (!pixels->createUint8Array(pixelData.size(), target).good()) | |
124 { | |
125 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
126 } | |
127 | |
128 if (pixelData.size() > 0) | |
129 { | |
130 if (target == NULL) | |
131 { | |
132 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
133 } | |
134 | |
135 // TODO Avoid this memcpy() | |
136 memcpy(target, pixelData.c_str(), pixelData.size()); | |
137 } | |
138 | |
139 if (!dicom.getDataset()->insert(pixels.release(), false, false).good()) | |
140 { | |
141 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
142 } | |
143 } | |
144 | |
145 | |
146 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset, | |
147 ImageCompression compression, | |
148 Orthanc::PixelFormat pixelFormat, | |
149 unsigned int width, | |
150 unsigned int height, | |
151 unsigned int tileWidth, | |
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152 unsigned int tileHeight, |
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Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
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153 Orthanc::PhotometricInterpretation photometric) : |
0 | 154 compression_(compression), |
155 width_(width), | |
156 height_(height) | |
157 { | |
158 switch (compression) | |
159 { | |
160 case ImageCompression_None: | |
161 transferSyntax_ = EXS_LittleEndianImplicit; | |
162 break; | |
163 | |
164 case ImageCompression_Jpeg: | |
165 // Default transfer syntax for lossy JPEG 8bit compression | |
14 | 166 transferSyntax_ = EXS_JPEGProcess1; |
0 | 167 break; |
168 | |
169 case ImageCompression_Jpeg2000: | |
170 // JPEG2000 compression (lossless only) | |
171 transferSyntax_ = EXS_JPEG2000LosslessOnly; | |
172 break; | |
173 | |
174 default: | |
175 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
176 } | |
177 | |
178 if (!sharedTags_.copyFrom(dataset).good()) | |
179 { | |
180 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
181 } | |
182 | |
183 // We only take care of grayscale or RGB images in 8bpp | |
184 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width); | |
185 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height); | |
186 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values | |
187 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth); | |
188 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight); | |
189 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8); | |
190 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8); | |
191 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7); | |
192 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values | |
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193 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, Orthanc::EnumerationToString(photometric)); |
0 | 194 |
195 switch (pixelFormat) | |
196 { | |
197 case Orthanc::PixelFormat_RGB24: | |
198 uncompressedFrameSize_ = 3 * tileWidth * tileHeight; | |
199 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3); | |
200 break; | |
201 | |
202 case Orthanc::PixelFormat_Grayscale8: | |
203 uncompressedFrameSize_ = tileWidth * tileHeight; | |
204 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1); | |
205 break; | |
206 | |
207 default: | |
208 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
209 } | |
210 | |
211 ResetImage(); | |
212 } | |
213 | |
214 | |
215 void MultiframeDicomWriter::AddFrame(const std::string& frame, | |
216 DcmItem* functionalGroup) // This takes the ownership | |
217 { | |
218 // Free the functional group on error | |
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219 std::unique_ptr<DcmItem> functionalGroupRaii(functionalGroup); |
0 | 220 |
221 if (compression_ == ImageCompression_None) | |
222 { | |
223 if (frame.size() != uncompressedFrameSize_) | |
224 { | |
225 LOG(ERROR) << "An uncompressed frame has not the proper size: " | |
226 << frame.size() << " instead of " << uncompressedFrameSize_; | |
227 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
228 } | |
229 | |
230 uncompressedPixelData_.AddChunk(frame); | |
231 } | |
232 else | |
233 { | |
234 uint8_t* bytes = const_cast<uint8_t*>(reinterpret_cast<const uint8_t*>(frame.c_str())); | |
235 | |
236 compressedPixelSequence_->storeCompressedFrame(*offsetList_, bytes, frame.size(), | |
237 0 /* unlimited fragment size */); | |
238 } | |
239 | |
240 if (functionalGroup != NULL) | |
241 { | |
242 perFrameFunctionalGroups_->insert(functionalGroupRaii.release()); | |
243 } | |
244 else | |
245 { | |
246 perFrameFunctionalGroups_->insert(new DcmItem); | |
247 } | |
248 | |
249 writtenSize_ += frame.size(); | |
250 framesCount_ += 1; | |
251 } | |
252 | |
253 | |
254 void MultiframeDicomWriter::Flush(std::string& target, | |
255 unsigned int instanceNumber) | |
256 { | |
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257 if (instanceNumber == 0) |
0 | 258 { |
259 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
260 } | |
261 | |
262 std::string tmp = boost::lexical_cast<std::string>(instanceNumber); | |
263 | |
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264 std::unique_ptr<DcmFileFormat> dicom(new DcmFileFormat); |
0 | 265 |
266 char uid[100]; | |
267 dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); | |
268 | |
269 if (!dicom->getDataset()->copyFrom(sharedTags_).good() || | |
270 !dicom->getDataset()->insert(perFrameFunctionalGroups_.release(), false, false).good() || | |
271 !dicom->getDataset()->putAndInsertString(DCM_SOPInstanceUID, uid).good() || | |
272 !dicom->getDataset()->putAndInsertString(DCM_InstanceNumber, tmp.c_str()).good()) | |
273 { | |
274 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
275 } | |
276 | |
277 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_NumberOfFrames, boost::lexical_cast<std::string>(framesCount_)); | |
278 | |
279 switch (compression_) | |
280 { | |
281 case ImageCompression_None: | |
282 InjectUncompressedPixelData(*dicom); | |
283 break; | |
284 | |
285 case ImageCompression_Jpeg: | |
286 case ImageCompression_Jpeg2000: | |
287 offsetTable_->createOffsetTable(*offsetList_); | |
288 dicom->getDataset()->insert(compressedPixelSequence_.release()); | |
289 break; | |
290 | |
291 default: | |
292 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
293 } | |
294 | |
295 ResetImage(); | |
296 | |
297 SaveDicomToMemory(target, *dicom, transferSyntax_); | |
298 } | |
299 } |