Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/MultiframeDicomWriter.cpp @ 170:cea9a4701fce
Support of grayscale images
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 02 Aug 2019 15:31:19 +0200 |
parents | 605247fc8758 |
children | e3cbf890b588 |
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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preparing for precompiled headers
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22 #include "../PrecompiledHeadersWSI.h" |
0 | 23 #include "MultiframeDicomWriter.h" |
24 | |
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25 #include <Core/OrthancException.h> |
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26 #include <Core/Logging.h> |
0 | 27 #include "../DicomToolbox.h" |
28 | |
29 #include <dcmtk/dcmdata/dcuid.h> | |
30 #include <dcmtk/dcmdata/dcdeftag.h> | |
31 #include <dcmtk/dcmdata/dcostrmb.h> | |
32 #include <dcmtk/dcmdata/dcpxitem.h> | |
33 #include <dcmtk/dcmdata/dcpixel.h> | |
34 #include <dcmtk/dcmdata/dcvrat.h> | |
35 | |
36 #include <boost/lexical_cast.hpp> | |
37 | |
14 | 38 #if DCMTK_VERSION_NUMBER <= 360 |
39 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax | |
40 #endif | |
41 | |
42 | |
0 | 43 namespace OrthancWSI |
44 { | |
45 static void SaveDicomToMemory(std::string& target, | |
46 DcmFileFormat& dicom, | |
47 E_TransferSyntax transferSyntax) | |
48 { | |
49 dicom.validateMetaInfo(transferSyntax); | |
50 dicom.removeInvalidGroups(); | |
51 | |
52 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
53 | |
54 // Create a memory buffer with the proper size | |
55 { | |
56 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*) | |
57 target.resize(estimatedSize); | |
58 } | |
59 | |
60 DcmOutputBufferStream ob(&target[0], target.size()); | |
61 | |
62 // Fill the memory buffer with the meta-header and the dataset | |
63 dicom.transferInit(); | |
64 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL, | |
65 /*opt_groupLength*/ EGL_recalcGL, | |
66 /*opt_paddingType*/ EPD_withoutPadding); | |
67 dicom.transferEnd(); | |
68 | |
69 if (!c.good()) | |
70 { | |
71 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
72 } | |
73 | |
74 // The DICOM file is successfully written, truncate the target | |
75 // buffer if its size was overestimated by (*) | |
76 ob.flush(); | |
77 | |
78 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
79 if (effectiveSize < target.size()) | |
80 { | |
81 target.resize(effectiveSize); | |
82 } | |
83 } | |
84 | |
85 | |
86 void MultiframeDicomWriter::ResetImage() | |
87 { | |
88 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence)); | |
89 | |
90 if (compression_ != ImageCompression_None) | |
91 { | |
92 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB))); | |
93 | |
94 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB); | |
95 compressedPixelSequence_->insert(offsetTable_); | |
96 offsetList_.reset(new DcmOffsetList); | |
97 } | |
98 | |
99 writtenSize_ = 0; | |
100 framesCount_ = 0; | |
101 } | |
102 | |
103 | |
104 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom) | |
105 { | |
106 static const size_t GIGABYTE = 1024 * 1024 * 1024; | |
107 | |
108 std::string pixelData; | |
109 uncompressedPixelData_.Flatten(pixelData); | |
110 | |
111 // Prevent the creation of too large DICOM files | |
112 // (uncompressed DICOM files are limited to 2GB) | |
113 if (pixelData.size() > GIGABYTE) | |
114 { | |
115 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); | |
116 } | |
117 | |
118 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData)); | |
119 | |
120 uint8_t* target = NULL; | |
121 if (!pixels->createUint8Array(pixelData.size(), target).good()) | |
122 { | |
123 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
124 } | |
125 | |
126 if (pixelData.size() > 0) | |
127 { | |
128 if (target == NULL) | |
129 { | |
130 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
131 } | |
132 | |
133 // TODO Avoid this memcpy() | |
134 memcpy(target, pixelData.c_str(), pixelData.size()); | |
135 } | |
136 | |
137 if (!dicom.getDataset()->insert(pixels.release(), false, false).good()) | |
138 { | |
139 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
140 } | |
141 } | |
142 | |
143 | |
144 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset, | |
145 ImageCompression compression, | |
146 Orthanc::PixelFormat pixelFormat, | |
147 unsigned int width, | |
148 unsigned int height, | |
149 unsigned int tileWidth, | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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150 unsigned int tileHeight, |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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151 Orthanc::PhotometricInterpretation photometric) : |
0 | 152 compression_(compression), |
153 width_(width), | |
154 height_(height) | |
155 { | |
156 switch (compression) | |
157 { | |
158 case ImageCompression_None: | |
159 transferSyntax_ = EXS_LittleEndianImplicit; | |
160 break; | |
161 | |
162 case ImageCompression_Jpeg: | |
163 // Default transfer syntax for lossy JPEG 8bit compression | |
14 | 164 transferSyntax_ = EXS_JPEGProcess1; |
0 | 165 break; |
166 | |
167 case ImageCompression_Jpeg2000: | |
168 // JPEG2000 compression (lossless only) | |
169 transferSyntax_ = EXS_JPEG2000LosslessOnly; | |
170 break; | |
171 | |
172 default: | |
173 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
174 } | |
175 | |
176 if (!sharedTags_.copyFrom(dataset).good()) | |
177 { | |
178 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
179 } | |
180 | |
181 // We only take care of grayscale or RGB images in 8bpp | |
182 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width); | |
183 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height); | |
184 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values | |
185 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth); | |
186 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight); | |
187 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8); | |
188 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8); | |
189 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7); | |
190 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
191 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, Orthanc::EnumerationToString(photometric)); |
0 | 192 |
193 switch (pixelFormat) | |
194 { | |
195 case Orthanc::PixelFormat_RGB24: | |
196 uncompressedFrameSize_ = 3 * tileWidth * tileHeight; | |
197 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3); | |
198 break; | |
199 | |
200 case Orthanc::PixelFormat_Grayscale8: | |
201 uncompressedFrameSize_ = tileWidth * tileHeight; | |
202 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1); | |
203 break; | |
204 | |
205 default: | |
206 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
207 } | |
208 | |
209 ResetImage(); | |
210 } | |
211 | |
212 | |
213 void MultiframeDicomWriter::AddFrame(const std::string& frame, | |
214 DcmItem* functionalGroup) // This takes the ownership | |
215 { | |
216 // Free the functional group on error | |
217 std::auto_ptr<DcmItem> functionalGroupRaii(functionalGroup); | |
218 | |
219 if (compression_ == ImageCompression_None) | |
220 { | |
221 if (frame.size() != uncompressedFrameSize_) | |
222 { | |
223 LOG(ERROR) << "An uncompressed frame has not the proper size: " | |
224 << frame.size() << " instead of " << uncompressedFrameSize_; | |
225 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
226 } | |
227 | |
228 uncompressedPixelData_.AddChunk(frame); | |
229 } | |
230 else | |
231 { | |
232 uint8_t* bytes = const_cast<uint8_t*>(reinterpret_cast<const uint8_t*>(frame.c_str())); | |
233 | |
234 compressedPixelSequence_->storeCompressedFrame(*offsetList_, bytes, frame.size(), | |
235 0 /* unlimited fragment size */); | |
236 } | |
237 | |
238 if (functionalGroup != NULL) | |
239 { | |
240 perFrameFunctionalGroups_->insert(functionalGroupRaii.release()); | |
241 } | |
242 else | |
243 { | |
244 perFrameFunctionalGroups_->insert(new DcmItem); | |
245 } | |
246 | |
247 writtenSize_ += frame.size(); | |
248 framesCount_ += 1; | |
249 } | |
250 | |
251 | |
252 void MultiframeDicomWriter::Flush(std::string& target, | |
253 unsigned int instanceNumber) | |
254 { | |
255 if (instanceNumber <= 0) | |
256 { | |
257 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
258 } | |
259 | |
260 std::string tmp = boost::lexical_cast<std::string>(instanceNumber); | |
261 | |
262 std::auto_ptr<DcmFileFormat> dicom(new DcmFileFormat); | |
263 | |
264 char uid[100]; | |
265 dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); | |
266 | |
267 if (!dicom->getDataset()->copyFrom(sharedTags_).good() || | |
268 !dicom->getDataset()->insert(perFrameFunctionalGroups_.release(), false, false).good() || | |
269 !dicom->getDataset()->putAndInsertString(DCM_SOPInstanceUID, uid).good() || | |
270 !dicom->getDataset()->putAndInsertString(DCM_InstanceNumber, tmp.c_str()).good()) | |
271 { | |
272 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
273 } | |
274 | |
275 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_NumberOfFrames, boost::lexical_cast<std::string>(framesCount_)); | |
276 | |
277 switch (compression_) | |
278 { | |
279 case ImageCompression_None: | |
280 InjectUncompressedPixelData(*dicom); | |
281 break; | |
282 | |
283 case ImageCompression_Jpeg: | |
284 case ImageCompression_Jpeg2000: | |
285 offsetTable_->createOffsetTable(*offsetList_); | |
286 dicom->getDataset()->insert(compressedPixelSequence_.release()); | |
287 break; | |
288 | |
289 default: | |
290 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
291 } | |
292 | |
293 ResetImage(); | |
294 | |
295 SaveDicomToMemory(target, *dicom, transferSyntax_); | |
296 } | |
297 } |