Mercurial > hg > orthanc-wsi
comparison Framework/Outputs/MultiframeDicomWriter.cpp @ 0:4a7a53257c7d
initial commit
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Sat, 22 Oct 2016 21:48:33 +0200 |
parents | |
children | d9c49ab82931 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:4a7a53257c7d |
---|---|
1 /** | |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
5 * | |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU Affero General Public License | |
8 * as published by the Free Software Foundation, either version 3 of | |
9 * the License, or (at your option) any later version. | |
10 * | |
11 * This program is distributed in the hope that it will be useful, but | |
12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
14 * Affero General Public License for more details. | |
15 * | |
16 * You should have received a copy of the GNU Affero General Public License | |
17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
18 **/ | |
19 | |
20 | |
21 #include "MultiframeDicomWriter.h" | |
22 | |
23 #include "../Orthanc/Core/OrthancException.h" | |
24 #include "../Orthanc/Core/Logging.h" | |
25 #include "../DicomToolbox.h" | |
26 | |
27 #include <dcmtk/dcmdata/dcuid.h> | |
28 #include <dcmtk/dcmdata/dcdeftag.h> | |
29 #include <dcmtk/dcmdata/dcostrmb.h> | |
30 #include <dcmtk/dcmdata/dcpxitem.h> | |
31 #include <dcmtk/dcmdata/dcpixel.h> | |
32 #include <dcmtk/dcmdata/dcvrat.h> | |
33 | |
34 #include <boost/lexical_cast.hpp> | |
35 | |
36 namespace OrthancWSI | |
37 { | |
38 static void SaveDicomToMemory(std::string& target, | |
39 DcmFileFormat& dicom, | |
40 E_TransferSyntax transferSyntax) | |
41 { | |
42 dicom.validateMetaInfo(transferSyntax); | |
43 dicom.removeInvalidGroups(); | |
44 | |
45 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
46 | |
47 // Create a memory buffer with the proper size | |
48 { | |
49 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*) | |
50 target.resize(estimatedSize); | |
51 } | |
52 | |
53 DcmOutputBufferStream ob(&target[0], target.size()); | |
54 | |
55 // Fill the memory buffer with the meta-header and the dataset | |
56 dicom.transferInit(); | |
57 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL, | |
58 /*opt_groupLength*/ EGL_recalcGL, | |
59 /*opt_paddingType*/ EPD_withoutPadding); | |
60 dicom.transferEnd(); | |
61 | |
62 if (!c.good()) | |
63 { | |
64 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
65 } | |
66 | |
67 // The DICOM file is successfully written, truncate the target | |
68 // buffer if its size was overestimated by (*) | |
69 ob.flush(); | |
70 | |
71 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
72 if (effectiveSize < target.size()) | |
73 { | |
74 target.resize(effectiveSize); | |
75 } | |
76 } | |
77 | |
78 | |
79 void MultiframeDicomWriter::ResetImage() | |
80 { | |
81 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence)); | |
82 | |
83 if (compression_ != ImageCompression_None) | |
84 { | |
85 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB))); | |
86 | |
87 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB); | |
88 compressedPixelSequence_->insert(offsetTable_); | |
89 offsetList_.reset(new DcmOffsetList); | |
90 } | |
91 | |
92 writtenSize_ = 0; | |
93 framesCount_ = 0; | |
94 } | |
95 | |
96 | |
97 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom) | |
98 { | |
99 static const size_t GIGABYTE = 1024 * 1024 * 1024; | |
100 | |
101 std::string pixelData; | |
102 uncompressedPixelData_.Flatten(pixelData); | |
103 | |
104 // Prevent the creation of too large DICOM files | |
105 // (uncompressed DICOM files are limited to 2GB) | |
106 if (pixelData.size() > GIGABYTE) | |
107 { | |
108 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); | |
109 } | |
110 | |
111 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData)); | |
112 | |
113 uint8_t* target = NULL; | |
114 if (!pixels->createUint8Array(pixelData.size(), target).good()) | |
115 { | |
116 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
117 } | |
118 | |
119 if (pixelData.size() > 0) | |
120 { | |
121 if (target == NULL) | |
122 { | |
123 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
124 } | |
125 | |
126 // TODO Avoid this memcpy() | |
127 memcpy(target, pixelData.c_str(), pixelData.size()); | |
128 } | |
129 | |
130 if (!dicom.getDataset()->insert(pixels.release(), false, false).good()) | |
131 { | |
132 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
133 } | |
134 } | |
135 | |
136 | |
137 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset, | |
138 ImageCompression compression, | |
139 Orthanc::PixelFormat pixelFormat, | |
140 unsigned int width, | |
141 unsigned int height, | |
142 unsigned int tileWidth, | |
143 unsigned int tileHeight) : | |
144 compression_(compression), | |
145 width_(width), | |
146 height_(height) | |
147 { | |
148 switch (compression) | |
149 { | |
150 case ImageCompression_None: | |
151 transferSyntax_ = EXS_LittleEndianImplicit; | |
152 break; | |
153 | |
154 case ImageCompression_Jpeg: | |
155 // Default transfer syntax for lossy JPEG 8bit compression | |
156 transferSyntax_ = EXS_JPEGProcess1TransferSyntax; | |
157 break; | |
158 | |
159 case ImageCompression_Jpeg2000: | |
160 // JPEG2000 compression (lossless only) | |
161 transferSyntax_ = EXS_JPEG2000LosslessOnly; | |
162 break; | |
163 | |
164 default: | |
165 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
166 } | |
167 | |
168 if (!sharedTags_.copyFrom(dataset).good()) | |
169 { | |
170 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
171 } | |
172 | |
173 // We only take care of grayscale or RGB images in 8bpp | |
174 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width); | |
175 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height); | |
176 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values | |
177 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth); | |
178 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight); | |
179 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8); | |
180 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8); | |
181 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7); | |
182 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values | |
183 | |
184 switch (pixelFormat) | |
185 { | |
186 case Orthanc::PixelFormat_RGB24: | |
187 uncompressedFrameSize_ = 3 * tileWidth * tileHeight; | |
188 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3); | |
189 | |
190 if (compression_ == ImageCompression_Jpeg) | |
191 { | |
192 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "YBR_FULL_422"); | |
193 } | |
194 else | |
195 { | |
196 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "RGB"); | |
197 } | |
198 | |
199 break; | |
200 | |
201 case Orthanc::PixelFormat_Grayscale8: | |
202 uncompressedFrameSize_ = tileWidth * tileHeight; | |
203 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1); | |
204 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "MONOCHROME2"); | |
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 | |
219 std::auto_ptr<DcmItem> functionalGroupRaii(functionalGroup); | |
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 { | |
257 if (instanceNumber <= 0) | |
258 { | |
259 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
260 } | |
261 | |
262 std::string tmp = boost::lexical_cast<std::string>(instanceNumber); | |
263 | |
264 std::auto_ptr<DcmFileFormat> dicom(new DcmFileFormat); | |
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 } |