Mercurial > hg > orthanc
annotate OrthancServer/Internals/DicomImageDecoder.cpp @ 858:ebc41566f742 jpeg
removed unneeded check
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 06 Jun 2014 15:25:31 +0200 |
parents | ff530685e46a |
children | 610a9a1ed855 |
rev | line source |
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845 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, | |
4 * Belgium | |
5 * | |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU General Public License as | |
8 * published by the Free Software Foundation, either version 3 of the | |
9 * License, or (at your option) any later version. | |
10 * | |
11 * In addition, as a special exception, the copyright holders of this | |
12 * program give permission to link the code of its release with the | |
13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
14 * that use the same license as the "OpenSSL" library), and distribute | |
15 * the linked executables. You must obey the GNU General Public License | |
16 * in all respects for all of the code used other than "OpenSSL". If you | |
17 * modify file(s) with this exception, you may extend this exception to | |
18 * your version of the file(s), but you are not obligated to do so. If | |
19 * you do not wish to do so, delete this exception statement from your | |
20 * version. If you delete this exception statement from all source files | |
21 * in the program, then also delete it here. | |
22 * | |
23 * This program is distributed in the hope that it will be useful, but | |
24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
26 * General Public License for more details. | |
27 * | |
28 * You should have received a copy of the GNU General Public License | |
29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
30 **/ | |
31 | |
32 | |
33 #include "../PrecompiledHeadersServer.h" | |
34 #include "DicomImageDecoder.h" | |
35 | |
846 | 36 |
37 /*========================================================================= | |
38 | |
39 This file is based on portions of the following project | |
40 (cf. function "DecodePsmctRle1()"): | |
41 | |
42 Program: GDCM (Grassroots DICOM). A DICOM library | |
43 Module: http://gdcm.sourceforge.net/Copyright.html | |
44 | |
45 Copyright (c) 2006-2011 Mathieu Malaterre | |
46 Copyright (c) 1993-2005 CREATIS | |
47 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) | |
48 All rights reserved. | |
49 | |
50 Redistribution and use in source and binary forms, with or without | |
51 modification, are permitted provided that the following conditions are met: | |
52 | |
53 * Redistributions of source code must retain the above copyright notice, | |
54 this list of conditions and the following disclaimer. | |
55 | |
56 * Redistributions in binary form must reproduce the above copyright notice, | |
57 this list of conditions and the following disclaimer in the documentation | |
58 and/or other materials provided with the distribution. | |
59 | |
60 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any | |
61 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to | |
62 endorse or promote products derived from this software without specific | |
63 prior written permission. | |
64 | |
65 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' | |
66 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
67 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
68 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR | |
69 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | |
70 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | |
71 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | |
72 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | |
73 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | |
74 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
75 | |
76 =========================================================================*/ | |
77 | |
78 | |
79 | |
845 | 80 #include "../../Core/OrthancException.h" |
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81 #include "../../Core/ImageFormats/ImageProcessing.h" |
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82 #include "../../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
845 | 83 #include "../ToDcmtkBridge.h" |
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84 #include "../FromDcmtkBridge.h" |
845 | 85 |
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86 #include <glog/logging.h> |
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87 |
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88 #include <boost/lexical_cast.hpp> |
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89 |
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90 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1 |
845 | 91 #include <dcmtk/dcmjpls/djcodecd.h> |
92 #include <dcmtk/dcmjpls/djcparam.h> | |
93 #include <dcmtk/dcmjpeg/djrplol.h> | |
94 #endif | |
95 | |
96 | |
97 namespace Orthanc | |
98 { | |
852 | 99 class DicomImageDecoder::ImageSource |
100 { | |
101 private: | |
102 std::string psmct_; | |
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103 std::auto_ptr<DicomIntegerPixelAccessor> slowAccessor_; |
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104 std::auto_ptr<ImageAccessor> fastAccessor_; |
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105 |
852 | 106 public: |
107 void Setup(DcmDataset& dataset, | |
108 unsigned int frame) | |
109 { | |
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110 psmct_.clear(); |
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111 slowAccessor_.reset(NULL); |
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112 fastAccessor_.reset(NULL); |
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113 |
852 | 114 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data |
115 | |
116 DicomMap m; | |
117 FromDcmtkBridge::Convert(m, dataset); | |
118 | |
119 /** | |
120 * Create an accessor to the raw values of the DICOM image. | |
121 **/ | |
122 | |
123 DcmElement* e; | |
124 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && | |
125 e != NULL) | |
126 { | |
127 Uint8* pixData = NULL; | |
128 if (e->getUint8Array(pixData) == EC_Normal) | |
129 { | |
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130 slowAccessor_.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); |
852 | 131 } |
132 } | |
133 else if (DicomImageDecoder::DecodePsmctRle1(psmct_, dataset)) | |
134 { | |
135 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded"; | |
136 Uint8* pixData = NULL; | |
137 if (psmct_.size() > 0) | |
138 { | |
139 pixData = reinterpret_cast<Uint8*>(&psmct_[0]); | |
140 } | |
141 | |
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142 slowAccessor_.reset(new DicomIntegerPixelAccessor(m, pixData, psmct_.size())); |
852 | 143 } |
144 | |
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145 if (slowAccessor_.get() == NULL) |
852 | 146 { |
147 throw OrthancException(ErrorCode_BadFileFormat); | |
148 } | |
149 | |
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150 slowAccessor_->SetCurrentFrame(frame); |
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151 |
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152 |
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153 /** |
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154 * If possible, create a fast ImageAccessor to the image buffer. |
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155 **/ |
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156 |
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157 |
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158 } |
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159 |
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160 unsigned int GetWidth() const |
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161 { |
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162 assert(slowAccessor_.get() != NULL); |
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163 return slowAccessor_->GetInformation().GetWidth(); |
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164 } |
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165 |
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166 unsigned int GetHeight() const |
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167 { |
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168 assert(slowAccessor_.get() != NULL); |
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169 return slowAccessor_->GetInformation().GetHeight(); |
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170 } |
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171 |
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172 unsigned int GetBytesPerPixel() const |
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173 { |
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174 assert(slowAccessor_.get() != NULL); |
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175 return slowAccessor_->GetInformation().GetBytesPerPixel(); |
852 | 176 } |
177 | |
178 unsigned int GetChannelCount() const | |
179 { | |
853
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180 assert(slowAccessor_.get() != NULL); |
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181 return slowAccessor_->GetInformation().GetChannelCount(); |
852 | 182 } |
183 | |
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184 const DicomIntegerPixelAccessor& GetAccessor() const |
852 | 185 { |
853
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186 assert(slowAccessor_.get() != NULL); |
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187 return *slowAccessor_; |
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188 } |
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189 |
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190 bool HasFastAccessor() const |
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191 { |
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192 return fastAccessor_.get() != NULL; |
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193 } |
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194 |
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195 const ImageAccessor& GetFastAccessor() const |
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196 { |
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197 assert(HasFastAccessor()); |
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198 return *fastAccessor_; |
852 | 199 } |
200 }; | |
201 | |
202 | |
846 | 203 static const DicomTag DICOM_TAG_CONTENT(0x07a1, 0x100a); |
204 static const DicomTag DICOM_TAG_COMPRESSION_TYPE(0x07a1, 0x1011); | |
205 | |
206 bool DicomImageDecoder::IsPsmctRle1(DcmDataset& dataset) | |
207 { | |
208 DcmElement* e; | |
209 char* c; | |
210 | |
211 // Check whether the DICOM instance contains an image encoded with | |
212 // the PMSCT_RLE1 scheme. | |
213 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_COMPRESSION_TYPE), e).good() || | |
214 e == NULL || | |
215 !e->isaString() || | |
216 !e->getString(c).good() || | |
217 c == NULL || | |
218 strcmp("PMSCT_RLE1", c)) | |
219 { | |
220 return false; | |
221 } | |
222 else | |
223 { | |
224 return true; | |
225 } | |
226 } | |
227 | |
228 | |
229 bool DicomImageDecoder::DecodePsmctRle1(std::string& output, | |
230 DcmDataset& dataset) | |
231 { | |
232 // Check whether the DICOM instance contains an image encoded with | |
233 // the PMSCT_RLE1 scheme. | |
234 if (!IsPsmctRle1(dataset)) | |
235 { | |
236 return false; | |
237 } | |
238 | |
239 // OK, this is a custom RLE encoding from Philips. Get the pixel | |
240 // data from the appropriate private DICOM tag. | |
241 Uint8* pixData = NULL; | |
242 DcmElement* e; | |
243 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_CONTENT), e).good() || | |
244 e == NULL || | |
245 e->getUint8Array(pixData) != EC_Normal) | |
246 { | |
247 return false; | |
248 } | |
249 | |
250 // The "unsigned" below IS VERY IMPORTANT | |
251 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData); | |
252 const size_t length = e->getLength(); | |
253 | |
254 /** | |
255 * The code below is an adaptation of a sample code for GDCM by | |
256 * Mathieu Malaterre (under a BSD license). | |
257 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html | |
258 **/ | |
259 | |
260 // RLE pass | |
261 std::vector<uint8_t> temp; | |
262 temp.reserve(length); | |
263 for (size_t i = 0; i < length; i++) | |
264 { | |
265 if (inbuffer[i] == 0xa5) | |
266 { | |
267 temp.push_back(inbuffer[i+2]); | |
268 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--) | |
269 { | |
270 temp.push_back(inbuffer[i+2]); | |
271 } | |
272 i += 2; | |
273 } | |
274 else | |
275 { | |
276 temp.push_back(inbuffer[i]); | |
277 } | |
278 } | |
279 | |
280 // Delta encoding pass | |
281 uint16_t delta = 0; | |
282 output.clear(); | |
283 output.reserve(temp.size()); | |
284 for (size_t i = 0; i < temp.size(); i++) | |
285 { | |
286 uint16_t value; | |
287 | |
288 if (temp[i] == 0x5a) | |
289 { | |
290 uint16_t v1 = temp[i + 1]; | |
291 uint16_t v2 = temp[i + 2]; | |
292 value = (v2 << 8) + v1; | |
293 i += 2; | |
294 } | |
295 else | |
296 { | |
297 value = delta + (int8_t) temp[i]; | |
298 } | |
299 | |
300 output.push_back(value & 0xff); | |
301 output.push_back(value >> 8); | |
302 delta = value; | |
303 } | |
304 | |
305 if (output.size() % 2) | |
306 { | |
307 output.resize(output.size() - 1); | |
308 } | |
309 | |
310 return true; | |
311 } | |
312 | |
313 | |
845 | 314 void DicomImageDecoder::SetupImageBuffer(ImageBuffer& target, |
315 DcmDataset& dataset) | |
316 { | |
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317 DicomMap m; |
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318 FromDcmtkBridge::Convert(m, dataset); |
845 | 319 |
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320 DicomImageInformation info(m); |
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321 PixelFormat format; |
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322 |
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323 if (!info.ExtractPixelFormat(format)) |
845 | 324 { |
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325 LOG(WARNING) << "Unsupported DICOM image: " << info.GetBitsStored() |
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326 << "bpp, " << info.GetChannelCount() << " channels, " |
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327 << (info.IsSigned() ? "signed" : "unsigned"); |
845 | 328 throw OrthancException(ErrorCode_NotImplemented); |
329 } | |
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330 |
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331 target.SetHeight(info.GetHeight()); |
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332 target.SetWidth(info.GetWidth()); |
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333 target.SetFormat(format); |
845 | 334 } |
335 | |
336 | |
337 bool DicomImageDecoder::IsJpegLossless(const DcmDataset& dataset) | |
338 { | |
851 | 339 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
845 | 340 return (dataset.getOriginalXfer() == EXS_JPEGLSLossless || |
341 dataset.getOriginalXfer() == EXS_JPEGLSLossy); | |
342 } | |
343 | |
344 | |
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345 bool DicomImageDecoder::IsUncompressedImage(const DcmDataset& dataset) |
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346 { |
851 | 347 // http://support.dcmtk.org/docs/dcxfer_8h-source.html |
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348 return (dataset.getOriginalXfer() == EXS_Unknown || |
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349 dataset.getOriginalXfer() == EXS_LittleEndianImplicit || |
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350 dataset.getOriginalXfer() == EXS_BigEndianImplicit || |
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351 dataset.getOriginalXfer() == EXS_LittleEndianExplicit || |
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352 dataset.getOriginalXfer() == EXS_BigEndianExplicit); |
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353 } |
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354 |
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355 |
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356 template <typename PixelType> |
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357 static void CopyPixels(ImageAccessor& target, |
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358 const DicomIntegerPixelAccessor& source) |
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359 { |
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360 const PixelType minValue = std::numeric_limits<PixelType>::min(); |
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361 const PixelType maxValue = std::numeric_limits<PixelType>::max(); |
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362 |
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363 for (unsigned int y = 0; y < source.GetInformation().GetHeight(); y++) |
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364 { |
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365 PixelType* pixel = reinterpret_cast<PixelType*>(target.GetRow(y)); |
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366 for (unsigned int x = 0; x < source.GetInformation().GetWidth(); x++) |
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367 { |
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368 for (unsigned int c = 0; c < source.GetInformation().GetChannelCount(); c++, pixel++) |
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369 { |
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370 int32_t v = source.GetValue(x, y, c); |
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371 if (v < static_cast<int32_t>(minValue)) |
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372 { |
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373 *pixel = minValue; |
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374 } |
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375 else if (v > static_cast<int32_t>(maxValue)) |
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376 { |
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377 *pixel = maxValue; |
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378 } |
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379 else |
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380 { |
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381 *pixel = static_cast<PixelType>(v); |
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382 } |
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383 } |
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384 } |
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385 } |
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386 } |
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387 |
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388 |
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389 void DicomImageDecoder::DecodeUncompressedImage(ImageBuffer& target, |
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390 DcmDataset& dataset, |
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391 unsigned int frame) |
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392 { |
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393 if (!IsUncompressedImage(dataset)) |
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394 { |
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395 throw OrthancException(ErrorCode_BadParameterType); |
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396 } |
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397 |
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398 DecodeUncompressedImageInternal(target, dataset, frame); |
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399 } |
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400 |
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401 |
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402 void DicomImageDecoder::DecodeUncompressedImageInternal(ImageBuffer& target, |
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403 DcmDataset& dataset, |
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404 unsigned int frame) |
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405 { |
852 | 406 ImageSource source; |
407 source.Setup(dataset, frame); | |
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408 |
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409 |
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410 /** |
858
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411 * Resize the target image. |
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412 **/ |
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413 |
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414 SetupImageBuffer(target, dataset); |
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415 |
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416 if (source.GetWidth() != target.GetWidth() || |
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417 source.GetHeight() != target.GetHeight()) |
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418 { |
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419 throw OrthancException(ErrorCode_InternalError); |
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420 } |
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421 |
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422 |
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423 /** |
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424 * If the format of the DICOM buffer is natively supported, use a |
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425 * direct access to copy its values. |
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426 **/ |
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427 |
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428 ImageAccessor targetAccessor(target.GetAccessor()); |
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429 const DicomImageInformation& info = source.GetAccessor().GetInformation(); |
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430 |
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431 bool fastVersionSuccess = false; |
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432 PixelFormat sourceFormat; |
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433 if (info.ExtractPixelFormat(sourceFormat)) |
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434 { |
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435 try |
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436 { |
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437 ImageAccessor sourceImage; |
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438 sourceImage.AssignReadOnly(sourceFormat, |
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439 info.GetWidth(), |
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440 info.GetHeight(), |
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441 info.GetWidth() * info.GetBytesPerPixel(), |
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442 source.GetAccessor().GetPixelData()); |
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443 |
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444 ImageProcessing::Convert(targetAccessor, sourceImage); |
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445 ImageProcessing::ShiftRight(targetAccessor, info.GetShift()); |
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446 fastVersionSuccess = true; |
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447 } |
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448 catch (OrthancException&) |
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449 { |
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450 // Unsupported conversion |
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451 } |
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452 } |
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453 |
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454 |
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455 /** |
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456 * Loop over the DICOM buffer, storing its value into the target |
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457 * image. |
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458 **/ |
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459 |
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460 if (!fastVersionSuccess) |
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461 { |
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462 switch (target.GetFormat()) |
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463 { |
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464 case PixelFormat_RGB24: |
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465 case PixelFormat_RGBA32: |
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466 case PixelFormat_Grayscale8: |
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467 CopyPixels<uint8_t>(targetAccessor, source.GetAccessor()); |
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468 break; |
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469 |
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470 case PixelFormat_Grayscale16: |
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471 CopyPixels<uint16_t>(targetAccessor, source.GetAccessor()); |
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472 break; |
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473 |
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474 case PixelFormat_SignedGrayscale16: |
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475 CopyPixels<int16_t>(targetAccessor, source.GetAccessor()); |
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476 break; |
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477 |
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478 default: |
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479 throw OrthancException(ErrorCode_InternalError); |
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480 } |
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481 } |
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482 } |
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483 |
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484 |
845 | 485 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1 |
486 void DicomImageDecoder::DecodeJpegLossless(ImageBuffer& target, | |
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487 DcmDataset& dataset, |
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488 unsigned int frame) |
845 | 489 { |
490 if (!IsJpegLossless(dataset)) | |
491 { | |
492 throw OrthancException(ErrorCode_BadParameterType); | |
493 } | |
494 | |
495 DcmElement *element = NULL; | |
496 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), element).good()) | |
497 { | |
498 throw OrthancException(ErrorCode_BadFileFormat); | |
499 } | |
500 | |
501 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
502 DcmPixelSequence* pixelSequence = NULL; | |
503 if (!pixelData.getEncapsulatedRepresentation | |
504 (dataset.getOriginalXfer(), NULL, pixelSequence).good()) | |
505 { | |
506 throw OrthancException(ErrorCode_BadFileFormat); | |
507 } | |
508 | |
509 SetupImageBuffer(target, dataset); | |
510 | |
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511 ImageAccessor targetAccessor(target.GetAccessor()); |
845 | 512 |
513 /** | |
514 * The "DJLSLosslessDecoder" and "DJLSNearLosslessDecoder" in DCMTK | |
515 * are exactly the same, except for the "supportedTransferSyntax()" | |
516 * virtual function. | |
517 * http://support.dcmtk.org/docs/classDJLSDecoderBase.html | |
518 **/ | |
519 | |
520 DJLSLosslessDecoder decoder; DJLSCodecParameter parameters; | |
521 //DJLSNearLosslessDecoder decoder; DJLSCodecParameter parameters; | |
522 | |
523 Uint32 startFragment = 0; // Default | |
524 OFString decompressedColorModel; // Out | |
525 DJ_RPLossless representationParameter; | |
526 OFCondition c = decoder.decodeFrame(&representationParameter, pixelSequence, ¶meters, | |
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527 &dataset, frame, startFragment, targetAccessor.GetBuffer(), |
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528 targetAccessor.GetSize(), decompressedColorModel); |
845 | 529 |
530 if (!c.good()) | |
531 { | |
532 throw OrthancException(ErrorCode_InternalError); | |
533 } | |
534 } | |
535 #endif | |
846 | 536 |
537 | |
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538 |
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539 bool DicomImageDecoder::Decode(ImageBuffer& target, |
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540 DcmDataset& dataset, |
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541 unsigned int frame) |
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542 { |
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543 if (IsUncompressedImage(dataset)) |
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544 { |
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545 DecodeUncompressedImage(target, dataset, frame); |
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546 return true; |
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547 } |
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548 |
852 | 549 |
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550 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1 |
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551 if (IsJpegLossless(dataset)) |
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552 { |
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553 LOG(INFO) << "Decoding a JPEG-LS image"; |
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554 DecodeJpegLossless(target, dataset, frame); |
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555 return true; |
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556 } |
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557 #endif |
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558 |
852 | 559 |
560 #if ORTHANC_JPEG_ENABLED == 1 | |
561 // TODO Implement this part to speed up JPEG decompression | |
562 #endif | |
563 | |
564 | |
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565 /** |
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566 * This DICOM image format is not natively supported by |
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567 * Orthanc. As a last resort, try and decode it through |
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568 * DCMTK. This will result in higher memory consumption. This is |
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569 * actually the second example of the following page: |
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570 * http://support.dcmtk.org/docs/mod_dcmjpeg.html#Examples |
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571 **/ |
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572 |
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573 { |
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574 LOG(INFO) << "Using DCMTK to decode a compressed image"; |
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575 |
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576 std::auto_ptr<DcmDataset> converted(dynamic_cast<DcmDataset*>(dataset.clone())); |
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577 converted->chooseRepresentation(EXS_LittleEndianExplicit, NULL); |
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578 |
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579 if (converted->canWriteXfer(EXS_LittleEndianExplicit)) |
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580 { |
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581 DecodeUncompressedImageInternal(target, *converted, frame); |
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582 return true; |
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583 } |
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584 } |
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585 |
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586 return false; |
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587 } |
845 | 588 } |