Mercurial > hg > orthanc
annotate OrthancServer/Internals/DicomImageDecoder.cpp @ 1909:21fcfc428dc2
another semantics for Originator Message ID
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 13 Jan 2016 15:15:51 +0100 |
parents | 8b1baa2315b8 |
children | 6c73df12ca51 |
rev | line source |
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845 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
1900 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
845 | 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 | |
863 | 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. | |
846 | 49 |
863 | 50 Redistribution and use in source and binary forms, with or without |
51 modification, are permitted provided that the following conditions are met: | |
846 | 52 |
863 | 53 * Redistributions of source code must retain the above copyright notice, |
54 this list of conditions and the following disclaimer. | |
846 | 55 |
863 | 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. | |
846 | 59 |
863 | 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. | |
846 | 64 |
863 | 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. | |
846 | 75 |
863 | 76 =========================================================================*/ |
846 | 77 |
78 | |
79 | |
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80 #include "../PrecompiledHeadersServer.h" |
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81 #include "DicomImageDecoder.h" |
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82 |
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83 #include "../../Core/Logging.h" |
845 | 84 #include "../../Core/OrthancException.h" |
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85 #include "../../Core/Images/Image.h" |
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86 #include "../../Core/Images/ImageProcessing.h" |
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87 #include "../../Core/Images/PngWriter.h" |
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88 #include "../../Core/Images/JpegWriter.h" |
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89 #include "../../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
845 | 90 #include "../ToDcmtkBridge.h" |
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91 #include "../FromDcmtkBridge.h" |
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92 #include "../ParsedDicomFile.h" |
845 | 93 |
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94 #include <boost/lexical_cast.hpp> |
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95 |
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96 #include <dcmtk/dcmdata/dcfilefo.h> |
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97 #include <dcmtk/dcmdata/dcrleccd.h> |
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98 #include <dcmtk/dcmdata/dcrlecp.h> |
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99 |
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100 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1 |
845 | 101 #include <dcmtk/dcmjpls/djcodecd.h> |
102 #include <dcmtk/dcmjpls/djcparam.h> | |
103 #include <dcmtk/dcmjpeg/djrplol.h> | |
104 #endif | |
105 | |
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106 #if ORTHANC_JPEG_ENABLED == 1 |
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107 #include <dcmtk/dcmjpeg/djcodecd.h> |
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108 #include <dcmtk/dcmjpeg/djcparam.h> |
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109 #include <dcmtk/dcmjpeg/djdecbas.h> |
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110 #include <dcmtk/dcmjpeg/djdecext.h> |
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111 #include <dcmtk/dcmjpeg/djdeclol.h> |
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112 #include <dcmtk/dcmjpeg/djdecpro.h> |
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113 #include <dcmtk/dcmjpeg/djdecsps.h> |
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114 #include <dcmtk/dcmjpeg/djdecsv1.h> |
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115 #endif |
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116 |
845 | 117 |
118 namespace Orthanc | |
119 { | |
846 | 120 static const DicomTag DICOM_TAG_CONTENT(0x07a1, 0x100a); |
121 static const DicomTag DICOM_TAG_COMPRESSION_TYPE(0x07a1, 0x1011); | |
122 | |
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123 |
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124 static bool IsPsmctRle1(DcmDataset& dataset) |
846 | 125 { |
126 DcmElement* e; | |
127 char* c; | |
128 | |
129 // Check whether the DICOM instance contains an image encoded with | |
130 // the PMSCT_RLE1 scheme. | |
131 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_COMPRESSION_TYPE), e).good() || | |
132 e == NULL || | |
133 !e->isaString() || | |
134 !e->getString(c).good() || | |
135 c == NULL || | |
136 strcmp("PMSCT_RLE1", c)) | |
137 { | |
138 return false; | |
139 } | |
140 else | |
141 { | |
142 return true; | |
143 } | |
144 } | |
145 | |
146 | |
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147 static bool DecodePsmctRle1(std::string& output, |
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148 DcmDataset& dataset) |
846 | 149 { |
150 // Check whether the DICOM instance contains an image encoded with | |
151 // the PMSCT_RLE1 scheme. | |
152 if (!IsPsmctRle1(dataset)) | |
153 { | |
154 return false; | |
155 } | |
156 | |
157 // OK, this is a custom RLE encoding from Philips. Get the pixel | |
158 // data from the appropriate private DICOM tag. | |
159 Uint8* pixData = NULL; | |
160 DcmElement* e; | |
161 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_CONTENT), e).good() || | |
162 e == NULL || | |
163 e->getUint8Array(pixData) != EC_Normal) | |
164 { | |
165 return false; | |
166 } | |
167 | |
168 // The "unsigned" below IS VERY IMPORTANT | |
169 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData); | |
170 const size_t length = e->getLength(); | |
171 | |
172 /** | |
173 * The code below is an adaptation of a sample code for GDCM by | |
174 * Mathieu Malaterre (under a BSD license). | |
175 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html | |
176 **/ | |
177 | |
178 // RLE pass | |
179 std::vector<uint8_t> temp; | |
180 temp.reserve(length); | |
181 for (size_t i = 0; i < length; i++) | |
182 { | |
183 if (inbuffer[i] == 0xa5) | |
184 { | |
185 temp.push_back(inbuffer[i+2]); | |
186 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--) | |
187 { | |
188 temp.push_back(inbuffer[i+2]); | |
189 } | |
190 i += 2; | |
191 } | |
192 else | |
193 { | |
194 temp.push_back(inbuffer[i]); | |
195 } | |
196 } | |
197 | |
198 // Delta encoding pass | |
199 uint16_t delta = 0; | |
200 output.clear(); | |
201 output.reserve(temp.size()); | |
202 for (size_t i = 0; i < temp.size(); i++) | |
203 { | |
204 uint16_t value; | |
205 | |
206 if (temp[i] == 0x5a) | |
207 { | |
208 uint16_t v1 = temp[i + 1]; | |
209 uint16_t v2 = temp[i + 2]; | |
210 value = (v2 << 8) + v1; | |
211 i += 2; | |
212 } | |
213 else | |
214 { | |
215 value = delta + (int8_t) temp[i]; | |
216 } | |
217 | |
218 output.push_back(value & 0xff); | |
219 output.push_back(value >> 8); | |
220 delta = value; | |
221 } | |
222 | |
223 if (output.size() % 2) | |
224 { | |
225 output.resize(output.size() - 1); | |
226 } | |
227 | |
228 return true; | |
229 } | |
230 | |
231 | |
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232 class DicomImageDecoder::ImageSource |
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233 { |
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234 private: |
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235 std::string psmct_; |
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236 std::auto_ptr<DicomIntegerPixelAccessor> slowAccessor_; |
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237 |
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238 public: |
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239 void Setup(DcmDataset& dataset, |
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240 unsigned int frame) |
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241 { |
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242 psmct_.clear(); |
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243 slowAccessor_.reset(NULL); |
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244 |
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245 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data |
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246 |
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247 DicomMap m; |
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248 FromDcmtkBridge::Convert(m, dataset); |
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249 |
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250 /** |
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251 * Create an accessor to the raw values of the DICOM image. |
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252 **/ |
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253 |
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254 DcmElement* e; |
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255 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
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256 e != NULL) |
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257 { |
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258 Uint8* pixData = NULL; |
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259 if (e->getUint8Array(pixData) == EC_Normal) |
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260 { |
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261 slowAccessor_.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); |
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262 } |
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263 } |
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264 else if (DecodePsmctRle1(psmct_, dataset)) |
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265 { |
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266 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded"; |
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267 Uint8* pixData = NULL; |
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268 if (psmct_.size() > 0) |
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269 { |
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270 pixData = reinterpret_cast<Uint8*>(&psmct_[0]); |
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271 } |
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272 |
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273 slowAccessor_.reset(new DicomIntegerPixelAccessor(m, pixData, psmct_.size())); |
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274 } |
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275 |
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276 if (slowAccessor_.get() == NULL) |
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277 { |
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278 throw OrthancException(ErrorCode_BadFileFormat); |
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279 } |
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280 |
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281 slowAccessor_->SetCurrentFrame(frame); |
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282 } |
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283 |
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284 unsigned int GetWidth() const |
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285 { |
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286 assert(slowAccessor_.get() != NULL); |
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287 return slowAccessor_->GetInformation().GetWidth(); |
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288 } |
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289 |
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290 unsigned int GetHeight() const |
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291 { |
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292 assert(slowAccessor_.get() != NULL); |
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293 return slowAccessor_->GetInformation().GetHeight(); |
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294 } |
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295 |
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296 unsigned int GetChannelCount() const |
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297 { |
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298 assert(slowAccessor_.get() != NULL); |
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299 return slowAccessor_->GetInformation().GetChannelCount(); |
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300 } |
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301 |
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302 const DicomIntegerPixelAccessor& GetAccessor() const |
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303 { |
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304 assert(slowAccessor_.get() != NULL); |
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305 return *slowAccessor_; |
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306 } |
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307 |
1190 | 308 unsigned int GetSize() const |
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309 { |
1190 | 310 assert(slowAccessor_.get() != NULL); |
311 return slowAccessor_->GetSize(); | |
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312 } |
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313 }; |
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314 |
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315 |
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316 ImageAccessor* DicomImageDecoder::CreateImage(DcmDataset& dataset, |
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317 bool ignorePhotometricInterpretation) |
845 | 318 { |
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319 DicomMap m; |
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320 FromDcmtkBridge::Convert(m, dataset); |
845 | 321 |
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322 DicomImageInformation info(m); |
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323 PixelFormat format; |
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324 |
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325 if (!info.ExtractPixelFormat(format, ignorePhotometricInterpretation)) |
845 | 326 { |
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327 LOG(WARNING) << "Unsupported DICOM image: " << info.GetBitsStored() |
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328 << "bpp, " << info.GetChannelCount() << " channels, " |
860 | 329 << (info.IsSigned() ? "signed" : "unsigned") |
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330 << (info.IsPlanar() ? ", planar, " : ", non-planar, ") |
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331 << EnumerationToString(info.GetPhotometricInterpretation()) |
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332 << " photometric interpretation"; |
845 | 333 throw OrthancException(ErrorCode_NotImplemented); |
334 } | |
874
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335 |
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336 return new Image(format, info.GetWidth(), info.GetHeight()); |
845 | 337 } |
338 | |
339 | |
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340 template <typename PixelType> |
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341 static void CopyPixels(ImageAccessor& target, |
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342 const DicomIntegerPixelAccessor& source) |
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343 { |
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344 const PixelType minValue = std::numeric_limits<PixelType>::min(); |
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345 const PixelType maxValue = std::numeric_limits<PixelType>::max(); |
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346 |
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347 for (unsigned int y = 0; y < source.GetInformation().GetHeight(); y++) |
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348 { |
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349 PixelType* pixel = reinterpret_cast<PixelType*>(target.GetRow(y)); |
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350 for (unsigned int x = 0; x < source.GetInformation().GetWidth(); x++) |
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351 { |
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352 for (unsigned int c = 0; c < source.GetInformation().GetChannelCount(); c++, pixel++) |
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353 { |
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354 int32_t v = source.GetValue(x, y, c); |
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355 if (v < static_cast<int32_t>(minValue)) |
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356 { |
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357 *pixel = minValue; |
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358 } |
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359 else if (v > static_cast<int32_t>(maxValue)) |
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360 { |
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361 *pixel = maxValue; |
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362 } |
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363 else |
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364 { |
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365 *pixel = static_cast<PixelType>(v); |
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366 } |
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367 } |
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368 } |
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369 } |
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370 } |
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371 |
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372 |
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373 ImageAccessor* DicomImageDecoder::DecodeUncompressedImage(DcmDataset& dataset, |
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374 unsigned int frame) |
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375 { |
852 | 376 ImageSource source; |
377 source.Setup(dataset, frame); | |
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378 |
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379 |
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380 /** |
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381 * Resize the target image. |
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382 **/ |
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383 |
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384 std::auto_ptr<ImageAccessor> target(CreateImage(dataset, false)); |
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385 |
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386 if (source.GetWidth() != target->GetWidth() || |
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387 source.GetHeight() != target->GetHeight()) |
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388 { |
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389 throw OrthancException(ErrorCode_InternalError); |
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390 } |
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391 |
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392 |
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393 /** |
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394 * If the format of the DICOM buffer is natively supported, use a |
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395 * direct access to copy its values. |
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396 **/ |
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397 |
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398 const DicomImageInformation& info = source.GetAccessor().GetInformation(); |
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399 |
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400 bool fastVersionSuccess = false; |
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401 PixelFormat sourceFormat; |
863 | 402 if (!info.IsPlanar() && |
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403 info.ExtractPixelFormat(sourceFormat, false)) |
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404 { |
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405 try |
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406 { |
1190 | 407 size_t frameSize = info.GetHeight() * info.GetWidth() * GetBytesPerPixel(sourceFormat); |
408 if ((frame + 1) * frameSize <= source.GetSize()) | |
409 { | |
410 const uint8_t* buffer = reinterpret_cast<const uint8_t*>(source.GetAccessor().GetPixelData()); | |
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411 |
1190 | 412 ImageAccessor sourceImage; |
413 sourceImage.AssignReadOnly(sourceFormat, | |
414 info.GetWidth(), | |
415 info.GetHeight(), | |
416 info.GetWidth() * GetBytesPerPixel(sourceFormat), | |
417 buffer + frame * frameSize); | |
418 | |
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419 ImageProcessing::Convert(*target, sourceImage); |
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420 ImageProcessing::ShiftRight(*target, info.GetShift()); |
1190 | 421 fastVersionSuccess = true; |
422 } | |
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423 } |
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424 catch (OrthancException&) |
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425 { |
859
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426 // Unsupported conversion, use the slow version |
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427 } |
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428 } |
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429 |
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430 /** |
859
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431 * Slow version : loop over the DICOM buffer, storing its value |
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432 * into the target image. |
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433 **/ |
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434 |
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435 if (!fastVersionSuccess) |
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436 { |
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437 switch (target->GetFormat()) |
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438 { |
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439 case PixelFormat_RGB24: |
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440 case PixelFormat_RGBA32: |
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441 case PixelFormat_Grayscale8: |
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442 CopyPixels<uint8_t>(*target, source.GetAccessor()); |
863 | 443 break; |
860 | 444 |
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445 case PixelFormat_Grayscale16: |
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446 CopyPixels<uint16_t>(*target, source.GetAccessor()); |
863 | 447 break; |
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448 |
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449 case PixelFormat_SignedGrayscale16: |
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450 CopyPixels<int16_t>(*target, source.GetAccessor()); |
863 | 451 break; |
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452 |
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453 default: |
863 | 454 throw OrthancException(ErrorCode_InternalError); |
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455 } |
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456 } |
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457 |
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458 return target.release(); |
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459 } |
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460 |
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461 |
1903 | 462 static DcmPixelSequence* GetPixelSequence(DcmDataset& dataset) |
845 | 463 { |
464 DcmElement *element = NULL; | |
465 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), element).good()) | |
466 { | |
467 throw OrthancException(ErrorCode_BadFileFormat); | |
468 } | |
469 | |
470 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
471 DcmPixelSequence* pixelSequence = NULL; | |
472 if (!pixelData.getEncapsulatedRepresentation | |
1903 | 473 (dataset.getOriginalXfer(), NULL, pixelSequence).good() || |
474 pixelSequence == NULL) | |
845 | 475 { |
476 throw OrthancException(ErrorCode_BadFileFormat); | |
477 } | |
478 | |
1903 | 479 return pixelSequence; |
480 } | |
481 | |
845 | 482 |
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483 ImageAccessor* DicomImageDecoder::ApplyCodec(const DcmCodec& codec, |
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484 const DcmCodecParameter& parameters, |
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485 DcmDataset& dataset, |
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486 unsigned int frame) |
1903 | 487 { |
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488 std::auto_ptr<ImageAccessor> target(CreateImage(dataset, true)); |
845 | 489 |
490 Uint32 startFragment = 0; // Default | |
491 OFString decompressedColorModel; // Out | |
492 DJ_RPLossless representationParameter; | |
1903 | 493 OFCondition c = codec.decodeFrame(&representationParameter, GetPixelSequence(dataset), ¶meters, |
494 &dataset, frame, startFragment, target->GetBuffer(), | |
495 target->GetSize(), decompressedColorModel); | |
845 | 496 |
1903 | 497 if (c.good()) |
845 | 498 { |
1903 | 499 return target.release(); |
845 | 500 } |
1903 | 501 else |
502 { | |
503 LOG(ERROR) << "Cannot decode an image"; | |
504 throw OrthancException(ErrorCode_BadFileFormat); | |
505 } | |
845 | 506 } |
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507 |
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508 |
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509 ImageAccessor* DicomImageDecoder::Decode(ParsedDicomFile& dicom, |
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510 unsigned int frame) |
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511 { |
1904 | 512 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
513 E_TransferSyntax syntax = dataset.getOriginalXfer(); | |
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514 |
1903 | 515 /** |
516 * Deal with uncompressed, raw images. | |
517 * http://support.dcmtk.org/docs/dcxfer_8h-source.html | |
518 **/ | |
1904 | 519 if (syntax == EXS_Unknown || |
520 syntax == EXS_LittleEndianImplicit || | |
521 syntax == EXS_BigEndianImplicit || | |
522 syntax == EXS_LittleEndianExplicit || | |
523 syntax == EXS_BigEndianExplicit) | |
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524 { |
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525 return DecodeUncompressedImage(dataset, frame); |
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526 } |
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527 |
1904 | 528 |
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529 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1 |
1904 | 530 /** |
531 * Deal with JPEG-LS images. | |
532 **/ | |
533 | |
534 if (syntax == EXS_JPEGLSLossless || | |
535 syntax == EXS_JPEGLSLossy) | |
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536 { |
1904 | 537 DJLSCodecParameter parameters; |
538 std::auto_ptr<DJLSDecoderBase> decoder; | |
1903 | 539 |
1904 | 540 switch (syntax) |
541 { | |
542 case EXS_JPEGLSLossless: | |
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543 LOG(INFO) << "Decoding a JPEG-LS lossless DICOM image"; |
1904 | 544 decoder.reset(new DJLSLosslessDecoder); |
545 break; | |
546 | |
547 case EXS_JPEGLSLossy: | |
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548 LOG(INFO) << "Decoding a JPEG-LS near-lossless DICOM image"; |
1904 | 549 decoder.reset(new DJLSNearLosslessDecoder); |
550 break; | |
1903 | 551 |
1904 | 552 default: |
553 throw OrthancException(ErrorCode_InternalError); | |
554 } | |
555 | |
556 return ApplyCodec(*decoder, parameters, dataset, frame); | |
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557 } |
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558 #endif |
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559 |
852 | 560 |
561 #if ORTHANC_JPEG_ENABLED == 1 | |
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562 /** |
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563 * Deal with JPEG images. |
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564 **/ |
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565 |
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566 if (syntax == EXS_JPEGProcess1TransferSyntax || // DJDecoderBaseline |
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567 syntax == EXS_JPEGProcess2_4TransferSyntax || // DJDecoderExtended |
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568 syntax == EXS_JPEGProcess6_8TransferSyntax || // DJDecoderSpectralSelection (retired) |
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569 syntax == EXS_JPEGProcess10_12TransferSyntax || // DJDecoderProgressive (retired) |
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570 syntax == EXS_JPEGProcess14TransferSyntax || // DJDecoderLossless |
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571 syntax == EXS_JPEGProcess14SV1TransferSyntax) // DJDecoderP14SV1 |
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572 { |
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573 // http://support.dcmtk.org/docs-snapshot/djutils_8h.html#a2a9695e5b6b0f5c45a64c7f072c1eb9d |
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574 DJCodecParameter parameters( |
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575 ECC_lossyYCbCr, // Mode for color conversion for compression, Unused for decompression |
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576 EDC_photometricInterpretation, // Perform color space conversion from YCbCr to RGB if DICOM photometric interpretation indicates YCbCr |
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577 EUC_default, // Mode for UID creation, unused for decompression |
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578 EPC_default); // Automatically determine whether color-by-plane is required from the SOP Class UID and decompressed photometric interpretation |
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579 std::auto_ptr<DJCodecDecoder> decoder; |
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580 |
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581 switch (syntax) |
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582 { |
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583 case EXS_JPEGProcess1TransferSyntax: |
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584 LOG(INFO) << "Decoding a JPEG baseline (process 1) DICOM image"; |
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585 decoder.reset(new DJDecoderBaseline); |
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586 break; |
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587 |
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588 case EXS_JPEGProcess2_4TransferSyntax : |
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589 LOG(INFO) << "Decoding a JPEG baseline (processes 2 and 4) DICOM image"; |
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590 decoder.reset(new DJDecoderExtended); |
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591 break; |
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592 |
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593 case EXS_JPEGProcess6_8TransferSyntax: // Retired |
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594 LOG(INFO) << "Decoding a JPEG spectral section, nonhierarchical (processes 6 and 8) DICOM image"; |
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595 decoder.reset(new DJDecoderSpectralSelection); |
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596 break; |
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597 |
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598 case EXS_JPEGProcess10_12TransferSyntax: // Retired |
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599 LOG(INFO) << "Decoding a JPEG full progression, nonhierarchical (processes 10 and 12) DICOM image"; |
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600 decoder.reset(new DJDecoderProgressive); |
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601 break; |
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602 |
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603 case EXS_JPEGProcess14TransferSyntax: |
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604 LOG(INFO) << "Decoding a JPEG lossless, nonhierarchical (process 14) DICOM image"; |
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605 decoder.reset(new DJDecoderLossless); |
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606 break; |
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607 |
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608 case EXS_JPEGProcess14SV1TransferSyntax: |
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609 LOG(INFO) << "Decoding a JPEG lossless, nonhierarchical, first-order prediction (process 14 selection value 1) DICOM image"; |
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610 decoder.reset(new DJDecoderP14SV1); |
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611 break; |
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612 |
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613 default: |
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614 throw OrthancException(ErrorCode_InternalError); |
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615 } |
1904 | 616 |
1905
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617 return ApplyCodec(*decoder, parameters, dataset, frame); |
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618 } |
852 | 619 #endif |
620 | |
1904 | 621 |
1905
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622 if (syntax == EXS_RLELossless) |
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623 { |
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624 LOG(INFO) << "Decoding a RLE lossless DICOM image"; |
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625 DcmRLECodecParameter parameters; |
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626 DcmRLECodecDecoder decoder; |
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627 return ApplyCodec(decoder, parameters, dataset, frame); |
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628 } |
1904 | 629 |
630 | |
847
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631 /** |
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632 * This DICOM image format is not natively supported by |
1905
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633 * Orthanc. As a last resort, try and decode it through DCMTK by |
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634 * converting its transfer syntax to Little Endian. This will |
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635 * result in higher memory consumption. This is actually the |
8b1baa2315b8
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636 * second example of the following page: |
847
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637 * http://support.dcmtk.org/docs/mod_dcmjpeg.html#Examples |
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638 **/ |
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639 |
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640 { |
1905
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641 LOG(INFO) << "Decoding a compressed image by converting its transfer syntax to Little Endian"; |
847
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642 |
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643 std::auto_ptr<DcmDataset> converted(dynamic_cast<DcmDataset*>(dataset.clone())); |
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644 converted->chooseRepresentation(EXS_LittleEndianExplicit, NULL); |
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645 |
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646 if (converted->canWriteXfer(EXS_LittleEndianExplicit)) |
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fully functional JPEG-LS conversion
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647 { |
1903 | 648 return DecodeUncompressedImage(*converted, frame); |
847
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649 } |
03ea55da7429
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|
650 } |
03ea55da7429
fully functional JPEG-LS conversion
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|
651 |
1902
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Refactoring leading to speedups with custom image decoders
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652 LOG(ERROR) << "Cannot decode a DICOM image with the built-in decoder"; |
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Refactoring leading to speedups with custom image decoders
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653 throw OrthancException(ErrorCode_BadFileFormat); |
847
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654 } |
859
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ImageProcessing::Convert
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|
655 |
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656 |
1015
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657 static bool IsColorImage(PixelFormat format) |
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658 { |
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659 return (format == PixelFormat_RGB24 || |
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660 format == PixelFormat_RGBA32); |
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661 } |
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|
662 |
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|
663 |
1826
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664 bool DicomImageDecoder::TruncateDecodedImage(std::auto_ptr<ImageAccessor>& image, |
1824
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diff
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|
665 PixelFormat format, |
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|
666 bool allowColorConversion) |
859
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ImageProcessing::Convert
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667 { |
1015
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668 // If specified, prevent the conversion between color and |
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669 // grayscale images |
1826
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670 bool isSourceColor = IsColorImage(image->GetFormat()); |
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671 bool isTargetColor = IsColorImage(format); |
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672 |
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673 if (!allowColorConversion) |
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674 { |
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|
675 if (isSourceColor ^ isTargetColor) |
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676 { |
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|
677 return false; |
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|
678 } |
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679 } |
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|
680 |
1826
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681 if (image->GetFormat() != format) |
863 | 682 { |
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683 // A conversion is required |
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684 std::auto_ptr<ImageAccessor> target(new Image(format, image->GetWidth(), image->GetHeight())); |
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685 ImageProcessing::Convert(*target, *image); |
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686 image = target; |
863 | 687 } |
859
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688 |
863 | 689 return true; |
690 } | |
691 | |
692 | |
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693 bool DicomImageDecoder::PreviewDecodedImage(std::auto_ptr<ImageAccessor>& image) |
863 | 694 { |
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695 switch (image->GetFormat()) |
861 | 696 { |
863 | 697 case PixelFormat_RGB24: |
859
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698 { |
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699 // Directly return color images without modification (RGB) |
859
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700 return true; |
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701 } |
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702 |
863 | 703 case PixelFormat_Grayscale8: |
704 case PixelFormat_Grayscale16: | |
705 case PixelFormat_SignedGrayscale16: | |
706 { | |
707 // Grayscale image: Stretch its dynamics to the [0,255] range | |
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708 int64_t a, b; |
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709 ImageProcessing::GetMinMaxValue(a, b, *image); |
863 | 710 |
711 if (a == b) | |
712 { | |
1826
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713 ImageProcessing::Set(*image, 0); |
863 | 714 } |
715 else | |
716 { | |
1826
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717 ImageProcessing::ShiftScale(*image, static_cast<float>(-a), 255.0f / static_cast<float>(b - a)); |
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718 } |
863 | 719 |
1826
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720 // If the source image is not grayscale 8bpp, convert it |
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721 if (image->GetFormat() != PixelFormat_Grayscale8) |
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722 { |
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723 std::auto_ptr<ImageAccessor> target(new Image(PixelFormat_Grayscale8, image->GetWidth(), image->GetHeight())); |
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724 ImageProcessing::Convert(*target, *image); |
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725 image = target; |
863 | 726 } |
727 | |
728 return true; | |
729 } | |
730 | |
859
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
731 default: |
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
732 throw OrthancException(ErrorCode_NotImplemented); |
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
733 } |
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
734 } |
1902
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
735 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
736 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
737 void DicomImageDecoder::ApplyExtractionMode(std::auto_ptr<ImageAccessor>& image, |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
738 ImageExtractionMode mode) |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
739 { |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
740 if (image.get() == NULL) |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
741 { |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
742 throw OrthancException(ErrorCode_ParameterOutOfRange); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
743 } |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
744 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
745 bool ok = false; |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
746 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
747 switch (mode) |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
748 { |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
749 case ImageExtractionMode_UInt8: |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
750 ok = TruncateDecodedImage(image, PixelFormat_Grayscale8, false); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
751 break; |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
752 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
753 case ImageExtractionMode_UInt16: |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
754 ok = TruncateDecodedImage(image, PixelFormat_Grayscale16, false); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
755 break; |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
756 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
757 case ImageExtractionMode_Int16: |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
758 ok = TruncateDecodedImage(image, PixelFormat_SignedGrayscale16, false); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
759 break; |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
760 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
761 case ImageExtractionMode_Preview: |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
762 ok = PreviewDecodedImage(image); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
763 break; |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
764 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
765 default: |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
766 throw OrthancException(ErrorCode_ParameterOutOfRange); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
767 } |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
768 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
769 if (ok) |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
770 { |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
771 assert(image.get() != NULL); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
772 } |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
773 else |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
774 { |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
775 throw OrthancException(ErrorCode_NotImplemented); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
776 } |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
777 } |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
778 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
779 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
780 void DicomImageDecoder::ExtractPngImage(std::string& result, |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
781 std::auto_ptr<ImageAccessor>& image, |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
782 ImageExtractionMode mode) |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
783 { |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
784 ApplyExtractionMode(image, mode); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
785 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
786 PngWriter writer; |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
787 writer.WriteToMemory(result, *image); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
788 } |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
789 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
790 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
791 void DicomImageDecoder::ExtractJpegImage(std::string& result, |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
792 std::auto_ptr<ImageAccessor>& image, |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
793 ImageExtractionMode mode, |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
794 uint8_t quality) |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
795 { |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
796 if (mode != ImageExtractionMode_UInt8 && |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
797 mode != ImageExtractionMode_Preview) |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
798 { |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
799 throw OrthancException(ErrorCode_ParameterOutOfRange); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
800 } |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
801 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
802 ApplyExtractionMode(image, mode); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
803 |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
804 JpegWriter writer; |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
805 writer.SetQuality(quality); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
806 writer.WriteToMemory(result, *image); |
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
807 } |
845 | 808 } |