Mercurial > hg > orthanc
annotate OrthancServer/Internals/DicomImageDecoder.cpp @ 1904:4be8accf8768
clarifications
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 05 Jan 2016 14:34:47 +0100 |
| parents | 554ec8422ec5 |
| children | 8b1baa2315b8 |
| rev | line source |
|---|---|
| 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 |
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98 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1 |
| 845 | 99 #include <dcmtk/dcmjpls/djcodecd.h> |
| 100 #include <dcmtk/dcmjpls/djcparam.h> | |
| 101 #include <dcmtk/dcmjpeg/djrplol.h> | |
| 102 #endif | |
| 103 | |
| 104 | |
| 105 namespace Orthanc | |
| 106 { | |
| 846 | 107 static const DicomTag DICOM_TAG_CONTENT(0x07a1, 0x100a); |
| 108 static const DicomTag DICOM_TAG_COMPRESSION_TYPE(0x07a1, 0x1011); | |
| 109 | |
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110 |
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111 static bool IsPsmctRle1(DcmDataset& dataset) |
| 846 | 112 { |
| 113 DcmElement* e; | |
| 114 char* c; | |
| 115 | |
| 116 // Check whether the DICOM instance contains an image encoded with | |
| 117 // the PMSCT_RLE1 scheme. | |
| 118 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_COMPRESSION_TYPE), e).good() || | |
| 119 e == NULL || | |
| 120 !e->isaString() || | |
| 121 !e->getString(c).good() || | |
| 122 c == NULL || | |
| 123 strcmp("PMSCT_RLE1", c)) | |
| 124 { | |
| 125 return false; | |
| 126 } | |
| 127 else | |
| 128 { | |
| 129 return true; | |
| 130 } | |
| 131 } | |
| 132 | |
| 133 | |
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134 static bool DecodePsmctRle1(std::string& output, |
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135 DcmDataset& dataset) |
| 846 | 136 { |
| 137 // Check whether the DICOM instance contains an image encoded with | |
| 138 // the PMSCT_RLE1 scheme. | |
| 139 if (!IsPsmctRle1(dataset)) | |
| 140 { | |
| 141 return false; | |
| 142 } | |
| 143 | |
| 144 // OK, this is a custom RLE encoding from Philips. Get the pixel | |
| 145 // data from the appropriate private DICOM tag. | |
| 146 Uint8* pixData = NULL; | |
| 147 DcmElement* e; | |
| 148 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_CONTENT), e).good() || | |
| 149 e == NULL || | |
| 150 e->getUint8Array(pixData) != EC_Normal) | |
| 151 { | |
| 152 return false; | |
| 153 } | |
| 154 | |
| 155 // The "unsigned" below IS VERY IMPORTANT | |
| 156 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData); | |
| 157 const size_t length = e->getLength(); | |
| 158 | |
| 159 /** | |
| 160 * The code below is an adaptation of a sample code for GDCM by | |
| 161 * Mathieu Malaterre (under a BSD license). | |
| 162 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html | |
| 163 **/ | |
| 164 | |
| 165 // RLE pass | |
| 166 std::vector<uint8_t> temp; | |
| 167 temp.reserve(length); | |
| 168 for (size_t i = 0; i < length; i++) | |
| 169 { | |
| 170 if (inbuffer[i] == 0xa5) | |
| 171 { | |
| 172 temp.push_back(inbuffer[i+2]); | |
| 173 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--) | |
| 174 { | |
| 175 temp.push_back(inbuffer[i+2]); | |
| 176 } | |
| 177 i += 2; | |
| 178 } | |
| 179 else | |
| 180 { | |
| 181 temp.push_back(inbuffer[i]); | |
| 182 } | |
| 183 } | |
| 184 | |
| 185 // Delta encoding pass | |
| 186 uint16_t delta = 0; | |
| 187 output.clear(); | |
| 188 output.reserve(temp.size()); | |
| 189 for (size_t i = 0; i < temp.size(); i++) | |
| 190 { | |
| 191 uint16_t value; | |
| 192 | |
| 193 if (temp[i] == 0x5a) | |
| 194 { | |
| 195 uint16_t v1 = temp[i + 1]; | |
| 196 uint16_t v2 = temp[i + 2]; | |
| 197 value = (v2 << 8) + v1; | |
| 198 i += 2; | |
| 199 } | |
| 200 else | |
| 201 { | |
| 202 value = delta + (int8_t) temp[i]; | |
| 203 } | |
| 204 | |
| 205 output.push_back(value & 0xff); | |
| 206 output.push_back(value >> 8); | |
| 207 delta = value; | |
| 208 } | |
| 209 | |
| 210 if (output.size() % 2) | |
| 211 { | |
| 212 output.resize(output.size() - 1); | |
| 213 } | |
| 214 | |
| 215 return true; | |
| 216 } | |
| 217 | |
| 218 | |
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219 class DicomImageDecoder::ImageSource |
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220 { |
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221 private: |
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222 std::string psmct_; |
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223 std::auto_ptr<DicomIntegerPixelAccessor> slowAccessor_; |
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224 |
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225 public: |
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226 void Setup(DcmDataset& dataset, |
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227 unsigned int frame) |
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228 { |
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229 psmct_.clear(); |
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230 slowAccessor_.reset(NULL); |
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231 |
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232 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data |
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233 |
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234 DicomMap m; |
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235 FromDcmtkBridge::Convert(m, dataset); |
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236 |
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237 /** |
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238 * Create an accessor to the raw values of the DICOM image. |
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239 **/ |
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240 |
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241 DcmElement* e; |
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242 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
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243 e != NULL) |
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244 { |
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245 Uint8* pixData = NULL; |
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246 if (e->getUint8Array(pixData) == EC_Normal) |
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247 { |
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248 slowAccessor_.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); |
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249 } |
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250 } |
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251 else if (DecodePsmctRle1(psmct_, dataset)) |
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252 { |
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253 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded"; |
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254 Uint8* pixData = NULL; |
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255 if (psmct_.size() > 0) |
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256 { |
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257 pixData = reinterpret_cast<Uint8*>(&psmct_[0]); |
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258 } |
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259 |
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260 slowAccessor_.reset(new DicomIntegerPixelAccessor(m, pixData, psmct_.size())); |
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261 } |
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262 |
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263 if (slowAccessor_.get() == NULL) |
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264 { |
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265 throw OrthancException(ErrorCode_BadFileFormat); |
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266 } |
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267 |
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268 slowAccessor_->SetCurrentFrame(frame); |
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269 } |
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270 |
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271 unsigned int GetWidth() const |
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272 { |
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273 assert(slowAccessor_.get() != NULL); |
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274 return slowAccessor_->GetInformation().GetWidth(); |
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275 } |
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276 |
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277 unsigned int GetHeight() const |
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278 { |
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279 assert(slowAccessor_.get() != NULL); |
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280 return slowAccessor_->GetInformation().GetHeight(); |
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281 } |
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282 |
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283 unsigned int GetChannelCount() const |
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284 { |
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285 assert(slowAccessor_.get() != NULL); |
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286 return slowAccessor_->GetInformation().GetChannelCount(); |
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287 } |
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288 |
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289 const DicomIntegerPixelAccessor& GetAccessor() const |
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290 { |
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291 assert(slowAccessor_.get() != NULL); |
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292 return *slowAccessor_; |
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293 } |
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294 |
| 1190 | 295 unsigned int GetSize() const |
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296 { |
| 1190 | 297 assert(slowAccessor_.get() != NULL); |
| 298 return slowAccessor_->GetSize(); | |
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299 } |
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300 }; |
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301 |
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302 |
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303 ImageAccessor* DicomImageDecoder::CreateImage(DcmDataset& dataset) |
| 845 | 304 { |
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305 DicomMap m; |
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306 FromDcmtkBridge::Convert(m, dataset); |
| 845 | 307 |
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308 DicomImageInformation info(m); |
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309 PixelFormat format; |
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310 |
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311 if (!info.ExtractPixelFormat(format)) |
| 845 | 312 { |
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313 LOG(WARNING) << "Unsupported DICOM image: " << info.GetBitsStored() |
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314 << "bpp, " << info.GetChannelCount() << " channels, " |
| 860 | 315 << (info.IsSigned() ? "signed" : "unsigned") |
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316 << (info.IsPlanar() ? ", planar, " : ", non-planar, ") |
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317 << EnumerationToString(info.GetPhotometricInterpretation()) |
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318 << " photometric interpretation"; |
| 845 | 319 throw OrthancException(ErrorCode_NotImplemented); |
| 320 } | |
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321 |
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322 return new Image(format, info.GetWidth(), info.GetHeight()); |
| 845 | 323 } |
| 324 | |
| 325 | |
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326 template <typename PixelType> |
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327 static void CopyPixels(ImageAccessor& target, |
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328 const DicomIntegerPixelAccessor& source) |
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329 { |
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330 const PixelType minValue = std::numeric_limits<PixelType>::min(); |
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331 const PixelType maxValue = std::numeric_limits<PixelType>::max(); |
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332 |
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333 for (unsigned int y = 0; y < source.GetInformation().GetHeight(); y++) |
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334 { |
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335 PixelType* pixel = reinterpret_cast<PixelType*>(target.GetRow(y)); |
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336 for (unsigned int x = 0; x < source.GetInformation().GetWidth(); x++) |
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337 { |
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338 for (unsigned int c = 0; c < source.GetInformation().GetChannelCount(); c++, pixel++) |
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339 { |
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340 int32_t v = source.GetValue(x, y, c); |
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341 if (v < static_cast<int32_t>(minValue)) |
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342 { |
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343 *pixel = minValue; |
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344 } |
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345 else if (v > static_cast<int32_t>(maxValue)) |
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346 { |
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347 *pixel = maxValue; |
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348 } |
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349 else |
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350 { |
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351 *pixel = static_cast<PixelType>(v); |
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352 } |
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353 } |
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354 } |
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355 } |
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356 } |
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357 |
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358 |
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359 ImageAccessor* DicomImageDecoder::DecodeUncompressedImage(DcmDataset& dataset, |
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360 unsigned int frame) |
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361 { |
| 852 | 362 ImageSource source; |
| 363 source.Setup(dataset, frame); | |
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364 |
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365 |
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366 /** |
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367 * Resize the target image. |
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368 **/ |
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369 |
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370 std::auto_ptr<ImageAccessor> target(CreateImage(dataset)); |
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371 |
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372 if (source.GetWidth() != target->GetWidth() || |
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373 source.GetHeight() != target->GetHeight()) |
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374 { |
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375 throw OrthancException(ErrorCode_InternalError); |
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376 } |
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377 |
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378 |
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379 /** |
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380 * If the format of the DICOM buffer is natively supported, use a |
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381 * direct access to copy its values. |
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382 **/ |
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383 |
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384 const DicomImageInformation& info = source.GetAccessor().GetInformation(); |
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385 |
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386 bool fastVersionSuccess = false; |
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387 PixelFormat sourceFormat; |
| 863 | 388 if (!info.IsPlanar() && |
| 389 info.ExtractPixelFormat(sourceFormat)) | |
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390 { |
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391 try |
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392 { |
| 1190 | 393 size_t frameSize = info.GetHeight() * info.GetWidth() * GetBytesPerPixel(sourceFormat); |
| 394 if ((frame + 1) * frameSize <= source.GetSize()) | |
| 395 { | |
| 396 const uint8_t* buffer = reinterpret_cast<const uint8_t*>(source.GetAccessor().GetPixelData()); | |
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397 |
| 1190 | 398 ImageAccessor sourceImage; |
| 399 sourceImage.AssignReadOnly(sourceFormat, | |
| 400 info.GetWidth(), | |
| 401 info.GetHeight(), | |
| 402 info.GetWidth() * GetBytesPerPixel(sourceFormat), | |
| 403 buffer + frame * frameSize); | |
| 404 | |
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405 ImageProcessing::Convert(*target, sourceImage); |
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406 ImageProcessing::ShiftRight(*target, info.GetShift()); |
| 1190 | 407 fastVersionSuccess = true; |
| 408 } | |
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409 } |
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410 catch (OrthancException&) |
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411 { |
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412 // Unsupported conversion, use the slow version |
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413 } |
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414 } |
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415 |
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416 /** |
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417 * Slow version : loop over the DICOM buffer, storing its value |
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418 * into the target image. |
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419 **/ |
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420 |
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421 if (!fastVersionSuccess) |
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422 { |
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423 switch (target->GetFormat()) |
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424 { |
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425 case PixelFormat_RGB24: |
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426 case PixelFormat_RGBA32: |
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427 case PixelFormat_Grayscale8: |
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428 CopyPixels<uint8_t>(*target, source.GetAccessor()); |
| 863 | 429 break; |
| 860 | 430 |
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431 case PixelFormat_Grayscale16: |
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432 CopyPixels<uint16_t>(*target, source.GetAccessor()); |
| 863 | 433 break; |
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434 |
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435 case PixelFormat_SignedGrayscale16: |
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436 CopyPixels<int16_t>(*target, source.GetAccessor()); |
| 863 | 437 break; |
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438 |
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439 default: |
| 863 | 440 throw OrthancException(ErrorCode_InternalError); |
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441 } |
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442 } |
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443 |
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444 return target.release(); |
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445 } |
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446 |
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447 |
| 1903 | 448 static DcmPixelSequence* GetPixelSequence(DcmDataset& dataset) |
| 845 | 449 { |
| 450 DcmElement *element = NULL; | |
| 451 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), element).good()) | |
| 452 { | |
| 453 throw OrthancException(ErrorCode_BadFileFormat); | |
| 454 } | |
| 455 | |
| 456 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 457 DcmPixelSequence* pixelSequence = NULL; | |
| 458 if (!pixelData.getEncapsulatedRepresentation | |
| 1903 | 459 (dataset.getOriginalXfer(), NULL, pixelSequence).good() || |
| 460 pixelSequence == NULL) | |
| 845 | 461 { |
| 462 throw OrthancException(ErrorCode_BadFileFormat); | |
| 463 } | |
| 464 | |
| 1903 | 465 return pixelSequence; |
| 466 } | |
| 467 | |
| 845 | 468 |
| 1903 | 469 static ImageAccessor* ApplyCodec(const DcmCodec& codec, |
| 470 const DcmCodecParameter& parameters, | |
| 471 DcmDataset& dataset, | |
| 472 unsigned int frame) | |
| 473 { | |
| 474 std::auto_ptr<ImageAccessor> target(DicomImageDecoder::CreateImage(dataset)); | |
| 845 | 475 |
| 476 Uint32 startFragment = 0; // Default | |
| 477 OFString decompressedColorModel; // Out | |
| 478 DJ_RPLossless representationParameter; | |
| 1903 | 479 OFCondition c = codec.decodeFrame(&representationParameter, GetPixelSequence(dataset), ¶meters, |
| 480 &dataset, frame, startFragment, target->GetBuffer(), | |
| 481 target->GetSize(), decompressedColorModel); | |
| 845 | 482 |
| 1903 | 483 if (c.good()) |
| 845 | 484 { |
| 1903 | 485 return target.release(); |
| 845 | 486 } |
| 1903 | 487 else |
| 488 { | |
| 489 LOG(ERROR) << "Cannot decode an image"; | |
| 490 throw OrthancException(ErrorCode_BadFileFormat); | |
| 491 } | |
| 845 | 492 } |
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493 |
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494 |
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495 ImageAccessor* DicomImageDecoder::Decode(ParsedDicomFile& dicom, |
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496 unsigned int frame) |
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497 { |
| 1904 | 498 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
| 499 E_TransferSyntax syntax = dataset.getOriginalXfer(); | |
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500 |
| 1903 | 501 /** |
| 502 * Deal with uncompressed, raw images. | |
| 503 * http://support.dcmtk.org/docs/dcxfer_8h-source.html | |
| 504 **/ | |
| 1904 | 505 if (syntax == EXS_Unknown || |
| 506 syntax == EXS_LittleEndianImplicit || | |
| 507 syntax == EXS_BigEndianImplicit || | |
| 508 syntax == EXS_LittleEndianExplicit || | |
| 509 syntax == EXS_BigEndianExplicit) | |
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510 { |
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511 return DecodeUncompressedImage(dataset, frame); |
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512 } |
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513 |
| 1904 | 514 |
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515 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1 |
| 1904 | 516 /** |
| 517 * Deal with JPEG-LS images. | |
| 518 **/ | |
| 519 | |
| 520 if (syntax == EXS_JPEGLSLossless || | |
| 521 syntax == EXS_JPEGLSLossy) | |
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522 { |
| 1904 | 523 DJLSCodecParameter parameters; |
| 524 std::auto_ptr<DJLSDecoderBase> decoder; | |
| 1903 | 525 |
| 1904 | 526 switch (syntax) |
| 527 { | |
| 528 case EXS_JPEGLSLossless: | |
| 529 LOG(INFO) << "Decoding a JPEG-LS lossless image"; | |
| 530 decoder.reset(new DJLSLosslessDecoder); | |
| 531 break; | |
| 532 | |
| 533 case EXS_JPEGLSLossy: | |
| 534 LOG(INFO) << "Decoding a JPEG-LS near-lossless image"; | |
| 535 decoder.reset(new DJLSNearLosslessDecoder); | |
| 536 break; | |
| 1903 | 537 |
| 1904 | 538 default: |
| 539 throw OrthancException(ErrorCode_InternalError); | |
| 540 } | |
| 541 | |
| 542 return ApplyCodec(*decoder, parameters, dataset, frame); | |
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543 } |
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544 #endif |
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545 |
| 852 | 546 |
| 547 #if ORTHANC_JPEG_ENABLED == 1 | |
| 1904 | 548 |
| 852 | 549 // TODO Implement this part to speed up JPEG decompression |
| 550 #endif | |
| 551 | |
| 1904 | 552 |
| 553 // TODO DcmRLECodecDecoder | |
| 554 | |
| 555 | |
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556 /** |
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557 * This DICOM image format is not natively supported by |
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558 * Orthanc. As a last resort, try and decode it through |
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559 * DCMTK. This will result in higher memory consumption. This is |
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560 * actually the second example of the following page: |
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561 * http://support.dcmtk.org/docs/mod_dcmjpeg.html#Examples |
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562 **/ |
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563 |
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564 { |
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565 LOG(INFO) << "Using DCMTK to decode a compressed image"; |
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566 |
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567 std::auto_ptr<DcmDataset> converted(dynamic_cast<DcmDataset*>(dataset.clone())); |
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568 converted->chooseRepresentation(EXS_LittleEndianExplicit, NULL); |
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569 |
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570 if (converted->canWriteXfer(EXS_LittleEndianExplicit)) |
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571 { |
| 1903 | 572 return DecodeUncompressedImage(*converted, frame); |
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573 } |
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574 } |
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575 |
|
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576 LOG(ERROR) << "Cannot decode a DICOM image with the built-in decoder"; |
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577 throw OrthancException(ErrorCode_BadFileFormat); |
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578 } |
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579 |
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580 |
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581 static bool IsColorImage(PixelFormat format) |
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582 { |
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583 return (format == PixelFormat_RGB24 || |
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584 format == PixelFormat_RGBA32); |
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585 } |
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586 |
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587 |
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588 bool DicomImageDecoder::TruncateDecodedImage(std::auto_ptr<ImageAccessor>& image, |
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589 PixelFormat format, |
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590 bool allowColorConversion) |
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591 { |
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592 // If specified, prevent the conversion between color and |
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593 // grayscale images |
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594 bool isSourceColor = IsColorImage(image->GetFormat()); |
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595 bool isTargetColor = IsColorImage(format); |
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596 |
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597 if (!allowColorConversion) |
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598 { |
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599 if (isSourceColor ^ isTargetColor) |
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600 { |
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601 return false; |
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602 } |
|
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
942
diff
changeset
|
603 } |
|
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
942
diff
changeset
|
604 |
|
1826
ac5b0b4e2434
refactoring of DicomImageDecoder
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parents:
1824
diff
changeset
|
605 if (image->GetFormat() != format) |
| 863 | 606 { |
|
1826
ac5b0b4e2434
refactoring of DicomImageDecoder
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parents:
1824
diff
changeset
|
607 // A conversion is required |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
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parents:
1824
diff
changeset
|
608 std::auto_ptr<ImageAccessor> target(new Image(format, image->GetWidth(), image->GetHeight())); |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
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parents:
1824
diff
changeset
|
609 ImageProcessing::Convert(*target, *image); |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
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parents:
1824
diff
changeset
|
610 image = target; |
| 863 | 611 } |
|
859
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
612 |
| 863 | 613 return true; |
| 614 } | |
| 615 | |
| 616 | |
|
1826
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
617 bool DicomImageDecoder::PreviewDecodedImage(std::auto_ptr<ImageAccessor>& image) |
| 863 | 618 { |
|
1826
ac5b0b4e2434
refactoring of DicomImageDecoder
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parents:
1824
diff
changeset
|
619 switch (image->GetFormat()) |
| 861 | 620 { |
| 863 | 621 case PixelFormat_RGB24: |
|
859
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
622 { |
|
1826
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
623 // Directly return color images without modification (RGB) |
|
859
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
624 return true; |
|
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
625 } |
|
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
626 |
| 863 | 627 case PixelFormat_Grayscale8: |
| 628 case PixelFormat_Grayscale16: | |
| 629 case PixelFormat_SignedGrayscale16: | |
| 630 { | |
| 631 // Grayscale image: Stretch its dynamics to the [0,255] range | |
|
1826
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
632 int64_t a, b; |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
633 ImageProcessing::GetMinMaxValue(a, b, *image); |
| 863 | 634 |
| 635 if (a == b) | |
| 636 { | |
|
1826
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
637 ImageProcessing::Set(*image, 0); |
| 863 | 638 } |
| 639 else | |
| 640 { | |
|
1826
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
641 ImageProcessing::ShiftScale(*image, static_cast<float>(-a), 255.0f / static_cast<float>(b - a)); |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
642 } |
| 863 | 643 |
|
1826
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
644 // If the source image is not grayscale 8bpp, convert it |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
645 if (image->GetFormat() != PixelFormat_Grayscale8) |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
646 { |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
647 std::auto_ptr<ImageAccessor> target(new Image(PixelFormat_Grayscale8, image->GetWidth(), image->GetHeight())); |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
648 ImageProcessing::Convert(*target, *image); |
|
ac5b0b4e2434
refactoring of DicomImageDecoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1824
diff
changeset
|
649 image = target; |
| 863 | 650 } |
| 651 | |
| 652 return true; | |
| 653 } | |
| 654 | |
|
859
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
655 default: |
|
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
656 throw OrthancException(ErrorCode_NotImplemented); |
|
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
657 } |
|
610a9a1ed855
ImageProcessing::Convert
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
858
diff
changeset
|
658 } |
|
1902
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
659 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
660 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
661 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
|
662 ImageExtractionMode mode) |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
663 { |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
664 if (image.get() == NULL) |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
665 { |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
666 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
667 } |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
668 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
669 bool ok = false; |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
670 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
671 switch (mode) |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
672 { |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
673 case ImageExtractionMode_UInt8: |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
674 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
|
675 break; |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
676 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
677 case ImageExtractionMode_UInt16: |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
678 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
|
679 break; |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
680 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
681 case ImageExtractionMode_Int16: |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
682 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
|
683 break; |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
684 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
685 case ImageExtractionMode_Preview: |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
686 ok = PreviewDecodedImage(image); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
687 break; |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
688 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
689 default: |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
690 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
691 } |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
692 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
693 if (ok) |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
694 { |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
695 assert(image.get() != NULL); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
696 } |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
697 else |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
698 { |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
699 throw OrthancException(ErrorCode_NotImplemented); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
700 } |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
701 } |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
702 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
703 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
704 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
|
705 std::auto_ptr<ImageAccessor>& image, |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
706 ImageExtractionMode mode) |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
707 { |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
708 ApplyExtractionMode(image, mode); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
709 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
710 PngWriter writer; |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
711 writer.WriteToMemory(result, *image); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
712 } |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
713 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
714 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
715 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
|
716 std::auto_ptr<ImageAccessor>& image, |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
717 ImageExtractionMode mode, |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
718 uint8_t quality) |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
719 { |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
720 if (mode != ImageExtractionMode_UInt8 && |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
721 mode != ImageExtractionMode_Preview) |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
722 { |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
723 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
724 } |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
725 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
726 ApplyExtractionMode(image, mode); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
727 |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
728 JpegWriter writer; |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
729 writer.SetQuality(quality); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
730 writer.WriteToMemory(result, *image); |
|
8b0ee8d5e6d0
Refactoring leading to speedups with custom image decoders
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
731 } |
| 845 | 732 } |