Mercurial > hg > orthanc
annotate Plugins/Samples/GdcmDecoder/GdcmImageDecoder.cpp @ 2919:2ca9cd064b15
PamReader::ReadFromMemory
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 06 Nov 2018 15:41:21 +0100 |
| parents | 5c83e5cf9d79 |
| children | 4e43e67f8ecf |
| rev | line source |
|---|---|
| 1834 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 1900 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
| 1834 | 4 * Department, University Hospital of Liege, Belgium |
|
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5 * Copyright (C) 2017-2018 Osimis S.A., Belgium |
| 1834 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU General Public License as | |
| 9 * published by the Free Software Foundation, either version 3 of the | |
| 10 * License, or (at your option) any later version. | |
| 11 * | |
| 12 * This program is distributed in the hope that it will be useful, but | |
| 13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 15 * General Public License for more details. | |
| 16 * | |
| 17 * You should have received a copy of the GNU General Public License | |
| 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 19 **/ | |
| 20 | |
| 21 | |
| 22 #include "GdcmImageDecoder.h" | |
| 23 | |
| 24 #include "OrthancImageWrapper.h" | |
| 25 | |
| 26 #include <gdcmImageReader.h> | |
| 27 #include <gdcmImageApplyLookupTable.h> | |
| 28 #include <gdcmImageChangePlanarConfiguration.h> | |
| 29 #include <gdcmImageChangePhotometricInterpretation.h> | |
| 30 #include <stdexcept> | |
| 31 #include <boost/iostreams/stream.hpp> | |
| 32 #include <boost/iostreams/device/array.hpp> | |
| 33 | |
| 34 | |
| 35 namespace OrthancPlugins | |
| 36 { | |
| 37 struct GdcmImageDecoder::PImpl | |
| 38 { | |
| 39 const void* dicom_; | |
| 40 size_t size_; | |
| 41 | |
| 42 gdcm::ImageReader reader_; | |
| 43 std::auto_ptr<gdcm::ImageApplyLookupTable> lut_; | |
| 44 std::auto_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_; | |
| 45 std::auto_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_; | |
| 46 std::string decoded_; | |
| 47 | |
| 48 PImpl(const void* dicom, | |
| 49 size_t size) : | |
| 50 dicom_(dicom), | |
| 51 size_(size) | |
| 52 { | |
| 53 } | |
| 54 | |
| 55 | |
| 56 const gdcm::DataSet& GetDataSet() const | |
| 57 { | |
| 58 return reader_.GetFile().GetDataSet(); | |
| 59 } | |
| 60 | |
| 61 | |
| 62 const gdcm::Image& GetImage() const | |
| 63 { | |
| 64 if (interleaved_.get() != NULL) | |
| 65 { | |
| 66 return interleaved_->GetOutput(); | |
| 67 } | |
| 68 | |
| 69 if (lut_.get() != NULL) | |
| 70 { | |
| 71 return lut_->GetOutput(); | |
| 72 } | |
| 73 | |
| 74 if (photometric_.get() != NULL) | |
| 75 { | |
| 76 return photometric_->GetOutput(); | |
| 77 } | |
| 78 | |
| 79 return reader_.GetImage(); | |
| 80 } | |
| 81 | |
| 82 | |
| 83 void Decode() | |
| 84 { | |
| 85 // Change photometric interpretation or apply LUT, if required | |
| 86 { | |
| 87 const gdcm::Image& image = GetImage(); | |
| 88 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
| 89 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::PALETTE_COLOR) | |
| 90 { | |
| 91 lut_.reset(new gdcm::ImageApplyLookupTable()); | |
| 92 lut_->SetInput(image); | |
| 93 if (!lut_->Apply()) | |
| 94 { | |
| 95 throw std::runtime_error( "GDCM cannot apply the lookup table"); | |
| 96 } | |
| 97 } | |
| 98 else if (image.GetPixelFormat().GetSamplesPerPixel() == 1) | |
| 99 { | |
| 100 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 && | |
| 101 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
| 102 { | |
| 103 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
| 104 photometric_->SetInput(image); | |
| 105 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); | |
| 106 if (!photometric_->Change() || | |
| 107 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
| 108 { | |
| 109 throw std::runtime_error("GDCM cannot change the photometric interpretation"); | |
| 110 } | |
| 111 } | |
| 112 } | |
| 113 else | |
| 114 { | |
| 115 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
|
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116 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB && |
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117 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_FULL && |
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118 (image.GetTransferSyntax() != gdcm::TransferSyntax::JPEG2000Lossless || |
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119 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_RCT)) |
| 1834 | 120 { |
| 121 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
| 122 photometric_->SetInput(image); | |
| 123 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); | |
| 124 if (!photometric_->Change() || | |
| 125 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
| 126 { | |
| 127 throw std::runtime_error("GDCM cannot change the photometric interpretation"); | |
| 128 } | |
| 129 } | |
| 130 } | |
| 131 } | |
| 132 | |
| 133 // Possibly convert planar configuration to interleaved | |
| 134 { | |
| 135 const gdcm::Image& image = GetImage(); | |
| 136 if (image.GetPlanarConfiguration() != 0 && | |
| 137 image.GetPixelFormat().GetSamplesPerPixel() != 1) | |
| 138 { | |
| 139 interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); | |
| 140 interleaved_->SetInput(image); | |
| 141 if (!interleaved_->Change() || | |
| 142 GetImage().GetPlanarConfiguration() != 0) | |
| 143 { | |
| 144 throw std::runtime_error("GDCM cannot change the planar configuration to interleaved"); | |
| 145 } | |
| 146 } | |
| 147 } | |
| 148 } | |
| 149 }; | |
| 150 | |
| 151 GdcmImageDecoder::GdcmImageDecoder(const void* dicom, | |
| 152 size_t size) : | |
| 153 pimpl_(new PImpl(dicom, size)) | |
| 154 { | |
| 155 // Setup a stream to the memory buffer | |
| 156 using namespace boost::iostreams; | |
| 157 basic_array_source<char> source(reinterpret_cast<const char*>(dicom), size); | |
| 158 stream<basic_array_source<char> > stream(source); | |
| 159 | |
| 160 // Parse the DICOM instance using GDCM | |
| 161 pimpl_->reader_.SetStream(stream); | |
| 162 if (!pimpl_->reader_.Read()) | |
| 163 { | |
| 164 throw std::runtime_error("Bad file format"); | |
| 165 } | |
| 166 | |
| 167 pimpl_->Decode(); | |
| 168 } | |
| 169 | |
| 170 | |
| 171 OrthancPluginPixelFormat GdcmImageDecoder::GetFormat() const | |
| 172 { | |
| 173 const gdcm::Image& image = pimpl_->GetImage(); | |
| 174 | |
| 175 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
| 176 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || | |
| 177 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) | |
| 178 { | |
| 179 switch (image.GetPixelFormat()) | |
| 180 { | |
| 181 case gdcm::PixelFormat::UINT16: | |
| 182 return OrthancPluginPixelFormat_Grayscale16; | |
| 183 | |
| 184 case gdcm::PixelFormat::INT16: | |
| 185 return OrthancPluginPixelFormat_SignedGrayscale16; | |
| 186 | |
| 187 case gdcm::PixelFormat::UINT8: | |
| 188 return OrthancPluginPixelFormat_Grayscale8; | |
| 189 | |
| 190 default: | |
| 191 throw std::runtime_error("Unsupported pixel format"); | |
| 192 } | |
| 193 } | |
| 194 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
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195 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB || |
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196 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_FULL || |
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197 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_RCT)) |
| 1834 | 198 { |
| 199 switch (image.GetPixelFormat()) | |
| 200 { | |
| 201 case gdcm::PixelFormat::UINT8: | |
| 202 return OrthancPluginPixelFormat_RGB24; | |
| 203 | |
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204 case gdcm::PixelFormat::UINT16: |
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205 #if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 3, 1) |
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206 return OrthancPluginPixelFormat_RGB48; |
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207 #else |
| 2428 | 208 throw std::runtime_error("RGB48 pixel format is only supported if compiled against Orthanc SDK >= 1.3.1"); |
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209 #endif |
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210 |
| 1834 | 211 default: |
| 212 break; | |
| 213 } | |
| 214 } | |
| 215 | |
| 216 throw std::runtime_error("Unsupported pixel format"); | |
| 217 } | |
| 218 | |
| 219 | |
| 220 unsigned int GdcmImageDecoder::GetWidth() const | |
| 221 { | |
| 222 return pimpl_->GetImage().GetColumns(); | |
| 223 } | |
| 224 | |
| 225 | |
| 226 unsigned int GdcmImageDecoder::GetHeight() const | |
| 227 { | |
| 228 return pimpl_->GetImage().GetRows(); | |
| 229 } | |
| 230 | |
| 231 | |
| 232 unsigned int GdcmImageDecoder::GetFramesCount() const | |
| 233 { | |
| 234 return pimpl_->GetImage().GetDimension(2); | |
| 235 } | |
| 236 | |
| 237 | |
| 238 size_t GdcmImageDecoder::GetBytesPerPixel(OrthancPluginPixelFormat format) | |
| 239 { | |
| 240 switch (format) | |
| 241 { | |
| 242 case OrthancPluginPixelFormat_Grayscale8: | |
| 243 return 1; | |
| 244 | |
| 245 case OrthancPluginPixelFormat_Grayscale16: | |
| 246 case OrthancPluginPixelFormat_SignedGrayscale16: | |
| 247 return 2; | |
| 248 | |
| 249 case OrthancPluginPixelFormat_RGB24: | |
| 250 return 3; | |
| 251 | |
| 2427 | 252 #if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 3, 1) |
| 253 case OrthancPluginPixelFormat_RGB48: | |
| 254 return 6; | |
| 255 #endif | |
| 256 | |
| 1834 | 257 default: |
| 258 throw std::runtime_error("Unsupport pixel format"); | |
| 259 } | |
| 260 } | |
| 261 | |
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262 static void ConvertYbrToRgb(uint8_t rgb[3], |
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263 const uint8_t ybr[3]) |
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264 { |
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265 // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.3.html#sect_C.7.6.3.1.2 |
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266 // https://en.wikipedia.org/wiki/YCbCr#JPEG_conversion |
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267 |
| 2485 | 268 // TODO - Check out the outcome of Mathieu's discussion about |
| 269 // truncation of YCbCr-to-RGB conversion: | |
| 270 // https://groups.google.com/forum/#!msg/comp.protocols.dicom/JHuGeyWbTz8/ARoTWrJzAQAJ | |
| 271 | |
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272 const float Y = ybr[0]; |
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273 const float Cb = ybr[1]; |
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274 const float Cr = ybr[2]; |
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275 |
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276 const float result[3] = { |
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277 Y + 1.402f * (Cr - 128.0f), |
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278 Y - 0.344136f * (Cb - 128.0f) - 0.714136f * (Cr - 128.0f), |
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279 Y + 1.772f * (Cb - 128.0f) |
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280 }; |
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281 |
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282 for (uint8_t i = 0; i < 3 ; i++) |
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283 { |
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284 if (result[i] < 0) |
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285 { |
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286 rgb[i] = 0; |
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287 } |
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288 else if (result[i] > 255) |
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289 { |
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290 rgb[i] = 255; |
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291 } |
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292 else |
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293 { |
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294 rgb[i] = static_cast<uint8_t>(result[i]); |
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295 } |
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296 } |
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297 } |
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298 |
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299 |
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300 static void FixPhotometricInterpretation(OrthancImageWrapper& image, |
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301 gdcm::PhotometricInterpretation interpretation) |
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302 { |
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303 switch (interpretation) |
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304 { |
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305 case gdcm::PhotometricInterpretation::MONOCHROME1: |
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306 case gdcm::PhotometricInterpretation::MONOCHROME2: |
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307 case gdcm::PhotometricInterpretation::RGB: |
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308 return; |
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309 |
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310 case gdcm::PhotometricInterpretation::YBR_FULL: |
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311 { |
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312 // Fix for Osimis issue WVB-319: Some images are not loading in US_MF |
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313 |
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314 uint32_t width = image.GetWidth(); |
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315 uint32_t height = image.GetHeight(); |
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316 uint32_t pitch = image.GetPitch(); |
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317 uint8_t* buffer = reinterpret_cast<uint8_t*>(image.GetBuffer()); |
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318 |
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319 if (image.GetFormat() != OrthancPluginPixelFormat_RGB24 || |
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320 pitch < 3 * width) |
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321 { |
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322 throw std::runtime_error("Internal error"); |
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323 } |
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324 |
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325 for (uint32_t y = 0; y < height; y++) |
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326 { |
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327 uint8_t* p = buffer + y * pitch; |
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328 for (uint32_t x = 0; x < width; x++, p += 3) |
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329 { |
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330 const uint8_t ybr[3] = { p[0], p[1], p[2] }; |
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331 uint8_t rgb[3]; |
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332 ConvertYbrToRgb(rgb, ybr); |
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333 p[0] = rgb[0]; |
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334 p[1] = rgb[1]; |
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335 p[2] = rgb[2]; |
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336 } |
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337 } |
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338 |
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339 return; |
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340 } |
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341 |
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342 default: |
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343 throw std::runtime_error("Unsupported output photometric interpretation"); |
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344 } |
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345 } |
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346 |
| 1834 | 347 |
| 348 OrthancPluginImage* GdcmImageDecoder::Decode(OrthancPluginContext* context, | |
| 349 unsigned int frameIndex) const | |
| 350 { | |
| 351 unsigned int frames = GetFramesCount(); | |
| 352 unsigned int width = GetWidth(); | |
| 353 unsigned int height = GetHeight(); | |
| 354 OrthancPluginPixelFormat format = GetFormat(); | |
| 355 size_t bpp = GetBytesPerPixel(format); | |
| 356 | |
| 357 if (frameIndex >= frames) | |
| 358 { | |
| 359 throw std::runtime_error("Inexistent frame index"); | |
| 360 } | |
| 361 | |
| 362 std::string& decoded = pimpl_->decoded_; | |
| 363 OrthancImageWrapper target(context, format, width, height); | |
| 364 | |
| 365 if (width == 0 || | |
| 366 height == 0) | |
| 367 { | |
| 368 return target.Release(); | |
| 369 } | |
| 370 | |
| 371 if (decoded.empty()) | |
| 372 { | |
| 373 decoded.resize(pimpl_->GetImage().GetBufferLength()); | |
| 374 pimpl_->GetImage().GetBuffer(&decoded[0]); | |
| 375 } | |
| 376 | |
| 377 const void* sourceBuffer = &decoded[0]; | |
| 378 | |
| 379 if (target.GetPitch() == bpp * width && | |
| 380 frames == 1) | |
| 381 { | |
| 382 assert(decoded.size() == target.GetPitch() * target.GetHeight()); | |
| 383 memcpy(target.GetBuffer(), sourceBuffer, decoded.size()); | |
| 384 } | |
| 385 else | |
| 386 { | |
| 387 size_t targetPitch = target.GetPitch(); | |
| 388 size_t sourcePitch = width * bpp; | |
| 389 | |
| 390 const char* a = &decoded[sourcePitch * height * frameIndex]; | |
| 391 char* b = target.GetBuffer(); | |
| 392 | |
| 393 for (uint32_t y = 0; y < height; y++) | |
| 394 { | |
| 395 memcpy(b, a, sourcePitch); | |
| 396 a += sourcePitch; | |
| 397 b += targetPitch; | |
| 398 } | |
| 399 } | |
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400 |
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401 FixPhotometricInterpretation(target, pimpl_->GetImage().GetPhotometricInterpretation()); |
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402 |
| 1834 | 403 return target.Release(); |
| 404 } | |
| 405 } |