Mercurial > hg > orthanc
annotate Plugins/Samples/GdcmDecoder/GdcmImageDecoder.cpp @ 3858:3ab2d48c8f69 c-get
integration mainline->c-get
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 21 Apr 2020 16:37:25 +0200 |
| parents | 6110a4995ace |
| children | 7e33516965f8 |
| 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) 2017-2020 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 | |
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24 #include "../../../Core/Compatibility.h" |
| 1834 | 25 #include "OrthancImageWrapper.h" |
| 26 | |
| 27 #include <gdcmImageReader.h> | |
| 28 #include <gdcmImageApplyLookupTable.h> | |
| 29 #include <gdcmImageChangePlanarConfiguration.h> | |
| 30 #include <gdcmImageChangePhotometricInterpretation.h> | |
| 31 #include <stdexcept> | |
| 32 #include <boost/iostreams/stream.hpp> | |
| 33 #include <boost/iostreams/device/array.hpp> | |
| 34 | |
| 35 | |
| 36 namespace OrthancPlugins | |
| 37 { | |
| 38 struct GdcmImageDecoder::PImpl | |
| 39 { | |
| 40 const void* dicom_; | |
| 41 size_t size_; | |
| 42 | |
| 43 gdcm::ImageReader reader_; | |
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44 std::unique_ptr<gdcm::ImageApplyLookupTable> lut_; |
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45 std::unique_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_; |
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46 std::unique_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_; |
| 1834 | 47 std::string decoded_; |
| 48 | |
| 49 PImpl(const void* dicom, | |
| 50 size_t size) : | |
| 51 dicom_(dicom), | |
| 52 size_(size) | |
| 53 { | |
| 54 } | |
| 55 | |
| 56 | |
| 57 const gdcm::DataSet& GetDataSet() const | |
| 58 { | |
| 59 return reader_.GetFile().GetDataSet(); | |
| 60 } | |
| 61 | |
| 62 | |
| 63 const gdcm::Image& GetImage() const | |
| 64 { | |
| 65 if (interleaved_.get() != NULL) | |
| 66 { | |
| 67 return interleaved_->GetOutput(); | |
| 68 } | |
| 69 | |
| 70 if (lut_.get() != NULL) | |
| 71 { | |
| 72 return lut_->GetOutput(); | |
| 73 } | |
| 74 | |
| 75 if (photometric_.get() != NULL) | |
| 76 { | |
| 77 return photometric_->GetOutput(); | |
| 78 } | |
| 79 | |
| 80 return reader_.GetImage(); | |
| 81 } | |
| 82 | |
| 83 | |
| 84 void Decode() | |
| 85 { | |
| 86 // Change photometric interpretation or apply LUT, if required | |
| 87 { | |
| 88 const gdcm::Image& image = GetImage(); | |
| 89 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
| 90 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::PALETTE_COLOR) | |
| 91 { | |
| 92 lut_.reset(new gdcm::ImageApplyLookupTable()); | |
| 93 lut_->SetInput(image); | |
| 94 if (!lut_->Apply()) | |
| 95 { | |
| 96 throw std::runtime_error( "GDCM cannot apply the lookup table"); | |
| 97 } | |
| 98 } | |
| 99 else if (image.GetPixelFormat().GetSamplesPerPixel() == 1) | |
| 100 { | |
| 101 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 && | |
| 102 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
| 103 { | |
| 104 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
| 105 photometric_->SetInput(image); | |
| 106 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); | |
| 107 if (!photometric_->Change() || | |
| 108 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
| 109 { | |
| 110 throw std::runtime_error("GDCM cannot change the photometric interpretation"); | |
| 111 } | |
| 112 } | |
| 113 } | |
| 114 else | |
| 115 { | |
| 116 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
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117 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB && |
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118 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_FULL && |
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119 (image.GetTransferSyntax() != gdcm::TransferSyntax::JPEG2000Lossless || |
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120 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_RCT)) |
| 1834 | 121 { |
| 122 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
| 123 photometric_->SetInput(image); | |
| 124 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); | |
| 125 if (!photometric_->Change() || | |
| 126 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
| 127 { | |
| 128 throw std::runtime_error("GDCM cannot change the photometric interpretation"); | |
| 129 } | |
| 130 } | |
| 131 } | |
| 132 } | |
| 133 | |
| 134 // Possibly convert planar configuration to interleaved | |
| 135 { | |
| 136 const gdcm::Image& image = GetImage(); | |
| 137 if (image.GetPlanarConfiguration() != 0 && | |
| 138 image.GetPixelFormat().GetSamplesPerPixel() != 1) | |
| 139 { | |
| 140 interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); | |
| 141 interleaved_->SetInput(image); | |
| 142 if (!interleaved_->Change() || | |
| 143 GetImage().GetPlanarConfiguration() != 0) | |
| 144 { | |
| 145 throw std::runtime_error("GDCM cannot change the planar configuration to interleaved"); | |
| 146 } | |
| 147 } | |
| 148 } | |
| 149 } | |
| 150 }; | |
| 151 | |
| 152 GdcmImageDecoder::GdcmImageDecoder(const void* dicom, | |
| 153 size_t size) : | |
| 154 pimpl_(new PImpl(dicom, size)) | |
| 155 { | |
| 156 // Setup a stream to the memory buffer | |
| 157 using namespace boost::iostreams; | |
| 158 basic_array_source<char> source(reinterpret_cast<const char*>(dicom), size); | |
| 159 stream<basic_array_source<char> > stream(source); | |
| 160 | |
| 161 // Parse the DICOM instance using GDCM | |
| 162 pimpl_->reader_.SetStream(stream); | |
| 163 if (!pimpl_->reader_.Read()) | |
| 164 { | |
| 165 throw std::runtime_error("Bad file format"); | |
| 166 } | |
| 167 | |
| 168 pimpl_->Decode(); | |
| 169 } | |
| 170 | |
| 171 | |
| 172 OrthancPluginPixelFormat GdcmImageDecoder::GetFormat() const | |
| 173 { | |
| 174 const gdcm::Image& image = pimpl_->GetImage(); | |
| 175 | |
| 176 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
| 177 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || | |
| 178 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) | |
| 179 { | |
| 180 switch (image.GetPixelFormat()) | |
| 181 { | |
| 182 case gdcm::PixelFormat::UINT16: | |
| 183 return OrthancPluginPixelFormat_Grayscale16; | |
| 184 | |
| 185 case gdcm::PixelFormat::INT16: | |
| 186 return OrthancPluginPixelFormat_SignedGrayscale16; | |
| 187 | |
| 188 case gdcm::PixelFormat::UINT8: | |
| 189 return OrthancPluginPixelFormat_Grayscale8; | |
| 190 | |
| 191 default: | |
| 192 throw std::runtime_error("Unsupported pixel format"); | |
| 193 } | |
| 194 } | |
| 195 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
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196 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB || |
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197 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_FULL || |
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198 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_RCT)) |
| 1834 | 199 { |
| 200 switch (image.GetPixelFormat()) | |
| 201 { | |
| 202 case gdcm::PixelFormat::UINT8: | |
| 203 return OrthancPluginPixelFormat_RGB24; | |
| 204 | |
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205 case gdcm::PixelFormat::UINT16: |
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206 #if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 3, 1) |
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207 return OrthancPluginPixelFormat_RGB48; |
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208 #else |
| 2428 | 209 throw std::runtime_error("RGB48 pixel format is only supported if compiled against Orthanc SDK >= 1.3.1"); |
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210 #endif |
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211 |
| 1834 | 212 default: |
| 213 break; | |
| 214 } | |
| 215 } | |
| 216 | |
| 217 throw std::runtime_error("Unsupported pixel format"); | |
| 218 } | |
| 219 | |
| 220 | |
| 221 unsigned int GdcmImageDecoder::GetWidth() const | |
| 222 { | |
| 223 return pimpl_->GetImage().GetColumns(); | |
| 224 } | |
| 225 | |
| 226 | |
| 227 unsigned int GdcmImageDecoder::GetHeight() const | |
| 228 { | |
| 229 return pimpl_->GetImage().GetRows(); | |
| 230 } | |
| 231 | |
| 232 | |
| 233 unsigned int GdcmImageDecoder::GetFramesCount() const | |
| 234 { | |
| 235 return pimpl_->GetImage().GetDimension(2); | |
| 236 } | |
| 237 | |
| 238 | |
| 239 size_t GdcmImageDecoder::GetBytesPerPixel(OrthancPluginPixelFormat format) | |
| 240 { | |
| 241 switch (format) | |
| 242 { | |
| 243 case OrthancPluginPixelFormat_Grayscale8: | |
| 244 return 1; | |
| 245 | |
| 246 case OrthancPluginPixelFormat_Grayscale16: | |
| 247 case OrthancPluginPixelFormat_SignedGrayscale16: | |
| 248 return 2; | |
| 249 | |
| 250 case OrthancPluginPixelFormat_RGB24: | |
| 251 return 3; | |
| 252 | |
| 2427 | 253 #if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 3, 1) |
| 254 case OrthancPluginPixelFormat_RGB48: | |
| 255 return 6; | |
| 256 #endif | |
| 257 | |
| 1834 | 258 default: |
| 259 throw std::runtime_error("Unsupport pixel format"); | |
| 260 } | |
| 261 } | |
| 262 | |
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263 static void ConvertYbrToRgb(uint8_t rgb[3], |
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264 const uint8_t ybr[3]) |
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265 { |
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266 // 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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267 // https://en.wikipedia.org/wiki/YCbCr#JPEG_conversion |
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268 |
| 2485 | 269 // TODO - Check out the outcome of Mathieu's discussion about |
| 270 // truncation of YCbCr-to-RGB conversion: | |
| 271 // https://groups.google.com/forum/#!msg/comp.protocols.dicom/JHuGeyWbTz8/ARoTWrJzAQAJ | |
| 272 | |
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273 const float Y = ybr[0]; |
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274 const float Cb = ybr[1]; |
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275 const float Cr = ybr[2]; |
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276 |
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277 const float result[3] = { |
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278 Y + 1.402f * (Cr - 128.0f), |
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279 Y - 0.344136f * (Cb - 128.0f) - 0.714136f * (Cr - 128.0f), |
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280 Y + 1.772f * (Cb - 128.0f) |
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281 }; |
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282 |
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283 for (uint8_t i = 0; i < 3 ; i++) |
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284 { |
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285 if (result[i] < 0) |
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286 { |
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287 rgb[i] = 0; |
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288 } |
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289 else if (result[i] > 255) |
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290 { |
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291 rgb[i] = 255; |
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292 } |
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293 else |
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294 { |
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295 rgb[i] = static_cast<uint8_t>(result[i]); |
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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 |
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301 static void FixPhotometricInterpretation(OrthancImageWrapper& image, |
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302 gdcm::PhotometricInterpretation interpretation) |
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303 { |
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304 switch (interpretation) |
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305 { |
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306 case gdcm::PhotometricInterpretation::MONOCHROME1: |
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307 case gdcm::PhotometricInterpretation::MONOCHROME2: |
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308 case gdcm::PhotometricInterpretation::RGB: |
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309 return; |
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310 |
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311 case gdcm::PhotometricInterpretation::YBR_FULL: |
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312 { |
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313 // Fix for Osimis issue WVB-319: Some images are not loading in US_MF |
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314 |
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315 uint32_t width = image.GetWidth(); |
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316 uint32_t height = image.GetHeight(); |
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317 uint32_t pitch = image.GetPitch(); |
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318 uint8_t* buffer = reinterpret_cast<uint8_t*>(image.GetBuffer()); |
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319 |
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320 if (image.GetFormat() != OrthancPluginPixelFormat_RGB24 || |
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321 pitch < 3 * width) |
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322 { |
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323 throw std::runtime_error("Internal error"); |
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324 } |
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325 |
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326 for (uint32_t y = 0; y < height; y++) |
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327 { |
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328 uint8_t* p = buffer + y * pitch; |
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329 for (uint32_t x = 0; x < width; x++, p += 3) |
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330 { |
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331 const uint8_t ybr[3] = { p[0], p[1], p[2] }; |
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332 uint8_t rgb[3]; |
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333 ConvertYbrToRgb(rgb, ybr); |
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334 p[0] = rgb[0]; |
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335 p[1] = rgb[1]; |
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336 p[2] = rgb[2]; |
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337 } |
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338 } |
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339 |
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340 return; |
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341 } |
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342 |
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343 default: |
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344 throw std::runtime_error("Unsupported output photometric interpretation"); |
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345 } |
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346 } |
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347 |
| 1834 | 348 |
| 349 OrthancPluginImage* GdcmImageDecoder::Decode(OrthancPluginContext* context, | |
| 350 unsigned int frameIndex) const | |
| 351 { | |
| 352 unsigned int frames = GetFramesCount(); | |
| 353 unsigned int width = GetWidth(); | |
| 354 unsigned int height = GetHeight(); | |
| 355 OrthancPluginPixelFormat format = GetFormat(); | |
| 356 size_t bpp = GetBytesPerPixel(format); | |
| 357 | |
| 358 if (frameIndex >= frames) | |
| 359 { | |
| 360 throw std::runtime_error("Inexistent frame index"); | |
| 361 } | |
| 362 | |
| 363 std::string& decoded = pimpl_->decoded_; | |
| 364 OrthancImageWrapper target(context, format, width, height); | |
| 365 | |
| 366 if (width == 0 || | |
| 367 height == 0) | |
| 368 { | |
| 369 return target.Release(); | |
| 370 } | |
| 371 | |
| 372 if (decoded.empty()) | |
| 373 { | |
| 374 decoded.resize(pimpl_->GetImage().GetBufferLength()); | |
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375 if (!pimpl_->GetImage().GetBuffer(&decoded[0])) |
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376 { |
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377 throw std::runtime_error("Image not properly decoded to a memory buffer"); |
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378 } |
| 1834 | 379 } |
| 380 | |
| 381 const void* sourceBuffer = &decoded[0]; | |
| 382 | |
| 383 if (target.GetPitch() == bpp * width && | |
| 384 frames == 1) | |
| 385 { | |
| 386 assert(decoded.size() == target.GetPitch() * target.GetHeight()); | |
| 387 memcpy(target.GetBuffer(), sourceBuffer, decoded.size()); | |
| 388 } | |
| 389 else | |
| 390 { | |
| 391 size_t targetPitch = target.GetPitch(); | |
| 392 size_t sourcePitch = width * bpp; | |
| 393 | |
| 394 const char* a = &decoded[sourcePitch * height * frameIndex]; | |
| 395 char* b = target.GetBuffer(); | |
| 396 | |
| 397 for (uint32_t y = 0; y < height; y++) | |
| 398 { | |
| 399 memcpy(b, a, sourcePitch); | |
| 400 a += sourcePitch; | |
| 401 b += targetPitch; | |
| 402 } | |
| 403 } | |
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404 |
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405 FixPhotometricInterpretation(target, pimpl_->GetImage().GetPhotometricInterpretation()); |
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406 |
| 1834 | 407 return target.Release(); |
| 408 } | |
| 409 } |