Mercurial > hg > orthanc-webviewer
annotate Orthanc/Plugins/Samples/GdcmDecoder/GdcmImageDecoder.cpp @ 128:e8cfda4c8a2f
Sync + support of JPEG2000 lossless images with YBR_RCT photometric interpretation
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 15 Apr 2016 21:44:03 +0200 |
| parents | 3809121c3290 |
| children | 5dc54316d68b |
| rev | line source |
|---|---|
| 107 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 122 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
| 107 | 4 * Department, University Hospital of Liege, Belgium |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 10 * | |
| 11 * This program is distributed in the hope that it will be useful, but | |
| 12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 14 * General Public License for more details. | |
| 15 * | |
| 16 * You should have received a copy of the GNU General Public License | |
| 17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 **/ | |
| 19 | |
| 20 | |
| 21 #include "GdcmImageDecoder.h" | |
| 22 | |
| 23 #include "OrthancImageWrapper.h" | |
| 24 | |
| 25 #include <gdcmImageReader.h> | |
| 26 #include <gdcmImageApplyLookupTable.h> | |
| 27 #include <gdcmImageChangePlanarConfiguration.h> | |
| 28 #include <gdcmImageChangePhotometricInterpretation.h> | |
| 29 #include <stdexcept> | |
| 30 #include <boost/iostreams/stream.hpp> | |
| 31 #include <boost/iostreams/device/array.hpp> | |
| 32 | |
| 33 | |
| 34 namespace OrthancPlugins | |
| 35 { | |
| 36 struct GdcmImageDecoder::PImpl | |
| 37 { | |
| 38 const void* dicom_; | |
| 39 size_t size_; | |
| 40 | |
| 41 gdcm::ImageReader reader_; | |
| 42 std::auto_ptr<gdcm::ImageApplyLookupTable> lut_; | |
| 43 std::auto_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_; | |
| 44 std::auto_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_; | |
| 45 std::string decoded_; | |
| 46 | |
| 47 PImpl(const void* dicom, | |
| 48 size_t size) : | |
| 49 dicom_(dicom), | |
| 50 size_(size) | |
| 51 { | |
| 52 } | |
| 53 | |
| 54 | |
| 55 const gdcm::DataSet& GetDataSet() const | |
| 56 { | |
| 57 return reader_.GetFile().GetDataSet(); | |
| 58 } | |
| 59 | |
| 60 | |
| 61 const gdcm::Image& GetImage() const | |
| 62 { | |
| 63 if (interleaved_.get() != NULL) | |
| 64 { | |
| 65 return interleaved_->GetOutput(); | |
| 66 } | |
| 67 | |
| 68 if (lut_.get() != NULL) | |
| 69 { | |
| 70 return lut_->GetOutput(); | |
| 71 } | |
| 72 | |
| 73 if (photometric_.get() != NULL) | |
| 74 { | |
| 75 return photometric_->GetOutput(); | |
| 76 } | |
| 77 | |
| 78 return reader_.GetImage(); | |
| 79 } | |
| 80 | |
| 81 | |
| 82 void Decode() | |
| 83 { | |
| 84 // Change photometric interpretation or apply LUT, if required | |
| 85 { | |
| 86 const gdcm::Image& image = GetImage(); | |
| 87 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
| 88 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::PALETTE_COLOR) | |
| 89 { | |
| 90 lut_.reset(new gdcm::ImageApplyLookupTable()); | |
| 91 lut_->SetInput(image); | |
| 92 if (!lut_->Apply()) | |
| 93 { | |
| 94 throw std::runtime_error( "GDCM cannot apply the lookup table"); | |
| 95 } | |
| 96 } | |
| 97 else if (image.GetPixelFormat().GetSamplesPerPixel() == 1) | |
| 98 { | |
| 99 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 && | |
| 100 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
| 101 { | |
| 102 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
| 103 photometric_->SetInput(image); | |
| 104 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); | |
| 105 if (!photometric_->Change() || | |
| 106 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
| 107 { | |
| 108 throw std::runtime_error("GDCM cannot change the photometric interpretation"); | |
| 109 } | |
| 110 } | |
| 111 } | |
| 112 else | |
| 113 { | |
| 114 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
|
128
e8cfda4c8a2f
Sync + support of JPEG2000 lossless images with YBR_RCT photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
122
diff
changeset
|
115 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB && |
|
e8cfda4c8a2f
Sync + support of JPEG2000 lossless images with YBR_RCT photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
122
diff
changeset
|
116 (image.GetTransferSyntax() != gdcm::TransferSyntax::JPEG2000Lossless || |
|
e8cfda4c8a2f
Sync + support of JPEG2000 lossless images with YBR_RCT photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
122
diff
changeset
|
117 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_RCT)) |
| 107 | 118 { |
| 119 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
| 120 photometric_->SetInput(image); | |
| 121 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); | |
| 122 if (!photometric_->Change() || | |
| 123 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
| 124 { | |
| 125 throw std::runtime_error("GDCM cannot change the photometric interpretation"); | |
| 126 } | |
| 127 } | |
| 128 } | |
| 129 } | |
| 130 | |
| 131 // Possibly convert planar configuration to interleaved | |
| 132 { | |
| 133 const gdcm::Image& image = GetImage(); | |
| 134 if (image.GetPlanarConfiguration() != 0 && | |
| 135 image.GetPixelFormat().GetSamplesPerPixel() != 1) | |
| 136 { | |
| 137 interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); | |
| 138 interleaved_->SetInput(image); | |
| 139 if (!interleaved_->Change() || | |
| 140 GetImage().GetPlanarConfiguration() != 0) | |
| 141 { | |
| 142 throw std::runtime_error("GDCM cannot change the planar configuration to interleaved"); | |
| 143 } | |
| 144 } | |
| 145 } | |
| 146 } | |
| 147 }; | |
| 148 | |
| 149 GdcmImageDecoder::GdcmImageDecoder(const void* dicom, | |
| 150 size_t size) : | |
| 151 pimpl_(new PImpl(dicom, size)) | |
| 152 { | |
| 153 // Setup a stream to the memory buffer | |
| 154 using namespace boost::iostreams; | |
| 155 basic_array_source<char> source(reinterpret_cast<const char*>(dicom), size); | |
| 156 stream<basic_array_source<char> > stream(source); | |
| 157 | |
| 158 // Parse the DICOM instance using GDCM | |
| 159 pimpl_->reader_.SetStream(stream); | |
| 160 if (!pimpl_->reader_.Read()) | |
| 161 { | |
| 162 throw std::runtime_error("Bad file format"); | |
| 163 } | |
| 164 | |
| 165 pimpl_->Decode(); | |
| 166 } | |
| 167 | |
| 168 | |
| 169 OrthancPluginPixelFormat GdcmImageDecoder::GetFormat() const | |
| 170 { | |
| 171 const gdcm::Image& image = pimpl_->GetImage(); | |
| 172 | |
| 173 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
| 174 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || | |
| 175 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) | |
| 176 { | |
| 177 switch (image.GetPixelFormat()) | |
| 178 { | |
| 179 case gdcm::PixelFormat::UINT16: | |
| 180 return OrthancPluginPixelFormat_Grayscale16; | |
| 181 | |
| 182 case gdcm::PixelFormat::INT16: | |
| 183 return OrthancPluginPixelFormat_SignedGrayscale16; | |
| 184 | |
| 185 case gdcm::PixelFormat::UINT8: | |
| 186 return OrthancPluginPixelFormat_Grayscale8; | |
| 187 | |
| 188 default: | |
| 189 throw std::runtime_error("Unsupported pixel format"); | |
| 190 } | |
| 191 } | |
| 192 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
|
128
e8cfda4c8a2f
Sync + support of JPEG2000 lossless images with YBR_RCT photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
122
diff
changeset
|
193 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB || |
|
e8cfda4c8a2f
Sync + support of JPEG2000 lossless images with YBR_RCT photometric interpretation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
122
diff
changeset
|
194 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_RCT)) |
| 107 | 195 { |
| 196 switch (image.GetPixelFormat()) | |
| 197 { | |
| 198 case gdcm::PixelFormat::UINT8: | |
| 199 return OrthancPluginPixelFormat_RGB24; | |
| 200 | |
| 201 default: | |
| 202 break; | |
| 203 } | |
| 204 } | |
| 205 | |
| 206 throw std::runtime_error("Unsupported pixel format"); | |
| 207 } | |
| 208 | |
| 209 | |
| 210 unsigned int GdcmImageDecoder::GetWidth() const | |
| 211 { | |
| 212 return pimpl_->GetImage().GetColumns(); | |
| 213 } | |
| 214 | |
| 215 | |
| 216 unsigned int GdcmImageDecoder::GetHeight() const | |
| 217 { | |
| 218 return pimpl_->GetImage().GetRows(); | |
| 219 } | |
| 220 | |
| 221 | |
| 222 unsigned int GdcmImageDecoder::GetFramesCount() const | |
| 223 { | |
| 224 return pimpl_->GetImage().GetDimension(2); | |
| 225 } | |
| 226 | |
| 227 | |
| 228 size_t GdcmImageDecoder::GetBytesPerPixel(OrthancPluginPixelFormat format) | |
| 229 { | |
| 230 switch (format) | |
| 231 { | |
| 232 case OrthancPluginPixelFormat_Grayscale8: | |
| 233 return 1; | |
| 234 | |
| 235 case OrthancPluginPixelFormat_Grayscale16: | |
| 236 case OrthancPluginPixelFormat_SignedGrayscale16: | |
| 237 return 2; | |
| 238 | |
| 239 case OrthancPluginPixelFormat_RGB24: | |
| 240 return 3; | |
| 241 | |
| 242 default: | |
| 243 throw std::runtime_error("Unsupport pixel format"); | |
| 244 } | |
| 245 } | |
| 246 | |
| 247 | |
| 248 OrthancPluginImage* GdcmImageDecoder::Decode(OrthancPluginContext* context, | |
| 249 unsigned int frameIndex) const | |
| 250 { | |
| 251 unsigned int frames = GetFramesCount(); | |
| 252 unsigned int width = GetWidth(); | |
| 253 unsigned int height = GetHeight(); | |
| 254 OrthancPluginPixelFormat format = GetFormat(); | |
| 255 size_t bpp = GetBytesPerPixel(format); | |
| 256 | |
| 257 if (frameIndex >= frames) | |
| 258 { | |
| 259 throw std::runtime_error("Inexistent frame index"); | |
| 260 } | |
| 261 | |
| 262 std::string& decoded = pimpl_->decoded_; | |
| 263 OrthancImageWrapper target(context, format, width, height); | |
| 264 | |
| 265 if (width == 0 || | |
| 266 height == 0) | |
| 267 { | |
| 268 return target.Release(); | |
| 269 } | |
| 270 | |
| 271 if (decoded.empty()) | |
| 272 { | |
| 273 decoded.resize(pimpl_->GetImage().GetBufferLength()); | |
| 274 pimpl_->GetImage().GetBuffer(&decoded[0]); | |
| 275 } | |
| 276 | |
| 277 const void* sourceBuffer = &decoded[0]; | |
| 278 | |
| 279 if (target.GetPitch() == bpp * width && | |
| 280 frames == 1) | |
| 281 { | |
| 282 assert(decoded.size() == target.GetPitch() * target.GetHeight()); | |
| 283 memcpy(target.GetBuffer(), sourceBuffer, decoded.size()); | |
| 284 } | |
| 285 else | |
| 286 { | |
| 287 size_t targetPitch = target.GetPitch(); | |
| 288 size_t sourcePitch = width * bpp; | |
| 289 | |
| 290 const char* a = &decoded[sourcePitch * height * frameIndex]; | |
| 291 char* b = target.GetBuffer(); | |
| 292 | |
| 293 for (uint32_t y = 0; y < height; y++) | |
| 294 { | |
| 295 memcpy(b, a, sourcePitch); | |
| 296 a += sourcePitch; | |
| 297 b += targetPitch; | |
| 298 } | |
| 299 } | |
| 300 | |
| 301 return target.Release(); | |
| 302 } | |
| 303 } |