Mercurial > hg > orthanc
annotate Plugins/Samples/GdcmDecoder/GdcmImageDecoder.cpp @ 2312:8700dcaa02e5 issue-46-anonymization
GenerateAnonymizationProfile.py
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 12 Jul 2017 16:44:33 +0200 |
| parents | a3a65de1840f |
| children | 7ef9207f31d4 |
| 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 |
|
2244
a3a65de1840f
shared copyright with osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1978
diff
changeset
|
5 * Copyright (C) 2017 Osimis, 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 && | |
|
1978
0c9c4e36c2b9
support of YBR_RCT photometric interpretation for JPEG2000 lossless
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
116 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB && |
|
0c9c4e36c2b9
support of YBR_RCT photometric interpretation for JPEG2000 lossless
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
117 (image.GetTransferSyntax() != gdcm::TransferSyntax::JPEG2000Lossless || |
|
0c9c4e36c2b9
support of YBR_RCT photometric interpretation for JPEG2000 lossless
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
118 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_RCT)) |
| 1834 | 119 { |
| 120 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
| 121 photometric_->SetInput(image); | |
| 122 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); | |
| 123 if (!photometric_->Change() || | |
| 124 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
| 125 { | |
| 126 throw std::runtime_error("GDCM cannot change the photometric interpretation"); | |
| 127 } | |
| 128 } | |
| 129 } | |
| 130 } | |
| 131 | |
| 132 // Possibly convert planar configuration to interleaved | |
| 133 { | |
| 134 const gdcm::Image& image = GetImage(); | |
| 135 if (image.GetPlanarConfiguration() != 0 && | |
| 136 image.GetPixelFormat().GetSamplesPerPixel() != 1) | |
| 137 { | |
| 138 interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); | |
| 139 interleaved_->SetInput(image); | |
| 140 if (!interleaved_->Change() || | |
| 141 GetImage().GetPlanarConfiguration() != 0) | |
| 142 { | |
| 143 throw std::runtime_error("GDCM cannot change the planar configuration to interleaved"); | |
| 144 } | |
| 145 } | |
| 146 } | |
| 147 } | |
| 148 }; | |
| 149 | |
| 150 GdcmImageDecoder::GdcmImageDecoder(const void* dicom, | |
| 151 size_t size) : | |
| 152 pimpl_(new PImpl(dicom, size)) | |
| 153 { | |
| 154 // Setup a stream to the memory buffer | |
| 155 using namespace boost::iostreams; | |
| 156 basic_array_source<char> source(reinterpret_cast<const char*>(dicom), size); | |
| 157 stream<basic_array_source<char> > stream(source); | |
| 158 | |
| 159 // Parse the DICOM instance using GDCM | |
| 160 pimpl_->reader_.SetStream(stream); | |
| 161 if (!pimpl_->reader_.Read()) | |
| 162 { | |
| 163 throw std::runtime_error("Bad file format"); | |
| 164 } | |
| 165 | |
| 166 pimpl_->Decode(); | |
| 167 } | |
| 168 | |
| 169 | |
| 170 OrthancPluginPixelFormat GdcmImageDecoder::GetFormat() const | |
| 171 { | |
| 172 const gdcm::Image& image = pimpl_->GetImage(); | |
| 173 | |
| 174 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
| 175 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || | |
| 176 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) | |
| 177 { | |
| 178 switch (image.GetPixelFormat()) | |
| 179 { | |
| 180 case gdcm::PixelFormat::UINT16: | |
| 181 return OrthancPluginPixelFormat_Grayscale16; | |
| 182 | |
| 183 case gdcm::PixelFormat::INT16: | |
| 184 return OrthancPluginPixelFormat_SignedGrayscale16; | |
| 185 | |
| 186 case gdcm::PixelFormat::UINT8: | |
| 187 return OrthancPluginPixelFormat_Grayscale8; | |
| 188 | |
| 189 default: | |
| 190 throw std::runtime_error("Unsupported pixel format"); | |
| 191 } | |
| 192 } | |
| 193 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
|
1978
0c9c4e36c2b9
support of YBR_RCT photometric interpretation for JPEG2000 lossless
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
194 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB || |
|
0c9c4e36c2b9
support of YBR_RCT photometric interpretation for JPEG2000 lossless
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1900
diff
changeset
|
195 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_RCT)) |
| 1834 | 196 { |
| 197 switch (image.GetPixelFormat()) | |
| 198 { | |
| 199 case gdcm::PixelFormat::UINT8: | |
| 200 return OrthancPluginPixelFormat_RGB24; | |
| 201 | |
| 202 default: | |
| 203 break; | |
| 204 } | |
| 205 } | |
| 206 | |
| 207 throw std::runtime_error("Unsupported pixel format"); | |
| 208 } | |
| 209 | |
| 210 | |
| 211 unsigned int GdcmImageDecoder::GetWidth() const | |
| 212 { | |
| 213 return pimpl_->GetImage().GetColumns(); | |
| 214 } | |
| 215 | |
| 216 | |
| 217 unsigned int GdcmImageDecoder::GetHeight() const | |
| 218 { | |
| 219 return pimpl_->GetImage().GetRows(); | |
| 220 } | |
| 221 | |
| 222 | |
| 223 unsigned int GdcmImageDecoder::GetFramesCount() const | |
| 224 { | |
| 225 return pimpl_->GetImage().GetDimension(2); | |
| 226 } | |
| 227 | |
| 228 | |
| 229 size_t GdcmImageDecoder::GetBytesPerPixel(OrthancPluginPixelFormat format) | |
| 230 { | |
| 231 switch (format) | |
| 232 { | |
| 233 case OrthancPluginPixelFormat_Grayscale8: | |
| 234 return 1; | |
| 235 | |
| 236 case OrthancPluginPixelFormat_Grayscale16: | |
| 237 case OrthancPluginPixelFormat_SignedGrayscale16: | |
| 238 return 2; | |
| 239 | |
| 240 case OrthancPluginPixelFormat_RGB24: | |
| 241 return 3; | |
| 242 | |
| 243 default: | |
| 244 throw std::runtime_error("Unsupport pixel format"); | |
| 245 } | |
| 246 } | |
| 247 | |
| 248 | |
| 249 OrthancPluginImage* GdcmImageDecoder::Decode(OrthancPluginContext* context, | |
| 250 unsigned int frameIndex) const | |
| 251 { | |
| 252 unsigned int frames = GetFramesCount(); | |
| 253 unsigned int width = GetWidth(); | |
| 254 unsigned int height = GetHeight(); | |
| 255 OrthancPluginPixelFormat format = GetFormat(); | |
| 256 size_t bpp = GetBytesPerPixel(format); | |
| 257 | |
| 258 if (frameIndex >= frames) | |
| 259 { | |
| 260 throw std::runtime_error("Inexistent frame index"); | |
| 261 } | |
| 262 | |
| 263 std::string& decoded = pimpl_->decoded_; | |
| 264 OrthancImageWrapper target(context, format, width, height); | |
| 265 | |
| 266 if (width == 0 || | |
| 267 height == 0) | |
| 268 { | |
| 269 return target.Release(); | |
| 270 } | |
| 271 | |
| 272 if (decoded.empty()) | |
| 273 { | |
| 274 decoded.resize(pimpl_->GetImage().GetBufferLength()); | |
| 275 pimpl_->GetImage().GetBuffer(&decoded[0]); | |
| 276 } | |
| 277 | |
| 278 const void* sourceBuffer = &decoded[0]; | |
| 279 | |
| 280 if (target.GetPitch() == bpp * width && | |
| 281 frames == 1) | |
| 282 { | |
| 283 assert(decoded.size() == target.GetPitch() * target.GetHeight()); | |
| 284 memcpy(target.GetBuffer(), sourceBuffer, decoded.size()); | |
| 285 } | |
| 286 else | |
| 287 { | |
| 288 size_t targetPitch = target.GetPitch(); | |
| 289 size_t sourcePitch = width * bpp; | |
| 290 | |
| 291 const char* a = &decoded[sourcePitch * height * frameIndex]; | |
| 292 char* b = target.GetBuffer(); | |
| 293 | |
| 294 for (uint32_t y = 0; y < height; y++) | |
| 295 { | |
| 296 memcpy(b, a, sourcePitch); | |
| 297 a += sourcePitch; | |
| 298 b += targetPitch; | |
| 299 } | |
| 300 } | |
| 301 | |
| 302 return target.Release(); | |
| 303 } | |
| 304 } |