Mercurial > hg > orthanc
annotate Plugins/Samples/GdcmDecoder/GdcmImageDecoder.cpp @ 2425:59b7aa77a8da
compatibility of GDCM sample with Orthanc SDK <= 1.3.0
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 10 Oct 2017 12:44:58 +0200 |
| parents | 7ef9207f31d4 |
| children | 23f5ff059ce2 |
| 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 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 | |
|
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35 // This is for compatibility with Orthanc SDK <= 1.3.0 |
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36 #if !defined(ORTHANC_PLUGINS_VERSION_IS_ABOVE) |
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37 #define ORTHANC_PLUGINS_VERSION_IS_ABOVE(major, minor, revision) \ |
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38 (ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER > major || \ |
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39 (ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER == major && \ |
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40 (ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER > minor || \ |
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41 (ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER == minor && \ |
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42 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER >= revision)))) |
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43 #endif |
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44 |
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45 |
| 1834 | 46 namespace OrthancPlugins |
| 47 { | |
| 48 struct GdcmImageDecoder::PImpl | |
| 49 { | |
| 50 const void* dicom_; | |
| 51 size_t size_; | |
| 52 | |
| 53 gdcm::ImageReader reader_; | |
| 54 std::auto_ptr<gdcm::ImageApplyLookupTable> lut_; | |
| 55 std::auto_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_; | |
| 56 std::auto_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_; | |
| 57 std::string decoded_; | |
| 58 | |
| 59 PImpl(const void* dicom, | |
| 60 size_t size) : | |
| 61 dicom_(dicom), | |
| 62 size_(size) | |
| 63 { | |
| 64 } | |
| 65 | |
| 66 | |
| 67 const gdcm::DataSet& GetDataSet() const | |
| 68 { | |
| 69 return reader_.GetFile().GetDataSet(); | |
| 70 } | |
| 71 | |
| 72 | |
| 73 const gdcm::Image& GetImage() const | |
| 74 { | |
| 75 if (interleaved_.get() != NULL) | |
| 76 { | |
| 77 return interleaved_->GetOutput(); | |
| 78 } | |
| 79 | |
| 80 if (lut_.get() != NULL) | |
| 81 { | |
| 82 return lut_->GetOutput(); | |
| 83 } | |
| 84 | |
| 85 if (photometric_.get() != NULL) | |
| 86 { | |
| 87 return photometric_->GetOutput(); | |
| 88 } | |
| 89 | |
| 90 return reader_.GetImage(); | |
| 91 } | |
| 92 | |
| 93 | |
| 94 void Decode() | |
| 95 { | |
| 96 // Change photometric interpretation or apply LUT, if required | |
| 97 { | |
| 98 const gdcm::Image& image = GetImage(); | |
| 99 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
| 100 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::PALETTE_COLOR) | |
| 101 { | |
| 102 lut_.reset(new gdcm::ImageApplyLookupTable()); | |
| 103 lut_->SetInput(image); | |
| 104 if (!lut_->Apply()) | |
| 105 { | |
| 106 throw std::runtime_error( "GDCM cannot apply the lookup table"); | |
| 107 } | |
| 108 } | |
| 109 else if (image.GetPixelFormat().GetSamplesPerPixel() == 1) | |
| 110 { | |
| 111 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 && | |
| 112 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
| 113 { | |
| 114 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
| 115 photometric_->SetInput(image); | |
| 116 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); | |
| 117 if (!photometric_->Change() || | |
| 118 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
| 119 { | |
| 120 throw std::runtime_error("GDCM cannot change the photometric interpretation"); | |
| 121 } | |
| 122 } | |
| 123 } | |
| 124 else | |
| 125 { | |
| 126 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
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127 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB && |
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128 (image.GetTransferSyntax() != gdcm::TransferSyntax::JPEG2000Lossless || |
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129 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_RCT)) |
| 1834 | 130 { |
| 131 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
| 132 photometric_->SetInput(image); | |
| 133 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); | |
| 134 if (!photometric_->Change() || | |
| 135 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
| 136 { | |
| 137 throw std::runtime_error("GDCM cannot change the photometric interpretation"); | |
| 138 } | |
| 139 } | |
| 140 } | |
| 141 } | |
| 142 | |
| 143 // Possibly convert planar configuration to interleaved | |
| 144 { | |
| 145 const gdcm::Image& image = GetImage(); | |
| 146 if (image.GetPlanarConfiguration() != 0 && | |
| 147 image.GetPixelFormat().GetSamplesPerPixel() != 1) | |
| 148 { | |
| 149 interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); | |
| 150 interleaved_->SetInput(image); | |
| 151 if (!interleaved_->Change() || | |
| 152 GetImage().GetPlanarConfiguration() != 0) | |
| 153 { | |
| 154 throw std::runtime_error("GDCM cannot change the planar configuration to interleaved"); | |
| 155 } | |
| 156 } | |
| 157 } | |
| 158 } | |
| 159 }; | |
| 160 | |
| 161 GdcmImageDecoder::GdcmImageDecoder(const void* dicom, | |
| 162 size_t size) : | |
| 163 pimpl_(new PImpl(dicom, size)) | |
| 164 { | |
| 165 // Setup a stream to the memory buffer | |
| 166 using namespace boost::iostreams; | |
| 167 basic_array_source<char> source(reinterpret_cast<const char*>(dicom), size); | |
| 168 stream<basic_array_source<char> > stream(source); | |
| 169 | |
| 170 // Parse the DICOM instance using GDCM | |
| 171 pimpl_->reader_.SetStream(stream); | |
| 172 if (!pimpl_->reader_.Read()) | |
| 173 { | |
| 174 throw std::runtime_error("Bad file format"); | |
| 175 } | |
| 176 | |
| 177 pimpl_->Decode(); | |
| 178 } | |
| 179 | |
| 180 | |
| 181 OrthancPluginPixelFormat GdcmImageDecoder::GetFormat() const | |
| 182 { | |
| 183 const gdcm::Image& image = pimpl_->GetImage(); | |
| 184 | |
| 185 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
| 186 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || | |
| 187 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) | |
| 188 { | |
| 189 switch (image.GetPixelFormat()) | |
| 190 { | |
| 191 case gdcm::PixelFormat::UINT16: | |
| 192 return OrthancPluginPixelFormat_Grayscale16; | |
| 193 | |
| 194 case gdcm::PixelFormat::INT16: | |
| 195 return OrthancPluginPixelFormat_SignedGrayscale16; | |
| 196 | |
| 197 case gdcm::PixelFormat::UINT8: | |
| 198 return OrthancPluginPixelFormat_Grayscale8; | |
| 199 | |
| 200 default: | |
| 201 throw std::runtime_error("Unsupported pixel format"); | |
| 202 } | |
| 203 } | |
| 204 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
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0c9c4e36c2b9
support of YBR_RCT photometric interpretation for JPEG2000 lossless
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parents:
1900
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205 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB || |
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206 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_RCT)) |
| 1834 | 207 { |
| 208 switch (image.GetPixelFormat()) | |
| 209 { | |
| 210 case gdcm::PixelFormat::UINT8: | |
| 211 return OrthancPluginPixelFormat_RGB24; | |
| 212 | |
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213 case gdcm::PixelFormat::UINT16: |
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214 #if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 3, 1) |
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215 return OrthancPluginPixelFormat_RGB48; |
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216 #else |
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217 throw std::runtime_error("RGB48 pixel format is only supported by Orthanc >= 1.3.1"); |
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218 #endif |
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219 |
| 1834 | 220 default: |
| 221 break; | |
| 222 } | |
| 223 } | |
| 224 | |
| 225 throw std::runtime_error("Unsupported pixel format"); | |
| 226 } | |
| 227 | |
| 228 | |
| 229 unsigned int GdcmImageDecoder::GetWidth() const | |
| 230 { | |
| 231 return pimpl_->GetImage().GetColumns(); | |
| 232 } | |
| 233 | |
| 234 | |
| 235 unsigned int GdcmImageDecoder::GetHeight() const | |
| 236 { | |
| 237 return pimpl_->GetImage().GetRows(); | |
| 238 } | |
| 239 | |
| 240 | |
| 241 unsigned int GdcmImageDecoder::GetFramesCount() const | |
| 242 { | |
| 243 return pimpl_->GetImage().GetDimension(2); | |
| 244 } | |
| 245 | |
| 246 | |
| 247 size_t GdcmImageDecoder::GetBytesPerPixel(OrthancPluginPixelFormat format) | |
| 248 { | |
| 249 switch (format) | |
| 250 { | |
| 251 case OrthancPluginPixelFormat_Grayscale8: | |
| 252 return 1; | |
| 253 | |
| 254 case OrthancPluginPixelFormat_Grayscale16: | |
| 255 case OrthancPluginPixelFormat_SignedGrayscale16: | |
| 256 return 2; | |
| 257 | |
| 258 case OrthancPluginPixelFormat_RGB24: | |
| 259 return 3; | |
| 260 | |
| 261 default: | |
| 262 throw std::runtime_error("Unsupport pixel format"); | |
| 263 } | |
| 264 } | |
| 265 | |
| 266 | |
| 267 OrthancPluginImage* GdcmImageDecoder::Decode(OrthancPluginContext* context, | |
| 268 unsigned int frameIndex) const | |
| 269 { | |
| 270 unsigned int frames = GetFramesCount(); | |
| 271 unsigned int width = GetWidth(); | |
| 272 unsigned int height = GetHeight(); | |
| 273 OrthancPluginPixelFormat format = GetFormat(); | |
| 274 size_t bpp = GetBytesPerPixel(format); | |
| 275 | |
| 276 if (frameIndex >= frames) | |
| 277 { | |
| 278 throw std::runtime_error("Inexistent frame index"); | |
| 279 } | |
| 280 | |
| 281 std::string& decoded = pimpl_->decoded_; | |
| 282 OrthancImageWrapper target(context, format, width, height); | |
| 283 | |
| 284 if (width == 0 || | |
| 285 height == 0) | |
| 286 { | |
| 287 return target.Release(); | |
| 288 } | |
| 289 | |
| 290 if (decoded.empty()) | |
| 291 { | |
| 292 decoded.resize(pimpl_->GetImage().GetBufferLength()); | |
| 293 pimpl_->GetImage().GetBuffer(&decoded[0]); | |
| 294 } | |
| 295 | |
| 296 const void* sourceBuffer = &decoded[0]; | |
| 297 | |
| 298 if (target.GetPitch() == bpp * width && | |
| 299 frames == 1) | |
| 300 { | |
| 301 assert(decoded.size() == target.GetPitch() * target.GetHeight()); | |
| 302 memcpy(target.GetBuffer(), sourceBuffer, decoded.size()); | |
| 303 } | |
| 304 else | |
| 305 { | |
| 306 size_t targetPitch = target.GetPitch(); | |
| 307 size_t sourcePitch = width * bpp; | |
| 308 | |
| 309 const char* a = &decoded[sourcePitch * height * frameIndex]; | |
| 310 char* b = target.GetBuffer(); | |
| 311 | |
| 312 for (uint32_t y = 0; y < height; y++) | |
| 313 { | |
| 314 memcpy(b, a, sourcePitch); | |
| 315 a += sourcePitch; | |
| 316 b += targetPitch; | |
| 317 } | |
| 318 } | |
| 319 | |
| 320 return target.Release(); | |
| 321 } | |
| 322 } |