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