annotate Plugins/Samples/GdcmDecoder/GdcmImageDecoder.cpp @ 3640:94f4a18a79cc

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 31 Jan 2020 17:14:59 +0100
parents 5069af20932a
children 6110a4995ace
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
1900
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
3640
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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21
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22 #include "GdcmImageDecoder.h"
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23
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24 #include "OrthancImageWrapper.h"
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25
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26 #include <gdcmImageReader.h>
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27 #include <gdcmImageApplyLookupTable.h>
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28 #include <gdcmImageChangePlanarConfiguration.h>
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29 #include <gdcmImageChangePhotometricInterpretation.h>
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30 #include <stdexcept>
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31 #include <boost/iostreams/stream.hpp>
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32 #include <boost/iostreams/device/array.hpp>
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35 namespace OrthancPlugins
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36 {
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37 struct GdcmImageDecoder::PImpl
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38 {
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39 const void* dicom_;
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40 size_t size_;
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41
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42 gdcm::ImageReader reader_;
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43 std::auto_ptr<gdcm::ImageApplyLookupTable> lut_;
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44 std::auto_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_;
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45 std::auto_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_;
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46 std::string decoded_;
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47
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48 PImpl(const void* dicom,
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49 size_t size) :
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50 dicom_(dicom),
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51 size_(size)
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52 {
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53 }
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54
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55
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56 const gdcm::DataSet& GetDataSet() const
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57 {
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58 return reader_.GetFile().GetDataSet();
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59 }
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60
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61
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62 const gdcm::Image& GetImage() const
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63 {
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64 if (interleaved_.get() != NULL)
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65 {
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66 return interleaved_->GetOutput();
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67 }
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68
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69 if (lut_.get() != NULL)
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70 {
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71 return lut_->GetOutput();
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72 }
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73
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74 if (photometric_.get() != NULL)
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75 {
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76 return photometric_->GetOutput();
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77 }
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78
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79 return reader_.GetImage();
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80 }
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81
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82
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83 void Decode()
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84 {
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85 // Change photometric interpretation or apply LUT, if required
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86 {
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87 const gdcm::Image& image = GetImage();
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88 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 &&
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89 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::PALETTE_COLOR)
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90 {
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91 lut_.reset(new gdcm::ImageApplyLookupTable());
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92 lut_->SetInput(image);
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93 if (!lut_->Apply())
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94 {
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95 throw std::runtime_error( "GDCM cannot apply the lookup table");
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96 }
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97 }
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98 else if (image.GetPixelFormat().GetSamplesPerPixel() == 1)
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99 {
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100 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 &&
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101 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2)
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102 {
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103 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation());
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104 photometric_->SetInput(image);
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105 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2);
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106 if (!photometric_->Change() ||
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107 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2)
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108 {
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109 throw std::runtime_error("GDCM cannot change the photometric interpretation");
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110 }
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111 }
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112 }
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113 else
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114 {
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115 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 &&
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116 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB &&
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117 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_FULL &&
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118 (image.GetTransferSyntax() != gdcm::TransferSyntax::JPEG2000Lossless ||
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119 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::YBR_RCT))
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120 {
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121 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation());
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122 photometric_->SetInput(image);
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123 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB);
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124 if (!photometric_->Change() ||
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125 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB)
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126 {
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127 throw std::runtime_error("GDCM cannot change the photometric interpretation");
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128 }
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129 }
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130 }
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131 }
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132
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133 // Possibly convert planar configuration to interleaved
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134 {
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135 const gdcm::Image& image = GetImage();
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136 if (image.GetPlanarConfiguration() != 0 &&
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137 image.GetPixelFormat().GetSamplesPerPixel() != 1)
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138 {
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139 interleaved_.reset(new gdcm::ImageChangePlanarConfiguration());
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140 interleaved_->SetInput(image);
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141 if (!interleaved_->Change() ||
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142 GetImage().GetPlanarConfiguration() != 0)
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143 {
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144 throw std::runtime_error("GDCM cannot change the planar configuration to interleaved");
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145 }
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146 }
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147 }
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148 }
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149 };
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150
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151 GdcmImageDecoder::GdcmImageDecoder(const void* dicom,
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152 size_t size) :
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153 pimpl_(new PImpl(dicom, size))
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154 {
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155 // Setup a stream to the memory buffer
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156 using namespace boost::iostreams;
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157 basic_array_source<char> source(reinterpret_cast<const char*>(dicom), size);
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158 stream<basic_array_source<char> > stream(source);
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159
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160 // Parse the DICOM instance using GDCM
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161 pimpl_->reader_.SetStream(stream);
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162 if (!pimpl_->reader_.Read())
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163 {
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164 throw std::runtime_error("Bad file format");
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165 }
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166
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167 pimpl_->Decode();
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168 }
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169
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170
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171 OrthancPluginPixelFormat GdcmImageDecoder::GetFormat() const
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172 {
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173 const gdcm::Image& image = pimpl_->GetImage();
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174
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175 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 &&
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176 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 ||
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177 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2))
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178 {
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179 switch (image.GetPixelFormat())
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180 {
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181 case gdcm::PixelFormat::UINT16:
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182 return OrthancPluginPixelFormat_Grayscale16;
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183
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184 case gdcm::PixelFormat::INT16:
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185 return OrthancPluginPixelFormat_SignedGrayscale16;
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186
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187 case gdcm::PixelFormat::UINT8:
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188 return OrthancPluginPixelFormat_Grayscale8;
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189
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190 default:
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191 throw std::runtime_error("Unsupported pixel format");
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192 }
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193 }
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194 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 &&
1978
0c9c4e36c2b9 support of YBR_RCT photometric interpretation for JPEG2000 lossless
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195 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB ||
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196 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_FULL ||
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197 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::YBR_RCT))
1834
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198 {
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199 switch (image.GetPixelFormat())
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200 {
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201 case gdcm::PixelFormat::UINT8:
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202 return OrthancPluginPixelFormat_RGB24;
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203
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204 case gdcm::PixelFormat::UINT16:
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205 #if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 3, 1)
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206 return OrthancPluginPixelFormat_RGB48;
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207 #else
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208 throw std::runtime_error("RGB48 pixel format is only supported if compiled against Orthanc SDK >= 1.3.1");
2424
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209 #endif
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210
1834
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211 default:
b1a6f49b21dd GDCM decoder sample
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212 break;
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213 }
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214 }
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215
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216 throw std::runtime_error("Unsupported pixel format");
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217 }
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218
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219
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220 unsigned int GdcmImageDecoder::GetWidth() const
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221 {
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222 return pimpl_->GetImage().GetColumns();
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223 }
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224
b1a6f49b21dd GDCM decoder sample
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225
b1a6f49b21dd GDCM decoder sample
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226 unsigned int GdcmImageDecoder::GetHeight() const
b1a6f49b21dd GDCM decoder sample
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227 {
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228 return pimpl_->GetImage().GetRows();
b1a6f49b21dd GDCM decoder sample
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229 }
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230
b1a6f49b21dd GDCM decoder sample
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231
b1a6f49b21dd GDCM decoder sample
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232 unsigned int GdcmImageDecoder::GetFramesCount() const
b1a6f49b21dd GDCM decoder sample
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233 {
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234 return pimpl_->GetImage().GetDimension(2);
b1a6f49b21dd GDCM decoder sample
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235 }
b1a6f49b21dd GDCM decoder sample
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236
b1a6f49b21dd GDCM decoder sample
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237
b1a6f49b21dd GDCM decoder sample
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diff changeset
238 size_t GdcmImageDecoder::GetBytesPerPixel(OrthancPluginPixelFormat format)
b1a6f49b21dd GDCM decoder sample
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239 {
b1a6f49b21dd GDCM decoder sample
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diff changeset
240 switch (format)
b1a6f49b21dd GDCM decoder sample
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241 {
b1a6f49b21dd GDCM decoder sample
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242 case OrthancPluginPixelFormat_Grayscale8:
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243 return 1;
b1a6f49b21dd GDCM decoder sample
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diff changeset
244
b1a6f49b21dd GDCM decoder sample
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diff changeset
245 case OrthancPluginPixelFormat_Grayscale16:
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246 case OrthancPluginPixelFormat_SignedGrayscale16:
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247 return 2;
b1a6f49b21dd GDCM decoder sample
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248
b1a6f49b21dd GDCM decoder sample
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249 case OrthancPluginPixelFormat_RGB24:
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250 return 3;
b1a6f49b21dd GDCM decoder sample
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251
2427
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252 #if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 3, 1)
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253 case OrthancPluginPixelFormat_RGB48:
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254 return 6;
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255 #endif
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diff changeset
256
1834
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257 default:
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258 throw std::runtime_error("Unsupport pixel format");
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259 }
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260 }
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261
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262 static void ConvertYbrToRgb(uint8_t rgb[3],
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263 const uint8_t ybr[3])
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264 {
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265 // 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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266 // https://en.wikipedia.org/wiki/YCbCr#JPEG_conversion
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267
2485
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268 // TODO - Check out the outcome of Mathieu's discussion about
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269 // truncation of YCbCr-to-RGB conversion:
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270 // https://groups.google.com/forum/#!msg/comp.protocols.dicom/JHuGeyWbTz8/ARoTWrJzAQAJ
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271
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272 const float Y = ybr[0];
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273 const float Cb = ybr[1];
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274 const float Cr = ybr[2];
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275
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diff changeset
276 const float result[3] = {
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277 Y + 1.402f * (Cr - 128.0f),
61fc5133e5d5 Fix for Osimis issue WVB-319: Some images are not loading in US_MF
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278 Y - 0.344136f * (Cb - 128.0f) - 0.714136f * (Cr - 128.0f),
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279 Y + 1.772f * (Cb - 128.0f)
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280 };
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281
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282 for (uint8_t i = 0; i < 3 ; i++)
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283 {
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284 if (result[i] < 0)
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285 {
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286 rgb[i] = 0;
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287 }
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288 else if (result[i] > 255)
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289 {
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290 rgb[i] = 255;
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291 }
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292 else
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293 {
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294 rgb[i] = static_cast<uint8_t>(result[i]);
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295 }
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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 static void FixPhotometricInterpretation(OrthancImageWrapper& image,
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301 gdcm::PhotometricInterpretation interpretation)
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302 {
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303 switch (interpretation)
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304 {
2798
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am@osimis.io
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305 case gdcm::PhotometricInterpretation::MONOCHROME1:
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306 case gdcm::PhotometricInterpretation::MONOCHROME2:
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307 case gdcm::PhotometricInterpretation::RGB:
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308 return;
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309
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310 case gdcm::PhotometricInterpretation::YBR_FULL:
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311 {
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312 // Fix for Osimis issue WVB-319: Some images are not loading in US_MF
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313
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314 uint32_t width = image.GetWidth();
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315 uint32_t height = image.GetHeight();
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316 uint32_t pitch = image.GetPitch();
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317 uint8_t* buffer = reinterpret_cast<uint8_t*>(image.GetBuffer());
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318
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319 if (image.GetFormat() != OrthancPluginPixelFormat_RGB24 ||
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320 pitch < 3 * width)
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321 {
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322 throw std::runtime_error("Internal error");
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323 }
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diff changeset
324
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diff changeset
325 for (uint32_t y = 0; y < height; y++)
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diff changeset
326 {
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327 uint8_t* p = buffer + y * pitch;
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328 for (uint32_t x = 0; x < width; x++, p += 3)
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diff changeset
329 {
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diff changeset
330 const uint8_t ybr[3] = { p[0], p[1], p[2] };
61fc5133e5d5 Fix for Osimis issue WVB-319: Some images are not loading in US_MF
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diff changeset
331 uint8_t rgb[3];
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332 ConvertYbrToRgb(rgb, ybr);
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diff changeset
333 p[0] = rgb[0];
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diff changeset
334 p[1] = rgb[1];
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335 p[2] = rgb[2];
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336 }
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337 }
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diff changeset
338
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diff changeset
339 return;
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340 }
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diff changeset
341
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diff changeset
342 default:
61fc5133e5d5 Fix for Osimis issue WVB-319: Some images are not loading in US_MF
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diff changeset
343 throw std::runtime_error("Unsupported output photometric interpretation");
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344 }
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345 }
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diff changeset
346
1834
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
347
b1a6f49b21dd GDCM decoder sample
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diff changeset
348 OrthancPluginImage* GdcmImageDecoder::Decode(OrthancPluginContext* context,
b1a6f49b21dd GDCM decoder sample
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349 unsigned int frameIndex) const
b1a6f49b21dd GDCM decoder sample
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350 {
b1a6f49b21dd GDCM decoder sample
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diff changeset
351 unsigned int frames = GetFramesCount();
b1a6f49b21dd GDCM decoder sample
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diff changeset
352 unsigned int width = GetWidth();
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
353 unsigned int height = GetHeight();
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
354 OrthancPluginPixelFormat format = GetFormat();
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
355 size_t bpp = GetBytesPerPixel(format);
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
356
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
357 if (frameIndex >= frames)
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
358 {
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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359 throw std::runtime_error("Inexistent frame index");
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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360 }
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
361
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
362 std::string& decoded = pimpl_->decoded_;
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
363 OrthancImageWrapper target(context, format, width, height);
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
364
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
365 if (width == 0 ||
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
366 height == 0)
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
367 {
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
368 return target.Release();
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
369 }
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
370
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
371 if (decoded.empty())
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
372 {
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
373 decoded.resize(pimpl_->GetImage().GetBufferLength());
3351
5069af20932a Web viewer: Check the return value of gdcm::Bitmap::GetBuffer()
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parents: 3060
diff changeset
374 if (!pimpl_->GetImage().GetBuffer(&decoded[0]))
5069af20932a Web viewer: Check the return value of gdcm::Bitmap::GetBuffer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
375 {
5069af20932a Web viewer: Check the return value of gdcm::Bitmap::GetBuffer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
376 throw std::runtime_error("Image not properly decoded to a memory buffer");
5069af20932a Web viewer: Check the return value of gdcm::Bitmap::GetBuffer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
377 }
1834
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
378 }
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
379
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
380 const void* sourceBuffer = &decoded[0];
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
381
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
382 if (target.GetPitch() == bpp * width &&
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
383 frames == 1)
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
384 {
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
385 assert(decoded.size() == target.GetPitch() * target.GetHeight());
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
386 memcpy(target.GetBuffer(), sourceBuffer, decoded.size());
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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387 }
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
388 else
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
389 {
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
390 size_t targetPitch = target.GetPitch();
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
391 size_t sourcePitch = width * bpp;
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
392
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
393 const char* a = &decoded[sourcePitch * height * frameIndex];
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
394 char* b = target.GetBuffer();
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
395
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
396 for (uint32_t y = 0; y < height; y++)
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
397 {
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
398 memcpy(b, a, sourcePitch);
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
399 a += sourcePitch;
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
400 b += targetPitch;
b1a6f49b21dd GDCM decoder sample
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diff changeset
401 }
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
402 }
2464
61fc5133e5d5 Fix for Osimis issue WVB-319: Some images are not loading in US_MF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2447
diff changeset
403
61fc5133e5d5 Fix for Osimis issue WVB-319: Some images are not loading in US_MF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
404 FixPhotometricInterpretation(target, pimpl_->GetImage().GetPhotometricInterpretation());
61fc5133e5d5 Fix for Osimis issue WVB-319: Some images are not loading in US_MF
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2447
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405
1834
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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406 return target.Release();
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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407 }
b1a6f49b21dd GDCM decoder sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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408 }