Mercurial > hg > orthanc-stone

annotate Framework/Toolbox/DicomFrameConverter.cpp @ 201:e9c7a78a3e77

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removed absolute paths
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 23 Mar 2018 11:59:22 +0100
parents fccffbf99ba1
children 5412adf19980
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1 /**
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2 * Stone of Orthanc
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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 * Copyright (C) 2017-2018 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 Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the 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 * Affero 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 Affero 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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20
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21
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22 #include "DicomFrameConverter.h"
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24 #include "LinearAlgebra.h"
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25
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26 #include "../../Resources/Orthanc/Core/Images/Image.h"
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27 #include "../../Resources/Orthanc/Core/Images/ImageProcessing.h"
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28 #include "../../Resources/Orthanc/Core/OrthancException.h"
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29 #include "../../Resources/Orthanc/Core/Toolbox.h"
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31 namespace OrthancStone
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32 {
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33 void DicomFrameConverter::SetDefaultParameters()
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34 {
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35 isSigned_ = true;
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36 isColor_ = false;
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37 hasRescale_ = false;
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38 rescaleIntercept_ = 0;
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39 rescaleSlope_ = 1;
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40 defaultWindowCenter_ = 128;
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41 defaultWindowWidth_ = 256;
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42 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
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43 }
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46 void DicomFrameConverter::ReadParameters(const Orthanc::DicomMap& dicom)
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47 {
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48 SetDefaultParameters();
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49
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50 Vector c, w;
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51 if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
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52 LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) &&
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53 c.size() > 0 &&
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54 w.size() > 0)
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55 {
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56 defaultWindowCenter_ = static_cast<float>(c[0]);
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57 defaultWindowWidth_ = static_cast<float>(w[0]);
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58 }
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60 int32_t tmp;
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61 if (!dicom.ParseInteger32(tmp, Orthanc::DICOM_TAG_PIXEL_REPRESENTATION))
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62 {
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63 // Type 1 tag, must be present
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64 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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65 }
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66
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67 isSigned_ = (tmp == 1);
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68
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69 double doseGridScaling;
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70 bool isRTDose = false;
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71
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72 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
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73 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
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74 {
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75 hasRescale_ = true;
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76 }
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77 else if (dicom.ParseDouble(doseGridScaling, Orthanc::DICOM_TAG_DOSE_GRID_SCALING))
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78 {
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79 // This is for RT-DOSE
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80 hasRescale_ = true;
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81 isRTDose = true;
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82 rescaleIntercept_ = 0;
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83 rescaleSlope_ = doseGridScaling;
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84
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85 if (!dicom.ParseInteger32(tmp, Orthanc::DICOM_TAG_BITS_STORED))
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86 {
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87 // Type 1 tag, must be present
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88 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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89 }
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90
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91 switch (tmp)
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92 {
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93 case 16:
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94 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
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95 break;
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96
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97 case 32:
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98 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32;
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99 break;
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100
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101 default:
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102 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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103 }
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104 }
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105
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106 std::string photometric;
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107 if (dicom.CopyToString(photometric, Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION, false))
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108 {
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109 photometric = Orthanc::Toolbox::StripSpaces(photometric);
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110 }
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111 else
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112 {
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113 // Type 1 tag, must be present
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114 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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115 }
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116
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117 isColor_ = (photometric != "MONOCHROME1" &&
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118 photometric != "MONOCHROME2");
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119
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120 // TODO Add more checks, e.g. on the number of bytes per value
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121 // (cf. DicomImageInformation.h in Orthanc)
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122
120
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123 if (!isRTDose)
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124 {
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125 if (isColor_)
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126 {
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127 expectedPixelFormat_ = Orthanc::PixelFormat_RGB24;
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128 }
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129 else if (isSigned_)
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130 {
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131 expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16;
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132 }
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133 else
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134 {
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135 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
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136 }
119
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137 }
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138 }
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139
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140
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141 void DicomFrameConverter::ConvertFrame(std::auto_ptr<Orthanc::ImageAccessor>& source) const
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142 {
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143 assert(sizeof(float) == 4);
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144
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145 if (source.get() == NULL)
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146 {
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147 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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148 }
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149
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150 Orthanc::PixelFormat sourceFormat = source->GetFormat();
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151
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152 if (sourceFormat != GetExpectedPixelFormat())
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153 {
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154 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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155 }
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156
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157 if (sourceFormat == Orthanc::PixelFormat_RGB24)
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158 {
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159 // No conversion has to be done
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160 return;
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161 }
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162
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163 assert(sourceFormat == Orthanc::PixelFormat_Grayscale16 ||
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164 sourceFormat == Orthanc::PixelFormat_Grayscale32 ||
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165 sourceFormat == Orthanc::PixelFormat_SignedGrayscale16);
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166
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167 // This is the case of a grayscale frame. Convert it to Float32.
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168 std::auto_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32,
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169 source->GetWidth(),
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170 source->GetHeight(),
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171 false));
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172 Orthanc::ImageProcessing::Convert(*converted, *source);
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173
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174 source.reset(NULL); // We don't need the source frame anymore
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175
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176 // Correct rescale slope/intercept if need be
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177 ApplyRescale(*converted, sourceFormat != Orthanc::PixelFormat_Grayscale32);
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178
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179 source = converted;
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180 }
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181
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182
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183 void DicomFrameConverter::ApplyRescale(Orthanc::ImageAccessor& image,
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184 bool useDouble) const
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185 {
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186 if (image.GetFormat() != Orthanc::PixelFormat_Float32)
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187 {
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188 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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189 }
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190
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191 if (hasRescale_)
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192 {
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193 for (unsigned int y = 0; y < image.GetHeight(); y++)
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194 {
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195 float* p = reinterpret_cast<float*>(image.GetRow(y));
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196
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197 if (useDouble)
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198 {
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199 // Slower, accurate implementation using double
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200 for (unsigned int x = 0; x < image.GetWidth(); x++, p++)
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201 {
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202 double value = static_cast<double>(*p);
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203 *p = static_cast<float>(value * rescaleSlope_ + rescaleIntercept_);
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204 }
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205 }
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206 else
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207 {
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208 // Fast, approximate implementation using float
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209 for (unsigned int x = 0; x < image.GetWidth(); x++, p++)
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210 {
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211 *p = (*p) * static_cast<float>(rescaleSlope_) + static_cast<float>(rescaleIntercept_);
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212 }
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213 }
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214 }
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215 }
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216 }
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217
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218
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219 double DicomFrameConverter::Apply(double x) const
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220 {
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221 return x * rescaleSlope_ + rescaleIntercept_;
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222 }
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223
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224 }