Mercurial > hg > orthanc-stone

annotate Framework/Deprecated/Toolbox/DicomFrameConverter.cpp @ 925:4639d0bf6390

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Added support for Grayscale16 in the multiframe loader (Victor)
author Benjamin Golinvaux <bgo@osimis.io>
date Mon, 22 Jul 2019 16:00:03 +0200
parents c35e98d22764
children 1f74bc3459ba
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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) 2017-2019 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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23
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24 #include "../../Toolbox/LinearAlgebra.h"
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25
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26 #include <Core/Images/Image.h>
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27 #include <Core/Images/ImageProcessing.h>
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28 #include <Core/OrthancException.h>
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29 #include <Core/Toolbox.h>
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31 namespace Deprecated
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32 {
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33 static const Orthanc::DicomTag IMAGE_TAGS[] =
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34 {
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35 Orthanc::DICOM_TAG_BITS_STORED,
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36 Orthanc::DICOM_TAG_DOSE_GRID_SCALING,
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37 Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION,
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38 Orthanc::DICOM_TAG_PIXEL_REPRESENTATION,
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39 Orthanc::DICOM_TAG_RESCALE_INTERCEPT,
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40 Orthanc::DICOM_TAG_RESCALE_SLOPE,
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41 Orthanc::DICOM_TAG_WINDOW_CENTER,
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42 Orthanc::DICOM_TAG_WINDOW_WIDTH
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43 };
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44
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45
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46 void DicomFrameConverter::SetDefaultParameters()
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47 {
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48 isSigned_ = true;
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49 isColor_ = false;
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50 hasRescale_ = false;
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51 rescaleIntercept_ = 0;
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52 rescaleSlope_ = 1;
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53 hasDefaultWindow_ = false;
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54 defaultWindowCenter_ = 128;
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55 defaultWindowWidth_ = 256;
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56 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
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57 }
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60 void DicomFrameConverter::ReadParameters(const Orthanc::DicomMap& dicom)
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61 {
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62 SetDefaultParameters();
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63
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64 OrthancStone::Vector c, w;
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65 if (OrthancStone::LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
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66 OrthancStone::LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) &&
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67 c.size() > 0 &&
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68 w.size() > 0)
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69 {
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70 hasDefaultWindow_ = true;
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71 defaultWindowCenter_ = static_cast<float>(c[0]);
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72 defaultWindowWidth_ = static_cast<float>(w[0]);
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73 }
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75 int32_t tmp;
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76 if (!dicom.ParseInteger32(tmp, Orthanc::DICOM_TAG_PIXEL_REPRESENTATION))
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77 {
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78 // Type 1 tag, must be present
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79 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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80 }
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81
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82 isSigned_ = (tmp == 1);
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83
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84 double doseGridScaling;
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85 bool isRTDose = false;
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86
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87 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
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88 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
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89 {
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90 hasRescale_ = true;
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91 }
119
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92 else if (dicom.ParseDouble(doseGridScaling, Orthanc::DICOM_TAG_DOSE_GRID_SCALING))
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93 {
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94 // This is for RT-DOSE
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95 hasRescale_ = true;
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96 isRTDose = true;
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97 rescaleIntercept_ = 0;
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98 rescaleSlope_ = doseGridScaling;
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99
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100 if (!dicom.ParseInteger32(tmp, Orthanc::DICOM_TAG_BITS_STORED))
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101 {
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102 // Type 1 tag, must be present
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103 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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104 }
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105
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106 switch (tmp)
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107 {
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108 case 16:
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109 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
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110 break;
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111
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112 case 32:
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113 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32;
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114 break;
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115
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116 default:
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117 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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118 }
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119 }
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121 std::string photometric;
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122 if (dicom.CopyToString(photometric, Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION, false))
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123 {
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124 photometric = Orthanc::Toolbox::StripSpaces(photometric);
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125 }
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126 else
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127 {
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128 // Type 1 tag, must be present
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129 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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130 }
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131
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132 photometric_ = Orthanc::StringToPhotometricInterpretation(photometric.c_str());
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133
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134 isColor_ = (photometric != "MONOCHROME1" &&
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135 photometric != "MONOCHROME2");
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136
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137 // TODO Add more checks, e.g. on the number of bytes per value
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138 // (cf. DicomImageInformation.h in Orthanc)
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139
120
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140 if (!isRTDose)
119
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141 {
120
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142 if (isColor_)
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143 {
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144 expectedPixelFormat_ = Orthanc::PixelFormat_RGB24;
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145 }
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146 else if (isSigned_)
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147 {
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148 expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16;
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149 }
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150 else
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151 {
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152 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
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153 }
119
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154 }
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155 }
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156
338
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157
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158 void DicomFrameConverter::ReadParameters(const OrthancPlugins::IDicomDataset& dicom)
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159 {
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160 Orthanc::DicomMap converted;
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161
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162 for (size_t i = 0; i < sizeof(IMAGE_TAGS) / sizeof(Orthanc::DicomTag); i++)
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163 {
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164 OrthancPlugins::DicomTag tag(IMAGE_TAGS[i].GetGroup(), IMAGE_TAGS[i].GetElement());
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165
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166 std::string value;
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167 if (dicom.GetStringValue(value, tag))
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168 {
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169 converted.SetValue(IMAGE_TAGS[i], value, false);
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170 }
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171 }
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172
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173 ReadParameters(converted);
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174 }
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175
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176
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177 void DicomFrameConverter::ConvertFrameInplace(std::auto_ptr<Orthanc::ImageAccessor>& source) const
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178 {
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179 assert(sizeof(float) == 4);
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180
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181 if (source.get() == NULL)
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182 {
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183 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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184 }
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185
338
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186 if (source->GetFormat() == GetExpectedPixelFormat() &&
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187 source->GetFormat() == Orthanc::PixelFormat_RGB24)
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188 {
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189 // No conversion has to be done, check out (*)
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190 return;
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191 }
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192 else
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193 {
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194 source.reset(ConvertFrame(*source));
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195 }
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196 }
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197
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198
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199 Orthanc::ImageAccessor* DicomFrameConverter::ConvertFrame(const Orthanc::ImageAccessor& source) const
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200 {
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201 assert(sizeof(float) == 4);
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202
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203 Orthanc::PixelFormat sourceFormat = source.GetFormat();
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204
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205 if (sourceFormat != GetExpectedPixelFormat())
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206 {
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207 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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208 }
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209
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210 if (sourceFormat == Orthanc::PixelFormat_RGB24)
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211 {
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212 // This is the case of a color image. No conversion has to be done (*)
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213 std::auto_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_RGB24,
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214 source.GetWidth(),
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215 source.GetHeight(),
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216 false));
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217 Orthanc::ImageProcessing::Copy(*converted, source);
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218 return converted.release();
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219 }
338
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220 else
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221 {
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222 assert(sourceFormat == Orthanc::PixelFormat_Grayscale16 ||
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223 sourceFormat == Orthanc::PixelFormat_Grayscale32 ||
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224 sourceFormat == Orthanc::PixelFormat_SignedGrayscale16);
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225
338
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226 // This is the case of a grayscale frame. Convert it to Float32.
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227 std::auto_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32,
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228 source.GetWidth(),
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229 source.GetHeight(),
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230 false));
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231 Orthanc::ImageProcessing::Convert(*converted, source);
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232
338
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233 // Correct rescale slope/intercept if need be
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234 ApplyRescale(*converted, sourceFormat != Orthanc::PixelFormat_Grayscale32);
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235
338
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236 return converted.release();
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237 }
119
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238 }
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239
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240
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241 void DicomFrameConverter::ApplyRescale(Orthanc::ImageAccessor& image,
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242 bool useDouble) const
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243 {
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244 if (image.GetFormat() != Orthanc::PixelFormat_Float32)
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245 {
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246 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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247 }
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248
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249 if (hasRescale_)
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250 {
119
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251 for (unsigned int y = 0; y < image.GetHeight(); y++)
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252 {
119
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253 float* p = reinterpret_cast<float*>(image.GetRow(y));
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254
119
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255 if (useDouble)
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256 {
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257 // Slower, accurate implementation using double
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258 for (unsigned int x = 0; x < image.GetWidth(); x++, p++)
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259 {
119
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260 double value = static_cast<double>(*p);
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261 *p = static_cast<float>(value * rescaleSlope_ + rescaleIntercept_);
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262 }
119
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263 }
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264 else
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265 {
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266 // Fast, approximate implementation using float
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267 for (unsigned int x = 0; x < image.GetWidth(); x++, p++)
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268 {
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269 *p = (*p) * static_cast<float>(rescaleSlope_) + static_cast<float>(rescaleIntercept_);
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270 }
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271 }
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272 }
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273 }
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274 }
119
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275
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276
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277 double DicomFrameConverter::Apply(double x) const
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278 {
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279 return x * rescaleSlope_ + rescaleIntercept_;
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280 }
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281
0
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282 }