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annotate Plugins/Samples/GdcmDecoding/Plugin.cpp @ 1272:7442097b41c9

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 12 Jan 2015 17:42:29 +0100
parents d06186cdc502
children 6e7e5ed91c2d
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege,
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4 * Belgium
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5 *
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6 * Permission is hereby granted, free of charge, to any person
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7 * obtaining a copy of this software and associated documentation
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8 * files (the "Software"), to deal in the Software without
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9 * restriction, including without limitation the rights to use, copy,
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10 * modify, merge, publish, distribute, sublicense, and/or sell copies
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11 * of the Software, and to permit persons to whom the Software is
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12 * furnished to do so, subject to the following conditions:
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13 *
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14 * The above copyright notice and this permission notice shall be
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15 * included in all copies or substantial portions of the Software.
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16 *
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17 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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18 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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19 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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20 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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21 * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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22 * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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23 * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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24 * SOFTWARE.
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25 **/
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26
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27
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28 #include <map>
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29 #include <string>
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30 #include <stdexcept>
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31 #include <sstream>
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32 #include <boost/lexical_cast.hpp>
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33
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34 #include "OrthancContext.h"
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35 #include "../../../Core/ImageFormats/ImageProcessing.h"
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36
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37 #include <gdcmReader.h>
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38 #include <gdcmImageReader.h>
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39 #include <gdcmImageChangePlanarConfiguration.h>
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40
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41
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42 static void AnswerUnsupportedImage(OrthancPluginRestOutput* output)
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43 {
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44 OrthancContext::GetInstance().Redirect(output, "/app/images/unsupported.png");
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45 }
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47
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48 static bool GetOrthancPixelFormat(Orthanc::PixelFormat& format,
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49 const gdcm::Image& image)
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50 {
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51 if (image.GetPlanarConfiguration() != 0 &&
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52 image.GetPixelFormat().GetSamplesPerPixel() != 1)
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53 {
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54 OrthancContext::GetInstance().LogError("Planar configurations are not supported");
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55 return false;
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56 }
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57
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58 if (image.GetPixelFormat().GetSamplesPerPixel() == 1)
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59 {
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60 switch (image.GetPixelFormat().GetScalarType())
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61 {
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62 case gdcm::PixelFormat::UINT8:
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63 format = Orthanc::PixelFormat_Grayscale8;
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64 return true;
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65
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66 case gdcm::PixelFormat::UINT16:
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67 format = Orthanc::PixelFormat_Grayscale16;
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68 return true;
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69
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70 case gdcm::PixelFormat::INT16:
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71 format = Orthanc::PixelFormat_SignedGrayscale16;
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72 return true;
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73
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74 default:
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75 return false;
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76 }
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77 }
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78 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 &&
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79 image.GetPixelFormat().GetScalarType() == gdcm::PixelFormat::UINT8)
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80 {
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81 format = Orthanc::PixelFormat_RGB24;
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82 return true;
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83 }
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84 else if (image.GetPixelFormat().GetSamplesPerPixel() == 4 &&
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85 image.GetPixelFormat().GetScalarType() == gdcm::PixelFormat::UINT8)
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86 {
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87 format = Orthanc::PixelFormat_RGBA32;
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88 return true;
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89 }
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90
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91 return false;
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92 }
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94
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95 ORTHANC_PLUGINS_API int32_t DecodeImage(OrthancPluginRestOutput* output,
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96 const char* url,
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97 const OrthancPluginHttpRequest* request)
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98 {
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99 std::string instance(request->groups[0]);
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100 std::string outputFormat(request->groups[1]);
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101 OrthancContext::GetInstance().LogWarning("Using GDCM to decode instance " + instance);
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102
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103 // Download the request DICOM instance from Orthanc into a memory buffer
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104 std::string dicom;
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105 OrthancContext::GetInstance().GetDicomForInstance(dicom, instance);
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106
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107 // Prepare a memory stream over the DICOM instance
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108 std::stringstream stream(dicom);
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109
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110 // Parse the DICOM instance using GDCM
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111 gdcm::ImageReader imageReader;
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112 imageReader.SetStream(stream);
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113 if (!imageReader.Read())
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114 {
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115 OrthancContext::GetInstance().LogError("GDCM cannot extract an image from this DICOM instance");
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116 AnswerUnsupportedImage(output);
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117 return 0;
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118 }
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119
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120 gdcm::Image& image = imageReader.GetImage();
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121
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122
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123 // Log information about the decoded image
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124 char tmp[1024];
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125 sprintf(tmp, "Image format: %dx%d %s with %d color channel(s)", image.GetRows(), image.GetColumns(),
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126 image.GetPixelFormat().GetScalarTypeAsString(), image.GetPixelFormat().GetSamplesPerPixel());
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127 OrthancContext::GetInstance().LogWarning(tmp);
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128
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129
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130 // Convert planar configuration
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131 gdcm::ImageChangePlanarConfiguration planar;
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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 OrthancContext::GetInstance().LogWarning("Converting planar configuration to interleaved");
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136 planar.SetInput(imageReader.GetImage());
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137 planar.Change();
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138 image = planar.GetOutput();
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139 }
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140
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141
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142 // Create a read-only accessor to the bitmap decoded by GDCM
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143 Orthanc::PixelFormat format;
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144 if (!GetOrthancPixelFormat(format, image))
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145 {
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146 OrthancContext::GetInstance().LogError("This sample plugin does not support this image format");
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147 AnswerUnsupportedImage(output);
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148 return 0;
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149 }
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150
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151 Orthanc::ImageAccessor decodedImage;
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152 std::vector<char> decodedBuffer(image.GetBufferLength());
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153
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154 if (decodedBuffer.size())
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155 {
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156 image.GetBuffer(&decodedBuffer[0]);
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157 unsigned int pitch = image.GetColumns() * ::Orthanc::GetBytesPerPixel(format);
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158 decodedImage.AssignWritable(format, image.GetColumns(), image.GetRows(), pitch, &decodedBuffer[0]);
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159 }
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160 else
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161 {
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162 // Empty image
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163 decodedImage.AssignWritable(format, 0, 0, 0, NULL);
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164 }
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165
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166
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167 // Convert the pixel format from GDCM to the format requested by the REST query
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168 Orthanc::ImageBuffer converted;
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169 converted.SetWidth(decodedImage.GetWidth());
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170 converted.SetHeight(decodedImage.GetHeight());
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171
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172 if (outputFormat == "preview")
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173 {
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174 if (format == Orthanc::PixelFormat_RGB24 ||
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175 format == Orthanc::PixelFormat_RGBA32)
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176 {
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177 // Do not rescale color image
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178 converted.SetFormat(Orthanc::PixelFormat_RGB24);
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179 }
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180 else
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181 {
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182 converted.SetFormat(Orthanc::PixelFormat_Grayscale8);
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183
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184 // Rescale the image to the [0,255] range
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185 int64_t a, b;
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186 Orthanc::ImageProcessing::GetMinMaxValue(a, b, decodedImage);
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187
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188 float offset = -a;
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189 float scaling = 255.0f / static_cast<float>(b - a);
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190 Orthanc::ImageProcessing::ShiftScale(decodedImage, offset, scaling);
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191 }
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192 }
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193 else
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194 {
993
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195 if (format == Orthanc::PixelFormat_RGB24 ||
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196 format == Orthanc::PixelFormat_RGBA32)
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197 {
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198 // Do not convert color images to grayscale values (this is Orthanc convention)
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199 AnswerUnsupportedImage(output);
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200 return 0;
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201 }
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202
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203 if (outputFormat == "image-uint8")
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204 {
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205 converted.SetFormat(Orthanc::PixelFormat_Grayscale8);
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206 }
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207 else if (outputFormat == "image-uint16")
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208 {
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209 converted.SetFormat(Orthanc::PixelFormat_Grayscale16);
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210 }
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211 else if (outputFormat == "image-int16")
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212 {
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213 converted.SetFormat(Orthanc::PixelFormat_SignedGrayscale16);
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214 }
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215 else
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216 {
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217 OrthancContext::GetInstance().LogError("Unknown output format: " + outputFormat);
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218 AnswerUnsupportedImage(output);
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219 return 0;
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220 }
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221 }
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222
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223 Orthanc::ImageAccessor convertedAccessor(converted.GetAccessor());
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224 Orthanc::ImageProcessing::Convert(convertedAccessor, decodedImage);
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225
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226 // Compress the converted image as a PNG file
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227 OrthancContext::GetInstance().CompressAndAnswerPngImage(output, convertedAccessor);
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228
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229 return 0; // Success
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230 }
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231
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232
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233 extern "C"
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234 {
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235 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context)
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236 {
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237 OrthancContext::GetInstance().Initialize(context);
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238 OrthancContext::GetInstance().LogWarning("Initializing GDCM decoding");
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239
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240 // Check the version of the Orthanc core
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241 if (OrthancPluginCheckVersion(context) == 0)
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242 {
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243 OrthancContext::GetInstance().LogError(
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244 "Your version of Orthanc (" + std::string(context->orthancVersion) +
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245 ") must be above " + boost::lexical_cast<std::string>(ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER) +
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246 "." + boost::lexical_cast<std::string>(ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER) +
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247 "." + boost::lexical_cast<std::string>(ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER) +
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248 " to run this plugin");
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249 return -1;
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250 }
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251
983
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252 OrthancContext::GetInstance().Register("/instances/([^/]+)/(preview|image-uint8|image-uint16|image-int16)", DecodeImage);
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253 return 0;
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254 }
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255
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256 ORTHANC_PLUGINS_API void OrthancPluginFinalize()
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257 {
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258 OrthancContext::GetInstance().LogWarning("Finalizing GDCM decoding");
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259 OrthancContext::GetInstance().Finalize();
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260 }
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261
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262 ORTHANC_PLUGINS_API const char* OrthancPluginGetName()
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263 {
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264 return "gdcm-decoding";
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265 }
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266
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267 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion()
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268 {
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269 return "1.0";
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270 }
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271 }