Mercurial > hg > orthanc

annotate Plugins/Samples/GdcmDecoding/Plugin.cpp @ 993:501880d76474 plugins

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improvements to GDCM plugin
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 02 Jul 2014 14:41:57 +0200
parents 0bfdfc0c6b9b
children d06186cdc502
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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
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33 #include "OrthancContext.h"
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34 #include "../../../Core/ImageFormats/ImageProcessing.h"
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35
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36 #include <gdcmReader.h>
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37 #include <gdcmImageReader.h>
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38 #include <gdcmImageChangePlanarConfiguration.h>
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39
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40
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41 static void AnswerUnsupportedImage(OrthancPluginRestOutput* output)
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42 {
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43 OrthancContext::GetInstance().Redirect(output, "/app/images/unsupported.png");
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44 }
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46
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47 static bool GetOrthancPixelFormat(Orthanc::PixelFormat& format,
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48 const gdcm::Image& image)
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49 {
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50 if (image.GetPlanarConfiguration() != 0 &&
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51 image.GetPixelFormat().GetSamplesPerPixel() != 1)
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52 {
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53 OrthancContext::GetInstance().LogError("Planar configurations are not supported");
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54 return false;
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55 }
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56
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57 if (image.GetPixelFormat().GetSamplesPerPixel() == 1)
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58 {
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59 switch (image.GetPixelFormat().GetScalarType())
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60 {
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61 case gdcm::PixelFormat::UINT8:
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62 format = Orthanc::PixelFormat_Grayscale8;
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63 return true;
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64
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65 case gdcm::PixelFormat::UINT16:
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66 format = Orthanc::PixelFormat_Grayscale16;
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67 return true;
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68
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69 case gdcm::PixelFormat::INT16:
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70 format = Orthanc::PixelFormat_SignedGrayscale16;
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71 return true;
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72
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73 default:
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74 return false;
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75 }
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76 }
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77 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 &&
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78 image.GetPixelFormat().GetScalarType() == gdcm::PixelFormat::UINT8)
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79 {
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80 format = Orthanc::PixelFormat_RGB24;
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81 return true;
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82 }
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83 else if (image.GetPixelFormat().GetSamplesPerPixel() == 4 &&
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84 image.GetPixelFormat().GetScalarType() == gdcm::PixelFormat::UINT8)
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85 {
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86 format = Orthanc::PixelFormat_RGBA32;
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87 return true;
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88 }
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89
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90 return false;
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91 }
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92
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93
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94 ORTHANC_PLUGINS_API int32_t DecodeImage(OrthancPluginRestOutput* output,
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95 const char* url,
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96 const OrthancPluginHttpRequest* request)
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97 {
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98 std::string instance(request->groups[0]);
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99 std::string outputFormat(request->groups[1]);
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100 OrthancContext::GetInstance().LogWarning("Using GDCM to decode instance " + instance);
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101
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102 // Download the request DICOM instance from Orthanc into a memory buffer
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103 std::string dicom;
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104 OrthancContext::GetInstance().GetDicomForInstance(dicom, instance);
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105
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106 // Prepare a memory stream over the DICOM instance
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107 std::stringstream stream(dicom);
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108
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109 // Parse the DICOM instance using GDCM
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110 gdcm::ImageReader imageReader;
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111 imageReader.SetStream(stream);
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112 if (!imageReader.Read())
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113 {
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114 OrthancContext::GetInstance().LogError("GDCM cannot extract an image from this DICOM instance");
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115 AnswerUnsupportedImage(output);
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116 return 0;
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117 }
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118
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119 gdcm::Image& image = imageReader.GetImage();
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120
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121
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122 // Log information about the decoded image
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123 char tmp[1024];
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124 sprintf(tmp, "Image format: %dx%d %s with %d color channel(s)", image.GetRows(), image.GetColumns(),
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125 image.GetPixelFormat().GetScalarTypeAsString(), image.GetPixelFormat().GetSamplesPerPixel());
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126 OrthancContext::GetInstance().LogWarning(tmp);
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127
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128
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129 // Convert planar configuration
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130 gdcm::ImageChangePlanarConfiguration planar;
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131 if (image.GetPlanarConfiguration() != 0 &&
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132 image.GetPixelFormat().GetSamplesPerPixel() != 1)
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133 {
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134 OrthancContext::GetInstance().LogWarning("Converting planar configuration to interleaved");
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135 planar.SetInput(imageReader.GetImage());
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136 planar.Change();
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137 image = planar.GetOutput();
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138 }
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139
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140
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141 // Create a read-only accessor to the bitmap decoded by GDCM
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142 Orthanc::PixelFormat format;
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143 if (!GetOrthancPixelFormat(format, image))
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144 {
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145 OrthancContext::GetInstance().LogError("This sample plugin does not support this image format");
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146 AnswerUnsupportedImage(output);
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147 return 0;
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148 }
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149
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150 Orthanc::ImageAccessor decodedImage;
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151 std::vector<char> decodedBuffer(image.GetBufferLength());
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152
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153 if (decodedBuffer.size())
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154 {
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155 image.GetBuffer(&decodedBuffer[0]);
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156 unsigned int pitch = image.GetColumns() * ::Orthanc::GetBytesPerPixel(format);
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157 decodedImage.AssignWritable(format, image.GetColumns(), image.GetRows(), pitch, &decodedBuffer[0]);
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158 }
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159 else
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160 {
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161 // Empty image
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162 decodedImage.AssignWritable(format, 0, 0, 0, NULL);
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163 }
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164
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165
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166 // Convert the pixel format from GDCM to the format requested by the REST query
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167 Orthanc::ImageBuffer converted;
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168 converted.SetWidth(decodedImage.GetWidth());
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169 converted.SetHeight(decodedImage.GetHeight());
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170
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171 if (outputFormat == "preview")
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172 {
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173 if (format == Orthanc::PixelFormat_RGB24 ||
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174 format == Orthanc::PixelFormat_RGBA32)
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175 {
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176 // Do not rescale color image
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177 converted.SetFormat(Orthanc::PixelFormat_RGB24);
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178 }
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179 else
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180 {
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181 converted.SetFormat(Orthanc::PixelFormat_Grayscale8);
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182
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183 // Rescale the image to the [0,255] range
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184 int64_t a, b;
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185 Orthanc::ImageProcessing::GetMinMaxValue(a, b, decodedImage);
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186
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187 float offset = -a;
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188 float scaling = 255.0f / static_cast<float>(b - a);
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189 Orthanc::ImageProcessing::ShiftScale(decodedImage, offset, scaling);
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190 }
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191 }
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192 else
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193 {
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194 if (format == Orthanc::PixelFormat_RGB24 ||
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195 format == Orthanc::PixelFormat_RGBA32)
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196 {
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197 // Do not convert color images to grayscale values (this is Orthanc convention)
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198 AnswerUnsupportedImage(output);
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199 return 0;
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200 }
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201
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202 if (outputFormat == "image-uint8")
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203 {
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204 converted.SetFormat(Orthanc::PixelFormat_Grayscale8);
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205 }
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206 else if (outputFormat == "image-uint16")
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207 {
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208 converted.SetFormat(Orthanc::PixelFormat_Grayscale16);
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209 }
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210 else if (outputFormat == "image-int16")
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211 {
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212 converted.SetFormat(Orthanc::PixelFormat_SignedGrayscale16);
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213 }
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214 else
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215 {
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216 OrthancContext::GetInstance().LogError("Unknown output format: " + outputFormat);
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217 AnswerUnsupportedImage(output);
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218 return 0;
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219 }
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220 }
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221
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222 Orthanc::ImageAccessor convertedAccessor(converted.GetAccessor());
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223 Orthanc::ImageProcessing::Convert(convertedAccessor, decodedImage);
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224
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225 // Compress the converted image as a PNG file
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226 OrthancContext::GetInstance().CompressAndAnswerPngImage(output, convertedAccessor);
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227
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228 return 0; // Success
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229 }
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230
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231
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232 extern "C"
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233 {
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234 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context)
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235 {
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236 OrthancContext::GetInstance().Initialize(context);
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237 OrthancContext::GetInstance().LogWarning("Initializing GDCM decoding");
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238 OrthancContext::GetInstance().Register("/instances/([^/]+)/(preview|image-uint8|image-uint16|image-int16)", DecodeImage);
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239 return 0;
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240 }
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241
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242 ORTHANC_PLUGINS_API void OrthancPluginFinalize()
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243 {
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244 OrthancContext::GetInstance().LogWarning("Finalizing GDCM decoding");
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245 OrthancContext::GetInstance().Finalize();
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246 }
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247
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248 ORTHANC_PLUGINS_API const char* OrthancPluginGetName()
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249 {
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250 return "gdcm-decoding";
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251 }
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252
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253 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion()
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254 {
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255 return "1.0";
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256 }
80d4f1618b33 Sample plugin to replace DCMTK by GDCM when decoding images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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