Mercurial > hg > orthanc

annotate Plugins/Samples/GdcmDecoding/Plugin.cpp @ 983:80d4f1618b33 plugins

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Sample plugin to replace DCMTK by GDCM when decoding images
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 01 Jul 2014 12:01:58 +0200
parents
children 0bfdfc0c6b9b
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983
80d4f1618b33 Sample plugin to replace DCMTK by GDCM when decoding images
Sebastien Jodogne <s.jodogne@gmail.com>
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1 /**
80d4f1618b33 Sample plugin to replace DCMTK by GDCM when decoding images
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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
80d4f1618b33 Sample plugin to replace DCMTK by GDCM when decoding images
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9 * restriction, including without limitation the rights to use, copy,
80d4f1618b33 Sample plugin to replace DCMTK by GDCM when decoding images
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10 * modify, merge, publish, distribute, sublicense, and/or sell copies
80d4f1618b33 Sample plugin to replace DCMTK by GDCM when decoding images
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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
80d4f1618b33 Sample plugin to replace DCMTK by GDCM when decoding images
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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
80d4f1618b33 Sample plugin to replace DCMTK by GDCM when decoding images
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19 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
80d4f1618b33 Sample plugin to replace DCMTK by GDCM when decoding images
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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
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39
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40 static bool GetOrthancPixelFormat(Orthanc::PixelFormat& format,
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41 const gdcm::Image& image)
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42 {
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43 if (image.GetPlanarConfiguration() != 0 &&
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44 image.GetPixelFormat().GetSamplesPerPixel() != 1)
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45 {
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46 OrthancContext::GetInstance().LogError("Planar configurations are not supported");
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47 return false;
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48 }
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49
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50 if (image.GetPixelFormat().GetSamplesPerPixel() == 1)
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51 {
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52 switch (image.GetPixelFormat().GetScalarType())
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53 {
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54 case gdcm::PixelFormat::UINT8:
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55 format = Orthanc::PixelFormat_Grayscale8;
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56 return true;
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57
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58 case gdcm::PixelFormat::UINT16:
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59 format = Orthanc::PixelFormat_Grayscale16;
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60 return true;
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61
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62 case gdcm::PixelFormat::INT16:
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63 format = Orthanc::PixelFormat_SignedGrayscale16;
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64 return true;
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65
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66 default:
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67 return false;
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68 }
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69 }
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70 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 &&
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71 image.GetPixelFormat().GetScalarType() == gdcm::PixelFormat::UINT8)
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72 {
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73 format = Orthanc::PixelFormat_RGB24;
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74 }
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75 else if (image.GetPixelFormat().GetSamplesPerPixel() == 4 &&
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76 image.GetPixelFormat().GetScalarType() == gdcm::PixelFormat::UINT8)
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77 {
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78 format = Orthanc::PixelFormat_RGBA32;
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79 }
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80
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81 return false;
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82 }
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83
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84
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85 ORTHANC_PLUGINS_API int32_t DecodeImage(OrthancPluginRestOutput* output,
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86 const char* url,
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87 const OrthancPluginHttpRequest* request)
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88 {
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89 std::string instance(request->groups[0]);
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90 std::string outputFormat(request->groups[1]);
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91 OrthancContext::GetInstance().LogWarning("Using GDCM to decode instance " + instance);
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92
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93 // Download the request DICOM instance from Orthanc into a memory buffer
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94 std::string dicom;
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95 OrthancContext::GetInstance().GetDicomForInstance(dicom, instance);
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96
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97 // Prepare a memory stream over the DICOM instance
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98 std::stringstream stream(dicom);
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99
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100 // Parse the DICOM instance using GDCM
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101 gdcm::ImageReader imageReader;
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102 imageReader.SetStream(stream);
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103 if (!imageReader.Read())
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104 {
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105 OrthancContext::GetInstance().LogError("GDCM cannot extract an image from this DICOM instance");
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106 return -1; // Error
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107 }
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108
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109 gdcm::Image& image = imageReader.GetImage();
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110
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111 // Log information about the decoded image
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112 char tmp[1024];
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113 sprintf(tmp, "Image format: %dx%d %s with %d color channel(s)", image.GetRows(), image.GetColumns(),
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114 image.GetPixelFormat().GetScalarTypeAsString(), image.GetPixelFormat().GetSamplesPerPixel());
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115 OrthancContext::GetInstance().LogWarning(tmp);
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116
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117 // Create a read-only accessor to the bitmap decoded by GDCM
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118 Orthanc::PixelFormat format;
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119 if (!GetOrthancPixelFormat(format, image))
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120 {
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121 OrthancContext::GetInstance().LogError("This sample plugin does not support this image format");
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122 return -1; // Error
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123 }
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124
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125 Orthanc::ImageAccessor decodedImage;
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126 std::vector<char> decodedBuffer(image.GetBufferLength());
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127
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128 if (decodedBuffer.size())
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129 {
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130 image.GetBuffer(&decodedBuffer[0]);
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131 unsigned int pitch = image.GetColumns() * ::Orthanc::GetBytesPerPixel(format);
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132 decodedImage.AssignWritable(format, image.GetColumns(), image.GetRows(), pitch, &decodedBuffer[0]);
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133 }
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134 else
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135 {
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136 // Empty image
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137 decodedImage.AssignWritable(format, 0, 0, 0, NULL);
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138 }
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139
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140
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141 // Convert the pixel format from GDCM to the format requested by the REST query
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142 Orthanc::ImageBuffer converted;
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143 converted.SetWidth(decodedImage.GetWidth());
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144 converted.SetHeight(decodedImage.GetHeight());
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145
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146 if (outputFormat == "preview")
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147 {
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148 if (format == Orthanc::PixelFormat_RGB24 ||
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149 format == Orthanc::PixelFormat_RGBA32)
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150 {
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151 // Do not rescale color image
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152 converted.SetFormat(Orthanc::PixelFormat_RGB24);
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153 }
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154 else
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155 {
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156 converted.SetFormat(Orthanc::PixelFormat_Grayscale8);
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157
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158 // Rescale the image to the [0,255] range
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159 int64_t a, b;
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160 Orthanc::ImageProcessing::GetMinMaxValue(a, b, decodedImage);
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161
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162 float offset = -a;
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163 float scaling = 255.0f / static_cast<float>(b - a);
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164 Orthanc::ImageProcessing::ShiftScale(decodedImage, offset, scaling);
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165 }
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166 }
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167 else if (outputFormat == "image-uint8")
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168 {
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169 converted.SetFormat(Orthanc::PixelFormat_Grayscale8);
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170 }
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171 else if (outputFormat == "image-uint16")
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172 {
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173 converted.SetFormat(Orthanc::PixelFormat_Grayscale16);
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174 }
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175 else if (outputFormat == "image-int16")
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176 {
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177 converted.SetFormat(Orthanc::PixelFormat_SignedGrayscale16);
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178 }
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179 else
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180 {
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181 OrthancContext::GetInstance().LogError("Unknown output format: " + outputFormat);
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182 return -1;
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183 }
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184
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185 Orthanc::ImageAccessor convertedAccessor(converted.GetAccessor());
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186 Orthanc::ImageProcessing::Convert(convertedAccessor, decodedImage);
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187
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188
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189 // Compress the converted image as a PNG file
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190 OrthancContext::GetInstance().CompressAndAnswerPngImage(output, convertedAccessor);
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191
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192 return 0; // Success
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193 }
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194
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195
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196 extern "C"
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197 {
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198 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context)
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199 {
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200 OrthancContext::GetInstance().Initialize(context);
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201 OrthancContext::GetInstance().LogWarning("Initializing GDCM decoding");
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202 OrthancContext::GetInstance().Register("/instances/([^/]+)/(preview|image-uint8|image-uint16|image-int16)", DecodeImage);
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203 return 0;
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204 }
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205
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206 ORTHANC_PLUGINS_API void OrthancPluginFinalize()
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207 {
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208 OrthancContext::GetInstance().LogWarning("Finalizing GDCM decoding");
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209 OrthancContext::GetInstance().Finalize();
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210 }
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211
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212 ORTHANC_PLUGINS_API const char* OrthancPluginGetName()
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213 {
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214 return "gdcm-decoding";
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215 }
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216
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217 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion()
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218 {
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219 return "1.0";
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220 }
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221 }