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documented transcoding
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 22 May 2020 11:19:41 +0200
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children 2922fb1bd65e
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1 .. _transcoding:
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2
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3 Transcoding of DICOM files
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4 ==========================
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5
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6 .. contents::
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7
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8
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9 General information
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10 -------------------
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11
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12 **DICOM transcoding** refers to the process of changing the
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13 :ref:`transfer syntax <dicom-pixel-data>` of some DICOM instance.
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15 Transcoding can be used to **compress** DICOM images, which is useful
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16 to reduce the required storage area or to optimize the network
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17 bandwidth for exchanges between sites. Conversely, transcoding can be
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18 used to **decompress** DICOM images, which is needed as many DICOM
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19 viewers or specialized analysis software do not provide support for
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20 compressed transfer syntaxes.
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21
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22 Support for transcoding was introduced in Orthanc 1.7.0.
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24
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25 Motivation for transcoding
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26 --------------------------
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27
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28 Let's consider the following basic workflow, in which some imaging
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29 workstation must access a medical image that originates from a PACS
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30 and that is served through an Orthanc proxy:
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31
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32 .. image:: ../images/Transcoding1.svg
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33 :align: center
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34 :width: 700px
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35
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36 This is quite a common situation, e.g. in university hospitals where
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37 researchers must access medical images without having authorization to
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38 log in the clinical PACS. It is also common if the main PACS restricts
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39 the number of workstations that can directly be connected to it, or if
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40 Orthanc acts as gateway through Internet.
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41
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42 The problem is that the software running on workstations might not be
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43 able to display some DICOM transfer syntaxes. This is especially true
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44 in research software, that is often limited to uncompressed transfer
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45 syntaxes. For instance, let's consider the following scenario where a
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46 workstation wants to access an image from the PACS:
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47
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48 .. image:: ../images/Transcoding2.svg
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49 :align: center
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50 :width: 700px
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51
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52 A typical PACS system will decide, when requested to export an image
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53 using DICOM C-Store, to compress the image in order to reduce the
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54 network bandwidth and the storage requirements. Orthanc is fine with
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55 it: As a vendor neutral archive, Orthanc can basically
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56 receive/store/transmit any DICOM transfer syntax. Unfortunately, this
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57 might not be the case of the target workstation, that is often limited
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58 to some selected transfer syntaxes. As a consequence, the workstation
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59 will complain about not being to use the DICOM file (in the situation
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60 depicted above, because the PACS has decided to send the DICOM image
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61 using the JPEG2k transfer syntax).
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62
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63
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64 Transcoding in Orthanc
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65 ----------------------
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66
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67 Orthanc 1.7.0 was the first release of Orthanc to feature built-in
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68 support for DICOM transcoding. Transcoding is available at multiple
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69 levels, as depicted by the green arrows on the following drawing:
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71 .. image:: ../images/Transcoding-1.7.0.svg
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72 :align: center
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73 :width: 500px
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75
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76 * **Automated transcoding while ingesting**. Orthanc can be configured
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77 to automatically transcode each DICOM instance it receives (either
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78 by DICOM protocol or by REST API) to a fixed transfer syntax. This
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79 is especially useful to either create an archive of compressed files
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80 (for long-term archiving), or to create a DICOM buffer with
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81 uncompressed files (for interfacing with DICOM modalities that do
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82 not support compressed transfer syntaxes). If the transcoding fails,
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83 the DICOM instance is still stored using its original transfer
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84 syntax.
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85
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86 Automated transcoding is enabled by setting the :ref:`configuration
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87 option <configuration>` ``IngestTranscoding`` to the transfer syntax
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88 UID of interest. For instance, setting ``IngestTranscoding`` to
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89 ``1.2.840.10008.1.2.1`` will decompress all the received DICOM
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90 instances. Conversely, setting it to ``1.2.840.10008.1.2.4.70`` will
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91 compress and store images using JPEG-LS (lossless).
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92
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93 * **Decompression while sending instances using the DICOM protocol**.
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94 Orthanc can be configured to automatically decompress DICOM images
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95 on its outgoing connections, if the remote modality does not support
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96 the compressed transfer syntax of the source DICOM instances. This
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97 feature is available for both :ref:`DICOM C-Move and C-Get commands
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98 <dicom-move>`. Note that Orthanc won't transcode DICOM instances to
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99 a compressed transfer syntax over the DICOM protocol.
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100
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101 By default, this automated decompression is enabled. This might be
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102 undesirable if you want to limit the resources that are used by
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103 Orthanc. As a consequence, you can disable this feature either
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104 globally (by setting configuration option ``TranscodeDicomProtocol``
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105 to ``false``), or on a per-modality basis (by setting the option
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106 ``AllowTranscoding`` to ``false`` in the ``DicomModalities``
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107 section).
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108
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109 .. highlight:: bash
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110
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111 * **Transcoding while sending instances to an Orthanc peer**. The
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112 ``/peers/{id}/store`` route in the Orthanc REST API allows to send
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113 DICOM resources (patients, studies, series or instances) to
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114 :ref:`another Orthanc server over HTTP/HTTPS <peering>`. Starting
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115 with Orthanc 1.7.0, the ``Transcode`` option can be used in the JSON
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116 POST body to instruct to transcode the DICOM files before they are
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117 sent. For instance::
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118
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119 $ curl -X POST http://localhost:8042/peers/sample/store -d '{"Transcode":"1.2.840.10008.1.2.4.70","Resources":["66c8e41e-ac3a9029-0b85e42a-8195ee0a-92c2e62e"]}'
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120
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121 * **Transcoding using the REST API**. Starting with Orthanc 1.7.0,
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122 some routes in the REST API also accept the ``Transcode`` option
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123 in their JSON POST body. Those routes notably include:
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124
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125 * The routes to create ZIP files or DICOMDIR archives (``.../media``
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126 and ``.../archive``).
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127
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128 * The routes to modify DICOM resources
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129 (``/{patients|studies|series|instances}/{id}/modify``).
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130
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131 Importantly, if you need to transcode JPEG2k DICOM instances, you'll
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132 have to install the :ref:`GDCM plugin <gdcm>` that replaces the
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133 built-in transcoder of Orthanc based on DCMTK, by the GDCM transcoder.
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134
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135 The following :ref:`advanced configuration options <configuration>`
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136 are also available to control transcoding:
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137
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138 * ``BuiltinDecoderTranscoderOrder`` controls the transcoder that is
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139 used by Orthanc. It specifies whether the built-in transcoder of
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140 Orthanc (that uses DCMTK) is applied before or after the transcoding
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141 plugins, or not applied at all. "After" means that the built-in
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142 transcoder is applied if all the transcoding plugins have failed to
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143 transcode the image.
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144
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145 * ``DicomLossyTranscodingQuality`` controls the quality level of lossy
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146 compression (notably for JPEG transcoding).
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147
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148
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149 Solutions to avoid transcoding
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150 ------------------------------
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151
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152 Up to release 1.6.1, Orthanc didn't feature support for transcoding
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153 DICOM instances. In other words, the Orthanc core never changed the
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154 :ref:`transfer syntax <dicom-pixel-data>` of some DICOM instance when
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155 it had to send it to another modality using the DICOM protocol.
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156
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157 Three workarounds were available to bypass the need for DICOM
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158 transcoding in Orthanc <= 1.6.1. These workarounds are still valid in
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159 Orthanc >= 1.7.0, if transcoding is undesirable (e.g. if Orthanc is
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160 being run on a computer with sparse CPU/RAM resources).
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161
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162
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163 Refusing transfer syntaxes
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164 ^^^^^^^^^^^^^^^^^^^^^^^^^^
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165
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166 The first solution consists in making Orthanc **refuse to accept the
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167 transfer syntaxes** that are not supported by the workstation. This is
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168 depicted in the following diagram:
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169
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170 .. image:: ../images/Transcoding3.svg
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171 :align: center
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172 :width: 700px
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173
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174 .. highlight:: json
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175
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176 If Orthanc tells the PACS that is doesn't accept, say, DICOM JPEG2k,
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177 the source PACS will be aware of this, and will take care of
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178 transcoding the DICOM files before they are sent to Orthanc. This is
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179 the role of the following :ref:`configuration options <configuration>`
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180 that specifies which transfer syntaxes are accepted by Orthanc::
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181
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182 {
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183 "DeflatedTransferSyntaxAccepted" : true,
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184 "JpegTransferSyntaxAccepted" : true,
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185 "Jpeg2000TransferSyntaxAccepted" : true,
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186 "JpegLosslessTransferSyntaxAccepted" : true,
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187 "JpipTransferSyntaxAccepted" : true,
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188 "Mpeg2TransferSyntaxAccepted" : true,
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189 "RleTransferSyntaxAccepted" : true,
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190 "UnknownSopClassAccepted" : false
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191 }
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192
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193 If all of those options are set to ``false``, Orthanc will only
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194 receive uncompressed transfer syntaxes (obviously provided that the
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195 source PACS itself supports DICOM transcoding).
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196
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197
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198 Using external conversion tools
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199 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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200
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201 The second solution consists in **applying an external conversion
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202 tool** to every DICOM image that is received by Orthanc. The standard
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203 command-line tools ``gdcmconv`` from `GDCM
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204 <http://gdcm.sourceforge.net/html/gdcmconv.html>`__ or ``dcmconv``
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205 from `DCMTK <https://support.dcmtk.org/docs/dcmconv.html>`__ can be
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206 used to change the transfer syntax of a given DICOM file. These tools
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207 can be invoked from a :ref:`Lua script <lua>` (check out
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208 ``OnStoredInstance()`` callback) or from an :ref:`Orthanc plugin
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209 <creating-plugins>` (check out
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210 ``OrthancPluginRegisterOnStoredInstanceCallback()`` function). A
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211 sample Lua script that converts every incoming DICOM file to the
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212 JPEG2k transfer syntax is `part of the Orthanc sources
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213 <https://hg.orthanc-server.com/orthanc/file/default/Resources/Samples/Lua/AutomatedJpeg2kCompression.lua>`__. Note
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214 that this solution makes no sense anymore in Orthanc 1.7.0, as it
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215 provides built-in support for transcoding.
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216
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217
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218 Transcoding buffer
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219 ^^^^^^^^^^^^^^^^^^
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220
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221 Finally, as a third solution, it is possible to **combine two Orthanc
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222 servers**, the first one being configured to accept any transfer
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223 syntax, and the second one being responsible to serve the DICOM files
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224 after conversion to uncompressed transfer syntax (which should be
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225 compatible with any workstation):
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226
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227 .. image:: ../images/Transcoding4.svg
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228 :align: center
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229 :width: 700px
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230
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231 In this solution, the first Orthanc server acts as a transient server
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232 that implements the decompression (i.e. it transcodes all the DICOM
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233 instances it receives to an uncompressed transfer syntax). To carry on
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234 the transcoding, this first Orthanc server can be:
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235
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236 * either an instance Orthanc >= 1.7.0, with transcoding enabled, or
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237
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238 * an instance of Orthanc (any version) equipped with a plugin or an
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239 external script to do the necessary conversions to an uncompressed
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240 transfer syntax, as explained in the second solution above.
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241
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242 Whenever a DICOM instance is received by the first Orthanc, the DICOM
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243 instance is thus transcoded. The first Orthanc server automatically
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244 forwards all the transcoded instances to the second instance of
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245 Orthanc, thanks to a :ref:`Lua script <lua>` or an :ref:`external
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246 script <rest>`, taking advantage of :ref:`Orthanc peering <peering>`.
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247
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248 Contrarily to the second solution, this solution has the advantage of
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249 better scalability (as decompression can be a time-consuming
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250 operation). The second instance of Orthanc can run even on a low-end
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251 computer, with any version of Orthanc.