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updating old documentation about transcoding
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 22 May 2020 10:10:21 +0200
parents 24b1c64002b8
children 943515b68158
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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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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 **uncompress** 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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23
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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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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.
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71
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72 * Explanation of DICOM protocol (transparent transcoding from
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73 compressed transfer syntaxes to uncompressed transfer syntaxes).
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74
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75 * ``TranscodeDicomProtocol`` global configuration option
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76
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77 * ``AllowTranscoding`` in ``DicomModalities`` configuration option
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78
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79 * ``/instances/.../modify`` route: ``Transcode`` option
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80
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81 * ``IngestTranscoding``
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82
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83 * ``BuiltinDecoderTranscoderOrder``
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84
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85 * ``DicomLossyCompressionLevel``
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86
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87 * Routes to create archives: ``Transcode`` option
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88
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89 You might therefore have to **disable
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90 transfer syntaxes** by setting the ``*TransferSyntaxAccepted`` options
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91 to ``false`` in the :ref:`configuration file of Orthanc
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92 <configuration>` (by default, all the transfer syntaxes are enabled).
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93
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94
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95 Solutions to avoid transcoding
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96 ------------------------------
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97
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98 Up to release 1.6.1, Orthanc didn't feature support for transcoding
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99 DICOM instances. In other words, the Orthanc core never changed the
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100 :ref:`transfer syntax <dicom-pixel-data>` of some DICOM instance when
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101 it had to send it to another modality using the DICOM protocol.
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102
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103 Three workarounds were available to bypass the need for DICOM
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104 transcoding in Orthanc <= 1.6.1. These workarounds are still valid in
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105 Orthanc >= 1.7.0, if transcoding is undesirable (e.g. if Orthanc is
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106 being run on a computer with sparse CPU/RAM resources).
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107
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108
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109 Refusing transfer syntaxes
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110 ^^^^^^^^^^^^^^^^^^^^^^^^^^
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111
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112 The first solution consists in making Orthanc **refuse to accept the
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113 transfer syntaxes** that are not supported by the workstation. This is
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114 depicted in the following diagram:
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115
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116 .. image:: ../images/Transcoding3.svg
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117 :align: center
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118 :width: 700px
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119
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120 .. highlight:: json
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121
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122 If Orthanc tells the PACS that is doesn't accept, say, DICOM JPEG2k,
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123 the source PACS will be aware of this, and will take care of
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124 transcoding the DICOM files before they are sent to Orthanc. This is
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125 the role of the following :ref:`configuration options <configuration>`
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126 that specifies which transfer syntaxes are accepted by Orthanc::
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127
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128 {
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129 "DeflatedTransferSyntaxAccepted" : true,
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130 "JpegTransferSyntaxAccepted" : true,
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131 "Jpeg2000TransferSyntaxAccepted" : true,
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132 "JpegLosslessTransferSyntaxAccepted" : true,
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133 "JpipTransferSyntaxAccepted" : true,
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134 "Mpeg2TransferSyntaxAccepted" : true,
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135 "RleTransferSyntaxAccepted" : true,
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136 "UnknownSopClassAccepted" : false
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137 }
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138
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139 If all of those options are set to ``false``, Orthanc will only
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140 receive uncompressed transfer syntaxes (obviously provided that the
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141 source PACS itself supports DICOM transcoding).
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142
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143
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144 Using external conversion tools
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145 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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146
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147 The second solution consists in **applying an external conversion
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148 tool** to every DICOM image that is received by Orthanc. The standard
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149 command-line tools ``gdcmconv`` from `GDCM
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150 <http://gdcm.sourceforge.net/html/gdcmconv.html>`__ or ``dcmconv``
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151 from `DCMTK <https://support.dcmtk.org/docs/dcmconv.html>`__ can be
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152 used to change the transfer syntax of a given DICOM file. These tools
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153 can be invoked from a :ref:`Lua script <lua>` (check out
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154 ``OnStoredInstance()`` callback) or from an :ref:`Orthanc plugin
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155 <creating-plugins>` (check out
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156 ``OrthancPluginRegisterOnStoredInstanceCallback()`` function). A
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157 sample Lua script that converts every incoming DICOM file to the
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158 JPEG2k transfer syntax is `part of the Orthanc sources
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159 <https://hg.orthanc-server.com/orthanc/file/default/Resources/Samples/Lua/AutomatedJpeg2kCompression.lua>`__. Note
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160 that this solution makes no sense anymore in Orthanc 1.7.0, as it
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161 provides built-in support for transcoding.
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162
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163
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164 Transcoding buffer
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165 ^^^^^^^^^^^^^^^^^^
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166
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167 Finally, as a third solution, it is possible to **combine two Orthanc
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168 servers**, the first one being configured to accept any transfer
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169 syntax, and the second one being responsible to serve the DICOM files
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170 after conversion to uncompressed transfer syntax (which should be
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171 compatible with any workstation):
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172
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173 .. image:: ../images/Transcoding4.svg
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174 :align: center
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175 :width: 700px
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176
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177 In this solution, the first Orthanc server acts as a transient server
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178 that implements the decompression (i.e. it transcodes all the DICOM
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179 instances it receives to an uncompressed transfer syntax). To carry on
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180 the transcoding, this first Orthanc server can be:
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181
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182 * either an instance Orthanc >= 1.7.0, with transcoding enabled, or
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183
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184 * an instance of Orthanc (any version) equipped with a plugin or an
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185 external script to do the necessary conversions to an uncompressed
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186 transfer syntax, as explained in the second solution above.
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187
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188 Whenever a DICOM instance is received by the first Orthanc, the DICOM
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189 instance is thus transcoded. The first Orthanc server automatically
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190 forwards all the transcoded instances to the second instance of
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191 Orthanc, thanks to a :ref:`Lua script <lua>` or an :ref:`external
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192 script <rest>`, taking advantage of :ref:`Orthanc peering <peering>`.
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193
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194 Contrarily to the second solution, this solution has the advantage of
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195 better scalability (as decompression can be a time-consuming
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196 operation). The second instance of Orthanc can run even on a low-end
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197 computer, with any version of Orthanc.