Mercurial > hg > orthanc-book
annotate Sphinx/source/faq/transcoding.rst @ 660:a6e371768a70
dicom-as-json
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 29 Apr 2021 12:41:31 +0200 |
| parents | 9bee264de083 |
| children | 1316bc62b5d5 |
| rev | line source |
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| 275 | 1 .. _transcoding: |
| 2 | |
| 3 Transcoding of DICOM files | |
| 4 ========================== | |
| 5 | |
| 411 | 6 .. contents:: |
| 7 | |
| 8 | |
| 275 | 9 General information |
| 10 ------------------- | |
| 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. |
| 275 | 14 |
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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. |
| 275 | 23 |
| 24 | |
| 25 Motivation for transcoding | |
| 26 -------------------------- | |
| 27 | |
| 28 Let's consider the following basic workflow, in which some imaging | |
| 29 workstation must access a medical image that originates from a PACS | |
| 30 and that is served through an Orthanc proxy: | |
| 31 | |
| 32 .. image:: ../images/Transcoding1.svg | |
| 33 :align: center | |
| 34 :width: 700px | |
| 35 | |
| 36 This is quite a common situation, e.g. in university hospitals where | |
| 37 researchers must access medical images without having authorization to | |
| 38 log in the clinical PACS. It is also common if the main PACS restricts | |
| 39 the number of workstations that can directly be connected to it, or if | |
| 40 Orthanc acts as gateway through Internet. | |
| 41 | |
| 42 The problem is that the software running on workstations might not be | |
| 43 able to display some DICOM transfer syntaxes. This is especially true | |
| 44 in research software, that is often limited to uncompressed transfer | |
| 45 syntaxes. For instance, let's consider the following scenario where a | |
| 46 workstation wants to access an image from the PACS: | |
| 47 | |
| 48 .. image:: ../images/Transcoding2.svg | |
| 49 :align: center | |
| 50 :width: 700px | |
| 51 | |
| 52 A typical PACS system will decide, when requested to export an image | |
| 53 using DICOM C-Store, to compress the image in order to reduce the | |
| 54 network bandwidth and the storage requirements. Orthanc is fine with | |
| 55 it: As a vendor neutral archive, Orthanc can basically | |
| 56 receive/store/transmit any DICOM transfer syntax. Unfortunately, this | |
| 57 might not be the case of the target workstation, that is often limited | |
| 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 |
| 275 | 60 depicted above, because the PACS has decided to send the DICOM image |
| 61 using the JPEG2k transfer syntax). | |
| 62 | |
| 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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70 |
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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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74 |
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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 Lossless. |
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92 |
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93 NB: Starting with Orthanc 1.8.2, the option |
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94 ``IngestTranscodingOfUncompressed`` |
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95 (resp. ``IngestTranscodingOfCompressed``) is available to control |
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96 whether the ingest transcoding is applied to uncompressed transfer |
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97 syntaxes (resp. compressed transfer syntaxes). By "uncompressed" |
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98 transfer syntaxes, we mean Little Endian Implicit, Little Endian |
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99 Explicit, or Big Endian Explicit. By default, these options are |
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100 considered as equal to ``true``, meaning that all the transfer |
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101 syntaxes are transcoded. |
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102 |
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103 * **Decompression while sending instances using the DICOM protocol**. |
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104 Orthanc can be configured to automatically decompress DICOM images |
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105 on its outgoing connections, if the remote modality does not support |
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106 the compressed transfer syntax of the source DICOM instances. This |
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107 feature is available for both :ref:`DICOM C-Move and C-Get commands |
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108 <dicom-move>`. Note that Orthanc won't transcode DICOM instances to |
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109 a compressed transfer syntax over the DICOM protocol. |
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110 |
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111 By default, this automated decompression is enabled. This might be |
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112 undesirable if you want to limit the resources that are used by |
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113 Orthanc. As a consequence, you can disable this feature either |
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114 globally (by setting configuration option ``TranscodeDicomProtocol`` |
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115 to ``false``), or on a per-modality basis (by setting the option |
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116 ``AllowTranscoding`` to ``false`` in the ``DicomModalities`` |
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117 section). |
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118 |
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119 .. highlight:: bash |
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120 |
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121 * **Transcoding while sending instances to an Orthanc peer**. The |
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122 ``/peers/{id}/store`` route in the Orthanc REST API allows to send |
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123 DICOM resources (patients, studies, series or instances) to |
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124 :ref:`another Orthanc server over HTTP/HTTPS <peering>`. Starting |
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125 with Orthanc 1.7.0, the ``Transcode`` option can be used in the JSON |
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126 POST body to instruct to transcode the DICOM files before they are |
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127 sent. For instance:: |
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128 |
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129 $ 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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130 |
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131 * **Transcoding using the REST API**. Starting with Orthanc 1.7.0, |
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132 some routes in the REST API also accept the ``Transcode`` option |
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133 in their JSON POST body. Those routes notably include: |
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134 |
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135 * The routes to create ZIP files or DICOMDIR archives (``.../media`` |
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136 and ``.../archive``). |
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137 |
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138 * The routes to modify DICOM resources |
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139 (``/{patients|studies|series|instances}/{id}/modify``). |
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140 |
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141 Importantly, if you need to transcode JPEG2k DICOM instances, you'll |
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142 have to install the :ref:`GDCM plugin <gdcm>` that replaces the |
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143 built-in transcoder of Orthanc based on DCMTK, by the GDCM transcoder. |
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144 |
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145 The following :ref:`advanced configuration options <configuration>` |
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146 are also available to control transcoding: |
| 275 | 147 |
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148 * ``BuiltinDecoderTranscoderOrder`` controls the transcoder that is |
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149 used by Orthanc. It specifies whether the built-in transcoder of |
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150 Orthanc (that uses DCMTK) is applied before or after the transcoding |
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151 plugins, or not applied at all. "After" means that the built-in |
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152 transcoder is applied if all the transcoding plugins have failed to |
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153 transcode the image. |
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154 |
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155 * ``DicomLossyTranscodingQuality`` controls the quality level of lossy |
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156 compression (notably for JPEG transcoding). |
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157 |
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158 |
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159 Solutions to avoid transcoding |
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160 ------------------------------ |
| 275 | 161 |
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162 Up to release 1.6.1, Orthanc didn't feature support for transcoding |
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163 DICOM instances. In other words, the Orthanc core never changed the |
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164 :ref:`transfer syntax <dicom-pixel-data>` of some DICOM instance when |
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165 it had to send it to another modality using the DICOM protocol. |
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166 |
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167 Three workarounds were available to bypass the need for DICOM |
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168 transcoding in Orthanc <= 1.6.1. These workarounds are still valid in |
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169 Orthanc >= 1.7.0, if transcoding is undesirable (e.g. if Orthanc is |
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170 being run on a computer with sparse CPU/RAM resources). |
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171 |
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172 |
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173 Refusing transfer syntaxes |
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174 ^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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175 |
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176 The first solution consists in making Orthanc **refuse to accept the |
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177 transfer syntaxes** that are not supported by the workstation. This is |
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178 depicted in the following diagram: |
| 275 | 179 |
| 180 .. image:: ../images/Transcoding3.svg | |
| 181 :align: center | |
| 182 :width: 700px | |
| 183 | |
| 184 .. highlight:: json | |
| 185 | |
| 186 If Orthanc tells the PACS that is doesn't accept, say, DICOM JPEG2k, | |
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187 the source PACS will be aware of this, and will take care of |
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188 transcoding the DICOM files before they are sent to Orthanc. This is |
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189 the role of the following :ref:`configuration options <configuration>` |
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190 that specifies which transfer syntaxes are accepted by Orthanc:: |
| 275 | 191 |
| 192 { | |
| 193 "DeflatedTransferSyntaxAccepted" : true, | |
| 194 "JpegTransferSyntaxAccepted" : true, | |
| 195 "Jpeg2000TransferSyntaxAccepted" : true, | |
| 196 "JpegLosslessTransferSyntaxAccepted" : true, | |
| 197 "JpipTransferSyntaxAccepted" : true, | |
| 198 "Mpeg2TransferSyntaxAccepted" : true, | |
| 199 "RleTransferSyntaxAccepted" : true, | |
| 200 "UnknownSopClassAccepted" : false | |
| 201 } | |
| 202 | |
| 203 If all of those options are set to ``false``, Orthanc will only | |
| 204 receive uncompressed transfer syntaxes (obviously provided that the | |
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205 source PACS itself supports DICOM transcoding). |
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206 |
| 275 | 207 |
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208 Using external conversion tools |
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209 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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210 |
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211 The second solution consists in **applying an external conversion |
| 275 | 212 tool** to every DICOM image that is received by Orthanc. The standard |
| 213 command-line tools ``gdcmconv`` from `GDCM | |
| 214 <http://gdcm.sourceforge.net/html/gdcmconv.html>`__ or ``dcmconv`` | |
| 215 from `DCMTK <https://support.dcmtk.org/docs/dcmconv.html>`__ can be | |
| 216 used to change the transfer syntax of a given DICOM file. These tools | |
| 217 can be invoked from a :ref:`Lua script <lua>` (check out | |
| 218 ``OnStoredInstance()`` callback) or from an :ref:`Orthanc plugin | |
| 219 <creating-plugins>` (check out | |
| 220 ``OrthancPluginRegisterOnStoredInstanceCallback()`` function). A | |
| 221 sample Lua script that converts every incoming DICOM file to the | |
| 222 JPEG2k transfer syntax is `part of the Orthanc sources | |
| 449 | 223 <https://hg.orthanc-server.com/orthanc/file/default/OrthancServer/Resources/Samples/Lua/AutomatedJpeg2kCompression.lua>`__. Note |
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224 that this solution makes no sense anymore in Orthanc 1.7.0, as it |
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225 provides built-in support for transcoding. |
| 275 | 226 |
| 227 | |
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228 Transcoding buffer |
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229 ^^^^^^^^^^^^^^^^^^ |
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230 |
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231 Finally, as a third solution, it is possible to **combine two Orthanc |
| 275 | 232 servers**, the first one being configured to accept any transfer |
| 233 syntax, and the second one being responsible to serve the DICOM files | |
| 234 after conversion to uncompressed transfer syntax (which should be | |
| 235 compatible with any workstation): | |
| 236 | |
| 237 .. image:: ../images/Transcoding4.svg | |
| 238 :align: center | |
| 239 :width: 700px | |
| 240 | |
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241 In this solution, the first Orthanc server acts as a transient server |
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242 that implements the decompression (i.e. it transcodes all the DICOM |
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243 instances it receives to an uncompressed transfer syntax). To carry on |
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244 the transcoding, this first Orthanc server can be: |
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245 |
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246 * either an instance Orthanc >= 1.7.0, with transcoding enabled, or |
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247 |
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248 * an instance of Orthanc (any version) equipped with a plugin or an |
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249 external script to do the necessary conversions to an uncompressed |
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250 transfer syntax, as explained in the second solution above. |
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251 |
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252 Whenever a DICOM instance is received by the first Orthanc, the DICOM |
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253 instance is thus transcoded. The first Orthanc server automatically |
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254 forwards all the transcoded instances to the second instance of |
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255 Orthanc, thanks to a :ref:`Lua script <lua>` or an :ref:`external |
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256 script <rest>`, taking advantage of :ref:`Orthanc peering <peering>`. |
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257 |
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258 Contrarily to the second solution, this solution has the advantage of |
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259 better scalability (as decompression can be a time-consuming |
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260 operation). The second instance of Orthanc can run even on a low-end |
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261 computer, with any version of Orthanc. |