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comparison Sphinx/source/users/docker.rst @ 1075:d2be251975d1 Orthanc-1.12.4

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Orthanc 1.12.4
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 05 Jun 2024 20:18:43 +0200
parents 60b0b7ea409b
children 567de375e89f
comparison
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1074:32ac45058512 1075:d2be251975d1
70 $ docker pull jodogne/orthanc 70 $ docker pull jodogne/orthanc
71 71
72 If more stability is required, you can select the official release of 72 If more stability is required, you can select the official release of
73 Orthanc to be run:: 73 Orthanc to be run::
74 74
75 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.3 75 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.4
76 76
77 Passing additional command-line options (e.g. to make Orthanc verbose) 77 Passing additional command-line options (e.g. to make Orthanc verbose)
78 can be done as follows (note the ``/etc/orthanc`` option that is 78 can be done as follows (note the ``/etc/orthanc`` option that is
79 required for Orthanc to find its configuration files):: 79 required for Orthanc to find its configuration files)::
80 80
81 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.3 /etc/orthanc --verbose 81 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.4 /etc/orthanc --verbose
82 82
83 83
84 Usage, with plugins enabled 84 Usage, with plugins enabled
85 --------------------------- 85 ---------------------------
86 86
92 92
93 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins 93 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins
94 94
95 Or you can also start a specific version of Orthanc for more stability:: 95 Or you can also start a specific version of Orthanc for more stability::
96 96
97 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.12.3 97 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.12.4
98 98
99 If you have an interest in the :ref:`Python plugin <python-plugin>`, 99 If you have an interest in the :ref:`Python plugin <python-plugin>`,
100 you can use the ``orthanc-python`` image. The latter image is a 100 you can use the ``orthanc-python`` image. The latter image is a
101 heavier version of the ``orthanc-plugins`` image, as it embeds the 101 heavier version of the ``orthanc-plugins`` image, as it embeds the
102 Python 3.7 interpreter. Here is how to start this image:: 102 Python 3.7 interpreter. Here is how to start this image::
103 103
104 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python 104 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python
105 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.12.3 105 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.12.4
106 106
107 107
108 Fine-tuning the configuration 108 Fine-tuning the configuration
109 ----------------------------- 109 -----------------------------
110 110
114 need to fine-tune other parameters, notably the list of the DICOM 114 need to fine-tune other parameters, notably the list of the DICOM
115 modalities Orthanc knows about. 115 modalities Orthanc knows about.
116 116
117 You can generate a custom configuration file for Orthanc as follows:: 117 You can generate a custom configuration file for Orthanc as follows::
118 118
119 $ docker run --rm --entrypoint=cat jodogne/orthanc:1.12.3 /etc/orthanc/orthanc.json > /tmp/orthanc.json 119 $ docker run --rm --entrypoint=cat jodogne/orthanc:1.12.4 /etc/orthanc/orthanc.json > /tmp/orthanc.json
120 120
121 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart 121 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart
122 Orthanc with your updated configuration:: 122 Orthanc with your updated configuration::
123 123
124 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc:1.12.3 124 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc:1.12.4
125 125
126 *Remark:* These Docker images automatically set the environment 126 *Remark:* These Docker images automatically set the environment
127 variable ``MALLOC_ARENA_MAX`` to ``5`` in order to :ref:`control 127 variable ``MALLOC_ARENA_MAX`` to ``5`` in order to :ref:`control
128 memory usage <scalability-memory>`. This default setting can be 128 memory usage <scalability-memory>`. This default setting can be
129 overriden by providing the option ``-e MALLOC_ARENA_MAX=1`` when 129 overriden by providing the option ``-e MALLOC_ARENA_MAX=1`` when
152 the `YAML file format <https://en.wikipedia.org/wiki/YAML>`__):: 152 the `YAML file format <https://en.wikipedia.org/wiki/YAML>`__)::
153 153
154 version: '3.1' # Secrets are only available since this version of Docker Compose 154 version: '3.1' # Secrets are only available since this version of Docker Compose
155 services: 155 services:
156 orthanc: 156 orthanc:
157 image: jodogne/orthanc-plugins:1.12.3 157 image: jodogne/orthanc-plugins:1.12.4
158 command: /run/secrets/ # Path to the configuration files (stored as secrets) 158 command: /run/secrets/ # Path to the configuration files (stored as secrets)
159 ports: 159 ports:
160 - 4242:4242 160 - 4242:4242
161 - 8042:8042 161 - 8042:8042
162 secrets: 162 secrets:
201 deleted once the container stops). You can make the Orthanc database 201 deleted once the container stops). You can make the Orthanc database
202 persistent by mapping the ``/var/lib/orthanc/db`` folder of the 202 persistent by mapping the ``/var/lib/orthanc/db`` folder of the
203 container to some path in the filesystem of your Linux host, e.g.:: 203 container to some path in the filesystem of your Linux host, e.g.::
204 204
205 $ mkdir /tmp/orthanc-db 205 $ mkdir /tmp/orthanc-db
206 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.12.3 206 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.12.4
207 207
208 208
209 Whole-slide imaging support 209 Whole-slide imaging support
210 --------------------------- 210 ---------------------------
211 211
212 The ``orthanc-plugins`` image includes support for :ref:`microscopic 212 The ``orthanc-plugins`` image includes support for :ref:`microscopic
213 whole-slide imaging (WSI) <wsi>`. For instance, the following command 213 whole-slide imaging (WSI) <wsi>`. For instance, the following command
214 will start the WSI viewer plugin transparently together with Orthanc:: 214 will start the WSI viewer plugin transparently together with Orthanc::
215 215
216 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins:1.12.3 216 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins:1.12.4
217 217
218 Note that we gave the name ``orthanc-wsi`` to this new Docker 218 Note that we gave the name ``orthanc-wsi`` to this new Docker
219 container. Then, the Dicomizer command-line tool can be invoked as 219 container. Then, the Dicomizer command-line tool can be invoked as
220 follows:: 220 follows::
221 221
222 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins:1.12.3 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif 222 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins:1.12.4 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif
223 223
224 This command needs a few explanations: 224 This command needs a few explanations:
225 225
226 * ``--link=orthanc-wsi:orthanc`` links the container running the 226 * ``--link=orthanc-wsi:orthanc`` links the container running the
227 Dicomizer, to the Docker container running Orthanc that we started 227 Dicomizer, to the Docker container running Orthanc that we started
245 245
246 If you have a source image that is not a hierarchical TIFF, you must 246 If you have a source image that is not a hierarchical TIFF, you must
247 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__ 247 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__
248 to decode it by adding the ``--openslide`` option:: 248 to decode it by adding the ``--openslide`` option::
249 249
250 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins:1.12.3 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs 250 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins:1.12.4 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs
251 251
252 252
253 PostgreSQL and Orthanc inside Docker 253 PostgreSQL and Orthanc inside Docker
254 ------------------------------------ 254 ------------------------------------
255 255
266 retrieve the IP and the port of the PostgreSQL container, together 266 retrieve the IP and the port of the PostgreSQL container, together
267 with the default Orthanc configuration file:: 267 with the default Orthanc configuration file::
268 268
269 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres 269 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres
270 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres 270 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres
271 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins:1.12.3 /etc/orthanc/orthanc.json > /tmp/orthanc.json 271 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins:1.12.4 /etc/orthanc/orthanc.json > /tmp/orthanc.json
272 272
273 .. highlight:: text 273 .. highlight:: text
274 274
275 Add the following section to ``/tmp/orthanc.json`` (adapting the 275 Add the following section to ``/tmp/orthanc.json`` (adapting the
276 values Host and Port to what docker inspect said above):: 276 values Host and Port to what docker inspect said above)::
287 287
288 .. highlight:: bash 288 .. highlight:: bash
289 289
290 Finally, you can start Orthanc:: 290 Finally, you can start Orthanc::
291 291
292 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins:1.12.3 292 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins:1.12.4
293 293
294 294
295 Debugging 295 Debugging
296 --------- 296 ---------
297 297
298 .. highlight:: text 298 .. highlight:: text
299 299
300 For debugging purpose, you can start an interactive bash session as 300 For debugging purpose, you can start an interactive bash session as
301 follows:: 301 follows::
302 302
303 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc:1.12.3 303 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc:1.12.4
304 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins:1.12.3 304 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins:1.12.4