Mercurial > hg > orthanc-book

comparison Sphinx/source/users/docker.rst @ 1021:a3436ae3709c Orthanc-1.12.3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Orthanc 1.12.3
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 31 Jan 2024 14:01:54 +0100
parents 23a54088d604
children 5d4701d8fe28
comparison
equal deleted inserted replaced
1020:3f4a7ee8033b 1021:a3436ae3709c
73 $ docker pull jodogne/orthanc 73 $ docker pull jodogne/orthanc
74 74
75 If more stability is required, you can select the official release of 75 If more stability is required, you can select the official release of
76 Orthanc to be run:: 76 Orthanc to be run::
77 77
78 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.2 78 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.3
79 79
80 Passing additional command-line options (e.g. to make Orthanc verbose) 80 Passing additional command-line options (e.g. to make Orthanc verbose)
81 can be done as follows (note the ``/etc/orthanc`` option that is 81 can be done as follows (note the ``/etc/orthanc`` option that is
82 required for Orthanc to find its configuration files):: 82 required for Orthanc to find its configuration files)::
83 83
84 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.2 /etc/orthanc --verbose 84 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.3 /etc/orthanc --verbose
85 85
86 86
87 Usage, with plugins enabled 87 Usage, with plugins enabled
88 --------------------------- 88 ---------------------------
89 89
95 95
96 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins 96 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins
97 97
98 Or you can also start a specific version of Orthanc for more stability:: 98 Or you can also start a specific version of Orthanc for more stability::
99 99
100 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.12.2 100 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.12.3
101 101
102 If you have an interest in the :ref:`Python plugin <python-plugin>`, 102 If you have an interest in the :ref:`Python plugin <python-plugin>`,
103 you can use the ``orthanc-python`` image. The latter image is a 103 you can use the ``orthanc-python`` image. The latter image is a
104 heavier version of the ``orthanc-plugins`` image, as it embeds the 104 heavier version of the ``orthanc-plugins`` image, as it embeds the
105 Python 3.7 interpreter. Here is how to start this image:: 105 Python 3.7 interpreter. Here is how to start this image::
106 106
107 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python 107 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python
108 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.12.2 108 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.12.3
109 109
110 110
111 Fine-tuning the configuration 111 Fine-tuning the configuration
112 ----------------------------- 112 -----------------------------
113 113
117 need to fine-tune other parameters, notably the list of the DICOM 117 need to fine-tune other parameters, notably the list of the DICOM
118 modalities Orthanc knows about. 118 modalities Orthanc knows about.
119 119
120 You can generate a custom configuration file for Orthanc as follows:: 120 You can generate a custom configuration file for Orthanc as follows::
121 121
122 $ docker run --rm --entrypoint=cat jodogne/orthanc:1.12.2 /etc/orthanc/orthanc.json > /tmp/orthanc.json 122 $ docker run --rm --entrypoint=cat jodogne/orthanc:1.12.3 /etc/orthanc/orthanc.json > /tmp/orthanc.json
123 123
124 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart 124 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart
125 Orthanc with your updated configuration:: 125 Orthanc with your updated configuration::
126 126
127 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc:1.12.2 127 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc:1.12.3
128 128
129 *Remark:* These Docker images automatically set the environment 129 *Remark:* These Docker images automatically set the environment
130 variable ``MALLOC_ARENA_MAX`` to ``5`` in order to :ref:`control 130 variable ``MALLOC_ARENA_MAX`` to ``5`` in order to :ref:`control
131 memory usage <scalability-memory>`. This default setting can be 131 memory usage <scalability-memory>`. This default setting can be
132 overriden by providing the option ``-e MALLOC_ARENA_MAX=1`` when 132 overriden by providing the option ``-e MALLOC_ARENA_MAX=1`` when
155 the `YAML file format <https://en.wikipedia.org/wiki/YAML>`__):: 155 the `YAML file format <https://en.wikipedia.org/wiki/YAML>`__)::
156 156
157 version: '3.1' # Secrets are only available since this version of Docker Compose 157 version: '3.1' # Secrets are only available since this version of Docker Compose
158 services: 158 services:
159 orthanc: 159 orthanc:
160 image: jodogne/orthanc-plugins:1.12.2 160 image: jodogne/orthanc-plugins:1.12.3
161 command: /run/secrets/ # Path to the configuration files (stored as secrets) 161 command: /run/secrets/ # Path to the configuration files (stored as secrets)
162 ports: 162 ports:
163 - 4242:4242 163 - 4242:4242
164 - 8042:8042 164 - 8042:8042
165 secrets: 165 secrets:
204 deleted once the container stops). You can make the Orthanc database 204 deleted once the container stops). You can make the Orthanc database
205 persistent by mapping the ``/var/lib/orthanc/db`` folder of the 205 persistent by mapping the ``/var/lib/orthanc/db`` folder of the
206 container to some path in the filesystem of your Linux host, e.g.:: 206 container to some path in the filesystem of your Linux host, e.g.::
207 207
208 $ mkdir /tmp/orthanc-db 208 $ mkdir /tmp/orthanc-db
209 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.12.2 209 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.12.3
210 210
211 211
212 Whole-slide imaging support 212 Whole-slide imaging support
213 --------------------------- 213 ---------------------------
214 214
215 The ``orthanc-plugins`` image includes support for :ref:`microscopic 215 The ``orthanc-plugins`` image includes support for :ref:`microscopic
216 whole-slide imaging (WSI) <wsi>`. For instance, the following command 216 whole-slide imaging (WSI) <wsi>`. For instance, the following command
217 will start the WSI viewer plugin transparently together with Orthanc:: 217 will start the WSI viewer plugin transparently together with Orthanc::
218 218
219 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins:1.12.2 219 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins:1.12.3
220 220
221 Note that we gave the name ``orthanc-wsi`` to this new Docker 221 Note that we gave the name ``orthanc-wsi`` to this new Docker
222 container. Then, the Dicomizer command-line tool can be invoked as 222 container. Then, the Dicomizer command-line tool can be invoked as
223 follows:: 223 follows::
224 224
225 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins:1.12.2 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif 225 $ 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
226 226
227 This command needs a few explanations: 227 This command needs a few explanations:
228 228
229 * ``--link=orthanc-wsi:orthanc`` links the container running the 229 * ``--link=orthanc-wsi:orthanc`` links the container running the
230 Dicomizer, to the Docker container running Orthanc that we started 230 Dicomizer, to the Docker container running Orthanc that we started
248 248
249 If you have a source image that is not a hierarchical TIFF, you must 249 If you have a source image that is not a hierarchical TIFF, you must
250 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__ 250 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__
251 to decode it by adding the ``--openslide`` option:: 251 to decode it by adding the ``--openslide`` option::
252 252
253 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins:1.12.2 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs 253 $ 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
254 254
255 255
256 PostgreSQL and Orthanc inside Docker 256 PostgreSQL and Orthanc inside Docker
257 ------------------------------------ 257 ------------------------------------
258 258
269 retrieve the IP and the port of the PostgreSQL container, together 269 retrieve the IP and the port of the PostgreSQL container, together
270 with the default Orthanc configuration file:: 270 with the default Orthanc configuration file::
271 271
272 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres 272 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres
273 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres 273 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres
274 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins:1.12.2 /etc/orthanc/orthanc.json > /tmp/orthanc.json 274 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins:1.12.3 /etc/orthanc/orthanc.json > /tmp/orthanc.json
275 275
276 .. highlight:: text 276 .. highlight:: text
277 277
278 Add the following section to ``/tmp/orthanc.json`` (adapting the 278 Add the following section to ``/tmp/orthanc.json`` (adapting the
279 values Host and Port to what docker inspect said above):: 279 values Host and Port to what docker inspect said above)::
290 290
291 .. highlight:: bash 291 .. highlight:: bash
292 292
293 Finally, you can start Orthanc:: 293 Finally, you can start Orthanc::
294 294
295 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins:1.12.2 295 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins:1.12.3
296 296
297 297
298 Debugging 298 Debugging
299 --------- 299 ---------
300 300
301 .. highlight:: text 301 .. highlight:: text
302 302
303 For debugging purpose, you can start an interactive bash session as 303 For debugging purpose, you can start an interactive bash session as
304 follows:: 304 follows::
305 305
306 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc:1.12.2 306 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc:1.12.3
307 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins:1.12.2 307 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins:1.12.3