Mercurial > hg > orthanc-book
annotate Sphinx/source/users/docker.rst @ 1027:60b0b7ea409b
migration to orthancteam
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
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| date | Fri, 02 Feb 2024 14:16:55 +0100 |
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| 54 | 1 .. _docker: |
| 2 .. highlight:: bash | |
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5 jodogne/orthanc Docker images |
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6 ============================= |
| 54 | 7 |
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8 .. toctree:: |
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9 :hidden: |
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11 docker-orthancteam.rst |
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13 |
| 54 | 14 .. contents:: |
| 15 :depth: 3 | |
| 16 | |
| 17 | |
| 18 Introduction | |
| 19 ------------ | |
| 20 | |
| 21 `Docker images <https://en.wikipedia.org/wiki/Docker_(software)>`__ | |
| 22 for the Orthanc core and its official plugins are freely available on | |
| 23 the `DockerHub platform <https://hub.docker.com/u/jodogne/>`__. The | |
| 24 source code of the corresponding Docker images is available on `GitHub | |
| 25 <https://github.com/jodogne/OrthancDocker>`__. | |
| 26 | |
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27 **Note about Orthanc vs. Orthanc Team Docker images:** |
| 229 | 28 |
| 29 * The ``jodogne/orthanc`` and ``jodogne/orthanc-plugins`` Docker | |
| 30 images that are described on this page are always kept in sync with | |
| 31 the latest releases of the Orthanc project, with a basic | |
| 32 configuration system that is inherited from the Debian packages | |
| 759 | 33 (i.e. manual edition of the configuration files). These images are |
| 34 most useful to **software developers and researchers**. | |
| 229 | 35 |
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36 * Our commercial partner `Orthanc Team <https://orthanc.team/>`__ also |
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37 `publishes separated Docker images |
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38 <https://hub.docker.com/r/orthancteam/orthanc>`__. These |
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39 ``orthancteam/orthanc`` images are used by the technical team of |
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40 the Orthanc Team company in order to provide professional support |
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41 to their customers, with a |
| 759 | 42 configuration system that can be tuned through **environment |
| 43 variables** (which is very handy if using ``docker-compose`` or | |
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44 Kubernetes). A :ref:`specific page <docker-orthancteam>` is |
| 759 | 45 available to describe how these images should be used. These images |
| 46 are targeted at **ops teams**. | |
| 229 | 47 |
| 48 **Note for CentOS users:** The Docker environment might be difficult to | |
| 54 | 49 configure on your platform. Hints are available on the `Orthanc Users |
| 50 discussion group | |
| 51 <https://groups.google.com/d/msg/orthanc-users/w-uPAknnRQc/-XhzBGSCAwAJ>`__. | |
| 52 | |
| 53 | |
| 54 Running the Orthanc core | |
| 55 ------------------------ | |
| 56 | |
| 57 The following command will start the core of Orthanc, with all the | |
| 58 plugins disabled:: | |
| 59 | |
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60 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc |
| 54 | 61 |
| 62 Once Orthanc is running, use Mozilla Firefox at URL | |
| 63 http://localhost:8042/ to interact with Orthanc. The default username | |
| 64 is ``orthanc`` and its password is ``orthanc``. | |
| 65 | |
| 66 The command above starts the mainline version of Orthanc, whose | |
| 69 | 67 development is in continuous progress. Do not forget to regularly |
| 68 update the Docker image to benefit from the latest features:: | |
| 69 | |
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70 $ docker pull jodogne/orthanc |
| 69 | 71 |
| 72 If more stability is required, you can select the official release of | |
| 73 Orthanc to be run:: | |
| 54 | 74 |
| 1021 | 75 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.3 |
| 54 | 76 |
| 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 | |
| 79 required for Orthanc to find its configuration files):: | |
| 80 | |
| 1021 | 81 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.3 /etc/orthanc --verbose |
| 54 | 82 |
| 83 | |
| 84 Usage, with plugins enabled | |
| 85 --------------------------- | |
| 86 | |
| 87 The following command will run the mainline version of the Orthanc | |
| 88 core, together with its :ref:`Web viewer <webviewer>`, its | |
| 89 :ref:`PostgreSQL support <postgresql>`, its :ref:`DICOMweb | |
| 90 implementation <dicomweb>`, and its :ref:`whole-slide imaging viewer | |
| 91 <wsi>`:: | |
| 92 | |
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93 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins |
| 54 | 94 |
| 365 | 95 Or you can also start a specific version of Orthanc for more stability:: |
| 96 | |
| 1021 | 97 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.12.3 |
| 365 | 98 |
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99 If you have an interest in the :ref:`Python plugin <python-plugin>`, |
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100 you can use the ``orthanc-python`` image. The latter image is a |
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101 heavier version of the ``orthanc-plugins`` image, as it embeds the |
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102 Python 3.7 interpreter. Here is how to start this image:: |
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103 |
| 365 | 104 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python |
| 1021 | 105 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.12.3 |
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106 |
| 54 | 107 |
| 108 Fine-tuning the configuration | |
| 109 ----------------------------- | |
| 110 | |
| 111 For security reasons, you should at least protect your instance of | |
| 112 Orthanc by changing this default user, in the ``RegisteredUsers`` | |
| 113 :ref:`configuration option <configuration>`. You will also probably | |
| 114 need to fine-tune other parameters, notably the list of the DICOM | |
| 115 modalities Orthanc knows about. | |
| 116 | |
| 117 You can generate a custom configuration file for Orthanc as follows:: | |
| 118 | |
| 1021 | 119 $ docker run --rm --entrypoint=cat jodogne/orthanc:1.12.3 /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 120 |
| 121 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart | |
| 122 Orthanc with your updated configuration:: | |
| 123 | |
| 1021 | 124 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc:1.12.3 |
| 54 | 125 |
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126 *Remark:* These Docker images automatically set the environment |
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127 variable ``MALLOC_ARENA_MAX`` to ``5`` in order to :ref:`control |
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128 memory usage <scalability-memory>`. This default setting can be |
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129 overriden by providing the option ``-e MALLOC_ARENA_MAX=1`` when |
| 386 | 130 invoking ``docker run`` (the value ``0`` corresponds to the default |
| 131 value). | |
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132 |
| 54 | 133 |
| 382 | 134 .. _docker-compose: |
| 135 | |
| 136 Configuration management using Docker Compose | |
| 137 --------------------------------------------- | |
| 138 | |
| 139 Depending on the context, the `Docker Compose tool | |
| 140 <https://docs.docker.com/compose/>`__ might be easier to use than the | |
| 141 plain Docker tool, as it allows replacing long command lines as above, | |
| 142 by plain configuration files. The trick here is to provide the JSON | |
| 143 configuration files to Orthanc as `secrets | |
| 144 <https://docs.docker.com/compose/compose-file/#secrets>`__ (note that | |
| 145 the related option ``configs`` could in theory be better, | |
| 146 unfortunately it is only available to `Docker Swarm | |
| 147 <https://github.com/docker/compose/issues/5110>`__). | |
| 148 | |
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149 .. highlight:: yaml |
| 382 | 150 |
| 151 First create the ``docker-compose.yml`` file as follows (this one uses | |
| 152 the `YAML file format <https://en.wikipedia.org/wiki/YAML>`__):: | |
| 153 | |
| 154 version: '3.1' # Secrets are only available since this version of Docker Compose | |
| 155 services: | |
| 156 orthanc: | |
| 1021 | 157 image: jodogne/orthanc-plugins:1.12.3 |
| 382 | 158 command: /run/secrets/ # Path to the configuration files (stored as secrets) |
| 159 ports: | |
| 402 | 160 - 4242:4242 |
| 382 | 161 - 8042:8042 |
| 162 secrets: | |
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163 - orthanc.json |
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164 environment: |
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165 - ORTHANC_NAME=HelloWorld |
| 382 | 166 secrets: |
| 167 orthanc.json: | |
| 168 file: orthanc.json | |
| 169 | |
| 170 .. highlight:: json | |
| 171 | |
| 172 Then, place the configuration file ``orthanc.json`` next to the | |
| 173 ``docker-compose.yml`` file. Here is a minimalist ``orthanc.json``:: | |
| 174 | |
| 175 { | |
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176 "Name" : "${ORTHANC_NAME} in Docker Compose", |
| 382 | 177 "RemoteAccessAllowed" : true |
| 178 } | |
| 179 | |
| 180 .. highlight:: bash | |
| 181 | |
| 182 This single configuration file should contain all the required | |
| 183 configuration options for Orthanc and all its plugins. The container | |
| 184 can then be started as follows:: | |
| 185 | |
| 186 $ docker-compose up | |
| 187 | |
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188 Note how the `environment variable |
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189 <https://docs.docker.com/compose/environment-variables/>`__ |
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190 ``ORTHANC_NAME`` has been used in order to easily adapt the |
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191 configuration of Orthanc. This results from the fact that Orthanc |
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192 injects :ref:`environment variables <orthanc-environment-variables>` |
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193 once reading the content of its configuration files (since Orthanc |
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194 1.5.0). |
| 382 | 195 |
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196 |
| 54 | 197 Making the Orthanc database persistent |
| 198 -------------------------------------- | |
| 199 | |
| 200 The filesystem of Docker containers is volatile (its content is | |
| 201 deleted once the container stops). You can make the Orthanc database | |
| 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.:: | |
| 204 | |
| 205 $ mkdir /tmp/orthanc-db | |
| 1021 | 206 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.12.3 |
| 54 | 207 |
| 208 | |
| 209 Whole-slide imaging support | |
| 210 --------------------------- | |
| 211 | |
| 212 The ``orthanc-plugins`` image includes support for :ref:`microscopic | |
| 213 whole-slide imaging (WSI) <wsi>`. For instance, the following command | |
| 214 will start the WSI viewer plugin transparently together with Orthanc:: | |
| 215 | |
| 1021 | 216 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins:1.12.3 |
| 54 | 217 |
| 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 | |
| 220 follows:: | |
| 221 | |
| 1021 | 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 |
| 54 | 223 |
| 224 This command needs a few explanations: | |
| 225 | |
| 226 * ``--link=orthanc-wsi:orthanc`` links the container running the | |
| 227 Dicomizer, to the Docker container running Orthanc that we started | |
| 228 just before. | |
| 229 * ``--entrypoint=OrthancWSIDicomizer`` specifies that the Dicomizer | |
| 230 must be run instead of the Orthanc server. | |
| 231 * ``-v /tmp/Source.tif:/tmp/Source.tif:ro`` maps the source image | |
| 232 ``/tmp/Source.tif`` on the host computer into the Orthanc container | |
| 233 as read-only file ``/tmp/Source.tif``. | |
| 234 * ``--orthanc=http://orthanc:8042/`` instructs the Dicomizer to push | |
| 235 images through the ``--link`` created above. | |
| 236 * ``--username=orthanc --password=orthanc`` correspond to the default | |
| 237 credentials of the ``orthanc-plugins`` image. | |
| 238 | |
| 239 Obviously, you are free to add all the options you wish (check out the | |
| 240 ``--help`` flag to list these options). In particular, the | |
| 241 ``--dataset`` option allows to specify DICOM tags, in the JSON file | |
| 242 format, so as to include them in the resulting DICOM series (the | |
| 243 option ``--sample-dataset`` prints a sample JSON file that has the | |
| 244 expected format). | |
| 245 | |
| 246 If you have a source image that is not a hierarchical TIFF, you must | |
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247 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__ |
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248 to decode it by adding the ``--openslide`` option:: |
| 54 | 249 |
| 1021 | 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 |
| 54 | 251 |
| 252 | |
| 253 PostgreSQL and Orthanc inside Docker | |
| 254 ------------------------------------ | |
| 255 | |
| 256 It is possible to run both Orthanc and PostgreSQL inside Docker. First, start the official PostgreSQL container:: | |
| 257 | |
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258 $ docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres |
| 54 | 259 |
| 260 Open another shell, and create a database to host the Orthanc database:: | |
| 261 | |
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262 $ docker run -it --link some-postgres:postgres --rm postgres sh -c 'echo "CREATE DATABASE orthanc;" | exec psql -h "$POSTGRES_PORT_5432_TCP_ADDR" -p "$POSTGRES_PORT_5432_TCP_PORT" -U postgres' |
| 54 | 263 |
| 264 You will have to type the password (cf. the environment variable | |
| 265 ``POSTGRES_PASSWORD`` above that it set to ``pgpassword``). Then, | |
| 266 retrieve the IP and the port of the PostgreSQL container, together | |
| 267 with the default Orthanc configuration file:: | |
| 268 | |
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269 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres |
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270 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres |
| 1021 | 271 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins:1.12.3 /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 272 |
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273 .. highlight:: text |
| 54 | 274 |
| 275 Add the following section to ``/tmp/orthanc.json`` (adapting the | |
| 276 values Host and Port to what docker inspect said above):: | |
| 277 | |
| 278 "PostgreSQL" : { | |
| 279 "EnableIndex" : true, | |
| 280 "EnableStorage" : true, | |
| 281 "Host" : "172.17.0.38", | |
| 282 "Port" : 5432, | |
| 283 "Database" : "orthanc", | |
| 284 "Username" : "postgres", | |
| 285 "Password" : "pgpassword" | |
| 286 } | |
| 287 | |
| 288 .. highlight:: bash | |
| 289 | |
| 290 Finally, you can start Orthanc:: | |
| 291 | |
| 1021 | 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 |
| 54 | 293 |
| 294 | |
| 295 Debugging | |
| 296 --------- | |
| 297 | |
| 176 | 298 .. highlight:: text |
| 299 | |
| 54 | 300 For debugging purpose, you can start an interactive bash session as |
| 301 follows:: | |
| 302 | |
| 1021 | 303 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc:1.12.3 |
| 304 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins:1.12.3 |