orthancteam/orthanc Docker images¶
Contents
Warning
Starting from February 2024, the osimis/orthanc
Docker images have been renamed
into orthancteam/orthanc
. The osimis/orthanc
images won’t be updated anymore
therefore you should switch to the orthancteam/orthanc
images.
Note that all old tags released prior to February 2024 have been copied into orthancteam/orthanc
as well so, even if you are using an old version, you should update the name in your setup.
The name is the only thing that has changed. The content and build procedure are identical.
The orthancteam/orthanc
images are updated regularly. The release notes are available here.
Warning
Starting from the 22.6.1
release, we are providing 2 types of images:
the default image with the usual tag: e.g
22.6.1
the full image with a e.g
22.6.1-full
tag
The default image is suitable for 99.9% of users.
You should use the full image only if you need to use one of these:
the Azure Blob storage plugin
the Google Cloud storage plugin
the ODBC plugin with SQL Server (msodbcsql18 is preinstalled)
Introduction¶
Our commercial partner Orthanc Team
publishes separated Docker images.
These images have been designed to be used with docker-compose
and
provide a configuration system through:
environment variables
Docker secrets
classical configuration files
a mix of these options
A comparison against the jodogne/orthanc
Docker images is
available.
This repository contains lots of examples on how to use these images. In particular, this example shows all the way that can be used to generate the same configuration in Orthanc.
Environment variables¶
Any part of the Orthanc configuration file can be configured through an environment variable. Now that Orthanc and its plugins have hundreds of configuration parameter, listing all these environment variable would be too long. That’s why we have defined a standard way of naming the variable:
Orthanc configuration |
Environment variable |
Sample value |
---|---|---|
StableAge |
ORTHANC__STABLE_AGE |
|
DicomWeb.Root |
ORTHANC__DICOM_WEB__ROOT |
|
DicomWeb.Servers |
ORTHANC__DICOM_WEB__SERVERS |
|
To find out an environment variable name from an Orthanc setting
(i.e. DicomWeb.StudiesMetadata
is the path
to a setting):
whenever a word contains a capital letter, insert an underscore
_
in front.DicomWeb.StudiesMetadata
now becomesDicom_Web.Studies_Metadata
whenever you go down one level in the JSON configuration, insert a double underscore
__
.Dicom_Web.Studies_Metadata
now becomesDicom_Web__Studies_Metadata
capitalize all letters.
Dicom_Web__Studies_Metadata
now becomesDICOM_WEB__STUDIES_METADATA
add
ORTHANC__
in front.DICOM_WEB__STUDIES_METADATA
now becomesORTHANC__DICOM_WEB__STUDIES_METADATA
Note that, this automatic rule might fail because of 2 capital letters one after each other in some Orthanc settings. Therefore, there are some exceptions to this rule that are however quite intuitive.
Special environment variables¶
Other environment variables are not related to the Orthanc configuration file but can be specified to control the way Orthanc is run.
VERBOSE_STARTUP=true
will allow you to debug the startup process and see the configuration that has been provided to Orthanc. This setup should be disabled in production since it might display secret information like passwords in your logsVERBOSE_ENABLED=true
will start Orthanc with the--verbose
optionTRACE_ENABLED=true
will start Orthanc with the--trace
optionNO_JOBS=true
will start Orthanc with the--no-jobs
optionLOGDIR=/logs
will start Orthanc with the--logdir=/logs
option (introduced in 21.9.1)LOGFILE=/logs
will start Orthanc with the--logfile=/logs/orthanc.log
option (introduced in 21.9.1)MALLOC_ARENA_MAX=10
will control memory usageORTHANC_JSON
can be used to pass a JSON “root” configuration (see below).BEFORE_ORTHANC_STARTUP_SCRIPT
can be used to run a custom script before starting Orthanc.FORCE_HOST_ID
andGENERATE_HOST_ID_IF_MISSING
can be used to control the content of /etc/hostid (introduced in 22.9.1). DCMTK calls gethostid() when generating DICOM UIDs (used, e.g, in modifications/anonymizations). When /etc/hostid is missing, the system tries to generate it from the IP of the system. On some system, in particular circumstances, we have observed that the system performs a DNS query to get the IP of the system. This DNS can timeout (after multiple with retries) and, in particular cases, we have observed a delay of 40 seconds to generate a single DICOM UID in Orthanc. Therefore, if /etc/hostid is missing, the startup script creates it and fill it with a random number (default behaviour). This behaviour can still be deactivated by definingGENERATE_HOST_ID_IF_MISSING=false
. The host id can also be forced by definingFORCE_HOST_ID
.
Configuration files¶
Configuration files should be stored in the /etc/orthanc/
folder inside the Docker image.
This is done by building an image thanks to a Dockerfile
:
FROM orthancteam/orthanc
COPY orthanc.json /etc/orthanc/
Configuration files can also be passed as secrets as shown in this docker-compose.yml
:
version: "3.3"
services:
orthanc-file-in-secrets:
image: orthancteam/orthanc
depends_on: [index-db]
ports: ["8201:8042"]
environment:
VERBOSE_STARTUP: "true"
secrets:
- orthanc.secret.json
secrets:
orthanc.secret.json:
file: orthanc.secret.json
Finally, a whole configuration file can be passed as a JSON through the ORTHANC_JSON
environment variable:
version: "3.3"
services:
orthanc-file-in-env-var:
image: orthancteam/orthanc
depends_on: [index-db]
ports: ["8200:8042"]
environment:
VERBOSE_ENABLED: "true"
OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED: "true"
ORTHANC_JSON: |
{
"Name": "orthanc-file-in-env-var",
"PostgreSQL" : {
"Host": "index-db",
"Password": "pg-password"
},
"RegisteredUsers": {
"demo": "demo"
}
}
Docker secrets¶
When using your container in a Docker Swarm
or Kubernetes
environment,
it is usually advised to pass sensitive information through Docker Secrets
.
For this purpose, any secret whose name is similar to the name of an
environment variable is considered as an environment variable:
version: "3.3"
services:
orthanc-with-direct-secret:
image: orthancteam/orthanc
depends_on: [index-db]
ports: ["8003:8042"]
environment:
ORTHANC__NAME: "orthanc-with-direct-secret"
VERBOSE_ENABLED: "true"
OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED: "true"
ORTHANC__POSTGRESQL__HOST: "index-db"
ORTHANC__REGISTERED_USERS: |
{"demo": "demo"}
secrets:
- ORTHANC__POSTGRESQL__PASSWORD
secrets:
ORTHANC__POSTGRESQL__PASSWORD:
file: ORTHANC__POSTGRESQL__PASSWORD
Mixing configuration¶
Parts of your configuration can be defined in a configuration file, another part in an environment variable and yet another in a secret. If the same setting is defined in multiple location, the latest one will overwrite the first. Settings are evaluated in this order:
JSON files from
/etc/orthanc/
JSON files from
/run/secrets
(Docker secrets are copied there by Docker)environment variables
secret environment variables
At this point, if some settings have not been defined yet, some defaults are applied (see below).
Default configuration¶
Orthanc and each plugin might have some default settings that might eventually be different from the defaults included in the Orthanc executable or the plugin library.
Orthanc non-standard defaults:
{
"StorageDirectory" : "/var/lib/orthanc/db",
"RemoteAccessAllowed": true,
"AuthenticationEnabled": true,
"HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt",
"Plugins" : ["/usr/share/orthanc/plugins/"]
}
Default Lua scripts¶
Some Lua scripts are already loaded in the image but are not configured to
be loaded by Orthanc automatically. You’ll have to add them to the "LuaScripts"
configuration if you want to use them.
/lua-scripts/filter-http-tools-reset.lua
can be used to regenerate the /tmp/orthanc.json
configuration file that is loaded by Orthanc every time
you POST to /tools/reset
. Note that it declares an IncomingHttpRequestFilter
callback that might conflict with your scripts.
Healthcheck probe¶
In version 21.10.0, the /probes/test-aliveness.py script has been added in order to perform healthchecks. Check the doc in the script itself for more details. A sample configuration is also available in this sample
Plugins¶
Plugins are automatically enabled as soon as you define a setting
in their JSON section or as soon as you define to true
their
specific environment variable.
Below is a list of all plugins, their environment variable and their default configuration (only when their default configuration is different from the plugin defaults):
Plugin |
Environment variable |
Default configuration |
---|---|---|
Authorization |
|
|
ConnectivityChecks |
|
|
DicomWeb |
|
{
"DicomWeb": {
"Enable": true
}
}
|
Gdcm |
|
{
"Gdcm": {
"Throttling": 4,
"RestrictTransferSyntaxes": [
"1.2.840.10008.1.2.4.90",
"1.2.840.10008.1.2.4.91",
"1.2.840.10008.1.2.4.92",
"1.2.840.10008.1.2.4.93"
]
}
}
|
OrthancWebViewer |
|
|
StoneWebViewer |
|
|
OsimisWebViewerBasic |
|
|
OsimisWebViewerBasicAlpha |
|
|
PostgreSQL |
|
{
"PostgreSQL": {
"EnableIndex": true,
"EnableStorage": false,
"Port": 5432,
"Host": "HOST MUST BE DEFINED",
"Database": "postgres",
"Username": "postgres",
"Password": "postgres",
"EnableSsl": false,
"Lock": false
}
}
|
MySQL |
|
{
"MySQL": {
"EnableIndex": true,
"EnableStorage": false,
"Port": 3306,
"Host": "HOST MUST BE DEFINED",
"Database": "mysql",
"Username": "root",
"Password": "mysql",
"Lock": false
}
}
|
Python |
|
|
ServeFolders |
|
|
Transfers |
|
|
Worklists |
|
{
"Worklists": {
"Enable": true,
"Database": "/var/lib/orthanc/worklists"
}
}
|
Housekeeper |
|
{
"Housekeeper": {
"Enable": true
}
}
|
DelayedDeletion |
|
{
"DelayedDeletion": {
"Enable": true
}
}
|
MultitenantDicom |
|
|
Wsi |
|
|
Odbc |
|
{
"Odbc": {
"EnableIndex": true,
"EnableStorage": false,
"IndexConnectionString": "MUST BE DEFINED",
"StorageConnectionString": "MUST BE DEFINED"
}
}
|
Tcia |
|
{
"Tcia": {
"Enable": true
}
}
|
Indexer |
|
{
"Indexer": {
"Enable": true
}
}
|
Neuro |
|
{
"Neuro": {
"Enable": true
}
}
|
AzureBlobStorage |
|
{
"AzureBlobStorage": {
"ConnectionString": "MUST BE DEFINED BY YOU",
"ContainerName": "MUST BE DEFINED BY YOU"
}
}
|
AwsS3Storage |
|
{
"AwsS3Storage": {
"BucketName": "MUST BE DEFINED BY YOU",
"Region": "MUST BE DEFINED BY YOU"
}
}
|
GoogleCloudStorage |
|
{
"GoogleCloudStorage": {
"ServiceAccountFile": "MUST BE DEFINED BY YOU",
"BucketName": "MUST BE DEFINED BY YOU"
}
}
|
OrthancExplorer2 |
|
{
"OrthancExplorer2": {
"Enable": true,
"IsDefaultOrthancUI": false
}
}
|
VolView |
|
|
Ohif |
|
|
STL |
|
{
"STL": {
"Enable": true
}
}
|
Java |
|
{
"Java": {
"Enable": true,
"Classpath": "MUST BE DEFINED BY YOU",
"InitializationClass": "MUST BE DEFINED BY YOU"
}
}
|
Under the hood¶
The source code that is used to generate the image can be found here.
The Python script that is used at startup can be found here