Terminology of advanced features

Peers

An “Orthanc peer” is another instance of Orthanc, possibly running on a remote computer.

Contrarily to a “modality”, it is possible to communicate with a peer through the HTTP/HTTPS protocol (i.e. through the REST API of Orthanc), and not through the DICOM protocol. This implies a much easier configuration: It is only required to know the URL, the username and the password to communicate with an Orthanc peer. This contrasts with DICOM query/retrieve, that is quite complex and that involves a lot of pitfalls (cf. the FAQ entry about troubleshooting DICOM communications) that can be bypassed if using HTTP.

Furthermore, as HTTP(S) communications are generally not blocked by firewalls (contrarily to the DICOM protocol that is inherently an Intranet protocol and that often requires the setup of VPN tunnels), it is much easier to setup communications of medical images through the Internet with Orthanc peers.

Recycling/Protection

Because of its focus on low-end computers, Orthanc implements disk space recycling: The patient that has been stored for the longest time inside Orthanc can be automatically deleted when the disk space used by Orthanc grows above a threshold, or when the number of stored patients grows above a threshold. This feature enables the automated control of the disk space dedicated to Orthanc. Note that each time a new instance is received for an existing patient, the patient will be marked as the most recent one in the recycling order.

Recycling is controlled by the MaximumStorageSize and the MaximumPatientCount options in the Orthanc configuration file. Setting both these values to 0 will disable recycling.

It is possible to prevent important data from being automatically recycled. This mechanism is called protection. Each patient can be individually protected against recycling by using the Unprotected/Protected switch that is available from Orthanc Explorer.

Note that protection is only available at the patient level. It protects all the studies/series/instances of the patient against recycling. The rationale is that we think it is important to keep available all the data related to one patient. Unwillingly losing a study/series that is part of the same patient might lead to a loss in consistency with respect to the medical history of this patient.

Compression

If your disk space is limited, besides Recycling/Protection, you should also consider using disk space compression. When compression is enabled, Orthanc compresses the incoming DICOM instances on-the-fly before writing them to the filesystem, using zlib. This is useful, because the images are often stored as raw, uncompressed arrays in DICOM instances: The size of a typical DICOM instance can hopefully be divided by a factor 2 through lossless compression. This compression process is transparent to the user, as Orthanc automatically decompresses the file before sending it back to the external world.

Compression is controlled by the StorageCompression option in the Orthanc configuration file.

Metadata & attachments

Metadata consists in an associative key-value array (mapping a integer key in the range [0,65535] to a string value) that is associated with each DICOM resource stored inside Orthanc (may it be a patient, a study, a series or a DICOM instance). Metadata can be either referred to using the integer key, or using a symbolic name (if configured). Metadata records information that is not readily available in the DICOM tags.

In spirit, the metadata mechanism is similar to the attachment mechanism. However, metadata is stored directly inside the database, whereas attachments are stored as separate files on the filesystem (the database only stores a reference to the attachments). Choosing between metadata and attachments is most often a matter of trade-off: Metadata must be kept small (as a rule of thumb, under 1KB) and used if fast access is needed, whereas attachments can be used to store arbitrarily large piece of data.

However, pay attention to the fact that metadata must be UTF-8 strings terminated by the \0 character. If you need to store arbitrary binary objects, use an attachment or use Base64 encoding.

Also note that metadata and attachments are only available for resources stored inside Orthanc. Once one DICOM instance leaves the Orthanc ecosystem, its associated metadata and attachments are lost.

Core metadata

Here are the main metadata handled by the Orthanc core:

  • ReceptionDate records when a DICOM instance was received by Orthanc. Similarly, LastUpdate records, for each patient/study/series, the last time a DICOM instance was added to this resource.
  • RemoteAET records the AET of the modality that has sent some DICOM instance to Orthanc using the DICOM protocol.
  • ModifiedFrom and AnonymizedFrom hold from which original resource, a resource was modified or anonymized. The presence of this metadata indicates that the resource is the result of a modification or anonymization that was carried on by Orthanc.
  • Origin records through which mechanism the instance was received by Orthanc (may be Unknown, DicomProtocol, RestApi, Plugins, or Lua).
  • IndexInSeries records the expected index of a DICOM instance inside its parent series. Conversely, ExpectedNumberOfInstances associates to each series, the number of DICOM instances this series is expected to contain. This information is not always available.
  • Starting with Orthanc 1.2.0, TransferSyntax and SopClassUid respectively stores the transfer syntax UID and the SOP class UID of DICOM instances, in order to speed up the access to this information.
  • RemoteIP (new in Orthanc 1.4.0): The IP address of the remote SCU (for REST API and DICOM protocol).
  • CalledAET (new in Orthanc 1.4.0): The AET that was called by the SCU, which normally matches the AET of Orthanc (for DICOM protocol).
  • HttpUsername (new in Orthanc 1.4.0): The username that created the instance (for REST API).
  • PixelDataOffset (new in Orthanc 1.9.1): Offset (in bytes) of the Pixel Data DICOM tag in the DICOM file, if available.

Metadata listed above are set privately by the Orthanc core. They are read-only from the perspective of the end user, as Orthanc internally relies on them.

User-defined metadata

The metadata described above where handled by the core of Orthanc. Orthanc users are however allowed to define their own user-defined metadata. Such metadata are associated with an integer key that is greater or equal to 1024 (whereas keys below 1023 are reserved for core metadata).

You can associate a symbolic name to user-defined metadata using the UserMetadata option inside the configuration of Orthanc:

"UserMetadata" : {
  "SampleMetaData1" : 1024,
  "SampleMetaData2" : 1025
}

Accessing metadata

Metadata associated with one DICOM resource can be accessed through the REST API, for instance:

$ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata
$ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/RemoteAet
$ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/SampleMetaData1

User-defined metadata can be modified by issuing a HTTP PUT against the REST API:

$ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024 -X PUT -d 'hello'
$ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024
hello

User-defined attachments

Orthanc users are allowed to define their own user-defined attachments. Such attachments are associated with an integer key that is greater or equal to 1024 (whereas keys below 1023 are reserved for core attachments).

You can associate a symbolic name to user-defined attachments using the UserContentType option inside the configuration of Orthanc. Optionally, the user may specify a MIME content type for the attachment:

"UserContentType" : {
  "samplePdf" : [1024, "application/pdf"],
  "sampleJson" : [1025, "application/json"],
  "sampleRaw" : 1026
}

Accessing attachments

Attachments associated with one DICOM resource can be accessed through the REST API, for instance:

$ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf/data
$ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleJson/data

User-defined attachments can be modified by issuing a HTTP PUT against the REST API:

$ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf -X PUT --data-binary @sample.pdf
$ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleRaw -X PUT -d 'raw data'

DICOM-as-JSON attachments

In the version of Orthanc <= 1.9.0, whenever Orthanc receives a DICOM file, it pre-computes a JSON summary of its DICOM tags, and caches this JSON file as an attachment to the DICOM instance (accessible at the /instances/{...}/attachments/dicom-as-json/ URI). This attachment is used as a cache to seep up future accesses to /instances/.../tags, lookups using /tools/find or C-FIND queries.

This caching might cause issues if the dictionary of DICOM tags is subsequently modified, which implies that the cached JSON file does not perfectly match the new dictionary.

Since Orthanc 1.2.0, you can force the re-generation of the cached JSON file by DELETE-ing it, for instance:

$ curl -X DELETE http://localhost:8042/instances/301896f2-1416807b-3e05dcce-ff4ce9bb-a6138832/attachments/dicom-as-json

The next time you open this particular instance with Orthanc Explorer, you will see messages in the Orthanc logs (in verbose mode) stating that the Orthanc server has reconstructed the JSON summary, which will match the new content of the dictionary:

I0222 08:56:00.923070 FilesystemStorage.cpp:155] Reading attachment "2309c47b-1cbd-4601-89b5-1be1ad80382c" of "DICOM" content type
I0222 08:56:00.923394 ServerContext.cpp:401] Reconstructing the missing DICOM-as-JSON summary for instance: 301896f2-1416807b-3e05dcce-ff4ce9bb-a6138832
I0222 08:56:00.929117 ServerContext.cpp:540] Adding attachment dicom-as-json to resource 301896f2-1416807b-3e05dcce-ff4ce9bb-a6138832
I0222 08:56:00.929425 FilesystemStorage.cpp:118] Creating attachment "3c830b66-8a00-42f0-aa3a-5e37b4a8b5a4" of "JSON summary of DICOM" type (size: 1MB)

These DICOM-as-JSON attachments are not automatically generated anymore starting with Orthanc 1.9.1.

Central registry of metadata and attachments

Obviously, one must pay attention to the fact that different applications might use the same key to store different user-defined metadata, which might result in incompatibilities between such applications. Similarly, incompatibilities might show up for user-defined attachments.

Developers of applications/plugins that use user-defined metadata, attachments or global properties (using OrthancPluginSetGlobalProperty()) are therefore kindly invited to complete the central registry below:

  • Attachment 1 is used by the core of Orthanc to store the DICOM file associated with one instance.
  • Attachment 2 was used by Orthanc <= 1.9.0 to cache the so-called DICOM-as-JSON information (as returned by the /instances/.../tags URI in the REST API) in order to speed up subsequent requests to the same URI. This attachment is not automatically generated anymore starting with Orthanc 1.9.1, in order to improve performance (creating two files for each DICOM instance has a cost) and consistency (if the DICOM dictionary gets modified in the future).
  • Attachment 3 is used since Orthanc 1.9.1 to store the DICOM instance until the Pixel Data (7fe0,0010) tag, if the global configuration option StorageCompression is true, or if the storage area plugin doesn’t support range reads. This allows to avoid downloading the full DICOM instance if not necessary.
  • Attachment 9997 is used by the Osimis WebViewer plugin to store series information.
  • Attachment 9998 is used by the Osimis WebViewer plugin to store instance information.
  • Attachment 9999 is used by the Osimis WebViewer plugin to store annotations.
  • Attachments 10000-13999 are used by the Osimis WebViewer plugin to store reduced quality images.
  • Global property 5467 is used by the Osimis Cloud plugin.
  • Global property 5468 is used by the DICOMweb plugin to store the DICOMweb servers into the Orthanc database.
  • Metadata 4200 is used by the plugin for whole-slide imaging with version <= 0.7.
  • Metadata 4201 is used by the plugin for whole-slide imaging with version >= 1.0.

Stable resources

A DICOM resource (patient, study or series) is referred to as stable if it has not received any new instance for a certain amount of time.

This amount of time is configured by the the option StableAge in the configuration file.

When some resource becomes stable, an event is generated as a log entry in the /changes URI in the REST API, a Lua callback is invoked, the callback function registered by OrthancPluginRegisterOnChangeCallback() in C/C++ plugins is executed, as well as the Python callback registered by orthanc.RegisterOnChangeCallback().

The IsStable field is also available to get the status of an individual patient/study/series using the REST API of Orthanc.

In the multiple readers/writers scenario enabled since Orthanc 1.9.2, each Orthanc server is considered separately: The “stable” information is monitored by threads inside the Orthanc process, and is not shared in the database. In other words, the “stable” information is local to the Orthanc server that is queried. Synchronization between multiple readers/writers must be implemented at a higher level (e.g. using a distributed message-broker system such as RabbitMQ that is fed by an Orthanc plugin).

Revisions

Higher-level applications built on the top of Orthanc might have to modify metadata and/or attachments. This can cause concurrency problems if multiple clients modify the same metadata/attachment simultaneously. To avoid such problems, Orthanc implements a so-called revision mechanism to protect from concurrent modifications.

The revision mechanism is optional, was introduced in Orthanc 1.9.2 and must be enabled by setting configuration option CheckRevisions to true. It is strongly inspired by the CouchDB API.

When the revision mechanism is enabled, each metadata and attachment is associated with a revision number. Whenever one sets a metadata for the first time using a PUT query, this revision number can be found in the HTTP header ETag that is reported by Orthanc:

$ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X PUT -d 'Hello'
[...]
< ETag: "0"

Any GET query will also return the current value of ETag:

$ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024
[...]
< ETag: "0"

If one needs to subsequently modify or delete this metadata, the HTTP client must set this value of ETag into the If-Match HTTP header:

$ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X PUT -d 'Hello 2' -H 'If-Match: "0"'
[...]
< ETag: "1"

Note how this second call has incremented the value of ETag: This is the new revision number to be used in future updates. If a bad revision number is provided, the HTTP error 409 Conflict is generated:

$ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X PUT -d 'Hello 3' -H 'If-Match: "0"'
[...]
< HTTP/1.1 409 Conflict

Such a 409 error must be handled by the higher-level application. The revision number must similarly be given if deleting a metadata/attachment:

$ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X DELETE -H 'If-Match: "1"'
[...]
< HTTP/1.1 200 OK

Check out the OpenAPI reference of the REST API of Orthanc for more information.

Warning: The database index back-end must support revisions. As of writing, only the PostgreSQL plugins in versions above 4.0 and the ODBC plugins implement support for revisions.

Synchronous vs. asynchronous C-MOVE SCP

The C-MOVE SCP of Orthanc (i.e. the component of the Orthanc server that is responsible for routing DICOM instances from Orthanc to other modalities) can be configured to run either in synchronous or in asynchronous mode, depending on the value of the SynchronousCMove configuration option:

  • In synchronous mode (if SynchronousCMove is true), Orthanc will interleave its C-STORE SCU commands with the C-MOVE instructions received from the remote modality. In other words, Orthanc immediately sends the DICOM instances while it handles the C-MOVE command from the remote modality. This mode is for compatibility with simple DICOM client software that considers that when its C-MOVE SCU is over, it should have received all the instructed DICOM instances. This is the default behavior of Orthanc.
  • In asynchronous mode (if SynchronousCMove is false), Orthanc will queue the C-MOVE instructions and creates a job that will issue the C-STORE SCU commands afterward. This behavior is typically encountered in hospital-wide PACS systems, but requires the client software to be more complex as it must be handle the delay between its C-MOVE queries and the actual reception of the DICOM instances through C-STORE.

As a consequence, by setting SynchronousCMove to true, Orthanc can be used as a buffer that enables communications between a simple C-MOVE client and a hospital-wide PACS. This can be interesting to introduce compatibility with specialized image processing applications.