How does Orthanc store its database?

Storage folder

By default (i.e. if no database plugin such as PostgreSQL or MySQL is used), Orthanc stores all the DICOM files it receives in a folder called OrthancStorage on the filesystem. Orthanc also associates each incoming DICOM file with a JSON file that summarizes all its DICOM tags, which speeds up subsequent processing by avoiding a costly DICOM parsing.

More generally, the OrthancStorage folder contains a set of so-called attachments, that may correspond to either a DICOM file, a JSON file, or any user-defined file. Internally, each attachment is automatically associated with an universally unique identifier (UUID). Orthanc can be configured to compress these files on-the-fly in order to save disk space (cf. the StorageCompression configuration option).

To reduce the number of files in a single directory (which is something that some operating systems might not like), a 3-level hierarchy of directories is created to store the attachments: The first two hexadecimal characters of the UUID give the first-level folder, and the two next characters give the second-level folder.

SQLite index

Inside the same OrthancStorage folder, Orthanc maintains a SQLite database called index that indexes all these attachments. The database records, for each attachment, its compression method, and its MD5 hashes before and after compression in order to detect disk corruption (cf. the StoreMD5ForAttachments configuration option).

One attachment must be associated with one DICOM resource (patient, study, series, or instance). Incoming DICOM files and associated JSON summary are associated with one instance-level resource, but user-defined attachments can be associated with any kind of resource.

Given one DICOM resource, all of its child attachments are identified by a number between 0 and 65535. Identifiers <= 1023 are reserved for the Orthanc core, whereas identifiers >= 1024 can be user-defined for external applications.

Besides the attachments, the database index maintains other information for each DICOM resource, notably the metadata, the history of changes, and an associative map that stores the so-called “main” DICOM tags (to avoid accessing the storage folder are when this is not needed). The SQLite database schema is kept as simple as possible, and can be found in the following two files of the source code of Orthanc: PrepareDatabase.sql and InstallTrackAttachmentsSize.sql.

Direct access

Directly accessing the content of the OrthancStorage folder and the content of the SQLite database is strongly discouraged for several reasons:

  • This internal organization is only true when no database plugin is used (e.g. the PostgreSQL and MySQL plugins can be configured to store the attachments inside a database).
  • Orthanc can be configured to compress the attachments before writing them on the disk (cf. the StorageCompression option).
  • By directly reading the content of OrthancStorage, you bypass all the locking mechanisms used by Orthanc, which might result in data corruption.
  • One SQLite database should be accessed by at most one process at any time to avoid any problem (e.g. with NFS filesystems), for reasons that are explained in the SQLite FAQ. Orthanc will stop if it receives the SQLITE_BUSY status.

As a consequence, it is HIGHLY recommended NOT to directly access the OrthancStorage folder and the SQLite database. Use the REST API instead, which contains primitives to access the attachments (cf. the .../attachments/... URIs).

The only exception to this rule is for read-only access when Orthanc is stopped, e.g. as a part of a backup or upgrade/replication process.