dicom

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dicom

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Extension descriptor (YAML)

DuckDB integration with medical imaging data (DICOM - Digital Imaging and Communication in Medicine).

Maintainer(s): nmontesg

Compatibility Matrix

This table covers all DuckDB releases that have not reached end-of-life, including LTS releases, and shows the 2 most recent patch releases of each. Older patch releases are not listed, but the extension may be available for them as well.

Platform	1.4.4	1.4.5	1.5.5	1.5.6	2.0.0
Linux AMD64
Linux ARM64
macOS AMD64
macOS ARM64
Windows AMD64
Windows ARM64
WebAssembly

Installing and Loading

INSTALL dicom FROM community;
LOAD dicom;

Example

INSTALL dicom FROM community;
LOAD dicom;
FROM read_dicom('path/to/dicom_file.dcm');

About dicom

The dicom extension for DuckDB provides functionality to import medical imaging data (DICOM, Digital Imaging and Communication in Medicine) directly into DuckDB. It uses the powerful DCMTK C++ library to read DICOM files and convert them into JSON format.

For full documentation and examples, see the project documentation.

Key functionality:

read_dicom() - Table function to import DICOM files directly into DuckDB, including support for local and remote files.
DICOM_TAG - Custom type to work with DICOM tags, including conversion to and from VARCHAR.
tag_group(), tag_element(), tag_name() - Scalar functions to work with DICOM tags.
dicom secret type - Store credentials to establish connection with remote DICOM modalities, such as PACS systems.
query_dicom() and retrieve_dicom() - Table functions to query and retrieve DICOM datasets from a remote modalities directly into DuckDB using C-FIND and C-MOVE commands.

Added Functions

function_name	function_type	description	comment	examples
query_dicom	table	Query remote DICOM nodes using C-FIND commands	NULL	[FROM query_dicom(host='localhost', port=4242, match_keys=MAP {'Modality': 'MR'}, retrieve_keys=['StudyInstanceUID']);, FROM query_dicom(secret='my_dicom_conn_secret', qr_level='series', match_keys=MAP {'SeriesDate': '20070101'});]
read_dicom	table	Load DICOM files into DuckDB. The contents of each file are loaded into a row in JSON format.	NULL	[SELECT * FROM read_dicom('/path/to/dicom_files/');, SELECT FROM read_dicom('/path/to/dicom_files/*', load_pixel_data = true);]
retrieve_dicom	table	Retrieve DICOM data from remote modalities using C-MOVE commands	NULL	[FROM retrieve_dicom('1.3.54.24.5…', host='localhost', port=4242, incoming_port=11112, qr_level='study');, FROM retrieve_dicom('1.95.3…', '1.56.7…', …, secret='my_dicom_conn_secret', qr_level='series');]
tag_element	scalar	Extracts the element of a DICOM tag, as a VARCHAR containing the element in hexadecimal representation.	NULL	[SELECT tag_element('0008,01DA')]
tag_group	scalar	Extracts the group of a DICOM tag, as a VARCHAR containing the group in hexadecimal representation.	NULL	[SELECT tag_group('0008,01DA')]
tag_name	scalar	Extracts the name of the DICOM tag. If it can't be found, a VARCHAR with format GGGG,EEEE is returned.	NULL	[SELECT tag_name('0008,0008')]

Overloaded Functions

This extension does not add any function overloads.

Added Types

type_name	type_size	logical_type	type_category	internal
DICOM_TAG	0	STRUCT	COMPOSITE	true

Added Settings

name	description	input_type	scope	aliases	typed_value
read_dicom_batch_size	Number of files to read in each batch of read_dicom.	UINTEGER	GLOBAL	[]	64
read_dicom_internal_buffer_size	The size of the internal buffer (in kB) used to cache remote read when calling read_dicom over remote storage.	UINTEGER	GLOBAL	[]	128
temp_directory	Set the directory to which temporary files are written.	VARCHAR	GLOBAL	[]	post.db.tmp

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