dicom index

Extracts DICOM information from files into a single sqlite file

Installation

pip install dicomindex

Usage

Index a DICOM in folder

To recursively read all DICOM files in /path/to/folder and add patient/study/series objects to index.

dicomindex index_full /tmp/myindex.sql /path/to/folder

Index faster

For big file collections over slow connections, indexing all files can easily take weeks. Annoying. You could use this to for a faster index:

dicomindex index_per_folder /tmp/myindex.sql /path/to/base_folder

This will find a single DICOM file to index in each folder recursively. This speeds up indexing significantly, but assumes base_folder contains sub-folders that are structured in a patient/series/study way.

Explore

I've indexed this folder. Now what?

What's in my index file? (quick overview)

dicomindex stats /path/to/folder

Detailed exploration - Datasette

Install datasette
From commandline, run datsette /tmp/myindex.sql

Detailed exploration - Python

Query the db file directly using dicomindex sqlalchemy ORM:

from dicomindex.orm import Study
from dicomindex.persistence import SQLiteSession

with SQLiteSession("/tmp/archive.sql") as session:
    studies = session.query(Study).all()
    print(f"found {len(studies)} studies")

Non-goals

dicomindex will not do the following:

Comprehensive storage. Use a PACS like orthanc
Exploration and browsing tools. Use datasette

Useful for

DICOM data exploration and sanitizing legacy archives
Messy, semi-structured data, 'archives' that are just collections of folders with DICOM files in them

sjoerdk / dicomindex