dicomselect

dicomselect: DICOM database and conversion software

dicomselect is a Python tool that simplifies the process of creating SQLite databases from directories containing .dcm files. Once the database is created, you can easily perform SQL-like queries on the data directly within Python. Additionally, dicomselect allows you to convert query results into various file formats supported by SimpleITK, providing flexibility in working with your DICOM data.

Installation

Python 3.10 or higher. You can install this project using pip. If you haven't already, it's recommended to create a virtual environment to isolate project dependencies.

pip install dicomselect

Documentation

Read the documentation.

Example

Clone this repo, install dicomselect, then run this example in the repo.

from dicomselect import Database
from pathlib import Path

db_path = Path('tests/output/example.db')
db_path.parent.mkdir(exist_ok=True)

# initialize the Database object with a path to the to-be-created SQLite database file
db = Database(db_path)

# create the .db file, using test data as the input directory.
db.create('tests/input/ProstateX', max_workers=4)

with db as query:
    # we only want to convert images with patient_id "ProstateX-0000" and image_direction "transverse"
    query_0000 = query.where('patient_id', '=', 'ProstateX-0000'
                             ).where('image_direction', '=', 'transverse')

    # print out a detailed extraction of our query
    print(query_0000)

# initialize the Plan object, with a template of DICOM headers for our conversion
# (note: dcm to dcm conversion is possible, if you only need restructuring of your data)
plan = db.plan('{patient_id}/prostateX_{series_description}_{instance_creation_time}', query_0000)

# ensure these properties are set
plan.target_dir = 'tests/output/example'
plan.extension = '.mha'
plan.max_workers = 4

# print out a detailed structure of our intended conversion
print(plan.to_string())

plan.execute()

Check out the results in tests/output/example.