nbiatoolkit 1.3.0

A python package to query the National Biomedical Imaging Archive (NBIA) database.

NBIA Toolkit

A python package that provides programmatic access to query and download images from the National Biomedical Imaging Archive (NBIA) and The Cancer Imaging Archive (TCIA) databases.

Table of Contents

• Features
• Installation
• Python Usage
• CLI Usage
• Contributing
• License
• User Agreements and Disclaimers

Features

[!TIP] For a thorough description of the package and its available features, please refer to the Documentation at NBIA-Toolkit Read The Docs

• Programmatic access to the National Biomedical Imaging Archive (NBIA) and The Cancer Imaging Archive (TCIA) databases

  • Use NBIA Guest account to access public data OR authenticate using OAuth with user credentials for limited access data (requires approved data access).
  • Custom OAuth2 class for NBIA, TCIA, including special handling for dedicated server for the NLST collection.

• Query NBIA database for metadata on collections, patients, studies, series, and images

• Download images from NBIA

  • Validate doownloads with MD5 checksums for downloaded images
  • Auto-sort DICOM files using a user-defined pattern of DICOM tags with specialized DICOMSorter class

See Developer Notes for more details on the features and the development process.

Installation

[!WARNING] nbiatoolkit is currently under development and is not guaranteed to be stable.

It is made available via PyPI and can be installed using pip:

pip install nbiatoolkit

Python Usage

Using a context manager, you can easily access the NBIA database and query for metadata on collections, patients, studies, and series.

from nbiatoolkit import NBIAClient

with NBIAClient() as client:
    # Get a list of collections
    collections = client.getCollections()
    print(collections)

    # Get a list of patients in a collection
    patients = client.getPatients(Collection="TCGA-KIRC")
    print(patients)

    # Get a list of studies for a patient
    studies = client.getStudies(PatientID="TCGA-BP-4989")
    print(studies)

    # Get a list of series for a study
    series = client.getSeries(StudyInstanceUID=studies[0]["StudyInstanceUID"])
    print(series[0:5])

CLI Usage

For quick access to the NBIA, the toolkit also provides a command line interface (CLI)

> NBIAToolkit --version

        _   ______  _______  ______            ____   _ __
       / | / / __ )/  _/   |/_  __/___  ____  / / /__(_) /_
      /  |/ / __  |/ // /| | / / / __ \/ __ \/ / //_/ / __/
     / /|  / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_
    /_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/

Version: 1.0.1

Available CLI tools:

getCollections [-h] [-u USERNAME] [-pw PASSWORD] [-p PREFIX]
               [-o OUTPUTFILE] [--version]

getBodyPartCounts [-h] [-u USERNAME] [-pw PASSWORD] [-c COLLECTION]
                  [-o OUTPUTFILE] [--version]

getPatients [-h] [-u USERNAME] [-pw PASSWORD] -c COLLECTION
            [-o OUTPUTFILE] [--version]

getNewPatients [-h] [-u USERNAME] [-pw PASSWORD] -c COLLECTION -d DATE
               [-o OUTPUTFILE] [--version]

getStudies [-h] [-u USERNAME] [-pw PASSWORD] -c COLLECTION
           [-p PATIENTID] [-s STUDYINSTANCEUID] [-o OUTPUTFILE]
           [--version]

getSeries [-h] [-u USERNAME] [-pw PASSWORD] [-c COLLECTION]
          [-p PATIENTID] [-m MODALITY] [-study STUDYINSTANCEUID]
          [--seriesInstanceUID SERIESINSTANCEUID]
          [--bodyPartExamined BODYPARTEXAMINED]
          [--manufacturerModelName MANUFACTURERMODELNAME]
          [--manufacturer MANUFACTURER] [-o OUTPUTFILE] [--version]

getNewSeries [-h] [-u USERNAME] [-pw PASSWORD] -d DATE [-o OUTPUTFILE]
             [--version]

Contributing

Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

nbiatoolkit was created by Jermiah Joseph. It is licensed under the terms of the MIT license.

User Agreements and Disclaimers

[!IMPORTANT] The NBIA-toolkit is NOT a product of the National Cancer Institute (NCI) and is not endorsed by the NCI. Users of the NBIA-toolkit are required to abide by the NBIA REST API Terms of Service and the NBIA Data Usage Policies and Restrictions The NBIA-toolkit is provided as an open-source tool based on the NBIA REST API and is provided "AS IS" without warranty of any kind. In no event shall the authors or contributors be liable for any claim, damages or other liability, arising from, out of or in connection with the NBIA-toolkit or the use or other dealings in the NBIA-toolkit.