nbiatoolkit 0.22.0

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

NBIA Toolkit

nbiatoolkit is 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.

Features

• Use NBIA Guest account to access public data OR authenticate using OAuth with user credentials for limited access data (requires approved data access).
• 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 Documentation at NBIA-Toolkit Read The Docs

Installation

nbiatoolkit is currently under development. It is made available via PyPI and can be installed using pip:

---

pip install nbiatoolkit

CLI Usage

getCollections Output

nbia-toolkit also provides a command line interface (CLI) to query the NBIA database for some queries.

> NBIAToolkit --version
    _   ______  _______  ______            ____   _ __ 
   / | / / __ )/  _/   |/_  __/___  ____  / / /__(_) /_
  /  |/ / __  |/ // /| | / / / __ \/ __ \/ / //_/ / __/
 / /|  / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_  
/_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/  
                                                       

Version: 0.21.1

Available CLI tools: 

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

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

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

downloadSingleSeries [-h] [-u USERNAME] [-p PASSWORD] --seriesUID
                     SERIESUID --downloadDir DOWNLOADDIR
                     [--filePattern FILEPATTERN] [--overwrite]

dicomsort [-h] [-u USERNAME] [-p PASSWORD]
          [--targetPattern TARGETPATTERN] [--truncateUID]
          [--sanitizeFilename] [--overwrite] [--nParallel NPARALLEL]
          sourceDir destinationDir

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

The NBIA-toolkit is NOT a product of the National Cancer Institute (NCI) and is not endorsed by the NCI. The NBIA-toolkit is provided as an open-source tool based on the NBIA REST API. The NBIA-toolkit 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.

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