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.

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

Installation

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

pip install nbiatoolkit

CLI Usage

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

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

Version: 0.25.3

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]

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

dicomsort [-h] [-u USERNAME] [-pw 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