imaging-research 0.1.5

Medical Imaginging Research structuring and automation

miresearch

Organisation and automation tools for medical imaging research data

Installation:

pip install imaging-research

Note: pypi reported naming conflicts for miresearch

[!IMPORTANT]
This package is currently undergoing frequent development and testing. Please check back regularly for version updates.

About

This is a collection of classes for following OOP principles for organisation of research data for medical imaging research studies.

It takes advantage of the dicom standard and the package spydcmtk for automating and generalising many typical steps with the intention of making the researcher's life easier.

This package may be easily adapted and expanded upon for a high level control over your research data. Or, it may be used as is for basic structure and organisation of data and automation of common tasks.

[!NOTE]
Version 0.1.0 release: Greater flexibility in subject ID naming and stability improvements to miresearch_watchdog.

Class structure

AbstractSubject class is top level class taking inputs:

• subjectNumber : an integer
• dataRoot : the root directory where subjects to be stored
• subjectPrefix : a prefix to be combined with subjectNumber for naming each subject
  • Optional: will be guessed from subjects already present in dataRoot if not given.
• DIRECTORY_STRUCTURE_TREE : DirectoryStructureTree class to define directory structure for each subject directory (see wiki for construction shortcuts)
  • Optional: Defaults to RAW and META directories.

This is the basic parent class containing fundamental methods for organisation and management. See miresearch docs for advanced usage, epsecially via inheritance and polymorphism.

Exposed commandline tool: miresearch

miresearch -h
usage: miresearch [-h] [-config CONFIGFILE] [-FORCE] [-QUIET] [-INFO] [-DEBUG] [-s [SUBJNLIST ...]] [-sf SUBJNLISTFILE] [-sR SUBJRANGE SUBJRANGE] [-y DATAROOT] [-sPrefix SUBJPREFIX] [-sSuffix SUBJSUFFIX]
                  [-anonName ANONNAME] [-Load LOADPATH] [-LOAD_MULTI] [-LOAD_MULTI_FORCE] [-RunPost] [-SubjInfo] [-SummaryCSV SUMMARYCSV] [-WatchDirectory WATCHDIRECTORY]

options:
  -h, --help            show this help message and exit

Management Parameters:
  -config CONFIGFILE    Path to configuration file to use.
  -FORCE                force action - use with caution
  -QUIET                Suppress progress bars and logging to terminal
  -INFO                 Provide setup (configuration) info and exit.
  -DEBUG                Run in DEBUG mode (save intermediate steps, increase log output)

Subject Definition:
  -s [SUBJNLIST ...]    Subject number
  -sf SUBJNLISTFILE     Subject numbers in file
  -sR SUBJRANGE SUBJRANGE
                        Subject range
  -y DATAROOT           Path of root data directory (where subjects are stored) [default None -> may be set in config file]
  -sPrefix SUBJPREFIX   Subject prefix [default None -> will get from config file OR dataRoot]
  -sSuffix SUBJSUFFIX   Subject suffix [default ""]
  -anonName ANONNAME    Set to anonymise newly loaded subject. Set to true to use for WatchDirectory. [default None]

Actions:
  -Load LOADPATH        Path to load dicoms from (file / directory / tar / tar.gz / zip)
  -LOAD_MULTI           Combine with "Load": Load new subject for each subdirectory under loadPath
  -LOAD_MULTI_FORCE     Combine with "Load": Force to ignore studyUIDs and load new ID per subdirectory
  -RunPost              Run post load pipeline
  -SubjInfo             Print info for each subject
  -SummaryCSV SUMMARYCSV
                        Write summary CSV file (give output file name)
  -WatchDirectory WATCHDIRECTORY
                        Will watch given directory for new data and load as new study

Configuration

miresearch uses a miresearch.conf file for configuration.

By default miresearch.conf files are search for in the following locations:

1. source_code_directory/miresearch.conf (file with default settings)
2. $HOME/miresearch.conf
3. $HOME/.miresearch.conf
4. $HOME/.config/miresearch.conf
5. Full file path defined at environment variable: "MIRESEARCH_CONF"
6. Full path passed as commandline argument to miresearch

Files are read in the above order with each subsequent variable present overwritting any previously defined. For information on files found and variables used run:

miresearch -INFO

Documentation

For full documentation see miresearch docs