hurahura 0.1.21

Medical Imaginging Research structuring and automation

hurahura - formerly miresearch

Organisation and automation tools for medical imaging research data

hurahura is māori for "to investigate" or "to look around"

Installation:

pip install hurahura
# formerly: pip install imaging-research

About

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

The intention is to provide a framework that will store imaging data on a "per examination" basis in a structured format. This structured format then permits simple interrogation, and automation.

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.

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 hurahura docs for advanced usage, epsecially via inheritance and polymorphism.

Configuration

hurahura 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 hurahura

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:

hurahura -INFO

systemctl

Running mi_watcher via systemctl is an attractive application:

Ubuntu instructions:

• Build a .service file in /etc/systemd/system:

[Unit]
Description=My mi_watcher Service
After=network.target

[Service]
Type=simple
ExecStart=/path/to/script
Restart=on-failure

[Install]
WantedBy=multi-user.target

• Build /path/to/script:

#!/bin/bash
source /myvenv/bin/activate
hurahura -WatchDirectory /path/to/watch_directory -config /path/to/my_proj.conf

• Reload systemd
• enable service
• start service

sudo systemctl daemon-reload
sudo systemctl enable myservice.service
sudo systemctl start myservice.service

Documentation

For full documentation see hurahura docs