Medical Imaginging Research structuring and automation
Project description
miresearch
Organisation and automation tools for medical imaging research data
Installation:
pip install imaging-research
Note: pypi reported naming conflicts for miresearch
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.
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 wiki for advanced usage, epsecially via inheritance and polymorphism.
Exposed commandline tool: miresearch
miresearch -h
usage: ...
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
-WatchDirectory WATCHDIRECTORY
Will watch given directory for new data and load as new study
-SummaryCSV SUMMARYCSV
Write summary CSV file (give output file name)
Configuration
miresearch uses a miresearch.conf file for configuration.
By default miresearch.conf files are search for in the following locations:
- source_code_directory/miresearch.conf (file with default settings)
- $HOME/miresearch.conf
- $HOME/.miresearch.conf
- $HOME/.config/miresearch.conf
- Full file path defined at environment variable: "MIRESEARCH_CONF"
- 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 wiki
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