# miresearch
Organisation and automation tools for medical imaging research data
## Installation:
```bash
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](https://github.com/fraser29/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](https://fraser29.github.io/miresearch/) for advanced usage, epsecially via inheritance and polymorphism.
# Exposed commandline tool: miresearch
```bash
miresearch -h
usage: miresearch [-h] [-config CONFIGFILE] [-FORCE] [-QUIET] [-INFO] [-DEBUG] [-s [SUBJNLIST ...]] [-sf SUBJNLISTFILE] [-sR SUBJRANGE SUBJRANGE] [-y DATAROOT] [-sPrefix SUBJPREFIX] [-anonName ANONNAME]CODE
[-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]
-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](https://fraser29.github.io/miresearch/)
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