ImageTrove python DICOM uploader

Andrew Janke - [email protected] - National Imaging Facility.

Auto-upload from instrument to an AAF authenticated ImageTrove/MyTardis respository (in NecTAR/AWS cloud) from an instrument. Works by watching a local dcmtk DICOM listener client that runs in the local network. Thus it can upload data past VPN's and all sorts of hard things has it only uses the HTTPS protocol. All data is identified by project (and thus a group of people) from there access to the data is granted to the group of users associated with the project.

Usage

This python listener client will connect to a single instance of Imagetrove/MyTardis but can back-end on multiple DICOM instruments (typically MRI/CT/PET).

Pre-requisites

Linux, Windows, Mac
Miniconda Recommended
pip install -r requirements.txt

Config file

Default config file location is HOME_DIR/imagetrove/imagetrove.ini

[Instrument Mapping]

Use the following syntax:
ManufacturerName-StationName = MyTardis Instrument Name

*Remove spaces from ManacturerName-StationName. Examples found in imagetrove.ini.example

[MyTardis Instrument Name]

experiment-tag = DICOM tag used as Experiment name
dataset-tag = DICOM tag used as Dataset name
facility-name = MyTardis Facility
storagebox = MyTardis Storagebox

Running

python run.py dicom {input-directory}

Optionals

Option	Description	Default value
--config	Config file path	~/imagetrove/imagetrove.ini
--tmproot	Temp dir	Default OS tmp directory
--cores	No. of cores for multiprocessing	All system cores
--experiment	Manual Experiment name override	From metadata, see experiment-tag in config
--dataset	Manual Dataset name override	From metadata, see dataset-tag in config
--instrument	Manual Instrument name override	See InstrumentMapping in config