Data Science Tools

A collection of Data Science Facility tools for data management and other tasks.

Introduction

This tool has been written to replace PhenoFront and allow a user to connect to a LemnaTec database and download snapshots without the requirement to use LemnaTec software.

Instructions

1. Open database.example-config and adjust parameters in the JSON file to suit your set-up. Save this file with a new name (eg: database.config.file). Note: the parameter "Colour" describes the colour conversion process that is required. This has an int code, which can be obtained from the OpenCV Colour Space Conversions list. For instance, the code for COLOR_BAYER_RG2BGR is 48.

2. Open the command prompt and run LT-db-extractor.py with the config file as input (-c) and specify an output directory (-o) plus experiment (-e, your measurement_label) to query. You can also select a range of dates using the optional -a (earliest date) and -z (latest date) flags. For example: C:/path/to/data-science-tools/LT-db-extractor.py -c T:/path/to/database.config.file -o T:/path/to/my/output/experiment47 -e Experiment47 -a 2019-06-21 -z 2019-09-24. The script will connect to the database server to query image and experimental metadata. It identifies raw LemnaTec images (in RAWX format) and transfers them to the local machine via SFTP, then it converts them to PNG files. Metadata will be saved to a CSV. Downloaded blob files will be deleted.

3. Utilise PlantCV to analyse your data.