Export and Filter Data from a PlantCV Database

Utility scripts are available to filter and export data from a PlantCV results database.

Database exporter

The utility script db-exporter-pcv2.py can be used to join tables from the SQLite database, filter data if angles are missing, and average signal data (by timestamp) Requires a PlantCV SQLite database.



-d, --database     <path to sqlite database>, required
-o, --outfile      <path and name of output files>, required
-f, --filter       Either 'filter' or 'raw' if filter is selected, there will be a check to make sure that each 
                   timepoint has the correct number of angles (-a flag), default='raw'
-i, --imgtype      Type of image either 'VIS', 'NIR', or 'BOTH', or 'NONE' if no type is specified in database, 
-a, --angles       Total number of angles (TV and SV), default=5
-s, --signal       If true outputs signal data as well as feature data, default=True
-n, --signalnorm   If true, normalizes signal data to area of object, default=True
-v, --signalavg    If true, also output data averaged by timestamp for seperated sv and tv files, default=True
-D, --debug        Turn on debugging mode, action="store_true"
-h, --help         Show the help message and exit
~/plantcv/utils/db-exporter-pcv2.py -d ~/plantcv.db.sqlite3 -o test-db.csv -f 'filter' -a 3 -i 'BOTH' -s True -n True -v True -D