phytooracle/environmental_association repository overview

⁠Environmental Association

This repo is used to associate the EnvironmentLogger data (containing weather and other ambient condition sensors) from the Maricopa Field Scanner to the plant detections resulting from the PhytoOracle processing pipelines.

⁠Download container

To download the environmental association container run:

singularity build environmental_association.simg docker://phytooracle/environmental_association:latest

You should now see a new file called environmental_association.simg within your working directory.

⁠Running the container

Run the container:

singularity run -B $(pwd):/mnt --pwd /mnt environmental_association.simg -s 14 -c sorghum -i FLIR

This command runs the container on FLIR (flirIrCamera) sensor data for the season 14 data collected on sorghum.

Command Line Arguments:

• Output directory (-o, --out_dir)

  • Required: False
  • Default: environmental_association

• Season during which data were collected (-s, --season)

  • Required: True
  • Choices: 10, 11, 12, 13, 14, 15, 16

• Crop name of data to download (-c, --crop)

  • Required: True
  • Choices: sorghum, lettuce

• Instrument (sensor) used to collect phenotype data (-i, --instrument)

  • Required: True
  • Choices: FLIR, PS2