Transformer Mean Temperature

Calculates mean temperature on a plot level for one or more IR (infrared) images

Sample Docker Command line

Below is a sample command line that shows how the mean temperature Docker image could be run. An explanation of the command line options used follows. Be sure to read up on the docker run command line for more information.

The files used in this example can be found on Google Drive.

docker run --rm --mount "src=/home/test,target=/mnt,type=bind" -e "BETYDB_URL=https://terraref.ncsa.illinois.edu/bety/" -e "BETYDB_KEY=<key value>" agpipeline/meantemp:3.0 --working_space "/mnt" --metadata "/mnt/e475911c-3f79-4ebb-807f-f623d5ae7783_metadata_cleaned.json" --citation_author "Me Myself" --citation_title "Something that's warm" --citation_year "2019" "/mnt/ir_fullfield_L2_ua-mac_2018-07-07_stereovis_ir_sensors_partialplots_sorghum6_shade_flir_eastedge_mn.tif"

This example command line assumes the source files are located in the /home/test folder of the local machine. The name of the image to run is agpipeline/meantemp:3.0.

We are using the same folder for the source metadata and the cleaned metadata. By using multiple --mount options, the source and output files can be separated.

Docker commands
Everything between 'docker' and the name of the image are docker commands.

• run indicates we want to run an image
• --rm automatically delete the image instance after it's run
• --mount "src=/home/test,target=/mnt,type=bind" mounts the /home/test folder to the /mnt folder of the running image
• -e "BETYDB_URL=https://terraref.ncsa.illinois.edu/bety/" the URL to the BETYdb instance to fetch plot boundaries, and other data, from
• -e "BETYDB_KEY=<key value>" the key associated with the BETYdb URL (replace <key value> with value of your key)

We mount the /home/test folder to the running image to make available the file to the software in the image.

Image's commands
The command line parameters after the image name are passed to the software inside the image. Note that the paths provided are relative to the running image (see the --mount option specified above).

• --working_space "/mnt" specifies the folder to use as a workspace
• --metadata "/mnt/e475911c-3f79-4ebb-807f-f623d5ae7783_metadata_cleaned.json" is the name of the cleaned metadata
• --citation_author "<author name>" the name of the author to cite in the resulting CSV file(s)
• --citation_title "<title>" the title of the citation to store in the resulting CSV file(s)
• --citation_year "<year>" the year of the citation to store in the resulting CSV file(s)
• "/mnt/ir_fullfield_L2_ua-mac_2018-07-07_stereovis_ir_sensors_partialplots_sorghum6_shade_flir_eastedge_mn.tif" the name of one or more IR (infrared) image files to use when calculating plot-level mean temperature