Transformer: PSII sensor files to PNG

Converts PSII sensor files to PNG and TIFF format. Also produces a combined histogram image and a combined false color image.

Sample Docker Command Line

Below is a sample command line that shows how the PSII to PNG 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 sample command line can be found on Google Drive.

docker run --rm --mount "src=/home/test,target=/mnt,type=bind" agpipeline/psii2png:2.0 --working_space /mnt --metadata /mnt/2018-06-19__02-30-22-631/30a2e41a-3af4-4ed2-8948-70bd1327d9b7_metadata_cleaned.json "/mnt/2018-06-19__02-30-22-631"

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/psii2png:2.0.

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

Docker commands
Everything between 'docker' and the name of the Docker 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

We mount the /home/test folder to the running image to make files available 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/2018-06-19__02-30-22-631/30a2e41a-3af4-4ed2-8948-70bd1327d9b7_metadata_cleaned.json specifies the metadata to use when processing the data
• "/mnt/2018-06-19__02-30-22-631" is the folder containing the sensor files to process