Batch mode

Batch files - sometimes called parameter files - let you create a PCOT graph and then run it several times from the command line, modifying its inputs, outputs or nodes each time.

For example, imagine that we have a graph like this to generate a false colour spectral parameter map across an entire image:

The expr node is set to the parameter we want to generate, which in this case is a$670/(a$440+0.1) and we've renamed it back to expr for reasons which will become apparent (expr nodes usually change their name to their expression).

The gradient node is set to the defaults, but with the legend in the left margin rather than inside the image.

When we run this on some data (assuming it has the two wavelengths we need), and right-click on the image inside the gradient node, we can save as a PDF. That PDF will look something like this:

This is great, but we might want to run this on multiple images. We can do that using batch files. For example, this file will use the same settings for all the nodes and inputs, but replace the input filenames with those specified (we're using a multifile input here):

inputs.0.multifile.directory = H:\PancamData\SamplesGeologyFilter
inputs.0.multifile.filenames.+ = R01.bin
.+ = R02.bin
.+ = R03.bin
.+ = R04.bin
.+ = R05.bin
.+ = R06.bin

outputs.+.node=gradient
.file=gradient.pdf
.annotations=y
.clobber=y

The inputs will keep their settings (e.g. raw loader parameters and filter) but new files will be used.

If we want to do this several times, we can either write multiple batch files, or we can run the graph several times in one file, changing it each time. Here's an example that runs the graph twice:

inputs.0.multifile.directory = H:\PancamData\SamplesGeologyFilter
inputs.0.multifile.filenames.+ = R01.bin
.+ = R02.bin
.+ = R03.bin
.+ = R04.bin
.+ = R05.bin
.+ = R06.bin

outputs.+.node=gradient
.file=gradient1.pdf
.annotations=y
.clobber=y

run

inputs.0.multifile.directory = H:\PancamData\Data2
expr.expr = a$440
gradient.preset = magma
reset inputs.0.multifile.filenames
inputs.0.multifile.filenames.+ = *1712*Training Model-R01*.bin
inputs.0.multifile.filenames.+ = *1713*Training Model-R05*.bin
outputs.0.file = gradient2.pdf
run

Here, we are running the graph once as above and then making some changes:

• changing the input directory
• changing the input to read different filenames, this time loaded using "wildcards"
• changing the expr node's expression to show just the 440nm channel
• changing the gradient's appearance with a preset
• changing the output to write to a different filename

• Parameter file format