Post processing

How to

Post processing functionality is provided by the makie_post_processing.makie_post_processing module. To run the post processing, call makie_post_processing.makie_post_process e.g.

julia> using makie_post_processing
julia> makie_post_process("runs/example-run/")

or

julia> makie_post_process("runs/example-run1/", "runs/example-run2/", "runs/example-run3/")

What this function does is controlled by the settings in an input file, by default post_processing_input.toml.

To run from the command line

julia --project run_makie_post_processing.jl dir1 [dir2 [dir3 ...]]

If multiple directories are passed, comparison plots will be made. This usually means that for line plots and animations the output for all the runs will be drawn on the same plot. For heatmap plots, the runs will be plotted side by side.

If there is output from several restarts of the same run in a directory, by default they will all be read and plotted. A single restart can be started by passing the restart_id argument to makie_post_process().

It is also possible to pass an output file (*.moments.h5 or *.dfns.h5) instead of a directory. The file name is just used to find the directory and run_name (which is the prefix of the file name), so for example you can pass a *.moments.h5 file and ask for distribution function plots (as long as the corresponding *.dfns.h5 file exists). This is useful if some output files were moved to a different directory, or the run directory was renamed (e.g. for backup, or to compare some different input options or code versions).

To see all the options that can be set, makie_post_processing.generate_example_input_file can be used to create an example file containing all the options with their default values. The options are all commented out when the file is created.

Interactive use

The functions in makie_post_processing.makie_post_processing can be used interactively (or in standalone scripts). To do so, first get the 'info' for a run (file names, metadata, etc.) using makie_post_processing.get_run_info

julia> using makie_post_processing
julia> run_info = get_run_info("runs/example-run/")

or to load from the distribution functions output file .dfns.h5

julia> run_info_dfns = get_run_info("runs/example-run/"; dfns=true)

Settings for post-processing are read from an input file, by default post_processing_input.toml (you can select a different one using the setup_input_file argument to get_run_info()). The relevant settings for interactive use are the default indices (iz0, ivpa0, etc.) that are used to select slices for 1D/2D plots and animations. The settings are read by setup_makie_post_processing!() which is called by default as part of get_run_info(). You might want to call it directly if you load both 'moments' and 'distribution functions' data, to get sensible settings for both at the same time.

Then you can make 1d or 2d plots, e.g.

julia> fig1 = plot_vs_z(run_info, "phi")
julia> fig2 = plot_vs_r_t(run_info, "density"; outfile="density_vs_r_t.pdf")

using makie_post_processing.plot_vs_t, etc. for 1d and makie_post_processing.plot_vs_r_t, etc. for 2d plots. The outfile argument can be used to save the plot. You can also change the default values used to select from the other dimensions

julia> plot_vs_z(run_info, "phi"; outfile="phi_vs_z.pdf", it=42, ir=7)

You can make animations in a similar way

julia> fig1 = animate_vs_z(run_info, "phi"; outfile="phi_vs_z.gif", it=8:12, ir=1)
julia> fig2 = animate_vs_z_r(run_info, "density"; outfile="density_vs_z_r.mp4")

using makie_post_processing.animate_vs_r, etc. for 1d and makie_post_processing.animate_vs_z_r, etc. for 2d animations. Note that outfile is required for animations.

API

See makie_post_processing.