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Usage in command line (CLI)

installation

Since nonos v0.19.0, nonos-cli is a separate package, which is not installed alongside the library by default. You can request it separately with pip install nonos-cli, although note that the recommended approach is to use a tool installer such as uv (uv tool install nonos-cli) or pipx (pipx install nonos-cli).

The nonos CLI gets its parameters from three sources:

  • command line parameters
  • a configuration file
  • default values

Priority

Command line parameters take priority over the configuration file, which itself takes priority over default values.

To get help, run 

$ nonos --help

This will give an idea of the current possibilities provided by nonos.

API

To have more control on the operations and plots you want to make, use the API

Command line parameters

In order to use the CLI, you need to do nonos followed by one or several arguments. We introduce some important arguments in the following subsections.

Type of output

  • -d: open a graphic window with the plot (only works with a single image)
  • -fmt FORMAT: save the output image in the selected file format (can be png, pdf, ...)
  • -dpi DPI: image file resolution (default: 200)

Field and output number

  • -field FIELD: What field do you want to visualize ? [ex: RHO (default), VX1, BX3, ...]
  • -on ON or -all: Either for one specific file (can be interactive or saved in a file), a range of files (start, end, [step]), or for all files in the working directory (only saved in a file).

Example (idefix, 2D, polar \(R\)-\(\phi\))

nonos -field VX1 -on 0 -d: will open the file data.0000.vtk and display a slice in the midplane of the radial velocity.

Log and diff

  • -log: compute the common logarithm (log10) of the field \(f\), i.e. \(\log(f)\)
  • -diff: compute the relative perturbation of the field (compared to the initial condition data.0000.vtk) \(f\), i.e. \(\displaystyle\frac{(f-f_0)}{f_0}\)

Example (idefix, 2D, polar \(R\)-\(\phi\))

nonos -log -all: will open all the VTK files in the directory and save the log of the density in the midplane in PNG format.

Operation

The -operation (or -op) command allows you to choose what operation is applied to the data, and can be paired with -z, -theta, -phi, or -distance depending on the operation.

API function corresponding CLI argument
latitudinal_projection(theta) -op lp [-theta THETA]
vertical_projection(z) -op vp [-z Z]
vertical_at_midplane() -op vm
latitudinal_at_theta(theta) -op lt [-theta THETA]
vertical_at_z(z) -op vz [-z Z]
azimuthal_at_phi(phi) -op ap [-phi PHI]
azimuthal_at_planet(planet_number) -op apl -corotate COROTATE
azimuthal_average() -op aa
radial_at_r(distance) -op rr [-distance DISTANCE]
radial_average_interval(vmin,vmax) -
remove_planet_hill(planet_number) -

Example (idefix, 3D, polar \(R\)-\(\phi\)-\(z\))

nonos -on 5 -field BX3 -diff -op aa -fmt pdf: will open the file data.0005.vtk, and perform an azimuthal average of the relative perturbation of the vertical component of the magnetic field \(B_z\) before saving it in a PDF file.

Chain the operations

You can cumulate some operations, like -op lp aa.

Plane

The -plane argument is based on the map("XDIR","YDIR") function. Depending on the native geometry of the data and the target geometry of the visualization, you may choose various values for the -plane argument.

Examples (idefix, 3D, polar \(R\)-\(\phi\)-\(z\))

  • nonos -d -on 0 -log -op vp -z 0.1-plane x y

    rhovp_xy
    Vertical projection of the logarithm of the density

  • nonos -d -on 0 -log -op vp -z 0.1-plane R phi

    rhovp_Rphi
    Vertical projection of the logarithm of the density

  • nonos -d -on 0 -log -op vp -z 0.1-plane phi R
    rhovp_phiR
    Vertical projection of the logarithm of the density
  • nonos -d -on 0 -log -op apl -corotate 0-plane R z
    rhoapl_Rz
    Logarithm of the density at the planet azimuth
  • nonos -d -on 0 -log -op apl -corotate 0-plane theta r
    rhoapl_thetar
    Logarithm of the density at the planet azimuth

Warning

Some target geometries may not be possible, or may not yet be implemented, or may give strange results. If so, try another one to check the result or use the API instead.

Some other arguments

Reference example (idefix, 2D, polar \(R\)-\(\phi\))

nonos -on 23 -diff -plane x y

rhovm_xy_nozoom
Density at the midplane

  • -corotate COROTATE: planet number that defines with which planet the grid corotates.

Comparison (idefix, 2D, polar \(R\)-\(\phi\))

nonos -on 23 -diff -plane x y -corotate 0

rhovm_xy_corotate
Density at the midplane

  • -range x x x x: range of matplotlib window

Comparison (idefix, 2D, polar \(R\)-\(\phi\))

nonos -on 23 -diff -plane x y -range x x -2 0 will perform a zoom in the y-axis

rhovm_xy_zoom
Density at the midplane

  • -vmin VMIN and -vmax VMAX: min and max values of the field

Comparison (idefix, 2D, polar \(R\)-\(\phi\))

nonos -on 23 -diff -plane x y -vmin -0.5 -vmax 0.5

rhovm_xy_minmax
Density at the midplane

  • -cpu NCPU or -ncpu NCPU: compute and save multiple images in parallel. You can also use -pbar to display a progress bar

Example (idefix)

nonos -on 0 6 2 -cpu 2 -pbar will produce 4 PNG files corresponding to ON = 0, 2, 4, 6 with 2 processors, and displaying a progress bar.

  • -title TITLE: name of the field in the colorbar

Comparison (idefix, 2D, polar \(R\)-\(\phi\))

nonos -on 23 -diff -plane x y -title "\frac{\rho-\rho_0}{\rho_0}"

rhovm_xy_title
Density at the midplane

  • -cmap CMAP: choice of the colormap

Comparison (idefix, 2D, polar \(R\)-\(\phi\))

nonos -on 23 -diff -plane x y -cmap inferno will perform a zoom in the y-axis

rhovm_xy_cmap
Density at the midplane

  • -scaling: scale the overall sizes of features in the graph (fonts, linewidth...)

Comparison (idefix, 2D, polar \(R\)-\(\phi\))

nonos -on 23 -diff -plane x y -cmap inferno -scaling 1.2

rhovm_xy_scaling
Density at the midplane

  • -dir DATADIR: location of output files and param files

Old outputs

For old idefix outputs, or if the geometry of the outputs is not recognized, you will need to add the -geometry command to process the data.

Configuration file

The CLI will read parameters from a local file named nonos.ini if it exists, or any other name specified using the -i/-input parameter. To ignore any existing nonos.ini file, use the -isolated flag.

One way to configure nonos is to use 

$ nonos -config

which prints the current configuration to stdout. You can then redirect it to get a working configuration file as 

$ nonos -config > nonos.ini
This method can also be used to store a complete configuration file from command line arguments: 
$ nonos -ncpu 8 -cmap viridis -operation vm -diff -vmin=-10 -vmax=+100 -config
As of nonos 0.19.0 + nonos-cli 0.1.0, this will print

# Generated with nonos 0.19.0 + nonos-cli 0.1.0
datadir            .
field              RHO
operation          vm
theta              unset
z                  unset
phi                unset
distance           unset
geometry           unset
on                 unset
diff               True
log                False
range              unset
vmin               -1e1
vmax               1e2
plane              unset
progressBar        False
corotate           unset
ncpu               8
scaling            1
cmap               viridis
title              unset
unit_conversion    1
format             unset
dpi                200