makie_post_processing
makie_post_processing.makie_post_processing — ModulePost processing functions using Makie.jl
Options are read by default from a file post_processing_input.toml, if it exists.
The plots can be generated from the command line by running
julia --project run_makie_post_processing.jl dir1 [dir2 [dir3 ...]]makie_post_processing.input_dict — ConstantGlobal dict containing settings for makiepostprocessing. Can be re-loaded at any time to change settings.
Is an OrderedDict so the order of sections is nicer if input_dict is written out as a TOML file.
makie_post_processing.input_dict_dfns — ConstantGlobal dict containing settings for makiepostprocessing for files with distribution function output. Can be re-loaded at any time to change settings.
Is an OrderedDict so the order of sections is nicer if input_dict_dfns is written out as a TOML file.
makie_post_processing.Chodura_condition_plots — FunctionChodura_condition_plots(run_info::Tuple; plot_prefix)
Chodura_condition_plots(run_info; plot_prefix=nothing, axes=nothing)Plot the criterion from the Chodura condition at the sheath boundaries.
The information for the runs to plot is passed in run_info (as returned by get_run_info). If run_info is a Tuple, comparison plots are made where line plots from the different runs are overlayed on the same axis, and heatmap plots are displayed in a horizontal row.
Settings are read from the [Chodura_condition] section of the input.
When run_info is a Tuple, plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf. When run_info is not a Tuple, plot_prefix is optional - plots will be saved only if it is passed.
When run_info is not a Tuple, a Vector of Axis objects can be passed to axes, and each plot will be added to one of axes.
makie_post_processing._MMS_pdf_plots — Method_MMS_pdf_plots(run_info, input, variable_name, plot_prefix, field_label,
field_sym_label, norm_label, plot_dims, animate_dims)Utility function for making plots to avoid duplicated code in compare_ion_pdf_symbolic_test and compare_neutral_pdf_symbolic_test.
The information for the run to analyse is passed in run_info (as returned by get_run_info).
input is a NamedTuple of settings to use.
variable_name is the name of the variable being plotted.
plot_prefix gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf for plots and plot_prefix<some_identifying_string>.gif, etc. for animations.
field_label is the label for the computed variable that will be used in plots/animations, field_sym_label is the label for the manufactured solution, and norm_label is the label for the error.
plot_dims are the dimensions of the variable, and animate_dims are the same but omitting :t.
makie_post_processing._get_steady_state_residual_fig_axes — Method _get_steady_state_residual_fig_axes(n_runs)Utility method to avoid code duplication when creating the figaxes OrderedDict for calculatesteadystateresidual.
n_runs sets the number of axes to create in each entry.
makie_post_processing.animate_1d — Methodanimate_1d(xcoord, data; frame_index=nothing, ax=nothing, fig=nothing,
xlabel=nothing, ylabel=nothing, title=nothing, yscale=nothing,
transform=identity, outfile=nothing, ylims=nothing,
axis_args=Dict{Symbol,Any}(), kwargs...)Make a 1d animation of data vs xcoord.
xlabel, ylabel and title can be passed to set axis labels and title for the (sub-)plot.
ylims can be passed a Tuple (ymin, ymax) to set the y-axis limits. By default the minimum and maximum of the data (over all time points) will be used.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
If ax is passed, the animation will be added to that existing Axis, otherwise a new Figure and Axis will be created. If ax is passed, you should also pass an Observable{mk_int} to frame_index so that the data for this animation can be updated when frame_index is changed.
If outfile is passed the animation will be saved to a file with that name. The suffix determines the file type. If ax is passed at the same time as outfile then the Figure containing ax must also be passed (to the fig argument) so that the animation can be saved.
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Other kwargs are passed to Makie's lines!() function.
If ax is not passed, returns the Figure, otherwise returns the object returned by lines!().
makie_post_processing.animate_2d — Methodanimate_2d(xcoord, ycoord, data; frame_index=nothing, ax=nothing, fig=nothing,
colorbar_place=nothing, xlabel=nothing, ylabel=nothing, title=nothing,
outfile=nothing, colormap="reverse_deep", colorscale=nothing,
transform=identity, axis_args=Dict{Symbol,Any}(), kwargs...)Make a 2d animation of data vs xcoord and ycoord.
xlabel, ylabel and title can be passed to set axis labels and title for the (sub-)plot.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
If ax is passed, the animation will be added to that existing Axis, otherwise a new Figure and Axis will be created. If ax is passed, you should also pass an Observable{mk_int} to frame_index so that the data for this animation can be updated when frame_index is changed.
If outfile is passed the animation will be saved to a file with that name. The suffix determines the file type. If ax is passed at the same time as outfile then the Figure containing ax must also be passed (to the fig argument) so that the animation can be saved.
colormap is included explicitly because we do some special handling so that extra Makie functionality can be specified by a prefix to the colormap string, rather than the standard Makie mechanism of creating a struct that modifies the colormap. For example Reverse("deep") can be passed as "reverse_deep". This is useful so that these extra colormaps can be specified in an input file, but is not needed for interactive use.
When xcoord and ycoord are both one-dimensional, uses Makie's heatmap!() function for the plot. If either or both of xcoord and ycoord are two-dimensional, instead uses irregular_heatmap!.
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Other kwargs are passed to Makie's heatmap!() function.
If ax is not passed, returns the Figure, otherwise returns the object returned by heatmap!().
makie_post_processing.animate_f_unnorm_vs_vpa — Functionanimate_f_unnorm_vs_vpa(run_info; input=nothing, electron=false, neutral=false, is=1,
iz=nothing, fig=nothing, ax=nothing, frame_index=nothing,
outfile=nothing, yscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), kwargs...)Plot an unnormalized distribution function against $v_\parallel$ at a fixed z.
This function is only needed for moment-kinetic runs. These are currently only supported for the 1D1V case.
The information for the runs to animate is passed in run_info (as returned by get_run_info). If run_info is a Tuple, comparison plots are made where plots from the different runs are overlayed on the same axis.
By default animates the ion distribution function. If electron=true is passed, animates the electron distribution function instead. If neutral=true is passed, animates the neutral distribution function instead.
is selects which species to analyse.
it and iz specify the indices of the time- and z-points to choose. By default they are taken from input.
If input is not passed, it is taken from input_dict_dfns["f"].
The data needed will be loaded from file.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When run_info is not a Tuple, an Axis can be passed to ax to have the plot added to ax. When ax is passed, if outfile is passed to save the plot, then the Figure containing ax must be passed to fig.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Any extra kwargs are passed to lines!() (which is used to create the plot, as we have to handle time-varying coordinates so cannot use animate_1d).
makie_post_processing.animate_f_unnorm_vs_vpa_z — Functionanimate_f_unnorm_vs_vpa_z(run_info; input=nothing, electron=false, neutral=false,
is=1, fig=nothing, ax=nothing, frame_index=nothing,
outfile=nothing, yscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), kwargs...)Animate an unnormalized distribution function against $v_\parallel$ and z.
This function is only needed for moment-kinetic runs. These are currently only supported for the 1D1V case.
The information for the runs to plot is passed in run_info (as returned by get_run_info). If run_info is a Tuple, comparison plots are made where plots from the different runs are displayed in a horizontal row.
By default animates the ion distribution function. If electron=true is passed, animates the electron distribution function instead. If neutral=true is passed, animates the neutral distribution function instead.
is selects which species to analyse.
If input is not passed, it is taken from input_dict_dfns["f"].
The data needed will be loaded from file.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When run_info is not a Tuple, an Axis can be passed to ax to have the animation created in ax. When ax is passed, if outfile is passed to save the animation, then the Figure containing ax must be passed to fig.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Any extra kwargs are passed to plot_2d (which is used to create the plot, as we have to handle time-varying coordinates so cannot use animate_2d).
makie_post_processing.animate_vs_r — Functionanimate_vs_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)
animate_vs_r(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing, label=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs r.
If a Tuple of run_info is passed, the animations from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
ylims can be passed a Tuple (ymin, ymax) to set the y-axis limits. By default the minimum and maximum of the data (over all time points) will be used.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
When a single run_info is passed, label can be passed to set a custom label for the line. By default the run_info.run_name is used.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vpa — Functionanimate_vs_vpa(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)
animate_vs_vpa(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing, label=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs vpa.
If a Tuple of run_info is passed, the animations from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
ylims can be passed a Tuple (ymin, ymax) to set the y-axis limits. By default the minimum and maximum of the data (over all time points) will be used.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
When a single run_info is passed, label can be passed to set a custom label for the line. By default the run_info.run_name is used.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vpa_r — Functionanimate_vs_vpa_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vpa_r(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vpa.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vpa_vperp — Functionanimate_vs_vpa_vperp(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vpa_vperp(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs vperp and vpa.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vpa_z — Functionanimate_vs_vpa_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vpa_z(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vpa.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vperp — Functionanimate_vs_vperp(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)
animate_vs_vperp(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing, label=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs vperp.
If a Tuple of run_info is passed, the animations from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
ylims can be passed a Tuple (ymin, ymax) to set the y-axis limits. By default the minimum and maximum of the data (over all time points) will be used.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
When a single run_info is passed, label can be passed to set a custom label for the line. By default the run_info.run_name is used.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vperp_r — Functionanimate_vs_vperp_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vperp_r(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vperp.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vperp_z — Functionanimate_vs_vperp_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vperp_z(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vperp.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vr — Functionanimate_vs_vr(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)
animate_vs_vr(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing, label=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs vr.
If a Tuple of run_info is passed, the animations from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
ylims can be passed a Tuple (ymin, ymax) to set the y-axis limits. By default the minimum and maximum of the data (over all time points) will be used.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
When a single run_info is passed, label can be passed to set a custom label for the line. By default the run_info.run_name is used.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vr_r — Functionanimate_vs_vr_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vr_r(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vr.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vr_vzeta — Functionanimate_vs_vr_vzeta(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vr_vzeta(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs vzeta and vr.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vr_z — Functionanimate_vs_vr_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vr_z(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vr.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vz — Functionanimate_vs_vz(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)
animate_vs_vz(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing, label=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs vz.
If a Tuple of run_info is passed, the animations from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
ylims can be passed a Tuple (ymin, ymax) to set the y-axis limits. By default the minimum and maximum of the data (over all time points) will be used.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
When a single run_info is passed, label can be passed to set a custom label for the line. By default the run_info.run_name is used.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vz_r — Functionanimate_vs_vz_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vz_r(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vz.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vz_vr — Functionanimate_vs_vz_vr(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vz_vr(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs vr and vz.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vz_vzeta — Functionanimate_vs_vz_vzeta(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vz_vzeta(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs vzeta and vz.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vz_z — Functionanimate_vs_vz_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vz_z(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vz.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vzeta — Functionanimate_vs_vzeta(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)
animate_vs_vzeta(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing, label=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs vzeta.
If a Tuple of run_info is passed, the animations from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
ylims can be passed a Tuple (ymin, ymax) to set the y-axis limits. By default the minimum and maximum of the data (over all time points) will be used.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
When a single run_info is passed, label can be passed to set a custom label for the line. By default the run_info.run_name is used.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vzeta_r — Functionanimate_vs_vzeta_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vzeta_r(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vzeta.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_vzeta_z — Functionanimate_vs_vzeta_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_vzeta_z(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vzeta.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_z — Functionanimate_vs_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)
animate_vs_z(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, outfile=nothing, yscale=nothing,
transform=identity, ylims=nothing, label=nothing,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing, iz=nothing,
ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing,
ivz=nothing, kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs z.
If a Tuple of run_info is passed, the animations from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
ylims can be passed a Tuple (ymin, ymax) to set the y-axis limits. By default the minimum and maximum of the data (over all time points) will be used.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
When a single run_info is passed, label can be passed to set a custom label for the line. By default the run_info.run_name is used.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.animate_vs_z_r — Functionanimate_vs_z_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
animate_vs_z_r(run_info, var_name; is=1, data=nothing,
input=nothing, frame_index=nothing, ax=nothing,
fig=nothing, colorbar_place=colorbar_place,
title=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)Animate var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and z.
If a Tuple of run_info is passed, the animations from each run are created in a horizontal row, with each sub-animation having the 'run name' as its subtitle.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be created in ax. When ax is passed, a colorbar will be created at colorbar_place if a GridPosition is passed to colorbar_place.
outfile is required for animations unless ax is passed. The animation will be saved to a file named outfile. The suffix determines the file type. If both outfile and ax are passed, then the Figure containing ax must be passed to fig to allow the animation to be saved.
When a single run_info is passed, the (sub-)title can be set with the title argument.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case returns nothing.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.calculate_steady_state_residual — Functioncalculatesteadystateresidual(runinfo, variablename; is=1, data=nothing, plotprefix=nothing, figaxes=nothing, irun=1)
Calculate and plot the 'residuals' for variable_name.
The information for the runs to plot is passed in run_info (as returned by get_run_info). If run_info is a Tuple, comparison plots are made where plots from the different runs are displayed in a horizontal row.
If the variable has a species dimension, is selects which species to analyse.
By default the variable will be loaded from file. If the data has already been loaded, it can be passed to data instead. data should be a Tuple of the same length as run_info if run_info is a Tuple.
If plot_prefix is passed, it gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf.
fig_axes can be passed an OrderedDict of Tuples as returned by _get_steady_state_residual_fig_axes - each tuple contains the Figure fig and Axis or Tuple{Axis} ax to which to add the plot corresponding to its key. If run_info is a Tuple, ax for each entry must be a Tuple of the same length.
makie_post_processing.clear_Dict! — Methodclear_Dict!(d::AbstractDict)Remove all entries from an AbstractDict, leaving it empty
makie_post_processing.compare_ion_pdf_symbolic_test — Methodcompare_ion_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
input=nothing)Compare the computed and manufactured solutions for the ion distribution function.
The information for the run to analyse is passed in run_info (as returned by get_run_info).
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf for plots and plot_prefix<some_identifying_string>.gif, etc. for animations.
If io is passed then error norms will be written to that file.
input is a NamedTuple of settings to use. If not given it will be read from the [manufactured_solns] section of [input_dict_dfns][@ref].
Note: when calculating error norms, data is loaded only for 1 time point and for an r-z chunk that is the same size as computed by 1 block of the simulation at run time. This should prevent excessive memory requirements for this function.
makie_post_processing.compare_moment_symbolic_test — Methodcompare_moment_symbolic_test(run_info, plot_prefix, field_label, field_sym_label,
norm_label, variable_name; io=nothing)Compare the computed and manufactured solutions for a field or moment variable variable_name.
The information for the run to analyse is passed in run_info (as returned by get_run_info).
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf for plots and plot_prefix<some_identifying_string>.gif, etc. for animations.
field_label is the label that will be used for the name of the computed variable in plots, field_sym_label is the label for the manufactured solution, and norm_label is the label for the error (the difference between the computed and manufactured solutions).
If io is passed then error norms will be written to that file.
makie_post_processing.compare_neutral_pdf_symbolic_test — Methodcompare_neutral_pdf_symbolic_test(run_info, plot_prefix; io=nothing,
input=nothing)Compare the computed and manufactured solutions for the neutral distribution function.
The information for the run to analyse is passed in run_info (as returned by get_run_info).
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf for plots and plot_prefix<some_identifying_string>.gif, etc. for animations.
If io is passed then error norms will be written to that file.
input is a NamedTuple of settings to use. If not given it will be read from the [manufactured_solns] section of [input_dict_dfns][@ref].
Note: when calculating error norms, data is loaded only for 1 time point and for an r-z chunk that is the same size as computed by 1 block of the simulation at run time. This should prevent excessive memory requirements for this function.
makie_post_processing.constraints_plots — Methodconstraints_plots(run_info; plot_prefix=plot_prefix)Plot and/or animate the coefficients used to correct the normalised distribution function(s) (aka shape functions) to obey the moment constraints.
If there were no discretisation errors, we would have $A=1$, $B=0$, $C=0$. The plots/animations show $(A-1)$ so that all three coefficients can be shown nicely on the same axes.
makie_post_processing.convert_to_OrderedDicts! — Methodconvert_to_OrderedDicts!(d::AbstractDict)Recursively convert an AbstractDict to OrderedDict.
Any nested AbstractDicts are also converted to OrderedDict.
makie_post_processing.curvilinear_grid_mesh — Methodcurvilinear_grid_mesh(xs, ys, zs, colors)Tesselates the grid defined by xs and ys in order to form a mesh with per-face coloring given by colors.
The grid defined by xs and ys must have dimensions (nx, ny) == size(colors) .+ 1, as is the case for heatmap/image.
Code from: https://github.com/MakieOrg/Makie.jl/issues/742#issuecomment-1415809653
makie_post_processing.generate_example_input_Dict — Methodgenerate_example_input_Dict()Create a Dict containing all the makie-post-processing options with default values
makie_post_processing.generate_example_input_file — Functiongenerate_example_input_file(filename::String=post_processing_input.toml;
overwrite::Bool=false)Create an example makie-post-processing input file.
Every option is commented out, but filled with the default value.
Pass filename to choose the name of the example file (defaults to the default input file name used by makie_post_process()).
Pass overwrite=true to overwrite any existing file at filename.
makie_post_processing.get_1d_ax — Functionget_1d_ax(n=nothing; title=nothing, subtitles=nothing, yscale=nothing,
get_legend_place=nothing, size=nothing, kwargs...)Create a new Figure fig and Axis ax intended for 1d plots.
title gives an overall title to the Figure.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10.
By default creates a single Axis, and returns (fig, ax). If a number of axes n is passed, then ax is a Vector{Axis} of length n (even if n is 1). The axes are created in a horizontal row, and the width of the figure is increased in proportion to n.
get_legend_place can be set to one of (:left, :right, :above, :below) to create a GridPosition for a legend in the corresponding place relative to each Axis. If get_legend_place is set, (fig, ax, legend_place) is returned where legend_place is a GridPosition (if n=nothing) or a Tuple of n GridPositions.
When n is passed, subtitles can be passed a Tuple of length n which will be used to set a subtitle for each Axis in ax.
size is passed through to the Figure constructor. Its default value is (600, 400) if n is not passed, or (600*n, 400) if n is passed.
Extra kwargs are passed to the Axis() constructor.
makie_post_processing.get_2d_ax — Functionget_2d_ax(n=nothing; title=nothing, subtitles=nothing, size=nothing, kwargs...)Create a new Figure fig and Axis ax intended for 2d plots.
title gives an overall title to the Figure.
By default creates a single Axis, and returns (fig, ax, colorbar_place), where colorbar_place is a location in the grid layout that can be passed to Colorbar() located immediately to the right of ax. If a number of axes n is passed, then ax is a Vector{Axis} and colorbar_place is a Vector{GridPosition} of length n (even if n is 1). The axes are created in a horizontal row, and the width of the figure is increased in proportion to n.
When n is passed, subtitles can be passed a Tuple of length n which will be used to set a subtitle for each Axis in ax.
size is passed through to the Figure constructor. Its default value is (600, 400) if n is not passed, or (600*n, 400) if n is passed.
Extra kwargs are passed to the Axis() constructor.
makie_post_processing.get_dimension_slice_indices — Methodgetdimensionsliceindices(keepdims...; input, it=nothing, is=nothing, ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing)
Get indices for dimensions to slice
The indices are taken from input, unless they are passed as keyword arguments
The dimensions in keep_dims are not given a slice (those are the dimensions we want in the variable after slicing).
makie_post_processing.get_run_info — Methodget_run_info(run_dir...; itime_min=1, itime_max=0,
itime_skip=1, dfns=false, initial_electron=false, do_setup=true,
setup_input_file=nothing)
get_run_info((run_dir, restart_index)...; itime_min=1, itime_max=0,
itime_skip=1, dfns=false, initial_electron=false, do_setup=true,
setup_input_file=nothing)Get file handles and other info for a single run
run_dir is either the directory to read output from (whose name should be the run_name), or a momentkinetics binary output file. If a file is passed, it is only used to infer the directory and `runname, so it is possible for example to pass a.moments.h5output file and alsodfns=trueand the.dfns.h5` file will be the one actually opened (as long as it exists).
restart_index can be given by passing a Tuple, e.g. ("runs/example", 42) as the positional argument. It specifies which restart to read if there are multiple restarts. If no restart_index is given or if nothing is passed, read all restarts and concatenate them. An integer value reads the restart with that index - -1 indicates the latest restart (which does not have an index).
Several runs can be loaded at the same time by passing multiple positional arguments. Each argument can be a String run_dir giving a directory to read output from or a Tuple (run_dir, restart_index) giving both a directory and a restart index (it is allowed to mix Strings and Tuples in a call).
By default load data from moments files, pass dfns=true to load from distribution functions files, or initial_electron=true and dfns=true to load from initial electron state files.
The itime_min, itime_max and itime_skip options can be used to select only a slice of time points when loading data. In makie_post_process these options are read from the input (if they are set) before get_run_info() is called, so that the run_info returned can be passed to setup_makie_post_processing_input!, to be used for defaults for the remaining options. If either itime_min or itime_max are ≤0, their values are used as offsets from the final time index of the run.
setup_makie_post_processing_input!() is called at the end of get_run_info(), for convenience when working interactively. Use moment_kinetics.load_data.get_run_info_no_setup if you do not want this. A post-processing input file can be passed to setup_input_file that will be passed to setup_makie_post_processing_input!() if you do not want to use the default input file.
makie_post_processing.get_variable_symbol — Methodget_variable_symbol(variable_name)Get a symbol corresponding to a variable_name
For example get_variable_symbol("phi") returns "ϕ".
If the symbol has not been defined, just return variable_name.
makie_post_processing.grid_points_to_faces — Functiongrid_points_to_faces(coord::AbstractVector)
grid_points_to_faces(coord::Observable{T} where T <: AbstractVector)
grid_points_to_faces(coord::AbstractMatrix)
grid_points_to_faces(coord::Observable{T} where T <: AbstractMatrix)Turn grid points in coord into 'cell faces'.
Returns faces, which has a length one greater than coord. The first and last values of faces are the first and last values of coord. The intermediate values are the mid points between grid points.
makie_post_processing.instability2D_plots — Functioninstability2D_plots(run_info::Tuple, variable_name; plot_prefix, zind=nothing)
instability2D_plots(run_info, variable_name; plot_prefix, zind=nothing,
axes_and_observables=nothing)Make plots of variable_name for analysis of 2D instability.
The information for the runs to analyse and plot is passed in run_info (as returned by get_run_info). If run_info is a Tuple, make plots comparing the runs, shown in a horizontal row..
Settings are read from the [instability2D] section of the input.
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf for plots and plot_prefix<some_identifying_string>.gif, etc. for animations.
When run_info is not a Tuple, axes_and_observables can be passed to add plots and animations to existing figures, although this is not very convenient - see the use of this argument when called from the run_info::Tuple method.
If zind is not passed, it is calculated as the z-index where the mode seems to have the maximum growth rate for this variable. Returns zind.
makie_post_processing.irregular_heatmap! — Methodirregular_heatmap!(ax, xs, ys, zs; kwargs...)Plot a heatmap onto the Axis ax where xs and ys are allowed to define irregularly spaced, 2d grids. zs gives the value in each cell of the grid.
The grid defined by xs and ys must have dimensions (nx, ny) == size(zs) .+ 1, as is the case for heatmap/image.
xs be an array of size (nx,ny) or a vector of size (nx).
ys be an array of size (nx,ny) or a vector of size (ny).
kwargs are passed to Makie's mesh() function.
Code adapted from: https://github.com/MakieOrg/Makie.jl/issues/742#issuecomment-1415809653
makie_post_processing.irregular_heatmap — Methodirregular_heatmap(xs, ys, zs; kwargs...)Plot a heatmap where xs and ys are allowed to define irregularly spaced, 2d grids. zs gives the value in each cell of the grid.
The grid defined by xs and ys must have dimensions (nx, ny) == size(zs) .+ 1, as is the case for heatmap/image.
xs be an array of size (nx,ny) or a vector of size (nx).
ys be an array of size (nx,ny) or a vector of size (ny).
kwargs are passed to Makie's mesh() function.
Code adapted from: https://github.com/MakieOrg/Makie.jl/issues/742#issuecomment-1415809653
makie_post_processing.makie_post_process — Methodmakie_post_process(run_dir...;
input_file::String=default_input_file_name,
restart_index::Union{Nothing,mk_int,Tuple}=nothing,
plot_prefix::Union{Nothing,AbstractString}=nothing)Run post processing with input read from a TOML file
run_dir... is the path to the directory to plot from. If more than one run_dir is given, plots comparing the runs in run_dir... are made. A momentkinetics binary output file can also be passed as `rundir, in which case the filename is only used to infer the directory andrun_name, so it is possible for example to pass a.moments.h5output file and still make distribution function plots (as long as the corresponding.dfns.h5` file exists).
restart_index specifies which restart to read if there are multiple restarts. The default (nothing) reads all restarts and concatenates them. An integer value reads the restart with that index - -1 indicates the latest restart (which does not have an index). A tuple with the same length as run_dir can also be passed to give a different restart_index for each run.
plot_prefix can be specified to give the prefix (directory and first part of file name) to use when saving plots/animations. By default the run directory and run name are used if there is only one run, and "comparisonplots/compare" is used if there are multiple runs.
If input_file does not exist, prints warning and uses default options.
makie_post_processing.makie_post_process — Methodmakie_post_process(run_dir::Union{String,Tuple},
new_input_dict::Dict{String,Any};
restart_index::Union{Nothing,mk_int,Tuple}=nothing,
plot_prefix::Union{Nothing,AbstractString}=nothing)Run post prossing, with (non-default) input given in a Dict
run_dir... is the path to the directory to plot from. If more than one run_dir is given, plots comparing the runs in run_dir... are made. A momentkinetics binary output file can also be passed as `rundir, in which case the filename is only used to infer the directory andrun_name, so it is possible for example to pass a.moments.h5output file and still make distribution function plots (as long as the corresponding.dfns.h5` file exists).
input_dict is a dictionary containing settings for the post-processing.
restart_index specifies which restart to read if there are multiple restarts. The default (nothing) reads all restarts and concatenates them. An integer value reads the restart with that index - -1 indicates the latest restart (which does not have an index). A tuple with the same length as run_dir can also be passed to give a different restart_index for each run.
plot_prefix can be specified to give the prefix (directory and first part of file name) to use when saving plots/animations. By default the run directory and run name are used if there is only one run, and "comparisonplots/compare" is used if there are multiple runs.
makie_post_processing.manufactured_solutions_analysis — Functionmanufactured_solutions_analysis(run_info; plot_prefix)
manufactured_solutions_analysis(run_info::Tuple; plot_prefix)Compare computed and manufactured solutions for field and moment variables for a 'method of manufactured solutions' (MMS) test.
The information for the run to analyse is passed in run_info (as returned by get_run_info).
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf for plots and plot_prefix<some_identifying_string>.gif, etc. for animations.
Settings are read from the [manufactured_solns] section of the input.
While a Tuple of run_info can be passed for compatibility with makie_post_process(), at present comparison of multiple runs is not supported - passing a Tuple of length greater than one will result in an error.
makie_post_processing.manufactured_solutions_analysis_dfns — Functionmanufactured_solutions_analysis_dfns(run_info; plot_prefix)
manufactured_solutions_analysis_dfns(run_info::Tuple; plot_prefix)Compare computed and manufactured solutions for distribution function variables for a 'method of manufactured solutions' (MMS) test.
The information for the run to analyse is passed in run_info (as returned by get_run_info).
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf for plots and plot_prefix<some_identifying_string>.gif, etc. for animations.
Settings are read from the [manufactured_solns] section of the input.
While a Tuple of run_info can be passed for compatibility with makie_post_process(), at present comparison of multiple runs is not supported - passing a Tuple of length greater than one will result in an error.
makie_post_processing.manufactured_solutions_get_field_and_field_sym — Method manufactured_solutions_get_field_and_field_sym(run_info, variable_name;
it=nothing, ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing)Get the data variable for variable_name from the output, and calculate the manufactured solution variable_sym.
The information for the runs to analyse and plot is passed in run_info (as returned by get_run_info).
it, ir, iz, ivperp, ivpa, ivzeta, ivr, ivz can be used to select a subset of the grid by passing an integer or range for any dimension.
Returns variable, variable_sym.
makie_post_processing.parse_colormap — Methodparse_colormap(colormap)Parse a colormap option
Allows us to have a string option which can be set in the input file and still use Reverse, etc. conveniently.
makie_post_processing.plot_1d — Methodplot_1d(xcoord, data; ax=nothing, xlabel=nothing, ylabel=nothing, title=nothing,
yscale=nothing, transform=identity, axis_args=Dict{Symbol,Any}(),
kwargs...)Make a 1d plot of data vs xcoord.
xlabel, ylabel and title can be passed to set axis labels and title for the (sub-)plot.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
If ax is passed, the plot will be added to that existing Axis, otherwise a new Figure and Axis will be created.
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Other kwargs are passed to Makie's lines!() function.
If ax is not passed, returns the Figure, otherwise returns the object returned by lines!().
makie_post_processing.plot_2d — Methodplot_2d(xcoord, ycoord, data; ax=nothing, colorbar_place=nothing, xlabel=nothing,
ylabel=nothing, title=nothing, colormap="reverse_deep",
colorscale=nothing, transform=identity, axis_args=Dict{Symbol,Any}(),
kwargs...)Make a 2d plot of data vs xcoord and ycoord.
xlabel, ylabel and title can be passed to set axis labels and title for the (sub-)plot.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
If ax is passed, the plot will be added to that existing Axis, otherwise a new Figure and Axis will be created.
colormap is included explicitly because we do some special handling so that extra Makie functionality can be specified by a prefix to the colormap string, rather than the standard Makie mechanism of creating a struct that modifies the colormap. For example Reverse("deep") can be passed as "reverse_deep". This is useful so that these extra colormaps can be specified in an input file, but is not needed for interactive use.
When xcoord and ycoord are both one-dimensional, uses Makie's heatmap!() function for the plot. If either or both of xcoord and ycoord are two-dimensional, instead uses irregular_heatmap!.
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Other kwargs are passed to Makie's heatmap!() function.
If ax is not passed, returns the Figure, otherwise returns the object returned by heatmap!().
makie_post_processing.plot_charged_pdf_2D_at_wall — Methodplot_charged_pdf_2D_at_wall(run_info; plot_prefix, electron=false)Make plots/animations of the ion distribution function at wall boundaries.
The information for the runs to plot is passed in run_info (as returned by get_run_info). If run_info is a Tuple, comparison plots are made where line plots/animations from the different runs are overlayed on the same axis, and heatmap plots/animations are displayed in a horizontal row.
Settings are read from the [wall_pdf] section of the input.
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf. When run_info is not a Tuple, plot_prefix is optional - plots/animations will be saved only if it is passed.
If electron=true is passed, plot electron distribution function instead of ion distribution function.
makie_post_processing.plot_f_unnorm_vs_vpa — Functionplot_f_unnorm_vs_vpa(run_info; input=nothing, electron=false, neutral=false,
it=nothing, is=1, iz=nothing, fig=nothing, ax=nothing,
outfile=nothing, yscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), kwargs...)Plot an unnormalized distribution function against $v_\parallel$ at a fixed z.
This function is only needed for moment-kinetic runs. These are currently only supported for the 1D1V case.
The information for the runs to plot is passed in run_info (as returned by get_run_info). If run_info is a Tuple, comparison plots are made where plots from the different runs are overlayed on the same axis.
By default plots the ion distribution function. If electron=true is passed, plots the electron distribution function instead. If neutral=true is passed, plots the neutral distribution function instead.
is selects which species to analyse.
it and iz specify the indices of the time- and z-points to choose. By default they are taken from input.
If input is not passed, it is taken from input_dict_dfns["f"].
The data needed will be loaded from file.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
When run_info is not a Tuple, an Axis can be passed to ax to have the plot added to ax. When ax is passed, if outfile is passed to save the plot, then the Figure containing ax must be passed to fig.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Any extra kwargs are passed to plot_1d.
makie_post_processing.plot_f_unnorm_vs_vpa_z — Functionplot_f_unnorm_vs_vpa_z(run_info; input=nothing, electron=false, neutral=false,
it=nothing, is=1, fig=nothing, ax=nothing, outfile=nothing,
yscale=identity, transform=identity, rasterize=true,
subtitles=nothing, axis_args=Dict{Symbol,Any}(), kwargs...)Plot unnormalized distribution function against $v_\parallel$ and z.
This function is only needed for moment-kinetic runs. These are currently only supported for the 1D1V case.
The information for the runs to plot is passed in run_info (as returned by get_run_info). If run_info is a Tuple, comparison plots are made where plots from the different runs are displayed in a horizontal row.
By default plots the ion distribution function. If electron=true is passed, plots the electron distribution function instead. If neutral=true is passed, plots the neutral distribution function instead.
is selects which species to analyse.
it specifies the time-index to choose. By default it is taken from input.
If input is not passed, it is taken from input_dict_dfns["f"].
The data needed will be loaded from file.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
When run_info is not a Tuple, an Axis can be passed to ax to have the plot created in ax. When ax is passed, if outfile is passed to save the plot, then the Figure containing ax must be passed to fig.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
rasterize is passed through to Makie's mesh!() function. The default is to rasterize plots as vectorized plots from mesh!() have a very large file size. Pass false to keep plots vectorized. Pass a number to increase the resolution of the rasterized plot by that factor.
When run_info is a Tuple, subtitles can be passed a Tuple (with the same length as run_info) to set the subtitle for each subplot.
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Any extra kwargs are passed to plot_2d.
makie_post_processing.plot_neutral_pdf_2D_at_wall — Methodplot_neutral_pdf_2D_at_wall(run_info; plot_prefix)Make plots/animations of the neutral particle distribution function at wall boundaries.
The information for the runs to plot is passed in run_info (as returned by get_run_info). If run_info is a Tuple, comparison plots are made where line plots/animations from the different runs are overlayed on the same axis, and heatmap plots/animations are displayed in a horizontal row.
Settings are read from the [wall_pdf_neutral] section of the input.
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf. When run_info is not a Tuple, plot_prefix is optional - plots/animations will be saved only if it is passed.
makie_post_processing.plot_vs_r — Functionplot_vs_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
plot_vs_r(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing, label=nothing,
outfile=nothing, yscale=nothing, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info) vs r.
If a Tuple of run_info is passed, the plots from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, label can be used to set the label for the line created by this plot, which would be used if it is added to a Legend.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's lines!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_r_t — Functionplot_vs_r_t(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_r_t(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs t and r.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_t — Functionplot_vs_t(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
plot_vs_t(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing, label=nothing,
outfile=nothing, yscale=nothing, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info) vs t.
If a Tuple of run_info is passed, the plots from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, label can be used to set the label for the line created by this plot, which would be used if it is added to a Legend.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's lines!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vpa — Functionplot_vs_vpa(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
plot_vs_vpa(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing, label=nothing,
outfile=nothing, yscale=nothing, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info) vs vpa.
If a Tuple of run_info is passed, the plots from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, label can be used to set the label for the line created by this plot, which would be used if it is added to a Legend.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's lines!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vpa_r — Functionplot_vs_vpa_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vpa_r(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vpa.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vpa_t — Functionplot_vs_vpa_t(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vpa_t(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs t and vpa.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vpa_vperp — Functionplot_vs_vpa_vperp(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vpa_vperp(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs vperp and vpa.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vpa_z — Functionplot_vs_vpa_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vpa_z(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vpa.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vperp — Functionplot_vs_vperp(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
plot_vs_vperp(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing, label=nothing,
outfile=nothing, yscale=nothing, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info) vs vperp.
If a Tuple of run_info is passed, the plots from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, label can be used to set the label for the line created by this plot, which would be used if it is added to a Legend.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's lines!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vperp_r — Functionplot_vs_vperp_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vperp_r(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vperp.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vperp_t — Functionplot_vs_vperp_t(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vperp_t(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs t and vperp.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vperp_z — Functionplot_vs_vperp_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vperp_z(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vperp.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vr — Functionplot_vs_vr(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
plot_vs_vr(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing, label=nothing,
outfile=nothing, yscale=nothing, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info) vs vr.
If a Tuple of run_info is passed, the plots from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, label can be used to set the label for the line created by this plot, which would be used if it is added to a Legend.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's lines!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vr_r — Functionplot_vs_vr_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vr_r(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vr.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vr_t — Functionplot_vs_vr_t(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vr_t(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs t and vr.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vr_vzeta — Functionplot_vs_vr_vzeta(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vr_vzeta(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs vzeta and vr.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vr_z — Functionplot_vs_vr_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vr_z(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vr.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vz — Functionplot_vs_vz(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
plot_vs_vz(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing, label=nothing,
outfile=nothing, yscale=nothing, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info) vs vz.
If a Tuple of run_info is passed, the plots from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, label can be used to set the label for the line created by this plot, which would be used if it is added to a Legend.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's lines!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vz_r — Functionplot_vs_vz_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vz_r(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vz.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vz_t — Functionplot_vs_vz_t(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vz_t(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs t and vz.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vz_vr — Functionplot_vs_vz_vr(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vz_vr(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs vr and vz.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vz_vzeta — Functionplot_vs_vz_vzeta(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vz_vzeta(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs vzeta and vz.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vz_z — Functionplot_vs_vz_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vz_z(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vz.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vzeta — Functionplot_vs_vzeta(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
plot_vs_vzeta(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing, label=nothing,
outfile=nothing, yscale=nothing, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info) vs vzeta.
If a Tuple of run_info is passed, the plots from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, label can be used to set the label for the line created by this plot, which would be used if it is added to a Legend.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's lines!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vzeta_r — Functionplot_vs_vzeta_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vzeta_r(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and vzeta.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vzeta_t — Functionplot_vs_vzeta_t(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vzeta_t(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs t and vzeta.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_vzeta_z — Functionplot_vs_vzeta_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_vzeta_z(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs z and vzeta.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_z — Functionplot_vs_z(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, yscale=nothing,
transform=identity, axis_args=Dict{Symbol,Any}(), it=nothing,
ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
ivzeta=nothing, ivr=nothing, ivz=nothing, kwargs...)
plot_vs_z(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing, label=nothing,
outfile=nothing, yscale=nothing, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info) vs z.
If a Tuple of run_info is passed, the plots from each run are overlayed on the same axis, and a legend is added.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
yscale can be used to set the scaling function for the y-axis. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_1d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's lines!() function.
When a single run_info is passed, label can be used to set the label for the line created by this plot, which would be used if it is added to a Legend.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's lines!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_z_r — Functionplot_vs_z_r(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_z_r(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs r and z.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plot_vs_z_t — Functionplot_vs_z_t(run_info::Tuple, var_name; is=1, data=nothing,
input=nothing, outfile=nothing, colorscale=identity,
transform=identity, axis_args=Dict{Symbol,Any}(),
it=nothing, ir=nothing, iz=nothing, ivperp=nothing,
ivpa=nothing, ivzeta=nothing, ivr=nothing, ivz=nothing,
kwargs...)
plot_vs_z_t(run_info, var_name; is=1, data=nothing,
input=nothing, ax=nothing,
colorbar_place=nothing, title=nothing,
outfile=nothing, colorscale=identity, transform=identity,
axis_args=Dict{Symbol,Any}(), it=nothing, ir=nothing,
iz=nothing, ivperp=nothing, ivpa=nothing, ivzeta=nothing,
ivr=nothing, ivz=nothing, kwargs...)Plot var_name from the run(s) represented by run_info (as returned by get_run_info)vs t and z.
If a Tuple of run_info is passed, the plots from each run are displayed in a horizontal row, and the subtitle for each subplot is the 'run name'.
it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, and ivz can be used to select different indices (for non-plotted dimensions) or range (for the plotted dimension) to use.
If outfile is given, the plot will be saved to a file with that name. The suffix determines the file type.
colorscale can be used to set the scaling function for the colors. Options are identity, log, log2, log10, sqrt, Makie.logit, Makie.pseudolog10 and Makie.Symlog10. transform is a function that is applied element-by-element to the data before it is plotted. For example when using a log scale on data that may contain some negative values it might be useful to pass transform=abs (to plot the absolute value) or transform=positive_or_nan (to ignore any negative or zero values).
axis_args are passed as keyword arguments to get_2d_ax(), and from there to the Axis constructor.
Extra kwargs are passed to Makie's heatmap!() function.
When a single run_info is passed, title can be used to set the title for the (sub-)plot.
When a single run_info is passed, an Axis can be passed to ax. If it is, the plot will be added to ax. A colorbar will be created in colorbar_place if it is given a GridPosition.
By default the data for the variable is loaded from the output represented by run_info. The data can optionally be passed to data if you have already loaded it.
Returns the Figure, unless ax was passed in which case the object returned by Makie's heatmap!() function is returned.
By default relevant settings are read from the var_name section of input_dict_dfns (if output that has distribution functions is being read) or input_dict (otherwise). The settings can also be passed as an AbstractDict or NamedTuple via the input argument. Sometimes needed, for example if var_name is not present in input_dict (in which case you would have had to create the array to be plotted and pass it to data).
makie_post_processing.plots_for_dfn_variable — Methodplots_for_dfn_variable(run_info, variable_name; plot_prefix, has_rdim=true,
has_zdim=true, is_1V=false)Make plots for the distribution function variable variable_name.
Which plots to make are determined by the settings in the section of the input whose heading is the variable name.
run_info is the information returned by get_run_info(). The dfns=true keyword argument must have been passed to get_run_info() so that output files containing the distribution functions are being read.
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf for plots and plot_prefix<some_identifying_string>.gif, etc. for animations.
has_rdim, has_zdim and/or is_1V can be passed to allow the function to skip some plots that do not make sense for 0D/1D or 1V simulations (regardless of the settings).
makie_post_processing.plots_for_variable — Methodplots_for_variable(run_info, variable_name; plot_prefix, has_rdim=true,
has_zdim=true, is_1V=false,
steady_state_residual_fig_axes=nothing)Make plots for the EM field or moment variable variable_name.
Which plots to make are determined by the settings in the section of the input whose heading is the variable name.
run_info is the information returned by get_run_info.
plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf for plots and plot_prefix<some_identifying_string>.gif, etc. for animations.
has_rdim, has_zdim and/or is_1V can be passed to allow the function to skip some plots that do not make sense for 0D/1D or 1V simulations (regardless of the settings).
steady_state_residual_fig_axes contains the figure, axes and legend places for steady state residual plots.
makie_post_processing.positive_or_nan — Methodpositive_or_nan(x; epsilon=0)If the argument x is zero or negative, replace it with NaN, otherwise return x.
epsilon can be passed if the number should be forced to be above some value (typically we would assume epsilon is small and positive, but nothing about this function forces it to be).
makie_post_processing.println_to_stdout_and_file — Methodprintln_to_stdout_and_file(io, stuff...)Print stuff both to stdout and to a file io.
makie_post_processing.put_legend_above — Methodputlegendabove(fig, ax; kwargs...)
Add a legend corresponding to the plot in ax to fig on the left of a new row at the top of the figure layout.
Additional kwargs are passed to the Legend() constructor.
makie_post_processing.put_legend_below — Methodputlegendbelow(fig, ax; kwargs...)
Add a legend corresponding to the plot in ax to fig on the left of a new row at the bottom of the figure layout.
Additional kwargs are passed to the Legend() constructor.
makie_post_processing.put_legend_left — Methodputlegendleft(fig, ax; kwargs...)
Add a legend corresponding to the plot in ax to fig on the bottom of a new column at the left of the figure layout.
Additional kwargs are passed to the Legend() constructor.
makie_post_processing.put_legend_right — Methodputlegendright(fig, ax; kwargs...)
Add a legend corresponding to the plot in ax to fig on the bottom of a new column at the right of the figure layout.
Additional kwargs are passed to the Legend() constructor.
makie_post_processing.save_animation — Methodsave_animation(fig, frame_index, nt, outfile)Animate fig and save the result in outfile.
frame_index is the Observable{mk_int} that updates the data used to make fig to a new time point. nt is the total number of time points to create.
The suffix of outfile determines the file type.
makie_post_processing.select_slice — Functionselect_slice(variable::AbstractArray, dims::Symbol...; input=nothing, it=nothing,
is=1, ir=nothing, iz=nothing, ivperp=nothing, ivpa=nothing,
ivzeta=nothing, ivr=nothing, ivz=nothing)Returns a slice of variable that includes only the dimensions given in dims..., e.g.
select_slice(variable, :t, :r)to get a two dimensional slice with t- and r-dimensions.
Any other dimensions present in variable have a single point selected. By default this point is set by the options in input (which must be a NamedTuple) (or the final point for time or the size of the dimension divided by 3 if input is not given). These defaults can be overridden using the keyword arguments it, is, ir, iz, ivperp, ivpa, ivzeta, ivr, ivz. Ranges can also be passed to these keyword arguments for the 'kept dimensions' in dims to select a subset of those dimensions.
This function only recognises what the dimensions of variable are by the number of dimensions in the array. It assumes that either the variable has already been sliced to the correct dimensions (if ndims(variable) == length(dims) it just returns variable) or that variable has the full number of dimensions it could have (i.e. 'field' variables have 3 dimensions, 'moment' variables 4, 'ion distribution function' variables 6 and 'neutral distribution function' variables 7).
makie_post_processing.setup_makie_post_processing_input! — Functionsetup_makie_post_processing_input!(input_file::Union{AbstractString,Nothing}=nothing;
run_info_moments=nothing, run_info_dfns=nothing,
allow_missing_input_file=false)
setup_makie_post_processing_input!(new_input_dict::AbstractDict{String,Any};
run_info_moments=nothing,
run_info_dfns=nothing)Pass input_file to read the input from an input file other than post_processing_input.toml. You can also pass a Dict{String,Any} of options.
Set up input, storing in the global input_dict and input_dict_dfns to be used in the various plotting and analysis functions.
The run_info that you are using (as returned by get_run_info) should be passed to run_info_moments (if it contains only the moments), or run_info_dfns (if it also contains the distributions functions), or both (if you have loaded both sets of output). This allows default values to be set based on the grid sizes and number of time points read from the output files. Note that setup_makie_post_processing_input!() is called by default at the end of get_run_info(), for conveinence in interactive use.
By default an error is raised if input_file does not exist. To continue anyway, using default options, pass allow_missing_input_file=true.
makie_post_processing.sound_wave_plots — Functionsound_wave_plots(run_info::Tuple; plot_prefix)
sound_wave_plots(run_info; outfile=nothing, ax=nothing, phi=nothing)Calculate decay rate and frequency for the damped 'sound wave' in a 1D1V simulation in a periodic box. Plot the mode amplitude vs. time along with the fitted decay rate.
The information for the runs to analyse and plot is passed in run_info (as returned by get_run_info). If run_info is a Tuple, comparison plots are made where line plots from the different runs are overlayed on the same axis.
Settings are read from the [sound_wave] section of the input.
When run_info is a Tuple, plot_prefix is required and gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix<some_identifying_string>.pdf. When run_info is not a Tuple, outfile can be passed, to save the plot to outfile.
When run_info is not a Tuple, ax can be passed to add the plot to an existing Axis.
When run_info is not a Tuple, the array containing data for phi can be passed to phi - by default this data is loaded from the output file.
makie_post_processing.timestep_diagnostics — Methodtimestep_diagnostics(run_info, run_info_dfns; plot_prefix=nothing, it=nothing)Plot a time-trace of some adaptive-timestep diagnostics: steps per output, timestep failures per output, how many times per output each variable caused a timestep failure, and which factor limited the length of successful timesteps (CFL, accuracy, max_timestep).
If plot_prefix is passed, it gives the path and prefix for plots to be saved to. They will be saved with the format plot_prefix_timestep_diagnostics.pdf.
it can be used to select a subset of the time points by passing a range.
makie_post_processing.timing_data — Methodtiming_data(run_info; plot_prefix=nothing, threshold=nothing,
include_patterns=nothing, exclude_patterns=nothing, ranks=nothing,
figsize=nothing, include_legend=true)Plot timings from different parts of the moment_kinetics code. Only timings from function calls during the time evolution loop are included, not from the setup, because we plot versus time.
To reduce clutter, timings whose total time (at the final time point) is less than threshold times the overall run time will be excluded. By default, threshold is 1.0e-3.
When there is more than one MPI rank present, the timings for each rank will be plotted separately. The lines will be labelled with the MPI rank, with the position of the labels moving along the lines one point at a time, to try to avoid overlapping many labels. If the curves all overlap, this will look like one curve labelled by many MPI ranks.
There are many timers, so it can be useful to filter them to see only the most relevant ones. By default all timers will be plotted. If include_patterns is passed, and exclude_patterns is not, then only the total time and any timers that match include_patterns (matches checked using occursin()) will be included in the plots. If exclude_patterns is passed, then any timers that match (matches checked using occursin()) exclude_patterns will be omitted, unless they match include_patterns in which case they will still be included. If ranks is passed, then only the MPI ranks with indices found in ranks will be included.
figsize can be passed to customize the size of the figures that plots are made on. This can be useful because the legends may become very large when many timers are plotted, in which case a larger figure might be needed.
threshold, exclude_patterns, include_patterns, ranks, and figsize can also be set in this_input_dict. When this function is called as part of makie_post_process, input_dict is passed as this_input_dict so that the settings are read from the post processing input file (by default post_processing_input.toml). The function arguments take precedence, if they are given.
If you load GLMakie by doing using GLMakie before running this function, but after calling using makie_post_processing (because CairoMakie is loaded when the module is loaded and would take over if you load GLMakie before makie_post_processing), the figures will be displayed in interactive windows. When you hover over a line some useful information will be displayed.
Pass include_legend=false to remove legends from the figures. This is mostly useful for interactive figures where hovering over the lines can show what they are, so that the legend is not needed.
makie_post_processing.shared_utils.calculate_and_write_frequencies — Method