plot

The plot module has all the functions related to plotting variables.

# Example:
import analysator as pt
pt.pt.
#press [tab] -> get the functions

analysator.plot.plot_colormap(filename=None, vlsvobj=None, filedir=None, step=None, outputdir=None, outputfile=None, nooverwrite=False, var=None, op=None, operator=None, title=None, cbtitle=None, draw=None, usesci=True, symlog=None, diff=None, boxm=None, boxre=None, colormap=None, run=None, nocb=False, internalcb=False, wmark=False, wmarkb=False, axisunit=None, thick=1.0, scale=1.0, tickinterval=0, noborder=False, noxlabels=False, noylabels=False, vmin=None, vmax=None, lin=None, external=None, expression=None, vscale=1.0, absolute=False, symmetric=False, pass_vars=None, pass_times=None, pass_full=False, fluxfile=None, fluxdir=None, flux_levels=None, fluxthick=1.0, fluxlines=1, fluxlinecolor='k', fsaved=None, nomask=False, Earth=None, highres=None, vectors=None, vectordensity=100, vectorcolormap='gray', vectorsize=1.0, streamlines=None, streamlinedensity=1, streamlinecolor='white', streamlinethick=1.0, axes=None, cbaxes=None, useimshow=False, imshowinterp='none')

Plots a coloured plot with axes and a colour bar.

Kword filename:

path to .vlsv file to use for input. Assumes a bulk file.

Kword vlsvobj:

Optionally provide a python vlsvfile object instead

Kword filedir:

Optionally provide directory where files are located and use step for bulk file name

Kword step:

output step index, used for constructing output (and possibly input) filename

Kword outputdir:

path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR) If directory does not exist, it will be created. If the string does not end in a forward slash, the final part will be used as a prefix for the files.

Kword outputfile:

Singular output file name

Kword nooverwrite:

Set to only perform actions if the target output file does not yet exist

Kword var:

variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms, E, B, v, V or others. Accepts any variable known by analysator. Per-population variables are simply given as “proton/rho” etc

Kword operator:

Operator to apply to variable: None, x, y, or z. Vector variables return either the queried component, or otherwise the magnitude.

Kword op:

duplicate of operator

Kword boxm:

zoom box extents [x0,x1,y0,y1] in metres (default and truncate to: whole simulation box)

Kword boxre:

zoom box extents [x0,x1,y0,y1] in Earth radii (default and truncate to: whole simulation box)

Kword colormap:

colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno, magma, parula, nipy_spectral, RdBu, bwr

Kword run:

run identifier, used for constructing output filename

Kword title:

string to use as plot title instead of time. Special case: Set to “msec” to plot time with millisecond accuracy or “musec” for microsecond accuracy. “sec” is integer second accuracy.

Kword cbtitle:

string to use as colorbar title instead of map name

Kword axisunit:

Plot axes using 10^{axisunit} m (default: Earth radius R_E)

Kword tickinterval:

Interval at which to have ticks on axes (not colorbar)

Kwird usesci:

Use scientific notation for colorbar ticks? (default: True)

Kword vmin,vmax:

min and max values for colour scale and colour bar. If no values are given, min and max values for whole plot (non-zero rho regions only) are used.

Kword symmetric:

Set the absolute value of vmin and vmax to the greater of the two

Kword lin:

Flag for using linear colour scaling instead of log. If an integer, defines number of colorbar ticks.

Kword symlog:

Use logarithmic scaling, but linear when abs(value) is below the value given to symlog. Allows symmetric quasi-logarithmic plots of e.g. transverse field components. A given of 0 or True translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can result in the innermost tick marks overlapping. In this case, using a larger value for symlog is suggested.

Kword wmark:

If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword wmarkb:

As for wmark, but uses an all-black Vlasiator logo.

Kword Earth:

If set, draws an earth at (0,0)

Kword highres:

Creates the image in high resolution, scaled up by this value (suitable for print).

Kword draw:

Set to anything but None or False in order to draw image on-screen instead of saving to file (requires x-windowing)

Kword noborder:

Plot figure edge-to-edge without borders (default off)

Kword noxlabels:

Suppress x-axis labels and title

Kword noylabels:

Suppress y-axis labels and title

Kword scale:

Scale text size (default=1.0)

Kword thick:

line and axis thickness, default=1.0

Kword nocb:

Set to suppress drawing of colourbar

Kword internalcb:

Set to draw colorbar inside plot instead of outside. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword external:

Optional function to use for external plotting of e.g. contours. The function receives the following arguments: ax, XmeshXY,YmeshXY, pass_maps If the function accepts a fifth variable, if set to true, it is expected to return a list of required variables for constructing the pass_maps dictionary.

Kword expression:

Optional function which calculates a custom expression to plot. The function receives the same dictionary of numpy arrays as external, as an argument pass_maps, the contents of which are maps of variables. Each is either of size [ysize,xsize] or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim]. If the function accepts a second variable, if set to true, it is expected to return a list of required variables for pass_maps.

Kword diff:

Instead of a regular plot, plot the difference between the selected plot type for the regular source file and the file given by this keyword. This overides external and expression keywords, as well as related pass_vars, pass_times, and pass_full.

Important note: the dictionaries of arrays passed to external and expression are of shape [ysize,xzize], so for some analysis transposing them is necessary. For pre-existing functions to use and to base new functions on, see the plot_helpers.py file.

Kword vscale:

Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3 or from tesla to nanotesla. Guesses correct units for colourbar for some known variables. Set to None to search for a default scaling settings.

Kword absolute:

Plot the absolute of the evaluated variable

Kword pass_vars:

Optional list of map names to pass to the external/expression functions as a dictionary of numpy arrays. Each is either of size [ysize,xsize] or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].

Kword pass_times:

Integer, how many timesteps in each direction should be passed to external/expression functions in pass_vars (e.g. pass_times=1 passes the values of three timesteps). If pass_times has two values, the first is the extent before, the second after. (e.g. pass_times=[2,1] passes the values of two preceding and one following timesteps for a total of four timesteps) This causes pass_vars to become a list of timesteps, with each timestep containing a dictionary of numpy arrays as for regular pass_vars. An additional dictionary entry is added as ‘dstep’ which gives the timestep offset from the master frame. Does not work if working from a vlsv-object.

Kword pass_full:

Set to anything but None in order to pass the full arrays instead of a zoomed-in section

Kword fluxfile:

Filename to plot fluxfunction from

Kword flux_levels:

A list of flux function values to plot as the contours (default: None, a set of constant intervals: np.linspace(-10,10,fluxlines*60))

Kword fluxdir:

Directory in which fluxfunction files can be found

Kword fluxthick:

Scale fluxfunction line thickness

Kword fluxlines:

Relative density of fluxfunction contours

Kword fluxlinecolor:

Set flux line color (default black)

Kword fsaved:

Overplot locations of fSaved. If keyword is set to a string, that will be the colour used.

Kword nomask:

Do not mask plotting based on proton density

Kword vectors:

Set to a vector variable to overplot (unit length vectors, color displays variable magnitude)

Kword vectordensity:

Aim for how many vectors to show in plot window (default 100)

Kword vectorcolormap:

Colormap to use for overplotted vectors (default: gray)

Kword vectorsize:

Scaling of vector sizes

Kword streamlines:

Set to a vector variable to overplot as streamlines

Kword streamlinedensity:

Set streamline density (default 1)

Kword streamlinecolor:

Set streamline color (default white)

Kword streamlinethick:

Set streamline thickness

Kword axes:

Provide the routine a set of axes to draw within instead of generating a new image. It is recommended to either also provide cbaxes or activate nocb, unless one wants a colorbar to be automatically added next to the panel (but this may affect the overall layout) Note that the aspect ratio of the colormap is made equal in any case, hence the axes proportions may change if the box and axes size are not designed to match by the user

Kword cbaxes:

Provide the routine a set of axes for the colourbar.

Kword useimshow:

Use imshow for raster background instead (default: False)

Kword imshowinterp:

Use this matplotlib interpolation for imshow (default: ‘none’)

Returns:

Outputs an image to a file or to the screen.

# Example usage:
plot_colormap(filename=fileLocation, var="MA", run="BCQ",
            colormap='nipy_spectral',step=j, outputdir=outputLocation,
            lin=True, wmark=1, vmin=2.7, vmax=10, 
            external=cavitoncontours, pass_vars=['rho','B','beta'])
# Where cavitoncontours is an external function which receives the arguments
#  ax, XmeshXY,YmeshXY, pass_maps
# where pass_maps is a dictionary of maps for the requested variables.

# example (simple) use of expressions:
def exprMA_cust(exprmaps, requestvariables=False):
    if requestvariables==True:
    return ['va']
    custombulkspeed=750000. # m/s
    va = exprmaps['va'][:,:]
    MA = custombulkspeed/va
    return MA
plot_colormap(filename=fileLocation, vmin=1 vmax=40, expression=exprMA_cust,lin=True)

analysator.plot.plot_colormap3dslice(filename=None, vlsvobj=None, filedir=None, step=None, run=None, outputdir=None, outputfile=None, nooverwrite=False, var=None, op=None, operator=None, title=None, cbtitle=None, draw=None, usesci=True, symlog=None, boxm=None, boxre=None, colormap=None, nocb=False, internalcb=False, wmark=False, wmarkb=False, axisunit=None, thick=1.0, scale=1.0, tickinterval=0, noborder=False, noxlabels=False, noylabels=False, vmin=None, vmax=None, lin=None, external=None, expression=None, diff=None, vscale=1.0, absolute=False, symmetric=False, pass_vars=None, pass_times=None, pass_full=False, fsaved=None, nomask=None, Earth=None, highres=None, vectors=None, vectordensity=100, vectorcolormap='gray', vectorsize=1.0, streamlines=None, streamlinedensity=1, streamlinecolor='white', streamlinethick=1.0, axes=None, cbaxes=None, normal='y', cutpoint=0.0, cutpointre=None, useimshow=False, imshowinterp='none')

Plots a coloured plot with axes and a colour bar.

Kword filename:

path to .vlsv file to use for input. Assumes a bulk file.

Kword vlsvobj:

Optionally provide a python vlsvfile object instead

Kword filedir:

Optionally provide directory where files are located and use step for bulk file name

Kword step:

output step index, used for constructing output (and possibly input) filename

Kword run:

run identifier, used for constructing output filename

Kword outputdir:

path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR) If directory does not exist, it will be created. If the string does not end in a forward slash, the final part will be used as a prefix for the files.

Kword outputfile:

Singular output file name

Kword nooverwrite:

Set to only perform actions if the target output file does not yet exist

Kword var:

variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms, E, B, v, V or others. Accepts any variable known by analysator. Per-population variables are simply given as “proton/rho” etc

Kword operator:

Operator to apply to variable: None, x, y, or z. Vector variables return either the queried component, or otherwise the magnitude.

Kword op:

duplicate of operator

Kword boxm:

zoom box extents [x0,x1,y0,y1] in metres (default and truncate to: whole simulation box)

Kword boxre:

zoom box extents [x0,x1,y0,y1] in Earth radii (default and truncate to: whole simulation box)

Kword colormap:

colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno, magma, parula, nipy_spectral, RdBu, bwr

Kword title:

string to use as plot title instead of time. Special case: Set to “msec” to plot time with millisecond accuracy or “musec” for microsecond accuracy. “sec” is integer second accuracy.

Kword cbtitle:

string to use as colorbar title instead of map name

Kword axisunit:

Plot axes using 10^{axisunit} m (default: Earth radius R_E)

Kword tickinterval:

Interval at which to have ticks on axes (not colorbar)

Kwird usesci:

Use scientific notation for colorbar ticks? (default: True)

Kword vmin,vmax:

min and max values for colour scale and colour bar. If no values are given, min and max values for whole plot (non-zero rho regions only) are used.

Kword symmetric:

Set the absolute value of vmin and vmax to the greater of the two

Kword lin:

Flag for using linear colour scaling instead of log

Kword symlog:

Use logarithmic scaling, but linear when abs(value) is below the value given to symlog. Allows symmetric quasi-logarithmic plots of e.g. transverse field components. A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can result in the innermost tick marks overlapping. In this case, using a larger value for symlog is suggested.

Kword wmark:

If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword wmarkb:

As for wmark, but uses an all-black Vlasiator logo.

Kword Earth:

If set, draws an earth at (0,0)

Kword highres:

Creates the image in high resolution, scaled up by this value (suitable for print).

Kword draw:

Set to nonzero in order to draw image on-screen instead of saving to file (requires x-windowing)

Kword noborder:

Plot figure edge-to-edge without borders (default off)

Kword noxlabels:

Suppress x-axis labels and title

Kword noylabels:

Suppress y-axis labels and title

Kword scale:

Scale text size (default=1.0)

Kword thick:

line and axis thickness, default=1.0

Kword nocb:

Set to suppress drawing of colourbar

Kword internalcb:

Set to draw colorbar inside plot instead of outside. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword external:

Optional function to use for external plotting of e.g. contours. The function receives the following arguments: ax, XmeshXY,YmeshXY, pass_maps If the function accepts a fifth variable, if set to true, it is expected to return a list of required variables for constructing the pass_maps dictionary.

Kword expression:

Optional function which calculates a custom expression to plot. The function receives the same dictionary of numpy arrays as external, as an argument pass_maps, the contents of which are maps of variables. Each is either of size [ysize,xsize] or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim]. If the function accepts a second variable, if set to true, it is expected to return a list of required variables for pass_maps.

Important note: the dictionaries of arrays passed to external and expression are of shape [ysize,xzize], so for some analysis transposing them is necessary. For pre-existing functions to use and to base new functions on, see the plot_helpers.py file.

Kword vscale:

Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3 or from tesla to nanotesla. Guesses correct units for colourbar for some known variables. Set to None to seek for a default scaling.

Kword absolute:

Plot the absolute of the evaluated variable

Kword pass_vars:

Optional list of map names to pass to the external/expression functions as a dictionary of numpy arrays. Each is either of size [ysize,xsize] or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].

Kword pass_times:

Integer, how many timesteps in each direction should be passed to external/expression functions in pass_vars (e.g. pass_times=1 passes the values of three timesteps). If pass_times has two values, the first is the extent before, the second after. (e.g. pass_times=[2,1] passes the values of two preceding and one following timesteps for a total of four timesteps) This causes pass_vars to become a list of timesteps, with each timestep containing a dictionary of numpy arrays as for regular pass_vars. An additional dictionary entry is added as ‘dstep’ which gives the timestep offset from the master frame. Does not work if working from a vlsv-object.

Kword pass_full:

Set to anything but None in order to pass the full arrays instead of a zoomed-in section

Kword diff:

Instead of a regular plot, plot the difference between the selected plot type for the regular source file and the file given by this keyword. This overides external and expression keywords, as well as related pass_vars, pass_times, and pass_full.

Kword fsaved:

Overplot locations of fSaved. If keyword is set to a string, that will be the colour used.

Kword nomask:

Do not mask plotting based on proton density

Kword vectors:

Set to a vector variable to overplot (unit length vectors, color displays variable magnitude)

Kword vectordensity:

Aim for how many vectors to show in plot window (default 100)

Kword vectorcolormap:

Colormap to use for overplotted vectors (default: gray)

Kword vectorsize:

Scaling of vector sizes

Kword streamlines:

Set to a vector variable to overplot as streamlines

Kword streamlinedensity:

Set streamline density (default 1)

Kword streamlinecolor:

Set streamline color (default white)

Kword streamlinethick:

Set streamline thickness

Kword axes:

Provide the routine a set of axes to draw within instead of generating a new image. It is recommended to either also provide cbaxes or activate nocb, unless one wants a colorbar to be automatically added next to the panel (but this may affect the overall layout) Note that the aspect ratio of the colormap is made equal in any case, hence the axes proportions may change if the box and axes size are not designed to match by the user

Kword cbaxes:

Provide the routine a set of axes for the colourbar.

Kword normal:

Direction of the normal of the 2D cut through (‘x’, ‘y’, or ‘z’ or a vector)

Kword cutpoint:

Coordinate (in normal direction) through which the cut must pass [m]

Kword cutpointre:

Coordinate (in normal direction) through which the cut must pass [rE]

Kword useimshow:

Use imshow for raster background instead (default: False)

Kword imshowinterp:

Use this matplotlib interpolation for imshow (default: ‘none’)

Returns:

Outputs an image to a file or to the screen.

# Example usage:
plot_colormap(filename=fileLocation, var="MA", run="BCQ",
            colormap='nipy_spectral',step=j, outputdir=outputLocation,
            lin=1, wmark=1, vmin=2.7, vmax=10, 
            external=cavitoncontours, pass_vars=['rho','B','beta'])
# Where cavitoncontours is an external function which receives the arguments
#  ax, XmeshXY,YmeshXY, pass_maps
# where pass_maps is a dictionary of maps for the requested variables.

# example (simple) use of expressions:
def exprMA_cust(exprmaps, requestvariables=False):
    if requestvariables==True:
    return ['va']
    custombulkspeed=750000. # m/s
    va = exprmaps['va'][:,:]
    MA = custombulkspeed/va
    return MA
plot_colormap(filename=fileLocation, vmin=1 vmax=40, expression=exprMA_cust,lin=1)

analysator.plot.plot_ionosphere(filename=None, vlsvobj=None, filedir=None, step=None, run=None, outputdir=None, outputfile=None, nooverwrite=False, var=None, op=None, operator=None, colormap=None, vmin=None, vmax=None, symmetric=False, absolute=None, usesci=True, log=None, lin=None, symlog=None, nocb=False, internalcb=False, minlatitude=60, cbtitle=None, title=None, cbaxes=None, thick=1.0, scale=1.0, vscale=1.0, wmark=False, wmarkb=False, viewdir=1.0, draw=None, axes=None)

Plots a 2d projection of an ionosphere variable

Kword filename:

path to .vlsv file to use for input. Assumes a bulk file.

Kword vlsvobj:

Optionally provide a python vlsvfile object instead

Kword filedir:

Optionally provide directory where files are located and use step for bulk file name

Kword step:

output step index, used for constructing output (and possibly input) filename

Kword run:

run identifier, used for constructing output filename

Kword outputdir:

path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR) If directory does not exist, it will be created. If the string does not end in a forward slash, the final part will be used as a prefix for the files.

Kword outputfile:

Singular output file name

Kword nooverwrite:

Set to only perform actions if the target output file does not yet exist

Kword var:

variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms, E, B, v, V or others. Accepts any variable known by analysator. Per-population variables are simply given as “proton/rho” etc

Kword operator:

Operator to apply to variable: None, x, y, or z. Vector variables return either the queried component, or otherwise the magnitude.

Kword op:

duplicate of operator

Kword colormap:

colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno, magma, parula, nipy_spectral, RdBu, bwr

Kword vmin,vmax:

min and max values for colour scale and colour bar. If no values are given, min and max values for whole plot (non-zero rho regions only) are used.

Kword symmetric:

Set the absolute value of vmin and vmax to the greater of the two

Kword absolute:

Plot the absolute of the evaluated variable

Kwird usesci:

Use scientific notation for colorbar ticks? (default: True)

Kword lin:

Flag for using linear colour scaling instead of log

Kword symlog:

Use logarithmic scaling, but linear when abs(value) is below the value given to symlog. Allows symmetric quasi-logarithmic plots of e.g. transverse field components. A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can result in the innermost tick marks overlapping. In this case, using a larger value for symlog is suggested.

Kword nocb:

Set to suppress drawing of colourbar

Kword internalcb:

Set to draw colorbar inside plot instead of outside. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword minlatitude:

Minimum plot latitude (default=60 degrees)

Kword title:

string to use as plot title instead of time. Special case: Set to “msec” to plot time with millisecond accuracy or “musec” for microsecond accuracy. “sec” is integer second accuracy.

Kword cbtitle:

string to use as colorbar title instead of map name

Kword viewdir:

view direction onto the sphere. Positive value: North pole. Negative values: South pole.

Kword scale:

Scale text size (default=1.0)

Kword vscale:

Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3 or from tesla to nanotesla. Guesses correct units for colourbar for some known variables.

Kword axes:

Provide the routine a set of axes to draw within instead of generating a new image.

Kword cbaxes:

Provide the routine a set of axes for the colourbar.

Kword thick:

line and axis thickness, default=1.0

Kword draw:

Set to anything but None or False in order to draw image on-screen instead of saving to file (requires x-windowing)

Kword wmark:

If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword wmarkb:

As for wmark, but uses an all-black Vlasiator logo.

analysator.plot.plot_isosurface(filename=None, vlsvobj=None, filedir=None, step=None, outputdir=None, nooverwrite=None, surf_var=None, surf_op=None, surf_level=None, color_var=None, color_op=None, surf_step=1, title=None, cbtitle=None, draw=None, usesci=None, symmetric=False, highres=None, boxm=[], boxre=[], colormap=None, run=None, wmark=None, nocb=False, unit=None, thick=1.0, scale=1.0, vscale=1.0, vmin=None, vmax=None, lin=None, symlog=None, angle=[30.0, 90.0], transparent=True)

Plots a coloured isosurface plot with axes and a colour bar.

Kword filename:

path to .vlsv file to use for input. Assumes a bulk file.

Kword vlsvobj:

Optionally provide a python vlsvfile object instead

Kword filedir:

Optionally provide directory where files are located and use step for bulk file name

Kword step:

output step index, used for constructing output (and possibly input) filename

Kword outputdir:

path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR) If directory does not exist, it will be created. If the string does not end in a forward slash, the final parti will be used as a perfix for the files.

Kword nooverwrite:

Set to only perform actions if the target output file does not yet exist

Kword surf_var:

Variable to read for defining surface

Kword surf_op:

Operator to use for variable to read surface

Kword surf_level:

Level at which to define surface

Kword surf_step:

Vertex stepping for surface generation: larger value returns coarser surface

Kword color_var:

Variable to read for coloring surface

Kword color_op:

Operator to use for variable to color surface (‘x’, ‘y’, ‘z’; if None and color_var is a vector, the magnitude is taken)

Kword boxm:

zoom box extents [x0,x1,y0,y1] in metres (default and truncate to: whole simulation box)

Kword boxre:

zoom box extents [x0,x1,y0,y1] in Earth radii (default and truncate to: whole simulation box)

Kword colormap:

colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno, magma, parula, nipy_spectral, RdBu, bwr

Kword run:

run identifier, used for constructing output filename

Kword title:

string to use as plot title instead of time

Kword cbtitle:

string to use as colorbar title instead of map name

Kword unit:

Plot axes using 10^{unit} m (default: Earth radius R_E)

Kwird usesci:

Use scientific notation for colorbar ticks? (default: 1)

Kword vscale:

Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3 or from tesla to nanotesla. Guesses correct units for colourbar for some known variables. Set to None to seek for a default scaling.

Kword vmin,vmax:

min and max values for colour scale and colour bar. If no values are given, min and max values for whole plot (non-zero rho regions only) are used.

Kword symmetric:

Set the absolute value of vmin and vmax to the greater of the two

Kword lin:

Flag for using linear colour scaling instead of log

Kword symlog:

Use logarithmic scaling, but linear when abs(value) is below the value given to symlog. Allows symmetric quasi-logarithmic plots of e.g. transverse field components. A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2.

Kword wmark:

If set to non-zero, will plot a Vlasiator watermark in the top left corner.

Kword highres:

Creates the image in high resolution, scaled up by this value (suitable for logging.info).

Kword draw:

Set to nonzero in order to draw image on-screen instead of saving to file (requires x-windowing)

Kword transparent:

Set to False in order to make the surface opaque

Kword scale:

Scale text size (default=1.0)

Kword thick:

line and axis thickness, default=1.0

Kword nocb:

Set to suppress drawing of colourbar

Kword angle:

Viewing elevation and azimuthal angles in degrees

Returns:

Outputs an image to a file or to the screen.

# Example usage:

analysator.plot.plot_multiple_variables(variables_x_list, variables_y_list, figure=[], clean_xticks=False)

Plots multiple variables from the input with pylab

Parameters:

• variables_x_list – Some list of variables to be plotted in the x-axis

• variables_y_list – Some list of variables to be plotted in the y-axis

• figure – If one wants to plot into an existing figure then the matplotlib figure should be passed as an argument (OPTIONAL)

Returns:

a pylab figure with the plot

#Example usage:
plot_multiple_variables( [distances, xcoordinates], [rho, B_x] )
# This would plot rho_values as a function of distance and B_x_values as a function of xcoordinates

Note

Multiplot expects variables to be saved in the VariableInfo class

Note

If for some reason some variable list (x or y) is empty, e.g. variables_x_list = [B_x, [], B_z, rho], then the variable will not be plotted. This can be used if one wants to plot only into certain subplots.

analysator.plot.plot_neutral_sheet(filename=None, vlsvobj=None, filedir=None, step=None, run=None, outputdir=None, outputfile=None, nooverwrite=False, var=None, op=None, operator=None, title=None, cbtitle=None, draw=None, usesci=True, symlog=None, boxm=None, boxre=None, colormap=None, nocb=False, internalcb=False, wmark=False, wmarkb=False, axisunit=None, thick=1.0, scale=1.0, tickinterval=0, noborder=False, noxlabels=False, noylabels=False, vmin=None, vmax=None, lin=None, external=None, expression=None, diff=None, vscale=1.0, absolute=False, symmetric=False, pass_vars=None, pass_times=None, pass_full=False, nomask=None, Earth=None, highres=None, vectors=None, vectordensity=100, vectorcolormap='gray', vectorsize=1.0, streamlines=None, streamlinedensity=1, streamlinecolor='white', streamlinethick=1.0, axes=None, cbaxes=None, useimshow=False, imshowinterp='none', folding_alpha=0.2, z_extent=[-5, 5], sheetlayer='above')

Plots a coloured plot along the neutral sheet with axes and a colour bar.

Kword filename:

path to .vlsv file to use for input. Assumes a bulk file.

Kword vlsvobj:

Optionally provide a python vlsvfile object instead

Kword filedir:

Optionally provide directory where files are located and use step for bulk file name

Kword step:

output step index, used for constructing output (and possibly input) filename

Kword run:

run identifier, used for constructing output filename

Kword outputdir:

path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR) If directory does not exist, it will be created. If the string does not end in a forward slash, the final part will be used as a prefix for the files.

Kword outputfile:

Singular output file name

Kword nooverwrite:

Set to only perform actions if the target output file does not yet exist

Kword var:

variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms, E, B, v, V or others. Accepts any variable known by analysator. Per-population variables are simply given as “proton/rho” etc

Kword operator:

Operator to apply to variable: None, x, y, or z. Vector variables return either the queried component, or otherwise the magnitude.

Kword op:

duplicate of operator

Kword boxm:

zoom box extents [x0,x1,y0,y1] in metres (default and truncate to: whole simulation box)

Kword boxre:

zoom box extents [x0,x1,y0,y1] in Earth radii (default and truncate to: whole simulation box)

Kword colormap:

colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno, magma, parula, nipy_spectral, RdBu, bwr

Kword title:

string to use as plot title instead of time. Special case: Set to “msec” to plot time with millisecond accuracy or “musec” for microsecond accuracy. “sec” is integer second accuracy.

Kword cbtitle:

string to use as colorbar title instead of map name

Kword axisunit:

Plot axes using 10^{axisunit} m (default: Earth radius R_E)

Kword tickinterval:

Interval at which to have ticks on axes (not colorbar)

Kwird usesci:

Use scientific notation for colorbar ticks? (default: True)

Kword vmin,vmax:

min and max values for colour scale and colour bar. If no values are given, min and max values for whole plot (non-zero rho regions only) are used.

Kword symmetric:

Set the absolute value of vmin and vmax to the greater of the two

Kword lin:

Flag for using linear colour scaling instead of log

Kword symlog:

Use logarithmic scaling, but linear when abs(value) is below the value given to symlog. Allows symmetric quasi-logarithmic plots of e.g. transverse field components. A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can result in the innermost tick marks overlapping. In this case, using a larger value for symlog is suggested.

Kword wmark:

If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword wmarkb:

As for wmark, but uses an all-black Vlasiator logo.

Kword Earth:

If set, draws an earth at (0,0)

Kword highres:

Creates the image in high resolution, scaled up by this value (suitable for print).

Kword draw:

Set to nonzero in order to draw image on-screen instead of saving to file (requires x-windowing)

Kword noborder:

Plot figure edge-to-edge without borders (default off)

Kword noxlabels:

Suppress x-axis labels and title

Kword noylabels:

Suppress y-axis labels and title

Kword scale:

Scale text size (default=1.0)

Kword thick:

line and axis thickness, default=1.0

Kword nocb:

Set to suppress drawing of colourbar

Kword internalcb:

Set to draw colorbar inside plot instead of outside. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword external:

Optional function to use for external plotting of e.g. contours. The function receives the following arguments: ax, XmeshXY,YmeshXY, pass_maps If the function accepts a fifth variable, if set to true, it is expected to return a list of required variables for constructing the pass_maps dictionary.

Kword expression:

Optional function which calculates a custom expression to plot. The function receives the same dictionary of numpy arrays as external, as an argument pass_maps, the contents of which are maps of variables. Each is either of size [ysize,xsize] or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim]. If the function accepts a second variable, if set to true, it is expected to return a list of required variables for pass_maps.

Important note: the dictionaries of arrays passed to external and expression are of shape [ysize,xzize], so for some analysis transposing them is necessary. For pre-existing functions to use and to base new functions on, see the plot_helpers.py file.

Kword vscale:

Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3 or from tesla to nanotesla. Guesses correct units for colourbar for some known variables. Set to None to seek for a default scaling.

Kword absolute:

Plot the absolute of the evaluated variable

Kword pass_vars:

Optional list of map names to pass to the external/expression functions as a dictionary of numpy arrays. Each is either of size [ysize,xsize] or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].

Kword pass_times:

Integer, how many timesteps in each direction should be passed to external/expression functions in pass_vars (e.g. pass_times=1 passes the values of three timesteps). If pass_times has two values, the first is the extent before, the second after. (e.g. pass_times=[2,1] passes the values of two preceding and one following timesteps for a total of four timesteps) This causes pass_vars to become a list of timesteps, with each timestep containing a dictionary of numpy arrays as for regular pass_vars. An additional dictionary entry is added as ‘dstep’ which gives the timestep offset from the master frame. Does not work if working from a vlsv-object.

Kword pass_full:

Set to anything but None in order to pass the full arrays instead of a zoomed-in section

Kword diff:

Instead of a regular plot, plot the difference between the selected plot type for the regular source file and the file given by this keyword. This overides external and expression keywords, as well as related pass_vars, pass_times, and pass_full.

Kword z_extent:

Search bracket for the neutral sheet in axisunit units

Kword folding_alpha:

If non-zero, plots transparent dots over the regions where the sheet has multiple separate z-values. A value of 1.0 is opaque, a value of 0.0 is transparent.

Kword sheetlayer:

If set to ‘above’, plots the topmost layer of the neutral sheet in case of folding. If set to anything else, the downmost layer is plotted.

Kword nomask:

Do not mask plotting based on proton density

Kword vectors:

Set to a vector variable to overplot (unit length vectors, color displays variable magnitude)

Kword vectordensity:

Aim for how many vectors to show in plot window (default 100)

Kword vectorcolormap:

Colormap to use for overplotted vectors (default: gray)

Kword vectorsize:

Scaling of vector sizes

Kword streamlines:

Set to a vector variable to overplot as streamlines

Kword streamlinedensity:

Set streamline density (default 1)

Kword streamlinecolor:

Set streamline color (default white)

Kword streamlinethick:

Set streamline thickness

Kword axes:

Provide the routine a set of axes to draw within instead of generating a new image. It is recommended to either also provide cbaxes or activate nocb, unless one wants a colorbar to be automatically added next to the panel (but this may affect the overall layout) Note that the aspect ratio of the colormap is made equal in any case, hence the axes proportions may change if the box and axes size are not designed to match by the user

Kword cbaxes:

Provide the routine a set of axes for the colourbar.

Kword normal:

Direction of the normal of the 2D cut through (‘x’, ‘y’, or ‘z’ or a vector)

Kword cutpoint:

Coordinate (in normal direction) through which the cut must pass [m]

Kword cutpointre:

Coordinate (in normal direction) through which the cut must pass [rE]

Kword useimshow:

Use imshow for raster background instead (default: False)

Kword imshowinterp:

Use this matplotlib interpolation for imshow (default: ‘none’)

Returns:

Outputs an image to a file or to the screen.

# Example usage:
plot_colormap(filename=fileLocation, var="MA", run="BCQ",
            colormap='nipy_spectral',step=j, outputdir=outputLocation,
            lin=1, wmark=1, vmin=2.7, vmax=10, 
            external=cavitoncontours, pass_vars=['rho','B','beta'])
# Where cavitoncontours is an external function which receives the arguments
#  ax, XmeshXY,YmeshXY, pass_maps
# where pass_maps is a dictionary of maps for the requested variables.

# example (simple) use of expressions:
def exprMA_cust(exprmaps, requestvariables=False):
    if requestvariables==True:
    return ['va']
    custombulkspeed=750000. # m/s
    va = exprmaps['va'][:,:]
    MA = custombulkspeed/va
    return MA
plot_colormap(filename=fileLocation, vmin=1 vmax=40, expression=exprMA_cust,lin=1)

analysator.plot.plot_threeslice(filename=None, vlsvobj=None, filedir=None, step=None, run=None, outputdir=None, outputfile=None, nooverwrite=False, var=None, op=None, operator=None, boxm=None, boxre=None, colormap=None, vmin=None, vmax=None, symmetric=False, absolute=None, lin=None, symlog=None, nocb=False, cbtitle=None, title=None, halfaxes=False, usesci=True, axisunit=None, axiscolor=None, shadings=None, draw=None, tickinterval=None, fixedticks=False, pass_full=None, wmark=False, wmarkb=False, nomask=None, Earth=True, thick=1.0, scale=1.0, expression=None, vscale=1.0, viewangle=(-60.0, 30.0), cutpointm=None, cutpointre=None, slices=None)

Plots a 3d plot constructed of three 2d cut throughs.

Kword filename:

path to .vlsv file to use for input. Assumes a bulk file.

Kword vlsvobj:

Optionally provide a python vlsvfile object instead

Kword filedir:

Optionally provide directory where files are located and use step for bulk file name

Kword step:

output step index, used for constructing output (and possibly input) filename

Kword run:

run identifier, used for constructing output filename

Kword outputdir:

path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR) If directory does not exist, it will be created. If the string does not end in a forward slash, the final part will be used as a prefix for the files.

Kword outputfile:

Singular output file name

Kword draw:

Set to anything but None or False in order to draw image on-screen instead of saving to file (requires x-windowing)

Kword nooverwrite:

Set to only perform actions if the target output file does not yet exist

Kword var:

variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms, E, B, v, V or others. Accepts any variable known by analysator. Per-population variables are simply given as “proton/rho” etc

Kword operator:

Operator to apply to variable: None, x, y, or z. Vector variables return either the queried component, or otherwise the magnitude.

Kword op:

duplicate of operator

Kword boxm:

zoom box extents [x0,x1,y0,y1,z0,z1] in metres (default and truncate to: whole simulation box)

Kword boxre:

zoom box extents [x0,x1,y0,y1,z0,z1] in Earth radii (default and truncate to: whole simulation box)

Kword colormap:

colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno, magma, parula, nipy_spectral, RdBu, bwr

Kword vmin,vmax:

min and max values for colour scale and colour bar. If no values are given, min and max values for whole plot (non-zero rho regions only) are used.

Kword symmetric:

Set the absolute value of vmin and vmax to the greater of the two

Kword absolute:

Plot the absolute of the evaluated variable

Kword lin:

Flag for using linear colour scaling instead of log

Kword symlog:

Use logarithmic scaling, but linear when abs(value) is below the value given to symlog. Allows symmetric quasi-logarithmic plots of e.g. transverse field components. A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can result in the innermost tick marks overlapping. In this case, using a larger value for symlog is suggested.

Kword nocb:

Set to suppress drawing of colourbar

Kword title:

string to use as plot title instead of time. Special case: Set to “msec” to plot time with millisecond accuracy or “musec” for microsecond accuracy. “sec” is integer second accuracy.

Kword cbtitle:

string to use as colorbar title instead of map name

Kword halfaxes:

Flag to prevent plotting the hidden half of the axes, otherwise shown as dashed lines (default: False)

Kwird usesci:

Use scientific notation for colorbar ticks? (default: True)

Kword axisunit:

Plot axes using 10^{axisunit} m (default: Earth radius R_E)

Kword axiscolor:

Color for drawing axes (default black)

Kword shadings:

Dimming values for the surfaces normal to the X, Y, Z directions, respectively, to better distinguish the slices, e.g. “(0.6,0.8,1.0). Default using the angles between the surface normal directions and the viewing angle.

Kword tickinterval:Axis tick interval, expressed in 10^{axisunit} (default:

10 Earth radii)

Kword fixedticks:

Set ticks at fixed locations instead of relative to the triple cut point (default: False)

Kword pass_full:

Set to anything but None in order to pass the full arrays instead of a zoomed-in section

Kword wmark:

If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword wmarkb:

As for wmark, but uses an all-black Vlasiator logo.

Kword nomask:

Do not mask plotting based on proton density

Kword Earth:

Draw Earth at origin (default True)

Kword scale:

Scale text size (default=1.0)

Kword thick:

line and axis thickness, default=1.0

Kword expression:

Optional function which calculates a custom expression to plot. The function receives the same dictionary of numpy arrays as external, as an argument pass_maps, the contents of which are maps of variables. Each is either of size [ysize,xsize] or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim]. If the function accepts a second variable, if set to true, it is expected to return a list of required variables for pass_maps.

Important note: the dictionaries of arrays passed to external and expression are of shape [ysize,xzize], so for some analysis transposing them is necessary. For pre-existing functions to use and to base new functions on, see the plot_helpers.py file.

Kword vscale:

Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3 or from tesla to nanotesla. Guesses correct units for colourbar for some known variables. Set to None to search for a default scaling.

Kword viewangle:

Azimuth and elevation angles giving the point of view on the 3D axes, in degrees. (default=(-60.,30.); corresponds to dayside, morningside, northern hemisphere)

Kword cutpointm:

Coordinates of the point through which all three 2D cuts must pass [m]

Kword cutpointre:

Coordinates of the point through which all three 2D cuts must pass [rE]

Kword slices:

Normal directions of the slices to plot, default=’xyz’

analysator.plot.plot_variables(x, y, figure=[])

Plots x and y variables from the input with pylab

Parameters:

• x – Some variable to be plotted in the x-axis

• y – Some variable to be plotted in the y-axis

• figure – If one wants to plot into an existing figure then the matplotlib figure should be passed as an argument (OPTIONAL)

Returns:

a pylab figure with the plot

# Example usage:
plot_variables( distances, rho )
# This would plot rho as a function of distance

analysator.plot.plot_vdf(filename=None, vlsvobj=None, filedir=None, step=None, cellids=None, pop='proton', coordinates=None, coordre=None, outputdir=None, outputfile=None, nooverwrite=None, draw=None, axisunit=None, axiskmps=None, title=None, cbtitle=None, tickinterval=None, colormap=None, box=None, nocb=None, internalcb=None, run=None, thick=1.0, wmark=None, wmarkb=None, fmin=None, fmax=None, slicethick=None, reducer='integrate', resampler=True, cellsize=None, xy=None, xz=None, yz=None, normal=None, normalx=None, bpara=None, bpara1=None, bperp=None, coordswap=None, bvector=None, bvectorscale=0.2, cbulk=None, cpeak=None, center=None, wflux=None, setThreshold=None, noborder=None, scale=1.0, scale_text=8.0, scale_title=10.0, scale_cb=5.0, scale_label=12.0, biglabel=None, biglabloc=None, noxlabels=None, noylabels=None, axes=None, cbaxes=None, contours=None)

Plots a coloured 2D plot of a VDF (a slice of given thickness or fully projected) with axes and a colour bar.

Kword filename:

path to .vlsv file to use for input. Assumes a bulk file.

Kword vlsvobj:

Optionally provide a python vlsvfile object instead

Kword filedir:

Optionally provide directory where files are located and use step for bulk file name

Kword step:

output step index, used for constructing output (and possibly input) filename

Kword outputdir:

path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR) If directory does not exist, it will be created. If the string does not end in a forward slash, the final parti will be used as a perfix for the files.

Kword nooverwrite:

Set to only perform actions if the target output file does not yet exist

Kword cellids:

LIST of cell IDs to plot VDF for

Kword coordinates:

LIST of 3-element spatial coordinate lusts to plot VDF for (given in metres)

Kword coordre:

LIST of 3-element spatial coordinate lists to plot VDF for (given in Earth radii)

Kword pop:

Population to plot, default proton

Kword colormap:

colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno, magma, parula, nipy_spectral, RdBu, bwr

Kword run:

run identifier, used for constructing output filename

Kword title:

string to use as plot title instead of time. Special case: Set to “msec” to plot time with millisecond accuracy or “musec” for microsecond accuracy. “sec” is integer second accuracy.

Kword cbtitle:

string to use as colorbar title instead of phase space density of flux

Kword contours:

Set to number of contours to draw

Kword fmin,fmax:

min and max values for colour scale and colour bar. If no values are given, min and max values for whole plot are used.

Kword box:

extents of plotted velocity grid as [x0,x1,y0,y1] (in m/s)

Kword axisunit:

Plot v-axes using 10^{axisunit} m/s (default: km/s)

Kword axiskmps:

Plot v-axes using 10^{axiskmps} km/s (default: km/s, when the kword has a value)

Kword tickinterval:

Interval at which to have ticks on axes

Kword xy:

Perform slice in x-y-direction

Kword xz:

Perform slice in x-z-direction

Kword yz:

Perform slice in y-z-direction

Kword normal:

Perform slice in plane perpendicular to given vector

Kword normalx:

X-axis direction for slice in plane perpendicular to given vector

Kword bpara:

Perform slice in B_para / B_perp2 plane

Kword bpara1:

Perform slice in B_para / B_perp1 plane

Kword bperp:

Perform slice in B_perp1 / B_perp2 plane If no plane is given, default is simulation plane (for 2D simulations)

Kword coordswap:

Swap the parallel and perpendicular coordinates

Kword bvector:

Plot a magnetic field vector projection in-plane

Kword bvectorscale:

Scale of bvector (default: 0.2 in units of axis lengths)

Kword cbulk:

Center plot on position of total bulk velocity (or if not available, bulk velocity for this population)

Kword cpeak:

Center plot on velocity associated with highest (peak) phase-space density for this population)

Kword center:

Center plot on provided 3-element velocity vector position (in m/s) If set instead to “bulk” will center on bulk velocity If set instead to “peak” will center on velocity with highest phase-space density

Kword wflux:

Plot flux instead of distribution function

Kword slicethick:

Thickness of slice as multiplier of cell size (default: 1 or minimum for good coverage). This can be set to zero in order to project the whole VDF to a plane.

Kword reducer:

How to reduce to 2D - default ‘integrate’ for LOS integration and reduced units, ‘average’ for old (slightly questionable) behaviour

Kword resampler:

Resample onto a regular grid? Default: yes, use False to disable.

Kword cellsize:

Plotting grid cell size as multiplier of input cell size (default: 1 or minimum for good coverage)

Kword setThreshold:

Use given setThreshold value instead of EffectiveSparsityThreshold or MinValue value read from file Useful if EffectiveSparsityThreshold wasn’t saved, or user wants to draw buffer cells with values below the sparsity threshold

Kword wmark:

If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword wmarkb:

As for wmark, but uses an all-black Vlasiator logo.

Kword draw:

Draw image on-screen instead of saving to file (requires x-windowing)

Kword nocb:

Suppress plotting of colourbar legend

Kword internalcb:

Set to draw colorbar inside plot instead of outside. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword biglabel:

Plot large label (in top-left corner)

Kword biglabloc:

Move large label to: 0: NW 1: NE 2: SE 3: SW corner

Kword axes:

Provide the routine a set of axes to draw within instead of generating a new image.

Kword cbaxes:

Provide the routine a set of axes for the colourbar.

Kword noborder:

Plot figure edge-to-edge without borders (default off)

Kword noxlabels:

Suppress x-axis labels and title

Kword noylabels:

Suppress y-axis labels and title

Kword scale:

Scale text size everywhere (default=1.0)

Kword scale_text:

Most text additional scale factor (default=8.0)

Kword scale_title:

Title additional scale factor (default=10.0)

Kword scale_cb:

Colour bar text additional scale factor (default=5.0)

Kword scale_label:

Big label text additional scale factor (default=12.0)

Kword thick:

line and axis thickness, default=1.0

Returns:

Outputs an image to a file or to the screen.

# Example usage:

pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,

coordre=[[11.7,-1.6,0.]], cbulk=1, bpara=1,box=[-2e6,2e6,-2e6,2e6],draw=1)

pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,

cellids=1670561, xy=1, box=[-2e6,2e6,-2e6,2e6], slicethick=5)

pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,

cellids=[1670561,], xz=1, box=[-2e6,2e6,-2e6,2e6], slicethick=0)

Note tilted slices: By default, the program samples the V-space with a slice where each cell is cube the dimensions of which are found by performing a rotation on a sample square and finding the maximum xyz-extent. This ensures adequate coverage and decreases sampling effects. This behaviour can be overridden with the slicethick and cellsize keywords.

Setting a value of slicethick=0 will result in the whole VDF being flattened into a single plane. This may result in some slight sampling artefacts, but is a good measure of complex populations.

analysator.plot.plot_vdf_profiles(filename=None, vlsvobj=None, filedir=None, step=None, cellids=None, pop='proton', coordinates=None, coordre=None, outputdir=None, outputfile=None, nooverwrite=None, draw=None, axisunit=None, title=None, tickinterval=None, lin=None, run=None, thick=1.0, wmark=None, wmarkb=None, fmin=None, fmax=None, vmin=None, vmax=None, xy=None, xz=None, yz=None, normal=None, bpara=None, bpara1=None, bperp=None, cbulk=None, cpeak=None, center=None, setThreshold=None, axes=None)

Plots vdf values along axis-aligned lines (see axis definitions).

Kword filename:

path to .vlsv file to use for input. Assumes a bulk file.

Kword vlsvobj:

Optionally provide a python vlsvfile object instead

Kword filedir:

Optionally provide directory where files are located and use step for bulk file name

Kword step:

output step index, used for constructing output (and possibly input) filename

Kword outputdir:

path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR) If directory does not exist, it will be created. If the string does not end in a forward slash, the final parti will be used as a perfix for the files.

Kword nooverwrite:

Set to only perform actions if the target output file does not yet exist

Kword cellids:

LIST of cell IDs to plot VDF for

Kword coordinates:

LIST of 3-element spatial coordinate lusts to plot VDF for (given in metres)

Kword coordre:

LIST of 3-element spatial coordinate lists to plot VDF for (given in Earth radii)

Kword pop:

Population to plot, default proton

Kword run:

run identifier, used for constructing output filename

Kword title:

string to use as plot title instead of time. Special case: Set to “msec” to plot time with millisecond accuracy or “musec” for microsecond accuracy. “sec” is integer second accuracy.

Kword fmin,fmax:

min and max values for colour scale and colour bar. If no values are given, min and max values for whole plot are used.

Kword vmin,vmax:

min and max values for x-axis

Kword axisunit:

Plot v-axes using 10^{axisunit} m/s (default: km/s)

Kword tickinterval:

Interval at which to have ticks on axes

Kword lin:

Plot using linear y-axis (default log)

Kword xy:

Perform slice in x-y-direction

Kword xz:

Perform slice in x-z-direction

Kword yz:

Perform slice in y-z-direction

Kword normal:

Perform slice in plane perpendicular to given vector

Kword bpara:

Perform slice in B_para / B_perp2 plane

Kword bpara1:

Perform slice in B_para / B_perp1 plane

Kword bperp:

Perform slice in B_perp1 / B_perp2 plane If no plane is given, default is simulation plane (for 2D simulations)

Kword cbulk:

Center plot on position of total bulk velocity (or if not available, bulk velocity for this population)

Kword cpeak:

Center plot on velocity with highest phase-space density

Kword center:

Center plot on provided 3-element velocity vector position (in m/s) If set instead to “bulk” will center on bulk velocity If set instead to “peak” will center on velocity with highest phase-space density

Kword setThreshold:

Use given setThreshold value instead of EffectiveSparsityThreshold or MinValue value read from file Useful if EffectiveSparsityThreshold wasn’t saved, or user wants to draw buffer cells with values below the sparsity threshold

Kword wmark:

If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword wmarkb:

As for wmark, but uses an all-black Vlasiator logo.

Kword draw:

Draw image on-screen instead of saving to file (requires x-windowing)

Kword axes:

Provide the routine a set of axes to draw within instead of generating a new image.

Kword scale:

Scale text size (default=1.0)

Kword thick:

line and axis thickness, default=1.0

Returns:

Outputs an image to a file or to the screen.

# Example usage:

pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,

coordre=[[11.7,-1.6,0.]], cbulk=1, bpara=1,box=[-2e6,2e6,-2e6,2e6],draw=1)

pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,

cellids=1670561, xy=1, box=[-2e6,2e6,-2e6,2e6], slicethick=5)

pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,

cellids=[1670561,], xz=1, box=[-2e6,2e6,-2e6,2e6], slicethick=0)

Note tilted slices: By default, the program samples the V-space with a slice where each cell is cube the dimensions of which are found by performing a rotation on a sample square and finding the maximum xyz-extent. This ensures adequate coverage and decreases sampling effects. This behaviour can be overridden with the slicethick and cellsize keywords.

Setting a value of slicethick=0 will result in the whole VDF being flattened into a single plane. This may result in some slight sampling artefacts, but is a good measure of complex populations.

analysator.plot.plot_vdfdiff(filename1=None, filename2=None, vlsvobj1=None, vlsvobj2=None, filedir=None, step=None, cellids=None, cellids2=None, pop='proton', coordinates=None, coordre=None, outputdir=None, outputfile=None, nooverwrite=None, draw=None, axisunit=None, axiskmps=None, title=None, cbtitle=None, tickinterval=None, colormap=None, box=None, nocb=None, internalcb=None, run=None, thick=1.0, wmark=None, wmarkb=None, fmin=None, fmax=None, slicethick=None, reducer='integrate', resampler=False, cellsize=None, xy=None, xz=None, yz=None, normal=None, normalx=None, bpara=None, bpara1=None, bperp=None, coordswap=None, bvector=None, bvectorscale=0.2, cbulk=None, center=None, wflux=None, setThreshold=None, noborder=None, scale=1.0, scale_text=8.0, scale_title=10.0, scale_cb=5.0, scale_label=12.0, biglabel=None, biglabloc=None, noxlabels=None, noylabels=None, axes=None, cbaxes=None, contours=None)

Plots the difference between VDFs as a coloured 2D plot with axes and a colour bar.

Kword filename1:

path to .vlsv file to use for input. Assumes a bulk file.

Kword filename2:

path to .vlsv file to use for input. Assumes a bulk file.

Kword vlsvobj1:

Optionally provide a python vlsvfile object instead

Kword vlsvobj2:

Optionally provide a python vlsvfile object instead

Kword filedir:

Optionally provide directory where files are located and use step for bulk file name

Kword step:

output step index, used for constructing output (and possibly input) filename

Kword outputdir:

path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR) If directory does not exist, it will be created. If the string does not end in a forward slash, the final parti will be used as a perfix for the files.

Kword nooverwrite:

Set to only perform actions if the target output file does not yet exist

Kword cellids:

LIST of cell IDs to plot VDF for

Kword cellids2:

Optional: LIST of cell IDs from input file 2. Same as cellids if omitted.

Kword coordinates:

LIST of 3-element spatial coordinate lusts to plot VDF for (given in metres)

Kword coordre:

LIST of 3-element spatial coordinate lists to plot VDF for (given in Earth radii)

Kword pop:

Population to plot, default proton

Kword colormap:

colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno, magma, parula, nipy_spectral, RdBu, bwr

Kword run:

run identifier, used for constructing output filename

Kword title:

string to use as plot title instead of time. Special case: Set to “msec” to plot time with millisecond accuracy or “musec” for microsecond accuracy. “sec” is integer second accuracy.

Kword cbtitle:

string to use as colorbar title instead of phase space density of flux

Kword contours:

Set to number of contours to draw

Kword fmin,fmax:

min and max values for colour scale and colour bar. If no values are given, min and max values for whole plot are used.

Kword box:

extents of plotted velocity grid as [x0,x1,y0,y1] (in m/s)

Kword axisunit:

Plot v-axes using 10^{axisunit} m/s (default: km/s)

Kword axiskmps:

Plot v-axes using 10^{axiskmps} km/s (default: km/s, when the kword has a value)

Kword tickinterval:

Interval at which to have ticks on axes

Kword xy:

Perform slice in x-y-direction

Kword xz:

Perform slice in x-z-direction

Kword yz:

Perform slice in y-z-direction

Kword normal:

Perform slice in plane perpendicular to given vector

Kword normalx:

X-axis direction for slice in plane perpendicular to given vector

Kword bpara:

Perform slice in B_para / B_perp2 plane

Kword bpara1:

Perform slice in B_para / B_perp1 plane

Kword bperp:

Perform slice in B_perp1 / B_perp2 plane If no plane is given, default is simulation plane (for 2D simulations)

Kword coordswap:

Swap the parallel and perpendicular coordinates

Kword bvector:

Plot a magnetic field vector projection in-plane

Kword bvectorscale:

Scale of bvector (default: 0.2 in units of axis lengths)

Kword cbulk:

Center plot on position of total bulk velocity (or if not available, bulk velocity for this population)

Kword center:

Center plot on provided 3-element velocity vector position (in m/s) If set instead to “bulk” will center on bulk velocity If set instead to “peak” will center on velocity with highest phase-space density

Kword wflux:

Plot flux instead of distribution function

Kword slicethick:

Thickness of slice as multiplier of cell size (default: 1 or minimum for good coverage). This can be set to zero in order to project the whole VDF to a plane.

Kword reducer:

How to reduce to 2D - default ‘integrate’ for LOS integration and reduced units, ‘average’ for old (slightly questionable) behaviour

Kword resampler:

Resample onto a regular grid? Default: yes, use False to disable.

Kword cellsize:

Plotting grid cell size as multiplier of input cell size (default: 1 or minimum for good coverage)

Kword setThreshold:

Use given setThreshold value instead of EffectiveSparsityThreshold or MinValue value read from file Useful if EffectiveSparsityThreshold wasn’t saved, or user wants to draw buffer cells with values below the sparsity threshold

Kword wmark:

If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword wmarkb:

As for wmark, but uses an all-black Vlasiator logo.

Kword draw:

Draw image on-screen instead of saving to file (requires x-windowing)

Kword nocb:

Suppress plotting of colourbar legend

Kword internalcb:

Set to draw colorbar inside plot instead of outside. If set to a text string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”

Kword biglabel:

Plot large label (in top-left corner)

Kword biglabloc:

Move large label to: 0: NW 1: NE 2: SE 3: SW corner

Kword axes:

Provide the routine a set of axes to draw within instead of generating a new image.

Kword cbaxes:

Provide the routine a set of axes for the colourbar.

Kword noborder:

Plot figure edge-to-edge without borders (default off)

Kword noxlabels:

Suppress x-axis labels and title

Kword noylabels:

Suppress y-axis labels and title

Kword scale:

Scale text size everywhere (default=1.0)

Kword scale_text:

Most text additional scale factor (default=8.0)

Kword scale_title:

Title additional scale factor (default=10.0)

Kword scale_cb:

Colour bar text additional scale factor (default=5.0)

Kword scale_label:

Big label text additional scale factor (default=12.0)

Kword thick:

line and axis thickness, default=1.0

Returns:

Outputs an image to a file or to the screen.

# Example usage:

pt.plot.plot_vdfdiff(“bulk.0000040.vlsv”,”bulk.0000048.vlsv”,cellids=1,xy=1,slicethick=1,colormap=”seismic”,

fmin=-1e-9,fmax=1e-9,cbulk=1)

See documentation of plot_vdf() for more usage information.