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plot_colormap3dslice
Markus Battarbee edited this page Jan 13, 2021
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Plot_colormap3dslice is a plotting routine used for generating 2D plots of 3D simulation data. It is capable of visualizing Cartesian slices from the 3D (AMR) simulation domain, but cannot currently plot diagonal slices.
In the most basic form, it's enough to provide a source file and the proton number density is plotted for the simulation domain. Output is generated by default in the standard Analysator output directory. It can be redirected to a defined file or directory or to the screen.
Plot_colormap3dslice allows for zooming into the simulation, adjusting the colorbar range, changing the variable to be plotted, adding vectors or streamlines on top, and much more.
plot_colormap3dslive(filename="/home/ad/ukko2-wrk/group/spacephysics/vlasiator/3D/EGE/bulk/bulk.0002193.vlsv", var="proton/vg_v", run="EGE",
colormap='seismic',lin=True, wmark=1, symmetric=1, normal='y', boxre=[-20,30,-30,20])
:kword filename: path to .vlsv file to use for input.
:kword outputfile: Output file name (and path)
:kword draw: Set to anything but None in order to draw image on-screen instead of saving to file (requires x-windowing)
: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/pytools.
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 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 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 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 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 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 fsaved: Overplot locations of fSaved (cells where VDFs are stored). If keyword is set to a string, that will be the colour used.
Plot_colormap3dslice allows calling external or expression functions for extended manipulation of variables and the plot window. Expressions are used to perform calculations (derivatives, subtractions, etc) on input data. External functions are used to draw on top of the plot window. Examples are available in the file examples/generate_panel.py and in pyPlot/plot_helpers.py with helper functions described in Plotting helper routines
: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 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
By default, variables passed to external functions and expressions are also only 2D slices of data. However, if the function returns the variable '3d' within it's list of required variables, the function receives the full 3D data cube. Note that this can be a very large amount of data, as all values are upsampled to the finest refinement level.
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 parti will be used as a perfix 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/pytools.
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
: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.
: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 fluxfile: Filename to plot fluxfunction from
:kword fluxdir: Directory in which fluxfunction files can be found
:kword fluxthick: Scale fluxfunction line thickness
:kword fluxlines: Relative density of fluxfunction contours
:kword fsaved: Overplot locations of fSaved. If keyword is set to a string, that will be the colour used.
: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]
:returns: Outputs an image to a file or to the screen.
.. code-block:: python
# 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)