Plotting options in Python ¶

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Plotting options in Python

Clawpack 4.4 includes utilities for plotting using Python. Most of these are defined in the file $CLAW/python/pyclaw/plotters/frametools.py In order to use these you will need to insure that you have the required modules installed (see Installation of required modules).

Clawpack 4.4 also includes the Matlab plotting tools from 4.3 and before, see Plotting using Matlab.

The advantages of using the Python options are:

Python and the graphics modules used in Clawpack are open source. Since Clawpack itself is open source we find it desirable to also have an open source plotting open for viewing the results.

The Python tools developed so far (mostly for 1d and 2d data sets) are more powerful than the Matlab versions they replace, and can be used for example to automatically generate html versions of multiple plots each frame over all frames of a computation, to generate latex versions of the output, as well as to step through the frames one by one as with the Matlab tools. It is easier to specify a set of multiple plots to be produced for each frame.

Matlab graphics are somewhat limited for 3d data sets, whereas several open source visualization tools such as VisIt (developed at Lawrence Livermore National Laboratory) are much better for dealing with large data sets, AMR grids, etc. VisIt has Python bindings and we are currently extending our tools to work with VisIt. If you are already a VisIt user, note that VisIt has a Claw reader that can be used to import data from Clawpack, see Application Toolkit Formats.

We are also considering developing tools for use with Mayavi.

Python is a powerful language that can be scripted to perform multiple runs, such as in a convergence test, and collect the results in tables or plots. We are developing tools to simplify this process.

See Python Hints for more information on Python and pointers to many tutorials.

Producing html plots from the command line ¶

In most Clawpack directories, typing:

$  make .plots

will compile the code and run it (if necessary) and then produce a set of html files that can be used to view the resulting plots. These will be in a subdirectory of the current directory as specified by CLAW_PLOTDIR in the Makefile.

Viewing plots via a local web server ¶

The best way to view the plots and associated web pages for each example is to first start a python web server in your main $CLAW directory with the commands:

$ cd $CLAW
$ xterm -e python python/startserver.py & # to start server in new X window

The main $CLAW directory will then be available at http://localhost:50005 and jsMath should work properly to display latex on the webpages (once you’ve downloaded the required fonts, see http://www.math.union.edu/locate/jsMath/users/fonts.html).

Producing a latex file with plots from the command line ¶

A latex file with all the plots can also be produced by printframes function, and is also typically controlled by options set in the file setplot.py.

Setting plot parameters with a setplot function ¶

Typically each applications directory contains a file setplot.py, see for example Plotting examples in 1d. This file should define a function setplot(plotdata) that sets various attributes of an object plotdata of class ClawPlotData.

Documentation on how to create a setplot function and the various plotting parameters that can be set can be found in the section Using setplot.py to specify the desired plots.

Examples can be found at Plotting examples in 1d.

Interactive plotting with `Iplotclaw`¶

For interactive plotting we suggest using IPython, which is a nicer shell than the pure python shell, with things like command completion and history. See the Quick IPython Tutorial

Here’s an example:

$  ipython
In [1]: from pyclaw.plotters.Iplotclaw import Iplotclaw
In [2]: ip = Iplotclaw()
In [3]: ip.plotloop()
New start
Executing setplot ...

Interactive plotclaw with ndim = 1 ...
Type ? at PLOTCLAW prompt for list of commands

    Start at which frame [default=0] ?
    Plotting frame 0 ...
PLOTCLAW >  n
    Plotting frame 1 ...
PLOTCLAW > q
quitting...
In [4]:

Type ? at the PLOTCLAW prompt or ?command-name for more information. Most commonly used are n for next frame, p for previous frame and j to jump to a different frame. Hitting return at the prompt repeats the previous command.

You can restart the plotloop later by doing:

In [4]: ip.plotloop()

Interactive plotclaw with ndim = 1 ...
Type ? at PLOTCLAW prompt for list of commands

    Start at which frame [default=1] ?
    Replot data for frame 1 [no] ?
PLOTCLAW >

By default it starts at the frame where you previously left off.

If you want to change plot parameters, the easiest way is to edit the file setplot.py, either in a different window or, if you use vi, by:

PLOTCLAW > vi setplot.py

and then re-execute the setplot function using:

PLOTCLAW > resetplot

If you recompute results by running the fortran code again and want to plot the new results (from this same directory), you may have to clear the frames that have already been viewed using:

PLOTCLAW > clearframes

Or you can redraw the frame you’re currently looking at without clearing the rest of the cached frame data by doing:

PLOTCLAW > rr

To see what figures, axes, and items have been defined by setplot:

PLOTCLAW > show

Current plot figures, axes, and items:
---------------------------------------
  figname = Pressure, figno = 1
     axesname = AXES1, axescmd = subplot(1,1,1)
        itemname = ITEM1,  plot_type = 1d_plot

  figname = Velocity, figno = 2
     axesname = AXES1, axescmd = subplot(1,1,1)
        itemname = ITEM1,  plot_type = 1d_plot

Type “help” or “help command-name” at the prompt for more options.

Access to current_data ¶

If you are viewing plots in using Iplotclaw and want to explore the data for some frame or make plots directly in your Python shell, the data that is being plotted is available to you in attributes of the Iplotclaw instance. For example:

>>> ip = Iplotclaw();  ip.plotloop()

Interactive plotting for Clawpack output...

Plotting data from outdir =  _output
    ...
    Plotting Frame 0 at t = 0.0
PLOTCLAW > q
quitting...

>>> pd = ip.plotdata
>>> cd = ip.current_data

The cd object contains the current_data used for the most recent plot, while pd is the ClawPlotData object that gives access to all the plotting parameters currently being used as well as to methods such as getframe for retrieving other frames of data from this computation.

If you want to change the directory outdir where the frame data is coming from, you could do, for example:

>>> pd.outdir = "_output2"
>>> ip.plotloop()
...
PLOTCLAW > clearframes    # to remove old frames from cache
PLOTCLAW > rr             # to redraw current frame number but with new data

ipyclaw ¶

If you use $CLAW/setenv.py to set up your environment, then an alias ipyclaw = ‘ipython -profile claw’ will be defined (or you can type the above command at the unix prompt). This automatically loads the function Iplotclaw and some other useful modules. You can reconfigure this in $CLAW/python/ipythondir/ipythonrc-claw if you wish to have other commands executed automatically every time you start ipython. If you use this, then the example above is simplified to:

$  ipyclaw
In [1]: ip = Iplotclaw()
In [2]: ip.plotloop()
...

printframes ¶

The function pyclaw.plotters.frametools.printframes can be used to produce html and latex versions of the plots:

>>> from pyclaw.plotters.data import ClawPlotData
>>> from pyclaw.plotters import frametools
>>> plotclaw = ClawPlotData()
>>> # set attributes as desired
>>> frametools.printframes(plotclaw)

A convenience method of ClawPlotData is defined to apply this function, e.g.:

>>> plotclaw.printframes()

This function is automatically called by the “make .plots” option available in most examples.

Specifying what and how to plot ¶

The first step in specifying how to plot is to create a ClawPlotData object to hold all the data required for plotting. This is generally done one of two ways:

In a script such as the plotclaw.py script included in most example directories, e.g., claw/examples/acoustics/1d/example1/plotclaw.py.html.
By creating an instance of Iplotclaw to do interactive plotting, e.g.:
>>> ip = Iplotclaw()
Then ip will have an attribute plotdata that is a ClawPlotData object. This object will have attribute setplot initialized to ‘setplot.py’, indicating that other attributes should be set by executing the setplot function defined in the file ‘setplot.py’ in this directory.

Once you have a ClawPlotData object you can set various attributes to control what is plotted. For example,:

>>> plotdata.plotdir = '_plots'
>>> plotdata.setplot = 'my_setplot_file.py'

will cause hardcopy to go to subdirectory _plots of the current directory and will cause the plotting routines to execute:

>>> from my_setplot_file import setplot
>>> plotdata = setplot(plotdata)

before doing the plotting.

There are many other ClawPlotData attributes and methods.

Most example directories contain a file setplot.py that contains a function setplot(). This function sets various attributes of the ClawPlotData object to control what figures, axes, and items should be plotted for each frame of the solution.

For an outline of how a typical set of plots is specified, see Using setplot.py to specify the desired plots.