-
Notifications
You must be signed in to change notification settings - Fork 4
Home
- summary How to install Cassius
- labels Featured,Phase-Deploy
The essential part of Cassius is pure Python with a standard `setup.py` script; thus, installation will usually be straight-forward. Most of the content of this page covers contingencies that may exist on your system.
Cassius requires at least [http://www.python.org/ Python 2.6], [http://numpy.scipy.org/ NumPy 1.3], [http://www.pythonware.com/products/pil/ PIL 1.1.7], and [http://code.google.com/p/augustus/ Augustus 0.4.2.1]. (Augustus is only needed for `inspect/InspectTable` and only works with Augustus <= 0.5.2.)
The Python dependencies can be installed in Ubuntu 10.04 (or later) with
linux> sudo apt-get install python python-numpy python-imaging
and Augustus can be installed by following the [http://code.google.com/p/augustus/wiki/Installation Augustus instructions].
- One more thing:* to use Augustus's !UniTable, we also need PyGSL (you would only notice this if you call the `cassius.inspect()` function). To get it, do the following:
linux> sudo apt-get install gsl-bin libgsl0-dev python-dev gcc linux> http://sourceforge.net/projects/pygsl/files/pygsl/pygsl-0.9.5/pygsl-0.9.5.tar.gz/download -O pygsl-0.9.5.tar.gz linux> tar -xzvf pygsl-0.9.5.tar.gz linux> cd pygsl-0.9.5/ linux> sudo python setup.py install linux> cd ..
While developing a plotting script, it is often useful to see updates in a plot without having to save a file and load it in another program. For this reason, Cassius has an interactive viewer module that can be invoked with
>>> view(plot_object)
The viewer has the following dependencies: [http://www.gtk.org/ GTK], [http://librsvg.sourceforge.net/ librsvg 2.32.0], and [http://www.cairographics.org/ Cairo], and it must be compiled as a C program. These dependencies can be satisfied in Ubuntu *10.10* or later with
linux> sudo apt-get install python-dev libgtk2.0-dev libglib2.0-dev librsvg2-dev libcairo2-dev
(The librsvg in Ubuntu 10.04 (librsvg 2.26.2) is not sufficient.)
_This viewer is optional._ Without it, Cassius can save plots as files with
>>> draw(plot_object, fileName="plot.svg")
Also, Cassius only directly outputs SVG files. If you do not have any software to view, edit, or convert SVG files, I recommend [http://inkscape.org/ Inkscape]:
linux> sudo apt-get install inkscape
linux> inkview plot.svg # quick viewer
linux> inkscape plot.svg # fully featured editor
linux> inkscape plot.svg --export-pdf=plot.pdf # convert to PDF
# convert to PNG at a given scale
linux> inkscape plot.svg --export-png=plot.png --export-width=400 --export-background=white1. Download a Cassius archive from [http://code.google.com/p/cassius/downloads/list?q=label:Cassius the downloads page]. The filename is cassius-x_y_z_b.tgz or cassius-x_y_z_b.zip.
2. Unpack the archive and enter the installation directory:
linux> tar -xzvf cassius-x_y_z_b.tgz linux> cd cassius-x_y_z_b/
or
windows> unzip cassius-x_y_z_b.zip windows> cd cassius-x_y_z_b
3. Invoke the setup.py script, either with normal user privileges (local installation) or as the superuser (system-wide installation).
linux> python setup.py install --home=/path/to/desired/location
where `/path/to/desired/location` can be your home directory, ``.
The installation script attempts to compile the optional viewer, but if the dependencies are not met, it will just present a warning message and install the rest of the package.
If `/path/to/desired/location` does not contain a `bin` and a `lib` directory, these directories will be created and filled with executable scripts and the Cassius libraries, respectively. To access the executable scripts from a commandline, you may need to add the `bin` directory to your `PATH` environment variable:
linux> export PATH=/path/to/desired/location/bin:$PATH
To access the Cassius libraries in Python, you may need to add the `lib` directory to your `PYTHONPATH`:
linux> export PYTHONPATH=/path/to/desired/location/lib/python:$PYTHONPATH
You can check your `PATH` by executing one of the scripts:
linux> CassiusScorePlane --help ...
and you can check your `PYTHONPATH` by loading the Cassius module from a directory other than the installation directory:
linux> cd / linux> python >>> import cassius
To be sure that these environment variables are correctly set in new terminals, add them to your login script. If your shell is `csh` or `tcsh` (check with `echo $SHELL`), use the
linux> setenv VARIABLE value
syntax instead.
linux> sudo python setup.py install
The installation script attempts to compile the optional viewer, but if the dependencies are not met, it will just present a warning message and install the rest of the package.
The scripts and Cassius module will be installed in your system's standard locations, so it is not necessary to set environment variables.
To verify your installation of Cassius, try the following simple commands:
>>> from cassius import * >>> dir() ['Auto', 'ClosePolygon', 'ColorField', 'Curve', 'DAY', 'EdgeTo', 'Grid', 'HLS', 'HOUR', 'HSV', 'Histogram', 'HistogramCategorical', 'HistogramNonUniform', 'Infinity', 'InspectTable', 'Layout', 'Legend', 'Line', 'MINUTE', 'MONTH', 'MinusInfinity', 'MoveTo', 'Overlay', 'RGB', 'Region', 'RegionMap', 'SECOND', 'Scatter', 'Stack', 'Style', 'TimeSeries', 'WEEK', 'YEAR', '__builtins__', '__doc__', '__name__', '__package__', 'asymptotic_shift', 'binning', 'calcrange', 'calcrange_quartile', 'color', 'colors', 'containers', 'correlation', 'covariance', 'darken', 'darkseries', 'draw', 'drawpdf', 'epsilon', 'erf', 'erfc', 'fromtimestring', 'gaussian_likelihood', 'gradient', 'gradients', 'inspect', 'lighten', 'lightseries', 'linearfit', 'mathtools', 'mean', 'poisson_likelihood', 'regular', 'rms', 'round_errpair', 'round_sigfigs', 'stdev', 'str_errpair', 'str_round', 'str_sigfigs', 'svgdraw', 'tickmarks', 'timeticks', 'totimestring', 'truncated_shift', 'ubiquitous', 'unicode_errpair', 'unicode_number', 'utilities', 'view', 'wmean'] # The above output will vary, depending on version. This is for 0.1.0.0. >>> histogram = Histogram(20, 0., 20.) >>> histogram.fill(range(2, 15)) >>> histogram.fill(range(10, 18)) >>> print histogram bin value ======================================== [0, 1) 0 [1, 2) 0 [2, 3) 1 [3, 4) 1 [4, 5) 1 [5, 6) 1 [6, 7) 1 [7, 8) 1 [8, 9) 1 [9, 10) 1 [10, 11) 2 [11, 12) 2 [12, 13) 2 [13, 14) 2 [14, 15) 2 [15, 16) 1 [16, 17) 1 [17, 18) 1 [18, 19) 0 [19, 20) 0 >>> view(histogram) >>> draw(histogram, fileName="/tmp/output.svg")
If the interactive viewer was compiled and installed, then `view(histogram)` would pop up a window containing the histogram. If not, you would get a message like the following:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "cassius/svgdraw.py", line 128, in view
raise RuntimeError, "The '_svgview' extension module has not been compiled; use \"draw(object, fileName='...')\" instead."
RuntimeError: The '_svgview' extension module has not been compiled; use "draw(object, fileName='...')" instead.To view the plot in `/tmp/output.svg`, try
linux> inkview /tmp/output.svg
It should look like this:
[http://cassius.googlecode.com/files/wiki_Installation_output.svg http://cassius.googlecode.com/files/wiki_Installation_output.png]
![http://cassius.googlecode.com/files/wiki_Installation_output.png]](http://cassius.googlecode.com/files/wiki_Installation_output.png]){kind=link}