Editing Reproducible computational experiments using SCons (section)

===Example 2===

The plan for this experiment is to add random noise to the test
"Lena" image and then attempt removing it by low-pass filtering
and hard thresholding of coefficients in the Fourier domain. The
resultant images are shown in the figures.

[[Image:panel1.png|frame|center|Top left: original image. Top right: random noise added. Bottom left: original image spectrum in the Fourier (<math>F</math>-<math>X</math>) domain. Bottom right: noisy image spectrum in the Fourier (<math>F</math>-<math>X</math>) domain.]]

[[Image:panel2.png|frame|center|Left: denoising by low-pass filtering.  Right: denoising by hard thresholding in the Fourier domain.]]

Since the <tt>SConstruct|</tt> file is a Python script, we can also use all the
flexibility and power of the Python language in our Madagascar
reproducible scripts. A demo script is available in the
<tt>rsf/scons/rsfpy</tt> subdirectory of the Madagascar <tt>book</tt>
directory. Rather than commenting on it line-by-line, we select some
parts of interest.
In the <tt>SConstruct</tt> script, we can declare
Python variables
<syntaxhighlight lang="python">
bias = 128
</syntaxhighlight>

and use them later, for example, to define our customized plot
command as a Python function
<syntaxhighlight lang="python">
def grey(title,transp='n',bias=bias):
    return '''
    sfgrey title="%s" transp=%s bias=%g clip=100
    screenht=10 screenwd=10 crowd2=0.85 crowd1=0.8
    label1= label2= 
    ''' % (title,transp,bias)
</syntaxhighlight>

This Python function, named <tt>grey()</tt>, can then be called in Plot or Result
commands, e.g.
<syntaxhighlight lang="python">
Plot('lplena',grey('Noisy Lena LP filtered'))
</syntaxhighlight>

We can define a Python dictionary, e.g.
<syntaxhighlight lang="python">
titles = {'lena':'Lena',
          'nlena':'Noisy Lena'}
</syntaxhighlight>
and loop over its entries, e.g.
<syntaxhighlight lang="python">
for name in titles.keys():
    Plot(name,grey(titles[name]) )
    cftitle = titles[name]+' in FX domain'
    Flow('fx'+name,name,'sfspectra')
    Plot('fx'+name,grey(cftitle,'y',100))
</syntaxhighlight>
Note that the title of the plots is obtained by concatenating Python
strings.
Python strings can also be used to define sequences of commands used
in several Flows, e.g.
<syntaxhighlight lang="python">
# 2-D FFT
fft2 = 'sffft1 sym=y | sffft3 sym=y'
Flow('fnlena','nlena',fft2)
</syntaxhighlight>

Finally, in our Madagascar reproducible script, we may want the option
to pass command line arguments when running SCons or use default
values otherwise, e.g.
<syntaxhighlight lang="python">
# denoising using thresholding in the Fourier domain
fthr = float(ARGUMENTS.get('fthr', 70))
Flow('fthrlena','fnlena','sfthr thr=%f mode="hard"' % fthr)
</syntaxhighlight>

Running <tt>scons</tt> only, the default value set for fthr (i.e. 70)
is used whereas running <tt>scons fthr=68</tt> set fthr to a command
line specified value.
This is by no means an exhaustive list of options, but hopefully, it
will give you a flavor of the powerful tool you have in your hands. Enjoy!
<!-- 
===Useful SCons commands for reproducible scripts===
On top of SCons standard options (<tt>scons --help</tt> for more
details), Madagascar has its own SCons options. We already saw
<tt>scons plot.view</tt> that displays <tt>plot.vpl</tt> (in the
<tt>Fig</tt> folder) obtained in a Result command. <tt>scons view</tt>
displays the result plots one after the other.
It is also possible to check the parameters for Madagascar programs in
SCons Flow commands using the CHECKPAR option (\texttt{scons
CHECKPAR=y target}). Note that CHECKPAR is an experimental option
and will be enhanced in the future to include parameter ranges and
other safety checks.
To time the execution of processing flows in a SConstruct, use the
TIMER option (<tt>scons TIMER=y target</tt>).
<tt>scons lock</tt> is used to secure result plots and copy them from
the <tt>Fig</tt> folder of your working directory to your
<tt>&#36;RSFFIGS</tt> folder where <tt>RSFFIGS</tt> is the environmental
variable to the directory where you want Madagascar to put your key
Madagascar result plots. Note that this is a necessary step before
creating reproducible documentation. <tt>scons plot.flip</tt> runs
<tt>xtpen Fig/plot.vpl /locked/figures/plot.vpl</tt> to flip between
the new and locked figure. This is useful when detecting changes.
 -->