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Reproducible computational experiments using SCons
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===Example 2=== The plan for this experiment is to add random noise to the test "Lena" image and then to attempt removing it by low-pass filtering and by hard thresholding of coefficients in the Fourier domain. The result 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 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 mean an exhaustive list of options but, hopefully, it gives you a flavor of the powerful tool you have in 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 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>$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 a 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. -->
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