Editing Reproducible computational experiments using SCons (section)

==Example experiments==

The main <tt>SConstruct</tt> commands defined in our reproducible research environment are collected in the table.

<center>
{| class="wikitable"
|+Basic methods of an <tt>rsf.proj</tt> object.
|- 
|style="background-color:#ffdead;"| '''<tt>Fetch(data_file,dir[,ftp_server_info])</tt>'''
|-
| A rule to download <tt><math><</math>data_file<math>></math></tt> from a specific directory <tt><math><</math>dir<math>></math></tt> of an FTP server
|-
|style="background-color:#ffdead;"| '''<tt>Flow(target[s],source[s],command[s][,stdin][,stdout])</tt> '''
|-
| A rule to generate <tt><math><</math>target[s]<math>></math></tt> from <tt><math><</math>source[s]<math>></math></tt> using <tt><math><</math>command[s]<math>></math></tt> 
|-
|style="background-color:#ffdead;"| '''<tt>Plot(intermediate_plot[,source],plot_command)</tt>''' or
'''<tt>Plot(intermediate_plot,intermediate_plots,combination)</tt>'''
|-  
| A rule to generate <tt><math><</math>intermediate_plot<math>></math></tt> in the working directory. 
|-
|style="background-color:#ffdead;"| '''<tt>Result(plot[,source],plot_command)</tt>''' or
'''<tt>Result(plot,intermediate_plots,combination)</tt>'''
|- 
| A rule to generate a final <tt><math><</math>plot<math>></math></tt> in the special <tt>Fig</tt> folder of the working directory. 
|-
|style="background-color:#ffdead;"| '''<tt>End()</tt>''' 
|- 
| A rule to collect default targets. 
|}
</center>

These commands are defined in <tt>&#36;PYTHONPATH/rsf/proj.py</tt> where
<tt>RSFROOT</tt> is the environmental variable to the Madagascar
installation directory. The source of this file is in
[http://sourceforge.net/p/rsf/code/HEAD/tree/trunk/framework/rsf/proj.py framework/rsf/proj.py].

===Example 1===


To follow the first example, select a working project directory and
copy the following code
to a file named <tt>SConstruct</tt><ref>The source of this file is also accessible at [http://sourceforge.net/p/rsf/code/HEAD/tree/trunk/book/rsf/scons/easystart/SConstruct $RSFSRC/book/rsf/scons/easystart/SConstruct].</ref>.

<syntaxhighlight lang="python">
from rsf.proj import *

# Download the input data file
Fetch('lena.img','imgs')

# Create RSF header
Flow('lena.hdr','lena.img',
     'echo n1=512 n2=513 in=$SOURCE data_format=native_uchar',
     stdin=0)

# Convert to floating point and window out the first trace
Flow('lena','lena.hdr','dd type=float | window f2=1')

# Display
Result('lena',
       '''
       sfgrey title="Hello, World!" transp=n color=b bias=128
       clip=100 screenratio=1 
       ''')

# Wrap up
End()
</syntaxhighlight>


This is our "hello world" example that illustrates the basic use of
some of the commands presented in Table~(tbl:commands). The plan
for this experiment is to download data from a public data
server, convert it to an appropriate file format, and generate a
figure for publication. But let us look at the
<tt>SConstruct</tt> script and try to decorticate it.


<syntaxhighlight lang="python">
from rsf.proj import *
</syntaxhighlight>


is a standard Python command that loads the Madagascar project
management module <tt>rsf/proj.py</tt> which provides our extension to
SCons.


<syntaxhighlight lang="python">
Fetch('lena.img','imgs')
</syntaxhighlight>


instructs SCons to connect to a public data server (the default server
if no FTP server information is provided) and to fetch the data file
<tt>lena.img</tt> from the <tt>data/imgs</tt> directory. 
<!-- 
Note that
Madagascar expects a <tt>data</tt> folder on top of the specified
directory (i.e.  <tt>imgs</tt>). In the directory where you have your
SConstruct, running <tt>scons lena.img</tt> on the command line will
download the file <tt>lena.img</tt>.  The equivalent command line is
<pre>
bash&#36; wget http://www.ahay.org/data/imgs/lena.img
</pre>
 -->

Try running "<tt>scons lena.img</tt>" on the command line. The successful output should look like
<pre>
bash&#36; scons lena.img
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
retrieve(["lena.img"], [])
scons: done building targets.
</pre>
with the target file <tt>lena.img</tt> appearing in your directory.
In the following examples, we will use <tt>-Q</tt> (quiet) option of
<tt>scons</tt> to suppress the verbose output.
<syntaxhighlight lang="python">
Flow('lena.hdr','lena.img',
     'echo n1=512 n2=513 in=$SOURCE data_format=native_uchar',
     stdin=0)
</syntaxhighlight>


prepares the Madagascar header file <tt>lena.hdr</tt> using the
standard Unix command <tt>echo</tt>. 

<pre>
bash&#36; scons -Q lena.hdr
echo n1=512 n2=513 in=lena.img data_format=native_uchar > lena.hdr
</pre>

Since <tt>echo</tt> does not take a standard input, stdin is set to 0
in the Flow command; otherwise, the first source is the standard input.
Likewise, the first target is the standard output unless otherwise
specified. 


Note that
<tt>lena.img</tt> is referred as <tt>&#36;SOURCE</tt> in the command. This
allows us to change the source file's name without changing the command.
The data format of the <tt>lena.img</tt> image file is <tt>uchar</tt>
(unsigned character), the image consists of 513 traces with 512
samples per trace. Our next step is to convert the image
representation to floating point numbers and to window out the first
trace so that the final image is 512 by 512 square. The two
transformations are conveniently combined into one with the help of a Unix pipe.
<syntaxhighlight lang="python">
Flow('lena','lena.hdr','dd type=float | window f2=1')
</syntaxhighlight>


<pre>
  bash&#36; scons -Q lena
  scons: *** Do not know how to make target `lena'. Stop.
</pre>
What happened? In the absence of the file suffix, the <tt>Flow</tt>
command assumes that the target file suffix is "<tt>.rsf</tt>". Let us try again.
<pre>
scons -Q lena.rsf
< lena.hdr /RSF/bin/sfdd type=float | /RSF/bin/sfwindow f2=1 > lena.rsf
</pre>
Notice that Madagascar modules <tt>sfdd</tt> and <tt>sfwindow</tt> get
substituted for the corresponding short names in the
<tt>SConstruct</tt> file. The file <tt>lena.rsf</tt> is in a regularly
sampled format<ref>See [[Guide to RSF file format]]</ref> and can be examined, for example, with <tt>sfin lena.rsf</tt><ref>See [[Guide_to_madagascar_programs#sfin]].</ref>.
<pre>
bash&#36; sfin lena.rsf
lena.rsf:
    in="/datapath/lena.rsf@"
    esize=4 type=float form=native
    n1=512         d1=1           o1=0
    n2=512         d2=1           o2=1
        262144 elements 1048576 bytes
</pre>
In the last step, we will create a plot file to display the image
on the screen and for including it in the publication.

<syntaxhighlight lang="python">
Result('lena',
       '''
       sfgrey title="Hello, World!" transp=n color=b bias=128
       clip=100 screenratio=1 
       ''')
</syntaxhighlight>


Notice that we broke the long command string into multiple lines by
using Python's triple quote syntax. All the extra white space will be
ignored when the multiple-line string gets translated into the command
line. The <tt>Result</tt> command has special targets associated with
it. Try, for example, "<tt>scons lena.view</tt>" to observe the
figure <tt>Fig/lena.vpl</tt> generated in a specially created
<tt>Fig</tt> directory and displayed on the screen. The output should
look like this figure.

[[Image:lena.png|frame|center|The output of the first numerical experiment.]]

The reproducible script ends with

<syntaxhighlight lang="python">
End()
</syntaxhighlight>

Ready to experiment? Try some of the following:
  
#Run <tt>scons -c</tt>. The <tt>-c</tt> (clean) option tells SCons to remove all default targets (the <tt>Fig/lena.vpl</tt> image file in our case) and also all intermediate targets that it generated.  
<pre> bash&#36; scons -c -Q 
Removed lena.img 
Removed lena.hdr 
Removed lena.rsf 
Removed /datapath/lena.rsf@ 
Removed Fig/lena.vpl 
</pre> Run <tt>scons</tt> again, and the default target will be regenerated. 
<pre>
bash&#36; scons -Q 
retrieve(["lena.img"], []) 
echo n1=512 n2=513 in=lena.img data_format=native_uchar > lena.hdr 
< lena.hdr /RSF/bin/sfdd type=float | /RSF/bin/sfwindow f2=1 > lena.rsf 
< lena.rsf /RSF/bin/sfgrey title="Hello, World!" transp=n color=b  bias=128 clip=100 screenratio=1 > Fig/lena.vpl </pre> 
#Edit your <tt>SConstruct</tt> file and change some of the plotting parameters. For example, change the value of <tt>clip</tt> from <tt>clip=100</tt> to <tt>clip=50</tt>. Run <tt>scons</tt> again and observe that only the last part of the processing flow (precisely, the part affected by the parameter change) is being run: 
<pre> bash&#36; scons -Q view 
< lena.rsf /RSF/bin/sfgrey title="Hello, World!" transp=n color=b  bias=128 clip=50 screenratio=1 > Fig/lena.vpl 
sfpen Fig/lena.vpl 
</pre> SCons is smart enough to recognize that your editing did not affect any of the previous results in the data flow chain! Keeping track of dependencies is the main feature that separates data processing and computational experimenting with SCons from using linear shell scripts. This feature can save you a lot of time for computationally demanding data processing and make your experiments more interactive and enjoyable. 
#A special parameter to SCons (defined in <tt>rsfproj.py</tt>) can time the execution of each step in the processing flow. Try running <tt>scons TIMER=y</tt>. 
#The <tt>rsfproj</tt> module has direct access to the database that stores the parameters of all Madagascar modules. Try running <tt>scons CHECKPAR=y</tt> to see parameter checking enforced before computations\footnote{This feature is new and experimental and may not work correctly yet}. 
The summary of our SCons commands is given in the table.

{| class="wikitable"
|+SCons commands and options defined in <tt>rsfproj</tt>.
|- 
|style="background-color:#ffdead;"| '''<tt>scons <math><</math>file<math>></math></tt>'''
|-
| Generate <tt><math><</math>file<math>></math></tt> (usually requires <tt>.rsf</tt> suffix for <tt>Flow</tt> targets and <tt>.vpl</tt> suffix for <tt>Plot</tt> targets.)
|- 
|style="background-color:#ffdead;"| '''<tt>scons</tt>'''
|-
| Generate default targets (usually figures specified in <tt>Result</tt>.) 
|- 
|style="background-color:#ffdead;"| '''<tt>scons view</tt>''' or '''<tt>scons <math><</math>result<math>></math>.view</tt> '''
|-
| Generate <tt>Result</tt> figures and display them on the screen. 
|- 
|style="background-color:#ffdead;"| '''<tt>scons print</tt>''' or '''<tt>scons <math><</math>result<math>></math>.print</tt>''' 
|-
| Generate <tt>Result</tt> figures and print them. 
|- 
|style="background-color:#ffdead;"| '''<tt>scons lock</tt>''' or '''<tt>scons <math><</math>result<math>></math>.lock</tt> ''' 
|-
| Generate <tt>Result</tt> figures and install them in a separate location. 
|- 
|style="background-color:#ffdead;"| '''<tt>scons test</tt>''' or '''<tt>scons <math><</math>result<math>></math>.test</tt>''' 
|-
| Generate <tt>Result</tt> figures and compare them with the corresponding "locked" figures stored in a separate location (regression testing). 
|- 
|style="background-color:#ffdead;"| '''<tt>scons <math><</math>result<math>></math>.flip</tt>''' 
|-
| Generate the <tt><math><</math>result<math>></math></tt> figure and compare it with the corresponding "locked" figure stored in a separate location by flipping between the two figures on the screen. 
|- 
|style="background-color:#ffdead;"| '''<tt>scons TIMER=y ...</tt> ''' 
|-
| Time the execution of each step in the processing flow (using the Unix <tt>time</tt> utility.) 
|- 
|style="background-color:#ffdead;"| '''<tt>scons CHECKPAR=y ...</tt> ''' 
|-
| Check the names and values of all parameters supplied to Madagascar modules in the processing flow before executing anything (guards against incorrect input.) This option is new and experimental.  
|}

===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.
 -->