Reproducible computational experiments using SCons - Revision history

Fomels: typos

2024-11-20T23:42:00Z

typos

Sfomel: /* Example */

2014-04-08T21:49:27Z

Example

← Older revision		Revision as of 21:49, 8 April 2014
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	in the directory above the projects directories.		in the directory above the projects directories.

	<python>		<syntaxhighlight lang="python">
	from rsf.tex import *		from rsf.tex import *
	Paper('velan',use='hyperref,listings,color')		Paper('velan',use='hyperref,listings,color')
	End(use='hyperref,listings,color')		End(use='hyperref,listings,color')
			</syntaxhighlight>
	</~~python~~>


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	translates as		translates as

	<latex>		<syntaxhighlight lang="latex">
	\inputdir{easystart}		\inputdir{easystart}
	\sideplot{lena}{height=.25\textheight}{The output of the first numerical experiment.}		\sideplot{lena}{height=.25\textheight}{The output of the first numerical experiment.}
	</~~latex~~>		</syntaxhighlight>

	The <math>\backslash</math>inputdir command points to the project directory and		The <math>\backslash</math>inputdir command points to the project directory and

Sfomel: /* Example 2 */

2014-04-08T21:48:17Z

Example 2

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	In the <tt>SConstruct</tt> script, we can declare		In the <tt>SConstruct</tt> script, we can declare
	Python variables		Python variables
	<python>		<syntaxhighlight lang="python">
	bias = 128		bias = 128
	</~~python~~>		</syntaxhighlight>

	and use them later, for example, to define our customized plot		and use them later, for example, to define our customized plot
	command as a Python function		command as a Python function
	<python>		<syntaxhighlight lang="python">
	def grey(title,transp='n',bias=bias):		def grey(title,transp='n',bias=bias):
	return '''		return '''
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	label1= label2=		label1= label2=
	''' % (title,transp,bias)		''' % (title,transp,bias)
	</~~python~~>		</syntaxhighlight>

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

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

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

	Running <tt>scons</tt> only, the default value set for fthr (i.e. 70)		Running <tt>scons</tt> only, the default value set for fthr (i.e. 70)

Sfomel: /* Example 1 */

2014-04-08T21:45:59Z

Example 1

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

Sfomel: /* Example 1 */

2014-04-08T21:45:22Z

Example 1

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	To follow the first example, select a working project directory and		To follow the first example, select a working project directory and
	copy the following code		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 book/rsf/scons/easystart/SConstruct].</ref>.		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>.

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

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	# Wrap up		# Wrap up
	End()		End()
	</~~python~~>		</syntaxhighlight>


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


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	In the following examples, we will use <tt>-Q</tt> (quiet) option of		In the following examples, we will use <tt>-Q</tt> (quiet) option of
	<tt>scons</tt> to suppress the verbose output.		<tt>scons</tt> to suppress the verbose output.
	<python>		<syntaxhighlight lang="python">
	Flow('lena.hdr','lena.img',		Flow('lena.hdr','lena.img',
	'echo n1=512 n2=513 in=$SOURCE data_format=native_uchar',		'echo n1=512 n2=513 in=$SOURCE data_format=native_uchar',
	stdin=0)		stdin=0)
	</~~python~~>		</syntaxhighlight>


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	trace so that the final image is a 512 by 512 square. The two		trace so that the final image is a 512 by 512 square. The two
	transformations are conveniently combined into one with the help of a Unix pipe.		transformations are conveniently combined into one with the help of a Unix pipe.
	<python>		<syntaxhighlight lang="python">
	Flow('lena','lena.hdr','dd type=float \| window f2=1')		Flow('lena','lena.hdr','dd type=float \| window f2=1')
	</~~python~~>		</syntaxhighlight>


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	on the screen and for including it in the publication.		on the screen and for including it in the publication.

	<python>		<syntaxhighlight lang="python">
	Result('lena',		Result('lena',
	'''		'''
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	clip=100 screenratio=1		clip=100 screenratio=1
	''')		''')
	</~~python~~>		</syntaxhighlight>


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	The reproducible script ends with		The reproducible script ends with

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

	Ready to experiment? Try some of the following:		Ready to experiment? Try some of the following:

Sfomel: /* Creating reproducible documentation */

2013-08-10T20:38:42Z

Creating reproducible documentation

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	<tt>RSFROOT</tt> is the environmental variable to the Madagascar		<tt>RSFROOT</tt> is the environmental variable to the Madagascar
	installation directory. The source of this file is in		installation directory. The source of this file is in
	[http://~~rsf.svn.~~sourceforge.net/~~viewvc~~/rsf/trunk/framework/rsf/tex.py~~?view=markup~~ framework/rsf/tex.py].		[http://sourceforge.net/p/rsf/code/HEAD/tree/trunk/framework/rsf/tex.py framework/rsf/tex.py].
	We summarize the basic methods and commands in the tables.		We summarize the basic methods and commands in the tables.

Sfomel: /* Example experiments */

2013-08-10T20:35:37Z

Example experiments

← Older revision		Revision as of 20:35, 10 August 2013
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	<tt>RSFROOT</tt> is the environmental variable to the Madagascar		<tt>RSFROOT</tt> is the environmental variable to the Madagascar
	installation directory. The source of this file is in		installation directory. The source of this file is in
	[http://~~rsf.svn.~~sourceforge.net/~~viewvc~~/rsf/trunk/framework/rsf/proj.py~~?view=markup~~ framework/rsf/proj.py].		[http://sourceforge.net/p/rsf/code/HEAD/tree/trunk/framework/rsf/proj.py framework/rsf/proj.py].

	===Example 1===		===Example 1===
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	To follow the first example, select a working project directory and		To follow the first example, select a working project directory and
	copy the following code		copy the following code
	to a file named <tt>SConstruct</tt><ref>The source of this file is also accessible at [http://~~svn.~~sourceforge.net/~~viewvc~~/rsf/trunk/book/rsf/scons/easystart/SConstruct~~?view=markup~~ book/rsf/scons/easystart/SConstruct].</ref>.		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 book/rsf/scons/easystart/SConstruct].</ref>.

	<python>		<python>
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	directory (i.e. <tt>imgs</tt>). In the directory where you have your		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		SConstruct, running <tt>scons lena.img</tt> on the command line will
	download the file <tt>lena.img</tt>. The equivalent command ~~lines are~~		download the file <tt>lena.img</tt>. The equivalent command line is
	~~<ref>use login: anonymous, password: anonymous</ref>~~
	<pre>		<pre>
	bash$ ~~ftp egl~~.~~beg~~.~~utexas.edu~~		bash$ wget http://www.ahay.org/data/imgs/lena.img
	~~ftp> bin~~
	~~ftp> cd~~ data/imgs
	~~ftp> get~~ lena.img
	~~ftp> bye~~
	</pre>		</pre>
	-->		-->

Sfomel at 20:28, 10 August 2013

2013-08-10T20:28:53Z

← Older revision		Revision as of 20:28, 10 August 2013
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	<center><font size="-1">''This page was created from the LaTeX source in [http://~~rsf.svn.~~sourceforge.net/~~viewvc~~/rsf/trunk/book/rsf/scons/paper.tex~~?view=markup~~ book/rsf/scons/paper.tex] using [[latex2wiki]]''</font></center>		<center><font size="-1">''This page was created from the LaTeX source in [http://sourceforge.net/p/rsf/code/HEAD/tree/trunk/book/rsf/scons/paper.tex book/rsf/scons/paper.tex] using [[latex2wiki]]''</font></center>

	SCons (from Software Construction) is a well-known open-source		SCons (from Software Construction) is a well-known open-source

Sfomel: /* Example 1 */

2011-07-16T15:59:21Z

Example 1

← Older revision		Revision as of 15:59, 16 July 2011
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	is a standard Python command that loads the Madagascar project		is a standard Python command that loads the Madagascar project
	management module <tt>~~rsfproj~~.py</tt> which provides our extension to		management module <tt>rsf/proj.py</tt> which provides our extension to
	SCons.		SCons.

Sfomel: /* Creating reproducible documentation */

2010-09-15T22:50:29Z

Creating reproducible documentation

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	computational results (figures) are integrated with papers written in		computational results (figures) are integrated with papers written in
	L<sup>A</sup>TEX\.		L<sup>A</sup>TEX\.
	The corresponding SCons extension is defined in <tt>$~~RSFROOT~~/~~lib~~/~~rsftex~~.py</tt> where		The corresponding SCons extension is defined in <tt>$PYTHONPATH/rsf/tex.py</tt> where
	<tt>RSFROOT</tt> is the environmental variable to the Madagascar		<tt>RSFROOT</tt> is the environmental variable to the Madagascar
	installation directory. The source of this file is in		installation directory. The source of this file is in
	[http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/framework/~~rsftex~~.py?view=markup framework/~~rsftex~~.py].		[http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/framework/rsf/tex.py?view=markup framework/rsf/tex.py].
	We summarize the basic methods and commands in the tables.		We summarize the basic methods and commands in the tables.

	{\| class="wikitable"		{\| class="wikitable"
	\|+Basic methods of an <tt>~~rsftex~~</tt> object.		\|+Basic methods of an <tt>rsf.tex</tt> object.
	\|-		\|-
	\|style="background-color:#ffdead;"\| '''<tt>Paper(paper_name,[,lclass][,use][,include][,options])</tt>'''		\|style="background-color:#ffdead;"\| '''<tt>Paper(paper_name,[,lclass][,use][,include][,options])</tt>'''
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	environment and related to documentation is		environment and related to documentation is

	This command is defined in <tt>$~~RSFROOT~~/~~lib~~/~~rsftex~~.py</tt>.		This command is defined in <tt>$PYTHONPATH/rsf/tex.py</tt>.
	-->		-->

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	<python>		<python>
	from ~~rsftex~~ import *		from rsf.tex import *
	Paper('velan',use='hyperref,listings,color')		Paper('velan',use='hyperref,listings,color')
	End(use='hyperref,listings,color')		End(use='hyperref,listings,color')