Tutorial - Revision history

Fomels at 23:12, 31 October 2024

2024-10-31T23:12:42Z

← Older revision		Revision as of 23:12, 31 October 2024
Line 30:		Line 30:

	=Users=		=Users=
	The Users tutorials demonstrate how to use the Madagascar framework to create, process and visualize data, and to create reproducible scripts for processing data. The main goals of the Users tutorials are to learn about:		The Users tutorials demonstrate how to use the Madagascar framework to create, process, and visualize data and to create reproducible scripts for processing data. The main goals of the Users tutorials are to learn about:

	*the Madagascar framework,		*the Madagascar framework,
Line 41:		Line 41:
	*how to use SCons and Python,		*how to use SCons and Python,
	*how to visualize your data.		*how to visualize your data.
	By the end of this tutorial group you should be able to fully use all of Madagascar's built-in tools for data processing and scripting. ~~By using these~~ tools, you~~'ll be able~~ to process data ranging from tens of megabytes to tens of terabytes in a reproducible fashion.		By the end of this tutorial group, you should be able to fully use all of Madagascar's built-in tools for data processing and scripting. These tools will allow you to process data ranging from tens of megabytes to tens of terabytes in a reproducible fashion.
	==Introduction to Madagascar==		==Introduction to Madagascar==
	To begin, let's talk about the core principles of Madagascar, and the RSF file format.		To begin, let's talk about the core principles of Madagascar and the RSF file format.
	[[Image:scheme.png\|frame\|center\|The hierarchy of Madagascar. Fundamentally, everything builds off of the RSF file format. As you go up the chain the complexity level may increase, but the capabilities of the processing package increase as well.]]		[[Image:scheme.png\|frame\|center\|The hierarchy of Madagascar. Fundamentally, everything builds off of the RSF file format. As you go up the chain the complexity level may increase, but the capabilities of the processing package increase as well.]]
	===Madagascar's design===		===Madagascar's design===
	There are a few layers to Madagascar. At the bottom-most layer, is the RSF file format, ~~which is~~ a common exchange format ~~that~~ all Madagascar programs ~~use~~. Non-Madagascar programs can also read/write to and from RSF because it is an open exchange format. The next level of Madagascar contains the actual Madagascar programs that manipulate RSF files to process data. Concurrent to this level is the VPLOT graphics library which allows users to plot and visualize RSF files. The scripting utilities in Python and SCons are up another level from the core programs. These scripting utilities ~~allow~~ users to make powerful scripts that can perform even the most advanced data processing tasks. The last level includes support for LaTeX which allows you to ~~make~~ documents combining the features of Madagascar with ~~the~~ powerful typesetting ~~of LaTeX~~. Throughout the course of these tutorials, we will examine all of these components, and demonstrate how they can be used individually~~, as well as~~ together. When combined, the individual components of Madagascar allow us to: conduct experiments, process data, visualize our results, make reproducible scripts that can be shared with others, and write papers to document our experiments. Thus, Madagascar provides a fully integrated research environment.		There are a few layers to Madagascar. At the bottom-most layer is the RSF file format, a common exchange format used by all Madagascar programs. Non-Madagascar programs can also read/write to and from RSF because it is an open exchange format. The next level of Madagascar contains the actual Madagascar programs that manipulate RSF files to process data. Concurrent to this level is the VPLOT graphics library which allows users to plot and visualize RSF files. The scripting utilities in Python and SCons are up another level from the core programs. These scripting utilities enable users to make powerful scripts that can perform even the most advanced data processing tasks. The last level includes support for LaTeX, which allows you to create documents combining the features of Madagascar with LaTeX's powerful typesetting. Throughout the course of these tutorials, we will examine all of these components and demonstrate how they can be used individually and together. When combined, the individual components of Madagascar allow us to: conduct experiments, process data, visualize our results, make reproducible scripts that can be shared with others, and write papers to document our experiments. Thus, Madagascar provides a fully integrated research environment.

	===RSF file format===		===RSF file format===
	As previously mentioned, the lowest level of Madagascar is the RSF file format, which is the format used to exchange information between Madagascar programs. Conceptually, the RSF file format is one of the easiest to understand, as RSF files are simply regularly sampled hypercubes of information. For reference, a hypercube is a ~~hyper dimensional~~ cube (or array) that can best be visualized as an <math>N</math>-dimensional array, where <math>N</math> is between 1 and 9 in Madagascar.		As previously mentioned, the lowest level of Madagascar is the RSF file format, which is the format used to exchange information between Madagascar programs. Conceptually, the RSF file format is one of the easiest to understand, as RSF files are simply regularly sampled hypercubes of information. For reference, a hypercube is a hyperdimensional cube (or array) that can best be visualized as an <math>N</math>-dimensional array, where <math>N</math> is between 1 and 9 in Madagascar.

	RSF hypercubes are defined by two files, the header file and the binary file. The header file contains information about the dimensionality of the hypercube as well as the data contained within the hypercube. Information contained in the header file may include the following:		RSF hypercubes are defined by two files, the header file and the binary file. The header file contains information about the dimensionality of the hypercube as well as the data contained within the hypercube. Information contained in the header file may include the following:
Line 56:		Line 56:
	*the origin of the axes,		*the origin of the axes,
	*the sampling interval of elements on the axes,		*the sampling interval of elements on the axes,
	*the type of elements in the axes (i.e. float, integer),		*the type of elements in the axes (i.e., float, integer),
	*the size of the elements (e.g. single or double precision),		*the size of the elements (e.g. single or double precision),
	*and the location of the actual binary file.		*and the location of the actual binary file.
	Since we often want to view this information about files without deciphering it, we store the header file as an ASCII text file in the local directory, usually with the suffix '''.rsf''' . At any time, you can view or edit the contents of the header files using a text editor such as gedit, VIM, or Emacs.		Since we often want to view this information about files without deciphering it, we store the header file as an ASCII text file in the local directory, usually with the suffix '''.rsf''' . At any time, you can view or edit the contents of the header files using a text editor such as gedit, VIM, or Emacs.

	The binary file is ~~a file~~ stored remotely (i.e. in a separate directory) ~~that contains~~ the actual hypercube data. Because the hypercube data can be very large (<math>10s</math> of GB or TB) we usually store the binary files in a remote directory with the suffix '''.rsf@''' . The remote directory ~~is specified by the user~~ using the '''DATAPATH''' environmental variable. The advantage to doing this, is that we can store ~~the~~ large binary data ~~file~~ on a fast remote filesystem if we want, and we can avoid working in local directories.		The binary file is stored remotely (i.e., in a separate directory) containing the actual hypercube data. Because the hypercube data can be very large (<math>10s</math> of GB or TB), we usually store the binary files in a remote directory with the suffix '''.rsf@''' . The user can specify the remote directory using the '''DATAPATH''' environmental variable. The advantage of doing this is that we can store large binary data files on a fast remote filesystem if we want, and we can avoid working in local directories.
	[[Image:format.png\|frame\|center\|Cartoon of the RSF file format. The header file points to the binary file, which can be separate from ~~one another~~. The header file, which is text, is ~~very small~~ compared to the binary file.]]		[[Image:format.png\|frame\|center\|Cartoon of the RSF file format. The header file points to the binary file, which can be separate from each other. The header file, which is text, is tiny compared to the binary file.]]

	Because the header and binary are separated from one another, it is possible that we can lose either the header or binary for a particular RSF file. If the header is lost, then we can simply reconstruct the header using our previous knowledge of the data and a text editor. However, if we lose the binary file, then we cannot reconstruct the data regardless of what we do. Therefore, you should try and avoid losing either the header or binary data. The best way to ~~avoid~~ data loss is to make your research reproducible so that your results can be replicated later.		Because the header and binary are separated from one another, it is possible that we can lose either the header or binary for a particular RSF file. If the header is lost, then we can simply reconstruct the header using our previous knowledge of the data and a text editor. However, if we lose the binary file, then we cannot reconstruct the data regardless of what we do. Therefore, you should try and avoid losing either the header or binary data. The best way to prevent data loss is to make your research reproducible so that your results can be replicated later.
	Sometimes ~~though~~ we need to store RSF files for archiving or to transfer to other machines. Fortunately, we can avoid transferring the header and binary separately by using the combined header/binary format for RSF files. Files can be constructed using the combined header/binary format by specifying additional parameters on the command line, in particular '''--out=stdout''' , for any Madagascar program. The output file will then be header/binary combined, which allows you to transfer the file without fear ~~for~~ losing either the header or binary. Be careful though: header/binary combined files can be very large, and might slow down your local filesystem. A best practice is to ~~only~~ use combined header/binary files when absolutely necessary for file transfers. Note: header/binary combined files are usually automatically converted to header/binary separate files when processed by a Madagascar program.		Sometimes, we need to store RSF files for archiving or transfer to other machines. Fortunately, we can avoid transferring the header and binary separately by using the combined header/binary format for RSF files. Files can be constructed using the combined header/binary format by specifying additional parameters on the command line, in particular '''--out=stdout''' , for any Madagascar program. The output file will then be header/binary combined, which allows you to transfer the file without fear of losing either the header or binary. Be careful, though: header/binary combined files can be very large and might slow down your local filesystem. A best practice is only to use combined header/binary files when absolutely necessary for file transfers. Note: header/binary combined files are usually automatically converted to header/binary separate files when processed by a Madagascar program.

	===Additional documentation===		===Additional documentation===
Line 79:		Line 79:
	line. Programmers create Madagascar programs (prefixed with the sf		line. Programmers create Madagascar programs (prefixed with the sf
	designation) that read and write Madagascar files. These programs are		designation) that read and write Madagascar files. These programs are
	designed to be as general as possible, so that each ~~one~~ could operate		designed to be as general as possible so that each could operate
	on any dataset in RSF format, provided you also supply the correct		on any dataset in RSF format, provided you also supply the correct
	parameters and have the right type ~~of data~~ for the program.		parameters and have the right data type for the program.

	===Using programs===		===Using programs===
	Madagascar programs follow the standard UNIX conventions for reading and writing RSF files to and from '''stdin''' and '''stdout''' . This is also the convention that Seismic Unix uses, so it should be familiar to SU users.		Madagascar programs follow the standard UNIX conventions for reading and writing RSF files to and from '''stdin''' and '''stdout'''. This is also the convention that Seismic Unix uses, so it should be familiar to SU users.
	For example: the program '''sfattr''' allows us to get attributes about an RSF file (mean, standard deviation, min, max, etc.) To get the attributes for a pre-computed file, we might use		For example: the program '''sfattr''' allows us to get attributes about an RSF file (mean, standard deviation, min, max, etc.) To get the attributes for a pre-computed file, we might use
	<pre>		<pre>

Sfomel at 15:33, 30 August 2016

2016-08-30T15:33:47Z

← Older revision		Revision as of 15:33, 30 August 2016
Line 1:		Line 1:
	<center><font size="-1">''This page was created from the LaTeX source in [~~http~~://~~rsf~~.~~svn.sourceforge.net~~/~~viewvc~~/~~rsf~~/~~trunk~~/book/tutorial/ book/tutorial/] using [[latex2wiki]]''</font></center>		<center><font size="-1">''This page was created from the LaTeX source in [https://github.com/ahay/src/tree/master/book/tutorial book/tutorial/] using [[latex2wiki]]''</font></center>

	=Introduction=		=Introduction=

Tieyuan: /* Downloading LATEX */

2014-09-26T15:11:24Z

Downloading LATEX

← Older revision		Revision as of 15:11, 26 September 2014
Line 753:		Line 753:
	*Mac - install MacTex http://www.tug.org/mactex/2011/.		*Mac - install MacTex http://www.tug.org/mactex/2011/.
	*Windows - install MikTex http://miktex.org/.		*Windows - install MikTex http://miktex.org/.
	The respective downloads typically are quite large and take a substantial amount of time to complete, so start the download and come back later. Once your download is done, test your installation by executing '''pdflatex''' at the command line. If everything works fine then continue onwards.		The respective downloads typically are quite large and take a substantial amount of time to complete, so start the download and come back later. Once your download is done, test your installation by executing '''pdflatex''' at the command line. If everything works fine then continue onwards. For Mac users, you may need "sudo port install texlive-latex-extra".

	===Downloading SEGTeX===		===Downloading SEGTeX===
	The next step is to download the SEG\TeX class files, which tells L<sup>A</sup>TEX how to build certain documents that we commonly use. To download SEG\TeX first '''cd''' to a directory where L<sup>A</sup>TEX can find additional class files. This directory is typically operating system dependent, and may be distribution dependent for Linux. Typically, you can place these files in '''$HOME/texmf''' . Otherwise, you will need to place them in the root installation for Latex which can be found by searching for the basic class files, such as article.cls. On a Mac the typical place to put these files is '''$HOME/Library/texmf''' . In any case, once you are in the proper location, then use the following command to download the class files (using subversion):		The next step is to download the SEG\TeX class files, which tells L<sup>A</sup>TEX how to build certain documents that we commonly use. To download SEG\TeX first '''cd''' to a directory where L<sup>A</sup>TEX can find additional class files. This directory is typically operating system dependent, and may be distribution dependent for Linux. Typically, you can place these files in '''$HOME/texmf''' . Otherwise, you will need to place them in the root installation for Latex which can be found by searching for the basic class files, such as article.cls. On a Mac the typical place to put these files is '''$HOME/Library/texmf''' . In any case, once you are in the proper location, then use the following command to download the class files (using subversion):

Tieyuan: /* Authors */ cleanup

2014-09-26T15:05:22Z

Authors: cleanup

← Older revision		Revision as of 15:05, 26 September 2014
Line 744:		Line 744:
	*and add/modify Latex class files to add your custom document formats to Madagascar.		*and add/modify Latex class files to add your custom document formats to Madagascar.
	After completing this tutorial series, you will be able to maximize your research productivity using Madagascar.		After completing this tutorial series, you will be able to maximize your research productivity using Madagascar.
	~~ewcommand{\maindir}{$RSFSRC/book/rsf/tutorial}~~

	~~ewcommand{\exampledir}{\maindir/authors}~~
	==Getting started==		==Getting started==
	Before you can get started writing reproducible documents, you need to ensure that your system is properly setup. This section of the tutorial will walk you through the setup process, which can be somewhat difficult and laborious depending on which operating system you are on, as you will need a full installation of L<sup>A</sup>TEX and additional L<sup>A</sup>TEX class files that Madagascar makes available to you. The good news is that this configuration only happens once.		Before you can get started writing reproducible documents, you need to ensure that your system is properly setup. This section of the tutorial will walk you through the setup process, which can be somewhat difficult and laborious depending on which operating system you are on, as you will need a full installation of L<sup>A</sup>TEX and additional L<sup>A</sup>TEX class files that Madagascar makes available to you. The good news is that this configuration only happens once.

Sfomel: /* Shell scripting */

2014-04-12T13:02:15Z

Shell scripting

← Older revision		Revision as of 13:02, 12 April 2014
Line 327:		Line 327:
	===Shell scripting===		===Shell scripting===
	Shell scripting is the first option for creating scripts. In shell scripting we simply copy the command lines that we would use and paste them into a file that is recognized by either BASH, C-shell or another shell of your choosing. Shell scripting may be familiar to users of other packages such as SU, because it is the primary method of scripting there. An example of a Madagascar shell script is shown below:		Shell scripting is the first option for creating scripts. In shell scripting we simply copy the command lines that we would use and paste them into a file that is recognized by either BASH, C-shell or another shell of your choosing. Shell scripting may be familiar to users of other packages such as SU, because it is the primary method of scripting there. An example of a Madagascar shell script is shown below:
	<bash>		<syntaxhighlight lang="bash">
	#!/bin/bash		#!/bin/bash
	sfspike n1=100 > file.rsf		sfspike n1=100 > file.rsf
	< file.rsf sfgraph > file.vpl		< file.rsf sfgraph > file.vpl
	</~~bash~~>		</syntaxhighlight>
	For simple processing flows, shell scripting is a quick and easy approach to saving your processing flow. However, shell scripts quickly become unmanageable when more complicated processing flows are used. Additionally, shell scripts have no way to avoid repeating commands that have already been successfully run, which causes shell scripts to spend a significant amount of time duplicating already completed work. Because of these issues, Madagascar's main scripting option is to use a build manager called SCons for scripting instead of shell scripts.		For simple processing flows, shell scripting is a quick and easy approach to saving your processing flow. However, shell scripts quickly become unmanageable when more complicated processing flows are used. Additionally, shell scripts have no way to avoid repeating commands that have already been successfully run, which causes shell scripts to spend a significant amount of time duplicating already completed work. Because of these issues, Madagascar's main scripting option is to use a build manager called SCons for scripting instead of shell scripts.

	===SCons===		===SCons===
	SCons is a build manager written in 100% Python. As a build manager, SCons keeps track of three items for each file built in the script: the name of the output file(s), the name of the input file(s), and the rule (Madagascar program(s) with options) used to build the output file(s) from the input file(s). The advantage to keeping track of these items is that SCons can then check to see if any of those items have changed and if so mark the output file to be rebuilt. If no changes are detected, and the output file already exists, then SCons ''skips'' the output file and goes onto building other files. This gives the user the ability to avoid re-running portions of their scripts that previously completed without issue, which is very important when working on processing flows with large datasets where individual commands may take hours to execute. SCons also tracks dependencies between various processing commands. For example, if command 2 depends on the ouptut of command 1, and the input to command 1 changes, then SCons will automatically know that the input to command 2 has changed and will re-run command 2 as well. Furthermore, SCons allows us to run multiple processing commands at the same time on computers with sufficient capabilities, further reducing the amount of time that it takes for us to process data in Madagascar. Now, we'll discuss how to create SCons scripts and use SCons on the command line.		SCons is a build manager written in 100% Python. As a build manager, SCons keeps track of three items for each file built in the script: the name of the output file(s), the name of the input file(s), and the rule (Madagascar program(s) with options) used to build the output file(s) from the input file(s). The advantage to keeping track of these items is that SCons can then check to see if any of those items have changed and if so mark the output file to be rebuilt. If no changes are detected, and the output file already exists, then SCons ''skips'' the output file and goes onto building other files. This gives the user the ability to avoid re-running portions of their scripts that previously completed without issue, which is very important when working on processing flows with large datasets where individual commands may take hours to execute. SCons also tracks dependencies between various processing commands. For example, if command 2 depends on the ouptut of command 1, and the input to command 1 changes, then SCons will automatically know that the input to command 2 has changed and will re-run command 2 as well. Furthermore, SCons allows us to run multiple processing commands at the same time on computers with sufficient capabilities, further reducing the amount of time that it takes for us to process data in Madagascar. Now, we'll discuss how to create SCons scripts and use SCons on the command line.

Sfomel: /* Variables */

2014-04-08T22:22:18Z

Variables

← Older revision		Revision as of 22:22, 8 April 2014
Line 629:		Line 629:
	===Variables===		===Variables===
	The most effective way to combine SCons and Python is to use Python to manage important variables for your scripts. For example, if you want to test a variety of values for a certain processing Flow, then you might save the value to a variable and then let Python format it correctly for you, instead of changing the string each time you want to run a new test. You can also save all your variables in a convenient location and then easily change them to test different parameters as well. For example:		The most effective way to combine SCons and Python is to use Python to manage important variables for your scripts. For example, if you want to test a variety of values for a certain processing Flow, then you might save the value to a variable and then let Python format it correctly for you, instead of changing the string each time you want to run a new test. You can also save all your variables in a convenient location and then easily change them to test different parameters as well. For example:
	<python>		<syntaxhighlight lang="python">
	nx = 100		nx = 100
	nz = 100		nz = 100
	Flow('model',None,'sfspike n1='+str(nx)+'n2='+str(nz))		Flow('model',None,'sfspike n1='+str(nx)+'n2='+str(nz))
	</~~python~~>		</syntaxhighlight>
	Note: variables must be converted to strings in order to be combined into the command statements. Because these variables are converted using string concatenation, there is a possibility that a user could give a value of a wrong type.		Note: variables must be converted to strings in order to be combined into the command statements. Because these variables are converted using string concatenation, there is a possibility that a user could give a value of a wrong type.

	===String substitution===		===String substitution===
	While using variables is convenient, formatting them in the fashion shown above is not convenient. An easier way to format variables for strings is to use string substitution. String substitution works in the same way as the C - printf function works, i.e. we place markers that indicate where values should be substituted and what format they should be in. The above example using string substitution is:		While using variables is convenient, formatting them in the fashion shown above is not convenient. An easier way to format variables for strings is to use string substitution. String substitution works in the same way as the C - printf function works, i.e. we place markers that indicate where values should be substituted and what format they should be in. The above example using string substitution is:

Sfomel: /* Plots with a different output name */

2014-04-08T22:21:56Z

Plots with a different output name

← Older revision		Revision as of 22:21, 8 April 2014
Line 617:		Line 617:
	===Plots with a different output name===		===Plots with a different output name===
	Occasionally, you might want to create a plot with a different name than the input file. For example, a file might have multiple axes, and you could window along one of the axes, to create multiple graphs from a single input file. To distinguish between the different plots, you can rename the output files from Plot and Result commands using a syntax similar to Flow:		Occasionally, you might want to create a plot with a different name than the input file. For example, a file might have multiple axes, and you could window along one of the axes, to create multiple graphs from a single input file. To distinguish between the different plots, you can rename the output files from Plot and Result commands using a syntax similar to Flow:
	<python>		<syntaxhighlight lang="python">
	Plot('output','input','sfgraph')		Plot('output','input','sfgraph')
	</~~python~~>		</syntaxhighlight>
	This Plot command will produce output.vpl instead of input.vpl. In this way, you can create multiple visualizations of the same file. This applies to Result commands as well.		This Plot command will produce output.vpl instead of input.vpl. In this way, you can create multiple visualizations of the same file. This applies to Result commands as well.

Sfomel: /* Creating an SConstruct */

2014-04-08T22:21:32Z

Creating an SConstruct

← Older revision		Revision as of 22:21, 8 April 2014
Line 396:		Line 396:

	Lastly, you must include the following statement at the end of your SConstruct:		Lastly, you must include the following statement at the end of your SConstruct:
	<python>		<syntaxhighlight lang="python">
	End()		End()
	</~~python~~>		</syntaxhighlight>
	This statement tells SCons that the script is done and that it should not look for anything else in the script. Make sure to include this statement as the very last item in every SConstruct.		This statement tells SCons that the script is done and that it should not look for anything else in the script. Make sure to include this statement as the very last item in every SConstruct.
	Here's a sample SConstruct:		Here's a sample SConstruct:

	<python>		<syntaxhighlight lang="python">
	from rsf.proj import * # Remember, this statement comes first... ALWAYS		from rsf.proj import * # Remember, this statement comes first... ALWAYS
	Flow("spike",None,"sfspike n1=100 k1=50")		Flow("spike",None,"sfspike n1=100 k1=50")
Line 413:		Line 413:
	Result("noise",'sfgraph title="noisy" pclip=75 ')		Result("noise",'sfgraph title="noisy" pclip=75 ')
	End() # Remember, this always ends the script.		End() # Remember, this always ends the script.
	</~~python~~>		</syntaxhighlight>
	Note: you do not have to order your '''Flow''' , '''Plot''' and '''Result''' commands as shown above. You can mix '''Flow''' , '''Plot''' and '''Result''' in any order. SCons automatically establishes the relationships between related files and commands.		Note: you do not have to order your '''Flow''' , '''Plot''' and '''Result''' commands as shown above. You can mix '''Flow''' , '''Plot''' and '''Result''' in any order. SCons automatically establishes the relationships between related files and commands.

Sfomel: /* SConstructs and commands */

2014-04-08T22:20:43Z

SConstructs and commands

← Older revision		Revision as of 22:20, 8 April 2014
Line 343:		Line 343:
	</pre>		</pre>
	Python functions can take many arguments, and arguments of different types, but the syntax is the same. Python strings are also very similar to other programming languages. In Python anything inside double quotes is automatically considered to be a string, and not a variable declaration. However, Python also supports a few notations to indicate strings (or long strings) as shown below:		Python functions can take many arguments, and arguments of different types, but the syntax is the same. Python strings are also very similar to other programming languages. In Python anything inside double quotes is automatically considered to be a string, and not a variable declaration. However, Python also supports a few notations to indicate strings (or long strings) as shown below:
	<python>		<syntaxhighlight lang="python">
	"this is a string"		"this is a string"
	'this is a string'		'this is a string'
	"""this is a string"""		"""this is a string"""
	"'this is a string"'		"'this is a string"'
	</~~python~~>		</syntaxhighlight>
	Somtimes in Python you will need to nest a string within a string. To do use one of the string representations for the outer string, and use a different one for the inner string. For example:		Somtimes in Python you will need to nest a string within a string. To do use one of the string representations for the outer string, and use a different one for the inner string. For example:
	<python>		<syntaxhighlight lang="python">
	"""sfgraph title="my plot" """ OR		"""sfgraph title="my plot" """ OR
	''' sfgraph title="my plot" ''' OR		''' sfgraph title="my plot" ''' OR
	' sfgraph title="my plot" '		' sfgraph title="my plot" '
	</~~python~~>		</syntaxhighlight>
	Fundamentally, Madagascar's data-processing SConstructs are composed of only four commands: '''Fetch''' , '''Flow''' , '''Plot''' and '''Result''' . The main command is '''Flow''' . A '''Flow''' creates a relationship between the input file, the output file, and the processing command used to create the output file from the input file. The syntax for a '''Flow''' is:		Fundamentally, Madagascar's data-processing SConstructs are composed of only four commands: '''Fetch''' , '''Flow''' , '''Plot''' and '''Result''' . The main command is '''Flow''' . A '''Flow''' creates a relationship between the input file, the output file, and the processing command used to create the output file from the input file. The syntax for a '''Flow''' is:
	<pre>		<pre>
Line 360:		Line 360:
	</pre>		</pre>
	where, target and source are file names (strings), and command is a string that contains the Madagascar program to be used, along with the command line parameters needed for that program to run. For example:		where, target and source are file names (strings), and command is a string that contains the Madagascar program to be used, along with the command line parameters needed for that program to run. For example:
	<python>		<syntaxhighlight lang="python">
	Flow("spike1","spike","scale dscale=4.0")		Flow("spike1","spike","scale dscale=4.0")
	</~~python~~>		</syntaxhighlight>
	creates a dependency relationship between the output file 'spike1' and the input file 'spike'. The dependency indicates that 'spike1' cannot be created without 'spike' and that if 'spike' changes then 'spike1' also changes. The relationship in this case is that 'spike1' should be 'spike' scaled by four times. The equivalent command on the command line would be:		creates a dependency relationship between the output file 'spike1' and the input file 'spike'. The dependency indicates that 'spike1' cannot be created without 'spike' and that if 'spike' changes then 'spike1' also changes. The relationship in this case is that 'spike1' should be 'spike' scaled by four times. The equivalent command on the command line would be:
	<pre>		<pre>
Line 377:		Line 377:
	</pre>		</pre>
	In both cases, the '''Plot''' or '''Result''' command tells SCons to build a VPLOT file with same file name as the input file (with the .vpl suffix instead) from the input file using the command provided. For example, if we want to make a graph of a file we could use:		In both cases, the '''Plot''' or '''Result''' command tells SCons to build a VPLOT file with same file name as the input file (with the .vpl suffix instead) from the input file using the command provided. For example, if we want to make a graph of a file we could use:
	<python>		<syntaxhighlight lang="python">
	Plot("spike1","sfgraph pclip=100")		Plot("spike1","sfgraph pclip=100")
	</~~python~~>		</syntaxhighlight>
	Behind the scenes, SCons establishes that we want to use "spike1.rsf" to create a '''Plot''' called "spike1.vpl" using sfgraph. The equivalent command line operation is:		Behind the scenes, SCons establishes that we want to use "spike1.rsf" to create a '''Plot''' called "spike1.vpl" using sfgraph. The equivalent command line operation is:
	<pre>		<pre>

Sfomel: /* Using the default LATEX class files */

2014-04-08T22:19:40Z

Using the default LATEX class files

← Older revision		Revision as of 22:19, 8 April 2014
Line 849:		Line 849:
	==Using the default L<sup>A</sup>TEX class files==		==Using the default L<sup>A</sup>TEX class files==
	Lastly, you can use any of the default L<sup>A</sup>TEX class files just by changing the options to the Paper object to the appropriate lclass and options. For example:		Lastly, you can use any of the default L<sup>A</sup>TEX class files just by changing the options to the Paper object to the appropriate lclass and options. For example:
	<python>		<syntaxhighlight lang="python">
	Paper('article',		Paper('article',
	lclass='article',		lclass='article',
	options='11pt',		options='11pt',
	use='times,natbib,color,amssymb,amsmath,amsbsy,graphicx,fancyhdr')		use='times,natbib,color,amssymb,amsmath,amsbsy,graphicx,fancyhdr')
	</~~python~~>		</syntaxhighlight>

	=Developers=		=Developers=