Tutorial

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Contents

Introduction

Welcome to a brief introduction to Madagascar. The purpose of this document is to teach new users how to use the powerful tools in Madagascar to: process data, produce documents and build your own Madagascar programs. To gradually introduce you to Madagascar, we have created a series of tutorials that are targeted to distinct audiences and designed to make you an experienced Madagascar user in a short-time period. The tutorials are divided by interest into three main categories:

  • Users learn about Madagascar, how to use the processing programs, and build scripts.
  • Authors learn how to build reproducible documents using Madagascar.
  • Developers build new Madagascar programs that add additional functionality to Madagascar.

Each tutorial is designed to be completed in a short period of time. Additionally, each tutorial has hands-on examples that you should be able to reproduce on your computer as you go along with the tutorials. Most tutorials will use scripts that you can edit, modify, or play with to further gain experience and understanding. By the end of the tutorial series, you should be able to use all of the tools inside of Madagascar. Please note that this tutorial series does not explicitly show you how to process certain types of data, or how to perform common data processing operations (e.g. CMP semblance picking, time migration,etc.). Additional tutorials on those specific subjects will be added over time. The purpose of this document is simply to familiarize you with the Madagascar framework in a general sense. Before you go on, here are some notes on notation:

  • important names, or program names are usually bold in the text. For example: sfwindow
  • code snippets are always in the following formatting:
     sfwindow 

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 Madagascar framework,
  • the RSF file format,
  • the command line interface,
  • how to interact with files on the command line,
  • commonly used programs,
  • how to make plots in Madagascar,
  • how to make reproducible scripts,
  • how to use SCons and Python,
  • 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.

Introduction to Madagascar

To begin, let's talk about the core principles of Madagascar, and the RSF file format.

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

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.

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 N-dimensional array, where N 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:

  • number of elements on all axes,
  • the origin of the axes,
  • the sampling interval of elements on the axes,
  • the type of elements in the axes (i.e. float, integer),
  • the size of the elements (e.g. single or double precision),
  • 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.

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 (10s 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.

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.

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. 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.

Additional documentation

For more complete documentation on the RSF file format see the following links:

A gentle guide to the RSF file format

A detailed guide to the RSF file format

Command line interface

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

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. 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

sfattr < file.rsf
     rms =       1.41316 
   mean =      0.999667 
 2-norm =       357.503 
 variance =      0.997693 
std dev =      0.998846 
    max =       5.05567 at 36 8 27 
    min =      -3.59936 at 18 9 6 
 nonzero samples = 64000 
 total samples = 64000 
 

We demonstrate how to read and write RSF files using sfwindow which is a program that allows us to select portions of an RSF file. When sfwindow is used without any additional parameters, we are able to make a copy of a file with a different filename. For example:

 sfwindow < file.rsf > file2.rsf
 

gives us two files, file.rsf and file2.rsf which are identical but not the same file. If your intention is simply to copy a file, you can also use sfcp . In addition to specifying files to read in and out on the command line we can specify the parameters for each program that are necessary for it to run, or to produce the desired result. The general format for specifying parameters on the command line is key=val , where key is the name of the parameter that you want to set, and val is the value of the parameter. There are four (4) types of values that are acceptable: integers, floating point numbers, booleans, or strings. Going back to the window program, we can specify the number of traces or pieces of the file that we want to keep like:

sfwindow < file.rsf n1=10 > file-win.rsf

Self-documentation

Of course, we can specify as many parameters as we'd like on the command line. To figure out which parameters are needed for a specific program, just type the name of the program with no input files our output files on the command line to bring up a program's self-documentation. For example, sfwindow 's self documentation is:

NAME
sfwindow
DESCRIPTION
Window a portion of a dataset. 
SYNOPSIS
sfwindow < in.rsf > out.rsf verb=n squeeze=y 
j#=(1,...) d#=(d1,d2,...) f#=(0,...) min#=(o1,o2,,...) 
n#=(0,...) max#=(o1+(n1-1)*d1,o2+(n1-1)*d2,,...)
PARAMETERS
float   d#=(d1,d2,...)  sampling in #-th dimension 
largeint f#=(0,...)     window start in #-th dimension 
int     j#=(1,...)      jump in #-th dimension 
float   max#=(o1+(n1-1)*d1,o2+(n1-1)*d2,,...)   
maximum in #-th dimension 
float   min#=(o1,o2,,...)       minimum in #-th dimension 
largeint n#=(0,...)     window size in #-th dimension 
bool    squeeze=y [y/n] 
if y, squeeze dimensions equal to 1 to the end 
bool    verb=n [y/n]    Verbosity flag
USED IN
bei/dpmv/krchdmo
bei/dpmv/matt
bei/dwnc/sigmoid
bei/fdm/kjartjac
bei/fld/cube
bei/fld/shotmovie
bei/fld/synmarine
bei/fld/yc
bei/ft1/autocor
bei/ft1/brad
bei/ft1/ft2d
bei/krch/sep73
bei/sg/denmark
bei/sg/toldi
bei/trimo/mod
bei/trimo/subsamp
bei/vela/stretch
bei/vela/vscan
bei/wvs/head
bei/wvs/vscan
cwp/geo2006TimeShiftImagingCondition/flat
cwp/geo2006TimeShiftImagingCondition/icomp
cwp/geo2006TimeShiftImagingCondition/zicig
cwp/geo2007StereographicImagingCondition/flat4
cwp/geo2007StereographicImagingCondition/gaus1
167 more examples listed in:
/usr/local/RSFROOT/share/doc/madagascar/html/sfwindow.html
SOURCE
system/main/window.c
DOCUMENTATION
http://ahay.org/wiki/Guide_to_madagascar_programs#sfwindow
VERSION
1.3-svn

The self-documentation tells us the function of the program, as well as the parameters that are available to be specified. The parameter format is type - name=default value [options] and then a short description of the parameter. File parameters request a name of a file. For example:

 
file=file.rsf 

Note: strings with spaces must be enclosed in quotation marks (e.g. 'my value') so that the Unix shell could interpret them correctly.

Piping

Sometimes we want to chain multiple commands together without writing intermediate Madagascar RSF files in the process. We can avoid making intermediate files by using another standard UNIX construct, pipes. Pipes allow us to connect the standard output from one Madagascar program to the standard input to another program without first writing to a file. For example we could do the following without pipes:

sfwindow < file.rsf > file-win.rsf
sftransp < file-win.rsf > file2.rsf

Or we could do the equivalent using pipes on one line:

sfwindow < file.rsf | sftransp > file2.rsf

Pipes simply make these statements more compact, and allow us to reduce the number of files that we need to save to disk. Piping is very powerful, because there is no limit to the number of statements that you can pipe together. For example:

sfwindow < file.rsf | sftransp | sfnoise var=1 > file2.rsf 

If you're using multiple programs, and do not want to save the intermediate files, then pipes will greatly reduce the number of files that you have to keep track of.

Interacting with files from the command line

Ultimately though, 95% of your time using Madagascar on the command line will be to inspect and view files that are output by your scripts. Some of the key commands that are used to interact with files on the command line are:

  • sfin , used to get header information,
  • sfattr , used to get file attributes,
  • sfwindow , used to select portions of RSF files,
  • and sftransp , used to reorder files.

Here are detailed usage examples and explanations of what the above programs do: sfin is one of the most used program on the command line, because most often we simply need to check the dimensionality of our files to make sure that we have them in the correct order.

sfin file.rsf
 
file.rsf:
    in="/var/tmp/file.rsf@"
    esize=4 type=float form=native 
    n1=100         d1=0.004       o1=0          label1="Time" unit1="s" 
    n2=34          d2=0.1         o2=0          label2="Distance" unit2="km" 
	3400 elements 13600 bytes

sfattr is also commonly used from the command line to check files for correct values. Most often, we use sfattr to ensure that files are not filled with zeros, or with NaN's after a long computation, or to make sure that the values are reasonable. sfattr can be used to obtain basic statistics about the files as well.

sfattr < file.rsf 
 
******************************************* 
     rms =             1 
    mean =             1 
  2-norm =       58.3095 
variance =             0 
 std dev =             0 
     max =             1 at 1 1 
     min =             1 at 1 1 
nonzero samples = 3400 
  total samples = 3400 
*******************************************

sfwindow is used to select subsets of the data contained in an RSF file for computation elsewhere. Typically, you specify the data subset you want to keep using, the n, j, and f parameters which specify the number of indices in the arrays to keep, the jump in indices, and the first index to keep from the file in the respective dimension. For example if we want to keep the 15th-30th time samples from the first axis in file.rsf, we might use the following command:

sfwindow < file.rsf f1=15 n1=15 j1=1 > file-win.rsf

sftransp is used to reorder RSF files for other programs to be used. For example:

sftransp < file.rsf plane=12 > file-transposed.rsf

swaps the first and second axes, so that now the first axis is distance and the second axis is time. For more information about commonly used Madagascar programs please see the guide to Madagascar programs.

Plotting

VPLOT provides a method for making plots that are small in size, aesthetically pleasing, and easily compatible with Latex for rapid creation of productio-quality images in Madagascar.

VPLOT

The VPLOT file format (.vpl suffix) is a self-contained binary data format that describes in vector format how to draw a plot on the screen or a page using an interpreter. Since VPLOT is not a standard imaging format, VPLOT files must be viewed with interpreter programs which, for historical reasons, are called pens. Each pen interfaces VPLOT with a third-party graphing library such as X11, plplot, opengl, and others. This flexibility makes VPLOT files almost as portable as standard image formats such as: EPS, GIF, JPEG, PDF, PNG, SVG, and TIFF. Unlike rasterized formats, VPLOT files can be scaled to any size without losing image quality.

Creating plots

To generate VPLOT files, we need to pass our computed RSF files through VPLOT filters, that convert RSF data files to VPLOT files. The VPLOT filters are named by the type of plot that they produce. The following table lists all of the available VPLOT filters.

List of available plotting programs in Madagascar.
sfbox make box-line plots
sfcontour make contour plots
sfcontour3 make contour plots of 3D surfaces
sfdots plot signal with lollipops
sfgraph create line plots, or scatter plots
sfgraph3 generate 3-D cube plots for surfaces.
sfgrey create raster plots or 2D image plots
sfgrey3 create 3D image plots of panels (or slices) of a 3D cube
sfgrey4 generate movies of 3-D cube plots
sfplotrays make plots of rays
sfthplot make hidden-line surface plots
sfwiggle plot data with wiggly traces

To actually create a plot, we can use the plotting programs on the command line in the same fashion that we would use a Madagascar program:

sfspike n1=100 | sfnoise > file.rsf
sfgraph < file.rsf title="noise" > file.vpl

Visualizing plots

In this example, we create a single trace full of noise and then send it to sfgraph to produce a single VPLOT file, file.vpl. As you may have noticed, this only creates the file which is useful for saving the plot, does not allow us to visualize the data. To visualize the data we need to use a pen , which tells your machine how to actually draw the plot. A typical Madagascar installation will have multiple pens available for you to use. By default, you should use sfpen which will pick the best pen available for you. You can use sfpen to visualize your plots in the following manner:

sfpen < file.vpl

This will pop up a screen on your window with the plot shown. Depending on which pen you are using you may be able to interact with the pen interface to control various parameters of the plot as shown by the buttons at the top of the screen. Depending on the pen that you are using, there may be keyboard shortcuts to many of the buttons. NOTE: oglpen uses a mouse interface that can be accessed by right-clicking on the plot.

Converting VPLOT to other formats

If you want to build reports or documents using other programs, or want to send your images to someone who does not have Madagascar you will need to convert your VPLOT files to other image formats for transfer. To convert a VPLOT plot to another format use the tool vpconvert . vpconvert allows you to convert VPLOT files to any of the following formats, provided that you have the appropriate third-party libraries installed:

  • avi,
  • eps,
  • gif,
  • jpeg/jpg,
  • mpeg/mpg (movie format),
  • pdf,
  • png,
  • ppm,
  • ps,
  • svg,
  • and tif.

Here's an example of how to use vpconvert :

vpconvert file.vpl format=jpeg

NOTE: details on how to install these third-party libraries are not included with the Madagascar library, and we provide no support on installing them. Most users will be able to install them using either package management software (on Linux, Windows, and Mac) or pre-compiled binaries. The PS and EPS support is provided by default.

Scripting Madagascar

Madagascar's command line interface allows us to create, manipulate and plot data. Often though, we want to create scripts that will perform these operations automatically for us. Scripting is especially important when processing large amounts of data, or performing a complex chain of file manipulations in order to ensure that operations are completed in the right order or with proper parameters. In Madagascar, there are two main ways of creating scripts: shell scripts, and Python scripts using SCons.

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:

#!/bin/bash
sfspike n1=100 > file.rsf
< file.rsf sfgraph > file.vpl

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 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.

SConstructs and commands

SCons scripts are called SConstructs. In order to use SCons, you must create an SConstruct in the local directory where you want to work. Since SCons is written in Python, an SConstruct is simply a text file written using Python syntax. If you don't know Python, you can still use SCons, because the syntax is simple. First, a primer on Python syntax. In SConstructs we are going to deal with Python functions and strings. Python functions are simple, and should be familiar to anyone who has used a programming language. For example, calling a Python function, foo, looks like:

One argument - foo(1).
Many arguments - foo(1,2,3,4,5,123)

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:

"this is a string"
'this is a string'
"""this is a string"""
"'this is a string"'

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:

"""sfgraph title="my plot" """  OR
''' sfgraph title="my plot" ''' OR
'   sfgraph title="my plot" '

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:

Flow(output file,input file,command)

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:

Flow("spike1","spike","scale dscale=4.0")

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:

< spike.rsf sfscale dscale=4.0 > spike1.rsf

Note: the file names of the input and output files do not need to include '.rsf' on the end of the files as SCons automatically adds the suffix to all of our file names. Now that we can create relationships between files using Flow s, we can create an SConstruct to do all of our data processing using SCons. However, we often want to visualize the results of our processing in order to quality control the results. In order to create Plot s (or other visualizations) in Madagascar we have two additional SCons commands: Plot and Result . Plot and Result tell SCons how to use Madagascar's plotting programs to create visualizations of files on the fly after they have been computed. The syntax for both Plot and Result is as follows:

Plot(input file, command)

OR

Result(input file, command)

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:

Plot("spike1","sfgraph pclip=100")

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:

< spike1.rsf sfgraph pclip=100 > spike1.vpl

Result can be used in the same way as Plot , illustrated above. At this point, you might be asking yourself, what's the difference between Plot and Result ? The answer is that Plot creates all VPLOT files in the local directory, whereas Result creates its VPLOT files in a subdirectory called Fig. Fig is a location used to store Plot s that we want to later use when creating papers using LATEX. By default, you should use Plot when creating visualizations. Only use Result when you want to save something to be used in a paper. Note: since the VPLOTs from Plot and Result are placed in different locations you can use both Plot and Result for a single RSF file, but create two different plots for the same file.

Creating an SConstruct

Now that we have the three SConstruct commands, we can write our first SConstruct. To do so, open the SConstruct file in your favorite text editor. Before we can create any Flow , Plot or Result statements we have to add a first statement to the SConstruct. Enter the following statement (verbatim) into your new SConstruct:

from rsf.proj import *

This statement tells SCons where to find the Flow , Plot and Result commands, and must be included in every SConstruct. After that statement has been entered, you can enter as many Flow , Plot and Result commands as you wish making sure to use proper syntax. It's helpful to use a text editor that has Python syntax highlighting, as that will help you find and remedy strings that are not closed. You can also create Python comments using the \# mark to indicate the beginning of a comment to help document your SConstructs.

Lastly, you must include the following statement at the end of your SConstruct:

End()

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:

from rsf.proj import *  # Remember, this statement comes first... ALWAYS
Flow("spike",None,"sfspike n1=100 k1=50") 
# None is a trick, see Advanced SCons for more information
Flow("spike1","spike","sfadd scale=4.0")
Flow("noise","spike1","sfnoise")
Plot("spike",'sfgraph title="spike" ' ) # Note string nesting
Plot("spike1",'sfgraph title="spike1" ') 
Plot("noise",'sfgraph title="noisy" ')
Result("noise",'sfgraph title="noisy" pclip=75 ')
End() # Remember, this always ends the script.

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.

Executing SCons

Now that you have an SConstruct, you can start processing data the Madagascar way. To do so open a terminal and navigate to the local directory where your SConstruct is located. To execute your SConstruct simply run: scons . When you run SCons, it will check to make sure that all necessary dependencies are found and that all of your commands inside the SConstruct are valid. If not, SCons will return an error message showing you where you made a mistake. If everything is OK, then SCons will begin creating your files in the local directory and will output its progress as it executes the Madagascar programs on the command line. For example, running the sample SConstruct from above should show something similar to the following output:

scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
/opt/rsf/bin/sfspike n1=100 k1=50 > spike.rsf
< spike.rsf /opt/rsf/bin/sfadd scale=4.0 > spike1.rsf
< spike1.rsf /opt/rsf/bin/sfnoise > noise.rsf
< spike.rsf /opt/rsf/bin/sfgraph title="spike" > spike.vpl
< spike1.rsf /opt/rsf/bin/sfgraph title="spike1" > spike1.vpl
< noise.rsf /opt/rsf/bin/sfgraph title="noisy" > noise.vpl
< noise.rsf /opt/rsf/bin/sfgraph title="noisy" pclip=75 > Fig/noise.vpl
scons: done building targets.

If the execution of scons ends with, "scons: done building targets" then the script completed successfully. Check your local directory for your output files.

Common errors in SConstructs

There are two common errors that most users will experience when executing SConstructs: missing dependency errors, and misconfiguration errors. We'll demonstrate both of these errors to help new users troubleshoot them below. The first error is caused by missing a dependency in the SConstruct. To introduce this error into your SConstruct modify the sample SConstruct from above to the following:

from rsf.proj import *  # Remember, this statement comes first... ALWAYS
Flow("spike1","spike","sfadd scale=4.0")
Flow("noise","spike1","sfnoise")
Plot("spike",'sfgraph title="spike" ' ) # Note string nesting
Plot("spike1",'sfgraph title="spike1" ') 
Plot("noise",'sfgraph title="noisy" ')
Result("noise",'sfgraph title="noisy" pclip=75 ')
End() # Remember, this always ends the script.

Now when you run scons , you should get an error message:

scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
scons: *** [spike1.rsf] Source `spike.rsf' not found, needed by target `spike1.rsf'.
scons: building terminated because of errors.

In this case, SCons tells you exactly which file is missing and which output file is missing one of its dependencies. To solve this problem, add the Flow to create 'spike' to the SConstruct. If your SConstruct uses a file that is not created inside the SConstruct, and is complaining about a missing dependency, then make sure the file you are looking for is in a location that the SConstruct can access. The second error, is caused by having a misconfigured command. To demonstrate this type of error change your SConstruct to:

from rsf.proj import *  # Remember, this statement comes first... ALWAYS
 
'''Flow''' ("spike",None,"sfspike n1=100 k1=50") 
# None is a trick, see Users 4 for more information
'''Flow''' ("spike1","spike","sfasd scale=4.0") 
# HERE IS THE ERROR, NOTE sfasd instead of sfadd
'''Flow''' ("noise","spike1","sfnoise")
 
'''Plot''' ("spike",'sfgraph title="spike" ' ) # Note string nesting
'''Plot''' ("spike1",'sfgraph title="spike1" ') 
'''Plot''' ("noise",'sfgraph title="noisy" ')
 
'''Result''' ("noise",'sfgraph title="noisy" pclip=75 ')
 
End() # Remember, this always ends the script.

In this case, we've introduced a typo into one of our commands. When running scons, the result is:

scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
/opt/rsf/bin/sfspike n1=100 k1=50 > spike.rsf
< spike.rsf sfasd scale=4.0 > spike1.rsf
sh: sfasd: command not found
scons: *** [spike1.rsf] Error 127
scons: building terminated because of errors.

Again, the error message is pretty descriptive and could help you track down the error relatively quickly. It's important to note that in this case, the error was caught after SCons tried to execute the command and failed to do so, whereas the dependency error was caught before any commands were executed. This means that this typo error would kill a script that's been running a long time without any issues up till that point. Fortunately, SCons would restart the script at the point of failure thereby saving you all the additional time to recompute everything before this point in the script. These are only two of the most common errors that novice users will see. For additional information about debugging SConstructs, or for exceptionally strange errors please consult the online documentation or the RSF users mailing list.

Additional SCons commands

Here are some additional SCons commands that are useful to know.

Viewing Plots

If you're running an SConstruct and want to view the plots that it generates as it creates them, then you can use: scons view to force SCons to show the plots interactively. Doing so allows you to view your output at runtime and to stop the SConstruct as it's running if you don't like what you see.

Viewing only one plot

If you want to view the plot associated with only a single file you can tell SCons to view that plot by using the command: scons file.view where file is the filename of the item that you want to view. For example: scons spike.view would show the plot of the spike.rsf file. The advantage to using this command is that SCons will only build the dependencies needed to view that specific plot, which can save you a lot of time in longer processing scripts.

Building specific targets

If you want to build a specific RSF file, or a few specific RSF files you can simply specify them on the command line when you execute SCons as follows: scons file.rsf file2.rsf file3.rsf ... . The advantage to doing this, is that SCons will only build those files and their dependencies instead of running through the entire script.

Cleaning up

After we've executed our SConstruct and viewed the results of the processings flow, we might decide that we want to clean up our project and go work on something else. Normally, one would have to delete all of the files and then move on, but SCons automates this process using the command: scons -c . Simply execute it in the local directory and SCons will remove all of the built RSF files, and VPLOT files. SCons will not remove files that it does not have rules for.

Dry-runs

Sometimes we want to test an SConstruct through the end of the script without waiting for it to run completely. To do so, we can use scons -n which tells SCons to simulate an actual execution. During a dry-run SCons will check all of the commands, and dependencies to ensure that they exist and are properly configured. If not, then SCons will tell you which commands are misconfigured. This command can save you hours of debugging! Use it liberally.

Parallel executions

For long scripts we can use parallel execution to run multiple processing commands at the same time. Parallel execution requires that the commands can function independently of one another (i.e. there are commands that do not depend on each other's output). To use parallel execution use: pscons which launches the maximum number of parallel jobs that your computer can handle at once. Parallel execution can greatly speed up your processing flows if SCons can parallelize it. In the worst case, SCons won't be able to parallelize your script and it will run at the same speed as if you just used scons.

Final thoughts

At this point you should have a solid understanding of how to use SCons and create SConstructs to script your Madagascar processing flows. Admittedly, SCons is somewhat complicated and difficult to understand at first, but don't give up. By using SCons, you are able to create powerful Madagascar scripts that are completely reproducible and enjoy the benefits of using a powerful build management system. However, we have not shown you the most useful aspects of SCons, which are demonstrated in the next tutorial, where we show how to integrate Python with SCons, thereby making processing flows that are even more powerful.

Advanced SCons

Now that you have a grasp of how to use SCons to put together simple processing flows, we're going to show you how to abuse SCons to make more advanced processing flows that can handle multiple input and output files properly. Additionally, we're going to demonstrate some SCons tricks that make your life easier, and allow you to work faster, and smarter.

Multiple input files

Many Madagascar programs require multiple input files and/or output multiple files. In order for SCons to properly recognize that these additional files are dependencies for a specific output file we have to change the syntax that we use for Flow , Plot and Result statements. To do so, we'll need to use Python lists to help us keep everything together when using our SCons commands. We first discuss the case where we need multiple input files. An example of a Madagascar program that requires multiple input files is sfcat . For reference, sfcat is used to concatenate multiple files together, essentially a file manipulation program. For example, we might use sfcat on the command line in the following fashion:

< file.rsf sfcat axis=2 
file1.rsf file2.rsf file3.rsf file4.rsf > catted.rsf

To replicate this behavior using SCons we need to tell our Flow statements about the presence of multiple input files. Important: if we do not indicate to SCons that we have multiple input files then the dependency chain will not be correct and we cannot guarantee our results are correct . We can easily tell SCons of the presence of multiple input files by using a Python list as our input file, instead of a string:

Flow('catted',['file','file1','file2','file3','file4'],'sfcat axis=2 ${SOURCES[1:-1]}')

or, equivalently,

Flow('catted','file file1 file2 file3 file4','sfcat axis=2 ${SOURCES[1:-1]}')

As you may have noticed, there are two new items in this Flow statement, but let's start by discussing only the list of file names: ['file','file1','file2','file3','file4'] . The list of file names is simply a Python list of strings that contains each of the names of the files that we want to use in this Flow command. As usual, we don't have to append the '.rsf' suffix to the end of these names because SCons adds it for us. The second new part to the Flow command is: ${SOURCES[1:-1] }, referred to as the SCons source list, which tells SCons about the presence of additional input files in the command, and to substitute the names into the command automatically. Without this command, SCons would not include the files in the final command. As an example of what the SCons source list does, compare the two SConstructs below against one another. The top is correct, the bottom is incorrectly configured:

# Correct
from rsf.proj import *
Flow('file',None,'spike n1=100')
Flow('file1',None,'spike n1=100 mag=2')
Flow('file2',None,'spike n1=100 mag=3')
Flow('file3',None,'spike n1=100 mag=4')
Flow('file4',None,'spike n1=100 mag=5')
Flow('catted',['file','file1','file2','file3','file4'],
'sfcat axis=2 ${SOURCES[1:-1]}')
End()
# Wrong
from rsf.proj import *
Flow('file',None,'spike n1=100')
Flow('file1',None,'spike n1=100')
Flow('file2',None,'spike n1=100')
Flow('file3',None,'spike n1=100')
Flow('file4',None,'spike n1=100')
Flow('catted',['file','file1','file2','file3','file4'],'sfcat axis=2')
End()

If you noticed the command line output from SCons, you would find that for the incorrect SConstruct, SCons ran the following command:

< file.rsf sfcat axis=2 > catted.rsf

which is not correct. This is because SCons was not informed that the additional sources actually are used inside the command and did not substitute them in. The SCons source list contains a reference to all of the file names that we passed in our Python list earlier. In order to access those names we have to use a specific notation, but it is essentially a Python list enclosed in curly brackets that begins with a $. Since the source list is a Python list, we can get the file names in a few ways if we follow standard Python list conventions. Standard Python list conventions are:

  • List indexing starts with index 0,
  • Lists may be negatively indexed, which returns the items from the end (e.g. LIST[-1]),
  • Lists may be sliced using the LIST[start:end] notation, where start and end are indices,
  • List slicing indices are inclusive for the starting index, and exclusive for the ending index (e.g. LIST[0:4] returns LIST[0],LIST[1],LIST[2],LIST[3] but NOT LIST[4],
  • Open slicing indices may be used (e.g. LIST[2:] gets everything from index 2 to the end, and LIST[:4] returns everything from 0 to but not including 4).
  • Negative and positive indices may be used together (e.g. LIST[1:-1] returns all elements but the first and last).

These are the most useful conventions to remember, and the ones you will most frequently see. Please see the Python documentation (freely available online) for more information about dealing with Lists. Using the above conventions the following Flow statements are all equivalent for lettings SCons know about the presence of multiple input files:

Flow('catted',['file','file1','file2','file3','file4'],
'''
sfcat axis=2 ${SOURCES[1]} ${SOURCES[2]} 
    ${SOURCES[3]} ${SOURCES[4]}
''')
Flow('catted',['file','file1','file2','file3','file4'],
'''
sfcat axis=2 ${SOURCES[1:5]}
''')
Flow('catted',['file','file1','file2','file3','file4'],
'''
sfcat axis=2 ${SOURCES[1:-1]}
''')

Note: never use SOURCES[0] because SOURCES[0] corresponds to 'file' which is already used by SCons for standard input. Also, never use open slicing on the SOURCES list, because at the end of the SOURCES list are extra items added by SCons for safe keeping that will break the command if accidentally used.

Multiple outputs

For multiple outputs, we can use the same conventions as before, except we specify a list of output files instead of input files, and we use the TARGETS SCons list, instead of SOURCES. For example:

Flow(['pef','lag'], 'dat', 'sflpef lag=${TARGETS[1]}').

None inputs

Sometimes, Flow s are created that don't have an input file. For example, files created using sfspike do not require input files. To get around the need for an input file, we can use the Python keyword None , equivalent to NULL in C or Java, to indicate to SCons that no input file is needed. For example:

Flow('spike',None,'sfspike n1=100')

Toggling standard input and standard output

When None inputs are used, then standard input is no longer needed and can be disabled. To turn off standard input on a Flow , add another argument to the Flow statement:

Flow('spike',None,'sfspike n1=100',stdin=0)

When SCons runs this Flow , the output command line will be:

sfspike n1=100 > spike.rsf

Likewise, we can toggle output to standard output as well. Standard output has two options, redirect to null or completely off. For some programs we need to redirect standard output to null, and others will require standard output to be completely off. To toggle standard output off use the following syntax:

Flow('spike',None,'sfspike n1=100',stdout=-1)

OR to redirect to /dev/null:

Flow('spike',None,'sfspike n1=100',stdout=0)

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:

Plot('output','input','sfgraph')

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.

Integrating Python with SCons

Because SCons is written in Python, we can take advantage of all the features of the Python programming language. By doing so, we are able to make our life a lot easier by: compartmentalizing build commands, creating functions for commonly used scripts, organizing our scripts to make them easier to understand. Instead of giving an exhaustive tutorial of the combination of SCons and Python, we're going to demonstrate a few of the more commonly features of Python inside of SConstructs. We leave it to the end user to develop additional techniques that further exploit the power of Python.

A forewarning

While Python and SCons are compatible with one another they are not completely interchangeable. To understand why that is the case, you need to understand the underlying design of SCons. SCons is a declarative language, which means that you tell SCons what to do through the: Flow, Plot, and Result commands, and then SCons decides how and when to execute those commands. Python on the other hand is imperative , which means that as Python reads a Python script, it executes the commands immediately. Python does not take time to decide how or when to execute your commands. This point causes a bit of confusion to users who start to combine Python and SCons together because they expect SCons commands to execute in the order that they place them, which is not the case. Because of this, you may not be able to use certain Python features in their native Python way. For example, loops which require repeated computation, and whose results depend on the result of the last iteration are not possible using SCons. It is also not usually possible to use Python variables that change during execution with SCons because the variable value that SCons will use is always the last value of the variable. Typically, you cannot use conditional statements in SCons, where the choice depends on a file that SCons will build. To be safe, you should always assume that whatever Python does happens before SCons starts running commands.

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:

nx = 100
nz = 100
Flow('model',None,'sfspike n1='+str(nx)+'n2='+str(nz))

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

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:

nx = 100
nz = 100
Flow('model',None,
'''
sfspike n1=%d n2=%d 
''' % (nx,nz) )

In this statement, both nx, and nz are formatted as integers, and contained inside a tuple. All variables to be used for string substitution must be contained within the tuple at the end of the string statement. For reference, all C-printf like formatting choices are available in Python as well. Note: treat booleans as integers in Python.

Dictionaries

When scripts have a large number of variables, it is often easier to contain them within a Python dictionary instead of letting them float around the script. Dictionaries are declared in key=value format in Python using the dict keyword. For example:

parameters = dict(nx=100,nz=100,verb=True,final_file='output123')

To access variables from within the dictionary, we use list-like indexing where the index given is the name of the variable that we want to access:

nx = parameters['nx'] # Returns 100

We can also set variables within the dictionary, or modify their values after the initial declaration:

parameters['nx'] = 200 # Sets nx to 200
parameters['ny'] = 150 # Adds ny, and sets it to 150

To use the dictionary for string substitution, we only need to modify our formatters to include the key names of the variables that we wish to access from the dictionary. For example:

Flow('model',None,
	'''
	sfspike n1=%(nx)d n2=%(nz)d 
	''' % parameters )

Notice that the formatters now have the name of the variable inside parentheses: %(nx)d before the formatting expression. Then, the entire dictionary is passed to the string for substitution. At runtime, Python places the values for the keys from the dictionary into the string. If the values are the wrong type, or the key does not exist in the dictionary, then Python will throw an error at runtime, and prevent you from running with a bad value.

By using dictionaries with string substitution, we can add flexibility to our scripts, and improve their readability, which ultimately improves the ability of others to reproduce our work. Thus, you should strive to use dictionaries wherever possible in your SConstructs.

Loops

Perhaps the most useful construct from Python that can be added to SConstructs are loops. By using loops, we can automate many redundant processes. To use a Python loop we just use the standard Python syntax in the following fashion:

from rsf.proj import *
for i in range(10):
    count = str(i) # Convert integer to string
    Flow('spike-'+count,None,'sfspike n1=100 mag='+count)
    Plot('spike-'+count,'sfgraph')
End()

In order for the loop to work, you need to make sure that all the files that are created have a unique file name. The easiest way to do so is to use the loop index in the filename, the count variable in this case. The count variable must be a string, because only strings can be concatenated together in Python. If you want to make more complicated file names (from nested loops) then examine the printf like syntax for Python strings. All the usual Python rules apply to these loops. Typically, for loops are easier to understand than while loops in Python, and so we recommend using for loops for most purposes.

Functions

Python functions are incredibly useful because you can compartmentalize repeated uses of commonly used Flow s, and then use them in multiple SConstructs. For the best use of Python functions you should use the following conventions:

  • always use keyword=value arguments to help document your code,
  • list file names for input and output first, then other arguments,
  • use default values for all arguments, even if they are None,
  • use the locals() dictionary to get the values of the arguments,
  • always perform an action inside the function (i.e. create a Flow, Plot or Result),
  • do not return anything from the function,
  • and always accept **kwargs as the last argument to allow for dictionary substitution.

Here's an example of a well-defined function to create a Ricker wavelet with a peak frequency specified by the user:

def ricker(out='wave',freq=20.0,kt=100,nt=1001,dt=0.01,ot=0.0,**kwargs):
    Flow(out,None,
    	 '''
	 spike n1=%(nt)d o1=%(ot)f d1=%(d1)f 
         nsp=1 mag=1.0 k1=%(kt)d l1=%(kt)d | 
	 ricker1 frequency=%(freq)f 
	 ''' % locals())

Notice that we use the python function locals() for string substitution. This function returns a dictionary that contains only the names and values of the named arguments for the function. To call this function, you can use it as a normal Python function. Since there are default arguments, not all arguments need to be passed as long as you are OK with the default value.

ricker('wave',freq=30,kt=50)

If you are using a dictionary that has all of your variables in it, then you can call the function using explicit parameter fetching:

ricker('wave',parameters['freq'],parameters['kt'],...)

where you have to explicitly grab certain variables from the parameter dictionary. Conversely, you can use automatic parameter fetching:

ricker('wave',**parameters)

which will look for all the named arguments to the ricker function in the parameter dictionary, and send their values to the function. When there are many parameters, and you have already set them in the dictionary, then automatic parameter fetching is the best way to go.

Modules

Of course, functions can be compiled into groups and then placed into Python modules for widespread re-use throughout your SConstructs. Commonly used Python modules are currently located in $RSFROOT/book/Recipes, which is where you should place your modules as well. As usual, you must use correct Python syntax to access functions contained within modules. For example, if you create a module called myutil.py, then you can access your functions in the following manner:

import myutil
myutil.ricker(...)

Classes

The least used, but most powerful part of Python that you can bring into your SConstructs are Python classes. For example, if you are writing a script to process multiple models in the exact same way, but that have different parameters you would have to write separate Flow statements to process each of them, OR you could write a Python class that takes the model parameters and uses those parameters to generate Flow statements automatically, similar to functions. However, a class can allow you to group functions together into a single coherent body and allow you to drastically reduce the amount of code that must be reused. We refer the reader to the Python documentation for more information on creating and using classes.

Final thoughts

Congratulations on completing the Madagascar User tutorial series. Now, you should have all the tools to: use Madagascar programs, write SConstructs to script your processing flows, and combine Python with SCons to make powerful scripts that can process data in ways not previously possible. From here, you can continue learning about how to write your own Madagascar programs, or learn about how to make reproducible documents using the Madagascar framework.

Authors

The Authors tutorials demonstrate how one can create reproducible documents using the Madagascar processing package and LATEX together. By the end of the Authors tutorials, you should be able to:

  • build papers, including: SEG and EAGE abstracts, manuscripts for Geophysics, and handouts,
  • build a CSM thesis,
  • build a CWP report,
  • build slides,
  • 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. ewcommand{\maindir}{$RSFSRC/book/rsf/tutorial}

ewcommand{\exampledir}{\maindir/authors}

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 LATEX and additional LATEX class files that Madagascar makes available to you. The good news is that this configuration only happens once.

Downloading LATEX

To begin, you need to download a full installation of LATEX for your operating system. To do so, you may need to contact your system administrator. If you have administrative rights, then you can download a full install for your platform from the following locations:

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.

Downloading SEGTeX

The next step is to download the SEG\TeX class files, which tells LATEX how to build certain documents that we commonly use. To download SEG\TeX first cd to a directory where LATEX 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):

svn co https://segtex.svn.sourceforge.net/svnroot/segtex/trunk texmf 

or download a stable release from http://sourceforge.net/projects/segtex/files/ and unpack it into the texmf directory.

Updating your LATEX install

Once the class files are successfully downloaded, you will need to run texhash or texconfig rehash to update LATEX about the new class files. For reference, a successful run of texhash produces the following output:

jgodwin$ texhash
texhash: Updating /usr/local/texlive/2010/../texmf-local/ls-R... 
texhash: Updating /usr/local/texlive/2010/texmf/ls-R... 
texhash: Updating /usr/local/texlive/2010/texmf-config/ls-R... 
texhash: Updating /usr/local/texlive/2010/texmf-dist/ls-R... 
texhash: Updating /usr/local/texlive/2010/texmf-var/ls-R... 
texhash: Done.

To determine if these files are found successfully, go into $RSFROOT/book/rsf/manual and run scons manual.read . If LATEX complains about being unable to find the class files then you should re-run texhash, or make sure that your class files are in the proper location. If you are still having difficulties, then contact the SEGTeX webpage or the user mailing list for further information.

Papers

With LATEX installed, we can now create reproducible documents using Madagascar. First, we will demonstrate how to build shorter, less complicated documents using Madagascar, such as SEG/EAGE abstracts, Geophysics articles, and handouts. All of these papers have similar build styles, so the rules for building each respective paper have only slight differences from one another. Instead of talking in detail about each of these documents, we illustrate the basic idea for each of the documents, and provide examples that demonstrate the particulars for each type of document.

Paper organization

All Madagascar papers expect a specific organization to your directories. In particular, you are expected to have a paper-level directory where your tex files and main SConstruct will exist. These files will tell Madagascar how to build your documents for a particular project. You can have multiple documents built from the same location, using the same SConstruct as we will demonstrate later. Below the paper directory, are the individual "chapters" that contain the processing flows used to generate the plots or process the data that you wish to use in your reproducible documents. Ideally, each "chapter" directory correlates to the processing flows or examples in each chapter or section for your paper. Additionally, each "chapter" contains its own SConstruct that operates independently of the paper SConstruct one level above it. Furthermore, inside the "chapter" folder, Madagascar needs to have a Fig folder that contains all of the VPLOT files that were created using Result commands during processing. This folder is automatically created during processing using SCons, so you don't need to manually create it. It is important to note that Madagascar can only locate VPLOT files that are in this file hierarchy for use in your papers. The figure below illustrates the folder hierarchy as well. Note: "chapter" folders may be symbolic links that point to folders elsewhere on the file system. This trick can be useful to reuse figures without copying files and folders around to various folders. If you use symlinks, make sure to avoid editing files that are symbolically linked, as your changes may propagate in unintended ways to other projects and papers.

The organizational hierarchy for Madagascar paper directories.

Locking figures

Once you have created the necessary folder hierarchy with your "chapters" and processing flows, then go ahead and run your processing SConstructs. After those are finished, you need to lock your figures using scons lock . scons lock tells Madagascar that the figures you have generated are ready to go into a publication, and will store them in a subfolder of the $RSFFIGS directory for safe keeping. Locked figures are used for document figures instead of the figures in your local directory, because they are locked and not still changing. If you change your plots but do not lock your figures, you will not see your figures change. Always make sure to lock your figures before building a document.

TeX files

Now that your figures are locked, you can create your first reproducible document in Madagascar. To do so, you will need to:

  • make your TeX files, and
  • make a paper SConstruct,

Before making a document, you need to create your TeX files in the paper level directory. For example, to create an EAGE abstract, you would create a main TeX file called: eageabs.tex which contains the content and TeX commands to build your abstract. Your TeX file can use all of the standard and expanded LATEX commands provided by any available packages on your system. It's important to remember that you should try and break apart your TeX files into manageable chunks, so that you can modify them independently, or reuse the content in other documents. For example, instead of having a single TeX file for your EAGE abstract, you could have a separate TeX file that contains: \input{...} statements that include additional TeX files for each section, such as the abstract, theory, discussion, conclusions, etc. Additionally, Madagascar provides some convenience commands for often used LATEX functions. Here is a short description of some of those convenience commands that you may run across. Here's a brief list of these convenience functions:

  • \plot,
  • \multiplot,
  • \sideplot,
  • and more.

These convenience functions are not available for every type of document, but are demonstrated in documents where they are available. The definition for the convenience functions may be found in the LATEX class definitions listed at the end of this tutorial.

Paper SConstructs

One of Madagascar's aims is to make TeX files as layout-agnostic as possible. To do so, Madagascar automatically adds the TeX document preamble (including the LATEX document class information), the LATEX package inclusions, and end of document information at runtime. This allows you to generate multiple documents from a single TeX file by simply changing the SConstruct, instead of the TeX file. Note: the paper SConstruct is only used to build papers. It contains no other information, and cannot be used to process data in the same SConstruct. This is why the paper SConstruct must exist in a separate directory from any processing SConstructs. The paper SConstruct is very simple compared to most processing SConstructs, in that it contains only a few lines as shown below (in an example for an EAGE abstract):

from rsf.tex import *
Paper('eageabs',
      lclass='eageabs',
      options='11pt',
      use='times,natbib,color,amssymb,amsmath,amsbsy,graphicx,fancyhdr')

The first section, from rsf.tex import * tells Madagascar to import Python packages for processing TeX files instead of the usual processing packages. Next, we call a Paper object, which takes the following parameters:

Paper(name,lclass,options,use)
name - name of the root tex file to build.
lclass - name of the LaTeX class file to use.
options - document options for LaTeX class file.
use - names of LaTeX packages to import during compilation.

All of the parameters are passed as strings to the Paper object. Parameters with more that one possible value (e.g. options and use) accept comma delimited strings as shown above. To generate different types of documents, you simply change the lclass and options sent to the Paper object in the SConstruct for the respective document type. Since the documents that we are creating use custom LATEX document classes that require additional TeX commands to function properly, it is easier for us to provide you with a template instead of discussing the details of each document class. The templates for the documents can be found in the following directory: $RSFSRC/book/tutorial/authors.

Templates

To run the templates, you first need to generate the data used for them in the data directory inside of the $RSFSRC/book/tutorial/authors . To do so, run scons lock which will produce and lock the figures necessary. Then go into the template directory that you are interested in, and make a symbolic link to the data directory: ln -s ../data and a symbolic link to the BibTeX file: ln -s ../demobib.bib in the template directory. After those steps are made you can build and view the paper using scons or scons paper.read where paper is the name of the root tex file. Of course, if you want to remove all the generated files, then you can use scons -c to clean the directory.

Handouts

Handouts are informal documents that are loosely formatted, and very flexible. The handout example is located in: $RSFSRC/book/tutorial/authors/handout . Handouts do not require many additional arguments and are the most flexible of the documents discussed here.

EAGE abstracts

EAGE abstracts are short documents, with a few particular formatting tricks. In particular, EAGE requires the logo of the current year's convention to appear in the abstract. A template is available in: $RSFSRC/book/tutorial/authors/eage .

SEG abstracts

SEG abstracts are different from EAGE abstracts in that they require two-column formatting and are strictly limited to four pages not including references. To build an SEG abstract, we first build the abstract, and then build another document using the segcut.tex file that removes the references from the final pdf. An example is found in: $RSFSRC/book/tutorial/authors/seg .

Geophysics manuscripts

Geophysics manuscripts come in two flavors: the first is the manuscript prepared for peer review, and the second is the final document that would appear in a print version of Geophysics. The example shows how to build both from the same TeX files, which makes it painless to transition the formatting between the two documents. An example is located in: $RSFSRC/book/tutorial/authors/geophys . Make sure to use the template as there are quite a few additional TeX commands that have to be used to get the correct formatting.

CWP reports

CWP reports are slightly more complicated then most documents in that they require substantial modification to get the proper formatting. The CWP template is available in $RSFSRC/book/tutorial/authors/cwp .

Slides

Additionally, one can create presentation slides using LATEX and Madagascar together. To create slides, we use the Beamer class files that have been customized for the CWP. Slides have distinctly different commands then regular documents, so be sure to examine the template before diving in. The template is in: $RSFSRC/book/tutorial/authors/slides .

Theses

One can also create very complex documents using Madagascar in a reproducible way. To iillustrate this point we provide a template for building a thesis for the Colorado School of Mines. This template is quite heavily modified, and requires substantial modification due to all the formatting requirements. If you want to include a thesis template for another institution then you can do so by examining this template along with the CSM class files. The template is located in: $RSFSRC/book/tutorial/authors/thesis .

Books

You can make whole books using Madagascar. The advantage to doing so, is that you can make individual chapters with examples of processing or workflows that can be run independently of one another. Then Madagascar will stitch the chapters together into a cohesive package seamlessly. The example for a book is this document itself, which is located in: $RSFSRC/book/tutorial/ . Note: creating a book is significantly different from creating a paper.

Adding/modifying LATEX class files

The LATEX class files made available from SEGtex are found in texmf/tex/latex . You can modify these files locally by changing the files inside this location. To add your own LATEX class files, place them in this same directory, and then request SEG\TeX access to commit them to the main repository.

Using the default LATEX class files

Lastly, you can use any of the default LATEX class files just by changing the options to the Paper object to the appropriate lclass and options. For example:

Paper('article',
lclass='article',
options='11pt',
use='times,natbib,color,amssymb,amsmath,amsbsy,graphicx,fancyhdr')

Developers

The goal of this brief tutorial is to demonstrate the key concepts behind writing programs for Madagascar. Since the Madagascar API is well documented, we focus on a high level view of the development process and the core design functionality. For technical details of how to interface with the Madagascar API for a specific programming language, we refer the reader to the current online documentation mentioned at the end of this tutorial. By the end of this tutorial, you should understand the basic design of Madagascar programs, and where to find more information about how to develop programs using your programming language of choice.

Core design

As previously mentioned, the main way for programs to communicate in Madagascar is through RSF files. Thus, Madagascar programs are expected to read RSF files, process them, and then write RSF files as outputs that can be then used in other RSF programs. At the highest level of abstraction, we can consider RSF programs as black boxes that simply input and output RSF files and do something to them in between. From a practical standpoint, your programs will first read RSF files from disk into memory (or progressively do so) as hypercubes. Once the file is read,the program processes the hypercubes using routines that you design or external libraries. After processing, you then write the hypercubes to RSF files on disk. In pseudocode this process looks something like:

data = make_array()

input = rsf_input()

rsf_read(input,data) 

. . . process data . . .

output = rsf_output()

rsf_write(output,data)

Core API

Madagascar provides core APIs for each language to ease the process of reading/writing files. Additionally, the core API provides functions to parse command line variables that can be used to control the execution of your programs. In some languages, the API is extended to allow you to access commonly used functions from the RSF main library. For example, you can use the FFT library that is contained in Madagascar.

Program design philosophy

While Madagascar does not strictly have a design requirement for programs to enter the main distribution, there are some general guidelines to programs that we would like developers to follow. In particular, we would like developers to: design programs that have error handling and parameter checking, that accept command line arguments to control important parameters in the program, and write programs that are limited in scope. For example, a program that is limited in scope is a program that computes the Fourier transform of a real-valued signal and outputs a complex-valued RSF file. Conversely, a program that overreaches in its scope, would be a program that conducts a long series of processing completely in another language (say C or Fortran). You should avoid designing programs with too much scope, because you cannot fully leverage the advantages of SCons and Python, if everything is happening inside a C or Fortran program.

A Madagascar program reads RSF files, processes them, and then outputs them at the most fundamental level.

Final thoughts

With this background, and some additional information provided below, you should be able to start writing your own Madagascar programs to process data and implement algorithms that are not provided with Madagascar by default. We welcome you to the developer community, and would greatly appreciate it if you would consider releasing your programs to the community as a whole. If you have further questions, please feel free to ask the RSF mailing lists.

Further information

Quick reference

Environmental variables that are used in Madagascar programs
RSFROOT location of the main Madagascar installation
RSFSRC location of the source for Madagascar
DATAPATH location where to put the binary RSF files
RSF_MEMSIZE maximum memory size for some programs to use
PYTHONPATH set to point to Python libraries
LD_LIBRARY_PATH set to point to RSF dynamic libraries


Using programs on the command line
sfprogram < input.rsf arg1=val1 arg2=val2 ... > output.rsf
sftransp < file.rsf plane=12 > file2.rsf
sftransp < file.rsf plane=12 | sftransp plane=23 | sftransp plane=34 > file2.rsf
Some useful programs
sfdoc -k . | less show program descriptions
sfbrowser show program browser
sfgui show tkMadagascar GUI
sfspike create RSF files
sfmath create and manipulate RSF files
sftransp change the order of axes in RSF files
sfwindow window out portions of RSF files
sfricker1 create a Ricker wavelet
sfft1 FFT on the first axis (real to complex)
sffft3 FFT on other axes (complex)
sfnoise add noise
sfdd convert datasets
sfgrey make raster plots
'sfcat concatenate datasets together
sfput modify header values
sfsegyread read SEGY/SU files
sfsegywrite write SEGY/SU files
SCons commands
scons run an SConstruct
scons view view the results from an SConstruct, run if necessary
scons lock lock the results from an SConstruct
scons -c clean the local directory, delete all target files
scons -n dry-run of an SConstruct
scons --debug=explain explain why SCons is doing what it does
pscons parallel execution of an SConstruct