Extracting scripts from these tutorials: Difference between revisions

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The series of commands shown in each tutorial can be thought of as a data reduction script that can be run in CASA like so:
The series of commands shown in each tutorial can be written to a single casapy script using the CASA Guides script extractor.  The script extractor is described here.


<pre>
__TOC__
execfile('scriptname.py')
</pre>
 
where 'scriptname.py' is the name of an ascii file containing all of the CASA commands you want to run.
 
Hopefully the scripts contained in this documentation are (a) useful and (b) work. They were however developed with CASA still a work in progress, and so scripts may break as commands, arguments, and keywords change. We developed this script extractor to allow us to easily extract scripts from these pages and run them. Feel free to try it--it's handy for general users too!


The only differences you will see between the commands in each tutorial and the extracted script are requests for response from you after each interactive  command (plotants, plotcal, plotms, etc.).  These are to ensure that the tables you access to make plots are closed properly before they are needed by some following task (otherwise, you may experience the dreaded "table lock" errors, that may cause problems with your script, or in some cases even your CASA session.)
== Introduction ==


<div style="background-color: #dddddd;">
The script extractor will produce a Python script that can be invoked inside casapy.  The extractor ignores all CASA Guide source code that is not Python.  Special UNIX commands (such as 'ls' and 'less') supported by CASA but not by Python are commented out, and interactive pauses are inserted when GUIs are invoked.  (The interactive pause is necessary to avoid table lock errors that are produced when multiple tasks are run simultaneously.)
'''Note:''' the intention is to extract CASA scripts for testing; commands which are to be run on the command line outside of CASA, or within other software packages, will not be extracted.
</div>


 
If you are using OSX, you must have Python 2.7.13 or greater. Due to OSX security updates, the script extractor will not work with earlier versions of Python.
 
__TOC__


== How to Get the Script Extractor ==
== How to Get the Script Extractor ==


For most uses, the single-module script extractor is all you will need.  You can download it from
<!--
https://raw.github.com/jaredcrossley/CASA-Guides-Script-Extractor/master/extractCASAscript.py.
[https://github.com/jaredcrossley/CASA-Guides-Script-Extractor/blob/master/extractCASAscript.py script extractor]
 
-->
This Python module is maintained in a github repository as part of a simple, automated benchmark testing system.  You can browse the whole repository at https://github.com/jaredcrossley/CASA-Guides-Script-Extractor.


The older, pre-github version of the script extractor can be obtianed from ftp://ftp.cv.nrao.edu:/NRAO-staff/jgallimo/extractCASAscript.py.
For most uses, the single python script [https://github.com/CasaGuides/CASA-Guides-Script-Extractor/blob/master/extractCASAscript.py script extractor] is all you will need.  This Python module is maintained in a github repository as part of a simple, automated benchmark testing system.  If you like, you can browse the [https://github.com/CasaGuides/CASA-Guides-Script-Extractor whole repository] also.


== How to Use the Script Extractor ==
== How to Use the Script Extractor ==


Make your newly acquired python script executable.
Make your newly acquired Python script executable.


<source lang="bash">
<source lang="bash">
Line 37: Line 26:
</source>
</source>


To run it, issue the python script name and give the URL as the argument. For example:
To run it, issue the Python script name and give the URL as the argument. For example:


<source lang="bash">
<source lang="bash">
# in bash
# in bash or csh
./extractCASAscript.py http://casaguides.nrao.edu/index.php?title=Calibrating_a_VLA_5_GHz_continuum_survey
./extractCASAscript.py 'http://casaguides.nrao.edu/index.php?title=Calibrating_a_VLA_5_GHz_continuum_survey'
</source>
</source>


In csh, you need quotes around the URL:
This command will automatically generate a script called <tt>CalibratingaVLA5GHzcontinuumsurvey.py</tt>.  This script can be run in CASA:


<source lang="dos">
<source lang="python">
# in csh
# in CASA
./extractCASAscript.py 'http://casaguides.nrao.edu/index.php?title=Calibrating_a_VLA_5_GHz_continuum_survey'
execfile('CalibratingaVLA5GHzcontinuumsurvey.py')
</source>
</source>


== Support ==


This command will automatically generate a script called "CalibratingaVLA5GHzcontinuumsurvey.py"
Questions and bug reports should be submitted to either the [https://help.nrao.edu/ NRAO] or [https://help.almascience.org/ ALMA] helpdesks.
 
There is a companion script called removeplots.py which will comment out all calls to
plotcal, plotms, plotants, plotbandpass and raw_input. This is useful for running a script
non-interactively as a regression test.  You can get this from here: ftp://ftp.cv.nrao.edu/pub/casaguides/removeplots.py.
There is a corresponding script called restoreplots.py which restores the calls: ftp://ftp.cv.nrao.edu/pub/casaguides/restoreplots.py
 
== Version Notes ==
 
* 30 Oct 2009: Script created -- jfg.
* 17 Dec 2009: Fixed a bug that caused the script to drop brackets [] & {} incorrectly. Added script pauses for interactive commands viewer, plotms, plotxy, and plotcal. -- jfg
* 25 Feb 2010: Some minor bug fixes. -- jfg
* 19 Apr 2010: Better handling of interactive commands; allows for multi-line interactive commands.
* 21 May 2010: On-going improvements, mostly handling conversion of html math symbols into usable characters.
* 10 Jun 2010: The script is stable, but I've noticed some characters appear that don't correctly translate from html. The script searches for html codes for symbols and replaces them with ASCII symbols --- for example, translating "&amp;#38;" to ">" --- but it is uncertain whether I have caught all of the html characters produced by the GeSHI plug-in. It should be hopefully obvious how to fix html symbols that leak through to the extracted python script.
* 20 Apr 2012: Added the scripts removeplots.py and restoreplots.py - trh
 
--[[User:Jgallimo|Jack Gallimore]] 21:13, 3 November 2009 (UTC)

Latest revision as of 21:17, 3 January 2024

The series of commands shown in each tutorial can be written to a single casapy script using the CASA Guides script extractor. The script extractor is described here.

Introduction

The script extractor will produce a Python script that can be invoked inside casapy. The extractor ignores all CASA Guide source code that is not Python. Special UNIX commands (such as 'ls' and 'less') supported by CASA but not by Python are commented out, and interactive pauses are inserted when GUIs are invoked. (The interactive pause is necessary to avoid table lock errors that are produced when multiple tasks are run simultaneously.)

If you are using OSX, you must have Python 2.7.13 or greater. Due to OSX security updates, the script extractor will not work with earlier versions of Python.

How to Get the Script Extractor

For most uses, the single python script script extractor is all you will need. This Python module is maintained in a github repository as part of a simple, automated benchmark testing system. If you like, you can browse the whole repository also.

How to Use the Script Extractor

Make your newly acquired Python script executable. 

# in bash
chmod u+x extractCASAscript.py

To run it, issue the Python script name and give the URL as the argument. For example: 

# in bash or csh
./extractCASAscript.py 'http://casaguides.nrao.edu/index.php?title=Calibrating_a_VLA_5_GHz_continuum_survey'

This command will automatically generate a script called CalibratingaVLA5GHzcontinuumsurvey.py. This script can be run in CASA: 

# in CASA
execfile('CalibratingaVLA5GHzcontinuumsurvey.py')

Support

Questions and bug reports should be submitted to either the NRAO or ALMA helpdesks.

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