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<h1>Common Options</h1>
<p class="abstract">
Commonly used options and switches.
</p>
<h2>Verbose Output</h2>
<code>
$ munipack --verbose ... action and so on ...
</code>
<p>
This switch enables detailed reports.
The additional information can be useful for exploring
of processing or in doubts.
</p>
<p>
Without this switch,
Munipack respects standard UNIX philosophy:
<b>Only errors are reported. A silent run means no errors.</b>
It is very usefully for processing of large datasets because
only important errors should be delivered to users.
</p>
<h2>Numerical Data Types</h2>
<pre>
-B [8|16|32|-32]
--bitpix[=8|16|32|-32]
</pre>
<p>
Select bits per pixel of output images. Possible values are: 8
(0-255), 16 (0-65535), 32 (0-4294967296) for integer non-negative numbers
of ℕ set
and -32 (-10<sup>-38</sup> .. 10<sup>38</sup>, 6 decimal digits) for real numbers
of ℝ set, (values in braces indicates numerical ranges).
</p>
<p>
The parameter is set according to BITPIX in original frames for photometric
pre-corrections or set to -32 for derived images.
Defaults are usually satisfactory.
</p>
<p>
General guidelines: An optimal
bitpix for raw (instrumental) data is 16 (default) which covers
a full range of digital cameras. The representation occupies
2 × width × height bytes. Some out of range (rare) values will
be cut-off.
</p>
<p>
The representing by real numbers (eg. -32)
is recommended value for images intended for further processing
because saves numerical precision and their numerical range (but
occupies of twice more space with respect to 16).
</p>
<p>
8-bits reduces range (eg. suppress dynamical range) and 32 wastes
a lot of storage place only.
</p>
<h2>Input Filenames For A Single Output</h2>
<pre>
file(s).fits
@[file.lst]
-
</pre>
<p>
The list of files to process. Usually as a names with wildcards (* or ?).
Use @ (at) or - (dash) to read from a standard input. (@ character
is used in the same meaning in classical softwares Iraf and Midas.)
</p>
<p>
For single output file (actions with <samp>-o|--output</samp> like
bias, dark, flat and timeseries), the input files can be passed as
command line arguments or in a file. Arguments can be used by many ways:
</p>
<ul>
<li>Filenames: <samp>munipack ... one.fits more.fits red.fits nightmare.fits</samp></li>
<li>Wildcards: <samp>munipack ... *.fits</samp></li>
<li>Generated: <samp>munipack ... `find dir/ -name '*.fits'`</samp></li>
</ul>
<p>
The input from file is initiated with @ character followed a file-name (file.lst).
The file is a plain text file with single file per line. As example,
the content of the file.lst equivalent to the previous example:
</p>
<pre>
one.fits
more.fits
red.fits
nightmare.fits
</pre>
<p>
The file can be prepared by hand or prepared by the command with using
of <a href="http://en.wikipedia.org/wiki/Redirection_(computing)">shell redirection</a>
and <a href="http://en.wikipedia.org/wiki/Find">find</a> utility:
</p>
<pre>
$ ls *.fits > file.lst # files in current directory
$ find dir/ -name '*.fits' > file.lst # all files in dir/, recursive
$ ls *.fits | munipack dark - # filenames are piped from ls
</pre>
<h2>Input Filenames For Multiple Outputs</h2>
<code>
file(s)[,result(s)]
@[file.lst]
-
</code>
<p>
The list of files to process. Usually as a names with wildcards (* or ?).
The optional parameter <samp>result(s)</samp> can be used for a direct
setting of a new filename. Use @ (at) or - (dash) to read from a standard input.
<p>
<p>
For multiple output (actions without <samp>-o|--output</samp> like
find, aphot, astrometry and phcal), the input files
are manipulated the same way as in previous example. Moreover,
the twines of files separated by a comma are recognized and result
files can be named differently.
</p>
<p>
Examples similar to previous ones:
</p>
<ul>
<li>Filenames: <samp>munipack ... one.fits,two.fits red.fits,green.fits</samp></li>
<li>Wildcards: <samp>munipack ... *.fits</samp></li>
<li>Generated: <samp>munipack ... `find /dir -name '*.fits'`</samp></li>
</ul>
<p>(No change for both wildcard and generated ones.)</p>
<pre>
one.fits,two.fits
red.fits,green.fits
</pre>
<pre>
$ for F in *.fits; do echo ${F},${F%.fits}_result.fits; done > file.lst
</pre>
<p>
Last example illustrates, how a lot of files can be easy renamed and used
</p>
<p>
Note, that renaming can be modified by a powerful way as
describes <a href="#advanced">Advanced Output Filenames</a> section.
</p>
<h2>Simple Output Filenames</h2>
<pre>
-o name
--output name
</pre>
<p>
Specify an output file name for a single file. If the option is not
presented, the output name
is derived from the particular action name.
<!--
Use dash '-' for redirection to
the standard output. Precede the filename with exclamation
point (!) to overwrite of an existing FITS file.
In case that the name
is a directory, newly created file(s) are stored here.
-->
</p>
<h2>Target Directory</h2>
<pre>
-t directory
--target-directory=directory
</pre>
<p>
It would be useful to store output files in a specified directory.
The most typical use is storing modified files in a working directory
when original files are untouched.
</p>
<h2>Backup Strategy</h2>
<p>Backup strategy for Munipack modifies traditional conventions.
Backups are <b>switched-on</b> by default
(equivalent to use of -b option in every command). This is the important difference
to other FITS relates utilities. The observed data are too unique, valuable and once-in-a-lifetime
for ignoring backups.
The default behavior can be switched-off by using option <samp>--backup off</samp>.
</p>
<p>
For a comfortable use of routines, the backup method with just only once-time
copy is chooses. This may by potentially dangerous to data because older (original)
files are replaced.
</p>
<p>
The recommended way for processing is to use a working directory, different
to a directory with original data. Moreover, it is highly recommended to
store original data with permission flag set to read-only.
</p>
<p>
The parameter <samp>-t</samp> (<samp>--target-directory</samp>) can be used for this:
</p>
<pre>
$ munipack -t ~/work dark flat.fits *.fits
</pre>
<p>
Ones simply reads original data as <samp>sources.fits</samp> and store results in
<samp>~/work/sources.fits</samp>.
</p>
<h2>Backup Options</h2>
<pre>
-b
--backup[=method]
</pre>
<p>Backup options (default: on). Their syntax, environment variables and behavior
exactly corresponds to GNU core util's
<a href="http://www.gnu.org/software/coreutils/manual/html_node/Backup-options.html">Backup options</a>.
</p>
<pre>
-S suffix
--suffix=suffix
</pre>
<p>
Specify a suffix for backup files. Defaults set to tilde (~).
</p>
<p>
Certain characters (%,#,..) may interfere with bash and general regular expression
syntax which is used to recognize text patterns and ones are not recommended
as suffixes.
</p>
<p>
Sometimes, perhaps to save a some disk space, backups can be just switch-off
with setting of the environment variable:
</p>
<pre>
$ export VERSION_CONTROL=off
</pre>
<h2 id="advanced">Advanced Output Filenames</h2>
<pre>
-O
--pattern pattern (default: (.+)\.(.+))
--mask mask (default: empty)
--format format (default: empty)
</pre>
<p>
Specify a regular expression or a format to describe of an output file name(s).
The <samp>-O</samp> switch-on the advanced functionality (else the simple backup
with suffix is used). The pattern is a regular expression used to matching and
on will usually include bracket expression for back-references. The back-references
can be used in mask with \number. To test a regular expression, use sed:
<samp>sed s/pattern/mask/</samp>. <samp>--mask</samp> is used for newly created
files whilst <samp>--backup</samp> for specify of backup files.
</p>
<p>
The default pattern splits filenames onto two parts name and extension separated
by a dot (\.). The pattern recognizing algorithm uses
<a href="http://en.wikipedia.org/wiki/Regular_expression">Regular Expression</a>
rules syntax.
The parts are accessible via \number operator. The \0 means original
filename, \1 name and \2 extension.
</p>
<p>
The format is a standard format for output of
sequence images. To test a format, use <samp>printf "out%d.fits",666</samp>.
</p>
<p>
When just only <samp>-O</samp> is specified, backups are disabled.
</p>
<p>
When the advanced filename processing is set, the options <samp>-t,-S,-b</samp>
are ignored, because their functionality can be simply simulated.
</p>
<!--
<p>
When <samp>-O</samp> is specified but no other specificators (like masks, format)
are set, backups are disabled and the original file is modified in place.
</p>
-->
<p>Examples:</p>
<pre>
# store outputs in /tmp directory : -O --mask '/tmp/\0'
barnard_0011R.fits -> /tmp/barnard_0011R.fits
# modify suffix: -O --pattern '(.+)\.fits' --mask '\1.fit'
barnard_0011R.fits -> barnard_0011R.fit
# modify filename: -O --pattern '(.+)\.(.+)' --mask '\1_D.\2'
barnard_0011R.fits -> barnard_0011R_D.fits
# alternate backups: -O --mask '\0.bak'
barnard_0011R.fits -> barnard_0011R.fits.bak
# overwrite output: -O --mask '!\0'
barnard_0011R.fits -> !barnard_0011R.fits
# list of numbered files: -O --format 'out_%02d.fits'
barnard_0001R.fits -> out_01.fits
# disable backups: -O
barnard_0001R.fits -> barnard_0001R.fits
</pre>
<p>See also: <a href="http://docs.wxwidgets.org/3.0/classwx_reg_ex.html">wxRegEx</a>,
<a href="http://docs.wxwidgets.org/3.0/classwx_string.html">wxString</a></p>
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