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<HTML>
<HEAD>
<TITLE>Funtools Programs</TITLE>
</HEAD>
<BODY>
<H2>Funtools Programs</H2>

<H2>Summary</H2>

<P>
<PRE>

<A HREF="./programs.html#funcalc">funcalc</A> [-n] [-a argstr] [-e expr] [-f file] [-l link] [-p prog] [-u] &lt;iname&gt; [oname [columns]]

<A HREF="./programs.html#funcen">funcen</A> [-i] [-n iter] [-t tol] [-v lev] &lt;iname&gt; &lt;region&gt;

<A HREF="./programs.html#funcnts">funcnts</A> [switches] &lt;source_file&gt; [source_region] [bkgd_file] [bkgd_region|bkgd_cnts]

<A HREF="./programs.html#funcone">funcone</A> [-n] [-x|-X|-j|-J] [[-l|-L] list] [-r ra_col] [-d dec_col]  &lt;iname&gt; &lt;oname&gt; &lt;ra[hdr]&gt; &lt;dec[hdr]&gt; &lt;radius[dr'"]&gt; [columns]

<A HREF="./programs.html#fundisp">fundisp</A> [-f format] [-l] [-n] [-T] &lt;iname&gt; [columns|bitpix=n]

<A HREF="./programs.html#funhead">funhead</A> [-a] [-l] [-s] [-t] [-L] &lt;iname&gt; [oname ename]

<A HREF="./programs.html#funhist">funhist</A> [-n|-w|-T] &lt;iname&gt; [column] [[lo_edge:hi_edge:]bins] 

<A HREF="./programs.html#funimage">funimage</A> [-a] [-l] [-p x|y] &lt;iname&gt; &lt;oname&gt;  [bitpix=n]

<A HREF="./programs.html#funindex">funindex</A> &lt;iname&gt; &lt;key&gt; [oname]

<A HREF="./programs.html#funjoin">funjoin</A> [switches] &lt;ifile1&gt; &lt;ifile2&gt; ... &lt;ifilen&gt; &lt;ofile&gt; 

<A HREF="./programs.html#funmerge">funmerge</A> &lt;iname1&gt; &lt;iname2&gt; ... &lt;oname&gt;

<A HREF="./programs.html#funsky">funsky</A> [switches] &lt;iname1&gt; [&lt;lname2&gt; &lt;col1&gt; &lt;col2&gt;]

<A HREF="./programs.html#funtable">funtable</A> [-a] [-i|-z] [-m] [-s cols] &lt;iname&gt; &lt;oname&gt; [columns]

<A HREF="./programs.html#funtbl">funtbl</A> [-c cols] [-h] [-n table] [-p prog] [-s sep] [-T] &lt;iname&gt;
</PRE>

<!-- =defdoc funcalc funcalc 1 -->

<!-- =section funcalc NAME -->
<H2><A NAME="funcalc">funcalc - Funtools calculator (for binary tables)</A></H2>
<!-- =section funcalc SYNOPSIS -->
<B>
<PRE>
funcalc [-n] [-a argstr] [-e expr] [-f file] [-l link] [-p prog] &lt;iname&gt; [oname [columns]]
</PRE>
</B>

<!-- =section funcalc OPTIONS -->
<P>
<PRE>
  -a argstr    # user arguments to pass to the compiled program
  -e expr      # funcalc expression
  -f file      # file containing funcalc expression
  -l libs      # libs to add to link command  
  -n           # output generated code instead of compiling and executing
  -p prog      # generate named program, no execution
  -u           # die if any variable is undeclared (don't auto-declare)
</PRE>

<!-- =section funcalc DESCRIPTION -->
<P>
<B>funcalc</B> is a calculator program that allows arbitrary
expressions to be constructed, compiled, and executed on columns in a
Funtools table (FITS binary table or raw event file). It works by
integrating user-supplied expression(s) into a template C program,
then compiling and executing the program. <B>funcalc</B> expressions
are C statements, although some important simplifications (such
as automatic declaration of variables) are supported.

<P>
<B>funcalc</B> expressions can be specified in three ways: on the
command line using the <B>-e [expression]</B> switch, in a file using
the <B>-f [file]</B> switch, or from stdin (if neither <B>-e</B> nor
<B>-f</B> is specified). Of course a file containing <B>funcalc</B>
expressions can be read from stdin.

<P>
Each invocation of <B>funcalc</B> requires an input Funtools table
file to be specified as the first command line argument.  The output
Funtools table file is the second optional argument. It is needed only
if an output FITS file is being created (i.e., in cases where the
<B>funcalc</B> expression only prints values, no output file is
needed). If input and output file are both specified, a third optional
argument can specify the list of columns to activate (using 
<A HREF="./library.html#funcolumnactivate">FunColumnActivate()</A>).  Note
that <B>funcalc</B> determines whether or not to generate code for
writing an output file based on the presence or absence of an
output file argument.

<P>
A <B>funcalc</B> expression executes on each row of a table and
consists of one or more C statements that operate on the columns of
that row (possibly using temporary variables).  Within an expression,
reference is made to a column of the <B>current</B> row using the C
struct syntax <B>cur->[colname]</B>, e.g. cur->x, cur->pha, etc.
Local scalar variables can be defined using C declarations at very the
beginning of the expression, or else they can be defined automatically
by <B>funcalc</B> (to be of type double). Thus, for example, a swap of
columns x and y in a table can be performed using either of the
following equivalent <B>funcalc</B> expressions:

<PRE>
  double temp;
  temp = cur->x;
  cur->x = cur->y;
  cur->y = temp;
</PRE>

or:

<PRE>
  temp = cur->x;
  cur->x = cur->y;
  cur->y = temp;
</PRE>

When this expression is executed using a command such as:
<PRE>
  funcalc -f swap.expr itest.ev otest.ev
</PRE>
the resulting file will have values of the x and y columns swapped.

<P>
By default, the data type of the variable for a column is the same as
the data type of the column as stored in the file. This can be changed
by appending ":[dtype]" to the first reference to that column. In the
example above, to force x and y to be output as doubles, specify the
type 'D' explicitly:
<PRE>
  temp = cur->x:D;
  cur->x = cur->y:D;
  cur->y = temp;
</PRE>

Data type specifiers follow standard FITS table syntax for defining
columns using TFORM:
<UL>
<LI>A: ASCII characters
<LI>B: unsigned 8-bit char
<LI>I: signed 16-bit int
<LI>U: unsigned 16-bit int (not standard FITS)
<LI>J: signed 32-bit int
<LI>V: unsigned 32-bit int (not standard FITS)
<LI>E: 32-bit float
<LI>D: 64-bit float
<LI>X: bits (treated as an array of chars)
</UL>
Note that only the first reference to a column should contain the
explicit data type specifier.

<P>
Of course, it is important to handle the data type of the columns
correctly.  One of the most frequent cause of error in <B>funcalc</B>
programming is the implicit use of the wrong data type for a column in
expression.  For example, the calculation:
<PRE>
  dx = (cur->x - cur->y)/(cur->x + cur->y);
</PRE>
usually needs to be performed using floating point arithmetic. In
cases where the x and y columns are integers, this can be done by
reading the columns as doubles using an explicit type specification:
<PRE>
  dx = (cur->x:D - cur->y:D)/(cur->x + cur->y);
</PRE>

Alternatively, it can be done using C type-casting in the expression:
<PRE>
  dx = ((double)cur->x - (double)cur->y)/((double)cur->x + (double)cur->y);
</PRE>

<P>
In addition to accessing columns in the current row, reference also
can be made to the <B>previous</B> row using <B>prev->[colname]</B>,
and to the <B>next</B> row using <B>next->[colname]</B>.  Note that if
<B>prev->[colname]</B> is specified in the <B>funcalc</B>
expression, the very first row is not processed.  If
<B>next->[colname]</B> is specified in the <B>funcalc</B>
expression, the very last row is not processed. In this way,
<B>prev</B> and <B>next</B> are guaranteed always to point to valid
rows.  For example, to print out the values of the current x column
and the previous y column, use the C fprintf function in a
<B>funcalc</B> expression:
<PRE>
  fprintf(stdout, "%d %d\n", cur->x, prev->y);
</PRE>

<P>
New columns can be specified using the same <B>cur->[colname]</B>
syntax by appending the column type (and optional tlmin/tlmax/binsiz
specifiers), separated by colons. For example, cur->avg:D will define
a new column of type double. Type specifiers are the same those
used above to specify new data types for existing columns.

<P>
For example, to create and output a new column that is the average value of the
x and y columns, a new "avg" column can be defined:
<PRE>
  cur->avg:D = (cur->x + cur->y)/2.0
</PRE>
Note that the final ';' is not required for single-line expressions.

<P>
As with FITS TFORM data type specification, the column data type
specifier can be preceded by a numeric count to define an array, e.g.,
"10I" means a vector of 10 short ints, "2E" means two single precision
floats, etc.  A new column only needs to be defined once in a
<B>funcalc</B> expression, after which it can be used without
re-specifying the type. This includes reference to elements of a
column array:

<PRE>
  cur->avg[0]:2D = (cur->x + cur->y)/2.0;
  cur->avg[1] = (cur->x - cur->y)/2.0;
</PRE>

<P>
The 'X' (bits) data type is treated as a char array of dimension
(numeric_count/8), i.e., 16X is processed as a 2-byte char array. Each
8-bit array element is accessed separately:
<PRE>
  cur->stat[0]:16X  = 1;
  cur->stat[1]      = 2;
</PRE>
Here, a 16-bit column is created with the MSB is set to 1 and the LSB set to 2.

<P>
By default, all processed rows are written to the specified output
file. If you want to skip writing certain rows, simply execute the C
"continue" statement at the end of the <B>funcalc</B> expression,
since the writing of the row is performed immediately after the
expression is executed. For example, to skip writing rows whose
average is the same as the current x value:

<PRE>
  cur->avg[0]:2D = (cur->x + cur->y)/2.0;
  cur->avg[1] = (cur->x - cur->y)/2.0;
  if( cur->avg[0] == cur->x )
    continue;
</PRE>

<P>
If no output file argument is specified on the <B>funcalc</B> command
line, no output file is opened and no rows are written. This is useful
in expressions that simply print output results instead of generating
a new file:
<PRE>
  fpv = (cur->av3:D-cur->av1:D)/(cur->av1+cur->av2:D+cur->av3);
  fbv =  cur->av2/(cur->av1+cur->av2+cur->av3);
  fpu = ((double)cur->au3-cur->au1)/((double)cur->au1+cur->au2+cur->au3);
  fbu =  cur->au2/(double)(cur->au1+cur->au2+cur->au3);
  fprintf(stdout, "%f\t%f\t%f\t%f\n", fpv, fbv, fpu, fbu);
</PRE>
In the above example, we use both explicit type specification
(for "av" columns) and type casting (for "au" columns) to ensure that
all operations are performed in double precision.

<P>
When an output file is specified, the selected input table is
processed and output rows are copied to the output file.  Note that
the output file can be specified as "stdout" in order to write the
output rows to the standard output.  If the output file argument is
passed, an optional third argument also can be passed to specify which
columns to process.

<p>
In a FITS binary table, it sometimes is desirable to copy all of the
other FITS extensions to the output file as well. This can be done by
appending a '+' sign to the name of the extension in the input file
name. See <B>funtable</B> for a related example.

<P>
<B>funcalc</B> works by integrating the user-specified expression
into a template C program called <A HREF="./tabcalc.c">tabcalc.c</A>.
The completed program then is compiled and executed. Variable
declarations that begin the <B>funcalc</B> expression are placed in
the local declaration section of the template main program.  All other
lines are placed in the template main program's inner processing
loop. Other details of program generation are handled
automatically. For example, column specifiers are analyzed to build a
C struct for processing rows, which is passed to 
<A HREF="./library.html#funcolumnselect">FunColumnSelect()</A> and used
in <A HREF="./library.html#funtablerowget">FunTableRowGet()</A>.  If
an unknown variable is used in the expression, resulting in a
compilation error, the program build is retried after defining the
unknown variable to be of type double.

<P>
Normally, <B>funcalc</B> expression code is added to
<B>funcalc</B> row processing loop. It is possible to add code
to other parts of the program by placing this code inside
special directives of the form:
<PRE>
  [directive name]
    ... code goes here ...
  end
</PRE>

The directives are:
<UL>
<LI><B>global</B> add code and declarations in global space, before the main routine.

<LI><B>local</B> add declarations (and code) just after the local declarations in
main

<LI><B>before</B> add code just before entering the main row processing loop

<LI><B>after</B> add code just after exiting the main row processing loop
</UL>

Thus, the following <B>funcalc</B> expression will declare global
variables and make subroutine calls just before and just after the
main processing loop:
<PRE>
  global
    double v1, v2;
    double init(void);
    double finish(double v);
  end
  before
    v1  = init();
  end
  ... process rows, with calculations using v1 ...
  after
    v2 = finish(v1);
    if( v2 < 0.0 ){
      fprintf(stderr, "processing failed %g -> %g\n", v1, v2);
      exit(1);
    }
  end
</PRE>
Routines such as init() and finish() above are passed to the generated
program for linking using the <B>-l [link directives ...]</B>
switch. The string specified by this switch will be added to the link
line used to build the program (before the funtools library). For
example, assuming that init() and finish() are in the library
libmysubs.a in the /opt/special/lib directory, use:
<PRE>
  funcalc  -l "-L/opt/special/lib -lmysubs" ...
</PRE>

<p>
User arguments can be passed to a compiled funcalc program using a string
argument to the "-a" switch.  The string should contain all of the
user arguments. For example, to pass the integers 1 and 2, use:
<PRE>
  funcalc -a "1 2" ...
</PRE>
The arguments are stored in an internal array and are accessed as
strings via the ARGV(n) macro.  For example, consider the following
expression:
<PRE>
  local
    int pmin, pmax;
  end

  before
    pmin=atoi(ARGV(0));
    pmax=atoi(ARGV(1));
  end

  if( (cur->pha >= pmin) && (cur->pha <= pmax) )
    fprintf(stderr, "%d %d %d\n", cur->x, cur->y, cur->pha);
</PRE>
This expression will print out x, y, and pha values for all rows in which
the pha value is between the two user-input values:
<PRE>
  funcalc -a '1 12' -f foo snr.ev'[cir 512 512 .1]'
  512 512 6
  512 512 8
  512 512 5
  512 512 5
  512 512 8

  funcalc -a '5 6' -f foo snr.ev'[cir 512 512 .1]'
  512 512 6
  512 512 5
  512 512 5
</PRE>

<P>
Note that it is the user's responsibility to ensure that the correct
number of arguments are passed. The ARGV(n) macro returns a NULL if a
requested argument is outside the limits of the actual number of args,
usually resulting in a SEGV if processed blindly.  To check the
argument count, use the ARGC macro:
<PRE>
  local
    long int seed=1;
    double limit=0.8;
  end

  before
    if( ARGC >= 1 ) seed = atol(ARGV(0));
    if( ARGC >= 2 ) limit = atof(ARGV(1));
    srand48(seed);
  end

  if ( drand48() > limit ) continue;
</PRE>

<P>
The macro WRITE_ROW expands to the FunTableRowPut() call that writes
the current row. It can be used to write the row more than once.  In
addition, the macro NROW expands to the row number currently being
processed. Use of these two macros is shown in the following example:
<PRE>
  if( cur->pha:I == cur->pi:I ) continue;
  a = cur->pha;
  cur->pha = cur->pi;
  cur->pi = a;
  cur->AVG:E  = (cur->pha+cur->pi)/2.0;
  cur->NR:I = NROW;
  if( NROW < 10 ) WRITE_ROW;
</PRE>

<p>
If the <B>-p [prog]</B> switch is specified, the expression is not
executed. Rather, the generated executable is saved with the specified
program name for later use.

<P>
If the <B>-n</B> switch is specified, the expression is not
executed. Rather, the generated code is written to stdout. This is
especially useful if you want to generate a skeleton file and add your
own code, or if you need to check compilation errors. Note that the
comment at the start of the output gives the compiler command needed
to build the program on that platform. (The command can change from
platform to platform because of the use of different libraries,
compiler switches, etc.)

<P>
As mentioned previously, <B>funcalc</B> will declare a scalar
variable automatically (as a double) if that variable has been used
but not declared.  This facility is implemented using a sed script
named <A HREF="./funcalc.sed">funcalc.sed</A>, which processes the
compiler output to sense an undeclared variable error.  This script
has been seeded with the appropriate error information for gcc, and for
cc on Solaris, DecAlpha, and SGI platforms. If you find that automatic
declaration of scalars is not working on your platform, check this sed
script; it might be necessary to add to or edit some of the error
messages it senses.

<P>
In order to keep the lexical analysis of <B>funcalc</B> expressions
(reasonably) simple, we chose to accept some limitations on how
accurately C comments, spaces, and new-lines are placed in the
generated program. In particular, comments associated with local
variables declared at the beginning of an expression (i.e., not in a
<B>local...end</B> block) will usually end up in the inner loop, not
with the local declarations:
<PRE>
  /* this comment will end up in the wrong place (i.e, inner loop) */
  double a; /* also in wrong place */
  /* this will be in the the right place (inner loop) */
  if( cur->x:D == cur->y:D ) continue; /* also in right place */
  a = cur->x;
  cur->x = cur->y;
  cur->y = a;
  cur->avg:E  = (cur->x+cur->y)/2.0;
</PRE>
Similarly, spaces and new-lines sometimes are omitted or added in a
seemingly arbitrary manner. Of course, none of these stylistic
blemishes affect the correctness of the generated code.

<P>
Because <B>funcalc</B> must analyze the user expression using the data
file(s) passed on the command line, the input file(s) must be opened
and read twice: once during program generation and once during
execution. As a result, it is not possible to use stdin for the
input file: <B>funcalc</B> cannot be used as a filter. We will
consider removing this restriction at a later time.

<P>
Along with C comments, <B>funcalc</B> expressions can have one-line
internal comments that are not passed on to the generated C
program. These internal comment start with the <B>#</B> character and
continue up to the new-line:
<PRE>
  double a; # this is not passed to the generated C file
  # nor is this
  a = cur->x;
  cur->x = cur->y;
  cur->y = a;
  /* this comment is passed to the C file */
  cur->avg:E  = (cur->x+cur->y)/2.0;
</PRE>

<P>
As previously mentioned, input columns normally are identified by
their being used within the inner event loop. There are rare cases
where you might want to read a column and process it outside the main
loop. For example, qsort might use a column in its sort comparison
routine that is not processed inside the inner loop (and therefore not
implicitly specified as a column to be read).  To ensure that such a
column is read by the event loop, use the <b>explicit</b> keyword.
The arguments to this keyword specify columns that should be read into
the input record structure even though they are not mentioned in the
inner loop. For example:
 <PRE>
  explicit pi pha
</PRE>
will ensure that the pi and pha columns are read for each row,
even if they are not processed in the inner event loop. The <b>explicit</b>
statement can be placed anywhere.

<P>
Finally, note that <B>funcalc</B> currently works on expressions
involving FITS binary tables and raw event files. We will consider
adding support for image expressions at a later point, if there is
demand for such support from the community.

<!-- =defdoc funcen funcen 1 -->

<!-- =section funcen NAME -->
<H2><A NAME="funcen">funcen - find centroid (for binary tables)</A></H2>
<!-- =section funcen SYNOPSIS -->
<B>
<PRE>
funcen [-i] [-n iter] [-t tol] [-v lev] &lt;iname&gt; &lt;region&gt;
</PRE>
</B>

<!-- =section funcen OPTIONS -->
<P>
<PRE>
  -i            # use image filtering (default: event filtering)
  -n iter       # max number of iterations (default: 0)
  -t tol        # pixel tolerance distance (default: 1.0)
  -v [0,1,2,3]  # output verbosity level (default: 0)
</PRE>

<!-- =section funcen DESCRIPTION -->
<P>
<B>funcen</B> iteratively calculates the centroid position within one
or more regions of a Funtools table (FITS binary table or raw event
file).  Starting with an input table, an initial region specification,
and an iteration count, the program calculates the average x and y
position within the region and then uses this new position as the
region center for the next iteration. Iteration terminates when the
maximum number of iterations is reached or when the input tolerance
distance is met for that region. A count of events in the final region
is then output, along with the pixel position value (and, where
available, WCS position).

<P>
The first argument to the program specifies the Funtools table file to
process.  Since the file must be read repeatedly, a value of "stdin"
is not permitted when the number of iterations is non-zero.  Use 
<A HREF="./files.html">Funtools Bracket Notation</A> to specify FITS
extensions and filters.

<P>
The second required argument is the initial region descriptor. Multiple
regions are permitted. However, compound regions (accelerators,
variable argument regions and regions connected via boolean algebra)
are not permitted. Points and polygons also are illegal. These
restrictions might be lifted in a future version, if warranted.

<p>
The <B>-n</B> (iteration number) switch specifies the maximum number of
iterations to perform. The default is 0, which means that the program will
simply count and display the number of events in the initial region(s).
Note that when iterations is 0, the data can be input via stdin.

<p>
The <B>-t</B> (tolerance) switch specifies a floating point tolerance
value. If the distance between the current centroid position value and
the last position values is less than this value, iteration terminates.
The default value is 1 pixel.

<p>
The <B>-v</B> (verbosity) switch specifies the verbosity level of the
output. The default is 0, which results in a single line of output for
each input region consisting of the following values:
<pre>
  counts x y [ra dec coordsys]
</pre>
The last 3 WCS values are output if WCS information is available in the
data file header. Thus, for example:
<pre>
  [sh] funcen -n 0 snr.ev "cir 505 508 5"
  915 505.00 508.00 345.284038 58.870920 j2000

  [sh] funcen -n 3 snr.ev "cir 505 508 5"
  1120 504.43 509.65 345.286480 58.874587 j2000
</pre>
The first example simply counts the number of events in the initial region.
The second example iterates the centroid calculation three times to determine
a final "best" position.

<p> 
Higher levels of verbosity obviously imply more verbose output. At
level 1, the output essentially contains the same information as level
0, but with keyword formatting:

  [sh] funcen -v 1 -n 3 snr.ev "cir 505 508 5"
  event_file:     snr.ev
  initial_region: cir 505 508 5
  tolerance:      1.0000
  iterations:     1

  events:         1120
  x,y(physical):  504.43 509.65
  ra,dec(j2000):  345.286480 58.874587
  final_region1:  cir 504.43 509.65 5
</pre>
Level 2 outputs results from intermediate calculations as well.

<p>
Ordinarily, region filtering is performed using analytic (event)
filtering, i.e. that same style of filtering as is performed by
<b>fundisp</b> and <b>funtable</b>. Use the <b>-i</b> switch to specify image
filtering, i.e. the same style filtering as is performed by <b>funcnts</b>.
Thus, you can perform a quick calculation of counts in regions, using
either the analytic or image filtering method, by specifying the
 <b>-n 0</b> and optional <b>-i</b> switches. These two method often
give different results because of how boundary events are processed:
<pre>
  [sh] funcen  snr.ev "cir 505 508 5"
  915 505.00 508.00 345.284038 58.870920 j2000

  [sh] funcen -i snr.ev "cir 505 508 5"
  798 505.00 508.00 345.284038 58.870920 j2000
</pre>
See <A HREF="./regbounds.html">Region Boundaries</A> for more information
about how boundaries are calculated using these two methods.

<!-- =defdoc funcnts funcnts 1 -->

<!-- =section funcnts NAME -->
<H2><A NAME="funcnts">funcnts - count photons in specified regions, with bkgd subtraction</A></H2>

<!-- =section funcnts SYNOPSIS -->
<B>
<PRE>
funcnts  [switches] &lt;source_file&gt; [source_region] [bkgd_file] [bkgd_region|bkgd_value]
</PRE>
</B>

<!-- =section funcnts OPTIONS -->
<P>
<PRE>
  -e "source_exposure[;bkgd_exposure]"
                # source (bkgd) FITS exposure image using matching files
  -w "source_exposure[;bkgd_exposure]"
                # source (bkgd) FITS exposure image using WCS transform
  -t "source_timecorr[;bkgd_timecorr]"
                # source (bkgd) time correction value or header parameter name
  -g            # output using nice g format
  -G            # output using %.14g format (maximum precision)
  -i "[column;]int1;int2..." # column-based intervals
  -m            # match individual source and bkgd regions
  -p            # output in pixels, even if wcs is present
  -r            # output inner/outer radii (and angles) for annuli (and pandas)
  -s            # output summed values
  -v "scol[;bcol]" # src and bkgd value columns for tables
  -T            # output in starbase/rdb format
  -z            # output regions with zero area
</B>
</PRE>

<!-- =section funcnts DESCRIPTION -->
<P>
<B>funcnts</B> counts photons in the specified source regions and
reports the results for each region. Regions are specified using the
<A HREF="./regions.html">Spatial Region Filtering</A> mechanism.
Photons are also counted in the specified bkgd regions applied to the
same data file or a different data file. (Alternatively, a constant
background value in counts/pixel**2 can be specified.)  The bkgd regions
are either paired one-to-one with source regions or pooled and
normalized by area, and then subtracted from the source counts in each
region.  Displayed results include the bkgd-subtracted counts in each
region, as well as the error on the counts, the area in
each region, and the surface brightness (cnts/area**2) calculated for
each region.

<P>
The first argument to the program specifies the FITS input image, array, or
raw event file to process.  If "stdin" is specified, data are read from
the standard input. Use <A HREF="./files.html">Funtools Bracket
Notation</A> to specify FITS extensions, image sections, and filters.

<P>
The optional second argument is the source region descriptor.  If no
region is specified, the entire field is used.

<P>
The background arguments can take one of two forms, depending on
whether a separate background file is specified. If the source
file is to be used for background as well, the third argument can be
either the background region, or a constant value denoting background
cnts/pixel.  Alternatively, the third argument can be a background
data file, in which case the fourth argument is the background region.
If no third argument is specified, a constant value of 0 is used
(i.e., no background).

<P>
In summary, the following command arguments are valid:
<PRE>
  [sh] funcnts sfile                        # counts in source file
  [sh] funcnts sfile sregion                # counts in source region
  [sh] funcnts sfile sregion bregion        # bkgd reg. is from source file
  [sh] funcnts sfile sregion bvalue         # bkgd reg. is constant
  [sh] funcnts sfile sregion bfile bregion  # bkgd reg. is from separate file
</PRE>

<P>
NB: unlike other Funtools programs, source and background regions are
specified as separate arguments on the command line, rather than being
placed inside brackets as part of the source and background filenames.
This is because regions in funcnts are not simply used as data
filters, but also are used to calculate areas, exposure, etc. If you
put the source region inside the brackets (i.e. use it simply as a
filter) rather than specifying it as argument two, the program still
will only count photons that pass the region filter. However, the area
calculation will be performed on the whole field, since field() is the
default source region. This rarely is the desired behavior. On the
other hand, with FITS binary tables, it often is useful to put a column
filter in the filename brackets, so that only events matching the
column filter are counted inside the region.

<P>
For example, to extract the counts within a radius of 22 pixels from the
center of the FITS binary table snr.ev and subtract the background determined
from the same image within an annulus of radii 50-100 pixels:
<PRE>
  [sh] funcnts snr.ev "circle(502,512,22)" "annulus(502,512,50,100)"
  # source
  #   data file:        snr.ev
  #   degrees/pix:      0.00222222
  # background
  #   data file:        snr.ev
  # column units
  #   area:             arcsec**2
  #   surf_bri:         cnts/arcsec**2
  #   surf_err:         cnts/arcsec**2

  # background-subtracted results
   reg   net_counts     error   background    berror      area  surf_bri  surf_err
  ---- ------------ --------- ------------ --------- --------- --------- ---------
     1     3826.403    66.465      555.597     5.972  96831.98     0.040     0.001
  

  # the following source and background components were used:
  source region(s)
  ----------------
  circle(502,512,22)
  
   reg       counts    pixels
  ---- ------------ ---------
     1     4382.000      1513
  
  background region(s)
  --------------------
  annulus(502,512,50,100)
  
   reg       counts    pixels
  ---- ------------ ---------
  all      8656.000     23572
</PRE>
The area units for the output columns labeled "area", "surf_bri"
(surface brightness) and "surf_err" will be given either in
arc-seconds (if appropriate WCS information is in the data file
header(s)) or in pixels. If the data file has WCS info, but you do not
want arc-second units, use the <B>-p</B> switch to force output in
pixels.  Also, regions having zero area are not normally included in
the primary (background-subtracted) table, but are included in the
secondary source and bkgd tables. If you want these regions to be
included in the primary table, use the <B>-z</B> switch.

<P>
Note that a simple sed command will extract the background-subtracted results
for further analysis:
<PRE>
  [sh] cat funcnts.sed
  1,/---- .*/d
  /^$/,$d

  [sh] sed -f funcnts.sed funcnts.out
  1     3826.403    66.465      555.597     5.972  96831.98     0.040     0.001
</PRE>

<P>
If separate source and background files are specified, <B>funcnts</B> will
attempt to normalize the the background area so that the background
pixel size is the same as the source pixel size. This normalization
can only take place if the appropriate WCS information is contained in
both files (e.g. degrees/pixel values in CDELT). If either
file does not contain the requisite size information, the normalization
is not performed. In this case, it is the user's responsibility to
ensure that the pixel sizes are the same for the two files.

<P>
Normally, if more than one background region is specified, <B>funcnts</B>
will combine them all into a single region and use this background
region to produce the background-subtracted results for each source
region. The <B>-m</B> (match multiple backgrounds) switch tells
<B>funcnts</B> to make a one to one correspondence between background and
source regions, instead of using a single combined background region.
For example, the default case is to combine 2 background
regions into a single region and then apply that region to each of the
source regions:

<PRE>
  [sh] funcnts snr.ev "annulus(502,512,0,22,n=2)" "annulus(502,512,50,100,n=2)"
  # source
  #   data file:        snr.ev
  #   degrees/pix:      0.00222222
  # background
  #   data file:        snr.ev
  # column units
  #   area:             arcsec**2
  #   surf_bri:         cnts/arcsec**2
  #   surf_err:         cnts/arcsec**2
  
  # background-subtracted results
   reg   net_counts     error   background    berror      area  surf_bri  surf_err
  ---- ------------ --------- ------------ --------- --------- --------- ---------
     1     3101.029    56.922      136.971     1.472  23872.00     0.130     0.002
     2      725.375    34.121      418.625     4.500  72959.99     0.010     0.000
  
  
  # the following source and background components were used:
  source region(s)
  ----------------
  annulus(502,512,0,22,n=2)
  
   reg       counts    pixels
  ---- ------------ ---------
     1     3238.000       373
     2     1144.000      1140
  
  background region(s)
  --------------------
  annulus(502,512,50,100,n=2)
  
   reg       counts    pixels
  ---- ------------ ---------
  all      8656.000     23572
</PRE>
Note that the basic region filter rule "each photon is counted once
and no photon is counted more than once" still applies when using The
<B>-m</B> to match background regions. That is, if two background
regions overlap, the overlapping pixels will be counted in only one of
them. In a worst-case scenario, if two background regions are the same
region, the first will get all the counts and area and the second
will get none.

<P>
Using the <B>-m</B> switch causes <B>funcnts</B> to use each of the two
background regions independently with each of the two source regions:

<PRE>
  [sh] funcnts -m snr.ev "annulus(502,512,0,22,n=2)" "ann(502,512,50,100,n=2)"
  # source
  #   data file:        snr.ev
  #   degrees/pix:      0.00222222
  # background
  #   data file:        snr.ev
  # column units
  #   area:             arcsec**2
  #   surf_bri:         cnts/arcsec**2
  #   surf_err:         cnts/arcsec**2
  
  # background-subtracted results
   reg   net_counts     error   background    berror      area  surf_bri  surf_err
  ---- ------------ --------- ------------ --------- --------- --------- ---------
     1     3087.015    56.954      150.985     2.395  23872.00     0.129     0.002
     2      755.959    34.295      388.041     5.672  72959.99     0.010     0.000
  
  
  # the following source and background components were used:
  source region(s)
  ----------------
  annulus(502,512,0,22,n=2)
  
   reg       counts    pixels
  ---- ------------ ---------
     1     3238.000       373
     2     1144.000      1140
  
  background region(s)
  --------------------
  ann(502,512,50,100,n=2)
  
   reg       counts    pixels
  ---- ------------ ---------
     1     3975.000      9820
     2     4681.000     13752
</PRE>

<P>
Note that most floating point quantities are displayed using "f"
format. You can change this to "g" format using the <B>-g</B>
switch.  This can be useful when the counts in each pixel is very
small or very large. If you want maximum precision and don't care
about the columns lining up nicely, use <B>-G</B>, which outputs
all floating values as %.14g.

<P>
When counting photons using the annulus and panda (pie and annuli)
shapes, it often is useful to have access to the radii (and panda
angles) for each separate region. The <B>-r</B> switch will add radii
and angle columns to the output table:

<PRE>
  [sh] funcnts -r snr.ev "annulus(502,512,0,22,n=2)" "ann(502,512,50,100,n=2)"
  # source
  #   data file:        snr.ev
  #   degrees/pix:      0.00222222
  # background
  #   data file:        snr.ev
  # column units
  #   area:             arcsec**2
  #   surf_bri:         cnts/arcsec**2
  #   surf_err:         cnts/arcsec**2
  #   radii:            arcsecs
  #   angles:           degrees
  
  # background-subtracted results
   reg   net_counts     error   background    berror      area  surf_bri  surf_err   radius1   radius2    angle1    angle2
  ---- ------------ --------- ------------ --------- --------- --------- --------- --------- --------- --------- ---------
     1     3101.029    56.922      136.971     1.472  23872.00     0.130     0.002      0.00     88.00        NA        NA
     2      725.375    34.121      418.625     4.500  72959.99     0.010     0.000     88.00    176.00        NA        NA
  
  
  # the following source and background components were used:
  source region(s)
  ----------------
  annulus(502,512,0,22,n=2)
  
   reg       counts    pixels
  ---- ------------ ---------
     1     3238.000       373
     2     1144.000      1140
  
  background region(s)
  --------------------
  ann(502,512,50,100,n=2)
  
   reg       counts    pixels
  ---- ------------ ---------
  all      8656.000     23572
</PRE>

<P>
Radii are given in units of pixels or arc-seconds (depending on the
presence of WCS info), while the angle values (when present) are in
degrees.  These columns can be used to plot radial profiles. For
example, the script <B>funcnts.plot</B> in the funtools
distribution) will plot a radial profile using gnuplot (version 3.7 or
above). A simplified version of this script is shown below:

<PRE>
  #!/bin/sh
  
  if [ x"$1" = xgnuplot ]; then
    if [ x`which gnuplot 2>/dev/null` = x ]; then
      echo "ERROR: gnuplot not available"
      exit 1
    fi
    awk '
    BEGIN{HEADER=1; DATA=0; FILES=""; XLABEL="unknown"; YLABEL="unknown"}
    HEADER==1{
      if( $1 == "#" && $2 == "data" && $3 == "file:" ){
        if( FILES != "" ) FILES = FILES ","
        FILES = FILES $4
      }
      else if( $1 == "#" && $2 == "radii:" ){
        XLABEL = $3
      }
      else if( $1 == "#" && $2 == "surf_bri:" ){
        YLABEL = $3
      }
      else if( $1 == "----" ){
        printf "set nokey; set title \"funcnts(%s)\"\n", FILES
        printf "set xlabel \" radius(%s)\"\n", XLABEL
        printf "set ylabel \"surf_bri(%s)\"\n", YLABEL
        print  "plot \"-\" using 3:4:6:7:8 with boxerrorbars"
        HEADER = 0
        DATA = 1
        next
      }
    }
    DATA==1{
      if( NF == 12 ){
        print $9, $10, ($9+$10)/2, $7, $8, $7-$8, $7+$8, $10-$9
      }
      else{
        exit
      }
    }
    ' | gnuplot -persist - 1>/dev/null 2>&1
  
  elif [ x"$1" = xds9 ]; then
    awk '
    BEGIN{HEADER=1; DATA=0; XLABEL="unknown"; YLABEL="unknown"}
    HEADER==1{
      if( $1 == "#" && $2 == "data" && $3 == "file:" ){
        if( FILES != "" ) FILES = FILES ","
        FILES = FILES $4
      }
      else if( $1 == "#" && $2 == "radii:" ){
        XLABEL = $3
      }
      else if( $1 == "#" && $2 == "surf_bri:" ){
        YLABEL = $3
      }
      else if( $1 == "----" ){
        printf "funcnts(%s) radius(%s) surf_bri(%s) 3\n", FILES, XLABEL, YLABEL
        HEADER = 0
        DATA = 1
        next
      }
    }
    DATA==1{
      if( NF == 12 ){
        print $9, $7, $8
      }
      else{
        exit
      }
    }
    '
  else
    echo "funcnts -r ... | funcnts.plot [ds9|gnuplot]"
    exit 1
  fi
</PRE>

Thus, to run <B>funcnts</B> and plot the results using gnuplot (version 3.7
or above), use:
<PRE>
  funcnts -r snr.ev "annulus(502,512,0,50,n=5)" ...  | funcnts.plot gnuplot
</PRE>

<P>
The <B>-s</B> (sum) switch causes <B>funcnts</B> to produce an
additional table of summed (integrated) background subtracted values,
along with the default table of individual values:

<PRE>
  [sh] funcnts -s snr.ev "annulus(502,512,0,50,n=5)" "annulus(502,512,50,100)"
  # source
  #   data file:        snr.ev
  #   degrees/pix:      0.00222222
  # background
  #   data file:        snr.ev
  # column units
  #   area:             arcsec**2
  #   surf_bri:         cnts/arcsec**2
  #   surf_err:         cnts/arcsec**2
  
  # summed background-subtracted results
  upto   net_counts     error   background    berror      area  surf_bri  surf_err
  ---- ------------ --------- ------------ --------- --------- --------- ---------
     1     2880.999    54.722      112.001     1.204  19520.00     0.148     0.003
     2     3776.817    65.254      457.183     4.914  79679.98     0.047     0.001
     3     4025.492    71.972     1031.508    11.087 179775.96     0.022     0.000
     4     4185.149    80.109     1840.851    19.786 320831.94     0.013     0.000
     5     4415.540    90.790     2873.460    30.885 500799.90     0.009     0.000
  
  
  # background-subtracted results
   reg       counts     error   background    berror      area  surf_bri  surf_err
  ---- ------------ --------- ------------ --------- --------- --------- ---------
     1     2880.999    54.722      112.001     1.204  19520.00     0.148     0.003
     2      895.818    35.423      345.182     3.710  60159.99     0.015     0.001
     3      248.675    29.345      574.325     6.173 100095.98     0.002     0.000
     4      159.657    32.321      809.343     8.699 141055.97     0.001     0.000
     5      230.390    37.231     1032.610    11.099 179967.96     0.001     0.000
  
  
  # the following source and background components were used:
  source region(s)
  ----------------
  annulus(502,512,0,50,n=5)
  
   reg       counts    pixels      sumcnts    sumpix
  ---- ------------ --------- ------------ ---------
     1     2993.000       305     2993.000       305
     2     1241.000       940     4234.000      1245
     3      823.000      1564     5057.000      2809
     4      969.000      2204     6026.000      5013
     5     1263.000      2812     7289.000      7825
  
  background region(s)
  --------------------
  annulus(502,512,50,100)
  
   reg       counts    pixels
  ---- ------------ ---------
  all      8656.000     23572
</PRE>

<P>
The <B>-t</B> and <B>-e</B> switches can be used to apply timing and
exposure corrections, respectively, to the data. Please note that
these corrections are meant to be used qualitatively, since
application of more accurate correction factors is a complex and
mission-dependent effort. The algorithm for applying these simple
corrections is as follows:
<PRE>
  C =  Raw Counts in Source Region
  Ac=  Area of Source Region
  Tc=  Exposure time for Source Data
  Ec=  Average exposure in Source Region, from exposure map

  B=   Raw Counts in Background Region
  Ab=  Area of Background Region
  Tb=  (Exposure) time for Background Data
  Eb=  Average exposure in Background Region, from exposure map
</PRE>
Then, Net Counts in Source region is
<PRE>
  Net=  C - B * (Ac*Tc*Ec)/(Ab*Tb*Eb)
</PRE>
with the standard propagation of errors for the Error on Net.
The net rate would then be
<PRE>
  Net Rate = Net/(Ac*Tc*Ec)
</PRE>
The average exposure in each region is calculated by summing up the
pixel values in the exposure map for the given region and then
dividing by the number of pixels in that region. Exposure maps often
are generated at a block factor > 1 (e.g., block 4 means that each
exposure pixel contains 4x4 pixels at full resolution) and
<B>funcnts</B> will deal with the blocking automatically. Using the
<B>-e</B> switch, you can supply both source and background exposure
files (separated by ";"), if you have separate source and background
data files. If you do not supply a background exposure file to go with
a separate background data file, <B>funcnts</B> assumes that exposure
already has been applied to the background data file. In addition, it
assumes that the error on the pixels in the background data file is
zero.

<P>
NB: The <B>-e</B> switch assumes that the exposure map overlays the
image file <B>exactly</B>, except for the block factor.  Each pixel in
the image is scaled by the block factor to access the corresponding
pixel in the exposure map. If your exposure map does not line up
exactly with the image, <B>do not use</B> the <B>-e</B> exposure
correction.  In this case, it still is possible to perform exposure
correction <B>if</B> both the image and the exposure map have valid
WCS information: use the <B>-w</B> switch so that the transformation
from image pixel to exposure pixel uses the WCS information. That is,
each pixel in the image region will be transformed first from image
coordinates to sky coordinates, then from sky coordinates to exposure
coordinates. Please note that using <B>-w</B> can increase the time
required to process the exposure correction considerably.

<P>
A time correction can be applied to both source and
background data using the <B>-t</B> switch. The value for the correction can
either be a numeric constant or the name of a header parameter in
the source (or background) file:
<PRE>
  [sh] funcnts -t 23.4 ...            # number for source
  [sh] funcnts -t "LIVETIME;23.4" ... # param for source, numeric for bkgd
</PRE>
When a time correction is specified, it is applied to the net counts
as well (see algorithm above), so that the units of surface brightness
become cnts/area**2/sec.

<P>
The <B>-i</B> (interval) switch is used to run <b>funcnts</b> on multiple
column-based intervals with only a single pass through the data. It is
equivalent to running <b>funcnts</b> several times with a different column
filter added to the source and background data each time. For each
interval, the full <b>funcnts</b> output is generated, with a linefeed
character (^L) inserted between each run.  In addition, the output for
each interval will contain the interval specification in its header.
Intervals are very useful for generating X-ray hardness ratios
efficiently.  Of course, they are only supported when the input data
are contained in a table.

<P>
Two formats are supported for interval specification. The most general
format is semi-colon-delimited list of filters to be used as intervals:
<PRE>
  funcnts -i "pha=1:5;pha=6:10;pha=11:15" snr.ev "circle(502,512,22)" ...
</PRE>
Conceptually, this will be equivalent to running <b>funcnts</b> three times:
<PRE>
  funcnts snr.ev'[pha=1:5]' "circle(502,512,22)"
  funcnts snr.ev'[pha=6:10]' "circle(502,512,22)"
  funcnts snr.ev'[pha=11:15]' "circle(502,512,22)"
</PRE>
However, using the <B>-i</B> switch will require only one pass through
the data.

<P>
Note that complex filters can be used to specify intervals:
<PRE>
  funcnts -i "pha=1:5&&pi=4;pha=6:10&&pi=5;pha=11:15&&pi=6" snr.ev ...
</PRE>
The program simply runs the data through each filter in turn and generates
three <b>funcnts</b> outputs, separated by the line-feed character.

<P>
In fact, although the intent is to support intervals for hardness ratios,
the specified filters do not have to be intervals at all. Nor does one
"interval" filter have to be related to another. For example:
<PRE>
  funcnts -i "pha=1:5;pi=6:10;energy=11:15" snr.ev "circle(502,512,22)" ...
</PRE>
is equivalent to running <b>funcnts</b> three times with unrelated filter
specifications.

<P>
A second interval format is supported for the simple case in which a
single column is used to specify multiple homogeneous intervals for
that column. In this format, a column name is specified first,
followed by intervals:
<PRE>
  funcnts -i "pha;1:5;6:10;11:15" snr.ev "circle(502,512,22)" ...
</PRE>
This is equivalent to the first example, but requires less typing. The
<b>funcnts</b> program will simply prepend "pha=" before each of the specified
intervals. (Note that this format does not contain the "=" character in
the column argument.)

<P>
Ordinarily, when <b>funcnts</b> is run on a FITS binary table (or a
raw event table), one integral count is accumulated for each row
(event) contained within a given region. The <B>-v "scol[;bcol]"</B>
(value column) switch will accumulate counts using the value from the
specified column for the given event. If only a single column is
specified, it is used for both the source and background regions. Two
separate columns, separated by a semi-colon, can be specified for source
and background. The special token '$none' can be used to specify that
a value column is to be used for one but not the other. For example,
'pha;$none' will use the pha column for the source but use integral
counts for the background, while '$none;pha' will do the converse.
If the value column is of type logical, then the value used will be 1
for T and 0 for F.  Value columns are used, for example, to integrate
probabilities instead of integral counts.

<P>
If the <B>-T</B> (rdb table) switch is used, the output will conform
to starbase/rdb data base format: tabs will be inserted between
columns rather than spaces and line-feed will be inserted between
tables.

<P>
Finally, note that <B>funcnts</B> is an image program, even though it
can be run directly on FITS binary tables. This means that image
filtering is applied to the rows in order to ensure that the same
results are obtained regardless of whether a table or the equivalent
binned image is used. Because of this, however, the number of counts
found using <B>funcnts</B> can differ from the number of events found
using row-filter programs such as <B>fundisp</B> or <B>funtable</B>
For more information about these difference, see the discussion of
<A HREF="./regbounds.html">Region Boundaries</A>.

<!-- =defdoc funcone funcone 1 -->

<!-- =section funcone NAME -->
<H2><A NAME="funcone">funcone - cone search of a binary table containing RA, Dec columns</A></H2>

<!-- =section funcone SYNOPSIS -->
<B>
<PRE>
funcone &lt;switches&gt;  &lt;iname&gt; &lt;oname&gt; &lt;ra[hdr]&gt; &lt;dec[hdr]&gt; &lt;radius[dr'"]&gt; [columns]
</PRE>
</B>

<!-- =section funcone OPTIONS -->
<P>
<PRE>
  -d deccol:[hdr]  # Dec column name, units (def: DEC:d)
  -j               # join columns from list file
  -J               # join columns from list file, output all rows
  -l listfile      # read centers and radii from a list
  -L listfile      # read centers and radii from a list, output list rows
  -n               # don't use cone limits as a filter
  -r  racol:[hdr]  # RA column name, units (def: RA:h)
  -x               # append RA_CEN, DEC_CEN, RAD_CEN, CONE_KEY cols
  -X               # append RA_CEN, DEC_CEN, RAD_CEN, CONE_KEY cols, output all rows
</PRE>

<!-- =section funcone DESCRIPTION -->
<P>
Funcone performs a cone search on the RA and Dec columns of a FITS
binary table. The distance from the center RA, Dec position to the RA,
Dec in each row in the table is calculated. Rows whose distance is
less than the specified radius are output.

<P>
The first argument to the program specifies the FITS file, raw event
file, or raw array file.  If "stdin" is specified, data are read from
the standard input. Use <A HREF="./files.html">Funtools Bracket
Notation</A> to specify FITS extensions, and filters.  The second
argument is the output FITS file.  If "stdout" is specified, the FITS
binary table is written to the standard output.  

<P> 
The third and fourth required arguments are the RA and Dec center
position.  By default, RA is specified in hours while Dec is specified
in degrees.  You can change the units of either of these by appending
the character "d" (degrees), "h" (hours) or "r" (radians). Sexagesimal
notation is supported, with colons or spaces separating hms and dms.
(When using spaces, please ensure that the entire string is quoted.)

<P>
The fifth required argument is the radius of the cone search. By default,
the radius value is given in degrees. The units can be changed by appending
the character "d" (degrees), "r" (radians), "'" (arc minutes) or
'"' (arc seconds).

<P>
By default, all
columns of the input file are copied to the output file.  Selected
columns can be output using an optional sixth argument in the form:
<PRE>
  "column1 column1 ... columnN"
</PRE>
A seventh argument allows you to output selected columns from the list
file when <B>-j</B> switch is used. Note that the RA and Dec columns
used in the cone calculation must not be de-selected.

<P>
Also by default, the RA and Dec column names are named "RA" and "Dec",
and are given in units of hours and degrees respectively. You can
change both the name and the units using the -r [RA] and/or -d [Dec]
switches. Once again, one of "h", "d", or "r" is appended to the
column name to specify units but in this case, there must be a colon ":"
between the name and the unit specification.

<P>
If the <B>-l [listfile]</B> switch is used, then one or more of the
center RA, center Dec, and radius can be taken from a list file (which
can be a FITS table or an ASCII column text file). In this case, the
third (center RA), fourth (center Dec), and fifth (radius) command
line arguments can either be a column name in the list file (if that
parameter varies) or else a numeric value (if that parameter is
static). When a column name is specified for the RA, Dec, or radius,
you can append a colon followed by "h", "d", or "r" to specify units
(also ' and " for radius). The cone search algorithm is run once for
each row in the list, taking RA, Dec, and radius values from the
specified columns or from static numeric values specified on the
command line.

<P>
When using a list, all valid rows from each iteration are written to a
single output file.  Use the <B>-x</B> switch to help delineate which
line of the list file was used to produce the given output row(s).
This switch causes the values for the center RA, Dec, radius, and row
number to be appended to the output file, in columns called RA_CEN,
DEC_CEN, RAD_CEN and CONE_KEY, respectively. Alternatively, the
<B>-j</B> (join) switch will append all columns from the list row to
the output row (essentially a join of the list row and input row),
along with the CONE_KEY row number. These two switches are mutually
exclusive.

<P>
The <b>-X</b> and <b>-J</b> switches write out the same data as their
lower case counterparts for each row satisfying a cone search. In
addition, these switches also write out rows from the event file that
do not satisfy any cone search.  In such cases, that CONE_KEY column
will be given a value of -1 and the center and list position information
will be set to zero for the given row. Thus, all rows of the input
event file are guaranteed to be output, with rows satisfying at least
one cone search having additional search information.

<p>
The <b>-L</b> switch acts similarly to the <b>-l</b> switch in that it
takes centers from a list file. However, it also implicitly sets the
-j switch, so that output rows are the join of the input event row and
the center position row.  In addition, this switch also writes out all
center position rows for which no event satisfies the cone search
criteria of that row.  The CONE_KEY column will be given a value of -2
for center rows that were not close to any data row and the event
columns will be zeroed out for such rows. In this way, all centers
rows are guaranteed to be output at least once.

<p>
If any of "all row" switches (<b>-X</b>, <b>-J</b>, or <b>-L</b>) are
specified, then a new column named JSTAT is added to the output table.
The positive values in this column indicate the center position row number
(starting from 1) in the list file that this data row successful matched
in a cone search. A value of -1 means that the data row did not match
any center position. A value of -2 means that the center position was
not matched by any data row.

<P>
Given a center position and radius, the cone search algorithm
calculates limit parameters for a box enclosing the specified cone,
and only tests rows whose positions values lie within those limits.
For small files, the overhead associated with this cone limit
filtering can cause the program to run more slowly than if all events
were tested. You can turn off cone limit filtering using the <B>-n</B>
switch to see if this speeds up the processing (especially useful when
processing a large list of positions).

<P>
For example, the default cone search uses columns "RA" and "Dec" in hours
and degrees (respectively) and RA position in hours, Dec and radius in degrees:
<PRE>
  funone in.fits out.fits 23.45 34.56 0.01
</PRE>
To specify the RA position in degrees:
<PRE>
  funcone in.fits out.fits 23.45d 34.56 0.01
</PRE>
To get RA and Dec from a list but use a static value for radius (and
also write identifying info for each row in the list):
<PRE>
  funcone -x -l list.txt in.fits out.fits MYRA MYDec 0.01
</PRE>
User specified columns in degrees, RA position in hours (sexagesimal
notation), Dec position in degrees (sexagesimal notation) and radius
in arc minutes:
<PRE>
  funcone -r myRa:d -d myDec in.fits out.fits 12:30:15.5 30:12 15'
</PRE>

<!-- =defdoc fundisp fundisp 1 -->

<!-- =section fundisp NAME -->
<H2><A NAME="fundisp">fundisp - display data in a Funtools data file</A></H2>

<!-- =section fundisp SYNOPSIS -->
<B>
<PRE>
fundisp  [-f format] [-l] [-n] [-T] &lt;iname&gt; [columns|bitpix=n]
</PRE>
</B>

<!-- =section fundisp OPTIONS -->
<P>
<PRE>
  -f      # format string for display
  -l      # display image as a list containing the columns X, Y, VAL
  -n      # don't output header
  -F [c]  # use specified character as column separator (def: space)
  -T      # output in rdb/starbase format (tab separators) 
</PRE>

<!-- =section fundisp DESCRIPTION -->
<P>
<B>fundisp</B> displays the data in the specified 
<A HREF="./files.html">FITS Extension</A>
and/or
<A HREF="./files.html#sections">Image Section</A>
of a FITS file, or in a
<A HREF="./files.html#sections">Section</A>
of a non-FITS array or raw event file.
<P>
The first argument to the program specifies the FITS input image, array, or
raw event file to display.  If "stdin" is specified, data are read from
the standard input. Use <A HREF="./files.html">Funtools Bracket
Notation</A> to specify FITS extensions, image sections, and filters.

<P>
If the data being displayed are columns (either in a FITS binary table
or a raw event file), the individual rows are listed. Filters can be
added using bracket notation. Thus:
<PRE>
  [sh] fundisp "test.ev[time-(int)time>.15]"
         X       Y     PHA        PI             TIME         DX         DY
   ------- ------- ------- --------- ---------------- ---------- ----------
        10       8      10         8          17.1600       8.50      10.50
         9       9       9         9          17.1600       9.50       9.50
        10       9      10         9          18.1600       9.50      10.50
        10       9      10         9          18.1700       9.50      10.50
         8      10       8        10          17.1600      10.50       8.50
         9      10       9        10          18.1600      10.50       9.50
         9      10       9        10          18.1700      10.50       9.50
        10      10      10        10          19.1600      10.50      10.50
        10      10      10        10          19.1700      10.50      10.50
        10      10      10        10          19.1800      10.50      10.50
</PRE>
[NB: The FITS binary table test file test.ev, as well as the FITS
image test.fits, are contained in the funtools funtest directory.]

<P>
When a table is being displayed using <B>fundisp</B>, a second optional
argument can be used to specify the columns to display.  For example:
<PRE>
  [sh] fundisp "test.ev[time-(int)time>=.99]" "x y time"
          X        Y                  TIME
   -------- -------- ---------------------
          5       -6           40.99000000
          4       -5           59.99000000
         -1        0          154.99000000
         -2        1          168.99000000
         -3        2          183.99000000
         -4        3          199.99000000
         -5        4          216.99000000
         -6        5          234.99000000
         -7        6          253.99000000
</PRE>

<P>
The special column <B>$REGION</B> can be specified to display the
region id of each row:
<PRE>
  [sh $] fundisp "test.ev[time-(int)time>=.99&&annulus(0 0 0 10 n=3)]" 'x y time $REGION'
          X        Y                  TIME     REGION
   -------- -------- --------------------- ----------
          5       -6           40.99000000          3
          4       -5           59.99000000          2
         -1        0          154.99000000          1
         -2        1          168.99000000          1
         -3        2          183.99000000          2
         -4        3          199.99000000          2
         -5        4          216.99000000          2
         -6        5          234.99000000          3
         -7        6          253.99000000          3
</PRE>
<P>
Here only rows with the proper fractional time and whose position also is
within one of the three annuli are displayed.
<P>
Columns can be excluded from display using a minus sign before the
column:
<PRE>
  [sh $] fundisp "test.ev[time-(int)time>=.99]" "-time"
          X        Y      PHA         PI          DX          DY
   -------- -------- -------- ---------- ----------- -----------
          5       -6        5         -6        5.50       -6.50
          4       -5        4         -5        4.50       -5.50
         -1        0       -1          0       -1.50        0.50
         -2        1       -2          1       -2.50        1.50
         -3        2       -3          2       -3.50        2.50
         -4        3       -4          3       -4.50        3.50
         -5        4       -5          4       -5.50        4.50
         -6        5       -6          5       -6.50        5.50
         -7        6       -7          6       -7.50        6.50
</PRE>
All columns except the time column are displayed.
<P>
The special column <B>$N</B> can be specified to display the
ordinal value of each row. Thus, continuing the previous example:
<PRE>
  fundisp "test.ev[time-(int)time>=.99]" '-time $n'
         X        Y      PHA         PI          DX          DY          N
   ------- -------- -------- ---------- ----------- ----------- ----------
         5       -6        5         -6        5.50       -6.50        337
         4       -5        4         -5        4.50       -5.50        356
        -1        0       -1          0       -1.50        0.50        451
        -2        1       -2          1       -2.50        1.50        465
        -3        2       -3          2       -3.50        2.50        480
        -4        3       -4          3       -4.50        3.50        496
        -5        4       -5          4       -5.50        4.50        513
        -6        5       -6          5       -6.50        5.50        531
        -7        6       -7          6       -7.50        6.50        550
</PRE>
Note that the column specification is enclosed in single quotes to protect
'$n' from begin expanded by the shell.

<P>
In general, the rules for activating and de-activating columns are:
<UL>
<LI> If only exclude columns are specified, then all columns but
the exclude columns will be activated.
<LI> If only include columns are specified, then only the specified columns
are activated.
<LI> If a mixture of include and exclude columns are specified, then
all but the exclude columns will be active; this last case
is ambiguous and the rule is arbitrary.
</UL>
In addition to specifying columns names explicitly, the special
symbols <B>+</B> and <B>-</B> can be used to activate and
de-activate <B>all</B> columns. This is useful if you want to
activate the $REGION column along with all other columns.  According
to the rules, the syntax "$REGION" only activates the region column
and de-activates the rest. Use "+ $REGION" to activate all
columns as well as the region column.

<P>
If the data being displayed are image data (either in a FITS primary
image, a FITS image extension, or an array file), an mxn pixel display
is produced, where m and n are the dimensions of the image.  By
default, pixel values are displayed using the same data type as in the
file. However, for integer data where the BSCALE and BZERO header parameters
are present, the data is displayed as floats.  In either case, the
display data type can be overridden using an optional second argument
of the form:
<PRE>
  bitpix=n
</PRE>
where n is 8,16,32,-32,-64, for unsigned char, short, int, float and double,
respectively. 

<P>
Of course, running <B>fundisp</B> on anything but the smallest image
usually results in a display whose size makes it unreadable.
Therefore, one can uses bracket notation (see below)
to apply section and/or blocking to the image before generating a
display. For example:
<PRE>
  [sh] fundisp "test.fits[2:6,2:7]" bitpix=-32
                     2          3          4          5          6
            ---------- ---------- ---------- ---------- ----------
         2:       3.00       4.00       5.00       6.00       7.00
         3:       4.00       5.00       6.00       7.00       8.00
         4:       5.00       6.00       7.00       8.00       9.00
         5:       6.00       7.00       8.00       9.00      10.00
         6:       7.00       8.00       9.00      10.00      11.00
         7:       8.00       9.00      10.00      11.00      12.00
</PRE>

<P>
Note that is is possible to display a FITS binary table as an image
simply by passing the table through <B>funimage</B> first:
<PRE>
  [sh] ./funimage test.ev stdout | fundisp "stdin[2:6,2:7]" bitpix=8
                  2       3       4       5       6
            ------- ------- ------- ------- -------
         2:       3       4       5       6       7
         3:       4       5       6       7       8
         4:       5       6       7       8       9
         5:       6       7       8       9      10
         6:       7       8       9      10      11
         7:       8       9      10      11      12
</PRE>

If the <B>-l</B> (list) switch is used, then an image is displayed as a
list containing the columns: X, Y, VAL. For example:
<PRE>
  fundisp -l "test1.fits[2:6,2:7]" bitpix=-32
            X          Y         VAL
   ---------- ---------- -----------
            2          2        6.00
            3          2        1.00
            4          2        1.00
            5          2        1.00
            6          2        1.00
            2          3        1.00
            3          3        5.00
            4          3        1.00
            5          3        1.00
            6          3        1.00
            2          4        1.00
            3          4        1.00
            4          4        4.00
            5          4        1.00
            6          4        1.00
            2          5        1.00
            3          5        1.00
            4          5        1.00
            5          5        3.00
            6          5        1.00
            2          6        1.00
            3          6        1.00
            4          6        1.00
            5          6        1.00
            6          6        2.00
            2          7        1.00
            3          7        1.00
            4          7        1.00
            5          7        1.00
            6          7        1.00
</PRE>

<p>
If the <B>-n</B> (nohead) switch is used, then no header is output for
tables. This is useful, for example, when fundisp output is being
directed into gnuplot.

<P>
The <B>fundisp</B> program uses a default set of display formats:
<PRE>
  datatype      TFORM   format
  --------      -----   --------
  double        D       "%21.8f"
  float         E       "%11.2f"
  int           J       "%10d"
  short         I       "%8d"
  byte          B       "%6d"
  string        A       "%12.12s"
  bits          X       "%8x"
  logical       L       "%1x"
</PRE>
Thus, the default display of 1 double and 2 shorts gives:
<PRE>
  [sh] fundisp snr.ev "time x y"
  
                    TIME        X        Y
   --------------------- -------- --------
       79494546.56818075      546      201
       79488769.94469175      548      201
       ...
</PRE>
You can change the display format for individual columns or for all
columns of a given data types by means of the -f switch.  The format
string that accompanies -f is a space-delimited list of keyword=format
values.  The keyword values can either be column names (in which case
the associated format pertains only to that column) or FITS table
TFORM specifiers (in which case the format pertains to all columns
having that data type). For example, you can change the double and
short formats for all columns like this:
<PRE>
  [sh] fundisp -f "D=%22.11f I=%3d" snr.ev "time x y"
  
                    TIME   X   Y
  ---------------------- --- ---
    79494546.56818075478 546 201
    79488769.94469174743 548 201
    ...
</PRE>

<p>
Alternatively, you can change the format of the time and x columns like this:
<pre>
  [sh] fundisp -f "time=%22.11f x=%3d" snr.ev "time x y"
  
                    TIME   X        Y
  ---------------------- --- --------
    79494546.56818075478 546      201
    79488769.94469174743 548      201
    ...
</pre>
Note that there is a potential conflict if a column has the same name
as one of the TFORM specifiers. In the examples above, the the "X"
column in the table has the same name as the X (bit) datatype.  To
resolve this conflict, the format string is processed such that
TFORM datatype specifiers are checked for first, using a
case-sensitive comparison. If the specified format value is not an
upper case TFORM value, then a case-insensitive check is made on the
column name.  This means that, in the examples above, "X=%3d" will refer
to the X (bit) datatype, while "x=%3d" will refer to the X column:
<pre>
  [sh] fundisp -f "X=%3d" snr.ev "x y"
  
         X        Y
  -------- --------
       546      201
       548      201
       ...
  
  [sh] fundisp -f "x=%3d" snr.ev "x y"
  
    X        Y
  --- --------
  546      201
  548      201
  ...
</pre>
As a rule, therefore, it is best always to specify the column name in
lower case and TFORM data types in upper case. 

<p>
The <B>-f [format]</B> will change the format for a single execution
of fundisp. You also can use the <B>FUN_FORMAT</B> envronment variable
to change the format for all invocations of fundisp. The format of this
environment variable's value is identical to that used with
the <B>-f</B> switch. This global value can be overridden in
individual cases by use of the <B>-f [format]</B> switch.

<P>
Caveats: Please also note that it is the user's responsibility to
match the format specifier to the column data type correctly. Also
note that, in order to maintain visual alignment between names and
columns, the column name will be truncated (on the left) if the
format width is less than the length of the name. However, truncation
is not performed if the output is in RDB format (using the -T switch).

<p>
[An older-style format string is supported but deprecated. It
consists of space-delimited C format statements for all data types,
specified in the following order:
<PRE>
 double float int short byte string bit.
</PRE>
This order of the list is based on the assumption that people generally
will want to change the float formats.
<P>
If "-" is entered instead of a format statement for a given data type, the
default format is used. Also, the format string can be terminated without
specifying all formats, and defaults will be used for the rest of the
list. Note that you must supply a minimum field width, i.e., "%6d" and
"%-6d" are legal, "%d" is not legal.

By using -f [format], you can change the double and short formats like this:
<PRE>
  [sh] fundisp -f "22.11f - - 3d" snr.ev "time x y"
  
                     TIME   X   Y
   ---------------------- --- ---
     79494546.56818075478 546 201
     79488769.94469174743 548 201
     ...
</PRE>
NB: This format is deprecated and will be removed in a future release.]

<P>
The <B>-F[c]</B> switch can be used to specify a (single-character)
column separator (where the default is a space). Note that column
formatting will almost certainly also add spaces to pad individual
columns to the required width. These can be removed with a program
such as sed, at the cost of generating unaligned columns. For example:
<PRE>
fundisp -F',' snr.ev'[cir 512 512 .1]'
       X,       Y,     PHA,      PI,                 TIME,      DX,      DY
--------,--------,--------,--------,---------------------,--------,--------
     512,     512,       6,       7,    79493997.45854475,     578,     574
     512,     512,       8,       9,    79494575.58943175,     579,     573
     512,     512,       5,       6,    79493631.03866175,     578,     575
     512,     512,       5,       5,    79493290.86521725,     578,     575
     512,     512,       8,       9,    79493432.00990875,     579,     573

fundisp -F',' snr.ev'[cir 512 512 .1]' | sed 's/ *, */,/g'
       X,Y,PHA,PI,TIME,DX,DY
--------,--------,--------,--------,---------------------,--------,--------
     512,512,6,7,79493997.45854475,578,574
     512,512,8,9,79494575.58943175,579,573
     512,512,5,6,79493631.03866175,578,575
     512,512,5,5,79493290.86521725,578,575
     512,512,8,9,79493432.00990875,579,573

fundisp -f "x=%3d y=%3d pi=%1d pha=%1d time=%20.11f dx=%3d dy=%3d" -F',' snr.ev'[cir 512 512 .1]' | sed 's/ *, */,/g'
  X,Y,A,I,TIME,DX,DY
---,---,-,-,--------------------,---,---
512,512,6,7,79493997.45854474604,578,574
512,512,8,9,79494575.58943174779,579,573
512,512,5,6,79493631.03866174817,578,575
512,512,5,5,79493290.86521725357,578,575
512,512,8,9,79493432.00990875065,579,573

</PRE>

<P>
If the <B>-T</B> (rdb table) switch is used, the output will conform
to starbase/rdb data base format: tabs will be inserted between
columns rather than spaces. This format is not available when
displaying image pixels (except in conjunction with the <B>-l</B>
switch).

<P>
Finally, note that <B>fundisp</B> can be used to create column filters from
the auxiliary tables in a FITS file. For example, the following shell code
will generate a good-time interval (GTI) filter for X-ray data files that
contain a standard GTI extension:
<PRE>
  #!/bin/sh
  sed '1,/---- .*/d
  /^$/,$d' | awk 'tot>0{printf "||"};{printf "time="$1":"$2; tot++}' 
</PRE>
If this script is placed in a file called "mkgti", it can be used in a
command such as:
<PRE>
  fundisp foo.fits"[GTI]" | mkgti > gti.filter
</PRE>
The resulting filter file can then be used in various funtools programs:
<PRE>
  funcnts foo.fits"[@gti.filter]" ...
</PRE>
to process only the events in the good-time intervals.

<!-- =defdoc funhead funhead 1 -->

<!-- =section funhead NAME -->
<H2><A NAME="funhead">funhead - display a header in a Funtools file</A></H2>

<!-- =section funhead SYNOPSIS -->
<B>
<PRE>
funhead  [-a] [-s] [-t] [-L] &lt;iname&gt; [oname ename]
</PRE>
</B>

<!-- =section funhead OPTIONS -->
<P>
<PRE>
  -a    # display all extension headers
  -s    # display 79 chars instead of 80 before the new-line
  -t    # prepend data type char to each line of output
  -L    # output in rdb/starbase list format
</PRE>

<!-- =section funhead DESCRIPTION -->
<P>
<B>funhead</B> displays the FITS header parameters in the specified 
<A HREF="./files.html">FITS Extension</A>.
<P>
The first argument to the program specifies the Funtools input file
to display.  If "stdin" is specified, data are read from
the standard input. <A HREF="./files.html">Funtools Bracket
Notation</A> is used to specify particular FITS extension to process.
Normally, the full 80 characters of each header card is output,
followed by a new-line. 

<P>
If the <B>-a</B> switch is specified, the header from each FITS
extensions in the file is displayed. Note, however, that the <B>-a</B>
switch does not work with FITS files input via stdin. We hope to
remove this restriction in a future release.

<P>
If the <B>-s</B> switch is specified, only 79 characters are output
before the new-line. This helps the display on 80 character terminals.

<P>
If the <B>-t</B> switch is specified, the data type of the parameter
is output as a one character prefix, followed by 77 characters of the
param.  The parameter data types are defined as: FUN_PAR_UNKNOWN
('u'), FUN_PAR_COMMENT ('c'), FUN_PAR_LOGICAL ('l'), FUN_PAR_INTEGER
('i'), FUN_PAR_STRING ('s'), FUN_PAR_REAL ('r'), FUN_PAR_COMPLEX ('x').

<P>
If the <B>-L</B> (rdb table) switch is used, the output will conform
to starbase/rdb data base list format.

<P>
For example to display the EVENTS extension (binary table):
<PRE>
  [sh] funhead "foo.fits[EVENTS]"
  XTENSION= 'BINTABLE'            /  FITS 3D BINARY TABLE                      
  BITPIX  =                    8  /  Binary data                               
  NAXIS   =                    2  /  Table is a matrix                         
  NAXIS1  =                   20  /  Width of table in bytes                   
  NAXIS2  =                30760  /  Number of entries in table                
  PCOUNT  =                    0  /  Random parameter count                    
  GCOUNT  =                    1  /  Group count                               
  TFIELDS =                    7  /  Number of fields in each row              
  EXTNAME = 'EVENTS  '            /  Table name                                
  EXTVER  =                    1  /  Version number of table                   
  TFORM1  = '1I      '            /  Data type for field                       
  TTYPE1  = 'X       '            /  Label for field                           
  TUNIT1  = '        '            /  Physical units for field                  
  TFORM2  = '1I      '            /  Data type for field                       
    etc. ...
  END                                                                          
</PRE>

<P>
To display the third header:
<PRE>
  [sh] funhead "foo.fits[3]"
  XTENSION= 'BINTABLE'            /  FITS 3D BINARY TABLE                      
  BITPIX  =                    8  /  Binary data                               
  NAXIS   =                    2  /  Table is a matrix                         
  NAXIS1  =                   32  /  Width of table in bytes                   
  NAXIS2  =                   40  /  Number of entries in table                
  PCOUNT  =                    0  /  Random parameter count                    
  GCOUNT  =                    1  /  Group count                               
  TFIELDS =                    7  /  Number of fields in each row              
  EXTNAME = 'TGR     '            /  Table name                                
  EXTVER  =                    1  /  Version number of table                   
  TFORM1  = '1D      '            /  Data type for field                       
    etc. ...
  END                                                                          
</PRE>

<P>
To display the primary header (i.e., extension 0):
<PRE>
  sh> funhead "coma.fits[0]"
  SIMPLE  =                    T /STANDARD FITS FORMAT                         
  BITPIX  =                   16 /2-BYTE TWOS-COMPL INTEGER                    
  NAXIS   =                    2 /NUMBER OF AXES                               
  NAXIS1  =                  800 /                                             
  NAXIS2  =                  800 /                                             
  DATATYPE= 'INTEGER*2'          /SHORT INTEGER                                
  END                                                                          
</PRE>

<P>
The funhead program also can edit (i.e. add, delete, or modify) or
display individual headers parameters. Edit mode is signalled by the
presence of two additional command-line arguments: output file and
edit command file, in that order. Edit mode acts as a filter: the
output file will contain the entire input FITS file, including other
extensions. The edit command file can be "stdin", in which case edit
command are read from the standard input.

<P>
The edit command file contains parameter comments (having '#' in the
first column) and delete and assignment(modify or add) operations.  A
delete operation is specified by preceding the parameter name with a
minus sign "-".  A display operation (very useful in interactive
sessions, i.e., where the edit commands are taken from stdin) is
specified by preceding the parameter name with a question mark "?". In
either case, a parameter value need not be specified.  An assignment
operation is specified in the same two ways that a parameter is
specified in a text header (but without the comment character that
precedes header params), i.e.:

<UL>
<LI> FITS-style comments have an equal sign "=" between the keyword and
value and an optional slash "/" to signify a comment. The strict FITS
rules on column positions are not enforced.

<LI> Free-form comments can have an optional colon separator between the
keyword and value. In the absence of quote, all tokens after the
keyword are part of the value, i.e. no comment is allowed.
</UL>

<P>
For example, the following interactive session checks for the
existence of parameters, adds new parameters, modifies them, and
modifies and deletes existing parameters:
<PRE>
  sh$ ./funhead snr.ev foo.fits -
  # look for FOO1
  ? FOO1
  WARNING: FOO1 not found
  # add new foo1
  FOO1 = 100
  # add foo2
  FOO2 = 200
  # reset foo1 to a different value
  FOO1 -1
  # delete foo2
  -FOO2
  # change existing value
  EXTVER 2
  ? XS-SORT
  XS-SORT = 'EOF     '            /  type of event sort
  # delete existing value
  -XS-SORT
  # exit
  ^D
</PRE>

<P>
See <A HREF="./text.html">Column-based Text Files</A>
for more information about header parameter format.

<P>

<P>
<!-- =defdoc funhist funhist 1 -->

<!-- =section funhist NAME -->
<H2><A NAME="funhist">funhist - create a 1D histogram of a column (from a FITS binary table or raw event file) or an image</A></H2>

<!-- =section funhist SYNOPSIS -->
<B>
<PRE>
funhist  [-n|-w|-T] &lt;iname&gt; [column] [[lo:hi:]bins]
</PRE>
</B>

<!-- =section funhist OPTIONS -->
<P>
<PRE>
  -n    # normalize bin value by the width of each bin
  -w    # specify bin width instead of number of bins in arg3
  -T    # output in rdb/starbase format (tab separators)
</PRE>

<!-- =section funhist DESCRIPTION -->
<P>
<B>funhist</B> creates a one-dimensional histogram from the specified
columns of a <A HREF="./files.html">FITS Extension</A>
binary table of a FITS file (or from a non-FITS raw event file), or
from a FITS image or array, and writes that histogram as an ASCII
table. Alternatively, the program can perform a 1D projection of one
of the image axes.

<P>
The first argument to the program is required, and specifies the
Funtools file: FITS table or image, raw event file, or array.  If
"stdin" is specified, data are read from the standard input. Use 
<A HREF="./files.html">Funtools Bracket Notation</A> to specify FITS
extensions, and filters.

<P>
For a table, the second argument also is required. It specifies the
column to use in generating the histogram.  If the data file is of
type image (or array), the column is optional: if "x" (or "X"), "y"
(or "Y") is specified, then a projection is performed over the x
(dim1) or y (dim2) axes, respectively. (That is, this projection will
give the same results as a histogram performed on a table containing
the equivalent x,y event rows.)  If no column name is specified or
"xy" (or "XY") is specified for the image, then a histogram is
performed on the values contained in the image pixels.

<P>
The argument that follows is optional and specifies the number of bins
to use in creating the histogram and, if desired, the range of bin
values.  For image and table histograms, the range should specify the
min and max data values.  For image histograms on the x and y axes,
the range should specify the min and max image bin values.  If this
argument is omitted, the number of output bins for a table is
calculated either from the TLMIN/TLMAX headers values (if these exist
in the table FITS header for the specified column) or by going through
the data to calculate the min and max value. For an image, the number
of output bins is calculated either from the DATAMIN/DATAMAX header
values, or by going through the data to calculate min and max value.
(Note that this latter calculation might fail if the image cannot be
fit in memory.)  If the data are floating point (table or image) and
the number of bins is not specified, an arbitrary default of 128 is
used.

<P>
For binary table processing, the <B>-w</B> (bin width) switch can be used
to specify the width of each bin rather than the number of bins. Thus:
<PRE>
  funhist test.ev pha 1:100:5
</PRE>
means that 5 bins of width 20 are used in the histogram, while:
<PRE>
  funhist -w test.ev pha 1:100:5
</PRE>
means that 20 bins of width 5 are used in the histogram.

<P>
The data are divvied up into the specified number of bins and the
resulting 1D histogram (or projection) is output in ASCII table
format. For a table, the output displays the low_edge (inclusive) and
hi_edge (exclusive) values for the data. For example, a 15-row table
containing a "pha" column whose values range from -7.5 to 7.5
can be processed thus:

<PRE>
  [sh] funhist test.ev pha
  # data file:        /home/eric/data/test.ev
  # column:           pha
  # min,max,bins:     -7.5 7.5 15
  
     bin     value               lo_edge               hi_edge
  ------ --------- --------------------- ---------------------
       1        22           -7.50000000           -6.50000000
       2        21           -6.50000000           -5.50000000
       3        20           -5.50000000           -4.50000000
       4        19           -4.50000000           -3.50000000
       5        18           -3.50000000           -2.50000000
       6        17           -2.50000000           -1.50000000
       7        16           -1.50000000           -0.50000000
       8        30           -0.50000000            0.50000000
       9        16            0.50000000            1.50000000
      10        17            1.50000000            2.50000000
      11        18            2.50000000            3.50000000
      12        19            3.50000000            4.50000000
      13        20            4.50000000            5.50000000
      14        21            5.50000000            6.50000000
      15        22            6.50000000            7.50000000
  
  [sh] funhist test.ev pha 1:6
  # data file:          /home/eric/data/test.ev
  # column:             pha
  # min,max,bins:       0.5 6.5 6
  
     bin     value               lo_edge               hi_edge
  ------ --------- --------------------- ---------------------
       1        16            0.50000000            1.50000000
       2        17            1.50000000            2.50000000
       3        18            2.50000000            3.50000000
       4        19            3.50000000            4.50000000
       5        20            4.50000000            5.50000000
       6        21            5.50000000            6.50000000
  
  [sh] funhist test.ev pha 1:6:3
  # data file:          /home/eric/data/test.ev
  # column:             pha
  # min,max,bins:       0.5 6.5 3
  
     bin     value               lo_edge               hi_edge
  ------ --------- --------------------- ---------------------
       1        33            0.50000000            2.50000000
       2        37            2.50000000            4.50000000
       3        41            4.50000000            6.50000000
</PRE>

<P>
For a table histogram, the <B>-n</B>(normalize) switch can be used to
normalize the bin value by the width of the bin (i.e., hi_edge-lo_edge):
<PRE>
  [sh] funhist -n test.ev pha 1:6:3 
  # data file:          test.ev
  # column:             pha
  # min,max,bins:       0.5 6.5 3
  # width normalization (val/(hi_edge-lo_edge)) is applied
  
     bin                 value               lo_edge               hi_edge
  ------ --------------------- --------------------- ---------------------
       1           16.50000000            0.50000000            2.50000000
       2            6.16666667            2.50000000            4.50000000
       3            4.10000000            4.50000000            6.50000000
</PRE>
This could used, for example, to produce a light curve with values
having units of counts/second instead of counts.

<P>
For an image histogram, the output displays the low and high image
values (both inclusive) used to generate the histogram.  For example,
in the following example, 184 pixels had a value of 1, 31 had a value
of 2, while only 2 had a value of 3,4,5,6, or 7:
<PRE>
  [sh] funhist test.fits
  # data file:           /home/eric/data/test.fits
  # min,max,bins:        1 7 7
  
     bin                 value                lo_val                hi_val
  ------ --------------------- --------------------- ---------------------
       1          184.00000000            1.00000000            1.00000000
       2           31.00000000            2.00000000            2.00000000
       3            2.00000000            3.00000000            3.00000000
       4            2.00000000            4.00000000            4.00000000
       5            2.00000000            5.00000000            5.00000000
       6            2.00000000            6.00000000            6.00000000
       7            2.00000000            7.00000000            7.00000000
</PRE>

<P>
For the axis projection of an image, the output displays the low and
high image bins (both inclusive) used to generate the projection.  For
example, in the following example, 21 counts had their X bin value of
2, etc.:
<PRE>
  [sh] funhist test.fits x 2:7
  # data file:            /home/eric/data/test.fits
  # column:               X
  # min,max,bins: 2 7 6
   
     bin                 value                lo_bin                hi_bin
  ------ --------------------- --------------------- ---------------------
       1           21.00000000            2.00000000            2.00000000
       2           20.00000000            3.00000000            3.00000000
       3           19.00000000            4.00000000            4.00000000
       4           18.00000000            5.00000000            5.00000000
       5           17.00000000            6.00000000            6.00000000
       6           16.00000000            7.00000000            7.00000000
  
  [sh] funhist test.fits x 2:7:2
  # data file:            /home/eric/data/test.fits
  # column:               X
  # min,max,bins: 2 7 2
   
     bin                 value                lo_bin                hi_bin
  ------ --------------------- --------------------- ---------------------
       1           60.00000000            2.00000000            4.00000000
       2           51.00000000            5.00000000            7.00000000
</PRE>

<P>
You can use gnuplot or other plotting programs to graph the
results, using a script such as:
<PRE>
  #!/bin/sh
  sed -e '1,/---- .*/d
  /^$/,$d' | \
  awk '\
  BEGIN{print "set nokey; set title \"funhist\"; set xlabel \"bin\"; set ylabel \"counts\"; plot \"-\" with boxes"}   \
  {print $3, $2, $4-$3}'        | \
  gnuplot -persist - 1>/dev/null 2>&1
</PRE>

Similar plot commands are supplied in the script <B>funhist.plot</B>:
<PRE>
  funhist test.ev pha ...  | funhist.plot gnuplot
</PRE>

<!-- =defdoc funimage funimage 1 -->

<!-- =section funimage NAME -->
<H2><A NAME="funimage">funimage - create a FITS image from a Funtools data file</A></H2>

<!-- =section funimage SYNOPSIS -->
<B>
<PRE>
funimage [-a] &lt;iname&gt; &lt;oname&gt; [bitpix=n]
funimage [-l] &lt;iname&gt; &lt;oname&gt; &lt;xcol:xdims&gt; &lt;ycol:ydims&gt; &lt;vcol&gt; [bitpix=n]
funimage [-p x|y] &lt;iname&gt; &lt;oname&gt; [bitpix=n]
</PRE>
</B>

<!-- =section funimage OPTIONS -->
<P>
<PRE>
  -a       # append to existing output file as an image extension
  -l       # input is a list file containing xcol, ycol, value
  -p [x|y] # project along x or y axis to create a 1D image
</PRE>

<!-- =section funimage DESCRIPTION -->
<P>
<B>funimage</B> creates a primary FITS image from the specified
<A HREF="./files.html">FITS Extension</A>
and/or
<A HREF="./files.html#sections">Image Section</A>
of a FITS file, or from an
<A HREF="./files.html#sections">Image Section</A>
of a non-FITS array, or from a raw event file.
<P>
The first argument to the program specifies the FITS input image,
array, or raw event file to process.  If "stdin" is specified, data are
read from the standard input. Use <A HREF="./files.html">Funtools
Bracket Notation</A> to specify FITS extensions, image sections, and
filters.  The second argument is the output FITS file.  If "stdout" is
specified, the FITS image is written to the standard output.  By
default, the output pixel values are of the same data type as those of the
input file (or type "int" when binning a table), but this can be
overridden using an optional third argument of the form:
<PRE>
  bitpix=n
</PRE>
where n is 8,16,32,-32,-64, for unsigned char, short, int, float and double,
respectively.

<P>
If the input data are of type image, the appropriate section is
extracted and blocked (based on how the 
<A HREF="./files.html#sections">Image Section</A> is specified), and
the result is written to the FITS primary image.  When an integer
image containing the BSCALE and BZERO keywords is converted to float,
the pixel values are scaled and the scaling keywords are deleted from the
output header. When converting integer scaled data to integer
(possibly of a different size), the pixels are not scaled and the
scaling keywords are retained.

<P>
If the input data is a binary table or raw event file, these are
binned into an image, from which a section is extracted and blocked,
and written to a primary FITS image.  In this case, it is necessary to
specify the two columns that will be used in the 2D binning.  This can
be done on the command line using the <B>bincols=(x,y)</B> keyword:
<PRE>
  funcnts "foo.ev[EVENTS,bincols=(detx,dety)]"
</PRE>
The full form of the <B>bincols=</B> specifier is:
<PRE>
  bincols=([xname[:tlmin[:tlmax:[binsiz]]]],[yname[:tlmin[:tlmax[:binsiz]]]])
</PRE>
where the tlmin, tlmax, and binsiz specifiers determine the image binning
dimensions:
<PRE>
  dim = (tlmax - tlmin)/binsiz     (floating point data)
  dim = (tlmax - tlmin)/binsiz + 1 (integer data)
</PRE>
Using this syntax, it is possible to bin any two columns of a binary
table at any bin size.  Note that the tlmin, tlmax, and binsiz
specifiers can be omitted if TLMIN, TLMAX, and TDBIN header parameters
(respectively) are present in the FITS binary table header for the
column in question. Note also that if only one parameter is specified,
it is assumed to be tlmax, and tlmin defaults to 1. If two parameters
are specified, they are assumed to be tlmin and tlmax.
See <A HREF="./files.html#binning">Binning FITS Binary Tables and Non-FITS
Event Files</A> for more information about binning parameters.

<p>
By default, a new 2D FITS image file is created and the image is written
to the primary HDU.  If the <B>-a</B> (append) switch is specified,
the image is appended to an existing FITS file as an IMAGE extension.
(If the output file does not exist, the switch is effectively ignored
and the image is written to the primary HDU.)  This can be useful in a
shell programming environment when processing multiple FITS images
that you want to combine into a single final FITS file.

<P>
<B>funimage</B> also can take input from a table containing columns of
x, y, and value (e.g., the output from <B>fundisp -l</B> which
displays each image x and y and the number of counts at that
position.) When the <B>-l</B> (list) switch is used, the input file is
taken to be a FITS or ASCII table containing (at least) three columns
that specify the x and y image coordinates and the value of that
image pixel. In this case, <B>funimage</B> requires four extra
arguments: xcolumn:xdims, ycolumn:ydims, vcolumn and bitpix=n. The x
and y col:dim information takes the form: 
<PRE>
  name:dim               # values range from 1 to dim
  name:min:max           # values range from min to max
  name:min:max:binsiz    # dimensions scaled by binsize
</PRE>
In particular, the min value should be used whenever the
minimum coordinate value is something other than one. For example:
<PRE> 
  funimage -l foo.lst foo.fits xcol:0:512 ycol:0:512 value bitpix=-32
</PRE>

<P>
The list feature also can be used to read unnamed columns from standard
input: simply replace the column name with a null string. Note
that the dimension information is still required:
<PRE>
  funimage -l stdin foo.fits "":0:512 "":0:512 "" bitpix=-32
  240 250 1
  255 256 2
  ...
  ^D
</PRE>

<P>
The list feature provides a simple way to generate a blank image.
If you pass a <A HREF="./text.html">Column-based Text File</A>
to funimage in which the text header contains the required image
information, then funimage will correctly make a blank image. For
example, consider the following text file (called foo.txt):
<PRE>
  x:I:1:10  y:I:1:10
  ------    ------
  0         0
</PRE>
This text file defines two columns, x and y, each of data type 32-bit int and
image dimension 10. The command:
<PRE>
  funimage foo.txt foo.fits bitpix=8
</PRE>
will create an empty FITS image called foo.fits containing a 10x10
image of unsigned char:
<PRE>
  fundisp foo.fits
           1      2      3      4      5      6      7      8      9     10
      ------ ------ ------ ------ ------ ------ ------ ------ ------ ------
  10:      0      0      0      0      0      0      0      0      0      0
   9:      0      0      0      0      0      0      0      0      0      0
   8:      0      0      0      0      0      0      0      0      0      0
   7:      0      0      0      0      0      0      0      0      0      0
   6:      0      0      0      0      0      0      0      0      0      0
   5:      0      0      0      0      0      0      0      0      0      0
   4:      0      0      0      0      0      0      0      0      0      0
   3:      0      0      0      0      0      0      0      0      0      0
   2:      0      0      0      0      0      0      0      0      0      0
   1:      1      0      0      0      0      0      0      0      0      0

</PRE>

Note that the text file must contain at least
one row of data. However, in the present example, event position 0,0 is
outside the limits of the image and will be ignored. (You can, of course,
use real x,y values to seed the image with data.)

<P>
Furthermore, you can use the TEXT filter specification to obviate the need for
an input text file altogether. The following command will create the same
10x10 char image without an actual input file:
<PRE>
  funimage stdin'[TEXT(x:I:10,y:I:10)]' foo.fits bitpix=8 < /dev/null
or
  funimage /dev/null'[TEXT(x:I:10,y:I:10)]' foo.fits bitpix=8
</PRE>

<P>
You also can use either of these methods to generate a region mask simply
by appending a region inside the filter brackets and specfying <B>mask=all</B>
along with the bitpix. For example, the following command will generate a
10x10 char mask using 3 regions:
<PRE>
  funimage stdin'[TEXT(x:I:10,y:I:10),cir(5,5,4),point(10,1),-cir(5,5,2)]' \
  foo.fits bitpix=8,mask=all < /dev/null
</PRE>
The resulting mask looks like this:
<PRE>
  fundisp foo.fits
           1      2      3      4      5      6      7      8      9     10
      ------ ------ ------ ------ ------ ------ ------ ------ ------ ------
  10:      0      0      0      0      0      0      0      0      0      0
   9:      0      0      0      0      0      0      0      0      0      0
   8:      0      0      1      1      1      1      1      0      0      0
   7:      0      1      1      1      1      1      1      1      0      0
   6:      0      1      1      0      0      0      1      1      0      0
   5:      0      1      1      0      0      0      1      1      0      0
   4:      0      1      1      0      0      0      1      1      0      0
   3:      0      1      1      1      1      1      1      1      0      0
   2:      0      0      1      1      1      1      1      0      0      0
   1:      0      0      0      0      0      0      0      0      0      2
</PRE>

<P>
You can use <B>funimage</B> to create 1D image projections along the x
or y axis using the <b>-p [x|y]</b> switch. This capability works for
both images and tables. For example consider a FITS table named ev.fits
containing the following rows:
<PRE>
         X        Y
  -------- --------
         1        1
         1        2
         1        3
         1        4
         1        5
         2        2
         2        3
         2        4
         2        5
         3        3
         3        4
         3        5
         4        4
         4        5
         5        5

</PRE>
A corresponding 5x5 image, called dim2.fits, would therefore contain:
<PRE>
              1          2          3          4          5
     ---------- ---------- ---------- ---------- ----------
  5:          1          1          1          1          1
  4:          1          1          1          1          0
  3:          1          1          1          0          0
  2:          1          1          0          0          0
  1:          1          0          0          0          0
</PRE>
A projection along the y axis can be performed on either the table or
the image:
<PRE>
  funimage -p y ev.fits stdout | fundisp stdin
              1          2          3          4          5
     ---------- ---------- ---------- ---------- ----------
  1:          1          2          3          4          5

  funimage -p y dim2.fits stdout | fundisp stdin
              1          2          3          4          5
     ---------- ---------- ---------- ---------- ----------
  1:          1          2          3          4          5
</PRE>

<P>
Furthermore, you can create a 1D image projection along any column of
a table by using the <b>bincols=[column]</b> filter specification and
specifying a single column. For example, the following command
projects the same 1D image along the y axis of a table as use of
the <b>-p y</b> switch:
<PRE>
  funimage ev.fits'[bincols=y]' stdout | fundisp stdin 
              1          2          3          4          5
     ---------- ---------- ---------- ---------- ----------
  1:          1          2          3          4          5
</PRE>

<P>
Examples:
<P>
Create a FITS image from a FITS binary table:
<PRE>
  [sh] funimage test.ev test.fits
</PRE>

<P>
Display the FITS image generated from a blocked section of FITS binary table:
<PRE>
  [sh]  funimage "test.ev[2:8,3:7,2]" stdout | fundisp stdin
                    1         2         3
            --------- --------- ---------
         1:        20        28        36
         2:        28        36        44
</PRE>

<!-- =defdoc funindex funindex 1 -->

<!-- =section funindex NAME -->
<H2><A NAME="funindex">funindex - create an index for a column of a FITS binary table</A></H2>

<!-- =section funindex SYNOPSIS -->
<B>
<PRE>
funindex &lt;switches&gt;  &lt;iname&gt; [oname]
</PRE>
</B>

<!-- =section funindex OPTIONS -->
<P>
<PRE>
  NB: these options are not compatible with Funtools processing. Please
  use the defaults instead.
  -c        # compress output using gzip"
  -a        # ASCII output, ignore -c (default: FITS table)"
  -f        # FITS table output (default: FITS table)"
  -l        # long output, i.e. with key value(s) (default: long)"
  -s        # short output, i.e. no key value(s) (default: long)"
</PRE>

<!-- =section funindex DESCRIPTION -->
<P>
The funindex script creates an index for the specified column (key) by
running funtable -s (sort) and then saving the column value and the
record number for each sorted row. This index will be used automatically
 by funtools filtering of that column, provided the index file's modification
date is later than that of the data file.

<p> 
The first required argument is the name of the FITS binary table
to index. Please note that text files cannot be indexed at this time.
The second required argument is the column (key) name to index. While
multiple keys can be specified in principle, the funtools index processing
assume a single key and will not recognize files containing multiple keys.

<P>
By default, the output index file name is [root]_[key].idx, where [root]
is the root of the input file. Funtools looks for this specific file name
when deciding whether to use an index for faster filtering. Therefore, the
optional third argument (output file name) should not be used for funtools
processing.

<P>
For example, to create an index on column Y for a given FITS file, use:
<PRE>
  funindex foo.fits Y
</PRE>
This will generate an index named foo_y.idx, which will be used by funtools
for filters involving the Y column.

<!-- =defdoc funjoin funjoin 1 -->

<!-- =section funjoin NAME -->
<H2><A NAME="funjoin">funjoin - join two or more FITS binary tables on specified columns</A></H2>

<!-- =section funjoin SYNOPSIS -->
<B>
<PRE>
funjoin [switches] &lt;ifile1&gt; &lt;ifile2&gt; ... &lt;ifilen&gt; &lt;ofile&gt; 
</PRE>
</B>

<!-- =section funjoin OPTIONS -->
<P>
<PRE>
  -a  cols             # columns to activate in all files
  -a1 cols ... an cols # columns to activate in each file
  -b  'c1:bvl,c2:bv2'  # blank values for common columns in all files
  -bn 'c1:bv1,c2:bv2'  # blank values for columns in specific files
  -j  col              # column to join in all files
  -j1 col ... jn col   # column to join in each file
  -m min               # min matches to output a row
  -M max               # max matches to output a row
  -s                   # add 'jfiles' status column
  -S col               # add col as status column
  -t tol               # tolerance for joining numeric cols [2 files only]
</PRE>

<!-- =section funjoin DESCRIPTION -->
<B>funjoin</B> joins rows from two or more (up to 32)
<A HREF="./files.html">FITS Binary Table files</A>, based on the values
of specified join columns in each file. NB: the join columns must have
an index file associated with it. These files are generated using the
<B>funindex</B> program.

<P>
The first argument to the program specifies the first input FITS table
or raw event file. If "stdin" is specified, data are read from the
standard input.  Subsequent arguments specify additional event files
and tables to join.  The last argument is the output FITS file.

<P>
NB: Do <B>not</B> use <A HREF="./files.html">Funtools Bracket
Notation</A> to specify FITS extensions and row filters when running
funjoin or you will get wrong results. Rows are accessed and joined
using the index files directly, and this bypasses all filtering.

<P>
The join columns are specified using the <B>-j col</B> switch (which
specifies a column name to use for all files) or with <B>-j1 col1</B>,
<B>-j2 col2</B>, ... <B>-jn coln</B> switches (which specify a column
name to use for each file). A join column must be specified for each file.
If both <B>-j col</B> and <B>-jn coln</B> are specified for a given
file, then the latter is used. Join columns must either be of type
string or type numeric; it is illegal to mix numeric and string
columns in a given join.  For example, to join three files using the
same key column for each file, use:
<PRE>
  funjoin -j key in1.fits in2.fits in3.fits out.fits
</PRE>
A different key can be specified for the third file in this way:
<PRE>
  funjoin -j key -j3 otherkey in1.fits in2.fits in3.fits out.fits
</PRE>

<P>
The <B>-a "cols"</B> switch (and <B>-a1 "col1"</B>,
<B>-a2 "cols2"</B> counterparts) can be used to specify columns to
activate (i.e. write to the output file) for each input file. By
default, all columns are output.

<P>
If two or more columns from separate files have the same name, the
second (and subsequent) columns are renamed to have an underscore
and a numeric value appended.

<P>
The <B>-m min</B> and <B>-M max</B> switches specify the minimum
and maximum number of joins required to write out a row. The default
minimum is 0 joins (i.e. all rows are written out) and the default maximum
is 63 (the maximum number of possible joins with a limit of 32 input files).
For example, to write out only those rows in which exactly two files
have columns that match (i.e. one join):
<PRE>
  funjoin -j key -m 1 -M 1 in1.fits in2.fits in3.fits ... out.fits
</PRE>

<P>
A given row can have the requisite number of joins without all of the
files being joined (e.g. three files are being joined but only two
have a given join key value). In this case, all of the columns of the
non-joined file are written out, by default, using blanks (zeros or NULLs).
The <B>-b c1:bv1,c2:bv2</B> and
<B>-b1 'c1:bv1,c2:bv2' -b2 'c1:bv1,c2:bv2' ...</B>
switches can be used to set the blank value for columns common to all
files and/or columns in a specified file, respectively. Each blank value
string contains a comma-separated list of column:blank_val specifiers.
For floating point values (single or double), a case-insensitive string
value of "nan" means that the IEEE NaN (not-a-number) should be
used. Thus, for example:
<PRE>
  funjoin -b "AKEY:???" -b1 "A:-1" -b3 "G:NaN,E:-1,F:-100" ...
</PRE>
means that a non-joined AKEY column in any file will contain the
string "???", the non-joined A column of file 1 will contain a value
of -1, the non-joined G column of file 3 will contain IEEE NaNs, while
the non-joined E and F columns of the same file will contain values -1
and -100, respectively. Of course, where common and specific blank values
are specified for the same column, the specific blank value is used.

<P>
To distinguish which files are non-blank components of a given row,
the <B>-s</B> (status) switch can be used to add a bitmask column named
"JFILES" to the output file. In this column, a bit is set for each
non-blank file composing the given row, with bit 0 corresponds to the
first file, bit 1 to the second file, and so on. The file names
themselves are stored in the FITS header as parameters named JFILE1,
JFILE2, etc.  The <B>-S col</B> switch allows you to change the name
of the status column from the default "JFILES".

<P>
A join between rows is the Cartesian product of all rows in one file
having a given join column value with all rows in a second file having
the same value for its join column and so on. Thus, if file1 has 2
rows with join column value 100, file2 has 3 rows with the same value,
and file3 has 4 rows, then the join results in 2*3*4=24 rows being output.

<P>
The join algorithm directly processes the index file associated with
the join column of each file. The smallest value of all the current
columns is selected as a base, and this value is used to join
equal-valued columns in the other files. In this way, the index files
are traversed exactly once.

<P>
The <B>-t tol</B> switch specifies a tolerance value for numeric
columns.  At present, a tolerance value can join only two files at a
time.  (A completely different algorithm is required to join more than
two files using a tolerance, somethng we might consider implementing
in the future.)

<P>
The following example shows many of the features of funjoin. The input files
t1.fits, t2.fits, and t3.fits contain the following columns:
<PRE>
  [sh] fundisp t1.fits
        AKEY    KEY      A      B 
 ----------- ------ ------ ------
         aaa      0      0      1
         bbb      1      3      4
         ccc      2      6      7
         ddd      3      9     10
         eee      4     12     13
         fff      5     15     16
         ggg      6     18     19
         hhh      7     21     22

fundisp t2.fits
        AKEY    KEY      C      D 
 ----------- ------ ------ ------
         iii      8     24     25
         ggg      6     18     19
         eee      4     12     13
         ccc      2      6      7
         aaa      0      0      1

fundisp t3.fits
        AKEY    KEY        E        F           G
------------ ------ -------- -------- -----------
         ggg      6       18       19      100.10
         jjj      9       27       28      200.20
         aaa      0        0        1      300.30
         ddd      3        9       10      400.40
</PRE>

<P>
Given these input files, the following funjoin command:
<PRE>

  funjoin -s -a1 "-B" -a2 "-D" -a3 "-E" -b \
  "AKEY:???" -b1 "AKEY:XXX,A:255" -b3 "G:NaN,E:-1,F:-100" \
  -j key t1.fits t2.fits t3.fits foo.fits
</PRE>
will join the files on the KEY column, outputting all columns except B
(in t1.fits), D (in t2.fits) and E (in t3.fits), and setting blank
values for AKEY (globally, but overridden for t1.fits) and A (in file
1) and G, E, and F (in file 3).  A JFILES column will be output to
flag which files were used in each row:
<PRE>

        AKEY    KEY      A       AKEY_2  KEY_2      C       AKEY_3  KEY_3        F           G   JFILES
  ------------ ------ ------ ------------ ------ ------ ------------ ------ -------- ----------- --------
         aaa      0      0          aaa      0      0          aaa      0        1      300.30        7
         bbb      1      3          ???      0      0          ???      0     -100         nan        1
         ccc      2      6          ccc      2      6          ???      0     -100         nan        3
         ddd      3      9          ???      0      0          ddd      3       10      400.40        5
         eee      4     12          eee      4     12          ???      0     -100         nan        3
         fff      5     15          ???      0      0          ???      0     -100         nan        1
         ggg      6     18          ggg      6     18          ggg      6       19      100.10        7
         hhh      7     21          ???      0      0          ???      0     -100         nan        1
         XXX      0    255          iii      8     24          ???      0     -100         nan        2
         XXX      0    255          ???      0      0          jjj      9       28      200.20        4

</PRE>
<!-- =defdoc funmerge funmerge 1 -->

<!-- =section funmerge NAME -->
<H2><A NAME="funmerge">funmerge - merge one or more Funtools table files</A></H2>

<!-- =section funmerge SYNOPSIS -->
<B>
<PRE>
funmerge  [-w|-x] -f [colname] &lt;iname1&gt; &lt;iname2&gt;  ... &lt;oname&gt;
</PRE>
</B>

<!-- =section funmerge OPTIONS -->
<P>
<PRE>
  -f    # output a column specifying file from which this event came
  -w    # adjust position values using WCS info
  -x    # adjust position values using WCS info and save old values
</PRE>

<!-- =section funmerge DESCRIPTION -->
<P>
<B>funmerge</B> merges FITS data from one or more
<A HREF="./files.html">FITS Binary Table files</A>
or raw event files.
<P>
The first argument to the program specifies the first input FITS table
or raw event file. If "stdin" is specified, data are read from the
standard input.  Use <A HREF="./files.html">Funtools Bracket
Notation</A> to specify FITS extensions and row filters.  Subsequent
arguments specify additional event files and tables to merge. (NB: Stdin
cannot not be used for any of these additional input file arguments.)
The last argument is the output FITS file. The columns in each input table
must be identical.

<P>
If an input file begins with the '@' character, it is processed as an
include file, i.e., as a text file containing event file names (as
well as blank lines and/or comment lines starting with the '#' sign).
If standard input is specified as an include file ('@stdin'), then
file names are read from the standard input until EOF (^D).  Event
files and include files can be mixed on a command line.

<P>
Rows from each table are written sequentially to the output
file.  If the switch <B>-f [colname]</B> is specified on the command
line, an additional column is added to each row containing the number
of the file from which that row was taken (starting from one). In
this case, the corresponding file names are stored in the header
parameters having the prefix <B>FUNFIL</B>, i.e., FUNFIL01,
FUNFIL02, etc.

<P>
Using the <B>-w</B> switch (or <B>-x</B> switch as described
below), <B>funmerge</B> also can adjust the position column values
using the WCS information in each file. (By position columns, we mean
the columns that the table is binned on, i.e., those columns defined
by the <B>bincols=</B> switch, or (X,Y) by default.) To perform WCS
alignment, the WCS of the first file is taken as the base WCS.  Each
position in subsequent files is adjusted by first converting it to the
sky coordinate in its own WCS coordinate system, then by converting
this sky position to the sky position of the base WCS, and finally
converting back to a pixel position in the base system. Note that in
order to perform WCS alignment, the appropriate WCS and TLMIN/TLMAX
keywords must already exist in each FITS file.
<P>
When performing WCS alignment, you can save the original positions in
the output file by using the <B>-x</B> (for "xtra") switch instead
of the <B>-w</B> switch (i.e., using this switch also implies using
<B>-w</B>) The old positions are saved in columns having the same
name as the original positional columns, with the added prefix "OLD_".
<P>
Examples:

<P>
Merge two tables, and preserve the originating file number for
each row in the column called "FILE" (along with the corresponding
file name in the header):
<PRE>
  [sh] funmerge -f "FILE" test.ev test2.ev merge.ev
</PRE>

<P>
Merge two tables with WCS alignment, saving the old position values in
2 additional columns:
<PRE>
  [sh] funmerge -x test.ev test2.ev merge.ev
</PRE>

<P>
This program only works on raw event files and binary tables. We have
not yet implemented image and array merging.

<!-- =defdoc funsky funsky 1 -->

<!-- =section funsky NAME -->
<H2><A NAME="funsky">funsky - convert between image and sky coordinates</A></H2>

<!-- =section funsky SYNOPSIS -->
<B>
<PRE>
  funsky iname[ext]               # RA,Dec (deg) or image pix from stdin
  funsky iname[ext] [lname]       # RA, Dec (deg) or image pix from list
  funsky iname[ext] [col1] [col2]         # named cols:units from stdin
  funsky iname[ext] [lname] [col1] [col2] # named cols:units from list
</PRE>
</B>

<!-- =section funsky OPTIONS -->
<P>
<PRE>
  -d        # always use integer tlmin conversion (as ds9 does)
  -r        # convert x,y to RA,Dec (default: convert RA,Dec to x,y)
  -o        # include offset from the nominal target position (in arcsec)
  -v        # display input values also (default: display output only)
  -T        # output display in rdb format (w/header,tab delimiters)
</PRE>

<!-- =section funsky DESCRIPTION -->
<P>
Funsky converts input sky coordinates (RA, Dec) to image coordinates (or vice
versa) using the WCS information contained in the specified FITS file. Several
calling sequences are supported in order to make it easy to specify
coordinate positions in different ways.

<P>
The first required argument is always the input FITS file (or
extension) containing the WCS information in an extension header. Note
that the data from this file is not used. By default, the program
converts input RA and Dec values to X and Y using this WCS
information. If the WCS is associated with a FITS image, then the X,Y
values are image values. If the WCS is associated with a binary table,
then the X, Y values are physical values.  To convert X,Y to RA and
Dec, use the <B>-r</B> (reverse) switch.

<P>
If no other command arguments are supplied, then the input positions
are read from the standard input. Each line is assumed to contain a
single coordinate position consisting of an RA in degrees (or X in
pixels) followed by a Dec in degrees (or Y in pixels). The usual
delimiters are supported (spaces, commas, tabs). For example:
<PRE>
 # read from stdin, default column names and units
 [sh] funsky snr.ev
 22.982695    58.606523   # input RA (hrs), Dec(deg)
    510.00       510.00
 22.982127    58.607634   # input
    512.00       510.50
 22.981700    58.614301   # input
    513.50       513.50
 ^D                       # end of input
</PRE>

<p>
If a second argument is supplied, this argument is assumed to be
a file containing RA (X) and Dec (Y) positions. The file can either be
an ASCII table or a FITS binary table. The order of columns is
unimportant, if the table has a column header. In this case, the
names of the columns must be one of "RA", "DEC", or "X", "Y" for sky
to image and image to sky conversions, respectively. If the table has
no header, then once again, RA (X) is assumed to first, followed
by DEC (Y).
For example:
<PRE>
  # read from file, default column names and units
  [sh] cat hd.in
         RA          DEC
  ---------    ---------
  22.982695    58.606523
  22.982127    58.607634
  22.981700    58.614301

  [sh] funsky snr.ev hd.in
        510.00       510.00
        512.00       510.50
        513.50       513.50
</PRE>

<P>
If three arguments are supplied, then the input positions again are
read from the standard input. Each line is assumed to contain a single
coordinate position consisting of an RA (or X in pixels) followed by a
Dec (or Y in pixels), with the usual delimiters supported. However,
the second and third arguments now specify the column names and/or
sky units using a colon-delimited syntax:
<PRE>
  [colname]:[h|d|r]
</PRE>
If the colname is omitted, the names default to "RA", "DEC", "X", "Y",
"COL1", or "COL2" as above. If the units are omitted, the default is degrees
for both RA and Dec. When the -r switch is used (convert from image
to sky) the units are applied to the output instead of the input. The following
examples will serve to illustrate the options:
<PRE>
  # read from stdin, specifying column names (def. units: degrees)
  [sh] cat hd.in
       MYRA        MYDEC
  ---------    ---------
  22.982695    58.606523
  22.982127    58.607634
  22.981700    58.614301

  [sh] funsky snr.ev MYRA MYDEC < hd.in
        510.00       510.00
        512.00       510.50
        513.50       513.50

  # read from stdin, specifying column names and units
  [sh] cat dd.in
       MYRA        MYDEC
  ---------    ---------
  344.740432    58.606523
  344.731900    58.607634
  344.725500    58.614301

  [sh] funsky snr.ev MYRA:d MYDEC:d < dd.in
        510.00       510.00
        512.00       510.50
        513.50       513.50

  # read stdin, convert image to sky, specifying output sky units
  [sh] cat im.in
        510.00       510.00
        512.00       510.50
        513.50       513.50

  [sh] cat im.in | funsky -r snr.ev :d :d
  344.740432    58.606523
  344.731900    58.607634
  344.725500    58.614301
</PRE>

<P>
Finally, four command arguments specify both and input file and column names
and/or units:
<PRE>
  [sh] cat dd.in
       MYRA        MYDEC
  ---------    ---------
  344.740432    58.606523
  344.731900    58.607634
  344.725500    58.614301

  [sh] funsky snr.ev dd.in MYRA:d MYDEC:d
        510.00       510.00
        512.00       510.50
        513.50       513.50

  # read file, convert image to sky, specifying output sky units
  [sh] cat im.in
        510.00       510.00
        512.00       510.50
        513.50       513.50

  [sh] funsky -r snr.ev im.in :d :d
    344.740432    58.606523
    344.731900    58.607634
    344.725500    58.614301
</PRE>

<P>
By default, the output of funsky consists only of the converted coordinate
position(s), one per output line. This makes parsing in shell scripts easy.
Use the <B>-v</B> (verbose) switch to specify that the input
coordinates should be pre-pended to each line. For example:
<PRE>
  [sh] cat dd.in
       MYRA        MYDEC
  ---------    ---------
  344.740432    58.606523
  344.731900    58.607634
  344.725500    58.614301

  [sh] funsky snr.ev dd.in MYRA:d MYDEC:d
        510.00       510.00
        512.00       510.50
        513.50       513.50

  [sh] funsky -v snr.ev dd.in MYRA:d MYDEC:d
    344.740432    58.606523       510.00       510.00
    344.731900    58.607634       512.00       510.50
    344.725500    58.614301       513.50       513.50
</PRE>

<P>
In addition, a full starbase table can be output using the <B>-T</B>
(table) switch.  This switch can be used with or without the -v
switch. If the -T and -v are both specified, then a descriptive header
parameters are output before the table (mainly to remind you of the
sky units):
<PRE>
  # output table in non-verbose mode
  [sh] funsky -T snr.ev dd.in MYRA:d MYDEC:d
             X               Y
  ------------    ------------
        510.00          510.00
        512.00          510.50
        513.50          513.50
  
  # output table in verbose mode
  [sh] funsky -T -v snr.ev dd.in MYRA:d MYDEC:d
  # IFILE = /Users/eric/data/snr.ev
  # ICOL1 = MYRA
  # ICOL2 = MYDEC
  # IUNITS1 = d
  # IUNITS2 = d
  # OCOL1 = X
  # OCOL2 = Y
  
          MYRA           MYDEC               X               Y
  ------------    ------------    ------------    ------------
    344.740432       58.606523          510.00          510.00
    344.731900       58.607634          512.00          510.50
    344.725500       58.614301          513.50          513.50
</PRE>

<P>
Finally, the <B>-d</B> (ds9) switch mimicks ds9's use of integer TLMIN
and TLMAX values for all coordinate transformations.  FITS conventions
seem to call for use of floating point TLMIN and TLMAX when the data are
floats. This convention is followed by funsky but results in a
small discrepancy with ds9's converted values for floating point
data. We will remedy this conflict in the future, maybe.

<!-- =defdoc funtable funtable 1 -->

<!-- =section funtable NAME -->
<H2><A NAME="funtable">funtable - copy selected rows from a Funtools file to a FITS binary table</A></H2>

<!-- =section funtable SYNOPSIS -->
<B>
<PRE>
funtable [-a] [-i|-z] [-m] [-s cols] &lt;iname&gt; &lt;oname&gt; [columns]
</PRE>
</B>

<!-- =section funtable OPTIONS -->
<P>
<PRE>
  -a    # append to existing output file as a table extension
  -i    # for image data, only generate X and Y columns
  -m    # for tables, write a separate file for each region
  -s "col1 ..." # columns on which to sort
  -z    # for image data, output zero-valued pixels
</PRE>

<!-- =section funtable DESCRIPTION -->
<P>
<B>funtable</B> selects rows from the specified
<A HREF="./files.html">FITS Extension</A>
(binary table only) of a FITS file, or from a non-FITS raw event
file, and writes those rows to a FITS binary table file. It also
will create a FITS binary table from an image or a raw array file.

<P>
The first argument to the program specifies the FITS file, raw event
file, or raw array file.  If "stdin" is specified, data are read from
the standard input. Use <A HREF="./files.html">Funtools Bracket
Notation</A> to specify FITS extensions, and filters.  The second
argument is the output FITS file.  If "stdout" is specified, the FITS
binary table is written to the standard output.  By default, all
columns of the input file are copied to the output file.  Selected
columns can be output using an optional third argument in the form:
<PRE>
  "column1 column1 ... columnN"
</PRE>

<P>
The <B>funtable</B> program generally is used to select rows from a
FITS binary table using
<A HREF="./filters.html">Table Filters</A>
and/or
<A HREF="./regions.html">Spatial Region Filters</A>.
For example, you can copy only selected rows (and output only selected
columns) by executing in a command such as:
<PRE>
  [sh] funtable "test.ev[pha==1&&pi==10]" stdout "x y pi pha" | fundisp stdin
         X       Y     PHA        PI
   ------- ------- ------- ---------
         1      10       1        10
         1      10       1        10
         1      10       1        10
         1      10       1        10
         1      10       1        10
         1      10       1        10
         1      10       1        10
         1      10       1        10
         1      10       1        10
         1      10       1        10
</PRE>
<P>
The special column <B>$REGION</B> can be specified to write the
region id of each row:
<PRE>
  [sh $] funtable "test.ev[time-(int)time>=.99&&annulus(0 0 0 10 n=3)]" stdout 'x y time $REGION' | fundisp stdin
          X        Y                  TIME     REGION
   -------- -------- --------------------- ----------
          5       -6           40.99000000          3
          4       -5           59.99000000          2
         -1        0          154.99000000          1
         -2        1          168.99000000          1
         -3        2          183.99000000          2
         -4        3          199.99000000          2
         -5        4          216.99000000          2
         -6        5          234.99000000          3
         -7        6          253.99000000          3
</PRE>
<P>
Here only rows with the proper fractional time and whose position also is
within one of the three annuli are written.
<P>
Columns can be excluded from display using a minus sign before the
column:
<PRE>
  [sh $] funtable "test.ev[time-(int)time>=.99]" stdout "-time" | fundisp stdin
          X        Y      PHA         PI          DX          DY
   -------- -------- -------- ---------- ----------- -----------
          5       -6        5         -6        5.50       -6.50
          4       -5        4         -5        4.50       -5.50
         -1        0       -1          0       -1.50        0.50
         -2        1       -2          1       -2.50        1.50
         -3        2       -3          2       -3.50        2.50
         -4        3       -4          3       -4.50        3.50
         -5        4       -5          4       -5.50        4.50
         -6        5       -6          5       -6.50        5.50
         -7        6       -7          6       -7.50        6.50
</PRE>
All columns except the time column are written.
<P>
In general, the rules for activating and de-activating columns are:
<UL>
<LI> If only exclude columns are specified, then all columns but
the exclude columns will be activated.
<LI> If only include columns are specified, then only the specified columns
are activated.
<LI> If a mixture of include and exclude columns are specified, then
all but the exclude columns will be active; this last case
is ambiguous and the rule is arbitrary.
</UL>
In addition to specifying columns names explicitly, the special
symbols <EM>+</EM> and <EM>-</EM> can be used to activate and
de-activate <EM>all</EM> columns. This is useful if you want to
activate the $REGION column along with all other columns.  According
to the rules, the syntax "$REGION" only activates the region column
and de-activates the rest. Use "+ $REGION" to activate all
columns as well as the region column.

<P>
Ordinarily, only the selected table is copied to the output file.  In
a FITS binary table, it sometimes is desirable to copy all of the
other FITS extensions to the output file as well. This can be done by
appending a '+' sign to the name of the extension in the input file
name. For example, the first command below copies only the EVENT table,
while the second command copies other extensions as well:
<PRE>
  [sh] funtable "/proj/rd/data/snr.ev[EVENTS]" events.ev
  [sh] funtable "/proj/rd/data/snr.ev[EVENTS+]" eventsandmore.ev
</PRE>

<P>
If the input file is an image or a raw array file, then
<B>funtable</B> will generate a FITS binary table from the pixel
values in the image. Note that it is not possible to specify the
columns to output (using command-line argument 3). Instead, there are
two ways to create such a binary table from an image. By default, a
3-column table is generated, where the columns are "X", "Y", and
"VALUE". For each pixel in the image, a single row (event) is
generated with the "X" and "Y" columns assigned the dim1 and dim2
values of the image pixel, respectively and the "VALUE" column
assigned the value of the pixel. With sort of table, running
<B>funhist</B> on the "VALUE" column will give the same results as
running <B>funhist</B> on the original image.

<P>
If the <B>-i</B> ("individual" rows) switch is specified, then only
the "X" and "Y" columns are generated. In this case, each positive
pixel value in the image generates n rows (events), where n is equal
to the integerized value of that pixel (plus 0.5, for floating point
data).  In effect, <B>-i</B> approximately recreates the rows of a
table that would have been binned into the input image. (Of course,
this is only approximately correct, since the resulting x,y positions
are integerized.)

<P>
If the <B>-s [col1 col2 ... coln]</B> ("sort") switch is specified,
the output rows of a binary table will be sorted using the
specified columns as sort keys. The sort keys must be scalar columns
and also must be part of the output file (i.e. you cannot sort on a
column but not include it in the output). This facility uses the
<B>_sort</B> program (included with funtools), which must be accessible
via your path.

<p>
For binary tables, the <B>-m</B> ("multiple files") switch will
generate a separate file for each region in the filter specification
i.e. each file contains only the rows from that region. Rows
which pass the filter but are not in any region also are put in a
separate file.

<P>
The separate output file names generated by the <B>-m</B> switch are
produced automatically from the root output file to contain the region id of
the associated region. (Note that region ids start at 1, so that the
file name associated with id 0 contains rows that pass the filter but
are not in any given region.) Output file names are generated as follows:

<UL>
<LI> A $n specification can be used anywhere in the root file name (suitably
quoted to protect it from the shell) and will be expanded to be the id
number of the associated region. For example:
<PRE>
  funtable -m input.fits'[cir(512,512,1);cir(520,520,1)...]' 'foo.goo_$n.fits'
</PRE>
will generate files named foo.goo_0.fits (for rows not in any region but
still passing the filter), foo.goo_1.fits (rows in region id #1, the first
region), foo.goo_2.fits (rows in region id #2), etc. Note that single quotes
in the output root are required to protect the '$' from the shell.

<LI> If $n is not specified, then the region id will be placed before
the first dot (.) in the filename. Thus:
<PRE>
  funtable -m input.fits'[cir(512,512,1);cir(520,520,1)...]' foo.evt.fits
</PRE>
will generate files named foo0.evt.fits (for rows not in any region but
still passing the filter), foo1.evt.fits (rows in region id #1),
foo2.evt.fits (rows in region id #2), etc.

<LI> If no dot is specified in the root output file name, then
the region id will be appended to the filename. Thus:
<PRE>
  funtable -m input.fits'[cir(512,512,1);cir(520,520,1)...]' 'foo_evt'
</PRE>
will generate files named foo_evt0 (for rows not in any region but
still passing the filter), foo_evt1 (rows in region id #1),
foo_evt2 (rows in region id #2), etc.
</UL>
The multiple file mechanism provide a simple way to generate
individual source data files with a single pass through the data.

<p>
By default, a new FITS file is created and the binary table is written
to the first extension.  If the <B>-a</B> (append) switch is specified,
the table is appended to an existing FITS file as a BINTABLE extension.
Note that the output FITS file must already exist.

<P>
If the <B>-z</B> ("zero" pixel values) switch is specified and
<B>-i</B> is not specified, then pixels having a zero value will
be output with their "VALUE" column set to zero. Obviously, this
switch does not make sense when individual events are output.

<!-- =defdoc funtbl funtbl 1 -->

<!-- =section funtbl NAME -->
<H2><A NAME="funtbl">funtbl - extract a table from Funtools ASCII output</A></H2>

<!-- =section funtbl SYNOPSIS -->
<B>
<PRE>
funtable [-c cols] [-h] [-n table] [-p prog] [-s sep] &lt;iname&gt;
</PRE>
</B>

<!-- =section funtbl DESCRIPTION -->
<P>
[NB: This program has been deprecated in favor of the ASCII text processing
support in funtools. You can now perform fundisp on funtools ASCII output
files (specifying the table using bracket notation) to extract tables
and columns.]

The <B>funtbl</B> script extracts a specified table (without the
header and comments) from a funtools ASCII output file and writes the
result to the standard output.  The first non-switch argument is the
ASCII input file name (i.e. the saved output from funcnts, fundisp,
funhist, etc.). If no filename is specified, stdin is read. The
-n switch specifies which table (starting from 1) to extract. The
default is to extract the first table.  The -c switch is a
space-delimited list of column numbers to output, e.g.  -c "1 3 5"
will extract the first three odd-numbered columns. The default is to
extract all columns. The -s switch specifies the separator string to
put between columns. The default is a single space. The -h switch
specifies that column names should be added in a header line before
the data is output. Without the switch, no header is prepended.  The
-p program switch allows you to specify an awk-like program to run
instead of the default (which is host-specific and is determined at
build time). The -T switch will output the data in rdb format (i.e.,
with a 2-row header of column names and dashes, and with data columns
separated by tabs). The -help switch will print out a message
describing program usage.

<P>
For example, consider the output from the following funcnts command:
<PRE>
  [sh] funcnts -sr snr.ev "ann 512 512 0 9 n=3"
  # source
  #   data file:        /proj/rd/data/snr.ev
  #   arcsec/pixel:     8
  # background
  #   constant value:   0.000000
  # column units
  #   area:             arcsec**2
  #   surf_bri:         cnts/arcsec**2
  #   surf_err:         cnts/arcsec**2
  
  # summed background-subtracted results
  upto   net_counts     error   background    berror      area  surf_bri  surf_err
  ---- ------------ --------- ------------ --------- --------- --------- ---------
     1      147.000    12.124        0.000     0.000   1600.00     0.092     0.008
     2      625.000    25.000        0.000     0.000   6976.00     0.090     0.004
     3     1442.000    37.974        0.000     0.000  15936.00     0.090     0.002
  
  
  # background-subtracted results
   reg   net_counts     error   background    berror      area  surf_bri  surf_err
  ---- ------------ --------- ------------ --------- --------- --------- ---------
     1      147.000    12.124        0.000     0.000   1600.00     0.092     0.008
     2      478.000    21.863        0.000     0.000   5376.00     0.089     0.004
     3      817.000    28.583        0.000     0.000   8960.00     0.091     0.003
  
  
  # the following source and background components were used:
  source_region(s)
  ----------------
  ann 512 512 0 9 n=3
  
   reg       counts    pixels      sumcnts    sumpix
  ---- ------------ --------- ------------ ---------
     1      147.000        25      147.000        25
     2      478.000        84      625.000       109
     3      817.000       140     1442.000       249
</PRE>
<P>
There are four tables in this output. To extract the last one, you
can execute:
<PRE>
  [sh] funcnts -s snr.ev "ann 512 512 0 9 n=3" | funtbl -n 4
  1 147.000 25 147.000 25
  2 478.000 84 625.000 109
  3 817.000 140 1442.000 249
</PRE>
Note that the output has been re-formatted so that only a single space
separates each column, with no extraneous header or comment information.

<P>
To extract only columns 1,2, and 4 from the last example (but with a header
prepended and tabs between columns), you can execute:
<PRE>
  [sh] funcnts -s snr.ev "ann 512 512 0 9 n=3" | funtbl -c "1 2 4" -h -n 4 -s "\t"
  #reg    counts  sumcnts
  1       147.000 147.000
  2       478.000 625.000
  3       817.000 1442.000
</PRE>
<P>
Of course, if the output has previously been saved in a file named
foo.out, the same result can be obtained by executing:
<PRE>
  [sh] funtbl -c "1 2 4" -h -n 4 -s "\t" foo.out
  #reg    counts  sumcnts
  1       147.000 147.000
  2       478.000 625.000
  3       817.000 1442.000
</PRE>

<!-- =section funcalc SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funcen SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funcnts SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funcone SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section fundisp SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funhead SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funhist SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funimage SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funindex SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funjoin SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funmerge SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funsky SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funtable SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =section funtbl SEE ALSO -->
<!-- =text See funtools(n) for a list of Funtools help pages -->
<!-- =stop -->

<P>
<A HREF="./help.html">Go to Funtools Help Index</A>

<H5>Last updated: April 1, 2007</H5>

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