% -----------------------------------------------------------------------
% app-paramEx.tex: Example input parameter files, and how the
%                  parameters are listed in the output.
% -----------------------------------------------------------------------
% Copyright (C) 2006, Matthew Whiting, ATNF
%
% This program is free software; you can redistribute it and/or modify it
% under the terms of the GNU General Public License as published by the
% Free Software Foundation; either version 2 of the License, or (at your
% option) any later version.
%
% Duchamp is distributed in the hope that it will be useful, but WITHOUT
% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
% FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
% for more details.
%
% You should have received a copy of the GNU General Public License
% along with Duchamp; if not, write to the Free Software Foundation,
% Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA
%
% Correspondence concerning Duchamp may be directed to:
%    Internet email: Matthew.Whiting [at] atnf.csiro.au
%    Postal address: Dr. Matthew Whiting
%                    Australia Telescope National Facility, CSIRO
%                    PO Box 76
%                    Epping NSW 1710
%                    AUSTRALIA
% -----------------------------------------------------------------------
\secA{Example parameter files}
\label{app-input}

This is what a typical parameter file would look like.

\begin{verbatim}
imageFile       /home/mduchamp/fountain.fits
logFile         logfile.txt
outFile         results.txt
spectraFile     spectra.ps
flagSubsection  false
flagOutputRecon false
flagOutputResid 0
flagTrim        1
flagMW          1
minMW           75
maxMW           112
flagGrowth      1
growthCut       1.5
flagATrous      1
reconDim        1          
scaleMin        1
snrRecon        4
flagFDR         1
alphaFDR        0.1
snrCut          3
threshSpatial   3
threshVelocity  7
\end{verbatim}

Note that, as in this example, the flag parameters can be entered as
strings (\texttt{true}/\texttt{false}) or integers
(\texttt{1}/\texttt{0}). Also, note that it is not necessary to
include all these parameters in the file, only those that need to be
changed from the defaults (as listed in Appendix~\ref{app-param}),
which in this case would be very few. A minimal parameter file might
look like:
\begin{verbatim}
imageFile       /home/mduchamp/fountain.fits
flagLog         false
flagATrous      1
snrRecon        3
snrCut          2.5
minChannels     4
\end{verbatim}
This will reconstruct the cube with a lower SNR value than the
default, select objects at a lower threshold,  with a looser minimum
channel requirement, and not keep a log of the intermediate
detections. 

The following page demonstrates how the parameters are presented to
the user, both on the screen at execution time, and in the output and
log files. On each line, there is a description on the parameter, the
relevant parameter name that is used in the input file (if there is
one that the user can enter), and the value of the parameter being
used.

%\begin{sideways}
%Typical presentation of parameters in output and log files:  
%\begin{minipage}{170mm}
%
% NOTE -- EXCISED THESE FROM THE EXAMPLE, AS THE SECOND LINE IS 18PT
% TOO LONG...
%Reconstructed array exists?................[reconExists]  =  true
%FITS file containing reconstruction..........[reconFile]  =  fountain.RECON-1-1-4-1.fits
{\scriptsize
\begin{verbatim}
---- Parameters ----
Image to be analysed.........................[imageFile]  =  fountain.fits
Intermediate Logfile...........................[logFile]  =  duchamp-Logfile.txt
Final Results file.............................[outFile]  =  duchamp-Results.txt
Spectrum file..............................[spectraFile]  =  duchamp-Spectra.ps
0th Moment Map...............................[momentMap]  =  duchamp-MomentMap.ps
Detection Map.............................[detectionMap]  =  duchamp-DetectionMap.ps
Display a map in a pgplot xwindow?.........[flagXOutput]  =  true
Saving reconstructed cube?.............[flagoutputrecon]  =  false
Saving residuals from reconstruction?..[flagoutputresid]  =  false
------
Blank Pixel Value.......................................  =  -8.00061
Trimming Blank Pixels?........................[flagTrim]  =  true
Searching for Negative features?..........[flagNegative]  =  false
Removing Milky Way channels?....................[flagMW]  =  true
Milky Way Channels.......................[minMW - maxMW]  =  75-112
Beam Size (pixels)......................................  =  10.1788
Removing baselines before search?.........[flagBaseline]  =  false
Smoothing each spectrum first?..............[flagSmooth]  =  false
Using A Trous reconstruction?...............[flagATrous]  =  true
Number of dimensions in reconstruction........[reconDim]  =  1
Minimum scale in reconstruction...............[scaleMin]  =  1
SNR Threshold within reconstruction...........[snrRecon]  =  4
Filter being used for reconstruction........[filterCode]  =  1 (B3 spline function)
Using FDR analysis?............................[flagFDR]  =  false
SNR Threshold (in sigma)........................[snrCut]  =  3
Minimum # Pixels in a detection.................[minPix]  =  2
Minimum # Channels in a detection..........[minChannels]  =  3
Growing objects after detection?............[flagGrowth]  =  false
Using Adjacent-pixel criterion?...........[flagAdjacent]  =  true
Max. velocity separation for merging....[threshVelocity]  =  7
Method of spectral plotting.............[spectralMethod]  =  peak
Type of object centre used in results......[pixelCentre]  =  centroid
--------------------
\end{verbatim}
}
%\end{minipage}
%\end{sideways}