##
## SPECDETECT -- locate peaks in 1-D grating data
## 
input_data_file,s,a,"",,,"input data file [root.dat]"
#
# Data columns are: col1=position, col2=optional bin width
# if bin width present: col3=counts or flux, col4=counts_err or flux_err
# if bin width not present: col2=counts or flux, col3=counts_err or flux_err
#     
num_cols_in_data,i,a,3,3,4,"number of columns in input data file"
flux_corrected,b,a,no,,,"Is the input file flux corrected?"
output_peaks_file,s,a,".",,,"output file name [root.peaks]"
output_continuum_file,s,a,".",,,"output continuum file name [root_cont.dat]"
data_minus_cont_file,s,a,".",,,"output (data-continuum) file name [root_nocont.dat]"
thresh_emission,r,a,4,0,,"emission line detect threshold = (thresh_emission * uncertainty)"
grating,s,a,"HEG","HEG|heg|MEG|meg|LEG|leg",,"Grating associated with the input data"
#
# If entering an input continuum spectrum, all 4 columns must be present:
# col1=lambda, col2=bin width, col3=counts or flux, col3=counts_err or flux_err
#
input_continuum_file,s,h,"NONE",,,"optional input continuum file name [root_cont.dat]"
thresh_absoption,r,h,2,0,,"absorption line detect threshold = (thresh_absorption * uncertainty)"
#
# The methods for calculating the continuum are:
#	median  -> running median using median_n_bins, with step size of 1 bin
#	tmedian -> running truncated median using median_n_bins, ""
#	spline3 -> cubic smoothing spline
# If using median or truncated median, must set the median_n_bins parameter
#
continuum_method,s,h,"median",median|spline3|tmedian|test,,"Continuum calculation method"
median_n_bins,i,h,50,4,,"Number of bins for median of continuum calc - EVEN number"
cont_offset,i,h,1,1,20,"Offset from line center to sample continuum [LSF width]"
#
# The of head and tail of the non cubic spline continuum calculations need to
# be determined by the user.  The head and tail sections are equivalent to
# median_n_bins/2 on each end of the spectrum.  Currently, the possible 
# values for those sections are:
#	default     -> sets the head and tail to = 0 counts
#	values      -> sets the head and tail to user values; values are set
#                      in the following paramerters called "head_value" and
#	               "tail_value"
#	extrapolate -> uses extrapolation of the neighbors to cal head/tail
#	copy        -> uses a copy of the neighbors data values to get the extra
#	               points in order to perform median/tmedian calculations 
#
head_tail_cont_method,s,h,"default",default|values|extrapolate|copy,,"Head and tail t/median continuum calc"
#
# If head_tail_cont_method=values, the values must be set here, using
# the parameters "head_value" and "tail_value".
#
head_value,r,h,0,,,"If head_tail_cont_method=values, set short wavelength (left) end"
tail_value,r,h,0,,,"If head_tail_cont_method=values, set long wavelength (right) end"
#
# If using the truncated median parameter, set the low and high cut offs.
# The (high_tmedian + low_tmedian) cut off, must be less than 1.
#
low_tmedian,r,h,0.2,0,1,"For truncated median, reject bin values <= (low_tmedian * median)"
high_tmedian,r,h,0,0,1,"For truncated median, reject bins values >= (high_tmedian * median)"
clobber,b,h,yes,,,"OK to overwrite existing output files?"
debug,i,h,1,0,6,"debug level (0 = no debug)"
mode,s,h,"ql",,,