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% app-param.tex: Section listing all the possible input parameters and
%                their defaults.
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\secA{Available parameters}
\label{app-param}

The full list of parameters that can be listed in the input file are
given here. Following each parameter name are listed three things: the
default parameter taken when not provided in the input file; the data
type that should be provided; and some indication (where applicable)
of the range of values required or the type of information expected.
Since the order of the parameters in the input file does not matter,
they are grouped here in logical sections.

\secB*{Input related}
\begin{Lentry}
\item[{ImageFile [no default | string | filename]}] The filename of
  the data cube to be analysed.
\item[{flagSubsection [false | bool | true/false/1/0]}] A flag to
  indicate whether one wants a subsection of the requested image.
\item[{Subsection [full field | string | Subsection string]}] The
  requested subsection -- see \S\ref{sec-input} for details on the
  subsection format.  If the full range of a dimension is required,
  use a \texttt{*} (thus the default is the full cube).
\item[{flagReconExists [false | bool | true/false/1/0]}] A flag to
  indicate whether the reconstructed array has been saved by a
  previous run of \duchamp. If set true, the reconstructed array will
  be read from the file given by \texttt{reconFile}, rather than
  calculated directly.
\item[{reconFile [no default | string | filename]}] The FITS file that
  contains the reconstructed array. If \texttt{flagReconExists} is
  true and this parameter is not defined, the default file that is
  looked for will be determined by the \atrous parameters (see
  \S\ref{sec-recon}).
\item[{flagSmoothExists [false | bool | true/false/1/0]}] A flag to
  indicate whether the Hanning-smoothed array has been saved by a
  previous run of \duchamp. If set true, the smoothed array will be
  read from the file given by \texttt{smoothFile}, rather than
  calculated directly.
\item[{smoothFile [no default | string | filename]}] The FITS file
  that has a previously smoothed array. If \texttt{flagSmoothExists}
  is true and this parameter is not defined, the default file that is
  looked for will be determined by the smoothing parameters (see
  \S\ref{sec-smoothing}).
\item[{usePrevious [false | bool | true/false/1/0]}] A flag to
  indicate that \duchamp should read the list of objects from a
  previously-created log file, rather than doing the searching
  itself. The set of outputs will be created according to the flags in
  the following section.
\item[{objectList [no default | string | comma-separated list]}] When
  \texttt{usePrevious=true}, this list is used to output individual
  spectral plots, as well as a postscript file for all spectral plots
  as given by \texttt{SpectraFile}. The filenames of the plots will be
  the same as \texttt{SpectraFile}, but with -XX at the end, where XX
  is the object number (\eg \texttt{duchamp-Spectra-07.ps}). The
  format of the parameter value should be a string listing individual
  objects or object ranges: \eg 1,2,4-7,8,14.
\end{Lentry}

\secB*{Output related}
\begin{Lentry}
\item[{OutFile [duchamp-\\Results.txt | string | filename]}] The file
  containing the final list of detections. This also records the list
  of input parameters.
\item[{flagSeparateHeader [false | bool | true/false/1/0]}] A flag to
  indicate that the header information that would normally be printed
  at the start of the results file (containing information on the
  parameters, image statistics and number of detections) should
  instead be written to a separate file.
\item[{HeaderFile [duchamp-\\Results.hdr | string | filename]}] The
  file to which the header information should be written when
  \texttt{flagSeparateHeader=true}.
\item[{flagWriteBinaryCatalogue [true | bool | true/false/1/0]}]
  Whether to write a binary catalogue of the detections, for later
  re-use (see \S\ref{sec-reuse} for details).
\item[{binaryCatalogue [duchamp-Catalogue.dpc | string | filename]}]
  The filename for the binary catalogue.
\item[{flagPlotSpectra [true | bool | true/false/1/0]}] Whether to
  produce a postscript file containing spectra of all detected
  objects. If PGPlot has not been enabled, this parameter defaults to
  \texttt{false}.
\item[{SpectraFile [duchamp-\\Spectra.ps | string | filename]}] The
  postscript file that contains the resulting integrated spectra and
  images of the detections.
\item[{flagPlotIndividualSpectra [false | bool | true/false/1/0]}]
  Whether to produce individual spectral plots for listed sources.
\item[{flagTextSpectra [false | bool | true/false/1/0]}] A flag to say
  whether the spectra should be saved in text form in a single
  file. See below for a description.
\item[{spectraTextFile [duchamp-\\Spectra.txt | string | filename]}]
  The file containing the spectra of each object in ascii format. This
  file will have a column showing the spectral coordinates, and one
  column for each of the detected objects, showing the flux values as
  plotted in the graphical output of \texttt{spectraFile}.
\item[{flagLog [false | bool | true/false/1/0]}] A flag to indicate
  whether the details of intermediate detections should be logged.
\item[{LogFile [duchamp-\\Logfile.txt | string | filename]}] The file
  in which intermediate detections and the pixel content of the final
  list of detections are logged. These are detections that have not
  been merged. This is primarily for use in debugging and diagnostic
  purposes: normal use of the program will probably not require it.
\item[{flagOutputMomentMap [false | bool | true/false/1/0]}] A flag to
  say whether or not to save a FITS file containing the moment-0 map.
\item[fileOutputMomentMap{ [see text | string | filename]}] The file
  to which the moment-0 array is written. If left blank (the default),
  the naming scheme detailed in \S\ref{sec-momentOut} is used.
\item[{flagOutputMomentMask [false | bool | true/false/1/0]}] A flag
  to say whether or not to save a FITS file containing the moment-0
  mask (a mask showing which spatial pixels are detected in one or
  more channels).
\item[fileOutputMomentMask{ [see text | string | filename]}] The file
  to which the moment-0 mask is written. If left blank (the default),
  the naming scheme detailed in \S\ref{sec-maskOut} is used.
\item[{flagOutputMask [false | bool | true/false/1/0]}] A flag to say
  whether or not to save a FITS file containing a mask array, with
  values 1 where there is a detected object and 0 elsewhere.
\item[fileOutputMask{ [see text | string | filename]}] The file to
  which the mask array is written. If left blank (the default), the
  naming scheme detailed in \S\ref{sec-maskOut} is used.
\item[{flagMaskWithObjectNum [false | bool | true/false/1/0]}] If this
  flag is true, the detected pixels in the mask image have the
  corresponding object ID as their value. If false, they have the
  value 1. All non-detected pixels have the value 0.
\item[{flagOutputRecon [false | bool | true/false/1/0]}] A flag to say
  whether or not to save the reconstructed cube as a FITS file.
\item[fileOutputRecon{ [see text | string | filename]}] The file to
  which the reconstructed array is written. If left blank (the
  default), the naming scheme detailed in \S\ref{sec-reconIO} is used.
\item[{flagOutputResid [false | bool | true/false/1/0]}] As for
  \texttt{flagOutputRecon}, but for the residual array -- the
  difference between the original cube and the reconstructed cube. 
\item[fileOutputResid{ [see text | string | filename]}] The file to
  which the residual array is written. If left blank (the default),
  the naming scheme detailed in \S\ref{sec-reconIO} is used.
\item[{flagOutputSmooth [false | bool | true/false/1/0]}] A flag to
  say whether or not to save the smoothed cube as a FITS file.
\item[fileOutputSmooth{ [see text | string | filename]}] The file to
  which the smoothed array is written. If left blank (the default),
  the naming scheme detailed in \S\ref{sec-reconIO} is used.
\item[{flagOutputBaseline [false | bool | true/false/1/0]}] A flag to
  say whether or not to save the cube of spectral baseline values as a
  FITS file.
\item[fileOutputBaseline{ [see text | string | filename]}] The file to
  which the baseline values are written. If left blank (the default),
  the naming scheme detailed in \S\ref{sec-baselineOut} is used.
\item[{flagVOT [false | bool | true/false/1/0]}] A flag to say whether
  to create a VOTable file with the detection information. This will
  be an XML file in the Virtual Observatory VOTable format.
\item[{votFile [duchamp-\\Results.xml | string | filename]}] The
  VOTable file with the list of final detections. Some input
  parameters are also recorded.
\item[{flagKarma [false | bool | true/false/1/0]}] A flag to say
  whether to create a Karma annotation file corresponding to the
  information in \texttt{outfile}. This can be used as an overlay in
  Karma programs such as \texttt{kvis}.
\item[{karmaFile [duchamp-\\Results.ann | string | filename]}] The
  Karma annotation file showing the list of final detections.
\item[{flagDS9 [false | bool | true/false/1/0]}] A flag to say whether
  to create a DS9 region file corresponding to the information in
  \texttt{outfile}. This can be used as an overlay in SAOImage DS9 or
  casaviewer.
\item[{ds9File [duchamp-\\Results.ann | string | filename]}] The DS9
  region file showing the list of final detections.
\item[{flagCasa [false | bool | true/false/1/0]}] A flag to say
  whether to create a CASA region file corresponding to the
  information in \texttt{outfile}. This can be used as an overlay in
  casaviewer (when this functionality is available) or import into
  casapy.
\item[{casaFile [duchamp-\\Results.crf | string | filename]}] The CASA
  region file showing the list of final detections.
\item[{annotationType [borders | string | borders/circles/ellipses]}]
  Which type of annotation plot to use. Specifying ``borders'' gives
  an outline around the detected spatial pixels, ``circles'' gives a
  circle centred on the centre of the object with radius large enough
  to encompass all spatial pixels, and ``ellipses'' gives an ellipse
  centred on the centre of the object of size given by the MAJ, MIN \&
  PA values.
\item[{flagMaps [true | bool | true/false/1/0]}] A flag to say whether
  to save postscript files showing the 0th moment map of the whole
  cube (\texttt{momentMap}) and the detection image
  (\texttt{detectionMap}). If PGPlot has not been enabled, this
  parameter defaults to \texttt{false}.
\item[{momentMap [duchamp-\\MomentMap.ps | string | filename]}] A
  postscript file containing a map of the 0th moment of the detected
  sources, as well as pixel and WCS coordinates.
\item[{detectionMap [duchamp-\\DetectionMap.ps | string | filename]}]
  A postscript file with a map showing each of the detected objects,
  coloured in greyscale by the number of detected channels in each
  spatial pixel. Also shows pixel and WCS coordinates.
\item[{flagXOutput [true | bool | true/false/1/0]}] A flag to say
  whether to display a 0th moment map in a PGPlot X-window. This will
  be in addition to any that are saved to a file. This parameter can
  be overridden by the use of the \texttt{-x} command-line option,
  which disables the X-windows output. If PGPlot has not been enabled,
  this parameter defaults to \texttt{false}.
\item[{newFluxUnits [no default | string | units string]}] Flux units
  that the pixel values should be converted into. These should be
  directly compatible with the units in the FITS header, given by the
  BUNIT keyword.
\item[{precFlux [3 | int | $> 0$]}] The desired precision (\ie number
  of decimal places) for flux values given in the output files and
  tables.
\item[{precVel [3 | int | $> 0$]}] The desired precision (\ie number
  of decimal places) for velocity/frequency values given in the output
  files and tables.
\item[{precSNR [2 | int | $> 0$]}] The desired precision (\ie number
  of decimal places) for the peak SNR value given in the output files
  and tables.
\end{Lentry}

\secB*{Modifying the cube}
\begin{Lentry}
\item[{flagTrim [false | bool | true/false/1/0]}] A flag to say
  whether to trim BLANK pixels from the edges of the cube -- these are
  typically pixels set to some particular value because they fall
  outside the imaged area, and trimming them can help speed up the
  execution.
\item[{flaggedChannels [no default | string | comma-separated list]}]
  Channels that are to be ignored by the source-finding. These should
  be specified by a comma-separated list of single values and ranges,
  such as 1,3,6-12,18. Channel numbers are zero-based, so that the
  first channel in the cube has value 0.
\item[{flagBaseline [false | bool | true/false/1/0]}] A flag to say
  whether to remove the baseline from each spectrum in the cube for
  the purposes of reconstruction and detection.
\item[{baselineType [atrous | string | atrous/median]}] The algorithm
  used to calculate the spectral baseline. Only \texttt{atrous} or
  \texttt{median} are accepted.
\item[{baselineBoxWidth [51 | int | odd integer $> 0$]}] The box width
  used by the \texttt{median} baseline algorithm. Needs to be odd - if
  even, it will be incremented by one.
\end{Lentry}

\secB*{Detection related}

\secC*{General detection}
\begin{Lentry}
\item[{searchType [spatial | string | spectral/spatial]}] How the
  searches are done. Only ``spatial'' and ``spectral'' are accepted. A
  value of ``spatial'' means each 2D channel map is searched, whereas
  ``spectral'' means each 1D spectrum is searched.
\item[{flagStatSec [false | bool | true/false/1/0]}] A flag indicating
  whether the statistics should be calculated on a subsection of the
  cube, rather than the full cube. Note that this only applies to the
  statistics used to determine the threshold, and not for other
  statistical calculations (such as those in the reconstruction
  phase).
\item[{StatSec [full field | string | Subsection string]}] The
  subsection of the cube used for calculating statistics -- see
  \S\ref{sec-input} for details on the subsection format. Only used if
  \texttt{flagStatSec=true}.
\item[{flagRobustStats [true | bool | true/false/1/0]}] A flag
  indicating whether to use the robust statistics (median and MADFM)
  to estimate the noise parameters of the cube, rather than the mean
  and rms. See \S\ref{sec-stats} for details.
\item[{flagNegative [false | bool | true/false/1/0]}] A flag
  indicating that the features of interest are negative. The cube is
  inverted prior to searching.
\item[{snrCut [5. | float | any]}] The threshold, in multiples of
  $\sigma$ above the mean.
\item[{threshold [no default | float | any]}] The actual value of the
  threshold. Normally the threshold is calculated from the cube's
  statistics, but the user can manually specify a value to be used
  that overrides the calculated value. If this is not specified, the
  calculated value is used, but this value will take precedence over
  other means of calculating the threshold (\ie via \texttt{snrCut} or
  the FDR method).
\item[{flagGrowth [false | bool | true/false/1/0]}] A flag indicating
  whether or not to grow the detected objects to a smaller threshold.
\item[{growthCut [3. | float | any]}] The smaller threshold using in
  growing detections. In units of $\sigma$ above the mean.
\item[{growthThreshold [no default | float | any]}] Alternatively, the
  threshold to which detections are grown can be specified in flux
  units (in the same manner as the \texttt{threshold} parameter). When
  the \texttt{threshold} parameter is given, this option \textbf{must}
  be used instead of \texttt{growthCut}.
\item[{beamFWHM [0. | float | $> 0.$]}] The full-width at half maximum
  of the beam, in pixels.  If the header keywords BMAJ and BMIN are
  present, then these will be used to calculate the beam area, and
  this parameter will be ignored. This will take precedence over
  \texttt{beamArea} (but is ignored if not specified).
\item[{beamArea [0. | float | $> 0.$]}] The \textbf{area} of the beam
  in pixels (\ie how many pixel does the beam cover?). As above, if
  the header keywords BMAJ and BMIN are present, then these will be
  used to calculate the beam area, and this parameter will be ignored.
\end{Lentry}

\secC*{\Atrous reconstruction}
\begin{Lentry}
\item[{flagATrous [false | bool | true/false/1/0]}] A flag indicating
  whether or not to reconstruct the cube using the \atrous wavelet
  reconstruction. See \S\ref{sec-recon} for details.
\item[{reconDim [1 | int | 1, 2 or 3]}] The number of dimensions to use in
  the reconstruction. 1 means reconstruct each spectrum separately, 2
  means each channel map is done separately, and 3 means do the whole
  cube in one go.
\item[{scaleMin [1 | int | $> 0$]}] The minimum wavelet scale to be
  used in the reconstruction. A value of 1 means ``use all scales''.
\item[{scaleMax [0 | int | any]}] The maximum wavelet scale to be used
  in the reconstruction. If the value is $\le0$ then the maximum scale
  is calculated from the size of the input array. Similarly, if the
  value given is larger than this calculated value, the calculated
  value is used instead.
\item[{snrRecon [4 | float | $> 0$]}] The thresholding cutoff used in
  the reconstruction -- only wavelet coefficients at least this many
  $\sigma$ above the mean are included in the reconstruction.
\item[{reconConvergence [0.005 | float | $> 0.$]}] The convergence
  criterion used in the reconstruction. The \atrous algorithm iterates
  until the relative change in the standard deviation of the residuals
  is less than this amount.
\item[{filterCode [1 | int | 1/2/3]}] The code number of the filter to
  use in the reconstruction. The options are:
  \begin{itemize}
  \item \textbf{1:} B$_3$-spline filter: coefficients = 
    $(\frac{1}{16}, \frac{1}{4}, \frac{3}{8}, \frac{1}{4}, \frac{1}{16})$
  \item \textbf{2:} Triangle filter: coefficients = 
    $(\frac{1}{4}, \frac{1}{2}, \frac{1}{4})$
  \item \textbf{3:} Haar wavelet: coefficients = 
    $(0, \frac{1}{2}, \frac{1}{2})$
  \end{itemize}
\end{Lentry}

\secC*{Smoothing the cube}
\begin{Lentry}
\item[{flagSmooth [false | bool | true/false/1/0]}] A flag indicating whether to
  smooth the cube. See \S\ref{sec-smoothing} for details. 
\item[{smoothType [spectral | string | spectral/spatial]}] The
  smoothing method used: either ``spectral'' (with a 1D Hanning
  filter) or ``spatial'' (with a 2D Gaussian filter).
\item[{hanningWidth [5 | int | $> 0$]}] The width of the Hanning
  smoothing kernel.
\item[{kernMaj [3 | float | $> 0.$]}] The full-width-half-maximum
  (FWHM), in pixels, of the 2D Gaussian smoothing kernel's major axis.
\item[{kernMin [3 | float | $> 0.$]}] The FWHM (in pixels) of the 2D Gaussian smoothing kernel's
  minor axis.
\item[{kernPA [0 | float | any]}] The position angle, in degrees,
  anticlockwise from vertical (\ie usually East of North).
\item[{smoothEdgeMethod [equal | string | equal/truncate/scale]}] What
  method to use for dealing with pixels on the edge of the spatial
  image (\ie within the width of the kernel). Can be one of
  \texttt{equal, truncate, scale}. See \S\ref{sec-smoothing} for
  details.
\item[{spatialSmoothCutoff [1.e-10 | float | $> 0.$]}] The cutoff
  value for determining the width of the smoothing kernel. See
  \S\ref{sec-smoothing} for details.
\end{Lentry}

\secC*{FDR method}
\begin{Lentry}
\item[{flagFDR [false | bool | true/false/1/0]}] A flag indicating whether or not to use
  the False Discovery Rate method in thresholding the pixels.
\item[{alphaFDR [0.01 | float | $0. - 1.$]}] The $\alpha$ parameter used in the FDR
  analysis. The average number of false detections, as a fraction of
  the total number, will be less than $\alpha$ (see
  \S\ref{sec-detection}).
\item[{FDRnumCorChan [2 | int | $> 0$]}] The number of neighbouring spectral
  channels that are assumed to be correlated. This is needed by the
  FDR algorithm to calculate the normalisation constant $c_N$ (see
  \S\ref{sec-detection}). 
\end{Lentry}

\secC*{Merging detections}
\begin{Lentry}
\item[{minPix [2 | int | $> 0$]}] The minimum number of spatial pixels for a
  single detection to be counted.
\item[{minChannels [3 | int | $> 0$]}] At least one contiguous set of this many
  channels must be present in the detection for it to be accepted.
\item[{minVoxels [minPix$+$minChannels$-$1 | int | $> 0$]}] The minimum size of
  the object, in terms of the total number of voxels, for it to be
  accepted. This will be \textit{at least} minPix$+$minChannels$-$1,
  but can be set higher.
\item[{maxPix [$-1$ | int | any]}] The maximum number of spatial pixels an object
  can have. No check is made if the value is negative.
\item[{maxChannels [-1 | int | any]}] The maximum number of channels an object can
  have. No check is made if the value is negative.
\item[{maxVoxels [$-1$ | int | any]}] The maximum size of
  the object, in terms of the total number of voxels, for it to be
  accepted. No check is made if the value is negative.
\item[{flagRejectBeforeMerge [false | bool | true/false/1/0]}] A flag
  indicating whether to reject sources that fail to meet the
  \texttt{minPix} or \texttt{minChannels} criteria \textbf{before} the
  merging stage. Default behaviour is to do the rejection last.
\item[{flagTwoStageMerging [true | bool | true/false/1/0]}] A flag
  indicating whether to do an initial merge of newly-detected sources
  into the source list as they are found. If \texttt{false}, new
  sources are simply added to the end of the list for later merging.
\item[{flagAdjacent [true | bool | true/false/1/0]}] A flag indicating
  whether to use the ``adjacent pixel'' criterion to decide whether to
  merge objects. If not, the next two parameters are used to determine
  whether objects are within the necessary thresholds.
\item[{threshSpatial [$3.$ | float | $\ge 0$]}] The maximum allowed
  minimum spatial separation (in pixels) between two detections for
  them to be merged into one. Only used if \texttt{flagAdjacent =
    false}.
\item[{threshVelocity [$7.$ | float | $\ge 0$]}] The maximum allowed
  minimum channel separation between two detections for them to be
  merged into one.
\end{Lentry}

\secC*{WCS parameters}
\begin{Lentry}
\item[{spectralType ["" | string | A valid WCS type]}] The user can
  specify an alternative WCS spectral type that the spectral axis can
  be expressed in. This specification should conform to the standards
  described in \citet{greisen06}, although it is possible to provide
  just the first four letters (the ``S-type'', \eg 'VELO').
\item[{restFrequency [-1 | float | any]}] If provided, this will be used in
  preference to the rest frequency given in the FITS header to
  calculate velocities and related quantities. A negative value (such
  as the default) will mean this is not used and the FITS header
  value, if present, is used instead.
\item[{spectralUnits ["" | string | A valid units string]}] The user
  can specify the units of the spectral axis, overriding those given
  in the FITS header. If the spectral type is being changed, these
  units should be appropriate for that quantity. If not provided, the
  FITS header information is used.
\end{Lentry}

\secC*{Other parameters}
\begin{Lentry}
\item[{spectralMethod [peak | string | peak/sum]}] This indicates
  which method is used to plot the output spectra: \texttt{peak} means
  plot the spectrum containing the detection's peak pixel;
  \texttt{sum} means sum the spectra of each detected spatial pixel,
  and correct for the beam size. Any other choice defaults to
  \texttt{peak}.
\item[{pixelCentre [centroid | string | centroid/peak/average]}] Which
  of the three ways of expressing the ``centre'' of a detection (see
  \S\ref{sec-results} for a description of the options) to use for the
  X, Y, \& Z columns in the output list. Alternatives are:
  \texttt{centroid, peak, average}.
\item[{sortingParam [vel | string | see text for options]}] The
  parameter on which to sort the output list of detected
  objects. Options are: xvalue, yvalue, zvalue, ra, dec, vel, w50,
  iflux, pflux (integrated and peak flux respectively), or snr. If the
  parameter begins with a '-' (\eg '-vel'), the order of the sort is
  reversed.
\item[{drawBorders [true | bool | true/false/1/0]}] A flag indicating whether to draw
  borders around the detected objects in the moment maps included in
  the output (see for example Fig.~\ref{fig-spect}).
\item[{drawBlankEdges [true | bool | true/false/1/0]}] A flag indicating whether to
  draw the dividing line between BLANK and non-BLANK pixels on the
  2D images (see for example Fig.~\ref{fig-moment}).
\item[{verbose [true | bool | true/false/1/0]}] A flag indicating whether to print the
  progress of any computationally intensive algorithms (\eg
  reconstruction, searching or merging algorithms) to the screen.
\end{Lentry}


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