[18] | 1 | \documentclass[12pt,a4paper]{article} |
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| 2 | |
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[101] | 3 | %%%%%% LINE SPACING %%%%%%%%%%%% |
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| 4 | \usepackage{setspace} |
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| 5 | \singlespacing |
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| 6 | %\onehalfspacing |
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| 7 | %\doublespacing |
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| 8 | |
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[18] | 9 | %Define a test for doing PDF format -- use different code below |
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| 10 | \newif\ifPDF |
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| 11 | \ifx\pdfoutput\undefined\PDFfalse |
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| 12 | \else\ifnum\pdfoutput > 0\PDFtrue |
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| 13 | \else\PDFfalse |
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| 14 | \fi |
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| 15 | \fi |
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| 16 | |
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[3] | 17 | \textwidth=161 mm |
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[71] | 18 | \textheight=245 mm |
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| 19 | \topmargin=-15 mm |
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[3] | 20 | \oddsidemargin=0 mm |
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| 21 | \parindent=6 mm |
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| 22 | |
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[18] | 23 | \usepackage[sort]{natbib} |
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| 24 | \usepackage{lscape} |
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| 25 | \bibpunct[,]{(}{)}{;}{a}{}{,} |
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| 26 | |
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[3] | 27 | \newcommand{\eg}{e.g.\ } |
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| 28 | \newcommand{\ie}{i.e.\ } |
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| 29 | \newcommand{\hi}{H{\sc i}} |
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| 30 | \newcommand{\hipass}{{\sc hipass}} |
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[101] | 31 | \newcommand{\duchamp}{\emph{Duchamp}} |
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| 32 | \newcommand{\atrous}{\textit{{\`a} trous}} |
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| 33 | \newcommand{\Atrous}{\textit{{\`A} trous}} |
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[3] | 34 | \newcommand{\diff}{{\rm d}} |
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| 35 | \newcommand{\entrylabel}[1]{\mbox{\textsf{\bf{#1:}}}\hfil} |
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| 36 | \newenvironment{entry} |
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| 37 | {\begin{list}{}% |
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| 38 | {\renewcommand{\makelabel}{\entrylabel}% |
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| 39 | \setlength{\labelwidth}{30mm}% |
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| 40 | \setlength{\labelsep}{5pt}% |
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| 41 | \setlength{\itemsep}{2pt}% |
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| 42 | \setlength{\parsep}{2pt}% |
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| 43 | \setlength{\leftmargin}{35mm}% |
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| 44 | }% |
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| 45 | }% |
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| 46 | {\end{list}} |
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| 47 | |
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[18] | 48 | |
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[101] | 49 | \title{A Guide to the \duchamp\ Source Finding Software} |
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[18] | 50 | \author{Matthew Whiting\\ |
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| 51 | %{\small \href{mailto:Matthew.Whiting@csiro.au}{Matthew.Whiting@csiro.au}}\\ |
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[15] | 52 | Australia Telescope National Facility\\CSIRO} |
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[3] | 53 | %\date{January 2006} |
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| 54 | \date{} |
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| 55 | |
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[18] | 56 | % If we are creating a PDF, use different options for graphicx, hyperref. |
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| 57 | \ifPDF |
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| 58 | \usepackage[pdftex]{graphicx,color} |
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| 59 | \usepackage[pdftex]{hyperref} |
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| 60 | \hypersetup{colorlinks=true,% |
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[80] | 61 | citecolor=red,% |
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| 62 | filecolor=red,% |
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| 63 | linkcolor=red,% |
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| 64 | urlcolor=red,% |
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| 65 | } |
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[18] | 66 | \else |
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| 67 | \usepackage[dvips]{graphicx} |
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| 68 | \usepackage[dvips]{hyperref} |
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| 69 | \fi |
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| 70 | |
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[80] | 71 | \pagestyle{headings} |
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[3] | 72 | \begin{document} |
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| 73 | |
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| 74 | \maketitle |
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[80] | 75 | \thispagestyle{empty} |
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| 76 | \begin{figure}[!h] |
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| 77 | \begin{center} |
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| 78 | \includegraphics[width=\textwidth]{cover_image} |
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| 79 | \end{center} |
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| 80 | \end{figure} |
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| 81 | |
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| 82 | \newpage |
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[3] | 83 | \tableofcontents |
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| 84 | |
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| 85 | \newpage |
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| 86 | \section{Introduction and getting going quickly} |
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| 87 | |
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[101] | 88 | This document gives details on the program \duchamp: how to use it and |
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| 89 | what it does. This has been designed to provide a source-detection |
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| 90 | facility for spectral-line data cubes. The basic execution of |
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| 91 | \duchamp\ is to read in a FITS data cube, find sources in the cube, |
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| 92 | and produce a text file of positions, velocities and fluxes of the |
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| 93 | detections, as well as a postscript file of the spectra of each |
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| 94 | detection. |
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[3] | 95 | |
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| 96 | So, you have a FITS cube, and you want to find the sources in it. What |
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| 97 | do you do? The first step is to make an input file that contains the |
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| 98 | list of parameters. Brief and detailed examples are shown in |
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| 99 | Appendix~\ref{app-input}. This provides the input file name, the various |
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| 100 | output files, and defines various parameters that control the |
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| 101 | execution. |
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| 102 | |
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[101] | 103 | The standard way to run \duchamp\ is by the command |
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[3] | 104 | \begin{quote} |
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[101] | 105 | \texttt{Duchamp -p [parameter file]} |
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[3] | 106 | \end{quote} |
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[101] | 107 | replacing \texttt{[parameter file]} with the name of the file you have |
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[85] | 108 | just created/copied. Alternatively, you can use the syntax |
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| 109 | \begin{quote} |
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[101] | 110 | \texttt{Duchamp -f [FITS file]} |
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[85] | 111 | \end{quote} |
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[101] | 112 | where \texttt{[FITS file]} is the file you wish to search. In the latter |
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| 113 | case, all parameters will take their default values detailed in |
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| 114 | Appendix~\ref{app-param}. In either case, the program will then work |
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| 115 | away and give you the list of detections and their spectra. The |
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| 116 | program execution is summarised below, and detailed in |
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[85] | 117 | \S\ref{sec-flow}. Information on inputs is in \S\ref{sec-param} and |
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| 118 | Appendix~\ref{app-param}, and descriptions of the output is in |
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| 119 | \S\ref{sec-output}. |
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[3] | 120 | |
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| 121 | \subsection{A summary of the execution steps} |
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| 122 | |
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[101] | 123 | The basic flow of the program is summarised here -- all steps are |
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| 124 | discussed in more detail in the following sections. |
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[3] | 125 | \begin{enumerate} |
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[101] | 126 | \item If the \texttt{-p} option is used, the parameter file given on |
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| 127 | the command line is read in, and the parameters absorbed. |
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| 128 | \item The FITS image is located and read in to memory. |
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[80] | 129 | \item If requested, a FITS image with a previously reconstructed array |
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| 130 | is read in. |
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[3] | 131 | \item If requested, blank pixels are trimmed from the edges, and |
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[101] | 132 | the baseline of each spectrum is removed. |
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[80] | 133 | \item If the reconstruction method is requested, and the reconstructed |
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| 134 | array has not been read in at Step 3 above, the cube is |
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[101] | 135 | reconstructed using the \atrous\ wavelet method. |
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[3] | 136 | \item Searching for objects then takes place, using the requested |
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| 137 | thresholding method. |
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[101] | 138 | \item The list of objects is condensed by merging neighbouring objects |
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[3] | 139 | and removing those deemed unacceptable. |
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| 140 | \item The baselines and trimmed pixels are replaced prior to output. |
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[96] | 141 | \item The details of the detections are written to screen and to the |
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[3] | 142 | requested output file. |
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| 143 | \item Maps showing the spatial location of the detections are written. |
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| 144 | \item The integrated spectra of each detection are written to a |
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| 145 | postscript file. |
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| 146 | \item If requested, the reconstructed array can be written to a new |
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| 147 | FITS file. |
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| 148 | \end{enumerate} |
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| 149 | |
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| 150 | \subsection{Guide to terminology} |
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| 151 | |
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[101] | 152 | First, a brief note on the use of terminology in this guide. \duchamp\ |
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[18] | 153 | is designed to work on FITS ``cubes''. These are FITS\footnote{FITS is |
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| 154 | the Flexible Image Transport System -- see \citet{hanisch01} or |
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| 155 | websites such as |
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| 156 | \href{http://fits.cv.nrao.edu/FITS.html}{http://fits.cv.nrao.edu/FITS.html} |
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| 157 | for details.} image arrays with three dimensions -- they are assumed |
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| 158 | to have the following form: the first two dimensions (referred to as |
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| 159 | $x$ and $y$) are spatial directions (that is, relating to the position |
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| 160 | on the sky), while the third dimension, $z$, is the spectral |
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[101] | 161 | direction, which can correspond to frequency, wavelength, or |
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| 162 | velocity. The three dimensional analogue of pixels are ``voxels'', or |
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| 163 | volume cells -- a voxel is defined by a unique $(x,y,z)$ location and |
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| 164 | has a unique flux or intensity value associated with it. |
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[3] | 165 | |
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| 166 | Each spatial pixel (a given $(x,y)$ coordinate) can be said to be a |
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| 167 | single spectrum, while a slice through the cube perpendicular to the |
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| 168 | spectral direction at a given $z$-value is a single channel (the 2-D |
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| 169 | image is a channel map). |
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| 170 | |
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[101] | 171 | Detection involves locating a contiguous group of voxels with fluxes |
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| 172 | above a certain threshold. \duchamp\ makes no assumptions as to the |
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| 173 | size or shape of the detected features, other than having |
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| 174 | user-selected minimum size criteria. |
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| 175 | |
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[60] | 176 | Features that are detected are assumed to be positive. The user can |
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| 177 | choose to search for negative features by setting an input parameter |
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| 178 | -- this inverts the cube prior to the search (see |
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[101] | 179 | \S\ref{sec-detection} for details). |
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[24] | 180 | |
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[101] | 181 | Note that it is possible to run \duchamp\ on a two-dimensional image |
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[18] | 182 | (\ie one with no frequency or velocity information), or indeed a |
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| 183 | one-dimensional array, and many of the features of the program will |
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| 184 | work fine. The focus, however, is on object detection in three |
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| 185 | dimensions. |
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| 186 | |
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[101] | 187 | \subsection{Why \duchamp?} |
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[15] | 188 | |
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[101] | 189 | Well, it's important for a program to have a name, and the initial |
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| 190 | working title of \emph{cubefind} was somewhat uninspiring. I wanted to |
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| 191 | avoid the classic astronomical approach of designing a cute acronym, |
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| 192 | and since it is designed to work on cubes, I looked at naming it after |
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| 193 | a cubist. \emph{Picasso}, sadly, was already taken \citep{minchin99}, |
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| 194 | so I settled on naming it after Marcel Duchamp, another cubist, but |
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| 195 | also one of the first artists to work with ``found objects''. |
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[15] | 196 | |
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[3] | 197 | \section{User Inputs} |
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| 198 | \label{sec-param} |
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| 199 | |
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[101] | 200 | Input to the program is provided by means of a parameter |
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| 201 | file. Parameters are listed in the file, followed by the value that |
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| 202 | should be assigned to them. The syntax used is \texttt{paramName |
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| 203 | value}. Parameter names are not case-sensitive, and lines in the input |
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| 204 | file that start with \texttt{\#} are ignored. If a parameter is listed |
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| 205 | more than once, the latter value is used, but otherwise the order in |
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| 206 | which the parameters are listed in the input file is arbitrary. |
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[3] | 207 | |
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| 208 | If a parameter is not listed, the default value is assumed. The |
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| 209 | defaults are chosen to provide a good result (using the reconstruction |
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[24] | 210 | method), so the user doesn't need to specify many new parameters in |
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[101] | 211 | the input file. Note that the image file \textbf{must} be specified! The |
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[24] | 212 | parameters that can be set are listed in Appendix~\ref{app-param}, |
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| 213 | with their default values in parentheses. |
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[3] | 214 | |
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[101] | 215 | The 'flag' parameters are stored as \texttt{bool} variables, and so are |
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| 216 | either \texttt{true = 1} or \texttt{false = 0}. \duchamp\ will only |
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| 217 | read them from the file as integers, and so they should be entered in |
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[3] | 218 | the file as 0 or 1 (see example file in Appendix~\ref{app-input}). |
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| 219 | |
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[101] | 220 | \section{What \duchamp\ is doing} |
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[3] | 221 | \label{sec-flow} |
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| 222 | |
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[101] | 223 | The execution flow of \duchamp\ is detailed here, indicating the |
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[3] | 224 | main algorithmic steps that are used. The program is written in C/C++ |
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| 225 | and makes use of the {\sc cfitsio}, {\sc wcslib} and {\sc pgplot} |
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| 226 | libraries. |
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| 227 | |
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| 228 | %\subsection{Parameter input} |
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| 229 | % |
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| 230 | %The user provides parameters that govern the selection of files and |
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| 231 | %the parameters used by the various subroutines in the program. This is |
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| 232 | %done via a parameter file, and the parameters are stored in a C++ |
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| 233 | %class for use throughout the program. The form of the parameter file is |
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| 234 | %discussed in \S\ref{sec-param}, and the parameters themselves are |
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| 235 | %listed in Appendix~\ref{app-param}. |
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| 236 | |
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| 237 | \subsection{Image input} |
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| 238 | |
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| 239 | The cube is read in using basic {\sc cfitsio} commands, and stored as |
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[101] | 240 | an array in a special C++ class. This class keeps track of |
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[3] | 241 | the list of detected objects, as well as any reconstructed arrays that |
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[18] | 242 | are made (see \S\ref{sec-recon}). The World Coordinate System (WCS) |
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| 243 | information for the cube is also obtained from the FITS header by {\sc |
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| 244 | wcslib} functions \citep{greisen02, calabretta02}, and this |
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[101] | 245 | information, in the form of a \texttt{wcsprm} structure, is also stored |
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[18] | 246 | in the same class. |
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[3] | 247 | |
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[101] | 248 | A sub-section of an image can be requested via the \texttt{subsection} |
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[80] | 249 | parameter in the parameter file -- this can be a good idea if the cube |
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| 250 | has very noisy edges, which may produce many spurious detections. The |
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| 251 | generalised form of the subsection that is used by {\sc cfitsio} is |
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[101] | 252 | \texttt{[x1:x2:dx,y1:y2:dy,z1:z2:dz]}, such that the x-coordinates run |
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| 253 | from \texttt{x1} to \texttt{x2} (inclusive), with steps of |
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| 254 | \texttt{dx}. The step value can be omitted (so a subsection of the |
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| 255 | form \texttt{[2:50,2:50,10:1000]} is still valid). \duchamp\ does not |
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| 256 | at this stage deal with the presence of steps in the subsection |
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| 257 | string, and any that are present are removed before the file is |
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| 258 | opened. |
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[3] | 259 | |
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[80] | 260 | If one wants the full range of a coordinate then replace the range |
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[101] | 261 | with an asterisk, \eg \texttt{[2:50,2:50,*]}. If one wants to use a |
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| 262 | subsection, one must set \texttt{flagSubsection = 1}. A complete |
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[3] | 263 | description of the section syntax can be found at the {\sc fitsio} web |
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| 264 | site |
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[15] | 265 | \footnote{ |
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| 266 | \href{http://heasarc.gsfc.nasa.gov/docs/software/fitsio/c/c\_user/node90.html}% |
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| 267 | {http://heasarc.gsfc.nasa.gov/docs/software/fitsio/c/c\_user/node90.html}}. |
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[3] | 268 | |
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| 269 | \subsection{Image modification} |
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| 270 | \label{sec-modify} |
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| 271 | |
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| 272 | Several modifications to the cube can be made that improve the |
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[101] | 273 | execution and efficiency of \duchamp\ (these are optional -- their |
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[3] | 274 | use is indicated by the relevant flags set in the input parameter |
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| 275 | file). |
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| 276 | |
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| 277 | \subsubsection{Blank pixel removal} |
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| 278 | |
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[96] | 279 | First, the cube is trimmed of any BLANK pixels that pad the image out |
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| 280 | to a rectangular shape. This is optional, its use determined by the |
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[101] | 281 | \texttt{flagBlankPix} parameter. The value for these pixels is read from |
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[3] | 282 | the FITS header (using the BLANK, BSCALE and BZERO keywords), but if |
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| 283 | these are not present then the value can be specified by the user in |
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[101] | 284 | the parameter file using \texttt{blankPixValue}. |
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[3] | 285 | |
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| 286 | This stage is particularly important for the reconstruction step, as |
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| 287 | lots of BLANK pixels on the edges will smooth out features in the |
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| 288 | wavelet calculation stage. The trimming will also reduce the size of |
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| 289 | the cube's array, speeding up the execution. The amount of trimming is |
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| 290 | recorded, and these pixels are added back in once the source-detection |
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| 291 | is completed (so that quoted pixel positions are applicable to the |
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| 292 | original cube). |
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| 293 | |
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| 294 | Rows and columns are trimmed one at a time until the first non-BLANK |
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| 295 | pixel is reached, so that the image remains rectangular. In practice, |
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| 296 | this means that there will be BLANK pixels left in the trimmed image |
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| 297 | (if the non-BLANK region is non-rectangular). However, these are |
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| 298 | ignored in all further calculations done on the cube. |
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| 299 | |
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| 300 | \subsubsection{Baseline removal} |
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| 301 | |
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[96] | 302 | Second, the user may request the removal of baselines from the |
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[101] | 303 | spectra, via the parameter \texttt{flagBaseline}. This may be necessary |
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[3] | 304 | if there is a strong baseline ripple present, which can result in |
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| 305 | spurious detections on the high points of the ripple. The baseline is |
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| 306 | calculated from a wavelet reconstruction procedure (see |
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| 307 | \S\ref{sec-recon}) that keeps only the two largest scales. This is |
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| 308 | done separately for each spatial pixel (\ie for each spectrum in the |
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| 309 | cube), and the baselines are stored and added back in before any |
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| 310 | output is done. In this way the quoted fluxes and displayed spectra |
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[24] | 311 | are as one would see from the input cube itself -- even though the |
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| 312 | detection (and reconstruction if applicable) is done on the |
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| 313 | baseline-removed cube. |
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[3] | 314 | |
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[43] | 315 | The presence of very strong signals (for instance, masers at several |
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| 316 | hundred Jy) can affect the determination of the baseline, leading to a |
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| 317 | large dip centred on the signal in the baseline-subtracted |
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| 318 | spectrum. To prevent this, the signal is trimmed prior to the |
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[80] | 319 | reconstruction process at some standard threshold (at $8\sigma$ above |
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| 320 | the mean). The baseline determined should thus be representative of |
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| 321 | the true, signal-free baseline. Note that this trimming is only a |
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[43] | 322 | temporary measure which does not affect the source-detection. |
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| 323 | |
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[101] | 324 | \subsubsection{Ignoring bright Milky Way emission} |
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[96] | 325 | |
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| 326 | Also, a single set of contiguous channels can be ignored -- these may |
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| 327 | exhibit very strong emission, such as that from the Milky Way as seen |
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| 328 | in extragalactic \hi\ cubes (hence the references to ``Milky Way'' in |
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| 329 | relation to this task -- apologies to Galactic astronomers!). Such |
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| 330 | dominant channels will both produce many unnecessary, uninteresting |
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| 331 | and large (in size and hence in memory usage) detections, and so will |
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| 332 | slow the program down and detract from the interesting detections. The |
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[101] | 333 | use of this feature is controlled by the \texttt{flagMW} parameter, and |
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[96] | 334 | the exact channels concerned are able to be set by the user (using |
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[101] | 335 | \texttt{maxMW} and \texttt{minMW} -- these give an inclusive range of |
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| 336 | channels). When employed, these channels are temporarily blanked out |
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| 337 | for the searching, and the scaling of the spectral output (see |
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| 338 | Fig.~\ref{fig-spect}) will not take them into account. They will be |
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| 339 | present in the reconstructed array, however, and so will be included |
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| 340 | in the saved FITS file (see \S\ref{sec-reconIO}). When the final |
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| 341 | spectra are plotted, the range of channels covered by these parameters |
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| 342 | is indicated by a green hashed box. |
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[96] | 343 | |
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[3] | 344 | \subsection{Image reconstruction} |
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| 345 | \label{sec-recon} |
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| 346 | |
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[88] | 347 | This is an optional step, but one that greatly enhances the |
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[101] | 348 | source-detection process. The user can direct \duchamp\ to reconstruct |
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| 349 | the data cube using the \atrous\ wavelet procedure. A good |
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[88] | 350 | description of the procedure can be found in |
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| 351 | \citet{starck02:book}. The reconstruction is an effective way of |
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| 352 | removing a lot of the noise in the image, allowing one to search |
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| 353 | reliably to fainter levels, and reducing the number of spurious |
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| 354 | detections. The payoff is that it can be relatively time- and |
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[96] | 355 | memory-intensive. |
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| 356 | |
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| 357 | \subsubsection{Algorithm} |
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| 358 | |
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[101] | 359 | The steps in the \atrous\ reconstruction are as follows: |
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[3] | 360 | \begin{enumerate} |
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| 361 | \item Set the reconstructed array to 0 everywhere. |
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[96] | 362 | \item The input array is discretely convolved with a given filter |
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[101] | 363 | function. This is determined from the parameter file via the |
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| 364 | \texttt{filterCode} parameter -- see Appendix~\ref{app-param} for |
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| 365 | details on the filters available. |
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[3] | 366 | \item The wavelet coefficients are calculated by taking the difference |
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| 367 | between the convolved array and the input array. |
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| 368 | \item If the wavelet coefficients at a given point are above the |
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[101] | 369 | requested threshold (given by \texttt{snrRecon} as the number of |
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| 370 | $\sigma$ above the mean and adjusted to the current scale -- see |
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| 371 | Appendix~\ref{app-scaling}), add these to the reconstructed array. |
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[3] | 372 | \item The separation of the filter coefficients is doubled. |
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| 373 | \item The procedure is repeated from step 2, using the convolved array |
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| 374 | as the input array. |
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| 375 | \item Continue until the required maximum number of scales is reached. |
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[24] | 376 | \item Add the final smoothed (\ie convolved) array to the |
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| 377 | reconstructed array. This provides the ``DC offset'', as each of the |
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| 378 | wavelet coefficient arrays will have zero mean. |
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[3] | 379 | \end{enumerate} |
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| 380 | |
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[96] | 381 | The reconstruction has at least two iterations. The first iteration |
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| 382 | makes a first pass at the wavelet reconstruction (the process outlined |
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| 383 | in the 8 stages above), but the residual array will inevitably have |
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| 384 | some structure still in it, so the wavelet filtering is done on the |
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| 385 | residual, and any significant wavelet terms are added to the final |
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| 386 | reconstruction. This step is repeated until the change in the $\sigma$ |
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| 387 | of the background is less than some fiducial amount. |
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| 388 | |
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[101] | 389 | It is important to note that the \atrous\ decomposition is an |
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[96] | 390 | example of a ``redundant'' transformation. If no thresholding is |
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| 391 | performed, the sum of all the wavelet coefficient arrays and the final |
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| 392 | smoothed array is identical to the input array. The thresholding thus |
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| 393 | removes only the unwanted structure in the array. |
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| 394 | |
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[71] | 395 | Note that any BLANK pixels that are still in the cube will not be |
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| 396 | altered by the reconstruction -- they will be left as BLANK so that |
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| 397 | the shape of the valid part of the cube is preserved. |
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| 398 | |
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[96] | 399 | \subsubsection{Statistics} |
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[3] | 400 | |
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[96] | 401 | The correct calculation of the reconstructed array needs good |
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| 402 | estimation of the underlying mean and standard deviation of the |
---|
| 403 | background noise distribution. These statistics are estimated using |
---|
| 404 | robust methods, to avoid corruption by strong outlying points. The |
---|
[101] | 405 | mean of the distribution is actually estimated by the median, while |
---|
| 406 | the median absolute deviation from the median (MADFM) is calculated |
---|
| 407 | and corrected assuming Gaussianity to estimate the underlying standard |
---|
| 408 | deviation $\sigma$. The Gaussianity (or Normality) assumption is |
---|
| 409 | critical, as the MADFM does not give the same value as the usual rms |
---|
| 410 | or standard deviation value -- for a normal distribution |
---|
| 411 | $N(\mu,\sigma)$ we find MADFM$=0.6744888\sigma$. The difference |
---|
| 412 | between the MADFM and $\sigma$ is corrected for, so the user need only |
---|
| 413 | think in the usual multiples of $\sigma$ when setting |
---|
| 414 | \texttt{snrRecon}. See Appendix~\ref{app-madfm} for a derivation of |
---|
| 415 | this value. |
---|
[3] | 416 | |
---|
| 417 | When thresholding the different wavelet scales, the value of $\sigma$ |
---|
[101] | 418 | as measured from the wavelet array needs to be scaled to account for the |
---|
[3] | 419 | increased amount of correlation between neighbouring pixels (due to |
---|
[80] | 420 | the convolution). See Appendix~\ref{app-scaling} for details on this |
---|
[24] | 421 | scaling. |
---|
[3] | 422 | |
---|
[101] | 423 | \subsubsection{User control of reconstruction parameters} |
---|
[96] | 424 | |
---|
| 425 | The most important parameter for the user to select in relation to the |
---|
| 426 | reconstruction is the threshold for each wavelet array. This is set |
---|
[101] | 427 | using the \texttt{snrRecon} parameter, and is given as a multiple of the |
---|
[96] | 428 | rms (estimated by the MADFM) above the mean (which for the wavelet |
---|
| 429 | arrays should be approximately zero). There are several other |
---|
| 430 | parameters that can be altered as well that affect the outcome of the |
---|
| 431 | reconstruction. |
---|
| 432 | |
---|
| 433 | By default, the cube is reconstructed in three dimensions, using a |
---|
| 434 | 3-dimensional filter and 3-dimensional convolution. This can be |
---|
[101] | 435 | altered, however, using the parameter \texttt{reconDim}. If set to 1, |
---|
[96] | 436 | this means the cube is reconstructed by considering each spectrum |
---|
[101] | 437 | separately, whereas \texttt{reconDim=2} will mean the cube is |
---|
[96] | 438 | reconstructed by doing each channel map separately. The merits of |
---|
[101] | 439 | these choices are discussed in \S\ref{sec-notes}, but it should be |
---|
[96] | 440 | noted that a 2-dimensional reconstruction can be susceptible to edge |
---|
| 441 | effects if the spatial shape is not rectangular. |
---|
| 442 | |
---|
[3] | 443 | The user can also select the minimum scale to be used in the |
---|
| 444 | reconstruction -- the first scale exhibits the highest frequency |
---|
| 445 | variations, and so ignoring this one can sometimes be beneficial in |
---|
| 446 | removing excess noise. The default, however, is to use all scales |
---|
[101] | 447 | (\texttt{minscale = 1}). |
---|
[3] | 448 | |
---|
[96] | 449 | Finally, the filter that is used for the convolution can be selected |
---|
[101] | 450 | by using \texttt{filterCode} and the relevant code number -- the choices |
---|
[96] | 451 | are listed in Appendix~\ref{app-param}. When multi-dimensional |
---|
| 452 | reconstruction is selected, this filter is used to construct a 2- or |
---|
| 453 | 3-dimensional equivalent. |
---|
[3] | 454 | |
---|
[80] | 455 | \subsection{Reconstruction I/O} |
---|
[96] | 456 | \label{sec-reconIO} |
---|
[80] | 457 | |
---|
[101] | 458 | The reconstruction stage can be relatively time-consuming, particularly |
---|
| 459 | for large cubes and reconstructions in 3-D. To get around this, \duchamp\ |
---|
| 460 | provides a shortcut to allow users to perform multiple searches (\eg with |
---|
| 461 | different thresholds) on the same reconstruction without calculating the |
---|
| 462 | reconstruction each time. |
---|
[80] | 463 | |
---|
[101] | 464 | The first step is to choose to save the reconstructed array as a FITS |
---|
| 465 | file by setting \texttt{flagOutputRecon = true}. The file will be saved |
---|
| 466 | in the same directory as the input image, so the user needs to have write |
---|
| 467 | permissions for that directory. |
---|
[3] | 468 | |
---|
[101] | 469 | The filename will be derived from the input filename, with extra information |
---|
| 470 | detailing the reconstruction that has been done. For example, suppose |
---|
| 471 | \texttt{image.fits} has been reconstructed using a 3-dimensional |
---|
| 472 | reconstruction with filter 2, thresholded at $4\sigma$ using all scales. The |
---|
| 473 | output filename will then be \texttt{image.RECON-3-2-4-1.fits} (\ie it uses |
---|
| 474 | the four parameters relevant for the \atrous\ reconstruction as listed in |
---|
| 475 | Appendix~\ref{app-param}). The new FITS file will also have these |
---|
| 476 | parameters as header keywords. |
---|
[3] | 477 | |
---|
[101] | 478 | Likewise, the residual image, defined as the difference between the input |
---|
| 479 | and reconstructed arrays, can also be saved in the same manner by setting |
---|
| 480 | \texttt{flagOutputResid = true}. Its filename will be the same as above, |
---|
| 481 | with RESID replacing RECON. |
---|
| 482 | |
---|
[80] | 483 | If a reconstructed image has been saved, it can be read in and used |
---|
| 484 | instead of redoing the reconstruction. To do so, the user should set |
---|
[101] | 485 | \texttt{flagReconExists = true}. The user can indicate the name of the |
---|
| 486 | reconstructed FITS file using the \texttt{reconFile} parameter, or, if |
---|
| 487 | this is not specified, \duchamp\ searches for the file with the name |
---|
| 488 | as defined above. If the file is not found, the reconstruction is |
---|
| 489 | performed as normal. Note that to do this, the user needs to set |
---|
| 490 | \texttt{flagAtrous = true} (obviously, if this is \texttt{false}, the |
---|
| 491 | reconstruction is not needed). |
---|
[71] | 492 | |
---|
[3] | 493 | \subsection{Searching the image} |
---|
| 494 | \label{sec-detection} |
---|
| 495 | |
---|
[24] | 496 | The image is searched for detections in two ways: spectrally (a |
---|
| 497 | 1-dimensional search in the spectrum in each spatial pixel), and |
---|
| 498 | spatially (a 2-dimensional search in the spatial image in each |
---|
| 499 | channel). In both cases, the algorithm finds connected pixels that are |
---|
| 500 | above the user-specified threshold. In the case of the spatial image |
---|
| 501 | search, the algorithm of \citet{lutz80} is used to raster scan through |
---|
| 502 | the image and connect groups of pixels on neighbouring rows. |
---|
[3] | 503 | |
---|
| 504 | Note that this algorithm cannot be applied directly to a 3-dimensional |
---|
| 505 | case, as it requires that objects are completely nested in a row: that |
---|
| 506 | is, if you are scanning along a row, and one object finishes and |
---|
| 507 | another starts, you know that you will not get back to the first one |
---|
[101] | 508 | (if at all) until the second is completely finished for that |
---|
[3] | 509 | row. Three-dimensional data does not have this property, which is why |
---|
| 510 | we break up the searching into 1- and 2-dimensional cases. |
---|
| 511 | |
---|
| 512 | The determination of the threshold is done in one of two ways. The |
---|
[101] | 513 | first way is a simple sigma-clipping, where a threshold is set at a |
---|
| 514 | fixed number $n$ of standard deviations above the mean, and pixels |
---|
| 515 | above this threshold are flagged as detected. The value of $n$ is set |
---|
| 516 | with the parameter \texttt{snrCut}. As before, the value of the |
---|
| 517 | standard deviation is estimated by the MADFM, and corrected by the |
---|
| 518 | ratio derived in Appendix~\ref{app-madfm}. |
---|
[3] | 519 | |
---|
| 520 | The second method uses the False Discovery Rate (FDR) technique |
---|
| 521 | \citep{miller01,hopkins02}, whose basis we briefly detail here. The |
---|
| 522 | false discovery rate (given by the number of false detections divided |
---|
| 523 | by the total number of detections) is fixed at a certain value |
---|
| 524 | $\alpha$ (\eg $\alpha=0.05$ implies 5\% of detections are false |
---|
| 525 | positives). In practice, an $\alpha$ value is chosen, and the ensemble |
---|
[101] | 526 | average FDR (\ie $\langle FDR \rangle$) when the method is used will |
---|
| 527 | be less than $\alpha$. One calculates $p$ -- the probability, |
---|
| 528 | assuming the null hypothesis is true, of obtaining a test statistic as |
---|
| 529 | extreme as the pixel value (the observed test statistic) -- for each |
---|
| 530 | pixel, and sorts them in increasing order. One then calculates $d$ |
---|
| 531 | where |
---|
[3] | 532 | \[ |
---|
[18] | 533 | d = \max_j \left\{ j : P_j < \frac{j\alpha}{c_N N} \right\}, |
---|
[3] | 534 | \] |
---|
[18] | 535 | and then rejects all hypotheses whose $p$-values are less than or equal |
---|
[3] | 536 | to $P_d$. (So a $P_i<P_d$ will be rejected even if $P_i \geq |
---|
| 537 | j\alpha/c_N N$.) Note that ``reject hypothesis'' here means ``accept |
---|
| 538 | the pixel as an object pixel'' (\ie we are rejecting the null |
---|
| 539 | hypothesis that the pixel belongs to the background). |
---|
| 540 | |
---|
| 541 | The $c_N$ values here are normalisation constants that depend on the |
---|
| 542 | correlated nature of the pixel values. If all the pixels are |
---|
| 543 | uncorrelated, then $c_N=1$. If $N$ pixels are correlated, then their |
---|
| 544 | tests will be dependent on each other, and so $c_N = \sum_{i=1}^N |
---|
| 545 | i^{-1}$. \citet{hopkins02} consider real radio data, where the pixels |
---|
| 546 | are correlated over the beam. In this case the sum is made over the |
---|
| 547 | $N$ pixels that make up the beam. The value of $N$ is calculated from |
---|
[24] | 548 | the FITS header (if the correct keywords -- BMAJ, BMIN -- are not |
---|
| 549 | present, a default value of 10 pixels is assumed). |
---|
[3] | 550 | |
---|
[101] | 551 | The theory behind the FDR method implies a direct connection between the |
---|
| 552 | choice of $\alpha$ and the fraction of detections that will be false |
---|
| 553 | positives. However, due to the merging process, this direct connection is |
---|
| 554 | lost when looking at the final number of detections -- see discussion in |
---|
| 555 | \S\ref{sec-notes}. The effect is that the number of false detections will |
---|
| 556 | be less than indicated by the $\alpha$ value used. |
---|
| 557 | |
---|
[3] | 558 | If a reconstruction has been made, the residuals (defined as original |
---|
| 559 | $-$ reconstruction) are used to estimate the noise parameters of the |
---|
| 560 | cube. Otherwise they are estimated directly from the cube itself. In |
---|
[101] | 561 | both cases, robust estimators are used as described above. |
---|
[3] | 562 | |
---|
[24] | 563 | Detections must have a minimum number of pixels to be counted. This |
---|
[101] | 564 | minimum number is given by the input parameters \texttt{minPix} (for |
---|
| 565 | 2-dimensional searches) and \texttt{minChannels} (for 1-dimensional |
---|
[60] | 566 | searches). |
---|
[24] | 567 | |
---|
[60] | 568 | The search only looks for positive features. If one is interested |
---|
| 569 | instead in negative features (such as absorption lines), set the |
---|
[101] | 570 | parameter \texttt{flagNegative = true}. This will invert the cube (\ie |
---|
[80] | 571 | multiply all pixels by $-1$) prior to the search, and then re-invert |
---|
| 572 | the cube (and the fluxes of any detections) after searching is |
---|
| 573 | complete. All outputs are done in the same manner as normal, so that |
---|
| 574 | fluxes of detections will be negative. |
---|
[60] | 575 | |
---|
[3] | 576 | \subsection{Merging detected objects} |
---|
| 577 | \label{sec-merger} |
---|
| 578 | |
---|
[101] | 579 | The searching step produces a list of detected objects that will have many |
---|
[3] | 580 | repeated detections of a given object -- for instance, spectral |
---|
[18] | 581 | detections in adjacent pixels of the same object and/or spatial |
---|
| 582 | detections in neighbouring channels. These are then combined in an |
---|
| 583 | algorithm that matches all objects judged to be ``close''. This |
---|
| 584 | determination is made in one of two ways. |
---|
[3] | 585 | |
---|
| 586 | One way is to define two thresholds -- one spatial and one in velocity |
---|
| 587 | -- and say that two objects should be merged if there is at least one |
---|
| 588 | pair of pixels that lie within these threshold distances of each |
---|
[101] | 589 | other. These thresholds are specified by the parameters |
---|
| 590 | \texttt{threshSpatial} and \texttt{threshVelocity} (in units of pixels |
---|
| 591 | and channels respectively). |
---|
[3] | 592 | |
---|
| 593 | Alternatively, the spatial requirement can be changed to say that |
---|
[101] | 594 | there must be a pair of pixels that are \emph{adjacent} -- a stricter, |
---|
| 595 | but perhaps more realistic requirement, particularly when the spatial pixels |
---|
[3] | 596 | have a large angular size (as is the case for \hi\ surveys). This |
---|
| 597 | method can be selected by setting the parameter |
---|
[101] | 598 | \texttt{flagAdjacent} to 1 (\ie \texttt{true}) in the parameter file. The |
---|
[3] | 599 | velocity thresholding is done in the same way as the first option. |
---|
| 600 | |
---|
[18] | 601 | Once the detections have been merged, they may be ``grown''. This is a |
---|
| 602 | process of increasing the size of the detection by adding adjacent |
---|
| 603 | pixels that are above some secondary threshold. This threshold is |
---|
| 604 | lower than the one used for the initial detection, but above the noise |
---|
| 605 | level, so that faint pixels are only detected when they are close to a |
---|
| 606 | bright pixel. The value of this threshold is a possible input |
---|
[101] | 607 | parameter (\texttt{growthCut}), with a default value of $1.5\sigma$. The |
---|
| 608 | use of the growth algorithm is controlled by the \texttt{flagGrowth} |
---|
| 609 | parameter -- the default value of which is \texttt{false}. If the |
---|
[18] | 610 | detections are grown, they are sent through the merging algorithm a |
---|
[24] | 611 | second time, to pick up any detections that now overlap or have grown |
---|
[18] | 612 | over each other. |
---|
[3] | 613 | |
---|
[101] | 614 | Finally, to be accepted, the detections must span \emph{both} a minimum |
---|
[18] | 615 | number of channels (to remove any spurious single-channel spikes that |
---|
[24] | 616 | may be present), and a minimum number of spatial pixels. These |
---|
[101] | 617 | numbers, as for the original detection step, are set with the |
---|
| 618 | \texttt{minChannels} and \texttt{minPix} parameters. The channel |
---|
| 619 | requirement means there must be at least one set of \texttt{minChannels} |
---|
| 620 | consecutive channels in the source for it to be accepted. |
---|
[18] | 621 | |
---|
[3] | 622 | \section{Outputs} |
---|
| 623 | \label{sec-output} |
---|
| 624 | |
---|
| 625 | \subsection{During execution} |
---|
| 626 | |
---|
[101] | 627 | \duchamp\ provides the user with feedback whilst it is running, to |
---|
[3] | 628 | keep the user informed on the progress of the analysis. Most of this |
---|
| 629 | consists of self-explanatory messages about the particular stage the |
---|
| 630 | program is up to. The relevant parameters are printed to the screen at |
---|
| 631 | the start (once the file has been successfully read in), so the user |
---|
[101] | 632 | is able to make a quick check that the setup is correct (see |
---|
| 633 | Appendix~{app-input} for an example). |
---|
[3] | 634 | |
---|
| 635 | If the cube is being trimmed (\S\ref{sec-modify}), the resulting |
---|
| 636 | dimensions are printed to indicate how much has been trimmed. If a |
---|
[96] | 637 | reconstruction is being done, a continually updating message shows |
---|
| 638 | either the current iteration and scale, compared to the maximum scale |
---|
[101] | 639 | (when \texttt{reconDim=3}), or a progress bar showing the amount of |
---|
| 640 | the cube that has been reconstructed (for smaller values of |
---|
| 641 | \texttt{reconDim}). |
---|
[3] | 642 | |
---|
| 643 | During the searching algorithms, the progress through the 1D and 2D |
---|
| 644 | searches are shown. When the searches have completed, |
---|
| 645 | the number of objects found in both the 1D and 2D searches are |
---|
| 646 | reported (see \S\ref{sec-detection} for details). |
---|
| 647 | |
---|
| 648 | In the merging process (where multiple detections of the same object |
---|
| 649 | are combined -- see \S\ref{sec-merger}), two stages of output |
---|
| 650 | occur. The first is when each object in the list is compared with all |
---|
| 651 | others. The output shows two numbers: the first being how far through |
---|
[101] | 652 | the list the current object is, and the second being the length of the |
---|
| 653 | list. As the algorithm proceeds, the first number should increase and |
---|
| 654 | the second should decrease (as objects are combined). When the numbers |
---|
| 655 | meet (\ie the whole list has been compared), the second phase begins, |
---|
| 656 | in which multiply-appearing pixels in each object are removed, as are |
---|
| 657 | objects not meeting the minimum channels requirement. During this |
---|
| 658 | phase, the total number of accepted objects is shown, which should |
---|
| 659 | steadily increase until all have been accepted or rejected. Note that |
---|
| 660 | these steps can be very quick for small numbers of detections. |
---|
[3] | 661 | |
---|
| 662 | Since this continual printing to screen has some overhead of time and |
---|
| 663 | CPU involved, the user can elect to not print this information by |
---|
[101] | 664 | setting the parameter \texttt{verbose = 0}. In this case, the user is |
---|
[3] | 665 | still informed as to the steps being undertaken, but the details of |
---|
| 666 | the progress are not shown. |
---|
| 667 | |
---|
| 668 | \subsection{Results} |
---|
| 669 | |
---|
[92] | 670 | \subsubsection{Table of Results} |
---|
| 671 | |
---|
[101] | 672 | Finally, we get to the results -- the reason for running \duchamp\ in |
---|
[18] | 673 | the first place. Once the detection list is finalised, it is sorted by |
---|
[80] | 674 | the mean velocity of the detections (or, if there is no good WCS |
---|
| 675 | associated with the cube, by the mean Z-pixel position). The results |
---|
[101] | 676 | are then printed to the screen and to the output file, given by the |
---|
| 677 | \texttt{OutFile} parameter. The results list, an example of which can be |
---|
[80] | 678 | seen in Appendix~\ref{app-output}, contains the following columns |
---|
| 679 | (note that the title of the columns depending on WCS information will |
---|
| 680 | depend on the projection of the WCS): |
---|
[15] | 681 | |
---|
[3] | 682 | \begin{entry} |
---|
| 683 | \item[Obj\#] The ID number of the detection (simply the sequential |
---|
| 684 | count for the list, which is ordered by increasing velocity). |
---|
[101] | 685 | \item[Name] The IAU-format name of the detection (derived from the WCS |
---|
[80] | 686 | projection). |
---|
[3] | 687 | \item[X] The average X-pixel position. |
---|
| 688 | \item[Y] The average Y-pixel position. |
---|
| 689 | \item[Z] The average Z-pixel position. |
---|
[80] | 690 | \item[RA/GLON] The Right Ascension or Galactic Longitude of the centre |
---|
| 691 | of the object. |
---|
| 692 | \item[DEC/GLAT] The Declination or Galactic Latitude of the centre of |
---|
| 693 | the object. |
---|
[101] | 694 | \item[VEL] The mean velocity of the object [units given by the |
---|
| 695 | \texttt{spectralUnits} parameter]. |
---|
[85] | 696 | \item[w\_RA/w\_GLON] The width of the object in Right Ascension or |
---|
| 697 | Galactic Longitude [arcmin]. |
---|
[80] | 698 | \item[w\_DEC/w\_GLAT] The width of the object in Declination Galactic |
---|
| 699 | Latitude [arcmin]. |
---|
[3] | 700 | \item[w\_VEL] The full velocity width of the detection (max channel |
---|
[92] | 701 | $-$ min channel, in velocity units [see note below]). |
---|
[96] | 702 | \item[F\_int] The integrated flux over the object, in the units of |
---|
[101] | 703 | flux times velocity, corrected for the beam if necessary. |
---|
[87] | 704 | \item[F\_peak] The peak flux over the object, in the units of flux. |
---|
[3] | 705 | \item[X1, X2] The minimum and maximum X-pixel coordinates. |
---|
| 706 | \item[Y1, Y2] The minimum and maximum Y-pixel coordinates. |
---|
| 707 | \item[Z1, Z2] The minimum and maximum Z-pixel coordinates. |
---|
[96] | 708 | \item[Npix] The number of voxels (\ie distinct $(x,y,z)$ coordinates) |
---|
| 709 | in the detection. |
---|
[87] | 710 | \item[Flag] Whether the detection has any warning flags (see below). |
---|
[3] | 711 | \end{entry} |
---|
[101] | 712 | The Name is derived from the WCS position. For instance, a source |
---|
| 713 | centred on the RA,Dec position 12$^h$53$^m$45$^s$, |
---|
| 714 | -36$^\circ$24$'$12$''$ will be called J1253$-$3624 (if the epoch is |
---|
| 715 | J2000) or B1253$-$3624 (if B1950). An alternative form is used for |
---|
| 716 | Galactic coordinates: a source centred on the position ($l$,$b$) = |
---|
| 717 | (323.1245, 5.4567) will be called G323.12$+$05.45. If the WCS is not |
---|
| 718 | valid (\ie is not present or does not have all the necessary |
---|
| 719 | information), the Name, RA, DEC, VEL and related columns are not |
---|
| 720 | printed, but the pixel coordinates are still provided. |
---|
[3] | 721 | |
---|
[92] | 722 | The velocity units can be specified by the user, using the parameter |
---|
[101] | 723 | \texttt{spectralUnits} (enter it as a single string). The default value |
---|
[92] | 724 | is km/s, which should be suitable for most users. These units are also |
---|
| 725 | used to give the units of integrated flux. |
---|
| 726 | |
---|
[87] | 727 | The last column contains any warning flags about the detection. There |
---|
| 728 | are currently two options here. An `E' is printed if the detection is |
---|
| 729 | next to the edge of the image, meaning either the limit of the pixels, |
---|
| 730 | or the limit of the non-BLANK pixel region. An `N' is printed if the |
---|
| 731 | total flux, summed over all the (non-BLANK) pixels in the smallest box |
---|
| 732 | that completely encloses the detection, is negative. Note that this |
---|
[101] | 733 | sum is likely to include non-detected pixels. It is of use in |
---|
[87] | 734 | pointing out detections that lie next to strongly negative pixels, |
---|
| 735 | such as might arise due to interference -- the detected pixels might |
---|
| 736 | then also be due to the interference, so caution is advised. |
---|
| 737 | |
---|
[92] | 738 | \subsubsection{Other results lists} |
---|
| 739 | |
---|
[21] | 740 | Two alternative results files can also be requested. One option is a |
---|
| 741 | VOTable-format XML file, containing just the RA, Dec, Velocity and the |
---|
| 742 | corresponding widths of the detections, as well as the fluxes. The |
---|
[101] | 743 | user should set \texttt{flagVOT = 1}, and put the desired filename in the |
---|
| 744 | parameter \texttt{votFile} -- note that the default is for it not to be |
---|
[21] | 745 | produced. This file should be compatible with all Virtual Observatory |
---|
| 746 | tools (such as Aladin\footnote{ Aladin can be found on the web at |
---|
| 747 | \href{http://aladin.u-strasbg.fr/}{http://aladin.u-strasbg.fr/}}). The |
---|
| 748 | second option is an annotation file for use with the Karma toolkit of |
---|
[101] | 749 | visualisation tools (in particular, with \texttt{kvis}). This will draw a |
---|
[21] | 750 | circle at the position of each detection, and number it according to |
---|
[92] | 751 | the Obj\# given above. To make use of this option, the user should |
---|
[101] | 752 | set \texttt{flagKarma = 1}, and put the desired filename in the parameter |
---|
| 753 | \texttt{karmaFile} -- again, the default is for it not to be produced. |
---|
[18] | 754 | |
---|
[3] | 755 | As the program is running, it also (optionally) records the detections |
---|
| 756 | made in each individual spectrum or channel (see |
---|
| 757 | \S\ref{sec-detection} for details on this process). This is |
---|
[101] | 758 | recorded in the file given by the parameter \texttt{LogFile}. This file |
---|
| 759 | does not include the columns \texttt{Name, RA, DEC, w\_RA, w\_DEC, VEL, |
---|
[3] | 760 | w\_VEL}. This file is designed primarily for diagnostic purposes: \eg |
---|
| 761 | to see if a given set of pixels is detected in, say, one channel |
---|
| 762 | image, but does not survive the merging process. The list of pixels |
---|
| 763 | (and their fluxes) in the final detection list are also printed to |
---|
| 764 | this file, again for diagnostic purposes. This feature can be turned |
---|
[101] | 765 | off by setting \texttt{flagLog = false}. (This may be a good idea if you |
---|
[3] | 766 | are not interested in its contents, as it can be a large file.) |
---|
| 767 | |
---|
[101] | 768 | \begin{figure}[t] |
---|
| 769 | \begin{center} |
---|
| 770 | \includegraphics[width=\textwidth]{example_spectrum} |
---|
| 771 | \end{center} |
---|
| 772 | \caption{\footnotesize An example of the spectrum output. Note several |
---|
| 773 | of the features discussed in the text: the red lines indicating the |
---|
| 774 | reconstructed spectrum; the blue dashed lines indicating the |
---|
| 775 | spectral extent of the detection; the green hashed area indicating |
---|
| 776 | the Milky Way channels that are ignored by the searching algorithm; |
---|
| 777 | the blue border showing its spatial extent on the 0th moment map; |
---|
| 778 | and the 15~arcmin-long scale bar.} |
---|
| 779 | \label{fig-spect} |
---|
| 780 | \end{figure} |
---|
| 781 | |
---|
[18] | 782 | \begin{figure}[!t] |
---|
| 783 | \begin{center} |
---|
| 784 | \includegraphics[width=\textwidth]{example_moment_map} |
---|
| 785 | \end{center} |
---|
| 786 | \caption{\footnotesize An example of the moment map created by |
---|
[101] | 787 | \duchamp. The full extent of the cube is covered, and the 0th moment |
---|
[18] | 788 | of each object is shown (integrated individually over all the |
---|
| 789 | detected channels).} |
---|
| 790 | \label{fig-moment} |
---|
| 791 | \end{figure} |
---|
| 792 | |
---|
[92] | 793 | \subsubsection{Graphical output -- spectra} |
---|
| 794 | |
---|
[3] | 795 | As well as the output data file, a postscript file is created that |
---|
[80] | 796 | shows the spectrum for each detection, together with a small cutout |
---|
[101] | 797 | image (the 0th moment) and basic information about the detection (note |
---|
[87] | 798 | that any flags are printed after the name of the detection, in the |
---|
[101] | 799 | format \texttt{[E]}). If the cube was reconstructed, the spectrum from |
---|
[92] | 800 | the reconstruction is shown in red, over the top of the original |
---|
[101] | 801 | spectrum. The spectral extent of the detected object is indicated by |
---|
| 802 | two dashed blue lines, and the region covered by the ``Milky Way'' |
---|
| 803 | channels is shown by a green hashed box. |
---|
[3] | 804 | |
---|
[101] | 805 | The spectrum that is plotted is governed by the |
---|
| 806 | \texttt{spectralMethod} parameter. It can be either \texttt{peak}, |
---|
| 807 | where the spectrum is from the spatial pixel containing the |
---|
| 808 | detection's peak flux; or \texttt{sum}, where the spectrum is summed |
---|
| 809 | over all spatial pixels, and then corrected for the beam size. |
---|
| 810 | |
---|
[45] | 811 | The spectral extent of the detection is indicated with blue lines, and |
---|
| 812 | a zoom is shown in a separate window. The cutout image can optionally |
---|
| 813 | include a border around the spatial pixels that are in the detection |
---|
[101] | 814 | (turned on and off by the parameter \texttt{drawBorders} -- the |
---|
| 815 | default is \texttt{true}). It also includes a scale bar in the bottom |
---|
| 816 | left corner to indicate size -- it is 15~arcmin long (note that due to |
---|
| 817 | projection effects it may be a slightly different physical length from |
---|
| 818 | object to object). An example detection can be seen below in |
---|
| 819 | Fig.~\ref{fig-spect}. |
---|
[45] | 820 | |
---|
[92] | 821 | \subsubsection{Graphical output -- maps} |
---|
| 822 | |
---|
[17] | 823 | Finally, a couple of images are optionally produced: a 0th moment map |
---|
[3] | 824 | of the cube, combining just the detected channels in each object, |
---|
| 825 | showing the integrated flux in grey-scale; and a ``detection image'', |
---|
| 826 | a grey-scale image where the pixel values are the number of channels |
---|
[101] | 827 | that spatial pixel is detected in. In both cases, if |
---|
| 828 | \texttt{drawBorders = true}, a border is drawn around the spatial |
---|
| 829 | extent of each detection. An example moment map is shown in |
---|
| 830 | Fig.~\ref{fig-moment}. The production or otherwise of these images is |
---|
| 831 | governed by the \texttt{flagMaps} parameter. |
---|
[3] | 832 | |
---|
| 833 | The purpose of these images are to provide a visual guide to where the |
---|
| 834 | detections have been made, and, particularly in the case of the moment |
---|
| 835 | map, to provide an indication of the strength of the source. In both |
---|
[96] | 836 | cases, the detections are numbered (in the same sense as the output |
---|
[3] | 837 | list), and the spatial borders are marked out as for the cutout images |
---|
| 838 | in the spectra file. Both these images are saved as postscript files |
---|
[101] | 839 | (given by the parameters \texttt{momentMap} and \texttt{detectionMap} |
---|
[3] | 840 | respectively), with the latter also displayed in a {\sc pgplot} |
---|
[101] | 841 | window (regardless of the state of \texttt{flagMaps}). |
---|
[3] | 842 | |
---|
[101] | 843 | \section{Notes and hints on the use of \duchamp} |
---|
[96] | 844 | \label{sec-notes} |
---|
[3] | 845 | |
---|
[101] | 846 | In using \duchamp, the user has to make a number of decisions about |
---|
[3] | 847 | the way the program runs. This section is designed to give the user |
---|
[80] | 848 | some idea about what to choose. |
---|
[3] | 849 | |
---|
| 850 | The main choice is whether or not to use the wavelet |
---|
| 851 | reconstruction. The main benefits of this are the marked reduction in |
---|
| 852 | the noise level, leading to regularly-shaped detections, and good |
---|
| 853 | reliability for faint sources. The main drawback with its use is the |
---|
| 854 | long execution time: to reconstruct a $170\times160\times1024$ |
---|
| 855 | (\hipass) cube often requires three iterations and takes about 20-25 |
---|
[101] | 856 | minutes to run completely. Note that this is for the three-dimensional |
---|
| 857 | reconstruction: using \texttt{reconDim=1} makes the reconstruction |
---|
| 858 | quicker (the full program then takes about 6 minutes), but it is still |
---|
| 859 | the largest part of the time. |
---|
[96] | 860 | |
---|
[101] | 861 | The searching part of the procedure is much quicker: searching an |
---|
| 862 | un-reconstructed cube leads to execution times of only a couple of |
---|
[71] | 863 | minutes. Alternatively, using the ability to read in previously-saved |
---|
| 864 | reconstructed arrays makes running the reconstruction more than once a |
---|
| 865 | more feasible prospect. |
---|
[3] | 866 | |
---|
[96] | 867 | On the positive side, the shape of the detections in a cube that has |
---|
| 868 | been reconstructed will be much more regular and smooth -- the ragged |
---|
| 869 | edges that objects in the raw cube possess are smoothed by the removal |
---|
| 870 | of most of the noise. This enables better determination of the shapes |
---|
| 871 | and characteristics of objects. |
---|
[3] | 872 | |
---|
[96] | 873 | A further point to consider when using the reconstruction is that if |
---|
[101] | 874 | the two-dimensional reconstruction is chosen (\texttt{reconDim=2}), it |
---|
[96] | 875 | can be susceptible to edge effects. If the valid area in the cube (\ie |
---|
| 876 | the part that is not BLANK) has non-rectangular edges, the convolution |
---|
| 877 | can produce artefacts in the reconstruction that mimic the edges and |
---|
| 878 | can lead (depending on the selection threshold) to some spurious |
---|
| 879 | sources. Caution is advised with such data -- the user is advised to |
---|
| 880 | check carefully the reconstructed cube for the presence of such |
---|
| 881 | artefacts. Note, however, that the 1- and 3-dimensional |
---|
[101] | 882 | reconstructions are \emph{not} susceptible in the same way, since the |
---|
[96] | 883 | spectral direction does not generally exhibit these BLANK edges, and |
---|
| 884 | so we recommend the use of either of these. |
---|
| 885 | |
---|
[3] | 886 | If one chooses the reconstruction method, a further decision is |
---|
| 887 | required on the signal-to-noise cutoff used in determining acceptable |
---|
| 888 | wavelet coefficients. A larger value will remove more noise from the |
---|
| 889 | cube, at the expense of losing fainter sources, while a smaller value |
---|
| 890 | will include more noise, which may produce spurious detections, but |
---|
| 891 | will be more sensitive to faint sources. Values of less than about |
---|
| 892 | $3\sigma$ tend to not reduce the noise a great deal and can lead to |
---|
[71] | 893 | many spurious sources (although this will depend on the nature of the |
---|
| 894 | cube). |
---|
[3] | 895 | |
---|
[101] | 896 | When it comes to searching, the FDR method produces more reliable results |
---|
| 897 | than simple sigma-clipping, particularly in the absence of reconstruction. |
---|
| 898 | However, it does not work in exactly the way one would expect for a |
---|
| 899 | given value of \texttt{alpha}. For instance, setting fairly liberal values |
---|
| 900 | of \texttt{alpha} (say, 0.1) will often lead to a much smaller fraction |
---|
| 901 | of false detections (\ie much less than 10\%). This is the effect of the |
---|
| 902 | merging algorithms, that combine the sources after the detection stage, |
---|
| 903 | and reject detections not meeting the minimum pixel or channel requirements. |
---|
| 904 | It is thus better to aim for larger \texttt{alpha} values than those derived |
---|
| 905 | from a straight conversion of the desired false detection rate. |
---|
[3] | 906 | |
---|
[101] | 907 | Finally, as \duchamp\ is still undergoing development, there are some |
---|
[24] | 908 | elements that are not fully developed. In particular, it is not as |
---|
| 909 | clever as I would like at avoiding interference. The ability to place |
---|
| 910 | requirements on the minimum number of channels and pixels partially |
---|
[101] | 911 | circumvents this problem, but work is being done to make \duchamp\ |
---|
[24] | 912 | smarter at rejecting signals that are clearly (to a human eye at |
---|
| 913 | least) interference. See the following section for further |
---|
| 914 | improvements that are planned. |
---|
[3] | 915 | |
---|
[24] | 916 | %\section{Drawbacks of the current program} |
---|
| 917 | % |
---|
| 918 | %The program currently has a few problems/drawbacks/things to be aware |
---|
| 919 | %of that will hopefully be fixed in the future: |
---|
| 920 | %\begin{itemize} |
---|
| 921 | % |
---|
| 922 | %\item Narrow interference spikes are still getting found, particularly |
---|
| 923 | % if there is no reconstruction, or reconstruction with a relatively |
---|
[101] | 924 | % low \texttt{snrRecon} (such as 2 or 3). Increasing the |
---|
| 925 | % \texttt{minChannels} parameter is one way to circumvent this, but |
---|
| 926 | % making the algorithm a bit more clever would be preferable. |
---|
[24] | 927 | % |
---|
| 928 | %\item Sources that have strong continuum ripple and/or artefacts often |
---|
| 929 | % generate many spurious detections. This needs some work to avoid |
---|
[101] | 930 | % \duchamp\ doing this, and until then users are advised to be aware |
---|
[24] | 931 | % of the possibility. Strong continuum ripples may generate many |
---|
| 932 | % sources on the same spatial pixel, and this will be apparent on the |
---|
| 933 | % detection images. |
---|
| 934 | % |
---|
| 935 | %\item Spectra are integrated over every spatial pixel of the |
---|
| 936 | % detection, and this may dilute the actual detection, making it |
---|
| 937 | % harder to see \ie the apparent strength of the line as plotted may |
---|
| 938 | % not give a true indication of how strong it really is. |
---|
| 939 | % |
---|
| 940 | %%\item A caution on the merging part of the procedure. This can be time |
---|
| 941 | %% consuming if there are many detections that do not require merging |
---|
| 942 | %% -- in this case, the time will go like $N^2$ ($N$ = number of |
---|
| 943 | %% detections). If there are plenty of mergers, the size of the list |
---|
| 944 | %% reduces quickly, so the execution time will be less. |
---|
| 945 | % |
---|
| 946 | % |
---|
| 947 | %\end{itemize} |
---|
[3] | 948 | |
---|
| 949 | |
---|
| 950 | %\section{Comparison with other software (to be developed further...)} |
---|
| 951 | % |
---|
| 952 | %\subsection{fred, by Matt Howlett} |
---|
| 953 | % |
---|
| 954 | %This is the program used in the \hipass\ analysis. It smoothes the |
---|
| 955 | %data spectrally with a boxcar filter of a size that varies over a |
---|
| 956 | %user-specified range, and then thresholds the data. |
---|
| 957 | % |
---|
| 958 | %Works effectively, but generally doesn't find as many sources as |
---|
[101] | 959 | %\duchamp, particularly when the reconstruction is used. Sensitive to |
---|
[3] | 960 | %faint, broad features that fall below the reconstruction threshold. |
---|
| 961 | % |
---|
| 962 | %Execution takes a long time, depending on the range of filter widths |
---|
| 963 | %that are used. |
---|
| 964 | % |
---|
| 965 | %\subsection{sfind} |
---|
| 966 | % |
---|
| 967 | %Hard to evaluate, as it does not (as far as I can see) output the |
---|
| 968 | %channel number at which detections are made, and does not merge |
---|
| 969 | %detections made at adjacent channels (\ie it just works in 2 |
---|
| 970 | %dimensions). |
---|
| 971 | % |
---|
| 972 | |
---|
| 973 | \section{Future Developments} |
---|
| 974 | |
---|
| 975 | This is both a list of planned improvements and a wish-list of |
---|
| 976 | features that would be nice to include (but are not planned in the |
---|
[71] | 977 | immediate future). Let me know if there are items not on this list, or |
---|
| 978 | items on the list you would like prioritised. |
---|
[3] | 979 | |
---|
| 980 | \begin{itemize} |
---|
| 981 | |
---|
| 982 | \item Better determination of the noise characteristics of |
---|
| 983 | spectral-line cubes, including understanding how the noise is |
---|
[101] | 984 | generated and developing a model for it. \textbf{Planned.} |
---|
[3] | 985 | |
---|
| 986 | \item Include more source analysis. Examples could be: shape |
---|
[101] | 987 | information; measurements of HI mass; more variety of measurements |
---|
| 988 | of velocity width and profile. \textbf{Some planned.} |
---|
[3] | 989 | |
---|
| 990 | \item Provide some indication of the significance of the detection |
---|
[101] | 991 | (\ie some S/N-like value). \textbf{Planned.} |
---|
[3] | 992 | |
---|
[24] | 993 | \item Improved ability to reject interference, possibly on the |
---|
[101] | 994 | spectral shape of features. \textbf{Planned.} |
---|
[24] | 995 | |
---|
[71] | 996 | \item Ability to separate (de-blend) distinct sources that have been |
---|
[101] | 997 | merged. \textbf{Planned.} |
---|
[71] | 998 | |
---|
[3] | 999 | \item Link to lists of possible counterparts (\eg via NED/SIMBAD/other |
---|
[101] | 1000 | VO tools?). \textbf{Wish-list.} |
---|
[3] | 1001 | |
---|
[101] | 1002 | \item On-line web service interface, so a user can upload a cube and |
---|
| 1003 | get back a source-list. \textbf{Wish-list}. |
---|
| 1004 | |
---|
| 1005 | \item Embed \duchamp\ in a GUI, to move away from the text-based |
---|
| 1006 | interaction. \textbf{Wish-list}. |
---|
[3] | 1007 | \end{itemize} |
---|
| 1008 | |
---|
| 1009 | |
---|
| 1010 | %\bibliographystyle{mn2e} |
---|
| 1011 | %\bibliographystyle{abbrvnat} |
---|
| 1012 | %\bibliography{mnrasmnemonic,sourceDetection} |
---|
| 1013 | \begin{thebibliography}{} |
---|
| 1014 | |
---|
| 1015 | \bibitem[\protect\citeauthoryear{{Calabretta} \& {Greisen}}{{Calabretta} \& |
---|
| 1016 | {Greisen}}{2002}]{calabretta02} |
---|
| 1017 | {Calabretta} M., {Greisen} E., 2002, A\&A, 395, 1077 |
---|
| 1018 | |
---|
| 1019 | \bibitem[\protect\citeauthoryear{{Greisen} \& {Calabretta}}{{Greisen} \& |
---|
| 1020 | {Calabretta}}{2002}]{greisen02} |
---|
| 1021 | {Greisen} E., {Calabretta} M., 2002, A\&A, 395, 1061 |
---|
| 1022 | |
---|
[18] | 1023 | \bibitem[\protect\citeauthoryear{{Hanisch}, {Farris}, {Greisen}, {Pence}, |
---|
| 1024 | {Schlesinger}, {Teuben}, {Thompson} \& {Warnock}}{{Hanisch} |
---|
| 1025 | et~al.}{2001}]{hanisch01} |
---|
| 1026 | {Hanisch} R., {Farris} A., {Greisen} E., {Pence} W., {Schlesinger} B., |
---|
| 1027 | {Teuben} P., {Thompson} R., {Warnock} A., 2001, A\&A, 376, 359 |
---|
| 1028 | |
---|
[3] | 1029 | \bibitem[\protect\citeauthoryear{{Hopkins}, {Miller}, {Connolly}, {Genovese}, |
---|
| 1030 | {Nichol} \& {Wasserman}}{{Hopkins} et~al.}{2002}]{hopkins02} |
---|
| 1031 | {Hopkins} A., {Miller} C., {Connolly} A., {Genovese} C., {Nichol} R., |
---|
| 1032 | {Wasserman} L., 2002, AJ, 123, 1086 |
---|
| 1033 | |
---|
| 1034 | \bibitem[\protect\citeauthoryear{Lutz}{Lutz}{1980}]{lutz80} |
---|
| 1035 | Lutz R., 1980, The Computer Journal, 23, 262 |
---|
| 1036 | |
---|
| 1037 | \bibitem[\protect\citeauthoryear{{Meyer} et~al.,}{{Meyer} |
---|
| 1038 | et~al.}{2004}]{meyer04:trunc} |
---|
| 1039 | {Meyer} M., et~al., 2004, MNRAS, 350, 1195 |
---|
| 1040 | |
---|
| 1041 | \bibitem[\protect\citeauthoryear{{Miller}, {Genovese}, {Nichol}, {Wasserman}, |
---|
| 1042 | {Connolly}, {Reichart}, {Hopkins}, {Schneider} \& {Moore}}{{Miller} |
---|
| 1043 | et~al.}{2001}]{miller01} |
---|
| 1044 | {Miller} C., {Genovese} C., {Nichol} R., {Wasserman} L., {Connolly} A., |
---|
| 1045 | {Reichart} D., {Hopkins} A., {Schneider} J., {Moore} A., 2001, AJ, 122, |
---|
| 1046 | 3492 |
---|
| 1047 | |
---|
| 1048 | \bibitem[\protect\citeauthoryear{Minchin}{Minchin}{1999}]{minchin99} |
---|
| 1049 | Minchin R., 1999, PASA, 16, 12 |
---|
| 1050 | |
---|
| 1051 | \bibitem[\protect\citeauthoryear{Starck \& Murtagh}{Starck \& |
---|
| 1052 | Murtagh}{2002}]{starck02:book} |
---|
| 1053 | Starck J.-L., Murtagh F., 2002, {``Astronomical Image and Data Analysis''}. |
---|
| 1054 | Springer |
---|
| 1055 | |
---|
| 1056 | \end{thebibliography} |
---|
| 1057 | |
---|
| 1058 | |
---|
| 1059 | \appendix |
---|
| 1060 | \newpage |
---|
| 1061 | \section{Available parameters} |
---|
| 1062 | \label{app-param} |
---|
| 1063 | |
---|
| 1064 | The full list of parameters that can be listed in the input file are |
---|
| 1065 | given here. If not listed, they take the default value given in |
---|
| 1066 | parentheses. Since the order of the parameters in the input file does |
---|
| 1067 | not matter, they are grouped here in logical sections. |
---|
| 1068 | |
---|
| 1069 | \subsection*{Input-output related} |
---|
| 1070 | \begin{entry} |
---|
| 1071 | \item[ImageFile (no default assumed)] The filename of the |
---|
| 1072 | data cube to be analysed. |
---|
[101] | 1073 | \item[flagSubsection \texttt{[false]}] A flag to indicate whether one |
---|
[71] | 1074 | wants a subsection of the requested image. |
---|
[101] | 1075 | \item[Subsection \texttt{[ [*,*,*] ]}] The requested subsection, which |
---|
| 1076 | should be specified in the format \texttt{[x1:x2,y1:y2,z1:z2]}, where |
---|
[71] | 1077 | the limits are inclusive. If the full range of a dimension is |
---|
[101] | 1078 | required, use a \texttt{*}, \eg if you want the full spectral range of |
---|
| 1079 | a subsection of the image, use \texttt{[30:140,30:140,*]}. |
---|
| 1080 | \item[flagReconExists \texttt{[false]}] A flag to indicate whether the |
---|
| 1081 | reconstructed array has been saved by a previous run of \duchamp. If |
---|
[71] | 1082 | set true, the reconstructed array will be read from the file given by |
---|
[101] | 1083 | \texttt{reconFile}, rather than calculated directly. |
---|
[71] | 1084 | \item[reconFile (no default assumed)] The FITS file that contains the |
---|
[101] | 1085 | reconstructed array. If \texttt{flagReconExists} is true and this |
---|
[71] | 1086 | parameter is not defined, the default file searched will be |
---|
[101] | 1087 | determined by the \atrous\ parameters (see \S\ref{sec-recon}). |
---|
| 1088 | \item[OutFile \texttt{[duchamp-Results.txt]}] The file containing the |
---|
[87] | 1089 | final list of detections. This also records the list of input |
---|
[3] | 1090 | parameters. |
---|
[101] | 1091 | \item[SpectraFile \texttt{[duchamp-Spectra.ps]}] The postscript file |
---|
[3] | 1092 | containing the resulting integrated spectra and images of the |
---|
| 1093 | detections. |
---|
[101] | 1094 | \item[flagLog \texttt{[true]}] A flag to indicate whether intermediate |
---|
[3] | 1095 | detections should be logged. |
---|
[101] | 1096 | \item[LogFile \texttt{[duchamp-Logfile.txt]}] The file in which intermediate |
---|
[3] | 1097 | detections are logged. These are detections that have not been |
---|
| 1098 | merged. This is primarily for use in debugging and diagnostic |
---|
| 1099 | purposes -- normal use of the program will probably not require |
---|
| 1100 | this. |
---|
[101] | 1101 | \item[flagOutputRecon \texttt{[false]}] A flag to say whether or not to |
---|
[3] | 1102 | save the reconstructed cube as a FITS file. The filename will be |
---|
[101] | 1103 | derived from the ImageFile -- the reconstruction of \texttt{image.fits} |
---|
| 1104 | will be saved as \texttt{image.RECON?.fits}, where \texttt{?} stands for |
---|
| 1105 | the value of \texttt{snrRecon} (see below). |
---|
| 1106 | \item[flagOutputResid \texttt{[false]}] As for \texttt{flagOutputRecon}, but |
---|
[3] | 1107 | for the residual array -- the difference between the original cube |
---|
[101] | 1108 | and the reconstructed cube. The filename will be \texttt{image.RESID?.fits}. |
---|
| 1109 | \item[flagVOT \texttt{[false]}] A flag to say whether to create a VOTable |
---|
| 1110 | file corresponding to the information in \texttt{outfile}. This will be |
---|
[3] | 1111 | an XML file in the Virtual Observatory VOTable format. |
---|
[101] | 1112 | \item[votFile \texttt{[duchamp-Results.xml]}] The VOTable file with the |
---|
[3] | 1113 | list of final detections. Some input parameters are also recorded. |
---|
[101] | 1114 | \item[flagKarma \texttt{[false]}] A flag to say whether to create a |
---|
| 1115 | Karma annotation file corresponding to the information in |
---|
| 1116 | \texttt{outfile}. This can be used as an overlay for the Karma |
---|
| 1117 | programs such as \texttt{kvis}. |
---|
| 1118 | \item[karmaFile \texttt{[duchamp-Results.ann]}] The Karma annotation |
---|
[20] | 1119 | file showing the list of final detections. |
---|
[101] | 1120 | \item[flagMaps \texttt{[true]}] A flag to say whether to save |
---|
| 1121 | postscript files showing the 0th moment map of the whole cube |
---|
| 1122 | (parameter \texttt{momentMap}) and the detection image |
---|
| 1123 | (\texttt{detectionMap}). |
---|
| 1124 | \item[momentMap \texttt{[duchamp-MomentMap.ps]}] A postscript file |
---|
[17] | 1125 | containing a map of the 0th moment of the detected sources, as well |
---|
[3] | 1126 | as pixel and WCS coordinates. |
---|
[101] | 1127 | \item[detectionMap \texttt{[duchamp-DetectionMap.ps]}] A postscript |
---|
[3] | 1128 | file showing each of the detected objects, coloured in greyscale by |
---|
[101] | 1129 | the number of channels spanned by each pixel. Also shows pixel and WCS |
---|
[3] | 1130 | coordinates. |
---|
| 1131 | \end{entry} |
---|
| 1132 | |
---|
| 1133 | \subsection*{Modifying the cube} |
---|
| 1134 | \begin{entry} |
---|
[101] | 1135 | \item[flagBlankPix \texttt{[true]}] A flag to say whether to remove BLANK |
---|
[3] | 1136 | pixels from the analysis -- these are pixels set to some particular |
---|
| 1137 | value because they fall outside the imaged area. |
---|
[101] | 1138 | \item[blankPixValue \texttt{[-8.00061]}] The value of the BLANK pixels, |
---|
[15] | 1139 | if this information is not contained in the FITS header (the usual |
---|
[3] | 1140 | procedure is to obtain this value from the header information -- in |
---|
| 1141 | which case the value set by this parameter is ignored). |
---|
[101] | 1142 | \item[flagMW \texttt{[false]}] A flag to say whether to ignore channels |
---|
[96] | 1143 | contaminated by Milky Way (or other) emission -- the searching |
---|
| 1144 | algorithms will not look at these channels. |
---|
[101] | 1145 | \item[maxMW \texttt{[112]}] The maximum channel number containing |
---|
| 1146 | ``Milky Way'' emission. |
---|
| 1147 | \item[minMW \texttt{[75]}] The minimum channel number containing |
---|
| 1148 | ``Milky Way'' emission. Note that the range specified by |
---|
| 1149 | \texttt{maxMW} and \texttt{minMW} is inclusive. |
---|
| 1150 | \item[flagBaseline \texttt{[false]}] A flag to say whether to remove the |
---|
[3] | 1151 | baseline from each spectrum in the cube for the purposes of |
---|
| 1152 | reconstruction and detection. |
---|
| 1153 | \end{entry} |
---|
| 1154 | |
---|
| 1155 | \subsection*{Detection related} |
---|
| 1156 | |
---|
| 1157 | \subsubsection*{General detection} |
---|
| 1158 | \begin{entry} |
---|
[101] | 1159 | \item[flagNegative \texttt{[false]}] A flag to indicate that the features |
---|
[80] | 1160 | being searched for are negative. The cube will be inverted prior to |
---|
| 1161 | searching. |
---|
[101] | 1162 | \item[snrCut \texttt{[3.]}] The cut-off value for thresholding, in terms |
---|
[3] | 1163 | of number of $\sigma$ above the mean. |
---|
[101] | 1164 | \item[flagGrowth \texttt{[false]}] A flag indicating whether or not to |
---|
[3] | 1165 | grow the detected objects to a smaller threshold. |
---|
[101] | 1166 | \item[growthCut \texttt{[2.]}] The smaller threshold using in growing |
---|
[3] | 1167 | detections. In units of $\sigma$ above the mean. |
---|
| 1168 | \end{entry} |
---|
| 1169 | |
---|
[101] | 1170 | \subsubsection*{\Atrous\ reconstruction} |
---|
[3] | 1171 | \begin{entry} |
---|
[101] | 1172 | \item [flagATrous \texttt{[true]}] A flag indicating whether or not to |
---|
| 1173 | reconstruct the cube using the \atrous\ wavelet |
---|
| 1174 | reconstruction. See \S\ref{sec-recon} for details. |
---|
| 1175 | \item[reconDim \texttt{[3]}] The number of dimensions to use in the |
---|
[96] | 1176 | reconstruction. 1 means reconstruct each spectrum separately, 2 |
---|
| 1177 | means each channel map is done separately, and 3 means do the whole |
---|
| 1178 | cube in one go. |
---|
[101] | 1179 | \item[scaleMin \texttt{[1]}] The minimum wavelet scale to be used in the |
---|
[3] | 1180 | reconstruction. A value of 1 means ``use all scales''. |
---|
[101] | 1181 | \item[snrRecon \texttt{[4]}] The thresholding cutoff used in the |
---|
[3] | 1182 | reconstruction -- only wavelet coefficients this many $\sigma$ above |
---|
| 1183 | the mean (or greater) are included in the reconstruction. |
---|
[101] | 1184 | \item[filterCode \texttt{[2]}] The code number of the filter to use in |
---|
[3] | 1185 | the reconstruction. The options are: |
---|
| 1186 | \begin{itemize} |
---|
[101] | 1187 | \item \textbf{1:} B$_3$-spline filter: coefficients = |
---|
[3] | 1188 | $(\frac{1}{16}, \frac{1}{4}, \frac{3}{8}, \frac{1}{4}, \frac{1}{16})$ |
---|
[101] | 1189 | \item \textbf{2:} Triangle filter: coefficients = $(\frac{1}{4}, \frac{1}{2}, \frac{1}{4})$ |
---|
| 1190 | \item \textbf{3:} Haar wavelet: coefficients = $(0, \frac{1}{2}, \frac{1}{2})$ |
---|
[3] | 1191 | \end{itemize} |
---|
| 1192 | \end{entry} |
---|
| 1193 | |
---|
| 1194 | \subsubsection*{FDR method} |
---|
| 1195 | \begin{entry} |
---|
[101] | 1196 | \item[flagFDR \texttt{[false]}] A flag indicating whether or not to use |
---|
[3] | 1197 | the False Discovery Rate method in thresholding the pixels. |
---|
[101] | 1198 | \item[alphaFDR \texttt{[0.01]}] The $\alpha$ parameter used in the FDR |
---|
[3] | 1199 | analysis. The average number of false detections, as a fraction of the |
---|
| 1200 | total number, will be less than $\alpha$ (see \S\ref{sec-detection}). |
---|
| 1201 | \end{entry} |
---|
| 1202 | |
---|
| 1203 | \subsubsection*{Merging detections} |
---|
| 1204 | \begin{entry} |
---|
[101] | 1205 | \item[minPix \texttt{[2]}] The minimum number of spatial pixels for a single |
---|
[17] | 1206 | detection to be counted. |
---|
[101] | 1207 | \item[minChannels \texttt{[3]}] The minimum number of consecutive |
---|
| 1208 | channels that must be present in a detection. |
---|
| 1209 | \item[flagAdjacent \texttt{[true]}] A flag indicating whether to use the |
---|
[80] | 1210 | ``adjacent pixel'' criterion to decide whether to merge objects. If |
---|
| 1211 | not, the next two parameters are used to determine whether objects |
---|
| 1212 | are within the necessary thresholds. |
---|
[101] | 1213 | \item[threshSpatial \texttt{[3.]}] The maximum allowed minimum spatial |
---|
[3] | 1214 | separation (in pixels) between two detections for them to be merged |
---|
[101] | 1215 | into one. Only used if \texttt{flagAdjacent = false}. |
---|
| 1216 | \item[threshVelocity \texttt{[7.]}] The maximum allowed minimum channel |
---|
[3] | 1217 | separation between two detections for them to be merged into |
---|
[96] | 1218 | one. |
---|
[3] | 1219 | \end{entry} |
---|
| 1220 | |
---|
| 1221 | \subsubsection*{Other parameters} |
---|
| 1222 | \begin{entry} |
---|
[101] | 1223 | \item[spectralMethod \texttt{[peak]}] This indicates which method is used |
---|
| 1224 | to plot the output spectra: \texttt{peak} means plot the spectrum |
---|
| 1225 | containing the detection's peak pixel; \texttt{sum} means sum the |
---|
[80] | 1226 | spectra of each detected spatial pixel, and correct for the beam |
---|
[101] | 1227 | size. Any other choice defaults to \texttt{peak}. |
---|
| 1228 | \item[spectralUnits \texttt{[km/s]}] The user can specify the units of |
---|
| 1229 | the spectral axis. Assuming the WCS of the FITS file is valid, the |
---|
| 1230 | spectral axis is transformed into velocity, and put into these units |
---|
| 1231 | for all output and for calculations such as the integrated flux of a |
---|
| 1232 | detection. |
---|
| 1233 | \item[drawBorders \texttt{[true]}] A flag indicating whether borders |
---|
[3] | 1234 | are to be drawn around the detected objects in the moment maps |
---|
| 1235 | included in the output (see for example Fig.~\ref{fig-spect}). |
---|
[101] | 1236 | \item[verbose \texttt{[true]}] A flag indicating whether to print the |
---|
[3] | 1237 | progress of computationally-intensive algorithms (such as the |
---|
| 1238 | searching and merging) to screen. |
---|
| 1239 | \end{entry} |
---|
| 1240 | |
---|
| 1241 | |
---|
| 1242 | \newpage |
---|
| 1243 | \section{Example parameter files} |
---|
| 1244 | \label{app-input} |
---|
| 1245 | |
---|
| 1246 | This is what a typical parameter file would look like. |
---|
| 1247 | |
---|
| 1248 | \begin{verbatim} |
---|
| 1249 | imageFile /DATA/SITAR_1/whi550/cubes/H201_abcde_luther_chop.fits |
---|
[80] | 1250 | logFile logfile.txt |
---|
| 1251 | outFile results.txt |
---|
[3] | 1252 | spectraFile spectra.ps |
---|
| 1253 | flagSubsection 0 |
---|
| 1254 | flagOutputRecon 0 |
---|
| 1255 | flagOutputResid 0 |
---|
| 1256 | flagBlankPix 1 |
---|
| 1257 | flagMW 1 |
---|
| 1258 | minMW 75 |
---|
| 1259 | maxMW 112 |
---|
| 1260 | minPix 3 |
---|
| 1261 | flagGrowth 1 |
---|
| 1262 | growthCut 1.5 |
---|
| 1263 | flagATrous 0 |
---|
| 1264 | scaleMin 1 |
---|
| 1265 | snrRecon 4 |
---|
| 1266 | flagFDR 1 |
---|
| 1267 | alphaFDR 0.1 |
---|
| 1268 | numPixPSF 20 |
---|
| 1269 | snrCut 3 |
---|
| 1270 | threshSpatial 3 |
---|
| 1271 | threshVelocity 7 |
---|
| 1272 | \end{verbatim} |
---|
| 1273 | |
---|
| 1274 | Note that it is not necessary to include all these parameters in the |
---|
| 1275 | file, only those that need to be changed from the defaults (as listed |
---|
| 1276 | in Appendix~\ref{app-param}), which in this case would be very few. A |
---|
| 1277 | minimal parameter file might look like: |
---|
| 1278 | \begin{verbatim} |
---|
| 1279 | imageFile /DATA/SITAR_1/whi550/cubes/H201_abcde_luther_chop.fits |
---|
| 1280 | flagLog 0 |
---|
| 1281 | snrRecon 3 |
---|
| 1282 | snrCut 2.5 |
---|
[87] | 1283 | minChannels 4 |
---|
[3] | 1284 | \end{verbatim} |
---|
| 1285 | This will reconstruct the cube with a lower SNR value than the |
---|
| 1286 | default, select objects at a lower threshold, with a looser minimum |
---|
| 1287 | channel requirement, and not keep a log of the intermediate |
---|
| 1288 | detections. |
---|
| 1289 | |
---|
[101] | 1290 | The following page demonstrates how the parameters are presented to the |
---|
| 1291 | user, both on the screen at execution time, and in the output and log |
---|
| 1292 | files. On each line, there is a description on the parameter, the relevant |
---|
| 1293 | parameter name that is used in the input file (if there is one that the |
---|
| 1294 | user can enter), and the value of the parameter being used. |
---|
[3] | 1295 | \newpage |
---|
| 1296 | \begin{landscape} |
---|
[101] | 1297 | Typical presentation of parameters in output and log files: |
---|
[3] | 1298 | \begin{verbatim} |
---|
[18] | 1299 | ---- Parameters ---- |
---|
[101] | 1300 | Image to be analysed.........................[imageFile] = input.fits |
---|
| 1301 | Intermediate Logfile...........................[logFile] = duchamp-Logfile.txt |
---|
| 1302 | Final Results file.............................[outFile] = duchamp-Results.txt |
---|
| 1303 | Spectrum file..............................[spectraFile] = duchamp-Spectra.ps |
---|
| 1304 | 0th Moment Map...............................[momentMap] = duchamp-MomentMap.ps |
---|
| 1305 | Detection Map.............................[detectionMap] = duchamp-DetectionMap.ps |
---|
| 1306 | Saving reconstructed cube?.............[flagoutputrecon] = false |
---|
| 1307 | Saving residuals from reconstruction?..[flagoutputresid] = false |
---|
[18] | 1308 | ------ |
---|
[101] | 1309 | Searching for Negative features?..........[flagNegative] = false |
---|
| 1310 | Fixing Blank Pixels?......................[flagBlankPix] = true |
---|
| 1311 | Blank Pixel Value....................................... = -8.00061 |
---|
| 1312 | Removing Milky Way channels?....................[flagMW] = true |
---|
| 1313 | Milky Way Channels.......................[minMW - maxMW] = 75-112 |
---|
| 1314 | Beam Size (pixels)...................................... = 10.1788 |
---|
| 1315 | Removing baselines before search?.........[flagBaseline] = false |
---|
| 1316 | Minimum # Pixels in a detection.................[minPix] = 2 |
---|
| 1317 | Minimum # Channels in a detection..........[minChannels] = 3 |
---|
| 1318 | Growing objects after detection?............[flagGrowth] = false |
---|
| 1319 | Using A Trous reconstruction?...............[flagATrous] = true |
---|
| 1320 | Number of dimensions in reconstruction........[reconDim] = 3 |
---|
| 1321 | Minimum scale in reconstruction...............[scaleMin] = 1 |
---|
| 1322 | SNR Threshold within reconstruction...........[snrRecon] = 4 |
---|
| 1323 | Filter being used for reconstruction........[filterCode] = 1 (B3 spline function) |
---|
| 1324 | Using FDR analysis?............................[flagFDR] = false |
---|
| 1325 | SNR Threshold...................................[snrCut] = 3 |
---|
| 1326 | Using Adjacent-pixel criterion?...........[flagAdjacent] = true |
---|
| 1327 | Max. velocity separation for merging....[threshVelocity] = 7 |
---|
| 1328 | Method of spectral plotting.............[spectralMethod] = peak |
---|
[3] | 1329 | \end{verbatim} |
---|
| 1330 | |
---|
| 1331 | \newpage |
---|
[101] | 1332 | \section{Example results file} |
---|
[3] | 1333 | \label{app-output} |
---|
[101] | 1334 | This the typical content of an output file, after running \duchamp\ |
---|
[80] | 1335 | with the parameters illustrated on the previous page. |
---|
[3] | 1336 | |
---|
| 1337 | {\scriptsize |
---|
| 1338 | \begin{verbatim} |
---|
[101] | 1339 | Results of the \duchamp\ source finder: Tue May 23 14:51:38 2006 |
---|
[18] | 1340 | ---- Parameters ---- |
---|
[96] | 1341 | (... omitted for clarity -- see previous page for examples...) |
---|
[18] | 1342 | -------------------- |
---|
[96] | 1343 | Total number of detections = 25 |
---|
[18] | 1344 | -------------------- |
---|
[96] | 1345 | ------------------------------------------------------------------------------------------------------------------------------------------------------ |
---|
| 1346 | Obj# Name X Y Z RA DEC VEL w_RA w_DEC w_VEL F_int F_peak X1 X2 Y1 Y2 Z1 Z2 Npix Flag |
---|
| 1347 | [km/s] [arcmin] [arcmin] [km/s] [Jy km/s] [Jy/beam] [pix] |
---|
| 1348 | ------------------------------------------------------------------------------------------------------------------------------------------------------ |
---|
| 1349 | 1 J0618-2532 30.2 86.0 113.3 06:18:12.54 -25:32:44.79 208.502 45.17 34.61 26.383 24.394 0.350 25 35 82 90 112 114 137 E |
---|
| 1350 | 2 J0609-2156 59.5 140.6 114.6 06:09:19.66 -21:56:31.20 225.572 44.39 31.47 65.957 16.128 0.213 55 65 137 144 113 118 153 |
---|
| 1351 | 3 J0545-2143 141.2 143.2 114.8 05:45:51.71 -21:43:36.20 228.470 19.61 16.66 26.383 2.412 0.090 139 143 142 145 114 116 29 |
---|
| 1352 | 4 J0617-2633 33.3 70.8 115.6 06:17:25.52 -26:33:33.83 238.736 65.02 30.10 26.383 9.776 0.117 26 41 68 75 115 117 104 E |
---|
| 1353 | 5 J0601-2500 86.2 94.9 117.9 06:01:39.54 -25:00:32.46 269.419 27.99 24.02 26.383 3.920 0.124 83 89 92 97 117 119 44 |
---|
| 1354 | 6 J0602-2547 84.0 83.1 118.0 06:02:18.29 -25:47:31.69 270.319 20.01 19.99 26.383 2.999 0.118 82 86 81 85 117 119 34 |
---|
| 1355 | 7 J0547-2448 133.0 97.2 118.7 05:47:52.53 -24:48:38.16 279.113 19.72 12.54 26.383 1.474 0.074 131 135 96 98 118 120 21 |
---|
| 1356 | 8 J0606-2719 71.1 60.0 121.3 06:06:10.99 -27:19:48.61 314.090 52.36 39.59 39.574 14.268 0.150 65 77 55 64 120 123 154 |
---|
| 1357 | 9 J0611-2137 52.4 145.3 162.5 06:11:20.92 -21:37:29.57 857.955 32.39 23.49 118.722 43.178 0.410 49 56 142 147 158 167 265 E |
---|
| 1358 | 10 J0600-2859 89.7 35.3 202.4 06:00:34.08 -28:59:00.43 1383.160 23.93 24.10 171.487 24.439 0.173 87 92 33 38 196 209 271 |
---|
| 1359 | 11 J0558-2638 95.4 70.3 223.1 05:58:53.03 -26:38:45.91 1656.140 11.93 12.07 92.339 1.045 0.063 94 96 69 71 220 227 18 |
---|
| 1360 | 12 J0617-2723 34.7 58.3 227.4 06:17:07.07 -27:23:50.65 1712.868 16.75 23.53 290.209 8.529 0.093 33 36 56 61 215 237 118 |
---|
| 1361 | 13 J0558-2525 95.8 88.6 231.7 05:58:49.27 -25:25:33.60 1770.134 27.87 24.16 237.444 12.863 0.115 92 98 86 91 221 239 175 |
---|
| 1362 | 14 J0600-2141 88.8 144.4 232.5 06:00:54.02 -21:41:57.06 1780.188 27.96 24.13 224.252 30.743 0.166 86 92 142 147 222 239 344 E |
---|
| 1363 | 15 J0615-2634 40.0 70.8 232.6 06:15:25.50 -26:34:20.04 1782.214 12.44 15.69 52.765 2.084 0.068 39 41 69 72 231 235 31 |
---|
| 1364 | 16 J0604-2606 76.0 78.4 233.0 06:04:41.13 -26:06:21.19 1787.226 24.13 23.87 211.061 23.563 0.155 73 78 76 81 225 241 278 |
---|
| 1365 | 17 J0601-2340 87.9 114.9 235.8 06:01:08.83 -23:40:19.37 1824.122 31.95 28.09 237.444 82.380 0.297 85 92 112 118 227 245 647 |
---|
| 1366 | 18 J0615-2235 38.2 130.5 254.5 06:15:32.09 -22:35:37.24 2070.934 12.29 11.70 105.531 1.555 0.070 37 39 129 131 249 257 24 |
---|
| 1367 | 19 J0617-2305 31.4 122.8 258.1 06:17:33.45 -23:05:28.94 2118.752 12.34 11.65 26.383 1.022 0.062 30 32 122 124 257 259 16 |
---|
| 1368 | 20 J0612-2149 49.6 142.2 270.3 06:12:11.04 -21:49:29.72 2279.926 16.27 15.73 395.740 15.156 0.101 48 51 141 144 257 287 204 |
---|
| 1369 | 21 J0616-2133 35.3 146.0 300.6 06:16:15.78 -21:33:09.69 2679.148 20.22 7.47 224.252 3.014 0.127 33 37 145 146 294 311 28 E |
---|
| 1370 | 22 J0555-2956 107.3 20.9 367.6 05:55:08.02 -29:56:09.08 3562.236 19.71 20.30 39.574 5.891 0.169 105 109 19 23 366 369 58 |
---|
| 1371 | 23 J0557-2246 99.8 128.2 434.0 05:57:43.77 -22:46:42.95 4438.776 11.88 16.12 105.531 1.703 0.167 99 101 127 130 430 438 17 N |
---|
| 1372 | 24 J0616-2648 38.1 67.2 546.8 06:16:02.10 -26:48:35.49 5926.464 12.35 11.67 26.383 1.276 0.064 37 39 66 68 546 548 18 |
---|
| 1373 | 25 J0552-2916 117.0 30.5 727.0 05:52:13.64 -29:16:58.02 8303.952 11.59 20.25 303.400 35.523 0.479 116 118 28 32 716 739 111 |
---|
[3] | 1374 | \end{verbatim} |
---|
| 1375 | } |
---|
[80] | 1376 | Note that the |
---|
| 1377 | width of the table can make it hard to read. A good trick for those |
---|
[101] | 1378 | using UNIX/Linux is to make use of the \texttt{a2ps} command. The |
---|
| 1379 | following works well, producing a postscript file \texttt{results.ps}: |
---|
[87] | 1380 | \\\verb|a2ps -1 -r -f8 -o duchamp-Results.ps duchamp-Results.txt| |
---|
[3] | 1381 | |
---|
| 1382 | %\end{landscape} |
---|
| 1383 | |
---|
| 1384 | \newpage |
---|
| 1385 | \section{Example VOTable output} |
---|
| 1386 | \label{app-votable} |
---|
| 1387 | This is part of the VOTable, in XML format, corresponding to the |
---|
[101] | 1388 | output file in Appendix~\ref{app-output} (the indentation has been |
---|
| 1389 | removed to make it fit on the page). |
---|
[3] | 1390 | |
---|
| 1391 | %\begin{landscape} |
---|
| 1392 | {\scriptsize |
---|
| 1393 | \begin{verbatim} |
---|
| 1394 | <?xml version="1.0"?> |
---|
| 1395 | <VOTABLE version="1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" |
---|
| 1396 | xsi:noNamespaceSchemaLocation="http://www.ivoa.net/xml/VOTable/VOTable/v1.1"> |
---|
[20] | 1397 | <COOSYS ID="J2000" equinox="J2000." epoch="J2000." system="eq_FK5"/> |
---|
| 1398 | <RESOURCE name="Duchamp Output"> |
---|
| 1399 | <TABLE name="Detections"> |
---|
| 1400 | <DESCRIPTION>Detected sources and parameters from running the Duchamp source finder.</DESCRIPTION> |
---|
| 1401 | <PARAM name="FITS file" datatype="char" ucd="meta.file;meta.fits" value="/DATA/SITAR_1/whi550/cubes/H201_abcde_luther_chop.fits"/> |
---|
[87] | 1402 | <PARAM name="Threshold" datatype="float" ucd="stat.snr" value="2.5"> |
---|
| 1403 | <PARAM name="ATrous note" datatype="char" ucd="meta.note" value="The a trous reconstruction method was used, with the following parameters."> |
---|
[101] | 1404 | <PARAM name="ATrous Dimension" datatype="int" ucd="meta.code;stat" value="3"> |
---|
[87] | 1405 | <PARAM name="ATrous Cut" datatype="float" ucd="stat.snr" value="4"> |
---|
| 1406 | <PARAM name="ATrous Minimum Scale" datatype="int" ucd="stat.param" value="1"> |
---|
| 1407 | <PARAM name="ATrous Filter" datatype="char" ucd="meta.code;stat" value="B3 spline function"> |
---|
[20] | 1408 | <FIELD name="ID" ID="col1" ucd="meta.id" datatype="int" width="4"/> |
---|
| 1409 | <FIELD name="Name" ID="col2" ucd="meta.id;meta.main" datatype="char" arraysize="14"/> |
---|
| 1410 | <FIELD name="RA" ID="col3" ucd="pos.eq.ra;meta.main" ref="J2000" datatype="float" width="10" precision="6" unit="deg"/> |
---|
| 1411 | <FIELD name="Dec" ID="col4" ucd="pos.eq.dec;meta.main" ref="J2000" datatype="float" width="10" precision="6" unit="deg"/> |
---|
| 1412 | <FIELD name="w_RA" ID="col3" ucd="phys.angSize;pos.eq.ra" ref="J2000" datatype="float" width="7" precision="2" unit="arcmin"/> |
---|
| 1413 | <FIELD name="w_Dec" ID="col4" ucd="phys.angSize;pos.eq.dec" ref="J2000" datatype="float" width="7" precision="2" unit="arcmin"/> |
---|
| 1414 | <FIELD name="Vel" ID="col4" ucd="phys.veloc;src.dopplerVeloc" datatype="float" width="9" precision="3" unit="km/s"/> |
---|
| 1415 | <FIELD name="w_Vel" ID="col4" ucd="phys.veloc;src.dopplerVeloc;spect.line.width" datatype="float" width="8" precision="3" unit="km/s"/> |
---|
| 1416 | <FIELD name="Integrated_Flux" ID="col4" ucd="phys.flux;spect.line.intensity" datatype="float" width="10" precision="3" unit="km/s"/> |
---|
| 1417 | <DATA> |
---|
| 1418 | <TABLEDATA> |
---|
| 1419 | <TR> |
---|
[101] | 1420 | <TD> 1</TD><TD> J0609-2200</TD><TD> 92.410416</TD><TD>-22.013390</TD><TD> 48.50</TD><TD> 39.42</TD><TD> 213.061</TD><TD> 65.957</TD><TD> 17.572</TD> |
---|
[20] | 1421 | </TR> |
---|
| 1422 | <TR> |
---|
[101] | 1423 | <TD> 2</TD><TD> J0608-2605</TD><TD> 92.042633</TD><TD>-26.085157</TD><TD> 44.47</TD><TD> 39.47</TD><TD> 233.119</TD><TD> 39.574</TD><TD> 4.144</TD> |
---|
[20] | 1424 | </TR> |
---|
| 1425 | <TR> |
---|
[101] | 1426 | <TD> 3</TD><TD> J0606-2724</TD><TD> 91.637840</TD><TD>-27.412022</TD><TD> 52.48</TD><TD> 47.57</TD><TD> 302.213</TD><TD> 39.574</TD><TD> 17.066</TD> |
---|
[20] | 1427 | </TR> |
---|
[3] | 1428 | (... table truncated for clarity ...) |
---|
[20] | 1429 | </TABLEDATA> |
---|
| 1430 | </DATA> |
---|
| 1431 | </TABLE> |
---|
| 1432 | </RESOURCE> |
---|
[3] | 1433 | </VOTABLE> |
---|
| 1434 | \end{verbatim} |
---|
| 1435 | } |
---|
| 1436 | \end{landscape} |
---|
| 1437 | |
---|
[87] | 1438 | \newpage |
---|
| 1439 | \section{Example Karma Annotation File output} |
---|
| 1440 | \label{app-karma} |
---|
| 1441 | |
---|
| 1442 | This is the format of the Karma Annotation file, showing the locations |
---|
| 1443 | of the detected objects. This can be loaded by the plotting tools of |
---|
[101] | 1444 | the Karma package (for instance, \texttt{kvis}) as an overlay on the FITS |
---|
[87] | 1445 | file. |
---|
| 1446 | |
---|
| 1447 | \begin{verbatim} |
---|
| 1448 | # Duchamp Source Finder results for |
---|
| 1449 | # cube /DATA/SITAR_1/whi550/cubes/H201_abcde_luther_chop.fits |
---|
| 1450 | COLOR RED |
---|
| 1451 | COORD W |
---|
| 1452 | CIRCLE 92.3376 -21.9475 0.403992 |
---|
| 1453 | TEXT 92.3376 -21.9475 1 |
---|
| 1454 | CIRCLE 91.9676 -26.0193 0.37034 |
---|
| 1455 | TEXT 91.9676 -26.0193 2 |
---|
| 1456 | CIRCLE 91.5621 -27.3459 0.437109 |
---|
| 1457 | TEXT 91.5621 -27.3459 3 |
---|
| 1458 | CIRCLE 92.8285 -21.6344 0.269914 |
---|
| 1459 | TEXT 92.8285 -21.6344 4 |
---|
| 1460 | CIRCLE 90.1381 -28.9838 0.234179 |
---|
| 1461 | TEXT 90.1381 -28.9838 5 |
---|
| 1462 | CIRCLE 89.72 -26.6513 0.132743 |
---|
| 1463 | TEXT 89.72 -26.6513 6 |
---|
| 1464 | CIRCLE 94.2743 -27.4003 0.195175 |
---|
| 1465 | TEXT 94.2743 -27.4003 7 |
---|
| 1466 | CIRCLE 92.2739 -21.6941 0.134538 |
---|
| 1467 | TEXT 92.2739 -21.6941 8 |
---|
| 1468 | CIRCLE 89.7133 -25.4259 0.232252 |
---|
| 1469 | TEXT 89.7133 -25.4259 9 |
---|
| 1470 | CIRCLE 90.2206 -21.6993 0.266247 |
---|
| 1471 | TEXT 90.2206 -21.6993 10 |
---|
| 1472 | CIRCLE 93.8581 -26.5766 0.163153 |
---|
| 1473 | TEXT 93.8581 -26.5766 11 |
---|
| 1474 | CIRCLE 91.176 -26.1064 0.234356 |
---|
| 1475 | TEXT 91.176 -26.1064 12 |
---|
| 1476 | CIRCLE 90.2844 -23.6716 0.299509 |
---|
| 1477 | TEXT 90.2844 -23.6716 13 |
---|
| 1478 | CIRCLE 93.8774 -22.581 0.130925 |
---|
| 1479 | TEXT 93.8774 -22.581 14 |
---|
| 1480 | CIRCLE 94.3882 -23.0934 0.137108 |
---|
| 1481 | TEXT 94.3882 -23.0934 15 |
---|
| 1482 | CIRCLE 93.0491 -21.8223 0.202928 |
---|
| 1483 | TEXT 93.0491 -21.8223 16 |
---|
| 1484 | CIRCLE 94.0685 -21.5603 0.168456 |
---|
| 1485 | TEXT 94.0685 -21.5603 17 |
---|
| 1486 | CIRCLE 86.0568 -27.6095 0.101113 |
---|
| 1487 | TEXT 86.0568 -27.6095 18 |
---|
| 1488 | CIRCLE 88.7932 -29.9453 0.202624 |
---|
| 1489 | TEXT 88.7932 -29.9453 19 |
---|
| 1490 | \end{verbatim} |
---|
| 1491 | |
---|
| 1492 | \newpage |
---|
[101] | 1493 | \section{Installing \duchamp\ (README file)} |
---|
[71] | 1494 | \begin{verbatim} |
---|
| 1495 | There is an executable (Duchamp) that has been compiled on a Debian |
---|
| 1496 | Linux kernel 2.6.8-2-686, with gcc version 3.3.5 (Debian 1:3.3.5-13) |
---|
| 1497 | |
---|
| 1498 | If that is no good to you, you can compile it yourself using the |
---|
| 1499 | Makefile included in this directory (sorry for not having a configure |
---|
| 1500 | script or similar yet!). |
---|
| 1501 | |
---|
| 1502 | Duchamp uses three main external libraries: pgplot, cfitsio and |
---|
| 1503 | wcslib. You will need to set the paths for the base directory and |
---|
| 1504 | three libraries, as they are currently configured for my use and will |
---|
[101] | 1505 | not be of much use to you. These are: |
---|
[71] | 1506 | |
---|
| 1507 | BASE --> the current directory |
---|
| 1508 | PGDIR --> where the pgplot libraries (and header files) are located |
---|
| 1509 | CFITSIODIR --> where the header file fitsio.h is |
---|
| 1510 | CFITSIOLDIR --> where the cfitsio library is located (libcfitsio.a) |
---|
| 1511 | WCSDIR --> where the wcslib header files are |
---|
| 1512 | WCSLDIR --> where the wcslib library is located (libwcs.a) |
---|
| 1513 | |
---|
| 1514 | If you do not have the libraries, they can be downloaded from the |
---|
| 1515 | following locations: |
---|
| 1516 | PGPlot -- http://www.astro.caltech.edu/~tjp/pgplot/ |
---|
| 1517 | cfitsio -- http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html |
---|
| 1518 | wcslib -- http://www.atnf.csiro.au/people/Mark.Calabretta/WCS/index.html |
---|
| 1519 | |
---|
| 1520 | Once you've set up the Makefile correctly, then simply typing |
---|
| 1521 | > make duchamp |
---|
| 1522 | will compile the program. |
---|
| 1523 | |
---|
| 1524 | To run it, you need to use the syntax |
---|
| 1525 | > Duchamp -p parameterFile |
---|
| 1526 | where parameterFile is a file with the input parameters, including the |
---|
| 1527 | name of the cube you want to search. |
---|
| 1528 | |
---|
| 1529 | There are two example input files included with the distribution. The |
---|
| 1530 | smaller one, InputExample, shows the typical parameters one might want |
---|
| 1531 | to set. The large one, InputComplete, lists all parameters that can be |
---|
| 1532 | entered, and a brief description of them. Refer to the documentation |
---|
| 1533 | for further details. |
---|
| 1534 | |
---|
| 1535 | To get going quickly, just replace the "your-file-here" in |
---|
| 1536 | InputExample with your image name, and type |
---|
| 1537 | > Duchamp -p InputExample |
---|
| 1538 | and you're off! |
---|
| 1539 | \end{verbatim} |
---|
| 1540 | |
---|
[3] | 1541 | \section{Robust statistics for a Normal distribution} |
---|
| 1542 | \label{app-madfm} |
---|
| 1543 | |
---|
| 1544 | The Normal, or Gaussian, distribution for mean $\mu$ and standard |
---|
| 1545 | deviation $\sigma$ can be written as |
---|
| 1546 | \[ |
---|
| 1547 | f(x) = \frac{1}{\sqrt{2\pi\sigma^2}}\ e^{-(x-\mu)^2/2\sigma^2}. |
---|
| 1548 | \] |
---|
| 1549 | |
---|
| 1550 | When one has a purely Gaussian signal, it is straightforward to |
---|
| 1551 | estimate $\sigma$ by calculating the standard deviation (or rms) of |
---|
| 1552 | the data. However, if there is a small amount of signal present on top |
---|
| 1553 | of Gaussian noise, and one wants to estimate the $\sigma$ for the |
---|
| 1554 | noise, the presence of the large values from the signal can bias the |
---|
| 1555 | estimator to higher values. |
---|
| 1556 | |
---|
| 1557 | An alternative way is to use the median ($m$) and median absolute deviation |
---|
| 1558 | from the median ($s$) to estimate $\mu$ and $\sigma$. The median is the |
---|
| 1559 | middle of the distribution, defined for a continuous distribution by |
---|
| 1560 | \[ |
---|
| 1561 | \int_{-\infty}^{m} f(x) \diff x = \int_{m}^{\infty} f(x) \diff x. |
---|
| 1562 | \] |
---|
| 1563 | From symmetry, we quickly see that for the continuous Normal |
---|
| 1564 | distribution, $m=\mu$. We consider the case henceforth of $\mu=0$, |
---|
| 1565 | without loss of generality. |
---|
| 1566 | |
---|
| 1567 | To find $s$, we find the distribution of the absolute deviation from |
---|
| 1568 | the median, and then find the median of that distribution. This |
---|
| 1569 | distribution is given by |
---|
| 1570 | \begin{eqnarray*} |
---|
| 1571 | g(x) &= &{\mbox{\rm distribution of }} |x|\\ |
---|
[18] | 1572 | &= &f(x) + f(-x),\ x\ge0\\ |
---|
[37] | 1573 | &= &\sqrt{\frac{2}{\pi\sigma^2}}\, e^{-x^2/2\sigma^2},\ x\ge0. |
---|
[3] | 1574 | \end{eqnarray*} |
---|
[18] | 1575 | So, the median absolute deviation from the median, $s$, is given by |
---|
[3] | 1576 | \[ |
---|
| 1577 | \int_{0}^{s} g(x) \diff x = \int_{s}^{\infty} g(x) \diff x. |
---|
| 1578 | \] |
---|
| 1579 | Now, $\int_{0}^{\infty}e^{-x^2/2\sigma^2} \diff x = \sqrt{\pi\sigma^2/2}$, and |
---|
| 1580 | so $\int_{s}^{\infty} e^{-x^2/2\sigma^2} \diff x = |
---|
| 1581 | \sqrt{\pi\sigma^2/2} - \int_{0}^{s} e^{-\frac{x^2}{2\sigma^2}} \diff x |
---|
| 1582 | $. Hence, to find $s$ we simply solve the following equation (setting $\sigma=1$ for |
---|
| 1583 | simplicity -- equivalent to stating $x$ and $s$ in units of $\sigma$): |
---|
| 1584 | \[ |
---|
| 1585 | \int_{0}^{s}e^{-x^2/2} \diff x - \sqrt{\pi/8} = 0. |
---|
| 1586 | \] |
---|
| 1587 | This is hard to solve analytically (no nice analytic solution exists |
---|
| 1588 | for the finite integral that I'm aware of), but straightforward to |
---|
| 1589 | solve numerically, yielding the value of $s=0.6744888$. Thus, to |
---|
| 1590 | estimate $\sigma$ for a Normally distributed data set, one can calculate |
---|
| 1591 | $s$, then divide by 0.6744888 (or multiply by 1.4826042) to obtain the |
---|
| 1592 | correct estimator. |
---|
| 1593 | |
---|
| 1594 | Note that this is different to solutions quoted elsewhere, |
---|
[37] | 1595 | specifically in \citet{meyer04:trunc}, where the same robust estimator |
---|
| 1596 | is used but with an incorrect conversion to standard deviation -- they |
---|
| 1597 | assume $\sigma = s\sqrt{\pi/2}$. This, in fact, is the conversion used |
---|
[101] | 1598 | to convert the \emph{mean} absolute deviation from the mean to the |
---|
[37] | 1599 | standard deviation. This means that the cube noise in the \hipass\ |
---|
[80] | 1600 | catalogue (their parameter Rms$_{\rm cube}$) should be 18\% larger |
---|
| 1601 | than quoted. |
---|
[3] | 1602 | |
---|
[24] | 1603 | \section{How Gaussian noise changes with wavelet scale.} |
---|
| 1604 | \label{app-scaling} |
---|
| 1605 | |
---|
| 1606 | The key element in the wavelet reconstruction of an array is the |
---|
| 1607 | thresholding of the individual wavelet coefficient arrays. This is |
---|
| 1608 | usually done by choosing a level to be some number of standard |
---|
| 1609 | deviations above the mean value. |
---|
| 1610 | |
---|
| 1611 | However, since the wavelet arrays are produced by convolving the input |
---|
| 1612 | array by an increasingly large filter, the pixels in the coefficient |
---|
| 1613 | arrays become increasingly correlated as the scale of the filter |
---|
| 1614 | increases. This results in the measured standard deviation from a |
---|
| 1615 | given coefficient array decreasing with increasing scale. To calculate |
---|
| 1616 | this, we need to take into account how many other pixels each pixel in |
---|
| 1617 | the convolved array depends on. |
---|
| 1618 | |
---|
| 1619 | To demonstrate, suppose we have a 1-D array with $N$ pixel values |
---|
| 1620 | given by $F_i,\ i=1,...,N$, and we convolve it with the B$_3$-spline |
---|
[87] | 1621 | filter, defined by the set of coefficients |
---|
| 1622 | $\{1/16,1/4,3/8,1/4,1/16\}$. The flux of the $i$th pixel in the |
---|
| 1623 | convolved array will be |
---|
[24] | 1624 | \[ |
---|
[101] | 1625 | F'_i = \frac{1}{16}F_{i-2} + \frac{1}{4}F_{i-1} + \frac{3}{8}F_{i} |
---|
| 1626 | + \frac{1}{4}F_{i+1} + \frac{1}{16}F_{i+2} |
---|
[24] | 1627 | \] |
---|
| 1628 | and the flux of the corresponding pixel in the wavelet array will be |
---|
| 1629 | \[ |
---|
[101] | 1630 | W'_i = F_i - F'_i = \frac{-1}{16}F_{i-2} - \frac{1}{4}F_{i-1} + \frac{5}{8}F_{i} |
---|
| 1631 | - \frac{1}{4}F_{i+1} - \frac{1}{16}F_{i+2} |
---|
[24] | 1632 | \] |
---|
| 1633 | Now, assuming each pixel has the same standard deviation |
---|
| 1634 | $\sigma_i=\sigma$, we can work out the standard deviation for the |
---|
[101] | 1635 | wavelet array: |
---|
[24] | 1636 | \[ |
---|
| 1637 | \sigma'_i = \sigma \sqrt{\left(\frac{1}{16}\right)^2 + \left(\frac{1}{4}\right)^2 |
---|
| 1638 | + \left(\frac{5}{8}\right)^2 + \left(\frac{1}{4}\right)^2 + \left(\frac{1}{16}\right)^2} |
---|
| 1639 | = 0.72349\ \sigma |
---|
| 1640 | \] |
---|
| 1641 | Thus, the first scale wavelet coefficient array will have a standard |
---|
| 1642 | deviation of 72.3\% of the input array. This procedure can be followed |
---|
| 1643 | to calculate the necessary values for all scales, dimensions and |
---|
[101] | 1644 | filters used by \duchamp. |
---|
[24] | 1645 | |
---|
[101] | 1646 | Calculating these values is clearly a critical step in performing the |
---|
| 1647 | reconstruction. \citet{starck02:book} did so by simulating data sets |
---|
[24] | 1648 | with Gaussian noise, taking the wavelet transform, and measuring the |
---|
| 1649 | value of $\sigma$ for each scale. We take a different approach, by |
---|
| 1650 | calculating the scaling factors directly from the filter coefficients |
---|
| 1651 | by taking the wavelet transform of an array made up of a 1 in the |
---|
| 1652 | central pixel and 0s everywhere else. The scaling value is then |
---|
[101] | 1653 | derived by taking the square root of the sum (in quadrature) of all |
---|
| 1654 | the wavelet coefficient values at each scale. We give the scaling |
---|
| 1655 | factors for the three filters available to \duchamp\ on the following |
---|
| 1656 | page. These values are hard-coded into \duchamp, so no on-the-fly |
---|
| 1657 | calculation of them is necessary. |
---|
[24] | 1658 | |
---|
| 1659 | Memory limitations prevent us from calculating factors for large |
---|
| 1660 | scales, particularly for the three-dimensional case (hence the -- |
---|
| 1661 | symbols in the tables). To calculate factors for |
---|
| 1662 | higher scales than those available, we note the following |
---|
| 1663 | relationships apply for large scales to a sufficient level of precision: |
---|
| 1664 | \begin{itemize} |
---|
| 1665 | \item 1-D: factor(scale $i$) = factor(scale $i-1$)$/\sqrt{2}$. |
---|
| 1666 | \item 2-D: factor(scale $i$) = factor(scale $i-1$)$/2$. |
---|
| 1667 | \item 1-D: factor(scale $i$) = factor(scale $i-1$)$/\sqrt{8}$. |
---|
| 1668 | \end{itemize} |
---|
| 1669 | |
---|
| 1670 | \newpage |
---|
| 1671 | \begin{itemize} |
---|
[101] | 1672 | \item \textbf{B$_3$-Spline Function:} $\{1/16,1/4,3/8,1/4,1/16\}$ |
---|
[24] | 1673 | |
---|
| 1674 | \begin{tabular}{llll} |
---|
| 1675 | Scale & 1 dimension & 2 dimension & 3 dimension\\ \hline |
---|
| 1676 | 1 & 0.723489806 & 0.890796310 & 0.956543592\\ |
---|
| 1677 | 2 & 0.285450405 & 0.200663851 & 0.120336499\\ |
---|
| 1678 | 3 & 0.177947535 & 0.0855075048 & 0.0349500154\\ |
---|
| 1679 | 4 & 0.122223156 & 0.0412474444 & 0.0118164242\\ |
---|
| 1680 | 5 & 0.0858113122 & 0.0204249666 & 0.00413233507\\ |
---|
| 1681 | 6 & 0.0605703043 & 0.0101897592 & 0.00145703714\\ |
---|
| 1682 | 7 & 0.0428107206 & 0.00509204670 & 0.000514791120\\ |
---|
| 1683 | 8 & 0.0302684024 & 0.00254566946 & --\\ |
---|
| 1684 | 9 & 0.0214024008 & 0.00127279050 & --\\ |
---|
| 1685 | 10 & 0.0151336781 & 0.000636389722 & --\\ |
---|
| 1686 | 11 & 0.0107011079 & 0.000318194170 & --\\ |
---|
| 1687 | 12 & 0.00756682272 & -- & --\\ |
---|
| 1688 | 13 & 0.00535055108 & -- & --\\ |
---|
| 1689 | %14 & 0.00378341085 & -- & --\\ |
---|
| 1690 | %15 & 0.00267527545 & -- & --\\ |
---|
| 1691 | %16 & 0.00189170541 & -- & --\\ |
---|
| 1692 | %17 & 0.00133763772 & -- & --\\ |
---|
| 1693 | %18 & 0.000945852704 & -- & -- |
---|
| 1694 | \end{tabular} |
---|
| 1695 | |
---|
[101] | 1696 | \item \textbf{Triangle Function:} $\{1/4,1/2,1/4\}$ |
---|
[24] | 1697 | |
---|
| 1698 | \begin{tabular}{llll} |
---|
| 1699 | Scale & 1 dimension & 2 dimension & 3 dimension\\ \hline |
---|
| 1700 | 1 & 0.612372436 & 0.800390530 & 0.895954449 \\ |
---|
| 1701 | 2 & 0.330718914 & 0.272878894 & 0.192033014\\ |
---|
| 1702 | 3 & 0.211947812 & 0.119779282 & 0.0576484078\\ |
---|
| 1703 | 4 & 0.145740298 & 0.0577664785 & 0.0194912393\\ |
---|
| 1704 | 5 & 0.102310944 & 0.0286163283 & 0.00681278387\\ |
---|
| 1705 | 6 & 0.0722128185 & 0.0142747506 & 0.00240175885\\ |
---|
| 1706 | 7 & 0.0510388224 & 0.00713319703 & 0.000848538128 \\ |
---|
| 1707 | 8 & 0.0360857673 & 0.00356607618 & 0.000299949455 \\ |
---|
| 1708 | 9 & 0.0255157615 & 0.00178297280 & -- \\ |
---|
| 1709 | 10 & 0.0180422389 & 0.000891478237 & -- \\ |
---|
| 1710 | 11 & 0.0127577667 & 0.000445738098 & -- \\ |
---|
| 1711 | 12 & 0.00902109930 & 0.000222868922 & -- \\ |
---|
| 1712 | 13 & 0.00637887978 & -- & -- \\ |
---|
| 1713 | %14 & 0.00451054902 & -- & -- \\ |
---|
| 1714 | %15 & 0.00318942978 & -- & -- \\ |
---|
| 1715 | %16 & 0.00225527449 & -- & -- \\ |
---|
| 1716 | %17 & 0.00159471988 & -- & -- \\ |
---|
| 1717 | %18 & 0.000112763724 & -- & -- |
---|
| 1718 | |
---|
| 1719 | \end{tabular} |
---|
| 1720 | |
---|
[101] | 1721 | \item \textbf{Haar Wavelet:} $\{0,1/2,1/2\}$ |
---|
[24] | 1722 | |
---|
| 1723 | \begin{tabular}{llll} |
---|
| 1724 | Scale & 1 dimension & 2 dimension & 3 dimension\\ \hline |
---|
| 1725 | 1 & 0.707167810 & 0.433012702 & 0.935414347 \\ |
---|
| 1726 | 2 & 0.500000000 & 0.216506351 & 0.330718914\\ |
---|
| 1727 | 3 & 0.353553391 & 0.108253175 & 0.116926793\\ |
---|
| 1728 | 4 & 0.250000000 & 0.0541265877 & 0.0413398642\\ |
---|
| 1729 | 5 & 0.176776695 & 0.0270632939 & 0.0146158492\\ |
---|
| 1730 | 6 & 0.125000000 & 0.0135316469 & 0.00516748303 |
---|
| 1731 | |
---|
| 1732 | \end{tabular} |
---|
| 1733 | |
---|
| 1734 | |
---|
| 1735 | \end{itemize} |
---|
| 1736 | |
---|
| 1737 | \end{document} |
---|