1 | \secA{Available parameters} |
---|
2 | \label{app-param} |
---|
3 | |
---|
4 | The full list of parameters that can be listed in the input file are |
---|
5 | given here. If not listed, they take the default value given in |
---|
6 | parentheses. Since the order of the parameters in the input file does |
---|
7 | not matter, they are grouped here in logical sections. |
---|
8 | |
---|
9 | \secB*{Input-output related} |
---|
10 | \begin{entry} |
---|
11 | \item[ImageFile (no default assumed)] The filename of the |
---|
12 | data cube to be analysed. |
---|
13 | \item[flagSubsection \texttt{[false]}] A flag to indicate whether one |
---|
14 | wants a subsection of the requested image. |
---|
15 | \item[Subsection \texttt{[ [*,*,*] ]}] The requested subsection, which |
---|
16 | should be specified in the format \texttt{[x1:x2,y1:y2,z1:z2]}, |
---|
17 | where the limits are inclusive. If the full range of a dimension is |
---|
18 | required, use a \texttt{*}, \eg if you want the full spectral range |
---|
19 | of a subsection of the image, use \texttt{[30:140,30:140,*]} (thus |
---|
20 | the default is the full cube). |
---|
21 | \item[flagReconExists \texttt{[false]}] A flag to indicate whether the |
---|
22 | reconstructed array has been saved by a previous run of \duchamp. If |
---|
23 | set true, the reconstructed array will be read from the file given |
---|
24 | by \texttt{reconFile}, rather than calculated directly. |
---|
25 | \item[reconFile (no default assumed)] The FITS file that contains the |
---|
26 | reconstructed array. If \texttt{flagReconExists} is true and this |
---|
27 | parameter is not defined, the default file searched will be |
---|
28 | determined by the \atrous\ parameters (see \S\ref{sec-recon}). |
---|
29 | \item[OutFile \texttt{[duchamp-Results.txt]}] The file containing the |
---|
30 | final list of detections. This also records the list of input |
---|
31 | parameters. |
---|
32 | \item[SpectraFile \texttt{[duchamp-Spectra.ps]}] The postscript file |
---|
33 | containing the resulting integrated spectra and images of the |
---|
34 | detections. |
---|
35 | \item[flagLog \texttt{[true]}] A flag to indicate whether intermediate |
---|
36 | detections should be logged. |
---|
37 | \item[LogFile \texttt{[duchamp-Logfile.txt]}] The file in which |
---|
38 | intermediate detections are logged. These are detections that have |
---|
39 | not been merged. This is primarily for use in debugging and |
---|
40 | diagnostic purposes -- normal use of the program will probably not |
---|
41 | require this. |
---|
42 | \item[flagOutputRecon \texttt{[false]}] A flag to say whether or not |
---|
43 | to save the reconstructed cube as a FITS file. The filename will be |
---|
44 | derived according to the naming scheme detailed in |
---|
45 | Section~\ref{sec-reconIO}. |
---|
46 | \item[flagOutputResid \texttt{[false]}] As for |
---|
47 | \texttt{flagOutputRecon}, but for the residual array -- the |
---|
48 | difference between the original cube and the reconstructed cube. The |
---|
49 | filename will be derived according to the naming scheme detailed in |
---|
50 | Section~\ref{sec-reconIO}. |
---|
51 | \item[flagVOT \texttt{[false]}] A flag to say whether to create a |
---|
52 | VOTable file corresponding to the information in |
---|
53 | \texttt{outfile}. This will be an XML file in the Virtual |
---|
54 | Observatory VOTable format. |
---|
55 | \item[votFile \texttt{[duchamp-Results.xml]}] The VOTable file with |
---|
56 | the list of final detections. Some input parameters are also |
---|
57 | recorded. |
---|
58 | \item[flagKarma \texttt{[false]}] A flag to say whether to create a |
---|
59 | Karma annotation file corresponding to the information in |
---|
60 | \texttt{outfile}. This can be used as an overlay for the Karma |
---|
61 | programs such as \texttt{kvis}. |
---|
62 | \item[karmaFile \texttt{[duchamp-Results.ann]}] The Karma annotation |
---|
63 | file showing the list of final detections. |
---|
64 | \item[flagMaps \texttt{[true]}] A flag to say whether to save |
---|
65 | postscript files showing the 0th moment map of the whole cube |
---|
66 | (parameter \texttt{momentMap}) and the detection image |
---|
67 | (\texttt{detectionMap}). |
---|
68 | \item[momentMap \texttt{[duchamp-MomentMap.ps]}] A postscript file |
---|
69 | containing a map of the 0th moment of the detected sources, as well |
---|
70 | as pixel and WCS coordinates. |
---|
71 | \item[detectionMap \texttt{[duchamp-DetectionMap.ps]}] A postscript |
---|
72 | file showing each of the detected objects, coloured in greyscale by |
---|
73 | the number of channels spanned by each pixel. Also shows pixel and |
---|
74 | WCS coordinates. |
---|
75 | \end{entry} |
---|
76 | |
---|
77 | \secB*{Modifying the cube} |
---|
78 | \begin{entry} |
---|
79 | \item[flagBlankPix \texttt{[true]}] A flag to say whether to remove |
---|
80 | BLANK pixels from the analysis -- these are pixels set to some |
---|
81 | particular value because they fall outside the imaged area. |
---|
82 | \item[blankPixValue \texttt{[-8.00061]}] The value of the BLANK |
---|
83 | pixels, if this information is not contained in the FITS header (the |
---|
84 | usual procedure is to obtain this value from the header information |
---|
85 | -- in which case the value set by this parameter is ignored). |
---|
86 | \item[flagMW \texttt{[false]}] A flag to say whether to ignore |
---|
87 | channels contaminated by Milky Way (or other) emission -- the |
---|
88 | searching algorithms will not look at these channels. |
---|
89 | \item[maxMW \texttt{[112]}] The maximum channel number containing |
---|
90 | ``Milky Way'' emission. |
---|
91 | \item[minMW \texttt{[75]}] The minimum channel number containing |
---|
92 | ``Milky Way'' emission. Note that the range specified by |
---|
93 | \texttt{maxMW} and \texttt{minMW} is inclusive. |
---|
94 | \item[flagBaseline \texttt{[false]}] A flag to say whether to remove |
---|
95 | the baseline from each spectrum in the cube for the purposes of |
---|
96 | reconstruction and detection. |
---|
97 | \end{entry} |
---|
98 | |
---|
99 | \secB*{Detection related} |
---|
100 | |
---|
101 | \secC*{General detection} |
---|
102 | \begin{entry} |
---|
103 | \item[flagNegative \texttt{[false]}] A flag to indicate that the |
---|
104 | features being searched for are negative. The cube will be inverted |
---|
105 | prior to searching. |
---|
106 | \item[snrCut \texttt{[3.]}] The cut-off value for thresholding, in |
---|
107 | terms of number of $\sigma$ above the mean. |
---|
108 | \item[flagGrowth \texttt{[false]}] A flag indicating whether or not to |
---|
109 | grow the detected objects to a smaller threshold. |
---|
110 | \item[growthCut \texttt{[2.]}] The smaller threshold using in growing |
---|
111 | detections. In units of $\sigma$ above the mean. |
---|
112 | \item[beamSize \texttt{[10.]}] The size of the beam in pixels. If the |
---|
113 | header keywords BMAJ and BMIN are present, then these will be used |
---|
114 | to calculate the beam size, and this parameter will be ignored. |
---|
115 | \end{entry} |
---|
116 | |
---|
117 | \secC*{\Atrous\ reconstruction} |
---|
118 | \begin{entry} |
---|
119 | \item [flagATrous \texttt{[true]}] A flag indicating whether or not to |
---|
120 | reconstruct the cube using the \atrous\ wavelet |
---|
121 | reconstruction. See \S\ref{sec-recon} for details. |
---|
122 | \item[reconDim \texttt{[3]}] The number of dimensions to use in the |
---|
123 | reconstruction. 1 means reconstruct each spectrum separately, 2 |
---|
124 | means each channel map is done separately, and 3 means do the whole |
---|
125 | cube in one go. |
---|
126 | \item[scaleMin \texttt{[1]}] The minimum wavelet scale to be used in the |
---|
127 | reconstruction. A value of 1 means ``use all scales''. |
---|
128 | \item[snrRecon \texttt{[4]}] The thresholding cutoff used in the |
---|
129 | reconstruction -- only wavelet coefficients this many $\sigma$ above |
---|
130 | the mean (or greater) are included in the reconstruction. |
---|
131 | \item[filterCode \texttt{[1]}] The code number of the filter to use in |
---|
132 | the reconstruction. The options are: |
---|
133 | \begin{itemize} |
---|
134 | \item \textbf{1:} B$_3$-spline filter: coefficients = |
---|
135 | $(\frac{1}{16}, \frac{1}{4}, \frac{3}{8}, \frac{1}{4}, \frac{1}{16})$ |
---|
136 | \item \textbf{2:} Triangle filter: coefficients = |
---|
137 | $(\frac{1}{4}, \frac{1}{2}, \frac{1}{4})$ |
---|
138 | \item \textbf{3:} Haar wavelet: coefficients = |
---|
139 | $(0, \frac{1}{2}, \frac{1}{2})$ |
---|
140 | \end{itemize} |
---|
141 | \end{entry} |
---|
142 | |
---|
143 | \secC*{FDR method} |
---|
144 | \begin{entry} |
---|
145 | \item[flagFDR \texttt{[false]}] A flag indicating whether or not to use |
---|
146 | the False Discovery Rate method in thresholding the pixels. |
---|
147 | \item[alphaFDR \texttt{[0.01]}] The $\alpha$ parameter used in the FDR |
---|
148 | analysis. The average number of false detections, as a fraction of the |
---|
149 | total number, will be less than $\alpha$ (see \S\ref{sec-detection}). |
---|
150 | \end{entry} |
---|
151 | |
---|
152 | \secC*{Merging detections} |
---|
153 | \begin{entry} |
---|
154 | \item[minPix \texttt{[2]}] The minimum number of spatial pixels for a |
---|
155 | single detection to be counted. |
---|
156 | \item[minChannels \texttt{[3]}] The minimum number of consecutive |
---|
157 | channels that must be present in a detection. |
---|
158 | \item[flagAdjacent \texttt{[true]}] A flag indicating whether to use |
---|
159 | the ``adjacent pixel'' criterion to decide whether to merge |
---|
160 | objects. If not, the next two parameters are used to determine |
---|
161 | whether objects are within the necessary thresholds. |
---|
162 | \item[threshSpatial \texttt{[3.]}] The maximum allowed minimum spatial |
---|
163 | separation (in pixels) between two detections for them to be merged |
---|
164 | into one. Only used if \texttt{flagAdjacent = false}. |
---|
165 | \item[threshVelocity \texttt{[7.]}] The maximum allowed minimum channel |
---|
166 | separation between two detections for them to be merged into |
---|
167 | one. |
---|
168 | \end{entry} |
---|
169 | |
---|
170 | \secC*{Other parameters} |
---|
171 | \begin{entry} |
---|
172 | \item[spectralMethod \texttt{[peak]}] This indicates which method is used |
---|
173 | to plot the output spectra: \texttt{peak} means plot the spectrum |
---|
174 | containing the detection's peak pixel; \texttt{sum} means sum the |
---|
175 | spectra of each detected spatial pixel, and correct for the beam |
---|
176 | size. Any other choice defaults to \texttt{peak}. |
---|
177 | \item[spectralUnits \texttt{[km/s]}] The user can specify the units of |
---|
178 | the spectral axis. Assuming the WCS of the FITS file is valid, the |
---|
179 | spectral axis is transformed into velocity, and put into these units |
---|
180 | for all output and for calculations such as the integrated flux of a |
---|
181 | detection. |
---|
182 | \item[drawBorders \texttt{[true]}] A flag indicating whether borders |
---|
183 | are to be drawn around the detected objects in the moment maps |
---|
184 | included in the output (see for example Fig.~\ref{fig-spect}). |
---|
185 | \item[drawBlankEdges \texttt{[true]}] A flag indicating whether to |
---|
186 | draw the dividing line between BLANK and non-BLANK pixels on the |
---|
187 | 2-dimensional images (see for example Fig.~\ref{fig-moment}). |
---|
188 | \item[verbose \texttt{[true]}] A flag indicating whether to print the |
---|
189 | progress of computationally-intensive algorithms (such as the |
---|
190 | searching and merging) to screen. |
---|
191 | \end{entry} |
---|
192 | |
---|