[303] | 1 | % ----------------------------------------------------------------------- |
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| 2 | % outputs.tex: Section detailing the different forms of text- and |
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| 3 | % plot-based output. |
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| 4 | % ----------------------------------------------------------------------- |
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| 5 | % Copyright (C) 2006, Matthew Whiting, ATNF |
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| 6 | % |
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| 7 | % This program is free software; you can redistribute it and/or modify it |
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| 8 | % under the terms of the GNU General Public License as published by the |
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| 9 | % Free Software Foundation; either version 2 of the License, or (at your |
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| 10 | % option) any later version. |
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| 11 | % |
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| 12 | % Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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| 13 | % ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 14 | % FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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| 15 | % for more details. |
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| 16 | % |
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| 17 | % You should have received a copy of the GNU General Public License |
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| 18 | % along with Duchamp; if not, write to the Free Software Foundation, |
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| 19 | % Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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| 20 | % |
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| 21 | % Correspondence concerning Duchamp may be directed to: |
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| 22 | % Internet email: Matthew.Whiting [at] atnf.csiro.au |
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| 23 | % Postal address: Dr. Matthew Whiting |
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| 24 | % Australia Telescope National Facility, CSIRO |
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| 25 | % PO Box 76 |
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| 26 | % Epping NSW 1710 |
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| 27 | % AUSTRALIA |
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| 28 | % ----------------------------------------------------------------------- |
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[158] | 29 | \secA{Outputs} |
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| 30 | \label{sec-output} |
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| 31 | |
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| 32 | \secB{During execution} |
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| 33 | |
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[258] | 34 | \duchamp provides the user with feedback whilst it is running, to |
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[158] | 35 | keep the user informed on the progress of the analysis. Most of this |
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| 36 | consists of self-explanatory messages about the particular stage the |
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| 37 | program is up to. The relevant parameters are printed to the screen at |
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| 38 | the start (once the file has been successfully read in), so the user |
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| 39 | is able to make a quick check that the setup is correct (see |
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| 40 | Appendix~{app-input} for an example). |
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| 41 | |
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| 42 | If the cube is being trimmed (\S\ref{sec-modify}), the resulting |
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| 43 | dimensions are printed to indicate how much has been trimmed. If a |
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| 44 | reconstruction is being done, a continually updating message shows |
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| 45 | either the current iteration and scale, compared to the maximum scale |
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[298] | 46 | (when \texttt{reconDim = 3}), or a progress bar showing the amount of |
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[158] | 47 | the cube that has been reconstructed (for smaller values of |
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| 48 | \texttt{reconDim}). |
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| 49 | |
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[298] | 50 | During the searching algorithms, the progress through the search is |
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| 51 | shown. When completed, the number of objects found is reported (this |
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| 52 | is the total number found, before any merging is done). |
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[158] | 53 | |
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| 54 | In the merging process (where multiple detections of the same object |
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| 55 | are combined -- see \S\ref{sec-merger}), two stages of output |
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| 56 | occur. The first is when each object in the list is compared with all |
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| 57 | others. The output shows two numbers: the first being how far through |
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| 58 | the list the current object is, and the second being the length of the |
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| 59 | list. As the algorithm proceeds, the first number should increase and |
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| 60 | the second should decrease (as objects are combined). When the numbers |
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[265] | 61 | meet, the whole list has been compared. If the objects are being |
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| 62 | grown, a similar output is shown, indicating the progress through the |
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| 63 | list. In the rejection stage, in which objects not meeting the minimum |
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| 64 | pixels/channels requirements are removed, the total number of objects |
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| 65 | remaining in the list is shown, which should steadily decrease with |
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| 66 | each rejection until all have been examined. Note that these steps can |
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| 67 | be very quick for small numbers of detections. |
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[158] | 68 | |
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| 69 | Since this continual printing to screen has some overhead of time and |
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| 70 | CPU involved, the user can elect to not print this information by |
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[298] | 71 | setting the parameter \texttt{verbose = false}. In this case, the user |
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| 72 | is still informed as to the steps being undertaken, but the details of |
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[158] | 73 | the progress are not shown. |
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| 74 | |
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[162] | 75 | There may also be Warning or Error messages printed to screen. The |
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| 76 | Warning messages occur when something happens that is unexpected (for |
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| 77 | instance, a desired keyword is not present in the FITS header), but |
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| 78 | not detrimental to the execution. An Error message is something more |
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| 79 | serious, and indicates some part of the program was not able to |
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| 80 | complete its task. The message will also indicate which function or |
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| 81 | subroutine generated it -- this is primarily a tool for debugging, but |
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| 82 | can be useful in determining what went wrong. |
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| 83 | |
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[285] | 84 | \secB{Text-based output files} |
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[158] | 85 | |
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| 86 | \secC{Table of results} |
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[285] | 87 | \label{sec-results} |
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[158] | 88 | |
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[258] | 89 | Finally, we get to the results -- the reason for running \duchamp in |
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[158] | 90 | the first place. Once the detection list is finalised, it is sorted by |
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| 91 | the mean velocity of the detections (or, if there is no good WCS |
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[162] | 92 | associated with the cube, by the mean $z$-pixel position). The results |
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[158] | 93 | are then printed to the screen and to the output file, given by the |
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[194] | 94 | \texttt{OutFile} parameter. |
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[158] | 95 | |
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[364] | 96 | The output consists of two sections. First, a list of the parameters |
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[194] | 97 | are printed to the output file, for future reference. Next, the |
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[285] | 98 | detection threshold that was used is given, so comparison can be made |
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[386] | 99 | with other searches. The statistics estimating the noise parameters |
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| 100 | are given (see \S\ref{sec-stats}). Thirdly, the number of detections |
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| 101 | are reported. |
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[194] | 102 | |
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[364] | 103 | All this information, known as the ``header'', can either be written |
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| 104 | to the start of the output file (denoted by the parameter |
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| 105 | \texttt{OutFile}), or written to a separate file from the list of |
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| 106 | detections. This second option is activated by the parameter |
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| 107 | \texttt{flagSeparateHeader}, and the information is written to the |
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| 108 | file given by \texttt{HeaderFile}. |
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| 109 | |
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[194] | 110 | The most interesting part, however, is the list of detected |
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| 111 | objects. This list, an example of which can be seen in |
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| 112 | Appendix~\ref{app-output}, contains the following columns (note that |
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| 113 | the title of the columns depending on WCS information will depend on |
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| 114 | the details of the WCS projection: they are shown below for the |
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| 115 | Equatorial and Galactic projection cases). |
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| 116 | |
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[306] | 117 | \begin{Lentry} |
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| 118 | \item[{Obj\#}] The ID number of the detection (simply the |
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[303] | 119 | sequential count for the list, which is ordered by increasing |
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| 120 | velocity, or channel number, if the WCS is not good enough to find |
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| 121 | the velocity). |
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[306] | 122 | \item[{Name}] The ``IAU''-format name of the detection (derived from the |
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[158] | 123 | WCS position -- see below for a description of the format). |
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[306] | 124 | \item[{X,Y,Z}] The ``centre'' pixel position, determined by the input |
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[285] | 125 | parameter \texttt{pixelCentre}. |
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[306] | 126 | \item[{RA/GLON}] The Right Ascension or Galactic Longitude of the centre |
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[285] | 127 | of the object. |
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[306] | 128 | \item[{DEC/GLAT}] The Declination or Galactic Latitude of the centre of |
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[285] | 129 | the object. |
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[306] | 130 | \item[{VEL}] The mean velocity of the object [units given by the |
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[158] | 131 | \texttt{spectralUnits} parameter]. |
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[306] | 132 | \item[{w\_RA/w\_GLON}] The width of the object in Right Ascension or |
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[285] | 133 | Galactic Longitude (depending on FITS coordinates) [arcmin]. |
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[306] | 134 | \item[{w\_DEC/w\_GLAT}] The width of the object in Declination Galactic |
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[158] | 135 | Latitude [arcmin]. |
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[306] | 136 | \item[{w\_VEL}] The full velocity width of the detection (max channel |
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[158] | 137 | $-$ min channel, in velocity units [see note below]). |
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[306] | 138 | \item[{F\_int}] The integrated flux over the object, in the units of |
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[158] | 139 | flux times velocity, corrected for the beam if necessary. |
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[306] | 140 | \item[{F\_tot}] The sum of the flux values of all detected voxels. |
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| 141 | \item[{F\_peak}] The peak flux over the object, in the units of flux. |
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| 142 | \item[{S/Nmax}] The signal-to-noise ratio at the peak pixel. |
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| 143 | \item[{X1, X2}] The minimum and maximum X-pixel coordinates. |
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| 144 | \item[{Y1, Y2}] The minimum and maximum Y-pixel coordinates. |
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| 145 | \item[{Z1, Z2}] The minimum and maximum Z-pixel coordinates. |
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| 146 | \item[{Npix}] The number of voxels (\ie distinct $(x,y,z)$ coordinates) |
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[158] | 147 | in the detection. |
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[306] | 148 | \item[{Flag}] Whether the detection has any warning flags (see below). |
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| 149 | \end{Lentry} |
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[162] | 150 | |
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[303] | 151 | Note that the \texttt{X, Y, Z} columns depend on the \texttt{pixelCentre} |
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[285] | 152 | parameter. This is because there are three alternative ways of |
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| 153 | expressing the centre of a detection, which are all listed in the list |
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| 154 | of detections written to the output file. These alternatives are: |
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[306] | 155 | \begin{Lentry} |
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| 156 | \item[{X\_av, Y\_av, Z\_av}] The average pixel value in each |
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[303] | 157 | axis direction \ie X\_av is the average of the $x$-values of all |
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| 158 | pixels in the detection. |
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[306] | 159 | \item[{X\_cent, Y\_cent, Z\_cent}] The centroid position, being |
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[303] | 160 | the flux-weighted average of the pixels. |
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[306] | 161 | \item[{X\_peak, Y\_peak, Z\_peak}] The location of the pixel |
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[303] | 162 | containing the peak flux value. |
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[306] | 163 | \end{Lentry} |
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[303] | 164 | These are also written to the table in the output file, although not |
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| 165 | to the screen (as it would make the width of the table |
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| 166 | unwieldy). Similarly, the \texttt{F\_tot} column is only written to the output |
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| 167 | file, and not at run-time. |
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[285] | 168 | |
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[303] | 169 | The \texttt{Name} is derived from the WCS position. For instance, a |
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| 170 | source that is centred on the RA,Dec position 12$^h$53$^m$45$^s$, |
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[231] | 171 | -36$^\circ$24$'$12$''$ will be given the name J125345$-$362412, if the |
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| 172 | epoch is J2000, or the name B125345$-$362412 if it is B1950. An |
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| 173 | alternative form is used for Galactic coordinates: a source centred on |
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| 174 | the position ($l$,$b$) = (323.1245, 5.4567) will be called |
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| 175 | G323.124$+$05.457. If the WCS is not valid (\ie is not present or does |
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[303] | 176 | not have all the necessary information), the \texttt{Name, RA, DEC, |
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| 177 | VEL} and related columns are not printed, but the pixel coordinates |
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| 178 | are still provided. |
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[158] | 179 | |
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| 180 | The velocity units can be specified by the user, using the parameter |
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[298] | 181 | \texttt{spectralUnits} (enter it as a single string with no |
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| 182 | spaces). The default value is km/s, which should be suitable for most |
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| 183 | users. These units are also used to give the units of integrated |
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| 184 | flux. Note that if there is no rest frequency specified in the FITS |
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| 185 | header, the \duchamp output will instead default to using Frequency, |
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| 186 | with units of MHz. |
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[158] | 187 | |
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[194] | 188 | If the WCS is absent or not sufficiently specified, then all columns |
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[303] | 189 | from \texttt{RA/GLON} to \texttt{w\_VEL} will be left blank. Also, |
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| 190 | \texttt{F\_int} will be replaced with the more simple \texttt{F\_tot}. |
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[158] | 191 | |
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[303] | 192 | The \texttt{Flag} column contains any warning flags, such as: |
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[195] | 193 | \begin{itemize} |
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| 194 | \item \textbf{E} -- The detection is next to the spatial edge of the image, |
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| 195 | meaning either the limit of the pixels, or the limit of the non-BLANK |
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| 196 | pixel region. |
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| 197 | \item \textbf{S} -- The detection lies at the edge of the spectral region. |
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| 198 | \item \textbf{N} -- The total flux, summed over all the (non-BLANK) |
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| 199 | pixels in the smallest box that completely encloses the detection, is |
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| 200 | negative. Note that this sum is likely to include non-detected |
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| 201 | pixels. It is of use in pointing out detections that lie next to |
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| 202 | strongly negative pixels, such as might arise due to interference -- |
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| 203 | the detected pixels might then also be due to the interference, so |
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| 204 | caution is advised. |
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| 205 | \end{itemize} |
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[194] | 206 | |
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[158] | 207 | \secC{Other results lists} |
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| 208 | |
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[162] | 209 | Two additional results files can also be requested. One option is a |
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[158] | 210 | VOTable-format XML file, containing just the RA, Dec, Velocity and the |
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| 211 | corresponding widths of the detections, as well as the fluxes. The |
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[298] | 212 | user should set \texttt{flagVOT = true}, and put the desired filename |
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| 213 | in the parameter \texttt{votFile} -- note that the default is for it |
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| 214 | not to be produced. This file should be compatible with all Virtual |
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[285] | 215 | Observatory tools (such as Aladin% |
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| 216 | \footnote{%Aladin can be found on the web at |
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| 217 | \href{http://aladin.u-strasbg.fr/}{http://aladin.u-strasbg.fr/}} |
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| 218 | or TOPCAT\footnote{%Tool for OPerations on Catalogues And Tables: |
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| 219 | \href{http://www.star.bristol.ac.uk/~mbt/topcat/}% |
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| 220 | {http://www.star.bristol.ac.uk/~mbt/topcat/}}). The second option is |
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| 221 | an annotation file for use with the Karma toolkit of visualisation |
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| 222 | tools (in particular, with \texttt{kvis}). This will draw a circle at |
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| 223 | the position of each detection, scaled by the spatial size of the |
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| 224 | detection, and number it according to the Obj\# given above. To make |
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| 225 | use of this option, the user should set |
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[298] | 226 | \texttt{flagKarma = true}, and put the desired filename in the parameter |
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[162] | 227 | \texttt{karmaFile} -- again, the default is for it not to be produced. |
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[158] | 228 | |
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| 229 | As the program is running, it also (optionally) records the detections |
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| 230 | made in each individual spectrum or channel (see \S\ref{sec-detection} |
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| 231 | for details on this process). This is recorded in the file given by |
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| 232 | the parameter \texttt{LogFile}. This file does not include the columns |
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| 233 | \texttt{Name, RA, DEC, w\_RA, w\_DEC, VEL, w\_VEL}. This file is |
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| 234 | designed primarily for diagnostic purposes: \eg to see if a given set |
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| 235 | of pixels is detected in, say, one channel image, but does not survive |
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| 236 | the merging process. The list of pixels (and their fluxes) in the |
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| 237 | final detection list are also printed to this file, again for |
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| 238 | diagnostic purposes. The file also records the execution time, as well |
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| 239 | as the command-line statement used to run \duchamp. The creation of |
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[280] | 240 | this log file can be prevented by setting \texttt{flagLog = false} |
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| 241 | (which is the default). |
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[158] | 242 | |
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[285] | 243 | \secB{Graphical output} |
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[380] | 244 | |
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| 245 | \secC{Mask image} |
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| 246 | \label{sec-maskOut} |
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| 247 | |
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| 248 | It is possible to create a FITS file containing a mask array. This |
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| 249 | array is designed to indicate the location of detected objects, by |
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| 250 | setting pixel values to 1 for pixels in a detected object and 0 |
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| 251 | elsewhere. To create this FITS file, set the input parameter |
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| 252 | \texttt{flagOutputMask=true}. The file will be given the name |
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| 253 | \texttt{image.MASK.fits} (where the input image is called |
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| 254 | \texttt{image.fits}). |
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| 255 | |
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[285] | 256 | \secC{Spectral plots} |
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[158] | 257 | |
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[373] | 258 | As well as the output data file, a postscript file (with the filename |
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| 259 | given by the \texttt{spectralFile} parameter) is created that shows |
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| 260 | the spectrum for each detection, together with a small cutout image |
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| 261 | (the 0th moment) and basic information about the detection (note that |
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| 262 | any flags are printed after the name of the detection, in the format |
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| 263 | \texttt{[E]}). If the cube was reconstructed, the spectrum from the |
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| 264 | reconstruction is shown in red, over the top of the original |
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[285] | 265 | spectrum. The spectral extent of the detected object is indicated by |
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| 266 | two dashed blue lines, and the region covered by the ``Milky Way'' |
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| 267 | channels is shown by a green hashed box. An example detection can be |
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| 268 | seen below in Fig.~\ref{fig-spect}. |
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| 269 | |
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[160] | 270 | \begin{figure}[t] |
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| 271 | \begin{center} |
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| 272 | \includegraphics[width=\textwidth]{example_spectrum} |
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| 273 | \end{center} |
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[285] | 274 | \caption{\footnotesize An example of the spectral output. Note several |
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[160] | 275 | of the features discussed in the text: the red lines indicating the |
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| 276 | reconstructed spectrum; the blue dashed lines indicating the |
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| 277 | spectral extent of the detection; the green hashed area indicating |
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| 278 | the Milky Way channels that are ignored by the searching algorithm; |
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| 279 | the blue border showing its spatial extent on the 0th moment map; |
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| 280 | and the 15~arcmin-long scale bar.} |
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| 281 | \label{fig-spect} |
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| 282 | \end{figure} |
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| 283 | |
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[158] | 284 | The spectrum that is plotted is governed by the |
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[162] | 285 | \texttt{spectralMethod} parameter. It can be either \texttt{peak} (the |
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| 286 | default), where the spectrum is from the spatial pixel containing the |
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[158] | 287 | detection's peak flux; or \texttt{sum}, where the spectrum is summed |
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| 288 | over all spatial pixels, and then corrected for the beam size. The |
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| 289 | spectral extent of the detection is indicated with blue lines, and a |
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| 290 | zoom is shown in a separate window. |
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| 291 | |
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| 292 | The cutout image can optionally include a border around the spatial |
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[231] | 293 | pixels that are in the detection (turned on and off by the |
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| 294 | \texttt{drawBorders} parameter -- the default is \texttt{true}). It |
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| 295 | includes a scale bar in the bottom left corner to indicate size -- its |
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| 296 | length is indicated next to it (the choice of length depends on the |
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| 297 | size of the image). |
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[158] | 298 | |
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| 299 | There may also be one or two extra lines on the image. A yellow line |
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[162] | 300 | shows the limits of the cube's spatial region: when this is shown, the |
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| 301 | detected object will lie close to the edge, and the image box will |
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| 302 | extend outside the region covered by the data. A purple line, however, |
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| 303 | shows the dividing line between BLANK and non-BLANK pixels. The BLANK |
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| 304 | pixels will always be shown in black. The first type of line is always |
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| 305 | drawn, while the second is governed by the parameter |
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| 306 | \texttt{drawBlankEdges} (whose default is \texttt{true}), and |
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| 307 | obviously whether there are any BLANK pixel present. |
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[158] | 308 | |
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[373] | 309 | \secC{Output for 2-dimensional images} |
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| 310 | |
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| 311 | When the input image is two-dimensional, with no spectral dimension, |
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| 312 | this spectral plot would not make much sense. Instead, \duchamp |
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| 313 | creates a similar postscript file that simply includes the text |
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| 314 | headers as well as the 0th-moment map of the detection. As for the |
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| 315 | normal spectral case, this file will be written to the filename given |
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| 316 | by the \texttt{spectralFile} parameter. |
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| 317 | |
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[285] | 318 | \secC{Spatial maps} |
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[158] | 319 | |
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[285] | 320 | \begin{figure}[!t] |
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| 321 | \begin{center} |
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| 322 | \includegraphics[width=\textwidth]{example_moment_map} |
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| 323 | \end{center} |
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| 324 | \caption{\footnotesize An example of the moment map created by |
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| 325 | \duchamp. The full extent of the cube is covered, and the 0th moment |
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| 326 | of each object is shown (integrated individually over all the |
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| 327 | detected channels). The purple line indicates the limit of the |
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| 328 | non-BLANK pixels.} |
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| 329 | \label{fig-moment} |
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| 330 | \end{figure} |
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| 331 | |
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[158] | 332 | Finally, a couple of images are optionally produced: a 0th moment map |
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| 333 | of the cube, combining just the detected channels in each object, |
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| 334 | showing the integrated flux in grey-scale; and a ``detection image'', |
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| 335 | a grey-scale image where the pixel values are the number of channels |
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| 336 | that spatial pixel is detected in. In both cases, if |
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| 337 | \texttt{drawBorders = true}, a border is drawn around the spatial |
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| 338 | extent of each detection, and if \texttt{drawBlankEdges = true}, the |
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| 339 | purple line dividing BLANK and non-BLANK pixels (as described above) |
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| 340 | is drawn. An example moment map is shown in Fig.~\ref{fig-moment}. |
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| 341 | The production or otherwise of these images is governed by the |
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| 342 | \texttt{flagMaps} parameter. |
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| 343 | |
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[285] | 344 | The moment map is also displayed in a PGPlot XWindow (with the |
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| 345 | \texttt{/xs} display option). This feature can be turned off by |
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[298] | 346 | setting \texttt{flagXOutput = false} -- this might be useful if |
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| 347 | running \duchamp on a terminal with no window display capability, or |
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| 348 | if you have set up a script to run it in a batch mode. |
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[195] | 349 | |
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[158] | 350 | The purpose of these images are to provide a visual guide to where the |
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| 351 | detections have been made, and, particularly in the case of the moment |
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| 352 | map, to provide an indication of the strength of the source. In both |
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| 353 | cases, the detections are numbered (in the same sense as the output |
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| 354 | list and as the spectral plots), and the spatial borders are marked |
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| 355 | out as for the cutout images in the spectra file. Both these images |
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| 356 | are saved as postscript files (given by the parameters |
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| 357 | \texttt{momentMap} and \texttt{detectionMap} respectively), with the |
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| 358 | latter also displayed in a \textsc{pgplot} window (regardless of the |
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| 359 | state of \texttt{flagMaps}). |
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