1 | \secA{Outputs} |
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2 | \label{sec-output} |
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3 | |
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4 | \secB{During execution} |
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5 | |
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6 | \duchamp\ provides the user with feedback whilst it is running, to |
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7 | keep the user informed on the progress of the analysis. Most of this |
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8 | consists of self-explanatory messages about the particular stage the |
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9 | program is up to. The relevant parameters are printed to the screen at |
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10 | the start (once the file has been successfully read in), so the user |
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11 | is able to make a quick check that the setup is correct (see |
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12 | Appendix~{app-input} for an example). |
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13 | |
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14 | If the cube is being trimmed (\S\ref{sec-modify}), the resulting |
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15 | dimensions are printed to indicate how much has been trimmed. If a |
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16 | reconstruction is being done, a continually updating message shows |
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17 | either the current iteration and scale, compared to the maximum scale |
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18 | (when \texttt{reconDim=3}), or a progress bar showing the amount of |
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19 | the cube that has been reconstructed (for smaller values of |
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20 | \texttt{reconDim}). |
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21 | |
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22 | During the searching algorithms, the progress through the 1D and 2D |
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23 | searches are shown. When the searches have completed, the number of |
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24 | objects found in both the 1D and 2D searches are reported (see |
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25 | \S\ref{sec-detection} for details). |
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26 | |
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27 | In the merging process (where multiple detections of the same object |
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28 | are combined -- see \S\ref{sec-merger}), two stages of output |
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29 | occur. The first is when each object in the list is compared with all |
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30 | others. The output shows two numbers: the first being how far through |
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31 | the list the current object is, and the second being the length of the |
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32 | list. As the algorithm proceeds, the first number should increase and |
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33 | the second should decrease (as objects are combined). When the numbers |
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34 | meet (\ie the whole list has been compared), the second phase begins, |
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35 | in which multiply-appearing pixels in each object are removed, as are |
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36 | objects not meeting the minimum channels requirement. During this |
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37 | phase, the total number of accepted objects is shown, which should |
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38 | steadily increase until all have been accepted or rejected. Note that |
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39 | these steps can be very quick for small numbers of detections. |
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40 | |
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41 | Since this continual printing to screen has some overhead of time and |
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42 | CPU involved, the user can elect to not print this information by |
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43 | setting the parameter \texttt{verbose = 0}. In this case, the user is |
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44 | still informed as to the steps being undertaken, but the details of |
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45 | the progress are not shown. |
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46 | |
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47 | \secB{Results} |
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48 | |
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49 | \secC{Table of results} |
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50 | |
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51 | Finally, we get to the results -- the reason for running \duchamp\ in |
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52 | the first place. Once the detection list is finalised, it is sorted by |
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53 | the mean velocity of the detections (or, if there is no good WCS |
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54 | associated with the cube, by the mean Z-pixel position). The results |
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55 | are then printed to the screen and to the output file, given by the |
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56 | \texttt{OutFile} parameter. The results list, an example of which can |
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57 | be seen in Appendix~\ref{app-output}, contains the following columns |
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58 | (note that the title of the columns depending on WCS information will |
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59 | depend on the projection of the WCS): |
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60 | |
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61 | \begin{entry} |
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62 | \item[Obj\#] The ID number of the detection (simply the sequential |
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63 | count for the list, which is ordered by increasing velocity, or |
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64 | channel number, if the WCS is not good enough to find the velocity). |
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65 | \item[Name] The ``IAU''-format name of the detection (derived from the |
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66 | WCS position -- see below for a description of the format). |
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67 | \item[X] The average X-pixel position (averaged over all detected |
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68 | voxels). |
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69 | \item[Y] The average Y-pixel position. |
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70 | \item[Z] The average Z-pixel position. |
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71 | \item[RA/GLON] The Right Ascension or Galactic Longitude of the centre |
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72 | of the object. |
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73 | \item[DEC/GLAT] The Declination or Galactic Latitude of the centre of |
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74 | the object. |
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75 | \item[VEL] The mean velocity of the object [units given by the |
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76 | \texttt{spectralUnits} parameter]. |
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77 | \item[w\_RA/w\_GLON] The width of the object in Right Ascension or |
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78 | Galactic Longitude [arcmin]. |
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79 | \item[w\_DEC/w\_GLAT] The width of the object in Declination Galactic |
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80 | Latitude [arcmin]. |
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81 | \item[w\_VEL] The full velocity width of the detection (max channel |
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82 | $-$ min channel, in velocity units [see note below]). |
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83 | \item[F\_int] The integrated flux over the object, in the units of |
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84 | flux times velocity, corrected for the beam if necessary. |
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85 | \item[F\_peak] The peak flux over the object, in the units of flux. |
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86 | \item[X1, X2] The minimum and maximum X-pixel coordinates. |
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87 | \item[Y1, Y2] The minimum and maximum Y-pixel coordinates. |
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88 | \item[Z1, Z2] The minimum and maximum Z-pixel coordinates. |
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89 | \item[Npix] The number of voxels (\ie distinct $(x,y,z)$ coordinates) |
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90 | in the detection. |
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91 | \item[Flag] Whether the detection has any warning flags (see below). |
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92 | \end{entry} |
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93 | The Name is derived from the WCS position. For instance, a source |
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94 | centred on the RA,Dec position 12$^h$53$^m$45$^s$, |
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95 | -36$^\circ$24$'$12$''$ will be called J125345$-$362412 (if the epoch |
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96 | is J2000) or B125345$-$362412 (if B1950). An alternative form is used |
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97 | for Galactic coordinates: a source centred on the position ($l$,$b$) = |
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98 | (323.1245, 5.4567) will be called G323.124$+$05.457. If the WCS is not |
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99 | valid (\ie is not present or does not have all the necessary |
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100 | information), the Name, RA, DEC, VEL and related columns are not |
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101 | printed, but the pixel coordinates are still provided. |
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102 | |
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103 | The velocity units can be specified by the user, using the parameter |
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104 | \texttt{spectralUnits} (enter it as a single string). The default |
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105 | value is km/s, which should be suitable for most users. These units |
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106 | are also used to give the units of integrated flux. Note that if there |
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107 | is no rest frequency specified in the FITS header, the \duchamp\ |
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108 | output will instead default to using Frequency, with units of MHz. |
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109 | |
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110 | If the WCS is not specified sufficiently to be used, then all columns |
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111 | from RA/GLON to w\_VEL will be left blank. Also, F\_int will be |
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112 | replaced with the more simple F\_tot -- the total flux in the |
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113 | detection, being the sum of all detected voxels. |
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114 | |
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115 | The last column contains any warning flags about the detection. There |
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116 | are currently two options here. An `E' is printed if the detection is |
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117 | next to the edge of the image, meaning either the limit of the pixels, |
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118 | or the limit of the non-BLANK pixel region. An `N' is printed if the |
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119 | total flux, summed over all the (non-BLANK) pixels in the smallest box |
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120 | that completely encloses the detection, is negative. Note that this |
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121 | sum is likely to include non-detected pixels. It is of use in pointing |
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122 | out detections that lie next to strongly negative pixels, such as |
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123 | might arise due to interference -- the detected pixels might then also |
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124 | be due to the interference, so caution is advised. |
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125 | |
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126 | \secC{Other results lists} |
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127 | |
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128 | Two alternative results files can also be requested. One option is a |
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129 | VOTable-format XML file, containing just the RA, Dec, Velocity and the |
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130 | corresponding widths of the detections, as well as the fluxes. The |
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131 | user should set \texttt{flagVOT = 1}, and put the desired filename in |
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132 | the parameter \texttt{votFile} -- note that the default is for it not |
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133 | to be produced. This file should be compatible with all Virtual |
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134 | Observatory tools (such as Aladin\footnote{ Aladin can be found on the |
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135 | web at |
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136 | \href{http://aladin.u-strasbg.fr/}{http://aladin.u-strasbg.fr/}}). The |
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137 | second option is an annotation file for use with the Karma toolkit of |
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138 | visualisation tools (in particular, with \texttt{kvis}). This will |
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139 | draw a circle at the position of each detection, and number it |
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140 | according to the Obj\# given above. To make use of this option, the |
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141 | user should set \texttt{flagKarma = 1}, and put the desired filename |
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142 | in the parameter \texttt{karmaFile} -- again, the default is for it |
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143 | not to be produced. |
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144 | |
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145 | As the program is running, it also (optionally) records the detections |
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146 | made in each individual spectrum or channel (see \S\ref{sec-detection} |
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147 | for details on this process). This is recorded in the file given by |
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148 | the parameter \texttt{LogFile}. This file does not include the columns |
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149 | \texttt{Name, RA, DEC, w\_RA, w\_DEC, VEL, w\_VEL}. This file is |
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150 | designed primarily for diagnostic purposes: \eg to see if a given set |
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151 | of pixels is detected in, say, one channel image, but does not survive |
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152 | the merging process. The list of pixels (and their fluxes) in the |
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153 | final detection list are also printed to this file, again for |
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154 | diagnostic purposes. The file also records the execution time, as well |
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155 | as the command-line statement used to run \duchamp. The creation of |
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156 | this log file can be prevented by setting \texttt{flagLog = |
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157 | false}. (This may be a good idea if you are not interested in its |
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158 | contents, as it can be a large file if many pixels are being |
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159 | detected.) |
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160 | |
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161 | \secC{Graphical output -- spectra} |
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162 | |
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163 | As well as the output data file, a postscript file is created that |
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164 | shows the spectrum for each detection, together with a small cutout |
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165 | image (the 0th moment) and basic information about the detection (note |
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166 | that any flags are printed after the name of the detection, in the |
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167 | format \texttt{[E]}). If the cube was reconstructed, the spectrum from |
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168 | the reconstruction is shown in red, over the top of the original |
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169 | spectrum. The spectral extent of the detected object is indicated by |
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170 | two dashed blue lines, and the region covered by the ``Milky Way'' |
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171 | channels is shown by a green hashed box. An example detection can be |
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172 | seen below in Fig.~\ref{fig-spect}. |
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173 | |
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174 | The spectrum that is plotted is governed by the |
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175 | \texttt{spectralMethod} parameter. It can be either \texttt{peak}, |
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176 | where the spectrum is from the spatial pixel containing the |
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177 | detection's peak flux; or \texttt{sum}, where the spectrum is summed |
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178 | over all spatial pixels, and then corrected for the beam size. The |
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179 | spectral extent of the detection is indicated with blue lines, and a |
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180 | zoom is shown in a separate window. |
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181 | |
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182 | The cutout image can optionally include a border around the spatial |
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183 | pixels that are in the detection (turned on and off by the parameter |
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184 | \texttt{drawBorders} -- the default is \texttt{true}). It includes a |
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185 | scale bar in the bottom left corner to indicate size -- its length is |
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186 | indicated next to it (the choice of length depends on the size of the |
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187 | image). |
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188 | |
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189 | There may also be one or two extra lines on the image. A yellow line |
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190 | shows the limits of the cube -- the detected object is obviously close |
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191 | to the edge of the cube, and the box size extends outside the region |
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192 | covered by the data. A purple line, however, shows the dividing line |
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193 | between BLANK and non-BLANK pixels. The BLANK pixels will always be |
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194 | shown in black. The first type of line is always drawn, while the |
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195 | second is governed by the parameter \texttt{drawBlankEdges} (whose |
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196 | default is \texttt{true}), and obviously whether there are any BLANK |
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197 | pixel present. |
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198 | |
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199 | \begin{figure}[t] |
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200 | \begin{center} |
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201 | \includegraphics[width=\textwidth]{example_spectrum} |
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202 | \end{center} |
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203 | \caption{\footnotesize An example of the spectrum output. Note several |
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204 | of the features discussed in the text: the red lines indicating the |
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205 | reconstructed spectrum; the blue dashed lines indicating the |
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206 | spectral extent of the detection; the green hashed area indicating |
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207 | the Milky Way channels that are ignored by the searching algorithm; |
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208 | the blue border showing its spatial extent on the 0th moment map; |
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209 | and the 15~arcmin-long scale bar.} |
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210 | \label{fig-spect} |
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211 | \end{figure} |
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212 | |
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213 | \secC{Graphical output -- maps} |
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214 | |
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215 | \begin{figure}[!t] |
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216 | \begin{center} |
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217 | \includegraphics[width=\textwidth]{example_moment_map} |
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218 | \end{center} |
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219 | \caption{\footnotesize An example of the moment map created by |
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220 | \duchamp. The full extent of the cube is covered, and the 0th moment |
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221 | of each object is shown (integrated individually over all the |
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222 | detected channels). The purple line indicates the limit of the |
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223 | non-BLANK pixels.} |
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224 | \label{fig-moment} |
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225 | \end{figure} |
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226 | |
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227 | Finally, a couple of images are optionally produced: a 0th moment map |
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228 | of the cube, combining just the detected channels in each object, |
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229 | showing the integrated flux in grey-scale; and a ``detection image'', |
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230 | a grey-scale image where the pixel values are the number of channels |
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231 | that spatial pixel is detected in. In both cases, if |
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232 | \texttt{drawBorders = true}, a border is drawn around the spatial |
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233 | extent of each detection, and if \texttt{drawBlankEdges = true}, the |
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234 | purple line dividing BLANK and non-BLANK pixels (as described above) |
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235 | is drawn. An example moment map is shown in Fig.~\ref{fig-moment}. |
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236 | The production or otherwise of these images is governed by the |
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237 | \texttt{flagMaps} parameter. |
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238 | |
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239 | The purpose of these images are to provide a visual guide to where the |
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240 | detections have been made, and, particularly in the case of the moment |
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241 | map, to provide an indication of the strength of the source. In both |
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242 | cases, the detections are numbered (in the same sense as the output |
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243 | list and as the spectral plots), and the spatial borders are marked |
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244 | out as for the cutout images in the spectra file. Both these images |
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245 | are saved as postscript files (given by the parameters |
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246 | \texttt{momentMap} and \texttt{detectionMap} respectively), with the |
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247 | latter also displayed in a \textsc{pgplot} window (regardless of the |
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248 | state of \texttt{flagMaps}). |
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