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2 | The Duchamp Source Finder |
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3 | ----------------------------------------------------------------------- |
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4 | Duchamp 1.6.1 -- an object finder for spectral-line data cubes |
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5 | Copyright (C) 2006-2014 |
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6 | Matthew Whiting, CSIRO Astronomy & Space Science |
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7 | |
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8 | Duchamp is free software; you can redistribute it and/or modify it |
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9 | under the terms of the GNU General Public License as published by the |
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10 | Free Software Foundation; either version 2 of the License, or (at your |
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11 | option) any later version. |
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12 | |
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13 | Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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14 | ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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15 | FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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16 | for more details. |
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17 | |
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18 | You should have received a copy of the GNU General Public License |
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19 | along with Duchamp; if not, write to the Free Software Foundation, |
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20 | Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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21 | |
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22 | Correspondence concerning Duchamp may be directed to: |
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23 | Internet email: Matthew.Whiting [at] atnf.csiro.au |
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24 | Postal address: Dr. Matthew Whiting |
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25 | Australia Telescope National Facility, CSIRO |
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26 | PO Box 76 |
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27 | Epping NSW 1710 |
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28 | AUSTRALIA |
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29 | ----------------------------------------------------------------------- |
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30 | |
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31 | Introduction |
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32 | ============ |
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33 | |
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34 | Duchamp is a stand-alone program designed to find objects in |
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35 | astronomical data cubes, particularly spectral-line observations. Its |
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36 | features include a wavelet-based reconstruction technique for reducing |
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37 | the noise in the cube (and thereby enhancing detectability of |
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38 | sources), easy-to-use text-based interface, flexibility to control all |
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39 | relevant parameters such as detection thresholds, and a useful range |
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40 | of text- and graphics-based output. |
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41 | |
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42 | Duchamp works on any FITS image using the CFITSIO package, and uses |
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43 | Mark Calabretta's WCSLIB library to provide accurate position and |
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44 | velocity information for all detected sources. |
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45 | |
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46 | |
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47 | Obtaining and Building Duchamp |
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48 | ============================== |
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49 | |
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50 | The Duchamp web page is at |
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51 | http://www.atnf.csiro.au/people/Matthew.Whiting/Duchamp |
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52 | where you can download a gzipped tar archive of the source code. |
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53 | |
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54 | Duchamp uses three main external libraries: pgplot (although see note |
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55 | below), cfitsio (version 2.5 and greater, version 3+ preferred) and |
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56 | wcslib. If you do not have the libraries, they can be downloaded from |
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57 | the following locations: |
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58 | |
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59 | PGPLOT -- http://www.astro.caltech.edu/~tjp/pgplot/ |
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60 | cfitsio -- http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html |
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61 | wcslib -- http://www.atnf.csiro.au/people/Mark.Calabretta/WCS/index.html |
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62 | |
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63 | Note that PGPLOT is optional. Duchamp can be compiled and run without |
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64 | PGPLOT, but you will miss out on the useful graphical outputs! The |
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65 | other two libraries, cftisio and wcslib, are essential. |
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66 | |
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67 | |
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68 | Basic Compilation and Installation |
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69 | ---------------------------------- |
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70 | |
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71 | Duchamp can be built and installed on Unix systems by typing (note |
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72 | that the terminal prompt here is represented by > -- don't type this |
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73 | character!): |
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74 | |
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75 | > ./configure |
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76 | > make |
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77 | > make lib (optional -- this makes libraries for use in code |
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78 | development) |
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79 | > make clean (again optional -- to remove the object files from the |
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80 | src directory) |
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81 | > make install |
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82 | |
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83 | This default setup will search in standard locations for the necessary |
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84 | libraries, and install the executable ("Duchamp") in /usr/local/bin (a |
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85 | copy will also be in the current directory). It also installs the |
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86 | libraries libduchamp.1.6.a and libduchamp.1.6.so in /usr/local/lib and |
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87 | the header (.hh) files in /usr/local/include/duchamp. If you want |
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88 | these to go somewhere else, eg if you don't have write-access to that |
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89 | directory, or you need to tweak the libraries, see the next |
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90 | section. Otherwise, jump to the testing section. |
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91 | |
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92 | |
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93 | Tweaking the installation setup |
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94 | ------------------------------- |
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95 | |
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96 | To install Duchamp in a directory other than /usr/local/bin, use the |
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97 | --prefix option with configure, specifying the directory above the |
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98 | \texttt{bin/} directory. eg: |
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99 | |
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100 | > ./configure --prefix=/home/mduchamp |
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101 | |
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102 | which, if you run "make" and "make install", will result in the binary |
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103 | being put in the directory /home/mduchamp/bin. Similarly the library |
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104 | will be put in /home/mduchamp/lib and the header files in |
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105 | /home/mduchamp/include/duchamp and subdirectories thereof. |
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106 | |
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107 | If the above-mentioned libraries have been installed in non-standard |
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108 | locations, or you have more than one version installed on your system, |
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109 | you can specify specific locations by using the --with-cfitsio=<dir>, |
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110 | --with-wcslib=<dir> or --with-pgplot=<dir> flags. For example: |
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111 | |
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112 | > ./configure --with-wcslib=/home/mduchamp/wcslib-4.2 |
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113 | |
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114 | And then just run make in the usual fashion: |
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115 | |
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116 | > make |
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117 | |
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118 | Duchamp can be compiled without PGPLOT if it is not installed on your |
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119 | system -- the searching and text-based output remains the same, but |
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120 | you will not have any graphical output. |
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121 | To manually specify this option, use the --without-pgplot flag, eg: |
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122 | |
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123 | > ./configure --without-pgplot |
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124 | |
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125 | (Note that CFITSIO and WCSLIB are essential, however, so |
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126 | --without-wcslib or --without-cfitsio will not work.). |
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127 | Even if you do not give the --without-pgplot option, and the PGPLOT |
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128 | library is not found, Duchamp will still compile (albeit without |
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129 | graphical capabilities). |
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130 | |
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131 | Troubleshooting the installation |
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132 | -------------------------------- |
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133 | |
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134 | There may be issues with the configure/make/install process that arise |
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135 | from non-standard locations of key libraries. The User's Guide has a |
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136 | section in Appendix A discussing some of the more common problems |
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137 | and potential solutions. |
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138 | |
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139 | Feeback is welcome if you have trouble getting Duchamp working -- see |
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140 | the feedback section below. |
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141 | |
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142 | |
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143 | Testing |
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144 | ======= |
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145 | |
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146 | There is a script included in the distribution that allows you to make |
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147 | sure Duchamp is running correctly. It will use a dummy FITS image in |
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148 | the verification/ directory -- this image has some Gaussian random |
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149 | noise, with five Gaussian sources present, plus a dummy WCS. The |
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150 | script runs Duchamp on this image with three different sets of inputs, |
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151 | and compares to known results, looking for differences and reporting |
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152 | any. There should be none reported if everything is working |
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153 | correctly. To run, enter the command |
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154 | |
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155 | > ./VerifyDuchamp.sh |
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156 | |
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157 | This performs basic checks on the output files, but ignoring most of |
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158 | the actual values of source parameters (to avoid picking up just |
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159 | differences due to precision errors). For complete checks of the |
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160 | files, run |
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161 | |
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162 | > ./VerifyDuchamp.sh -f |
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163 | |
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164 | Be warned that on some systems this could provide a large number of |
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165 | apparent errors which may only be due to precision differences. |
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166 | |
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167 | Once you know it is working, you can install Duchamp on your system |
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168 | with the command |
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169 | |
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170 | > make install |
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171 | |
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172 | (this may need to be run as sudo depending on your system setup and |
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173 | your prefix directory). |
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174 | |
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175 | You can also use the dummy image for your own testing if you like (for |
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176 | instance, testing different thresholds to get a feel for how the |
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177 | program works). |
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178 | |
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179 | |
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180 | Using Duchamp |
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181 | ============= |
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182 | |
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183 | There are two possible ways to run Duchamp. The first is: |
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184 | |
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185 | > Duchamp -f image.fits |
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186 | |
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187 | where image.fits is the data cube to be searched. This method simply |
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188 | uses the default values of all parameters. |
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189 | |
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190 | The second method allows some determination of the parameter values by |
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191 | the user. Type: |
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192 | |
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193 | > Duchamp -p parameterFile |
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194 | |
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195 | where parameterFile is a file with the input parameters, including the |
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196 | name of the cube you want to search. There are two example input files |
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197 | included with the distribution. The smaller one, InputExample, shows |
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198 | the typical parameters one might want to set. The large one, |
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199 | InputComplete, lists all possible parameters that can be entered, and |
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200 | a brief description of them. To get going quickly, just replace the |
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201 | "your-file-here" in InputExample with your image name, and type |
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202 | |
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203 | > Duchamp -p InputExample |
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204 | |
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205 | By default, a map of detections is displayed in a PGPLOT |
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206 | X-window. This can be disabled by using the flagXOutput parameter, or |
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207 | using the -x command-line option along with the -f or -p options. The |
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208 | -x option will override the setting in the parameter file. |
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209 | |
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210 | You can specify a flux threshold from the command line by using the -t |
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211 | option. This is particularly useful when combined with -f to enable a |
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212 | quick search to some flux level: |
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213 | |
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214 | > Duchamp -f image.fits -t 0.001 |
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215 | |
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216 | A User's Guide in the docs/ directory provides complete |
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217 | documentation. It comes in both postscript and portable document |
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218 | format (pdf -- note that this contains hyperlinks). This guide will |
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219 | provide full descriptions of all parameters, and of all steps in the |
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220 | execution of Duchamp. |
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221 | |
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222 | Feedback |
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223 | ======== |
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224 | |
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225 | Any questions, please contact me. To report problems or bugs, or to |
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226 | suggest improvements, please go to the Duchamp Trac wiki site: |
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227 | http://svn.atnf.csiro.au/trac/duchamp/newticket |
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228 | and submit a "ticket", or view previously submitted reports. |
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229 | |
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230 | Acknowledging the use of Duchamp |
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231 | ================================ |
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232 | |
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233 | Duchamp is provided in the hope that it will be useful for your |
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234 | research. If you find that it is, I would ask that you acknowledge it |
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235 | in your publication by using the following: |
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236 | "This research made use of the Duchamp source finder, produced at |
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237 | the Australia Telescope National Facility, CSIRO, by M. Whiting." |
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238 | |
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239 | The journal paper describing Duchamp, and providing basic comparative |
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240 | tests of its different functions, is Whiting 2012, MNRAS 421, |
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241 | 3242, which can be found online at |
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242 | http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2966.2012.20548.x/full. |
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243 | This paper should be cited when describing Duchamp. |
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244 | |
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245 | An earlier conference proceedings paper briefly describing it was: |
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246 | "Astronomers! Do you know where your galaxies are?", M.Whiting, in |
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247 | "Galaxies in the Local Volume", Eds. B.Koribalski & H.Jerjen, |
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248 | Astrophysics & Space Science Proceedings, Springer, 2008, p.343-344 |
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249 | http://adsabs.harvard.edu/abs/2008glv..book..343W |
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250 | |
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251 | Those interested in the development of a source-finder for ASKAP |
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252 | (known for now as Selavy), which make use of the Duchamp code, should |
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253 | read Whiting & Humphreys 2012, PASA 29, 371, which can be found online |
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254 | at http://www.publish.csiro.au/paper/AS12028.htm |
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255 | |
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256 | ------- |
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257 | Author: |
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258 | Matthew Whiting, Australia Telescope National Facility, April 2014 |
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259 | Matthew.Whiting [at] csiro.au |
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260 | |
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