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2 | The Duchamp Source Finder |
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3 | ----------------------------------------------------------------------- |
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4 | Duchamp 1.2-beta -- an object finder for spectral-line data cubes |
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5 | Copyright (C) 2006, Matthew Whiting, ATNF |
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6 | |
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7 | Duchamp 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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29 | |
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30 | Introduction |
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31 | ============ |
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32 | |
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33 | Duchamp is a stand-alone program designed to find objects in |
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34 | astronomical data cubes, particularly spectral-line observations. Its |
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35 | features include a wavelet-based reconstruction technique for reducing |
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36 | the noise in the cube (and thereby enhancing detectability of |
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37 | sources), easy-to-use text-based interface, flexibility to control all |
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38 | relevant parameters such as detection thresholds, and a useful range |
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39 | of text- and graphics-based output. |
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40 | |
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41 | Duchamp works on any FITS image using the CFITSIO package, and uses |
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42 | Mark Calabretta's WCSLIB library to provide accurate position and |
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43 | velocity information for all detected sources. |
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44 | |
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45 | |
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46 | The "Beta" Version |
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47 | ================== |
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48 | |
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49 | This distribution of Duchamp, dated 11/5/2009, is known as the beta |
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50 | version. It is more recent than the most recent release (v1.1.7), as |
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51 | it has several new functions and features. It is being released as a |
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52 | beta version as it is close to a full release, but there are a few |
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53 | checks and so on that still need to be done. When 1.2 is released, |
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54 | it should be used instead. |
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55 | |
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56 | The beta version is provided more for testing purposes -- if users |
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57 | want a reliable version of the code that matches the documentation, |
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58 | please use the latest release available from the webpage given below. |
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59 | |
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60 | Having said all that, do note that I won't post a beta version on the |
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61 | website unless I know that it is functioning in most cases, so it |
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62 | should work to a large degree (and if it doesn't -- let me know!) |
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63 | |
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64 | |
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65 | |
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66 | Obtaining and Building Duchamp |
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67 | ============================== |
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68 | |
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69 | The Duchamp web page is at |
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70 | http://www.atnf.csiro.au/people/Matthew.Whiting/Duchamp |
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71 | where you can download a gzipped tar archive of the source code. |
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72 | |
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73 | Duchamp uses three main external libraries: pgplot (although see note |
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74 | below), cfitsio (version 2.5 and greater, version 3+ preferred) and |
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75 | wcslib. If you do not have the libraries, they can be downloaded from |
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76 | the following locations: |
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77 | |
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78 | PGPLOT -- http://www.astro.caltech.edu/~tjp/pgplot/ |
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79 | cfitsio -- http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html |
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80 | wcslib -- http://www.atnf.csiro.au/people/Mark.Calabretta/WCS/index.html |
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81 | |
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82 | Note that PGPLOT is optional. Duchamp can be compiled and run without |
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83 | PGPLOT, but you will miss out on the useful graphical outputs! The |
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84 | other two libraries, cftisio and wcslib, are essential. |
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85 | |
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86 | |
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87 | Basic Compilation and Installation |
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88 | ---------------------------------- |
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89 | |
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90 | Duchamp can be built and installed on Unix systems by typing (note |
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91 | that the terminal prompt here is represented by > -- don't type this |
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92 | character!): |
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93 | |
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94 | > ./configure |
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95 | > make |
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96 | > make clean (optional -- to remove the object files from the src |
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97 | directory) |
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98 | > make install |
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99 | |
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100 | This default setup will search in standard locations for the necessary |
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101 | libraries, and install the executable ("Duchamp") in /usr/local/bin (a |
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102 | copy will also be in the current directory). If you want this to go |
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103 | somewhere else, eg if you don't have write-access to that directory, |
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104 | or you need to tweak the libraries, see the next section. Otherwise, |
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105 | jump to the testing section. |
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106 | |
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107 | |
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108 | Tweaking the installation setup |
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109 | ------------------------------- |
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110 | |
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111 | To install Duchamp in a directory other than /usr/local/bin, use the |
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112 | --prefix option with configure, specifying the directory above the |
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113 | \texttt{bin/} directory. eg: |
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114 | |
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115 | > ./configure --prefix=/home/mduchamp |
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116 | |
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117 | which, if you run "make" and "make install", will result in the binary |
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118 | being put in the directory /home/mduchamp/bin. |
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119 | |
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120 | If the above-mentioned libraries have been installed in non-standard |
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121 | locations, or you have more than one version installed on your system, |
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122 | you can specify specific locations by using the --with-cfitsio=<dir>, |
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123 | --with-wcslib=<dir> or --with-pgplot=<dir> flags. For example: |
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124 | |
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125 | > ./configure --with-wcslib=/home/mduchamp/wcslib-4.2 |
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126 | And then just run make in the usual fashion: |
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127 | > make |
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128 | |
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129 | Duchamp can be compiled without PGPLOT if it is not installed on your |
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130 | system -- the searching and text-based output remains the same, but |
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131 | you will not have any graphical output. |
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132 | To manually specify this option, use the --without-pgplot flag, eg: |
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133 | |
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134 | > ./configure --without-pgplot |
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135 | |
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136 | (Note that CFITSIO and WCSLIB are essential, however, so |
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137 | --without-wcslib or --without-cfitsio will not work.). |
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138 | Even if you do not give the --without-pgplot option, and the PGPLOT |
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139 | library is not found, Duchamp will still compile (albeit without |
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140 | graphical capabilities). |
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141 | |
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142 | |
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143 | Installing on Mac OS X with gfortran |
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144 | ------------------------------------ |
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145 | |
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146 | Some recent testing on a Mac with OS X and gfortran has shown that |
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147 | slight tweaking needs to be done with the use of configure. In |
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148 | addition to the options noted above, configure should be run with F77 |
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149 | set to the desired fortran compiler command. Note that this should be |
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150 | the same as that used to compile the pgplot package, if you are using |
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151 | it: gfortran is probably the best choice. |
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152 | This is done simply by: |
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153 | |
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154 | > ./configure F77=gfortran ...[other options]... |
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155 | |
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156 | |
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157 | Testing |
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158 | ======= |
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159 | |
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160 | There is a script included in the distribution that allows you to make |
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161 | sure Duchamp is running correctly. It will use a dummy FITS image in |
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162 | the verification/ directory -- this image has some Gaussian random |
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163 | noise, with five Gaussian sources present, plus a dummy WCS. The |
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164 | script runs Duchamp on this image with three different sets of inputs, |
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165 | and compares to known results, looking for differences and reporting |
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166 | any. There should be none reported if everything is working |
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167 | correctly. To run, enter the command |
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168 | |
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169 | > VerifyDuchamp.sh |
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170 | |
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171 | Once you know it is working, you can install Duchamp on your system |
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172 | with the command |
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173 | |
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174 | > make install |
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175 | |
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176 | You can also use the dummy image for your own testing if you like (for |
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177 | instance, testing different thresholds to get a feel for how the |
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178 | program works). |
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179 | |
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180 | |
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181 | Using Duchamp |
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182 | ============= |
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183 | |
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184 | There are two possible ways to run Duchamp. The first is: |
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185 | |
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186 | > Duchamp -f image.fits |
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187 | |
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188 | where image.fits is the data cube to be searched. This method simply |
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189 | uses the default values of all parameters. |
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190 | |
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191 | The second method allows some determination of the parameter values by |
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192 | the user. Type: |
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193 | |
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194 | > Duchamp -p parameterFile |
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195 | |
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196 | where parameterFile is a file with the input parameters, including the |
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197 | name of the cube you want to search. There are two example input files |
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198 | included with the distribution. The smaller one, InputExample, shows |
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199 | the typical parameters one might want to set. The large one, |
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200 | InputComplete, lists all possible parameters that can be entered, and |
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201 | a brief description of them. To get going quickly, just replace the |
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202 | "your-file-here" in InputExample with your image name, and type |
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203 | |
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204 | > Duchamp -p InputExample |
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205 | |
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206 | By default, a map of detections is displayed in a PGPLOT |
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207 | X-window. This can be disabled by using the flagXOutput parameter, or |
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208 | using the -x command-line option along with the -f or -p options. The |
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209 | -x option will override the setting in the parameter file. |
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210 | |
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211 | A User's Guide in the docs/ directory provides complete |
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212 | documentation. It comes in both postscript and portable document |
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213 | format (pdf -- note that this contains hyperlinks). This guide will |
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214 | provide full descriptions of all parameters, and of all steps in the |
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215 | execution of Duchamp. |
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216 | |
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217 | Any questions, please contact me. To report problems or bugs, or to |
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218 | suggest improvements, please go to the Duchamp Trac wiki site: |
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219 | http://svn.atnf.csiro.au/trac/duchamp/newticket |
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220 | and submit a "ticket", or view previously submitted reports. |
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221 | |
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222 | ------- |
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223 | Author: |
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224 | Matthew Whiting, Australia Telescope National Facility, May 2009 |
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225 | Matthew.Whiting [at] csiro.au |
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226 | |
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