Mercurial > repos > astroteam > source_extractor_astro_tool

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 89e20bd2ec941d1d362da85bd81230419a1a4b2a
author astroteam
date Fri, 18 Jul 2025 14:23:35 +0000
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f4648bd69d48 planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 89e20bd2ec941d1d362da85bd81230419a1a4b2a
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1 <tool id="source_extractor_astro_tool" name="source-extractor" version="0.0.1+galaxy0" profile="24.0">
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2 <requirements>
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3 <requirement type="package" version="6.1.4">astropy</requirement>
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4 <requirement type="package" version="3.10.3">matplotlib</requirement>
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5 <requirement type="package" version="1.21.4">wget</requirement>
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6 <requirement type="package" version="1.4.1">sep</requirement>
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7 <requirement type="package" version="1.2.33">oda-api</requirement>
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8 <requirement type="package" version="2025.6.11">tifffile</requirement>
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9 <requirement type="package" version="9.4.0">ipython</requirement>
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10 <!--Requirements string 'nb2workflow>=1.3.30' can't be converted automatically. Please add the galaxy/conda requirement manually or modify the requirements file!-->
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11 </requirements>
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12 <command detect_errors="exit_code">ipython '$__tool_directory__/source_extraction.py'</command>
f4648bd69d48 planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 89e20bd2ec941d1d362da85bd81230419a1a4b2a
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13 <environment_variables>
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14 <environment_variable name="BASEDIR">$__tool_directory__</environment_variable>
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15 <environment_variable name="GALAXY_TOOL_DIR">$__tool_directory__</environment_variable>
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16 </environment_variables>
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17 <configfiles>
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18 <inputs name="inputs" filename="inputs.json" data_style="paths" />
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19 </configfiles>
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20 <inputs>
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21 <param name="input_file" type="data" label="Input file" format="data" optional="false" />
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22 <param name="mask_file" type="data" label="Mask file" format="data" optional="true" />
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23 <param name="thresh" type="float" value="1.5" label="thresh" optional="false" />
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24 <param name="err_option" type="select" label="err_option" optional="false">
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25 <option value="array_rms">array_rms</option>
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26 <option value="float_globalrms" selected="true">float_globalrms</option>
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27 <option value="none">none</option>
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28 </param>
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29 <param name="maskthresh" type="float" value="0.0" label="maskthresh" optional="false" />
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30 <param name="minarea" type="integer" value="5" label="minarea" optional="false" />
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31 <param name="filter_case" type="select" label="Filter Case" optional="false">
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32 <option value="default" selected="true">default</option>
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33 <option value="file">file</option>
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34 <option value="none">none</option>
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35 </param>
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36 <param name="filter_file" type="data" label="Filter file" format="data" optional="true" />
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37 <param name="filter_type" type="select" label="filter_type" optional="false">
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38 <option value="conv">conv</option>
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39 <option value="matched" selected="true">matched</option>
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40 </param>
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41 <param name="deblend_nthresh" type="integer" value="32" label="deblend_nthresh" optional="false" />
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42 <param name="deblend_cont" type="float" value="0.005" label="deblend_cont" optional="false" />
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43 <param name="clean" type="boolean" checked="true" label="clean" optional="false" />
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44 <param name="clean_param" type="float" value="1.0" label="clean_param" optional="false" />
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45 <param name="bw" type="integer" value="64" label="bw" optional="false" />
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46 <param name="bh" type="integer" value="64" label="bh" optional="false" />
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47 <param name="fw" type="integer" value="3" label="fw" optional="false" />
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48 <param name="fh" type="integer" value="3" label="fh" optional="false" />
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49 <param name="fthresh" type="float" value="0.0" label="fthresh" optional="false" />
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50 </inputs>
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51 <outputs>
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52 <data label="${tool.name} -&gt; source_extraction bkg_picture" name="out_source_extraction_bkg_picture" format="auto" from_work_dir="bkg_picture_galaxy.output" />
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53 <data label="${tool.name} -&gt; source_extraction rms_picture" name="out_source_extraction_rms_picture" format="auto" from_work_dir="rms_picture_galaxy.output" />
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54 <data label="${tool.name} -&gt; source_extraction data_picture" name="out_source_extraction_data_picture" format="auto" from_work_dir="data_picture_galaxy.output" />
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55 <data label="${tool.name} -&gt; source_extraction sources_picture" name="out_source_extraction_sources_picture" format="auto" from_work_dir="sources_picture_galaxy.output" />
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56 <data label="${tool.name} -&gt; source_extraction segmentation_map_picture" name="out_source_extraction_segmentation_map_picture" format="auto" from_work_dir="segmentation_map_picture_galaxy.output" />
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57 <data label="${tool.name} -&gt; source_extraction segmentation_map" name="out_source_extraction_segmentation_map" format="auto" from_work_dir="segmentation_map_galaxy.output" />
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58 <data label="${tool.name} -&gt; source_extraction bkg_array" name="out_source_extraction_bkg_array" format="auto" from_work_dir="bkg_array_galaxy.output" />
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59 <data label="${tool.name} -&gt; source_extraction rms_array" name="out_source_extraction_rms_array" format="auto" from_work_dir="rms_array_galaxy.output" />
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60 <data label="${tool.name} -&gt; source_extraction catalog_table" name="out_source_extraction_catalog_table" format="auto" from_work_dir="catalog_table_galaxy.output" />
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61 </outputs>
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62 <tests>
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63 <test expect_num_outputs="9">
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64 <param name="input_file" location="https://gitlab.renkulab.io/astronomy/mmoda/source-extractor/-/raw/5680fc685979c56c69f98eec8153673422abfa72/input.fits" />
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65 <param name="thresh" value="1.5" />
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66 <param name="err_option" value="float_globalrms" />
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67 <param name="maskthresh" value="0.0" />
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68 <param name="minarea" value="5" />
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69 <param name="filter_case" value="default" />
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70 <param name="filter_type" value="matched" />
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71 <param name="deblend_nthresh" value="32" />
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72 <param name="deblend_cont" value="0.005" />
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73 <param name="clean" value="True" />
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74 <param name="clean_param" value="1.0" />
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75 <param name="bw" value="64" />
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76 <param name="bh" value="64" />
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77 <param name="fw" value="3" />
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78 <param name="fh" value="3" />
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79 <param name="fthresh" value="0.0" />
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80 <assert_stdout>
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81 <has_text text="*** Job finished successfully ***" />
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82 </assert_stdout>
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83 </test>
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84 </tests>
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85 <help>Source extractor
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86 ================
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87
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88 This tool can be used to extract luminous sources from sky images. It is
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89 entirely based on the
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90 `sep &lt;https://sep.readthedocs.io/en/stable/index.html&gt;`__ package, which
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91 is built on `Source
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92 Extractor &lt;https://sextractor.readthedocs.io/en/latest/Introduction.html&gt;`__.
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93
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94 Input
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95 -----
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96
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97 Important input parameters:
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98
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99 1. **Input file** (``.fits`` or ``.tiff``) - A single-channel sky image
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100 to analyze.
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101
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102 2. **Mask file** (``.fits`` or ``.tiff``; optional) - A 2D numpy array.
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103 True values, or numeric values greater than **maskthresh**, are
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104 considered masked. Masking a pixel is equivalent to setting data to
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105 zero and noise (if present) to infinity.
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106
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107 3. **thresh** - Threshold pixel value for detection:
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108 ``thresh * err[j, i]``, where ``err[j, i]`` is given by the
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109 **err_option** parameter; ``j`` and ``i`` represent the pixel indices
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110
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111 4. **err_option** - Sets the error that is taken into account into the
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112 detection of sources:
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113
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114 - ``none`` - The value of **thresh** is taken as an absolute
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115 threshold.
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116 - ``array_rms`` - An array of the background RMS, i.e.&#160;for each
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117 individual pixel.
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118 - ``float_globalrms`` - A float value of the global background RMS.
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119
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120 The rest of the parameters are described in the documentations of
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121 `sep.Background &lt;https://sep.readthedocs.io/en/stable/api/sep.Background.html#sep.Background&gt;`__
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122 and
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123 `sep.extract &lt;https://sep.readthedocs.io/en/stable/api/sep.extract.html#sep.extract&gt;`__.
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124
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125 Output
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126 ------
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127
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128 Source Catalog
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129 ~~~~~~~~~~~~~~
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130
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131 The catalogue of sources is explained
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132 `here &lt;https://sep.readthedocs.io/en/stable/api/sep.extract.html#sep.extract&gt;`__.
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133
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134 Images
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135 ~~~~~~
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136
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137 There are 4 images as output:
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138
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139 - **Background**:
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140
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141 - ``.fits``: The output of ``sep.Background`` function, i.e.&#160;the
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142 estimated 2D background of the input image.
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143 - ``.png``: The gray-scale image of the previously described array
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144
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145 - **Background noise**:
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146
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147 - ``.fits``: The RMS of the background image.
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148 - ``.png``: The gray-scale image of the previously described array
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149
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150 - **Input image** - The gray-scale input image.
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151 - **Sources** - The sources on the background subtracted input image
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152 - **Segmentation map**:
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153
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154 - ``.fits``: Each pixel is labeled with 0 or object ID (``0`` =
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155 background; ``i+1`` = object ``i``).
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156 - ``.png``: Binary mask (``1`` = source, ``0`` = background).
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157
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158 Acknowledgement
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159 ---------------
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160
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161 Bertin, E. &amp; Arnouts, S. 1996: `SExtractor: Software for source
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162 extraction &lt;https://ui.adsabs.harvard.edu/abs/1996A%26AS..117..393B/abstract&gt;`__,
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163 Astronomy &amp; Astrophysics Supplement 317, 393
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164
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165 Barbary, (2016), SEP: Source Extractor as a library, Journal of Open
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166 Source Software, 1(6), 58, doi:10.21105/joss.00058
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167 </help>
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168 <citations>
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169 <citation type="doi">10.1051/aas:1996164</citation>
f4648bd69d48 planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 89e20bd2ec941d1d362da85bd81230419a1a4b2a
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170 <citation type="doi">10.21105/joss.00058</citation>
f4648bd69d48 planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 89e20bd2ec941d1d362da85bd81230419a1a4b2a
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171 </citations>
f4648bd69d48 planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 89e20bd2ec941d1d362da85bd81230419a1a4b2a
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172 </tool>