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