Mercurial > repos > astroteam > astropy_fits2csv

annotate fits2table.xml @ 3:f02f62944fa9 draft default tip

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author astroteam
date Fri, 04 Jul 2025 13:18:34 +0000
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1 <tool id="astropy_fits2csv" name="astropy fits2csv" version="0.2.0+galaxy2" profile="21.05">
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2 <requirements>
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3 <requirement type="package" version="6.1.7">astropy</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 python '$py_script_file'
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7 ]]></command>
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8
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9 <configfiles>
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10 <configfile name="py_script_file">
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11 from astropy.io import fits
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12 from astropy.table import Table
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13
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14 if '$output_format' == 'csv':
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15 output_separator = ','
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16 elif '$output_format' == 'tabular':
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17 output_separator = '\t'
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18 else:
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19 raise ValueError('Unknown output format: ' + '$output_format')
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21 with fits.open("$input_fits", memmap=True) as hdu_list:
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23 # select the HDU you want
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24 hdu = hdu_list[$hdu]
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25
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26 # read into an astropy Table object
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27 table = Table(hdu.data)
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28
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29 # write to a CSV file
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30 table.write('$output', delimiter=output_separator, format='ascii', overwrite=True)
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31 </configfile>
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32 </configfiles>
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34 <inputs>
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35 <param type="data" name="input_fits" format="fits" label="FITS file to dump"/>
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36 <param type="integer" name="hdu" value="1" min="1" label="Select input HDU number"/>
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37 <param type="select" name="output_format" label="Output format">
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38 <option value="tabular" selected="true">tabular, tab-separated values</option>
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39 <option value="csv">CSV, coma-separated values</option>
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40 </param>
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41 </inputs>
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42 <outputs>
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43 <data name="output" format="tabular">
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44 <change_format>
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45 <when input="output_separator" value="," format="csv" />
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46 </change_format>
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47 </data>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="input_fits" value="WFPC2u5780205r_c0fx.fits"/>
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52 <param name="hdu" value="1"/>
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53 <param name="output_format" value="csv"/>
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54 <output name="output" file="fitstable.csv"/>
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55 </test>
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56 <test>
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57 <param name="input_fits" value="WFPC2u5780205r_c0fx.fits"/>
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58 <param name="hdu" value="1"/>
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59 <param name="output_format" value="tabular"/>
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60 <output name="output" file="fitstable.tsv"/>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 Extract a text table (CSV, SSV, or TSV) from FITS file HDU Table. Resulting CSV file can be used by many existing Galaxy tools and visualisation plugins.
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65
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66 ---------
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67
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68 **Example:**
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69
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70 For example, here is the output for on of the sample fits files, https://fits.gsfc.nasa.gov/samples/WFPC2u5780205r_c0fx.fits
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71
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73 .. code-block::
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74
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75 CRVAL1 CRVAL2 CRPIX1 CRPIX2 CD1_1 CD1_2 CD2_1 CD2_2 DATAMIN DATAMAX MIR_REVR ORIENTAT FILLCNT ERRCNT FPKTTIME LPKTTIME CTYPE1 CTYPE2 DETECTOR DEZERO BIASEVEN BIASODD GOODMIN GOODMAX DATAMEAN GPIXELS SOFTERRS CALIBDEF STATICD ATODSAT DATALOST BADPIXEL OVERLAP PHOTMODE PHOTFLAM PHOTZPT PHOTPLAM PHOTBW MEDIAN MEDSHADO HISTWIDE SKEWNESS MEANC10 MEANC25 MEANC50 MEANC100 MEANC200 MEANC300 BACKGRND
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76 182.6311886308 39.39633673411 420.0 424.5 -1.06704e-06 -1.25958e-05 -1.26016e-05 1.06655e-06 -73.19537 3777.701 T -85.16 0 0 51229.798573999986 51229.798742000006 RA---TAN DEC--TAN 1 316.6452 316.6715 316.6189 -5.064006 2552.17 0.4182382 632387 0 1466 0 16 0 0 0 WFPC2,1,A2D7,LRF#4877.0,,CAL 3.44746e-16 -21.1 4884.258 20.20996 -0.175651 -0.121681 1.033711 -1.983727 0.12958 0.3129676 0.4577668 0.3916293 0.3115222 0.3295493 -0.3676353
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77 182.6255233634 39.41214313815 423.5 414.0 -2.75605e-05 2.08221e-06 2.08021e-06 2.75871e-05 -19.95751 3740.623 T 4.31638 0 0 51229.798742000006 51229.79891000002 RA---TAN DEC--TAN 2 354.0573 354.0761 354.0386 -3.379329 3720.573 0.6385469 631340 0 2072 0 25 0 0 0 WFPC2,2,A2D7,LRF#4877.0,,CAL 3.382652e-16 -21.1 4884.261 20.20992 -0.1896807 -0.1899146 1.053666 -1.947547 0.2564496 0.1057321 0.9952926 0.8409855 0.6534808 0.5836062 0.2101429
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78 182.6523792305 39.410944281389995 436.0 424.5 2.23913e-06 2.75426e-05 2.75684e-05 -2.23704e-06 -58.53249 3282.136 T 94.6434 0 0 51229.79891000002 51229.799078 RA---TAN DEC--TAN 3 306.6676 306.6541 306.681 -3.713645 3282.136 0.5217843 633259 0 1551 0 7 0 0 0 WFPC2,3,A2D7,LRF#4877.0,,CAL 3.372288e-16 -21.1 4884.255 20.21006 0.01109185 0.06184989 1.003236 28.21703 1.669304 0.3472891 0.327215 0.6145074 0.7027547 0.5681439 0.4761558
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79 182.650022355 39.38946044168 423.0 421.0 2.75358e-05 -2.50931e-06 -2.50689e-06 -2.75624e-05 -72.41166 3420.24 T -174.798 0 0 51229.799079 51229.79924599999 RA---TAN DEC--TAN 4 311.7072 311.7648 311.6496 -3.289304 3420.24 0.7084697 628289 0 1816 0 57 0 0 0 WFPC2,4,A2D7,LRF#4877.0,,CAL 3.46466e-16 -21.1 4884.256 20.20999 -0.06813275 -0.03253493 0.9846212 -4.591252 0.1359666 0.04015671 0.1129934 1.897491 0.9687142 1.05377 0.3466465
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80
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81
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82 This tool is a simple script based on Astropy package. See `astropy help <https://docs.astropy.org/en/latest/io/fits/>`_
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83 for further documentation.
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84 ]]></help>
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85 <citations>
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86 <citation type="doi">
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87 10.3847/1538-4357/ac7c74
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88 </citation>
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89 </citations>
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90 </tool>