Mercurial > repos > astroteam > hess_astro_tool
diff hess_astro_tool.xml @ 1:593c4b45eda5 draft default tip
planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2f23ec010eab8d33d2760f061286756e17015af7
| author | astroteam |
|---|---|
| date | Thu, 18 Apr 2024 09:26:15 +0000 |
| parents | 02e4bb4fa10c |
| children |
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--- a/hess_astro_tool.xml Mon Feb 19 10:56:44 2024 +0000 +++ b/hess_astro_tool.xml Thu Apr 18 09:26:15 2024 +0000 @@ -1,102 +1,88 @@ -<tool id="hess_astro_tool" name="HESS" version="0.0.1+galaxy0" profile="23.0"> +<tool id="hess_astro_tool" name="HESS" version="0.0.2+galaxy0" profile="23.0"> <requirements> - <requirement type="package" version="8.21.0">ipython</requirement> + <requirement type="package" version="8.22.2">ipython</requirement> <requirement type="package" version="5.3.4">astropy</requirement> <requirement type="package" version="1.11.4">scipy</requirement> - <requirement type="package" version="1.10.13">pydantic</requirement> + <requirement type="package" version="1.10.14">pydantic</requirement> <requirement type="package" version="4.66.2">tqdm</requirement> <requirement type="package" version="1.1">gammapy</requirement> - <requirement type="package" version="3.8.3">matplotlib</requirement> - <requirement type="package" version="1.2.12">oda-api</requirement> + <requirement type="package" version="3.8.4">matplotlib</requirement> + <requirement type="package" version="1.2.15">oda-api</requirement> <!--Requirements string 'nb2workflow[cwl,service,rdf,mmoda]>=1.3.30 ' can't be converted automatically. Please add the galaxy/conda requirement manually or modify the requirements file!--> - <requirement type="package" version="7.16.0">nbconvert</requirement> - <requirement type="package" version="1.20.3">wget</requirement> + <requirement type="package" version="7.16.3">nbconvert</requirement> + <requirement type="package" version="1.21.4">wget</requirement> </requirements> <command detect_errors="exit_code">ipython '$__tool_directory__/${_data_product._selector}.py'</command> <configfiles> - <inputs name="inputs" filename="inputs.json" /> + <inputs name="inputs" filename="inputs.json" data_style="paths" /> </configfiles> <inputs> <conditional name="_data_product"> <param name="_selector" type="select" label="Data Product"> <option value="Image" selected="true">Image</option> <option value="Spectrum" selected="false">Spectrum</option> - <option value="Spectrum_gammapy" selected="false">Spectrum_gammapy</option> <option value="Lightcurve" selected="false">Lightcurve</option> </param> <when value="Image"> <param name="src_name" type="text" value="Crab" label="src_name" /> - <param name="RA" type="float" value="83.6287" label="RA Units: deg" /> - <param name="DEC" type="float" value="22.0147" label="DEC Units: deg" /> + <param name="RA" type="float" value="83.6287" label="RA (unit: deg)" /> + <param name="DEC" type="float" value="22.0147" label="DEC (unit: deg)" /> <param name="T1" type="text" value="2000-10-09T13:16:00.0" label="T1" /> <param name="T2" type="text" value="2022-10-10T13:16:00.0" label="T2" /> - <param name="Radius" type="float" value="2.5" label="Radius Units: deg" /> - <param name="pixsize" type="float" value="0.1" label="Pixel size Units: deg" /> - <param name="Emin" type="float" value="100.0" label="Emin Units: GeV" /> - <param name="Emax" type="float" value="10000.0" label="Emax Units: GeV" /> + <param name="Radius" type="float" value="1.0" label="Radius (unit: deg)" /> + <param name="pixsize" type="float" value="0.05" label="Pixel size (unit: deg)" /> + <param name="Emin" type="integer" value="1" label="Emin (unit: TeV)" /> + <param name="Emax" type="float" value="100.0" label="Emax (unit: TeV)" /> </when> <when value="Spectrum"> <param name="src_name" type="text" value="PKS 2155-304" label="src_name" /> - <param name="RA" type="float" value="329.716938" label="RA Units: deg" /> - <param name="DEC" type="float" value="-30.225588" label="DEC Units: deg" /> + <param name="RA" type="float" value="329.716938" label="RA (unit: deg)" /> + <param name="DEC" type="float" value="-30.225588" label="DEC (unit: deg)" /> <param name="T1" type="text" value="2000-10-09T13:16:00.0" label="T1" /> <param name="T2" type="text" value="2022-10-10T13:16:00.0" label="T2" /> - <param name="Radius" type="float" value="2.5" label="Radius Units: deg" /> - <param name="R_s" type="float" value="0.2" label="R_s Units: deg" /> - <param name="Emin" type="float" value="100.0" label="Emin Units: GeV" /> - <param name="Emax" type="float" value="10000.0" label="Emax Units: GeV" /> - <param name="NEbins" type="integer" value="20" label="NEbins" /> - </when> - <when value="Spectrum_gammapy"> - <param name="src_name" type="text" value="PKS 2155-304" label="src_name" /> - <param name="RA" type="float" value="329.716938" label="RA Units: deg" /> - <param name="DEC" type="float" value="-30.225588" label="DEC Units: deg" /> - <param name="T1" type="text" value="2000-10-09T13:16:00.0" label="T1" /> - <param name="T2" type="text" value="2022-10-10T13:16:00.0" label="T2" /> - <param name="Radius" type="float" value="2.5" label="Radius Units: deg" /> - <param name="R_s" type="float" value="0.5" label="R_s Units: deg" /> - <param name="Emin" type="float" value="100.0" label="Emin Units: GeV" /> - <param name="Emax" type="float" value="10000.0" label="Emax Units: GeV" /> - <param name="NEbins" type="integer" value="20" label="NEbins" /> + <param name="Radius" type="float" value="2.5" label="Radius (unit: deg)" /> + <param name="R_s" type="float" value="0.2" label="R_s (unit: deg)" /> + <param name="Emin" type="float" value="0.1" label="Emin (unit: TeV)" /> + <param name="Emax" type="float" value="100.0" label="Emax (unit: TeV)" /> + <param name="NEbins" type="integer" value="30" label="NEbins" /> + <param name="Efit_min" type="float" value="0.2" label="Efit_min (unit: TeV)" /> + <param name="Efit_max" type="float" value="10.0" label="Efit_max (unit: TeV)" /> </when> <when value="Lightcurve"> <param name="src_name" type="text" value="Crab" label="src_name" /> - <param name="RA" type="float" value="83.6287" label="RA Units: deg" /> - <param name="DEC" type="float" value="22.0147" label="DEC Units: deg" /> - <param name="T1" type="text" value="2003-10-09T13:16:00.0" label="T1" /> - <param name="T2" type="text" value="2005-10-10T13:16:00.0" label="T2" /> - <param name="Radius" type="float" value="2.5" label="Radius Units: deg" /> - <param name="R_s" type="float" value="0.2" label="R_s Units: deg" /> - <param name="Emin" type="float" value="100.0" label="Emin Units: GeV" /> - <param name="Emax" type="float" value="10000.0" label="Emax Units: GeV" /> - <param name="NTbins" type="integer" value="10" label="NTbins" /> + <param name="RA" type="float" value="83.6287" label="RA (unit: deg)" /> + <param name="DEC" type="float" value="22.0147" label="DEC (unit: deg)" /> + <param name="T1" type="text" value="2004-11-20T13:16:00.0" label="T1" /> + <param name="T2" type="text" value="2004-12-20T13:16:00.0" label="T2" /> + <param name="Radius" type="float" value="2.5" label="Radius (unit: deg)" /> + <param name="R_s" type="float" value="0.2" label="R_s (unit: deg)" /> + <param name="Emin" type="integer" value="1" label="Emin (unit: TeV)" /> + <param name="Emax" type="float" value="100.0" label="Emax (unit: TeV)" /> + <param name="NTbins" type="integer" value="30" label="NTbins" /> </when> </conditional> </inputs> <outputs> - <data label="${tool.name} -> Image picture" name="out_Image_picture" format="auto" from_work_dir="picture_galaxy.output"> + <data label="${tool.name} -> Image png" name="out_Image_png" format="auto" from_work_dir="png_galaxy.output"> <filter>_data_product['_selector'] == 'Image'</filter> </data> - <data label="${tool.name} -> Image image" name="out_Image_image" format="auto" from_work_dir="image_galaxy.output"> + <data label="${tool.name} -> Image fits" name="out_Image_fits" format="auto" from_work_dir="fits_galaxy.output"> <filter>_data_product['_selector'] == 'Image'</filter> </data> - <data label="${tool.name} -> Spectrum picture_png" name="out_Spectrum_picture_png" format="auto" from_work_dir="picture_png_galaxy.output"> + <data label="${tool.name} -> Spectrum png" name="out_Spectrum_png" format="auto" from_work_dir="png_galaxy.output"> <filter>_data_product['_selector'] == 'Spectrum'</filter> </data> - <data label="${tool.name} -> Spectrum spectrum_astropy_table" name="out_Spectrum_spectrum_astropy_table" format="auto" from_work_dir="spectrum_astropy_table_galaxy.output"> + <data label="${tool.name} -> Spectrum table_confidence_contour" name="out_Spectrum_table_confidence_contour" format="auto" from_work_dir="table_confidence_contour_galaxy.output"> <filter>_data_product['_selector'] == 'Spectrum'</filter> </data> - <data label="${tool.name} -> Spectrum_gammapy picture_png" name="out_Spectrum_gammapy_picture_png" format="auto" from_work_dir="picture_png_galaxy.output"> - <filter>_data_product['_selector'] == 'Spectrum_gammapy'</filter> + <data label="${tool.name} -> Spectrum table_spectrum" name="out_Spectrum_table_spectrum" format="auto" from_work_dir="table_spectrum_galaxy.output"> + <filter>_data_product['_selector'] == 'Spectrum'</filter> </data> - <data label="${tool.name} -> Spectrum_gammapy spectrum_astropy_table" name="out_Spectrum_gammapy_spectrum_astropy_table" format="auto" from_work_dir="spectrum_astropy_table_galaxy.output"> - <filter>_data_product['_selector'] == 'Spectrum_gammapy'</filter> - </data> - <data label="${tool.name} -> Lightcurve picture" name="out_Lightcurve_picture" format="auto" from_work_dir="picture_galaxy.output"> + <data label="${tool.name} -> Lightcurve png" name="out_Lightcurve_png" format="auto" from_work_dir="png_galaxy.output"> <filter>_data_product['_selector'] == 'Lightcurve'</filter> </data> - <data label="${tool.name} -> Lightcurve lightcurve_astropy_table" name="out_Lightcurve_lightcurve_astropy_table" format="auto" from_work_dir="lightcurve_astropy_table_galaxy.output"> + <data label="${tool.name} -> Lightcurve table" name="out_Lightcurve_table" format="auto" from_work_dir="table_galaxy.output"> <filter>_data_product['_selector'] == 'Lightcurve'</filter> </data> </outputs> @@ -109,16 +95,16 @@ <param name="DEC" value="22.0147" /> <param name="T1" value="2000-10-09T13:16:00.0" /> <param name="T2" value="2022-10-10T13:16:00.0" /> - <param name="Radius" value="2.5" /> - <param name="pixsize" value="0.1" /> - <param name="Emin" value="100.0" /> - <param name="Emax" value="10000.0" /> + <param name="Radius" value="1.0" /> + <param name="pixsize" value="0.05" /> + <param name="Emin" value="1" /> + <param name="Emax" value="100.0" /> </conditional> <assert_stdout> <has_text text="*** Job finished successfully ***" /> </assert_stdout> </test> - <test expect_num_outputs="2"> + <test expect_num_outputs="3"> <conditional name="_data_product"> <param name="_selector" value="Spectrum" /> <param name="src_name" value="PKS 2155-304" /> @@ -128,27 +114,11 @@ <param name="T2" value="2022-10-10T13:16:00.0" /> <param name="Radius" value="2.5" /> <param name="R_s" value="0.2" /> - <param name="Emin" value="100.0" /> - <param name="Emax" value="10000.0" /> - <param name="NEbins" value="20" /> - </conditional> - <assert_stdout> - <has_text text="*** Job finished successfully ***" /> - </assert_stdout> - </test> - <test expect_num_outputs="2"> - <conditional name="_data_product"> - <param name="_selector" value="Spectrum_gammapy" /> - <param name="src_name" value="PKS 2155-304" /> - <param name="RA" value="329.716938" /> - <param name="DEC" value="-30.225588" /> - <param name="T1" value="2000-10-09T13:16:00.0" /> - <param name="T2" value="2022-10-10T13:16:00.0" /> - <param name="Radius" value="2.5" /> - <param name="R_s" value="0.5" /> - <param name="Emin" value="100.0" /> - <param name="Emax" value="10000.0" /> - <param name="NEbins" value="20" /> + <param name="Emin" value="0.1" /> + <param name="Emax" value="100.0" /> + <param name="NEbins" value="30" /> + <param name="Efit_min" value="0.2" /> + <param name="Efit_max" value="10.0" /> </conditional> <assert_stdout> <has_text text="*** Job finished successfully ***" /> @@ -160,13 +130,13 @@ <param name="src_name" value="Crab" /> <param name="RA" value="83.6287" /> <param name="DEC" value="22.0147" /> - <param name="T1" value="2003-10-09T13:16:00.0" /> - <param name="T2" value="2005-10-10T13:16:00.0" /> + <param name="T1" value="2004-11-20T13:16:00.0" /> + <param name="T2" value="2004-12-20T13:16:00.0" /> <param name="Radius" value="2.5" /> <param name="R_s" value="0.2" /> - <param name="Emin" value="100.0" /> - <param name="Emax" value="10000.0" /> - <param name="NTbins" value="10" /> + <param name="Emin" value="1" /> + <param name="Emax" value="100.0" /> + <param name="NTbins" value="30" /> </conditional> <assert_stdout> <has_text text="*** Job finished successfully ***" /> @@ -185,31 +155,37 @@ the time range that can be adjusted setting the ``T1`` (start time) and ``T2`` (stop time) parameters. +For the spectra, the analysis performs histogramming of events in +energy, in the number ``NEbins`` of energy bins homogeneously spaces in +logarithm of energy, beterrn ``Emin`` and ``Emax``. Conversion of the +counts to the physical flux units is done by dividing by the exposure +time and effective area that is extracted from the Instrument Response +Functions (IRF). The result is shown with black data points. This simple +estimate of flux in energy bins does not take into account the event +energy estimation errors. + +The source signal is extracted from a circular region of the radius +``R_s``\ (adjustable parameter) around the source posiiton. The +background estimate is done using the “wobble” method, from a position +opposite with respect to the signal extraction region in the camera, +with respect to the center of the telescope field-of-view. + +A powerlaw fit to the spectrum is done using forward folding method, +properly taking into account the error of energy estimation. The results +of the spectral fitting include the 68% confidence contour for the +spectral parameters (slope and normalisaiton of the powerlaw spectrum). +The first entry in the “contour” table is the best-fit value of the fit. +The energy range of fitting can be adjusted with the ``Efit_min``, +``Efit_max`` parameters. + The lightcurves are produced by hystrogramming of the events in time, in the number ``NTbins`` of time intervals of equalt time width between ``T1`` (start time) and ``T2`` (stop time). The events are selected in a -desired energy range between ``Emin`` and ``Emax`` from a circular -region of the radius ``R_s`` (in degrees) around the source position -``RA``,\ ``DEC``. Conversion of the counts to the physical flux units is -done by dividing by the exposure time and effective area that is -extracted from the Instrument Response Functions (IRF). - -For the spectra, two alternative tools are considered. The service -``Spectrum`` performs histogramming of the events in energy, in the -number ``NEbins`` of energy bins homogeneously spaces in logarithm of -energy, beterrn ``Emin`` and ``Emax``. Conversion of the counts to the -physical flux units is done by dividing by the exposure time and -effective area that is extracted from the IRF. This method does not take -into account the energy bias and can result in a wrong spectral shape at -the low-energy threshold where the bias is strongest. - -An alternative spectral extraction is done using -`Gammapy <https://gammapy.org/>`__, following the script `Spectrum -Analysis <https://docs.gammapy.org/0.18.2/tutorials/spectrum_analysis.html>`__. -It performs forward folding of the spectral model (a cut-off powerlaw by -default) with the IRF and fits the folded model to the binned count data -in the energy range between ``Emin`` and ``Emax`` in ``NEbins`` -logarithmically spaced energy bins. +desired energy range between ``Emin`` and ``Emax``. The source and +backgorund counts are computed in the same way as for the spectral +fitting. Conversion of the counts to the physical flux units is done by +dividing by the exposure time and effective area that is extracted from +the IRF. </help> <citations> <citation type="doi">10.5281/zenodo.1421098</citation>