Commit 2f7c4f3c authored by Matthieu BETHERMIN's avatar Matthieu BETHERMIN
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Documentation of the pySIDES code
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pySIDES is the new Python version of the Simulated Infrared Dusty Extragalctic Sky. This code generates mock catalogs of galaxies in the (sub-)millimeter domain and associates spectral cubes (e.g., intensity mapping experiments). It produces both continuum and bright line emission (CO, [CII], [CI]). The scientific paper describing the continuum model and its validation is `Béthermin et al. (2017)`__. The line emission will be described in a paper in preparation.
pySIDES is the new Python version of the Simulated Infrared Dusty Extragalactic Sky (SIDES). This code generates mock catalogs of galaxies in the (sub-)millimeter domain and associates spectral cubes (e.g., for intensity mapping experiments). It produces both continuum and CO, [CII], and [CI] line emission . The scientific paper describing the continuum model and its validation is `Béthermin et al. (2017)`__. The line emission is described in Bethermin et al. (2022).
__ https://ui.adsabs.harvard.edu/abs/2017A%26A...607A..89B/abstract
......@@ -11,14 +11,14 @@ Matthieu Béthermin, Mathilde Van Cuyck, Alexandre Beelen, Athanasia Gkogkou
How is the repository organized?
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The PYSIDES folder contains all the machinery of pySIDES. Inside this, there are a couple of scripts to generate catalogs of cubes and Jupyter notebooks used to validate the results. The pysides sub-folder contains the actual code with the routine used to generate galaxy properties. The PAR_FILES sub-folder contains the parameter files used to run the standard simulations and produce the CONCERTO standard cubes. OUTPUTS will contain the results of the runs if standard parameters are used.
The PYSIDES folder contains all the machinery of pySIDES. Inside this, there are a couple of scripts to generate catalogs of cubes and Jupyter notebooks used to validate the results. The pysides sub-folder contains the actual code with the routine used to generate galaxy properties. The PAR_FILES sub-folder contains the parameter files used to run the standard simulations and produce the CONCERTO-like standard cubes. OUTPUTS will contain the results of the runs if standard parameters are used.
The LINEPLOT directory contains the codes used to validate the line emission recipes of the standard simulation. If you are just interested to produce mock catalog with standard parameters, you do not care about it. But, it can save you time, if you want to validate your own modified line recipes.
How to generate a catalog without clustering?
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Before the first use, you need to regenerate the filter grids used to derive fluxes efficiently as a function of Umean, z, and the galaxy type. You can do this by running the following script: PYSIDES/pysides/SEDfiles/gen_useful_filter_grids.py.
Before the first use and if you want to generate photometric products, you need to regenerate the filter grids which is the way of deriving efficiently the fluxes as a function of Umean, z, and the galaxy type. You can do this by running the following script: PYSIDES/pysides/SEDfiles/gen_useful_filter_grids.py.
To generate a catalog without clustering, you just need to run the gen_psysides_cat.py script. By default, this script will generate the galaxy properties using parameters in PAR_FILES/SIDES_unclustered_1deg2_standard.par. You will probably have to modify the path the script and pysides_path in the parameter file. You can also use the keyword force_pysides_path = '/my/path/to/PYSIDES' in load_params if you do not want to modify the paramater file. You also may use your own custom parameter file. If so, you should change the path of files read by the load_params function.
......@@ -33,13 +33,9 @@ How to generate a catalog with clustering?
The procedure is similar as for the unclustered catalog, except that you have to load a catalog containing the 'redshift', 'ra', 'dec', 'Mhalo', 'Mstar' columns in a pandas object before producing IR properties. This is done by the gen_pysides_from_original.py script.
By default, you can load the 2 sq deg simulation of the original SIDES (coded in IDL). The CSV file can be downloaded at this `address`__. Do not forget to modify csv_idl_path to have the correct path.
By default, you can load the 2 sq deg simulation of the original SIDES published in 2017 (coded in IDL). The CSV file can be downloaded at this `address`__. Do not forget to modify csv_idl_path to have the correct path.
__ http://cesam.lam.fr/sides/index/download
You may need to add this line at the beginning of the file:
redshift,ra,dec,Mhalo,Mstar,qflag,SFR,mu,issb,Umean,SMIPS24,SPACS70,SPACS100,SPACS160,SSPIRE250,SSPIRE350,SSPIRE500,SNIKA1200,SNIKA2000,SCCAT200,SCCAT350,SCCAT450,SCCAT750,SCCAT850,SCCAT1100,SCCAT1300,SCCAT2000,SCCAT3300,SSPIRE250ext,SSPIRE350ext,SSPIRE500ext
__ https://cesamsi.lam.fr/server/download-file/catalogue_2017/SIDES_Bethermin2017_short.csv.gz
If you want to use another dark-matter simulation, you have to produce a piece of code doing something equivalent to line 10 to 14 of gen_pysides_from_original.py. The critical part is to perform an abundance matching producing the exact same stellar mass function as used in Béthermin et al. 2017 (also generated by gen_mass.py in the pysides folder and used by the unclustered version). If the stellar mass function is not the same, the IR properties may not be well reproduced.
......@@ -48,7 +44,7 @@ How to generate a cube?
An example of script to generate a cube for the CONCERTO experiment is provided: gen_CONCERTO_cubes.py. To generate a cube you need to load both the parameter file used to generate the catalog (e.g., PAR_FILES/SIDES_from_original.par) and the parameter file of the cube/instrument (e.g., PAR_FILES/CONCERTO_cubes.par). The cube generator can produce simulations smoothed or not by the beam (assuming a Gaussian beam with FWHM = 1.22 lambda/D). No noise is included in these simulations.
The parameters in CONCERTO_cubes.par provide the pixel size, the size of the telescope, the frequency range and spectral resolution. By default the cubes are saved in OUTPUTS/CUBES/. You can produce cubes in various units with and/or without beam. The slowest step of the process is the beam smoothing. Use it only if you need it. You can generate cubes with the De Looze et al. and/or the Lagache et al. relation between SFR and L[CII]. Finally, you can decide, which cubes you want to save (each transition, each species, all lines, continuum only, and/or everything).
The parameters in CONCERTO_cubes.par provide the pixel size, the size of the telescope, the frequency range and spectral resolution. You can produce cubes in various units with and/or without beam. The slowest step of the process is the beam smoothing. Use it only if you need it. You can generate cubes with the De Looze et al. and/or the Lagache et al. relation between SFR and L[CII]. Finally, you can decide, which cubes you want to save (each transition, each species, all lines, continuum only, and/or everything). The flux of a line is placed in a single spectral element (no line width taken into account) and resolutions better than 1 GHz should be used with caution.
How to add new broadband filters?
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......@@ -62,15 +58,15 @@ We provide some example scripts, which can be adapted to produce your own custom
- gen_pysides_cat.py: Script to generate a 1 deg2 simulation without clustering.
- gen_pysides_from_original.py: Script to generate luminous properties to the base catalog of the SIDES-Bolshoi run (Béthermin et al. 2017). You need to download SIDES_Bethermin2017.csv at http://cesam.lam.fr/sides/.
- gen_pysides_from_original.py: Script to generate luminous properties to the base catalog of the SIDES-Bolshoi run (Béthermin et al. 2017). You need to download SIDES_Bethermin2017_short.csv at https://cesamsi.lam.fr/server/download-file/catalogue_2017/SIDES_Bethermin2017_short.csv.gz.
- gen_CONCERTO_cubes.py: Generate simulated CONCERTO cubes without noise from the catalog generated by the previous script.
- gen_CONCERTO_cubes_masked.py: Generate simulated CONCERTO cubes without including the known sources.
- gen_CONCERTO_cubes_masked.py: Generate simulated CONCERTO cubes without including the known sources (see Sect. 5.4 of Bethermin et al. 2022).
- gen_Herschel_maps.py: Generate the Herschel maps from the catalogs.
The scripts tagged as uchuu correspond to another analysis, which will be released later.
The scripts tagged as uchuu correspond to another analysis, which will be released later.
Contact
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......@@ -78,3 +74,7 @@ If you have any question, please contact `Matthieu Béthermin`__.
__ mailto:matthieu.bethermin@lam.fr
Acknowledgments
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This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 788212). It also received support from the Excellence Initiative of Aix-Marseille University-AMidex, a French "Investissements d’Avenir.
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