Examples¶

List file types handled by all collaborator packages¶

The current list considers projects aosss, ariastro, f311, and PyFANT.

"""Lists different subsets of DataFile subclasses"""
import f311

titles = ("text", "binary", "1D spectrum")
allclasses = (f311.classes_txt(), f311.classes_bin(), f311.classes_sp())

for title, classes in zip(titles, allclasses):
    print("\n*** Classes that can handle {} files***".format(title))
    for cls in classes:
        print("{:25}: {}".format(cls.__name__, cls.__doc__.strip().split("\n")[0]))

*** Classes that can handle text files***
FileAbXFwhm              : `x.py` Differential Abundances X FWHMs (Python source)
FileAbonds               : PFANT Stellar Chemical Abundances
FileAbsoru2              : PFANT "Absoru2" file
FileAtoms                : PFANT Atomic Lines
FileConfigConvMol        : Configuration file for molecular lines conversion GUI (Python code)
FileDissoc               : PFANT Stellar Dissociation Equilibrium Information
FileHmap                 : PFANT Hydrogen Lines Map
FileKuruczMolecule       : Kurucz molecular lines file
FileKuruczMolecule1      : Kurucz molecular lines file following format of file "c2dabrookek.asc"
FileKuruczMoleculeBase   : Base class for the two types of Kurucz molecular lines file
FileKuruczMoleculeOld    : Kurucz molecular lines file, old format #0
FileKuruczMoleculeOld1   : Kurucz molecular lines file, old format #1
FileMain                 : PFANT Main Stellar Configuration
FileModTxt               : MARCS Atmospheric Model (text file)
FileMolConsts            : Molecular constants config file (Python code)
FileMolecules            : PFANT Molecular Lines
FileOpa                  : MARCS ".opa" (opacity model) file format.
FileOptions              : PFANT Command-line Options
FilePar                  : WebSim-COMPASS ".par" (parameters) file
FilePartit               : PFANT Partition Function
FilePlezTiO              : Plez molecular lines file, TiO format
FilePy                   : Configuration file saved as a .py Python source script
FilePyConfig             : Base class for config files. Inherit and set class variable 'modulevarname' besides usual
FileSpectrum             : Base class for all files representing a single 1D spectrum
FileSpectrumNulbad       : PFANT Spectrum (`nulbad` output)
FileSpectrumPfant        : PFANT Spectrum (`pfant` output)
FileSpectrumXY           : "Lambda-flux" Spectrum (2-column text file)
FileTRAPRBInput          : Input file for the TRAPRB Fortran code (which calculates Franck-Condon factors)
FileTRAPRBOutput         : Output file for the TRAPRB Fortran code (which calculates Franck-Condon factors)
FileToH                  : PFANT Hydrogen Line Profile
FileVald3                : VALD3 atomic or molecular lines file

*** Classes that can handle binary files***
FileFullCube             : FITS WebSim Compass Data Cube
FileHitranDB             : HITRAN Molecules Catalogue
FileModBin               : PFANT Atmospheric Model (binary file)
FileMolDB                : Database of Molecular Constants
FileMoo                  : Atmospheric model or grid of models (with opacities included)
FileSQLiteDB             : Represents a SQLite database file.
FileSparseCube           : FITS Sparse Data Cube (storage to take less disk space)
FileSpectrumFits         : FITS Spectrum
FileSpectrumList         : FITS Spectrum List
FileGalfit               : FITS file with frames named INPUT_*, MODEL_*, RESIDUAL_* (Galfit software output)

*** Classes that can handle 1D spectrum files***
FileSpectrum             : Base class for all files representing a single 1D spectrum
FileSpectrumFits         : FITS Spectrum
FileSpectrumNulbad       : PFANT Spectrum (`nulbad` output)
FileSpectrumPfant        : PFANT Spectrum (`pfant` output)
FileSpectrumXY           : "Lambda-flux" Spectrum (2-column text file)


By the way, the table above was generated with the following code:

Another way to list the file types (as ReST table)¶

import f311.filetypes as ft
print("\n".join(ft.tabulate_filetypes_rest(description_width=55)))

Description	Default filename	Class name	Editors
“Lambda-flux” Spectrum (2-column text file)		FileSpectrumXY	`splisted.py`
Atmospheric model or grid of models (with opacities included)	grid.moo	FileMoo
Configuration file for molecular lines conversion GUI (Python code)	configconvmol.py	FileConfigConvMol
Database of Molecular Constants	moldb.sqlite	FileMolDB	`convmol.py`, `moldbed.py`
FITS Sparse Data Cube (storage to take less disk space)	default.sparsecube	FileSparseCube
FITS Spectrum		FileSpectrumFits	`splisted.py`
FITS Spectrum List	default.splist	FileSpectrumList	`splisted.py`
FITS WebSim Compass Data Cube	default.fullcube	FileFullCube	`cubeed.py`
FITS file with frames named INPUT_, MODEL_, RESIDUAL_* (Galfit software output)		FileGalfit
File containing Franck-Condon Factors (FCFs)		FileFCF
HITRAN Molecules Catalogue	hitrandb.sqlite	FileHitranDB
Kurucz molecular lines file		FileKuruczMolecule
Kurucz molecular lines file, old format #0		FileKuruczMoleculeOld
Kurucz molecular lines file, old format #1		FileKuruczMoleculeOld1
MARCS “.opa” (opacity model) file format.	modeles.opa	FileOpa
MARCS Atmospheric Model (text file)		FileModTxt
Molecular constants config file (Python code)	configmolconsts.py	FileMolConsts	`mced.py`
PFANT “Absoru2” file	absoru2.dat	FileAbsoru2
PFANT Atmospheric Model (binary file)	modeles.mod	FileModBin
PFANT Atomic Lines	atoms.dat	FileAtoms	`ated.py`
PFANT Command-line Options	options.py	FileOptions	`x.py`
PFANT Hydrogen Line Profile	thalpha	FileToH
PFANT Hygrogen Lines Map	hmap.dat	FileHmap
PFANT Main Stellar Configuration	main.dat	FileMain	`mained.py`, `x.py`
PFANT Molecular Lines	molecules.dat	FileMolecules	`mled.py`
PFANT Partition Function	partit.dat	FilePartit
PFANT Spectrum (nulbad output)		FileSpectrumNulbad	`splisted.py`
PFANT Spectrum (pfant output)	flux.norm	FileSpectrumPfant	`splisted.py`
PFANT Stellar Chemical Abundances	abonds.dat	FileAbonds	`abed.py`, `x.py`
PFANT Stellar Dissociation Equilibrium Information	dissoc.dat	FileDissoc
Plez molecular lines file, TiO format		FilePlezTiO
VALD3 atomic or molecular lines file		FileVald3
WebSim-COMPASS “.par” (parameters) file		FilePar
x.py Differential Abundances X FWHMs (Python source)	abxfwhm.py	FileAbXFwhm	`x.py`

Convert 1D spectral file to FITS format¶

#!/usr/bin/env python
"""Converts 1D spectral file of any supported type to FITS format.

The new file is saved with name "<original-filename>.fits".

TODO handle non-equally spaced wavelength values
"""

import f311
import sys
import logging

if __name__ == "__main__":
    if len(sys.argv) < 2 or any([x.startswith("-") for x in sys.argv[1:]]):
        print(__doc__+"\nUsage:\n\n    convert-to-fits.py filename0 [filename1 [filename2 [...]]]\n")
        sys.exit()

    for filename in sys.argv[1:]:
        print("Converting file '{}'...".format(filename))

        try:
            spectrum = f311.load_spectrum(filename)

            if spectrum is None:
                print("File '{}' not recognized as a 1D spectral file".format(filename))
                continue

            filename_new = filename+".fits"

            fnew = f311.FileSpectrumFits()
            fnew.spectrum = spectrum
            fnew.save_as(filename_new)

            print("Successfully saved '{}'".format(filename_new))
        except:
            logging.exception("Error converting file '{}'".format(filename))

Todo

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