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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