def to_dict(self):
""" Generate a dict from the sub-system
Returns
-------
outdict : dict
JSON capatible
"""
import datetime
import getpass
date = str(datetime.date.today().strftime('%Y-%b-%d'))
user = getpass.getuser()
# Generate the dict
outdict = dict(abs_type='SubSystem', Name=self.name, zabs=self.zabs,
vlim=self.vlim.to('km/s').value,
lbl=self.lbl,
CreationDate=date,
user=user
)
# Components
outdict['components'] = {}
for component in self._components:
outdict['components'][component.name] = component.to_dict()
# Polish
outdict = ltu.jsonify_dict(outdict)
# Return
return outdict
def to_dict(self):
""" Convert component data to a dict
Returns
-------
cdict : dict
"""
cdict = dict(Zion=self.Zion, zcomp=self.zcomp, vlim=self.vlim.to('km/s').value,
Name=self.name,
RA=self.coord.ra.value, DEC=self.coord.dec.value,
A=self.A, Ej=self.Ej.to('1/cm').value, comment=self.comment,
flag_N=self.flag_N, logN=self.logN, sig_logN=self.sig_logN)
# AbsLines
cdict['lines'] = {}
for iline in self._abslines:
cdict['lines'][iline.wrest.value] = iline.to_dict()
# Polish
cdict = ltu.jsonify_dict(cdict)
# Return
return cdict
def to_dict(self):
""" Write AbsSystem data to a dict
"""
import datetime
import getpass
date = str(datetime.date.today().strftime('%Y-%b-%d'))
user = getpass.getuser()
# Generate the dict
outdict = dict(Name=self.name, abs_type=self.abs_type, zabs=self.zabs,
vlim=self.vlim.to('km/s').value, zem=self.zem,
NHI=self.NHI, sig_NHI=self.sig_NHI,
RA=self.coord.ra.value, DEC=self.coord.dec.value,
kin=self.kin, Refs=self.Refs, CreationDate=date,
user=user
)
# Components
outdict['components'] = {}
for component in self._components:
outdict['components'][component.name] = component.to_dict()
# Polish
outdict = ltu.jsonify_dict(outdict)
# Return
return outdict
def write_to_fits(self, outfil, clobber=True, add_wave=False):
""" Write to a FITS file
Should generate a separate code to make a Binary FITS table format
Parameters
----------
outfil: String
Name of the FITS file
clobber: bool (True)
Clobber existing file?
add_wave: bool (False)
Force writing of wavelength array
"""
# TODO
# 1. Add unit support for wavelength arrays
from specutils.wcs.specwcs import Spectrum1DPolynomialWCS, Spectrum1DLookupWCS
from specutils.io import write_fits as sui_wf
prihdu = sui_wf._make_hdu(self.data) # Not for binary table format
prihdu.name = "FLUX"
hdu = fits.HDUList([prihdu])
# Type
if type(self.wcs) is Spectrum1DPolynomialWCS: # CRVAL1, etc. WCS
# WCS
wcs = self.wcs
wcs.write_fits_header(prihdu.header)
# Error array?
if self.sig is not None:
sighdu = fits.ImageHDU(self.sig)
sighdu.name = "ERROR"
hdu.append(sighdu)
#
if add_wave:
wvhdu = fits.ImageHDU(self.dispersion.value)
wvhdu.name = "WAVELENGTH"
hdu.append(wvhdu)
elif type(self.wcs) is Spectrum1DLookupWCS:
# Wavelengths as an array (without units for now)
# Add sig, wavelength to HDU
if self.sig is not None:
sighdu = fits.ImageHDU(self.sig)
sighdu.name = "ERROR"
hdu.append(sighdu)
wvhdu = fits.ImageHDU(self.dispersion.value)
wvhdu.name = "WAVELENGTH"
hdu.append(wvhdu)
else:
raise ValueError("write_to_fits: Not ready for this type of spectrum wavelengths")
if hasattr(self, "co") and self.co is not None:
cohdu = fits.ImageHDU(self.co)
cohdu.name = "CONTINUUM"
hdu.append(cohdu)
# Deal with header
if hasattr(self, "head"):
hdukeys = prihdu.header.keys()
# Append ones to avoid
hdukeys = hdukeys + ["BUNIT", "COMMENT", "", "NAXIS2", "HISTORY"]
for key in self.head.keys():
# Use new ones
if key in hdukeys:
continue
# Update unused ones
try:
prihdu.header[key] = self.head[key]
except ValueError:
raise ValueError("l.spectra.utils: Bad header key card")
# History
if "HISTORY" in self.head.keys():
# Strip \n
tmp = str(self.head["HISTORY"]).replace("\n", " ")
try:
prihdu.header.add_history(str(tmp))
except ValueError:
import pdb
pdb.set_trace()
if self.meta is not None and len(self.meta) > 0:
d = liu.jsonify_dict(self.meta)
prihdu.header["METADATA"] = json.dumps(d)
hdu.writeto(outfil, clobber=clobber)
print("Wrote spectrum to {:s}".format(outfil))