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))
def write_to_fits(self, outfil, clobber=True, add_wave=False):
''' Write to a FITS file.
Note that this does not generate a binary FITS table format.
Parameters
----------
outfil : str
Name of the FITS file
clobber : bool (True)
Clobber existing file?
add_wave : bool (False)
Force writing of wavelengths as array, instead of using FITS
header keywords to specify a wcs.
'''
# 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.wavelength.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.wavelength.value)
wvhdu.name = 'WAVELENGTH'
hdu.append(wvhdu)
else:
raise ValueError(
'write_to_fits: Not ready for this for wavelength WCS')
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 = list(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(self.meta)
prihdu.header['METADATA'] = json.dumps(d)
hdu.writeto(outfil, clobber=clobber)
print('Wrote spectrum to {:s}'.format(outfil))
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.io import write_fits as sui_wf
prihdu = sui_wf._make_hdu(self.data) # Not for binary table format
prihdu.name = 'FLUX'
multi = 0 # Multi-extension?
# 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'
#
if add_wave:
wvhdu = fits.ImageHDU(self.dispersion.value)
wvhdu.name = 'WAVELENGTH'
hdu = fits.HDUList([prihdu, sighdu, wvhdu])
else:
hdu = fits.HDUList([prihdu, sighdu])
multi=1
else:
hdu = prihdu
elif type(self.wcs) is Spectrum1DLookupWCS: # Wavelengths as an array (without units for now)
# Add sig, wavelength to HDU
sighdu = fits.ImageHDU(self.sig)
sighdu.name='ERROR'
wvhdu = fits.ImageHDU(self.dispersion.value)
wvhdu.name = 'WAVELENGTH'
hdu = fits.HDUList([prihdu, sighdu, wvhdu])
multi=1
else:
raise ValueError('write_to_fits: Not ready for this type of spectrum wavelengths')
# Deal with header
if hasattr(self,'head'):
hdukeys = prihdu.header.keys()
# Append ones to avoid
hdukeys = hdukeys +ZZ ['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:
xdb.set_trace()
# History
if 'HISTORY' in self.head.keys():
prihdu.header.add_history(str(self.head['HISTORY']))
# Write
hdu.writeto(outfil, clobber=clobber)
print('Wrote spectrum to {:s}'.format(outfil))
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.io import write_fits as sui_wf
prihdu = sui_wf._make_hdu(self.data) # Not for binary table format
prihdu.name = 'FLUX'
multi = 0 # Multi-extension?
# 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'
#
if add_wave:
wvhdu = fits.ImageHDU(self.dispersion.value)
wvhdu.name = 'WAVELENGTH'
hdu = fits.HDUList([prihdu, sighdu, wvhdu])
else:
hdu = fits.HDUList([prihdu, sighdu])
multi = 1
else:
hdu = prihdu
elif type(
self.wcs
) is Spectrum1DLookupWCS: # Wavelengths as an array (without units for now)
# Add sig, wavelength to HDU
sighdu = fits.ImageHDU(self.sig)
sighdu.name = 'ERROR'
wvhdu = fits.ImageHDU(self.dispersion.value)
wvhdu.name = 'WAVELENGTH'
hdu = fits.HDUList([prihdu, sighdu, wvhdu])
multi = 1
else:
raise ValueError(
'write_to_fits: Not ready for this type of spectrum wavelengths'
)
# Deal with header
if hasattr(self, 'head'):
hdukeys = prihdu.header.keys()
# Append ones to avoid
hdukeys = hdukeys + ZZ['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:
xdb.set_trace()
# History
if 'HISTORY' in self.head.keys():
prihdu.header.add_history(str(self.head['HISTORY']))
# Write
hdu.writeto(outfil, clobber=clobber)
print('Wrote spectrum to {:s}'.format(outfil))