# NIRSpec specific rountines go here
import numpy as np
from astropy.io import fits
import astraeus.xarrayIO as xrio
from . import nircam, sigrej
from ..lib.util import read_time, supersample
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def read(filename, data, meta, log):
'''Reads single FITS file from JWST's NIRSpec instrument.
Parameters
----------
filename : str
Single filename to read.
data : Xarray Dataset
The Dataset object in which the fits data will stored.
meta : eureka.lib.readECF.MetaClass
The metadata object.
log : logedit.Logedit
The current log.
Returns
-------
data : Xarray Dataset
The updated Dataset object with the fits data stored inside.
meta : eureka.lib.readECF.MetaClass
The metadata object
log : logedit.Logedit
The current log.
'''
hdulist = fits.open(filename)
# Load master and science headers
data.attrs['filename'] = filename
data.attrs['mhdr'] = hdulist[0].header
data.attrs['shdr'] = hdulist['SCI', 1].header
meta.filter = data.attrs['mhdr']['GRATING']
sci = hdulist['SCI', 1].data
err = hdulist['ERR', 1].data
dq = hdulist['DQ', 1].data
v0 = hdulist['VAR_RNOISE', 1].data
wave_2d = hdulist['WAVELENGTH', 1].data
try:
data.attrs['intstart'] = data.attrs['mhdr']['INTSTART']-1
data.attrs['intend'] = data.attrs['mhdr']['INTEND']
except:
# FINDME: Need to only catch the particular exception we expect
log.writelog(' WARNING: Manually setting INTSTART to 0 and INTEND '
'to NINTS')
data.attrs['intstart'] = 0
data.attrs['intend'] = sci.shape[0]
meta.photometry = False # Photometry for NIRSpec not implemented yet.
# Increase pixel resolution along cross-dispersion direction
if meta.expand > 1:
log.writelog(f' Super-sampling y axis from {sci.shape[1]} ' +
f'to {sci.shape[1]*meta.expand} pixels...',
mute=(not meta.verbose))
sci = supersample(sci, meta.expand, 'flux', axis=1)
err = supersample(err, meta.expand, 'err', axis=1)
dq = supersample(dq, meta.expand, 'cal', axis=1)
v0 = supersample(v0, meta.expand, 'flux', axis=1)
wave_2d = supersample(wave_2d, meta.expand, 'wave', axis=0)
# Record integration mid-times in BMJD_TDB
int_times = hdulist['INT_TIMES', 1].data
if meta.time_file is not None:
time = read_time(meta, data, log)
elif len(int_times['int_mid_BJD_TDB']) == 0:
# There is no time information in the simulated NIRSpec data
if meta.firstFile:
log.writelog(' WARNING: The timestamps for simulated MIRI data '
'are not in the .fits files, so using integration '
'number as the time value instead.')
time = np.linspace(data.mhdr['EXPSTART'], data.mhdr['EXPEND'],
data.intend)
else:
time = int_times['int_mid_BJD_TDB']
if len(time) > len(sci):
# This line is needed to still handle the simulated data
# which had the full time array for all segments
time = time[data.attrs['intstart']:data.attrs['intend']]
# Record units
flux_units = data.attrs['shdr']['BUNIT']
time_units = 'BMJD_TDB'
wave_units = 'microns'
if (meta.firstFile and meta.spec_hw == meta.spec_hw_range[0] and
meta.bg_hw == meta.bg_hw_range[0]):
# Only apply super-sampling expansion once
meta.ywindow[0] *= meta.expand
meta.ywindow[1] *= meta.expand
data['flux'] = xrio.makeFluxLikeDA(sci, time, flux_units, time_units,
name='flux')
data['err'] = xrio.makeFluxLikeDA(err, time, flux_units, time_units,
name='err')
data['dq'] = xrio.makeFluxLikeDA(dq, time, "None", time_units,
name='dq')
data['v0'] = xrio.makeFluxLikeDA(v0, time, flux_units, time_units,
name='v0')
data['wave_2d'] = (['y', 'x'], wave_2d)
data['wave_2d'].attrs['wave_units'] = wave_units
return data, meta, log
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def flag_bg(data, meta, log):
'''Outlier rejection of sky background along time axis.
Parameters
----------
data : Xarray Dataset
The Dataset object.
meta : eureka.lib.readECF.MetaClass
The metadata object.
log : logedit.Logedit
The current log.
Returns
-------
data : Xarray Dataset
The updated Dataset object with outlier background pixels flagged.
'''
log.writelog(' Performing background outlier rejection...',
mute=(not meta.verbose))
bgdata1 = data.flux[:, :meta.bg_y1]
bgmask1 = data.mask[:, :meta.bg_y1]
bgdata2 = data.flux[:, meta.bg_y2:]
bgmask2 = data.mask[:, meta.bg_y2:]
if meta.use_estsig:
# This might not be necessary for real data
bgerr1 = np.ma.median(np.ma.masked_equal(data.err[:, :meta.bg_y1], 0))
bgerr2 = np.ma.median(np.ma.masked_equal(data.err[:, meta.bg_y2:], 0))
estsig1 = [bgerr1 for j in range(len(meta.bg_thresh))]
estsig2 = [bgerr2 for j in range(len(meta.bg_thresh))]
else:
estsig1 = None
estsig2 = None
data['mask'][:, :meta.bg_y1] = sigrej.sigrej(bgdata1, meta.bg_thresh,
bgmask1, estsig1)
data['mask'][:, meta.bg_y2:] = sigrej.sigrej(bgdata2, meta.bg_thresh,
bgmask2, estsig2)
return data
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def flag_ff(data, meta, log):
'''Outlier rejection of full frame along time axis.
For data with deep transits, there is a risk of masking good transit data.
Proceed with caution.
Parameters
----------
data : Xarray Dataset
The Dataset object.
meta : eureka.lib.readECF.MetaClass
The metadata object.
log : logedit.Logedit
The current log.
Returns
-------
data : Xarray Dataset
The updated Dataset object with outlier pixels flagged.
'''
return nircam.flag_ff(data, meta, log)
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def fit_bg(dataim, datamask, n, meta, isplots=0):
"""Fit for a non-uniform background.
Uses the code written for NIRCam which works for NIRSpec.
Parameters
----------
dataim : ndarray (2D)
The 2D image array.
datamask : ndarray (2D)
A boolean array of which data (set to True) should be masked.
n : int
The current integration.
meta : eureka.lib.readECF.MetaClass
The metadata object.
isplots : int; optional
The plotting verbosity, by default 0.
Returns
-------
bg : ndarray (2D)
The fitted background level.
mask : ndarray (2D)
The updated boolean mask after background subtraction, where True
values should be masked.
n : int
The current integration number.
"""
return nircam.fit_bg(dataim, datamask, n, meta, isplots=isplots)
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def cut_aperture(data, meta, log):
"""Select the aperture region out of each trimmed image.
Uses the code written for NIRCam which works for NIRSpec.
Parameters
----------
data : Xarray Dataset
The Dataset object.
meta : eureka.lib.readECF.MetaClass
The metadata object.
log : logedit.Logedit
The current log.
Returns
-------
apdata : ndarray
The flux values over the aperture region.
aperr : ndarray
The noise values over the aperture region.
apmask : ndarray
The mask values over the aperture region. True values should be masked.
apbg : ndarray
The background flux values over the aperture region.
apv0 : ndarray
The v0 values over the aperture region.
Notes
-----
History:
- 2022-06-17, Taylor J Bell
Initial version based on the code in s3_reduce.py
"""
return nircam.cut_aperture(data, meta, log)
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def calibrated_spectra(data, meta, log, cutoff=1e-4):
"""Modify data to compute calibrated spectra in units of mJy.
Parameters
----------
data : Xarray Dataset
The Dataset object.
meta : eureka.lib.readECF.MetaClass
The metadata object.
log : logedit.Logedit
The current log.
cutoff : float
Flux values above the cutoff will be set to zero.
Returns
-------
data : ndarray
The flux values in mJy
Notes
-----
History:
- 2023-07-17, KBS
Initial version.
"""
# Mask uncalibrated BG region
log.writelog(" Setting uncalibrated pixels to zero...",
mute=(not meta.verbose))
boolmask = np.abs(data.flux.data) > cutoff
data['flux'].data = np.where(boolmask, 0, data.flux.data)
log.writelog(f" Zeroed {np.sum(boolmask)} " +
"pixels in total.", mute=(not meta.verbose))
# Convert from MJy to mJy
log.writelog(" Converting from MJy to mJy...",
mute=(not meta.verbose))
data['flux'].data *= 1e9
data['err'].data *= 1e9
data['v0'].data *= 1e9
# Update units
data['flux'].attrs["flux_units"] = 'mJy'
data['err'].attrs["flux_units"] = 'mJy'
data['v0'].attrs["flux_units"] = 'mJy'
return data