"""
Module for JWST NIRSpec specific methods.
.. include:: ../include/links.rst
"""
import numpy as np
from pypeit import msgs
from pypeit import telescopes
from pypeit import utils
from pypeit.core import framematch
from pypeit import io
from pypeit.par import pypeitpar
from pypeit.spectrographs import spectrograph
from pypeit.core import parse
from pypeit.images import detector_container
from IPython import embed
[docs]class JWSTNIRSpecSpectrograph(spectrograph.Spectrograph):
"""
Child to handle JWST NIRSpec specific code
"""
ndet = 2
name = 'jwst_nirspec'
header_name = 'jwst_nirspec'
telescope = telescopes.JWSTTelescopePar()
camera = 'NIRSPEC'
url = 'https://jwst-docs.stsci.edu/jwst-near-infrared-spectrograph'
supported = True
[docs] def get_detector_par(self, det, hdu=None):
"""
Return metadata for the selected detector.
Args:
det (:obj:`int`):
1-indexed detector number.
hdu (`astropy.io.fits.HDUList`_, optional):
The open fits file with the raw image of interest. If not
provided, frame-dependent parameters are set to a default.
Returns:
:class:`~pypeit.images.detector_container.DetectorContainer`:
Object with the detector metadata.
"""
# Detector 1, i.e. NRS1 from
# https://jwst-docs.stsci.edu/jwst-near-infrared-spectrograph/nirspec-instrumentation/nirspec-detectors/nirspec-detector-performance
detector_dict1 = dict(
binning='1,1',
det=1,
dataext=1,
specaxis=1,
specflip=False,
spatflip=False,
xgap=180.,
ygap=0.,
ysize=1.,
platescale=0.1,
darkcurr=33.12, # e-/pixel/hour (=0.0092 e-/pixel/s)
saturation=55100.,
nonlinear=0.95, # need to look up and update
mincounts=-1e10,
numamplifiers=1,
gain=np.atleast_1d(0.996),
ronoise=np.atleast_1d(5.17),
datasec=None,
oscansec=None
)
# Detector 2
detector_dict2 = detector_dict1.copy()
detector_dict2.update(dict(
det=2,
dataext=1,
darkcurr=20.52, # e-/pixel/hour, (=0.0057 e-/pixel/s)
saturation=60400.,
gain=np.atleast_1d(1.137),
ronoise=np.atleast_1d(6.60),
))
detector_dicts = [detector_dict1, detector_dict2]
return detector_container.DetectorContainer(**detector_dicts[det-1])
[docs] @classmethod
def default_pypeit_par(cls):
"""
Return the default parameters to use for this instrument.
Returns:
:class:`~pypeit.par.pypeitpar.PypeItPar`: Parameters required by
all of PypeIt methods.
"""
par = super().default_pypeit_par()
# Reduce
par['reduce']['trim_edge'] = [0,0]
# Object finding
par['reduce']['findobj']['find_trim_edge'] = [0,0]
par['reduce']['findobj']['maxnumber_sci'] = 2
par['reduce']['findobj']['snr_thresh'] = 10.0
par['reduce']['findobj']['trace_npoly'] = 5
par['reduce']['findobj']['snr_thresh'] = 10.0
par['reduce']['findobj']['find_fwhm'] = 2.0
# Sky-subtraction
par['reduce']['skysub']['bspline_spacing'] = 5.0 # JWST sky is smooth
par['reduce']['skysub']['max_mask_frac'] = 0.95
par['reduce']['skysub']['mask_by_boxcar'] = True
par['reduce']['skysub']['sky_sigrej'] = 4.0
# Extraction
par['reduce']['extraction']['model_full_slit'] = True
par['reduce']['extraction']['sn_gauss'] = 5.0
par['reduce']['extraction']['boxcar_radius'] = 0.2 # extent in calwebb is 0.55" source and on NIRSpec website
par['reduce']['extraction']['use_2dmodel_mask'] = False # Don't use 2d mask in local skysub
# Cosmic ray rejection parameters for science frames
par['scienceframe']['process']['sigclip'] = 5.0
par['scienceframe']['process']['objlim'] = 2.0
par['scienceframe']['process']['mask_cr'] = False # Turn off for now since we coadd.
# Skip reference frame correction for now.
par['calibrations']['wavelengths']['refframe'] = 'observed'
return par
[docs] def configuration_keys(self):
"""
Return the metadata keys that define a unique instrument
configuration.
This list is used by :class:`~pypeit.metadata.PypeItMetaData` to
identify the unique configurations among the list of frames read
for a given reduction.
Returns:
:obj:`list`: List of keywords of data pulled from file headers
and used to constuct the :class:`~pypeit.metadata.PypeItMetaData`
object.
"""
return ['dispname', 'filter1', 'decker']
[docs] def pypeit_file_keys(self):
"""
Define the list of keys to be output into a standard ``PypeIt`` file.
Returns:
:obj:`list`: The list of keywords in the relevant
:class:`~pypeit.metadata.PypeItMetaData` instance to print to the
:ref:`pypeit_file`.
"""
pypeit_keys = super().pypeit_file_keys()
pypeit_keys.remove('airmass')
pypeit_keys.remove('binning')
return pypeit_keys
[docs] def check_frame_type(self, ftype, fitstbl, exprng=None):
"""
Check for frames of the provided type.
Args:
ftype (:obj:`str`):
Type of frame to check. Must be a valid frame type; see
frame-type :ref:`frame_type_defs`.
fitstbl (`astropy.table.Table`_):
The table with the metadata for one or more frames to check.
exprng (:obj:`list`, optional):
Range in the allowed exposure time for a frame of type
``ftype``. See
:func:`pypeit.core.framematch.check_frame_exptime`.
Returns:
`numpy.ndarray`_: Boolean array with the flags selecting the
exposures in ``fitstbl`` that are ``ftype`` type frames.
"""
if ftype == 'science':
return np.ones(len(fitstbl), dtype=bool)
msgs.warn('Cannot determine if frames are of type {0}.'.format(ftype))
return np.zeros(len(fitstbl), dtype=bool)
@property
def allowed_mosaics(self):
"""
Return the list of allowed detector mosaics.
JWST/NIRSpec only allows for mosaicing the NRS1 and NRS2 detectors.
Returns:
:obj:`list`: List of tuples, where each tuple provides the 1-indexed
detector numbers that can be combined into a mosaic and processed by
``PypeIt``.
"""
return [(1,2)]
[docs] def get_rawimage(self, raw_file, det):
"""
Read raw images and generate a few other bits and pieces
that are key for image processing.
Based on readmhdufits.pro
Parameters
----------
raw_file : :obj:`str`
File to read
det : :obj:`int`
1-indexed detector to read
Returns
-------
detector_par : :class:`pypeit.images.detector_container.DetectorContainer`
Detector metadata parameters.
raw_img : `numpy.ndarray`_
Raw image for this detector.
hdu : `astropy.io.fits.HDUList`_
Opened fits file
exptime : :obj:`float`
Exposure time read from the file header
rawdatasec_img : `numpy.ndarray`_
Data (Science) section of the detector as provided by setting the
(1-indexed) number of the amplifier used to read each detector
pixel. Pixels unassociated with any amplifier are set to 0.
oscansec_img : `numpy.ndarray`_
Overscan section of the detector as provided by setting the
(1-indexed) number of the amplifier used to read each detector
pixel. Pixels unassociated with any amplifier are set to 0.
"""
fil = utils.find_single_file(f'{raw_file}*', required=True)
# Read
msgs.info(f'Reading JWST/NIRSpec file: {fil}')
hdu = io.fits_open(fil)
head0 = hdu[0].header
detector = self.get_detector_par(det if det is not None else 1, hdu=hdu)
raw_img = hdu[detector['dataext']].data.astype(float)
# Need the exposure time
exptime = hdu[self.meta['exptime']['ext']].header[self.meta['exptime']['card']]
# Return
return detector, raw_img.T, hdu, exptime, None, None