def test_parse_binning():
""" Test parse binning algorithm
"""
bin1, bin2 = parse.parse_binning('2,2')
assert bin1 == 2
assert bin2 == 2
# Other input
bin1, bin2 = parse.parse_binning((2,2))
assert bin1 == 2
assert bin2 == 2
def config_specific_par(self, par, scifile):
# Templates
if self.get_meta_value(scifile, 'dispname') == '600ZD':
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_deimos_600.fits'
par['calibrations']['wavelengths']['lamps'] += [
'CdI', 'ZnI', 'HgI'
]
elif self.get_meta_value(scifile, 'dispname') == '830G':
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_deimos_830G.fits'
elif self.get_meta_value(scifile, 'dispname') == '1200G':
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_deimos_1200G.fits'
# FWHM
binning = parse.parse_binning(self.get_meta_value(scifile, 'binning'))
par['calibrations']['wavelengths']['fwhm'] = 6.0 / binning[1]
# Return
return par
def order_platescale(self, binning=None):
"""
Returns the plate scale in arcseconds for each order
Parameters
----------
None
Optional Parameters
--------------------
binning: str
Returns
-------
order_platescale: ndarray, float
"""
# VIS has no binning, but for an instrument with binning we would do this
binspectral, binspatial = parse.parse_binning(binning)
# ToDO Either assume a linear trend or measure this
# X-shooter manual says, but gives no exact numbers per order.
# VIS: 65.9 pixels (0.167"/pix) at order 17 to 72.0 pixels (0.153"/pix) at order 30.
# Right now I just assume a simple linear trend
slit_vec = np.arange(self.norders)
order_vec = self.slit2order(slit_vec)
plate_scale = 0.153 + (order_vec - 30)*(0.153-0.167)/(30 - 17)
return plate_scale*binspatial
def compound_meta(self, headarr, meta_key):
if meta_key == 'binning':
binspatial, binspec = parse.parse_binning(headarr[0]['BINNING'])
binning = parse.binning2string(binspec, binspatial)
return binning
else:
msgs.error("Not ready for this compound meta")
def compound_meta(self, headarr, meta_key):
"""
Methods to generate metadata requiring interpretation of the header
data, instead of simply reading the value of a header card.
Args:
headarr (:obj:`list`):
List of `astropy.io.fits.Header`_ objects.
meta_key (:obj:`str`):
Metadata keyword to construct.
Returns:
object: Metadata value read from the header(s).
"""
if meta_key == 'binning':
# binning in the raw frames
ccdsum = headarr[1].get('CCDSUM')
if ccdsum is not None:
binspatial, binspec = parse.parse_binning(ccdsum)
binning = parse.binning2string(binspec, binspatial)
else:
# binning in the spec2d file
binning = headarr[0].get('BINNING')
if binning is None:
msgs.error('Binning not found')
return binning
def config_specific_par(self, scifile, inp_par=None):
"""
Modify the ``PypeIt`` parameters to hard-wired values used for
specific instrument configurations.
Args:
scifile (:obj:`str`):
File to use when determining the configuration and how
to adjust the input parameters.
inp_par (:class:`~pypeit.par.parset.ParSet`, optional):
Parameter set used for the full run of PypeIt. If None,
use :func:`default_pypeit_par`.
Returns:
:class:`~pypeit.par.parset.ParSet`: The PypeIt parameter set
adjusted for configuration specific parameter values.
"""
par = super().config_specific_par(scifile, inp_par=inp_par)
headarr = self.get_headarr(scifile)
# Turn PCA off for long slits
if 'arcsec' in self.get_meta_value(headarr, 'decker'):
par['calibrations']['slitedges']['sync_predict'] = 'nearest'
# Allow for various binning
binning = parse.parse_binning(self.get_meta_value(headarr, 'binning'))
par['calibrations']['wavelengths']['fwhm_fromlines'] = True
return par
def order_platescale(self, order_vec, binning=None):
"""
Return the platescale for each echelle order.
This routine is only defined for echelle spectrographs, and it is
undefined in the base class.
Args:
order_vec (`numpy.ndarray`_):
The vector providing the order numbers.
binning (:obj:`str`, optional):
The string defining the spectral and spatial binning.
Returns:
`numpy.ndarray`_: An array with the platescale for each order
provided by ``order``.
"""
binspectral, binspatial = parse.parse_binning(binning)
# ToDO Either assume a linear trend or measure this
# X-shooter manual says, but gives no exact numbers per order.
# UVB: 65.9 pixels (0.167“/pix) at order 14 to 70.8 pixels (0.155”/pix) at order 24
# Assume a simple linear trend
plate_scale = 0.155 + (order_vec - 24) * (0.155 - 0.167) / (24 - 14)
# Right now I just took the average
return np.full(self.norders, 0.161) * binspatial
def order_platescale(self, order_vec, binning=None):
"""
Return the platescale for each echelle order.
This routine is only defined for echelle spectrographs, and it is
undefined in the base class.
Args:
order_vec (`numpy.ndarray`_):
The vector providing the order numbers.
binning (:obj:`str`, optional):
The string defining the spectral and spatial binning.
Returns:
`numpy.ndarray`_: An array with the platescale for each order
provided by ``order``.
"""
# VIS has no binning, but for an instrument with binning we would do this
binspectral, binspatial = parse.parse_binning(binning)
# ToDO Either assume a linear trend or measure this
# X-shooter manual says, but gives no exact numbers per order.
# VIS: 65.9 pixels (0.167"/pix) at order 17 to 72.0 pixels (0.153"/pix) at order 30.
# Right now I just assume a simple linear trend
plate_scale = 0.153 + (order_vec - 30) * (0.153 - 0.167) / (30 - 17)
return plate_scale * binspatial
def order_platescale(self, binning=None):
"""
Returns the plate scale in arcseconds for each order
Parameters
----------
None
Optional Parameters
--------------------
binning: str
Returns
-------
order_platescale: ndarray, float
"""
msgs.error("REFACTOR")
binspectral, binspatial = parse.parse_binning(binning)
# ToDO Either assume a linear trend or measure this
# X-shooter manual says, but gives no exact numbers per order.
# UVB: 65.9 pixels (0.167“/pix) at order 14 to 70.8 pixels (0.155”/pix) at order 24
# Right now I just took the average
return np.full(self.norders, 0.161) * binspatial
def bpm(self, shape=None, filename=None, det=None, **null_kwargs):
"""
Override parent bpm function with BPM specific to X-Shooter VIS.
.. todo::
Allow for binning changes.
Parameters
----------
det : int, REQUIRED
**null_kwargs:
Captured and never used
Returns
-------
bpix : ndarray
0 = ok; 1 = Mask
"""
msgs.info("Custom bad pixel mask for MAGE")
self.empty_bpm(shape=shape, filename=filename, det=det)
# Get the binning
hdu = fits.open(filename)
binspatial, binspec = parse.parse_binning(hdu[0].header['BINNING'])
hdu.close()
# Do it
self.bpm_img[:, :10 // binspatial] = 1.
self.bpm_img[:, 1020 // binspatial:] = 1.
# Return
return self.bpm_img
def compound_meta(self, headarr, meta_key):
"""
Args:
headarr: list
meta_key: str
Returns:
value
"""
if meta_key == 'binning':
binspatial, binspec = parse.parse_binning(headarr[0]['BINNING'])
binning = parse.binning2string(binspec, binspatial)
return binning
elif meta_key == 'dispangle':
if headarr[0]['GRATEPOS'] == 3:
return headarr[0]['G3TLTWAV']
elif headarr[0]['GRATEPOS'] == 4:
return headarr[0]['G4TLTWAV']
else:
msgs.warn(
'This is probably a problem. Non-standard DEIMOS GRATEPOS={0}.'
.format(headarr[0]['GRATEPOS']))
else:
msgs.error("Not ready for this compound meta")
def wavegrid(self, binning=None, midpoint=False, samp_fact=1.0):
r"""
Construct a fixed wavelength grid in :math:`\log_{10} \lambda`. This
method is mostly used for echelle spectrographs.
This is primarily a wrapper for
:func:`pypeit.core.wavecal.wvutils.wavegrid`.
Args:
binning (:obj:`str`, optional):
String representation of the spectral and spatial binning. If
None, assumed to be ``'1,1'``.
midpoint (:obj:`bool`, optional):
Increment the grid to the spectral mid-point.
samp_fact (:obj:`float`, optional):
The pixel-sampling factor. If 1., the spectra are sampled by
the logarithmic step associated with a single binned pixel
(:attr:`dloglam`).
Returns:
`numpy.ndarray`_: The logarithmically sampled wavelength grid;
grid points are in wavelength, *not* ``log10(wavelength)``.
"""
binspectral, binspatial = parse.parse_binning(binning)
logmin, logmax = self.loglam_minmax
loglam_grid = wvutils.wavegrid(logmin,
logmax,
self.dloglam * binspectral,
samp_fact=samp_fact)
if midpoint:
loglam_grid = loglam_grid + self.dloglam * binspectral / samp_fact / 2.0
return np.power(10.0, loglam_grid)
def get_wv_calib(self):
"""
Load or generate the 1D wavelength calibrations
Requirements:
msarc, msbpm, slits, det, par
Returns:
dict: :attr:`wv_calib` calibration dict and the updated slit mask array
"""
# Check for existing data
if not self._chk_objs(['msarc', 'msbpm', 'slits']):
msgs.warn(
'Not enough information to load/generate the wavelength calibration. Skipping and may crash down the line'
)
return None
# Check internals
self._chk_set(['det', 'calib_ID', 'par'])
if 'arc' not in self.master_key_dict.keys():
msgs.error('Arc master key not set. First run get_arc.')
# No wavelength calibration requested
if self.par['wavelengths']['reference'] == 'pixel':
msgs.info("A wavelength calibration will not be performed")
self.wv_calib = None
return self.wv_calib
# Grab arc binning (may be different from science!)
# TODO : Do this internally when we have a wv_calib DataContainer
binspec, binspat = parse.parse_binning(self.msarc.detector.binning)
# Instantiate
self.waveCalib = wavecalib.WaveCalib(
self.msarc,
self.slits,
self.spectrograph,
self.par['wavelengths'],
binspectral=binspec,
det=self.det,
master_key=self.master_key_dict['arc'], # For QA naming
qa_path=self.qa_path,
msbpm=self.msbpm)
# Load from disk (MasterFrame)?
masterframe_name = masterframe.construct_file_name(
wavecalib.WaveCalib,
self.master_key_dict['arc'],
master_dir=self.master_dir)
if os.path.isfile(masterframe_name) and self.reuse_masters:
# Load from disk
self.wv_calib = self.waveCalib.load(masterframe_name)
self.slits.mask_wvcalib(self.wv_calib)
else:
self.wv_calib = self.waveCalib.run(skip_QA=(not self.write_qa))
# Save to Masters
self.waveCalib.save(outfile=masterframe_name)
# Return
return self.wv_calib
def config_specific_par(self, scifile, inp_par=None):
"""
Modify the PypeIt parameters to hard-wired values used for
specific instrument configurations.
.. todo::
Document the changes made!
Args:
scifile (str):
File to use when determining the configuration and how
to adjust the input parameters.
inp_par (:class:`pypeit.par.parset.ParSet`, optional):
Parameter set used for the full run of PypeIt. If None,
use :func:`default_pypeit_par`.
Returns:
:class:`pypeit.par.parset.ParSet`: The PypeIt paramter set
adjusted for configuration specific parameter values.
"""
# Start with instrument wide
par = super(KeckLRISRSpectrograph,
self).config_specific_par(scifile, inp_par=inp_par)
# Lacosmic CR settings
# Grab the defaults for LRISr
binning = self.get_meta_value(scifile, 'binning')
# Unbinned LRISr needs very aggressive LACosmics parameters for 1x1 binning
if binning == '1,1':
sigclip = 3.0
objlim = 0.5
par['scienceframe']['process']['sigclip'] = sigclip
par['scienceframe']['process']['objlim'] = objlim
# Wavelength calibrations
if self.get_meta_value(
scifile,
'dispname') == '400/8500': # This is basically a reidentify
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_red_400.fits'
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths']['sigdetect'] = 20.0
par['calibrations']['wavelengths']['nsnippet'] = 1
elif self.get_meta_value(scifile, 'dispname') == '600/5000':
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_red_600_5000.fits'
par['calibrations']['wavelengths']['method'] = 'full_template'
elif self.get_meta_value(scifile, 'dispname') == '1200/9000':
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_red_1200_9000.fits'
par['calibrations']['wavelengths']['method'] = 'full_template'
# FWHM
binning = parse.parse_binning(self.get_meta_value(scifile, 'binning'))
par['calibrations']['wavelengths']['fwhm'] = 8.0 / binning[0]
# Return
return par
def config_specific_par(self, scifile, inp_par=None):
"""
Modify the PypeIt parameters to hard-wired values used for
specific instrument configurations.
.. todo::
Document the changes made!
Args:
scifile (str):
File to use when determining the configuration and how
to adjust the input parameters.
inp_par (:class:`pypeit.par.parset.ParSet`, optional):
Parameter set used for the full run of PypeIt. If None,
use :func:`default_pypeit_par`.
Returns:
:class:`pypeit.par.parset.ParSet`: The PypeIt paramter set
adjusted for configuration specific parameter values.
"""
par = self.default_pypeit_par() if inp_par is None else inp_par
headarr = self.get_headarr(scifile)
# Turn PCA off for long slits
# TODO: I'm a bit worried that this won't catch all
# long-slits...
if ('Long' in self.get_meta_value(
headarr, 'decker')) or ('LVMslit' in self.get_meta_value(
headarr, 'decker')):
par['calibrations']['slitedges']['sync_predict'] = 'nearest'
# Templates
if self.get_meta_value(headarr, 'dispname') == '600ZD':
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_deimos_600.fits'
par['calibrations']['wavelengths']['lamps'] += [
'CdI', 'ZnI', 'HgI'
]
elif self.get_meta_value(headarr, 'dispname') == '830G':
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_deimos_830G.fits'
elif self.get_meta_value(headarr, 'dispname') == '1200G':
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_deimos_1200G.fits'
# FWHM
binning = parse.parse_binning(self.get_meta_value(headarr, 'binning'))
par['calibrations']['wavelengths']['fwhm'] = 6.0 / binning[1]
# Return
return par
def config_specific_par(self, scifile, inp_par=None):
"""
Modify the PypeIt parameters to hard-wired values used for
specific instrument configurations.
.. todo::
Document the changes made!
Args:
scifile (str):
File to use when determining the configuration and how
to adjust the input parameters.
inp_par (:class:`pypeit.par.parset.ParSet`, optional):
Parameter set used for the full run of PypeIt. If None,
use :func:`default_pypeit_par`.
Returns:
:class:`pypeit.par.parset.ParSet`: The PypeIt paramter set
adjusted for configuration specific parameter values.
"""
par = self.default_pypeit_par() if inp_par is None else inp_par
# TODO: Should we allow the user to override these?
# Wavelength calibrations
if self.get_meta_value(scifile, 'dispname') == '300/5000':
par['calibrations']['wavelengths']['reid_arxiv'] = 'keck_lris_blue_300_d680.fits'
par['flexure']['spectrum'] = os.path.join(resource_filename('pypeit', 'data/sky_spec/'),
'sky_LRISb_400.fits')
elif self.get_meta_value(scifile, 'dispname') == '400/3400':
par['calibrations']['wavelengths']['reid_arxiv'] = 'keck_lris_blue_400_d560.fits'
par['flexure']['spectrum'] = os.path.join(resource_filename('pypeit', 'data/sky_spec/'),
'sky_LRISb_400.fits')
elif self.get_meta_value(scifile, 'dispname') == '600/4000':
par['calibrations']['wavelengths']['reid_arxiv'] = 'keck_lris_blue_600_d560.fits'
par['flexure']['spectrum'] = os.path.join(resource_filename('pypeit', 'data/sky_spec/'),
'sky_LRISb_600.fits')
elif self.get_meta_value(scifile, 'dispname') == '1200/3400':
par['calibrations']['wavelengths']['reid_arxiv'] = 'keck_lris_blue_1200_d460.fits'
par['flexure']['spectrum'] = os.path.join(resource_filename('pypeit', 'data/sky_spec/'),
'sky_LRISb_600.fits')
# FWHM
binning = parse.parse_binning(self.get_meta_value(scifile, 'binning'))
par['calibrations']['wavelengths']['fwhm'] = 8.0 / binning[0]
# Slit tracing
# Reduce the slit parameters because the flux does not span the full detector
# It is primarily on the upper half of the detector (usually)
if self.get_meta_value(scifile, 'dispname') == '300/5000':
par['calibrations']['slits']['mask_frac_thresh'] = 0.45
par['calibrations']['slits']['smash_range'] = [0.5, 1.]
# Return
return par
def _fill_tslits_dict(self):
"""
Build a simple dictionary holding the key trace bits and pieces that PypeIt wants
Returns:
dict: Trace slits dict
"""
self.tslits_dict = {}
# Have the slit boundaries been tweaked? If so use the tweaked
# boundaries. TODO: Have the dict keys have the same name as
# the attribute
self.tslits_dict['slit_left_orig'] = self.slit_left
self.tslits_dict['slit_righ_orig'] = self.slit_righ
if self.slit_left_tweak is not None:
self.tslits_dict['slit_left_tweak'] = self.slit_left_tweak
self.tslits_dict['slit_righ_tweak'] = self.slit_righ_tweak
self.tslits_dict['slit_left'] = self.slit_left_tweak
self.tslits_dict['slit_righ'] = self.slit_righ_tweak
else:
self.tslits_dict['slit_left'] = self.slit_left
self.tslits_dict['slit_righ'] = self.slit_righ
# Fill in the rest of the keys that were generated by
# make_pixel_arrays from the slit boundaries. This was done with
# tweaked boundaries if they exist. TODO: Some of these
# quantities may be deprecated.
#for key in ['slitcen', 'pixwid', 'lordpix','rordpix', 'extrapord']:
# self.tslits_dict[key] = getattr(self, key)
# add in the image size and some stuff to create the slitmask
self.tslits_dict['maskslits'] = self.maskslits
self.tslits_dict['slitcen'] = self.slitcen
self.tslits_dict['nspec'] = self.mstrace.shape[0]
self.tslits_dict['nspat'] = self.mstrace.shape[1]
self.tslits_dict['nslits'] = self.slit_left.shape[1]
self.tslits_dict['pad'] = self.par['pad']
binspectral, binspatial = parse.parse_binning(self.binning)
self.tslits_dict['binspectral'] = binspectral
self.tslits_dict['binspatial'] = binspatial
self.tslits_dict['spectrograph'] = self.spectrograph.spectrograph
slit_spat_pos = trace_slits.slit_spat_pos(self.tslits_dict)
spec_min_max = self.spectrograph.slit_minmax(slit_spat_pos, binspectral = binspectral)
self.tslits_dict['spec_min'], self.tslits_dict['spec_max'] = spec_min_max[0, :], spec_min_max[1, :]
# Now extrapolate the traces JFH turning this off for now.
#self.tslits_dict['slit_left'] = trace_slits.extrapolate_trace(self.tslits_dict['slit_left'], spec_min_max)
#self.tslits_dict['slit_righ'] = trace_slits.extrapolate_trace(self.tslits_dict['slit_righ'], spec_min_max)
return self.tslits_dict
def config_specific_par(self, par, scifile):
"""
Set par values according to the specific frame
Args:
par: ParSet
scifile: str
Name of the science file to use
Returns:
par
"""
# Wavelength calibrations
if self.get_meta_value(scifile, 'dispname') == '300/5000':
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_blue_300_d680.fits'
par['flexure']['spectrum'] = os.path.join(
resource_filename('pypeit', 'data/sky_spec/'),
'sky_LRISb_400.fits')
elif self.get_meta_value(scifile, 'dispname') == '400/3400':
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_blue_400_d560.fits'
par['flexure']['spectrum'] = os.path.join(
resource_filename('pypeit', 'data/sky_spec/'),
'sky_LRISb_400.fits')
elif self.get_meta_value(scifile, 'dispname') == '600/4000':
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_blue_600_d560.fits'
par['flexure']['spectrum'] = os.path.join(
resource_filename('pypeit', 'data/sky_spec/'),
'sky_LRISb_600.fits')
elif self.get_meta_value(scifile, 'dispname') == '1200/3400':
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_blue_1200_d460.fits'
par['flexure']['spectrum'] = os.path.join(
resource_filename('pypeit', 'data/sky_spec/'),
'sky_LRISb_600.fits')
# FWHM
binning = parse.parse_binning(self.get_meta_value(scifile, 'binning'))
par['calibrations']['wavelengths']['fwhm'] = 8.0 / binning[0]
# Slit tracing
# Reduce the slit parameters because the flux does not span the full detector
# It is primarily on the upper half of the detector (usually)
if self.get_meta_value(scifile, 'dispname') == '300/5000':
par['calibrations']['slits']['mask_frac_thresh'] = 0.45
par['calibrations']['slits']['smash_range'] = [0.5, 1.]
# Return
return par
def slitmask(self, tslits_dict, pad=None):
"""
Generic routine ton construct a slitmask image from a tslits_dict. Children of this class can
overload this function to implement instrument specific slitmask behavior, for example setting
where the orders on an echelle spectrograph end
Parameters
-----------
tslits_dict: dict
Trace slits dictionary with slit boundary information
Optional Parameters
pad: int or float
Padding of the slit boundaries
binning: tuple
Spectrograph binning in spectral and spatial directions
Returns
-------
slitmask: ndarray int
Image with -1 where there are no slits/orders, and an integer where there are slits/order with the integer
indicating the slit number going from 0 to nslit-1 from left to right.
"""
# These lines are always the same
pad = tslits_dict['pad'] if pad is None else pad
nslits = tslits_dict['lcen'].shape[1]
if nslits != self.norders:
msgs.error('Not all the orders were identified!')
slitmask = pixels.slit_pixels(tslits_dict['lcen'],
tslits_dict['rcen'],
tslits_dict['nspat'],
pad=pad)
spec_img = np.outer(
np.arange(tslits_dict['nspec'], dtype=int),
np.ones(tslits_dict['nspat'],
dtype=int)) # spectral position everywhere along image
binning = tslits_dict['binning']
binspectral, binspatial = parse.parse_binning(binning)
# These are the order boundaries determined by eye by JFH.
order_max = np.asarray([4000] * 14 + [3000]) // binspectral
order_min = np.asarray([2000, 1000] + [0] * 13) // binspectral
# TODO add binning adjustments to these
for iorder in range(self.norders):
orderbad = (slitmask == iorder) & ((spec_img < order_min[iorder]) |
(spec_img > order_max[iorder]))
slitmask[orderbad] = -1
return slitmask
def compound_meta(self, headarr, meta_key):
"""
Args:
headarr: list
meta_key: str
Returns:
value
"""
if meta_key == 'binning':
binspatial, binspec = parse.parse_binning(headarr[0]['BINNING'])
return parse.binning2string(binspec, binspatial)
def compound_meta(self, headarr, meta_key):
"""
Methods to generate metadata requiring interpretation of the header
data, instead of simply reading the value of a header card.
Args:
headarr (:obj:`list`):
List of `astropy.io.fits.Header`_ objects.
meta_key (:obj:`str`):
Metadata keyword to construct.
Returns:
object: Metadata value read from the header(s).
"""
if meta_key == 'binning':
binspatial, binspec = parse.parse_binning(headarr[0]['BINNING'])
binning = parse.binning2string(binspec, binspatial)
return binning
elif meta_key == 'slitwid':
# Get the slice scale
slicescale = 0.00037718 # Degrees per 'large slicer' slice
ifunum = headarr[0]['IFUNUM']
if ifunum == 2:
slicescale /= 2.0
elif ifunum == 3:
slicescale /= 4.0
return slicescale
elif meta_key == 'ra' or meta_key == 'dec':
try:
if self.is_nasmask(headarr[0]):
hdrstr = 'RABASE' if meta_key == 'ra' else 'DECBASE'
else:
hdrstr = 'RA' if meta_key == 'ra' else 'DEC'
except KeyError:
try:
hdrstr = 'TARGRA' if meta_key == 'ra' else 'TARGDEC'
except KeyError:
hdrstr = ''
return headarr[0][hdrstr]
elif meta_key == 'pressure':
return headarr[0]['WXPRESS'] * 0.001 * units.bar
elif meta_key == 'temperature':
return headarr[0]['WXOUTTMP'] * units.deg_C
elif meta_key == 'humidity':
return headarr[0]['WXOUTHUM'] / 100.0
elif meta_key == 'obstime':
return Time(headarr[0]['DATE-END'])
else:
msgs.error("Not ready for this compound meta")
def order_platescale(self, order_vec, binning=None):
"""
Returns the plate scale in arcseconds for each order
Args:
order_vec (np.ndarray): Order numbers
binning (optional):
Returns:
np.ndarray: Platescale
"""
norders = len(order_vec)
binspatial, binspec = parse.parse_binning(binning)
return np.full(norders, 0.30 * binspatial)
def compound_meta(self, headarr, meta_key):
"""
Args:
headarr: list
meta_key: str
Returns:
value
"""
if meta_key == 'binning':
binspatial, binspec = parse.parse_binning(np.array([headarr[0]['CCDXBIN'], headarr[0]['CCDYBIN']]))
binning = parse.binning2string(binspatial, binspec)
return binning
msgs.error("Not ready for this compound meta")
def config_specific_par(self, par, scifile):
"""
Set par values according to the specific frame
Args:
par: ParSet
scifile: str
Name of the science file to use
Returns:
par
"""
# Lacosmic CR settings
# Grab the defaults for LRISr
binning = self.get_meta_value(scifile, 'binning')
# Unbinned LRISr needs very aggressive LACosmics parameters for 1x1 binning
if binning == '1,1':
sigclip = 3.0
objlim = 0.5
par['scienceframe']['process']['sigclip'] = sigclip
par['scienceframe']['process']['objlim'] = objlim
# Wavelength calibrations
if self.get_meta_value(
scifile,
'dispname') == '400/8500': # This is basically a reidentify
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_red_400.fits'
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths']['sigdetect'] = 20.0
par['calibrations']['wavelengths']['nsnippet'] = 1
elif self.get_meta_value(scifile, 'dispname') == '600/5000':
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_red_600_5000.fits'
par['calibrations']['wavelengths']['method'] = 'full_template'
elif self.get_meta_value(scifile, 'dispname') == '1200/9000':
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_lris_red_1200_9000.fits'
par['calibrations']['wavelengths']['method'] = 'full_template'
# FWHM
binning = parse.parse_binning(self.get_meta_value(scifile, 'binning'))
par['calibrations']['wavelengths']['fwhm'] = 8.0 / binning[0]
# Return
return par
def config_specific_par(self, scifile, inp_par=None):
"""
Modify the PypeIt parameters to hard-wired values used for
specific instrument configurations.
.. todo::
Document the changes made!
Args:
scifile (str):
File to use when determining the configuration and how
to adjust the input parameters.
inp_par (:class:`pypeit.par.parset.ParSet`, optional):
Parameter set used for the full run of PypeIt. If None,
use :func:`default_pypeit_par`.
Returns:
:class:`pypeit.par.parset.ParSet`: The PypeIt paramter set
adjusted for configuration specific parameter values.
"""
par = self.default_pypeit_par() if inp_par is None else inp_par
# TODO: Should we allow the user to override these?
# Templates
if self.get_meta_value(scifile, 'dispname') == '600ZD':
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_deimos_600.fits'
par['calibrations']['wavelengths']['lamps'] += [
'CdI', 'ZnI', 'HgI'
]
elif self.get_meta_value(scifile, 'dispname') == '830G':
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_deimos_830G.fits'
elif self.get_meta_value(scifile, 'dispname') == '1200G':
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'keck_deimos_1200G.fits'
# FWHM
binning = parse.parse_binning(self.get_meta_value(scifile, 'binning'))
par['calibrations']['wavelengths']['fwhm'] = 6.0 / binning[1]
# Return
return par
def compound_meta(self, headarr, meta_key):
"""
Methods to generate metadata requiring interpretation of the header
data, instead of simply reading the value of a header card.
Args:
headarr (:obj:`list`):
List of `astropy.io.fits.Header`_ objects.
meta_key (:obj:`str`):
Metadata keyword to construct.
Returns:
object: Metadata value read from the header(s).
"""
if meta_key == 'binning':
binspatial, binspec = parse.parse_binning(headarr[0]['CCDSUM'])
binning = parse.binning2string(binspec, binspatial)
return binning
def compound_meta(self, headarr, meta_key):
"""
Args:
headarr: list
meta_key: str
Returns:
value
"""
if meta_key == 'binning':
binspatial, binspec = parse.parse_binning(headarr[0]['BINNING'])
return parse.binning2string(binspec, binspatial)
elif meta_key == 'mjd':
time = '{:s}T{:s}'.format(headarr[0]['UT-DATE'], headarr[0]['UT-TIME'])
ttime = Time(time, format='isot')
return ttime.mjd
else:
msgs.error("Not ready for this compound meta")
def order_platescale(self, order_vec, binning=None):
"""
Return the platescale for each echelle order.
This routine is only defined for echelle spectrographs, and it is
undefined in the base class.
Args:
order_vec (`numpy.ndarray`_):
The vector providing the order numbers.
binning (:obj:`str`, optional):
The string defining the spectral and spatial binning.
Returns:
`numpy.ndarray`_: An array with the platescale for each order
provided by ``order``.
"""
norders = len(order_vec)
binspatial, binspec = parse.parse_binning(binning)
return np.full(norders, 0.30 * binspatial)
def wavegrid(self, binning=None, midpoint=False,samp_fact=1.0):
"""
Routine to generate a fixed wavelength grid in log_10 lambda. Mostly used by echelle spectrographs
Args:
binning:
midpoint:
samp_fact:
Returns:
"""
binspectral, binspatial = parse.parse_binning(binning)
logmin, logmax = self.loglam_minmax
loglam_grid = wvutils.wavegrid(logmin, logmax, self.dloglam*binspectral, samp_fact=samp_fact)
if midpoint:
loglam_grid = loglam_grid + self.dloglam*binspectral/samp_fact/2.0
return np.power(10.0,loglam_grid)
def bpm(self, filename, det, shape=None, msbias=None):
"""
Generate a default bad-pixel mask.
Even though they are both optional, either the precise shape for
the image (``shape``) or an example file that can be read to get
the shape (``filename`` using :func:`get_image_shape`) *must* be
provided.
Args:
filename (:obj:`str` or None):
An example file to use to get the image shape.
det (:obj:`int`):
1-indexed detector number to use when getting the image
shape from the example file.
shape (tuple, optional):
Processed image shape
Required if filename is None
Ignored if filename is not None
msbias (`numpy.ndarray`_, optional):
Master bias frame used to identify bad pixels
Returns:
`numpy.ndarray`_: An integer array with a masked value set
to 1 and an unmasked value set to 0. All values are set to
0.
"""
# Call the base-class method to generate the empty bpm
bpm_img = super().bpm(filename, det, shape=shape, msbias=msbias)
# Get the binning
msgs.info("Custom bad pixel mask for MAGE")
hdu = io.fits_open(filename)
binspatial, binspec = parse.parse_binning(hdu[0].header['BINNING'])
hdu.close()
# Do it
bpm_img[:, :10 //
binspatial] = 1. # Setting BPM on the edge of the detector often leads to false edges
bpm_img[:, 1020 // binspatial:] = 1.
# Return
return bpm_img
