def default_pypeit_par():
"""
Set default parameters for Shane Kast reductions.
"""
par = pypeitpar.PypeItPar()
# Frame numbers
par['calibrations']['standardframe']['number'] = 1
par['calibrations']['biasframe']['number'] = 5
par['calibrations']['pixelflatframe']['number'] = 5
par['calibrations']['traceframe']['number'] = 5
par['calibrations']['arcframe']['number'] = 1
# Scienceimage default parameters
par['scienceimage'] = pypeitpar.ScienceImagePar()
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Always correct for flexure, starting with default parameters
par['flexure'] = pypeitpar.FlexurePar()
# Set the default exposure time ranges for the frame typing
par['calibrations']['biasframe']['exprng'] = [None, 1]
par['calibrations']['darkframe']['exprng'] = [999999,
None] # No dark frames
par['calibrations']['pinholeframe']['exprng'] = [999999, None
] # No pinhole frames
par['calibrations']['pixelflatframe']['exprng'] = [0, None]
par['calibrations']['traceframe']['exprng'] = [0, None]
par['calibrations']['arcframe']['exprng'] = [None, 60]
par['calibrations']['standardframe']['exprng'] = [1, 200]
par['scienceframe']['exprng'] = [200, None]
return par
def default_pypeit_par():
"""
Set default parameters for Keck LRISr reductions.
"""
par = pypeitpar.PypeItPar()
# Set wave tilts order
par['calibrations']['slitedges']['edge_thresh'] = 15.
par['calibrations']['slitedges']['fit_order'] = 3
par['calibrations']['slitedges']['sync_center'] = 'gap'
# TODO: I had to increase this from 1. to 2. to deal with
# Keck_LRIS_red/multi_1200_9000_d680_1x2/ . May need a
# different solution given that this is binned data and most of
# the data in the dev suite is unbinned.
# JXP -- Increased to 6 arcsec. I don't know how 2 (or 1!) could have worked.
par['calibrations']['slitedges']['minimum_slit_length'] = 6
# 1D wavelengths
par['calibrations']['wavelengths']['rms_threshold'] = 0.20 # Might be grism dependent
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Always correct for flexure, starting with default parameters
par['flexure']['method'] = 'boxcar'
# Set the default exposure time ranges for the frame typing
par['calibrations']['biasframe']['exprng'] = [None, 1]
par['calibrations']['darkframe']['exprng'] = [999999, None] # No dark frames
par['calibrations']['pinholeframe']['exprng'] = [999999, None] # No pinhole frames
par['calibrations']['pixelflatframe']['exprng'] = [None, 30] # This may be too low for LRISb
par['calibrations']['traceframe']['exprng'] = [None, 30]
par['scienceframe']['exprng'] = [29, None]
return par
def default_pypeit_par(self):
"""
Set default parameters for magellan MagE reduction.
"""
par = pypeitpar.PypeItPar()
par['rdx']['spectrograph'] = 'magellan_mage'
# Frame numbers
par['calibrations']['standardframe']['number'] = 1
par['calibrations']['biasframe']['number'] = 0
par['calibrations']['pixelflatframe']['number'] = 3
par['calibrations']['traceframe']['number'] = 3
par['calibrations']['arcframe']['number'] = 1
# Bias
par['calibrations']['biasframe']['useframe'] = 'overscan'
# Wavelengths
# 1D wavelength solution
par['calibrations']['wavelengths'][
'rms_threshold'] = 0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['sigdetect'] = 5.0
par['calibrations']['wavelengths']['lamps'] = ['ThAr']
par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[
0]['nonlinear'] * self.detector[0]['saturation']
#par['calibrations']['wavelengths']['method'] = 'reidentify'
# Reidentification parameters
#par['calibrations']['wavelengths']['reid_arxiv'] = 'magellan_thar.json'
par['calibrations']['wavelengths']['ech_fix_format'] = True
# Echelle parameters
par['calibrations']['wavelengths']['echelle'] = True
par['calibrations']['wavelengths']['ech_nspec_coeff'] = 4
par['calibrations']['wavelengths']['ech_norder_coeff'] = 4
par['calibrations']['wavelengths']['ech_sigrej'] = 3.0
# Always correct for flexure, starting with default parameters
par['flexure'] = pypeitpar.FlexurePar()
par['scienceframe']['process']['sigclip'] = 20.0
par['scienceframe']['process']['satpix'] = 'nothing'
# Set slits and tilts parameters
# par['calibrations']['tilts']['order'] = 2
par['calibrations']['tilts']['tracethresh'] = [
10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10
]
par['calibrations']['slits']['trace_npoly'] = 5
par['calibrations']['slits']['maxshift'] = 3.
par['calibrations']['slits']['pcatype'] = 'order'
# Scienceimage default parameters
par['scienceimage'] = pypeitpar.ScienceImagePar()
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Do not correct for flexure
par['flexure'] = pypeitpar.FlexurePar()
par['flexure']['method'] = 'skip'
# Set the default exposure time ranges for the frame typing
par['calibrations']['standardframe']['exprng'] = [None, 20]
par['calibrations']['arcframe']['exprng'] = [20, None]
par['calibrations']['darkframe']['exprng'] = [20, None]
par['scienceframe']['exprng'] = [20, None]
return par
def default_pypeit_par():
"""
Set default parameters for Shane Kast reductions.
"""
par = pypeitpar.PypeItPar()
# Ignore PCA
par['calibrations']['slitedges']['sync_predict'] = 'nearest'
# Flux calibration parset
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Always correct for flexure, starting with default parameters
par['flexure']['method'] = 'boxcar'
# Set the default exposure time ranges for the frame typing
par['calibrations']['biasframe']['exprng'] = [None, 1]
par['calibrations']['darkframe']['exprng'] = [999999,
None] # No dark frames
par['calibrations']['pinholeframe']['exprng'] = [999999, None
] # No pinhole frames
par['calibrations']['pixelflatframe']['exprng'] = [0, None]
par['calibrations']['traceframe']['exprng'] = [0, None]
par['calibrations']['arcframe']['exprng'] = [None, 61]
par['calibrations']['standardframe']['exprng'] = [1, 61]
par['scienceframe']['exprng'] = [61, None]
return par
def default_pypeit_par():
"""
Set default parameters for Keck LRISr reductions.
"""
par = pypeitpar.PypeItPar()
# Set wave tilts order
par['calibrations']['slits']['sigdetect'] = 30.
# 1D wavelengths
par['calibrations']['wavelengths']['rms_threshold'] = 0.20 # Might be grism dependent
# Always sky subtract, starting with default parameters
par['scienceimage'] = pypeitpar.ScienceImagePar()
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Always correct for flexure, starting with default parameters
par['flexure']['method'] = 'boxcar'
# Set the default exposure time ranges for the frame typing
par['calibrations']['biasframe']['exprng'] = [None, 1]
par['calibrations']['darkframe']['exprng'] = [999999, None] # No dark frames
par['calibrations']['pinholeframe']['exprng'] = [999999, None] # No pinhole frames
par['calibrations']['pixelflatframe']['exprng'] = [None, 30] # This may be too low for LRISb
par['calibrations']['traceframe']['exprng'] = [None, 30]
par['scienceframe']['exprng'] = [29, None]
return par
def default_pypeit_par():
"""
Set default parameters for Keck LRISb reductions.
"""
par = pypeitpar.PypeItPar()
# Set wave tilts order
par['calibrations']['slits']['sigdetect'] = 20.
par['calibrations']['slits']['trace_npoly'] = 3
# TODO: No longer a parameter
# par['calibrations']['slits']['fracignore'] = 0.02
# par['calibrations']['slits']['pcapar'] = [3,2,1,0]
# 1D wavelength solution
par['calibrations']['wavelengths']['rms_threshold'] = 0.40 # Might be grating dependent..
par['calibrations']['wavelengths']['sigdetect'] = 5. # Doesn't work for reddest chip
par['calibrations']['wavelengths']['lamps'] = ['CuI', 'ArI', 'ArII']
# Overscan subtract the images
#par['calibrations']['biasframe']['useframe'] = 'overscan'
# Alter the method used to combine pixel flats
par['calibrations']['pixelflatframe']['process']['combine'] = 'median'
par['calibrations']['pixelflatframe']['process']['sig_lohi'] = [10.,10.]
# Scienceimage default parameters
par['scienceimage'] = pypeitpar.ScienceImagePar()
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Always correct for flexure, starting with default parameters
par['flexure'] = pypeitpar.FlexurePar()
# Set the default exposure time ranges for the frame typing
#par['scienceframe']['exprng'] = [30, None]
return par
def default_pypeit_par(self):
"""
Set default parameters for magellan MagE reduction.
"""
par = pypeitpar.PypeItPar()
par['rdx']['spectrograph'] = 'magellan_mage'
# Bias
#par['calibrations']['biasframe']['useframe'] = 'overscan'
# Wavelengths
# 1D wavelength solution
par['calibrations']['wavelengths'][
'rms_threshold'] = 0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['sigdetect'] = 5.0
par['calibrations']['wavelengths']['lamps'] = ['ThAr_MagE']
par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[
0]['nonlinear'] * self.detector[0]['saturation']
par['calibrations']['wavelengths']['method'] = 'reidentify'
par['calibrations']['wavelengths']['cc_thresh'] = 0.50
par['calibrations']['wavelengths']['cc_local_thresh'] = 0.50
# Reidentification parameters
par['calibrations']['wavelengths']['reid_arxiv'] = 'magellan_mage.fits'
par['calibrations']['wavelengths']['ech_fix_format'] = True
# Echelle parameters
par['calibrations']['wavelengths']['echelle'] = True
par['calibrations']['wavelengths']['ech_nspec_coeff'] = 4
par['calibrations']['wavelengths']['ech_norder_coeff'] = 4
par['calibrations']['wavelengths']['ech_sigrej'] = 3.0
# Always correct for flexure, starting with default parameters
par['flexure'] = pypeitpar.FlexurePar()
par['scienceframe']['process']['sigclip'] = 20.0
par['scienceframe']['process']['satpix'] = 'nothing'
# Set slits and tilts parameters
par['calibrations']['tilts']['tracethresh'] = [10] * self.norders
par['calibrations']['slitedges']['fit_order'] = 5
par['calibrations']['slitedges']['max_shift_adj'] = 3.
par['calibrations']['slitedges'][
'edge_thresh'] = 10. # Tough to get the bluest orders
par['calibrations']['slitedges']['left_right_pca'] = True
par['calibrations']['slitedges'][
'fit_min_spec_length'] = 0.3 # Allow for a short detected blue order
# Find object parameters
par['scienceimage']['findobj']['find_trim_edge'] = [
4, 4
] # Slit is too short to trim 5,5 especially with 2x binning
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Do not correct for flexure
par['flexure'] = pypeitpar.FlexurePar()
par['flexure']['method'] = 'skip'
# Set the default exposure time ranges for the frame typing
par['calibrations']['standardframe']['exprng'] = [None, 20]
par['calibrations']['arcframe']['exprng'] = [20, None]
par['calibrations']['darkframe']['exprng'] = [20, None]
par['scienceframe']['exprng'] = [20, None]
return par
def default_pypeit_par(self):
"""
Set default parameters for Keck LRISb reductions.
"""
par = pypeitpar.PypeItPar()
par['rdx']['spectrograph'] = 'keck_deimos'
# Set wave tilts order
par['calibrations']['slits']['sigdetect'] = 50.
par['calibrations']['slits']['trace_npoly'] = 3
par['calibrations']['slits']['fracignore'] = 0.02
par['calibrations']['slits']['pcapar'] = [3, 2, 1, 0]
# Overscan subtract the images
par['calibrations']['biasframe']['useframe'] = 'overscan'
# 1D wavelength solution
par['calibrations']['wavelengths']['lamps'] = [
'ArI', 'NeI', 'KrI', 'XeI'
]
par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[
0]['nonlinear'] * self.detector[0]['saturation']
# Alter the method used to combine pixel flats
par['calibrations']['pixelflatframe']['process']['combine'] = 'median'
par['calibrations']['pixelflatframe']['process']['sig_lohi'] = [
10., 10.
]
# Scienceimage default parameters
par['scienceimage'] = pypeitpar.ScienceImagePar()
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Always correct for flexure, starting with default parameters
par['flexure'] = pypeitpar.FlexurePar()
# Set the default exposure time ranges for the frame typing
par['calibrations']['biasframe']['exprng'] = [None, 2]
par['calibrations']['darkframe']['exprng'] = [999999,
None] # No dark frames
par['calibrations']['pinholeframe']['exprng'] = [999999, None
] # No pinhole frames
par['calibrations']['pixelflatframe']['exprng'] = [None, 30]
par['calibrations']['traceframe']['exprng'] = [None, 30]
par['scienceframe']['exprng'] = [30, None]
# LACosmics parameters
par['scienceframe']['process']['sigclip'] = 4.0
par['scienceframe']['process']['objlim'] = 1.5
return par
def default_pypeit_par():
"""
Set default parameters for TNG Dolores reductions.
"""
par = pypeitpar.PypeItPar()
#par['calibrations']['tilts']['params'] = [1,1,1]
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Always correct for flexure, starting with default parameters
par['flexure'] = pypeitpar.FlexurePar()
# Set the default exposure time ranges for the frame typing
par['calibrations']['biasframe']['exprng'] = [None, 0.1]
par['calibrations']['darkframe']['exprng'] = [999999, None] # No dark frames
par['calibrations']['pinholeframe']['exprng'] = [999999, None] # No pinhole frames
par['scienceframe']['exprng'] = [1, None]
return par
def default_pypeit_par():
"""
Set default parameters for Keck LRISb reductions.
"""
par = pypeitpar.PypeItPar()
par['calibrations']['slitedges']['edge_thresh'] = 20.
par['calibrations']['slitedges']['fit_order'] = 3
# 1D wavelength solution
par['calibrations']['wavelengths'][
'rms_threshold'] = 0.40 # Might be grating dependent..
par['calibrations']['wavelengths'][
'sigdetect'] = 5. # Doesn't work for reddest chip
par['calibrations']['wavelengths']['lamps'] = ['CuI', 'ArI', 'ArII']
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'nsnippet'] = 1 # 3 detectors splitting is already a lot
par['calibrations']['tilts'][
'tracethresh'] = 10. # Deals with faint CuAr lines
# IF YOU CHANGE THIS, YOU WILL NEED TO DEAL WITH THE OVERSCAN GOING ALONG ROWS
#for key in par['calibrations'].keys():
# if 'frame' in key:
# par['calibrations'][key]['process']['overscan'] = 'median'
# Overscan subtract the images
#par['calibrations']['biasframe']['useframe'] = 'overscan'
# Alter the method used to combine pixel flats
par['calibrations']['pixelflatframe']['process']['combine'] = 'median'
par['calibrations']['pixelflatframe']['process']['sig_lohi'] = [
10., 10.
]
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibrationPar()
# Always correct for flexure, starting with default parameters
par['flexure'] = pypeitpar.FlexurePar()
# Always correct for flexure, starting with default parameters
par['flexure']['method'] = 'boxcar'
# Set the default exposure time ranges for the frame typing
#par['scienceframe']['exprng'] = [30, None]
return par
# Read the baseline file that is not changed and must be edited by
# the person building the documentation as necessary.
pypeit_root = os.path.dirname(resource_filename('pypeit', ''))
input_base = os.path.join(pypeit_root, 'doc', 'scripts', 'base_par_rst.txt')
with open(input_base, 'r') as f:
lines = [ l.replace('\n','') for l in f.readlines() ]
lines += ['']
# Start to append the automatically generated documentation
lines += ['Current PypeItPar Parameter Hierarchy']
lines += ['++++++++++++++++++++++++++++++++++++']
lines += ['']
p = pypeitpar.PypeItPar(flexure=pypeitpar.FlexurePar(),
fluxcalib=pypeitpar.FluxCalibrationPar())
lines += par_hierarchy(p)
lines += ['']
lines += ['----']
lines += ['']
lines += p.to_rst_table()
lines += ['']
lines += ['Instrument-Specific Default Configuration']
lines += ['+++++++++++++++++++++++++++++++++++++++++']
lines += ['']
lines += textwrap.wrap('The following provides the changes to the global default parameters '
'provided above for each instrument. That is, if one were to include '
def test_fluxcalibration():
pypeitpar.FluxCalibrationPar()
