def default_pypeit_par():
"""
Set default parameters for LBT/LUCI reductions.
OLD CODE from LBT MODS
"""
par = pypeitpar.PypeItPar()
# Scienceimage default parameters
par['reduce'] = pypeitpar.ReducePar()
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibratePar()
# 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(self):
"""
Set default parameters for the reductions.
"""
par = pypeitpar.PypeItPar()
par['rdx']['spectrograph'] = 'gemini_flamingos2'
# No overscan
for key in par['calibrations'].keys():
if 'frame' in key:
par['calibrations'][key]['process']['overscan'] = 'none'
# Wavelengths
# 1D wavelength solution with arc lines
par['calibrations']['wavelengths']['rms_threshold'] = 0.5
par['calibrations']['wavelengths']['sigdetect']=5
par['calibrations']['wavelengths']['fwhm'] = 5
par['calibrations']['wavelengths']['n_first']=2
par['calibrations']['wavelengths']['n_final']=4
par['calibrations']['wavelengths']['lamps'] = ['OH_NIRES']
par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[0]['nonlinear'] * self.detector[0]['saturation']
#par['calibrations']['wavelengths']['method'] = 'reidentify'
#par['calibrations']['wavelengths']['method'] = 'full_template'
#par['calibrations']['wavelengths']['reid_arxiv'] = 'magellan_fire_long.fits'
par['calibrations']['wavelengths']['match_toler']=5.0
# Set slits and tilts parameters
par['calibrations']['tilts']['tracethresh'] = 5
par['calibrations']['tilts']['spat_order'] = 4
par['calibrations']['slitedges']['trace_thresh'] = 10.
par['calibrations']['slitedges']['edge_thresh'] = 200.
#par['calibrations']['slitedges']['det_min_spec_length'] = 0.3
par['calibrations']['slitedges']['fit_min_spec_length'] = 0.4
par['calibrations']['slitedges']['sync_predict'] = 'nearest'
# Overscan but not bias
# This seems like a kludge of sorts
par['calibrations']['biasframe']['useframe'] = 'none'
# No overscan
par['scienceframe']['process']['overscan'] ='none'
for key in par['calibrations'].keys():
if 'frame' in key:
par['calibrations'][key]['process']['overscan'] = 'none'
# Set the default exposure time ranges for the frame typing
par['calibrations']['standardframe']['exprng'] = [None, 30]
par['calibrations']['tiltframe']['exprng'] = [50, None]
par['calibrations']['arcframe']['exprng'] = [50, None]
par['calibrations']['darkframe']['exprng'] = [20, None]
par['scienceframe']['exprng'] = [20, None]
# Scienceimage parameters
#par['reduce']['sig_thresh'] = 5
#par['reduce']['maxnumber'] = 2
par['reduce']['skysub']['sky_sigrej'] = 5.0
par['reduce']['findobj']['find_trim_edge'] = [10,10]
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibratePar()
# Do not correct for flexure
par['flexure'] = None
return par
def test_flux(monkeypatch):
def mock_get_header(file):
if file == "fail_grating.fits":
return {"DISPNAME": "Unknown"}
else:
return {"DISPNAME": "600ZD"}
def mock_get_flux_calib_instance(spec1d_files, sens_files, par):
if spec1d_files[0] == "fail_flux.fits":
raise PypeItError("Test failure")
else:
# The collate_1d caller doesn't use the output, it just
# depends on the side effect of fluxing
return None
# Test success
with monkeypatch.context() as m:
monkeypatch.setattr(fits, "getheader", mock_get_header)
monkeypatch.setattr(fluxcalibrate.FluxCalibrate, "get_instance",
mock_get_flux_calib_instance)
spectrograph = load_spectrograph('keck_deimos')
# This could break if we start supporting it
unsupported_spectrograph = load_spectrograph('shane_kast_red')
par = pypeitpar.PypeItPar()
par['fluxcalib'] = pypeitpar.FluxCalibratePar()
# Test success
failed_messages = []
flux(par, spectrograph, ["no_fail.fits"], failed_messages)
assert len(failed_messages) == 0
# Test failure due to no archived sensfunc
flux(par, spectrograph, ["fail_grating.fits"], failed_messages)
assert failed_messages[
0] == "Could not find archived sensfunc to flux fail_grating.fits, skipping it."
failed_messages = []
# Test failure in fluxing
flux(par, spectrograph, ["fail_flux.fits"], failed_messages)
assert failed_messages[
0] == "Failed to flux calibrate fail_flux.fits, skipping it."
# Test failure due to unsupported spectrograph
with pytest.raises(PypeItError):
flux(par, unsupported_spectrograph, ["600ZD_file.fits"],
failed_messages)
def default_pypeit_par(self):
"""
Set default parameters.
"""
par = pypeitpar.PypeItPar()
par['rdx']['spectrograph'] = 'magellan_fire_long'
# No overscan
for key in par['calibrations'].keys():
if 'frame' in key:
par['calibrations'][key]['process']['overscan'] = 'none'
# Wavelengths
# 1D wavelength solution with arc lines
par['calibrations']['wavelengths']['rms_threshold'] = 1.0
par['calibrations']['wavelengths']['sigdetect'] = 3
par['calibrations']['wavelengths']['fwhm'] = 20
par['calibrations']['wavelengths']['n_first'] = 2
par['calibrations']['wavelengths']['n_final'] = 4
par['calibrations']['wavelengths']['lamps'] = [
'ArI', 'ArII', 'ThAr', 'NeI'
]
par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[
0]['nonlinear'] * self.detector[0]['saturation']
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths'][
'reid_arxiv'] = 'magellan_fire_long.fits'
par['calibrations']['wavelengths']['match_toler'] = 5.0
# Set slits and tilts parameters
par['calibrations']['tilts']['tracethresh'] = 5
par['calibrations']['slitedges']['trace_thresh'] = 10.
par['calibrations']['slitedges']['sync_predict'] = 'nearest'
# Scienceimage parameters
par['reduce']['findobj']['sig_thresh'] = 5
#par['reduce']['maxnumber'] = 2
par['reduce']['findobj']['find_trim_edge'] = [50, 50]
# Always flux calibrate, starting with default parameters
par['fluxcalib'] = pypeitpar.FluxCalibratePar()
# Do not correct for flexure
par['flexure'] = None
# Set the default exposure time ranges for the frame typing
par['calibrations']['standardframe']['exprng'] = [None, 60]
par['calibrations']['arcframe']['exprng'] = [1, 50]
par['calibrations']['darkframe']['exprng'] = [20, None]
par['scienceframe']['exprng'] = [20, None]
return par
def test_fluxcalibrate():
pypeitpar.FluxCalibratePar()
# 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.FluxCalibratePar())
lines += par_hierarchy(p)
lines += ['']
lines += ['----']
lines += ['']
lines += p.to_rst_table()
lines += ['']
lines += [' .. _instr_par:']
lines += ['']
lines += ['Instrument-Specific Default Configuration']
lines += ['+++++++++++++++++++++++++++++++++++++++++']
lines += ['']