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mv flexure_diagnostics into each relevant class
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@kbwestfall
kbwestfall committed Aug 29, 2024
1 parent 01aed2e commit 25c7e35
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160 changes: 80 additions & 80 deletions pypeit/core/flexure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
from pypeit.datamodel import DataContainer
from pypeit.images.detector_container import DetectorContainer
from pypeit.images.mosaic import Mosaic
from pypeit import specobj, specobjs, spec2dobj
from pypeit import specobj, specobjs #, spec2dobj
from pypeit import wavemodel

from IPython import embed
Expand Down Expand Up @@ -1395,85 +1395,85 @@ def sky_em_residuals(wave:np.ndarray, flux:np.ndarray,
return dwave[m], diff[m], diff_err[m], los[m], los_err[m]


def flexure_diagnostic(file, file_type='spec2d', flexure_type='spec', chk_version=False):
"""
Print the spectral or spatial flexure of a spec2d or spec1d file.
Args:
file (:obj:`str`, `Path`_):
Filename of the spec2d or spec1d file to check
file_type (:obj:`str`, optional):
Type of the file to check. Options are 'spec2d' or 'spec1d'. Default is 'spec2d'.
flexure_type (:obj:`str`, optional):
Type of flexure to check. Options are 'spec' or 'spat'. Default is 'spec'.
chk_version (:obj:`bool`, optional):
If True, raise an error if the datamodel version or type check failed.
If False, throw a warning only. Default is False.
Returns:
:obj:`astropy.table.Table`, :obj:`float`: Type depends on the keyword
arguments:
- If file_type is 'spec2d' and flexure_type is 'spec', return a
table with the spectral flexure
- If file_type is 'spec2d' and flexure_type is 'spat', return the
spatial flexure
- If file_type is 'spec1d', return a table with the spectral flexure
"""

# value to return
return_flex = None

if file_type == 'spec2d':
# load the spec2d file
allspec2D = spec2dobj.AllSpec2DObj.from_fits(file, chk_version=chk_version)
# Loop on Detectors
for det in allspec2D.detectors:
print('')
print('=' * 50 + f'{det:^7}' + '=' * 51)
# get and print the spectral flexure
if flexure_type == 'spec':
spec_flex = allspec2D[det].sci_spec_flexure
spec_flex.rename_column('sci_spec_flexure', 'global_spec_shift')
if np.all(spec_flex['global_spec_shift'] != None):
spec_flex['global_spec_shift'].format = '0.3f'
# print the table
spec_flex.pprint_all()
# return the table
return_flex = spec_flex
# get and print the spatial flexure
if flexure_type == 'spat':
spat_flex = allspec2D[det].sci_spat_flexure
# print the value
print(f'Spat shift: {spat_flex}')
# return the value
return_flex = spat_flex
elif file_type == 'spec1d':
# no spat flexure in spec1d file
if flexure_type == 'spat':
msgs.error("Spat flexure not available in the spec1d file, try with a spec2d file")
# load the spec1d file
sobjs = specobjs.SpecObjs.from_fitsfile(file, chk_version=chk_version)
spec_flex = Table()
spec_flex['NAME'] = sobjs.NAME
spec_flex['global_spec_shift'] = sobjs.FLEX_SHIFT_GLOBAL
if np.all(spec_flex['global_spec_shift'] != None):
spec_flex['global_spec_shift'].format = '0.3f'
spec_flex['local_spec_shift'] = sobjs.FLEX_SHIFT_LOCAL
if np.all(spec_flex['local_spec_shift'] != None):
spec_flex['local_spec_shift'].format = '0.3f'
spec_flex['total_spec_shift'] = sobjs.FLEX_SHIFT_TOTAL
if np.all(spec_flex['total_spec_shift'] != None):
spec_flex['total_spec_shift'].format = '0.3f'
# print the table
spec_flex.pprint_all()
# return the table
return_flex = spec_flex

return return_flex
#def flexure_diagnostic(file, file_type='spec2d', flexure_type='spec', chk_version=False):
# """
# Print the spectral or spatial flexure of a spec2d or spec1d file.
#
# Args:
# file (:obj:`str`, `Path`_):
# Filename of the spec2d or spec1d file to check
# file_type (:obj:`str`, optional):
# Type of the file to check. Options are 'spec2d' or 'spec1d'. Default is 'spec2d'.
# flexure_type (:obj:`str`, optional):
# Type of flexure to check. Options are 'spec' or 'spat'. Default is 'spec'.
# chk_version (:obj:`bool`, optional):
# If True, raise an error if the datamodel version or type check failed.
# If False, throw a warning only. Default is False.
#
# Returns:
# :obj:`astropy.table.Table`, :obj:`float`: Type depends on the keyword
# arguments:
#
# - If file_type is 'spec2d' and flexure_type is 'spec', return a
# table with the spectral flexure
#
# - If file_type is 'spec2d' and flexure_type is 'spat', return the
# spatial flexure
#
# - If file_type is 'spec1d', return a table with the spectral flexure
#
# """
#
# # value to return
# return_flex = None
#
# if file_type == 'spec2d':
# # load the spec2d file
# allspec2D = spec2dobj.AllSpec2DObj.from_fits(file, chk_version=chk_version)
# # Loop on Detectors
# for det in allspec2D.detectors:
# print('')
# print('=' * 50 + f'{det:^7}' + '=' * 51)
# # get and print the spectral flexure
# if flexure_type == 'spec':
# spec_flex = allspec2D[det].sci_spec_flexure
# spec_flex.rename_column('sci_spec_flexure', 'global_spec_shift')
# if np.all(spec_flex['global_spec_shift'] != None):
# spec_flex['global_spec_shift'].format = '0.3f'
# # print the table
# spec_flex.pprint_all()
# # return the table
# return_flex = spec_flex
# # get and print the spatial flexure
# if flexure_type == 'spat':
# spat_flex = allspec2D[det].sci_spat_flexure
# # print the value
# print(f'Spat shift: {spat_flex}')
# # return the value
# return_flex = spat_flex
# elif file_type == 'spec1d':
# # no spat flexure in spec1d file
# if flexure_type == 'spat':
# msgs.error("Spat flexure not available in the spec1d file, try with a spec2d file")
# # load the spec1d file
# sobjs = specobjs.SpecObjs.from_fitsfile(file, chk_version=chk_version)
# spec_flex = Table()
# spec_flex['NAME'] = sobjs.NAME
# spec_flex['global_spec_shift'] = sobjs.FLEX_SHIFT_GLOBAL
# if np.all(spec_flex['global_spec_shift'] != None):
# spec_flex['global_spec_shift'].format = '0.3f'
# spec_flex['local_spec_shift'] = sobjs.FLEX_SHIFT_LOCAL
# if np.all(spec_flex['local_spec_shift'] != None):
# spec_flex['local_spec_shift'].format = '0.3f'
# spec_flex['total_spec_shift'] = sobjs.FLEX_SHIFT_TOTAL
# if np.all(spec_flex['total_spec_shift'] != None):
# spec_flex['total_spec_shift'].format = '0.3f'
# # print the table
# spec_flex.pprint_all()
# # return the table
# return_flex = spec_flex
#
# return return_flex


# TODO -- Consider separating the methods from the DataContainer as per calibrations
Expand Down
33 changes: 18 additions & 15 deletions pypeit/scripts/chk_flexure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,13 @@ def get_parser(cls, width=None):
parser = super().get_parser(description='Print QA on flexure to the screen',
width=width)

parser.add_argument('input_file', type=str, nargs='+', help='One or more PypeIt spec2d or spec1d file')
parser.add_argument('input_file', type=str, nargs='+',
help='One or more PypeIt spec2d or spec1d file')
inp = parser.add_mutually_exclusive_group(required=True)
inp.add_argument('--spec', default=False, action='store_true', help='Check the spectral flexure')
inp.add_argument('--spat', default=False, action='store_true', help='Check the spatial flexure')
inp.add_argument('--spec', default=False, action='store_true',
help='Check the spectral flexure')
inp.add_argument('--spat', default=False, action='store_true',
help='Check the spatial flexure')
parser.add_argument('--try_old', default=False, action='store_true',
help='Attempt to load old datamodel versions. A crash may ensue..')
return parser
Expand All @@ -29,9 +32,11 @@ def main(args):
from IPython import embed
from astropy.io import fits
from pypeit import msgs
from pypeit.core import flexure
from pypeit import specobjs
from pypeit import spec2dobj

chk_version = not args.try_old
flexure_type = 'spat' if args.spat else 'spec'

# Loop over the input files
for in_file in args.input_file:
Expand All @@ -43,21 +48,19 @@ def main(args):
head0 = hdul[0].header
file_type = None
if 'PYP_CLS' in head0.keys() and head0['PYP_CLS'].strip() == 'AllSpec2DObj':
file_type = 'spec2d'
# load the spec2d file
allspec2D = spec2dobj.AllSpec2DObj.from_fits(file, chk_version=chk_version)
allspec2D.flexure_diagnostics(flexure_type=flexure_type)
elif 'DMODCLS' in head0.keys() and head0['DMODCLS'].strip() == 'SpecObjs':
file_type = 'spec1d'
if flexure_type == 'spat':
msgs.error("Spat flexure not available in the spec1d file, try with a "
"spec2d file")
# load the spec1d file
sobjs = specobjs.SpecObjs.from_fitsfile(file, chk_version=chk_version)
sobjs.flexure_diagnostics()
else:
msgs.error("Bad file type input!")

# Check the flexure
flexure.flexure_diagnostic(in_file, file_type=file_type, flexure_type='spat' if args.spat else 'spec',
chk_version=chk_version)

# space between files for clarity
print('')






41 changes: 41 additions & 0 deletions pypeit/spec2dobj.py
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Original file line number Diff line number Diff line change
Expand Up @@ -728,3 +728,44 @@ def __repr__(self):
txt += ') >'
return txt

def flexure_diagnostics(self, flexure_type='spat'):
"""
Print the spectral or spatial flexure of a spec2d or spec1d file.
Args:
flexure_type (:obj:`str`, optional):
Type of flexure to check. Options are 'spec' or 'spat'. Default
is 'spec'.
Returns:
:obj:`astropy.table.Table`, :obj:`float`: If flexure_type is
'spec', return a table with the spectral flexure. If flexure_type is
'spat', return the spatial flexure
"""
if flexure_type not in ['spat', 'spec']:
msgs.error(f'flexure_type must be spat or spec, not {flexure_type}')
# Loop on Detectors
for det in self.detectors:
print('')
print('=' * 50 + f'{det:^7}' + '=' * 51)
# get and print the spectral flexure
if flexure_type == 'spec':
spec_flex = self[det].sci_spec_flexure
spec_flex.rename_column('sci_spec_flexure', 'global_spec_shift')
if np.all(spec_flex['global_spec_shift'] != None):
spec_flex['global_spec_shift'].format = '0.3f'
# print the table
spec_flex.pprint_all()
# return the table
return_flex = spec_flex
# get and print the spatial flexure
if flexure_type == 'spat':
spat_flex = self[det].sci_spat_flexure
# print the value
print(f'Spat shift: {spat_flex}')
# return the value
return_flex = spat_flex

# TODO: Was this supposed to be a list for all detectors, or just the last detector?
return return_flex

23 changes: 23 additions & 0 deletions pypeit/specobjs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1027,6 +1027,29 @@ def get_extraction_groups(self, model_full_slit=False) -> List[List[int]]:

return groups

def flexure_diagnostics(self):
"""
Print the spectral or spatial flexure of a spec2d or spec1d file.
Returns:
:obj:`astropy.table.Table`: Table with the spectral flexure.
"""
spec_flex = Table()
spec_flex['NAME'] = self.NAME
spec_flex['global_spec_shift'] = self.FLEX_SHIFT_GLOBAL
if np.all(spec_flex['global_spec_shift'] != None):
spec_flex['global_spec_shift'].format = '0.3f'
spec_flex['local_spec_shift'] = self.FLEX_SHIFT_LOCAL
if np.all(spec_flex['local_spec_shift'] != None):
spec_flex['local_spec_shift'].format = '0.3f'
spec_flex['total_spec_shift'] = self.FLEX_SHIFT_TOTAL
if np.all(spec_flex['total_spec_shift'] != None):
spec_flex['total_spec_shift'].format = '0.3f'
# print the table
spec_flex.pprint_all()
# return the table
return spec_flex


#TODO Should this be a classmethod on specobjs??
def get_std_trace(detname, std_outfile, chk_version=True):
Expand Down

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