diff --git a/pypeit/core/flexure.py b/pypeit/core/flexure.py index 02265a3426..a36e581ec4 100644 --- a/pypeit/core/flexure.py +++ b/pypeit/core/flexure.py @@ -17,6 +17,7 @@ from astropy import stats from astropy import units from astropy.io import ascii +from astropy.table import Table import scipy.signal import scipy.optimize as opt from scipy import interpolate @@ -36,7 +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 +from pypeit import specobj, specobjs, spec2dobj from pypeit import wavemodel from IPython import embed @@ -1394,6 +1395,80 @@ 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` or :obj:`float`: + - 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 class MultiSlitFlexure(DataContainer): """ diff --git a/pypeit/scripts/chk_flexure.py b/pypeit/scripts/chk_flexure.py index 027acd3d27..d384dc8e29 100644 --- a/pypeit/scripts/chk_flexure.py +++ b/pypeit/scripts/chk_flexure.py @@ -27,16 +27,12 @@ def get_parser(cls, width=None): def main(args): from IPython import embed - import numpy as np from astropy.io import fits - from astropy.table import Table - from pypeit import spec2dobj, specobjs, msgs + from pypeit import msgs + from pypeit.core import flexure chk_version = not args.try_old - # tables to return - return_tables = [] - # Loop over the input files for in_file in args.input_file: @@ -47,61 +43,18 @@ def main(args): head0 = hdul[0].header file_type = None if 'PYP_CLS' in head0.keys() and head0['PYP_CLS'].strip() == 'AllSpec2DObj': - file_type = 'AllSpec2D' + file_type = 'spec2d' elif 'DMODCLS' in head0.keys() and head0['DMODCLS'].strip() == 'SpecObjs': - file_type = 'SpecObjs' + file_type = 'spec1d' else: msgs.error("Bad file type input!") - if file_type == 'AllSpec2D': - # load the spec2d file - allspec2D = spec2dobj.AllSpec2DObj.from_fits(in_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 args.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_tables.append(spec_flex) - # get and print the spatial flexure - if args.spat: - spat_flex = allspec2D[det].sci_spat_flexure - # print the value - print(f'Spat shift: {spat_flex}') - # return the value - return_tables.append(spat_flex) - elif file_type == 'SpecObjs': - # no spat flexure in spec1d file - if args.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(in_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_tables.append(spec_flex) - + # 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('') - return return_tables