diff --git a/pypeit/core/flexure.py b/pypeit/core/flexure.py index 7fda7bf2b4..487dd504bf 100644 --- a/pypeit/core/flexure.py +++ b/pypeit/core/flexure.py @@ -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 from pypeit import wavemodel from IPython import embed @@ -1395,87 +1395,6 @@ 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 - - # 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 d384dc8e29..74faf77b01 100644 --- a/pypeit/scripts/chk_flexure.py +++ b/pypeit/scripts/chk_flexure.py @@ -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 @@ -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: @@ -41,23 +46,21 @@ def main(args): # What kind of file are we?? hdul = fits.open(in_file) 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(in_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(in_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('') - - - - - diff --git a/pypeit/spec2dobj.py b/pypeit/spec2dobj.py index 6aaae67396..5e693e44c0 100644 --- a/pypeit/spec2dobj.py +++ b/pypeit/spec2dobj.py @@ -728,3 +728,45 @@ def __repr__(self): txt += ') >' return txt + def flexure_diagnostics(self, flexure_type='spat'): + """ + Print and return the spectral or spatial flexure of a spec2d file. + + Args: + flexure_type (:obj:`str`, optional): + Type of flexure to check. Options are 'spec' or 'spat'. Default + is 'spec'. + + Returns: + :obj:`dict`: Dictionary with the flexure values for each detector. If + flexure_type is 'spec', the spectral flexure is stored in an astropy table. + If flexure_type is 'spat', the spatial flexure is stored in a float. + + """ + if flexure_type not in ['spat', 'spec']: + msgs.error(f'flexure_type must be spat or spec, not {flexure_type}') + return_flex = {} + # 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[det] = 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[det] = spat_flex + + return return_flex + diff --git a/pypeit/specobjs.py b/pypeit/specobjs.py index 4b6da7ef36..a5a51411e7 100644 --- a/pypeit/specobjs.py +++ b/pypeit/specobjs.py @@ -1027,6 +1027,29 @@ def get_extraction_groups(self, model_full_slit=False) -> List[List[int]]: return groups + def flexure_diagnostics(self): + """ + Print and return the spectral flexure of a 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):