""" Calibrate selected target with specific calibrator. Synopsis: run_gravi_recalibrate.py --calibrator= --science= Explanation: This script will look for vis-reduced files (PRO.CATG=*_SCI_VIS and *_CAL_VIS) on and in and copy these files to , including "_calibrator" and "_science" in the copied file names. It will also change PRO.CATG in the various files to *_CAL_VIS for the calibrator files and *_SCI_VIS for the science files. It will then do the equivalent of running run_gravi_trend.py in outdir. The calibrator targets must be specified using the --calibrator/-c option and the science targets using the --science/-s option. Both may be used several times. See details below. Example: Let "reduced" be a directory containing reduced data for a calibrator named INS.SOBJ.NAME=="A" and for two science targets named INS.SOBJ.NAME=="B" and "C". Assume that the user would like to calibrate all data (A, B and C) using B as a calibrator. They may do: run_gravi_recalibrate.py reduced reduced_B -cB -sA -sB -sC """ import argparse import os import glob import sys try: import pyfits as fits except ModuleNotFoundError: import astropy.io.fits as fits from gravi_reduce import gravi_esorex as ge from gravi_reduce import (log, ERROR, WARNING, NOTICE, set_verbose_type) log = log.Log().log parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter, prefix_chars='-+') parser.add_argument('indir', help="input directory") parser.add_argument('outdir', help="output directory") parser.add_argument("-c", "--calibrator", type=str, action="append", help="target to use as a calibrator. May be used several time. " "May be -cINS.SOBJ.NAME or -cINS.ROBJ.NAME:INS.SOBJ.NAME or -cFILENAME. " "Only files with INS.SOBJ.OFFX==0 and INS.SOBJ.OFFY will be considered," "exept if --calibratorOFFX is set.", default=[]) parser.add_argument("-s", "--science", type=str, action="append", help="target to use as a science target. May be used several time. " "May be -cINS.SOBJ.NAME or -cINS.ROBJ.NAME:INS.SOBJ.NAME or -cFILENAME. " "All files will be considered, independent on INS.SOBJ.OFFX " "and INS.SOBJ.OFFY. if the argument is 'all' all files are considered.", default=[]) parser.add_argument("-cOFFX", "--calibratorOFFX", type=float, default=0.0, help="INS SOBJ OFFX of the calibrator, only to be used when calibrator" "files do not have OFFX==0.0.") parser.add_argument("-phasec", "--phasecalib", type=str, help="If set file to be used for separate phase calibration. " "Only one file can be given", default=None) parser.add_argument("-m", "--mindate", type=str, help="minimum date in PCR.ACQ.START format") parser.add_argument("-M", "--maxdate", type=str, help="maximum date in PCR.ACQ.START format") parser.add_argument("--commoncalib-dir", dest="commoncalibdir", default="../../common_calibration", help="Add this directory in the search path for common" "calibration files [../../common_calibration]") options =[['gravity_viscal.force-calib',None], ['gravity_viscal.nsmooth-tfvis-sc',None], ['gravity_viscal.nsmooth-tfflux-sc',None], ['gravity_viscal.maxdeg-tfvis-sc',None], ['gravity_viscal.smoothing',None], ['esorex.msg-level','info'], ['esorex.time','TRUE'], ['esorex.mem-check','TRUE'], ['esorex.recipe-dir',None]] ge.implement_recipe_options (parser,options) def recalibrate(args): msg_level = vars(args)['esorex.msg-level'] if msg_level == 'error': set_verbose_type(ERROR) elif msg_level == 'warning': set_verbose_type(ERROR+WARNING) else: set_verbose_type(ERROR+WARNING+NOTICE) copydata(args.indir, args.outdir, args.calibrator, args.science, args.calibratorOFFX, args.phasecalib, args.mindate, args.maxdate) calibrate(args) def calibrate(args): common = [] reduced = [] calibrated = [] if args.phasecalib is not None: setattr(args, 'gravity_viscal.separate-phase-calib', 'TRUE') reduceddir=args.outdir commoncalibdir=args.commoncalibdir calibrateddir=args.outdir+'/calibrated' ge.add_gravity (common, glob.glob(commoncalibdir+'/GRAVI*fits')) ge.add_gravity (reduced, glob.glob(reduceddir+'/GRAVI*.fits')) ge.compute_tf (reduced, reduced+common, calibrateddir, options=args, overwrite=True) ge.add_gravity (calibrated, glob.glob(calibrateddir+'/GRAVI*.fits')) ge.add_gravity (reduced, glob.glob(reduceddir+'/GRAVI*.fits')) ge.calibrate_vis (reduced, calibrated, calibrateddir, options=args, overwrite=True) def copydata(indir, outdir, calibrator, science, calibratorOFFX, phasecalib, mindate=None, maxdate=None): if not os.path.exists(outdir): print(f'Creating directory {outdir}') os.makedirs(outdir) else: print(f'{outdir} exists') allfiles=sorted(glob.glob(indir+'/GRAVI*.fits')) for fname in allfiles: try: hdulist = fits.open(fname) except(IOError): continue header=hdulist[0].header try: FTname=header["HIERARCH ESO FT ROBJ NAME"] SCname=header["HIERARCH ESO INS SOBJ NAME"] PRO_CATG=header["HIERARCH ESO PRO CATG"] ACQ_START=header["HIERARCH ESO PCR ACQ START"] except (IOError, KeyError): continue if ( (mindate is not None and ACQ_START < mindate) or (maxdate is not None and ACQ_START > maxdate)): continue try: OFFX=header["HIERARCH ESO INS SOBJ OFFX"] OFFY=header["HIERARCH ESO INS SOBJ OFFY"] except (IOError, KeyError): OFFX=0. OFFY=0. pair=FTname.replace(':', '::') + ':' + SCname.replace(':', '::') if calibratorOFFX == 0.0: if ((pair in calibrator or SCname in calibrator or fname in calibrator or fname[len(indir):] in calibrator) and PRO_CATG in ['DUAL_CAL_VIS', 'DUAL_SCI_VIS', 'SINGLE_SCI_VIS', 'SINGLE_CAL_VIS'] and OFFX == 0. and OFFY == 0.): print(("Copying file "+fname+" as calibrator")) if PRO_CATG == 'DUAL_SCI_VIS': header['HIERARCH ESO PRO CATG']='DUAL_CAL_VIS' elif PRO_CATG == 'SINGLE_SCI_VIS': header['HIERARCH ESO PRO CATG']='SINGLE_CAL_VIS' outfname=outdir+'/'+fname[len(indir):-5]+'_calibrator.fits' try: hdulist.writeto(outfname, overwrite=True) except (TypeError): hdulist.writeto(outfname, clobber=True) if PRO_CATG in ['DUAL_CAL_VIS', 'SINGLE_SCI_VIS']: print(("Copying file "+fname+" as science")) if PRO_CATG == 'DUAL_CAL_VIS': header['HIERARCH ESO PRO CATG']='DUAL_SCI_VIS' elif PRO_CATG == 'SINGLE_CAL_VIS': header['HIERARCH ESO PRO CATG']='SINGLE_SCI_VIS' outfname=outdir+'/'+fname[len(indir):-5]+'_science.fits' try: hdulist.writeto(outfname, overwrite=True) except (TypeError): hdulist.writeto(outfname, clobber=True) header["HIERARCH ESO PRO CATG"]=PRO_CATG else: if ((pair in calibrator or SCname in calibrator or fname in calibrator or fname[len(indir):] in calibrator) and PRO_CATG in ['DUAL_CAL_VIS', 'DUAL_SCI_VIS', 'SINGLE_SCI_VIS', 'SINGLE_CAL_VIS'] and OFFX == calibratorOFFX): print(("Copying file "+fname+" as calibrator")) if PRO_CATG == 'DUAL_SCI_VIS': header['HIERARCH ESO PRO CATG']='DUAL_CAL_VIS' elif PRO_CATG == 'SINGLE_SCI_VIS': header['HIERARCH ESO PRO CATG']='SINGLE_CAL_VIS' outfname=outdir+'/'+fname[len(indir):-5]+'_calibrator.fits' try: hdulist.writeto(outfname, overwrite=True) except (TypeError): hdulist.writeto(outfname, clobber=True) if PRO_CATG in ['DUAL_CAL_VIS', 'SINGLE_SCI_VIS']: print(("Copying file "+fname+" as science")) if PRO_CATG == 'DUAL_CAL_VIS': header['HIERARCH ESO PRO CATG']='DUAL_SCI_VIS' elif PRO_CATG == 'SINGLE_CAL_VIS': header['HIERARCH ESO PRO CATG']='SINGLE_SCI_VIS' outfname=outdir+'/'+fname[len(indir):-5]+'_science.fits' try: hdulist.writeto(outfname, overwrite=True) except (TypeError): hdulist.writeto(outfname, clobber=True) header["HIERARCH ESO PRO CATG"]=PRO_CATG if phasecalib is not None: if (fname[len(indir):] in phasecalib and PRO_CATG in ['DUAL_CAL_VIS', 'DUAL_SCI_VIS', 'SINGLE_SCI_VIS', 'SINGLE_CAL_VIS']): print(("Copying file "+fname+" as phase calibrator")) if PRO_CATG in ['DUAL_SCI_VIS', 'DUAL_CAL_VIS']: header['HIERARCH ESO PRO CATG']='DUAL_CAL_VISPHI' elif PRO_CATG in ['SINGLE_SCI_VIS', 'SINGLE_CAL_VIS']: header['HIERARCH ESO PRO CATG']='SINGLE_CAL_VISPHI' outfname=outdir+'/'+fname[len(indir):-5]+'_phasecalibrator.fits' try: hdulist.writeto(outfname, overwrite=True) except (TypeError): hdulist.writeto(outfname, clobber=True) header["HIERARCH ESO PRO CATG"]=PRO_CATG if ((pair in science or SCname in science or fname in science or fname[len(indir):] in science) and PRO_CATG in ['DUAL_CAL_VIS', 'DUAL_SCI_VIS', 'SINGLE_SCI_VIS', 'SINGLE_CAL_VIS']): print(("Copying file "+fname+" as science")) if PRO_CATG == 'DUAL_CAL_VIS': header['HIERARCH ESO PRO CATG']='DUAL_SCI_VIS' elif PRO_CATG == 'SINGLE_CAL_VIS': header['HIERARCH ESO PRO CATG']='SINGLE_SCI_VIS' outfname=outdir+'/'+fname[len(indir):-5]+'_science.fits' try: hdulist.writeto(outfname, overwrite=True) except (TypeError): hdulist.writeto(outfname, clobber=True) header["HIERARCH ESO PRO CATG"]=PRO_CATG if 'all' in science and PRO_CATG in ['DUAL_CAL_VIS', 'DUAL_SCI_VIS', 'SINGLE_SCI_VIS', 'SINGLE_CAL_VIS']: print(("Copying file "+fname+" as science")) if PRO_CATG == 'DUAL_CAL_VIS': header['HIERARCH ESO PRO CATG']='DUAL_SCI_VIS' elif PRO_CATG == 'SINGLE_CAL_VIS': header['HIERARCH ESO PRO CATG']='SINGLE_SCI_VIS' outfname=outdir+'/'+fname[len(indir):-5]+'_science.fits' try: hdulist.writeto(outfname, overwrite=True) except (TypeError): hdulist.writeto(outfname, clobber=True) header["HIERARCH ESO PRO CATG"]=PRO_CATG