config.py

"""
Written by Avet Harutyunyan for the old GIANO pipeline
Implemented in the GIANOB DRS by Monica Rainer
"""

import os, tempfile, datetime
from collections import OrderedDict
from __version__ import __version__


def getdate(date_time=None):
    tlimit = datetime.time(9, 0, 0)
    oneday = datetime.timedelta(days=1)
    if date_time:
        if isinstance(date_time, datetime.datetime):
            pass
        elif isinstance(date_time, basestring): 
            date_time = datetime.datetime.strptime(date_time, '%Y-%m-%dT%H:%M:%S.%f')
    else:
        date_time = datetime.datetime.utcnow()
    date_, time_ = date_time.date(), date_time.time()
    if time_ < tlimit:
        date_ = date_ - oneday
    return date_.strftime('%Y-%m-%d')


def read_usr_config(path):
    f = open(path, 'r')
    cntnt = f.readlines()
    f.close()
    usrconfig = {}
    for aline in cntnt:
        aline = aline.strip()
        #print aline
        if aline:
            if aline[0] != '#':
                key, value = aline.split(':::')
                #print key
                #print value
                usrconfig[key.strip()] = eval(value.strip())
    return usrconfig

usr_cfg_path = os.path.join(os.getcwd(), 'gofio.cfg')
if os.path.isfile(usr_cfg_path):
    try:
        USRCONFIG = read_usr_config(usr_cfg_path)
    except:
        USRCONFIG = {}
        USRCONFIG['OFFLINE'] = False
else:
    USRCONFIG ={}
    USRCONFIG['OFFLINE'] = False


#
# pipeline configuration
#

CONFIG = {}
CONFIG['APPNAME'] = 'GOFIO'
#CONFIG['VERSION'] = 1.0
CONFIG['VERSION'] = __version__
CONFIG['DATE'] = getdate()
CONFIG['OFFLINE'] = False

#
# Directories 
#

CONFIG['TMP_DIR'] = tempfile.gettempdir()
CONFIG['APP_DIR'] = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))

#CONFIG['BASE_RAW'] = '/mnt/nfs/RAW'
CONFIG['BASE_RAW'] = '/home/monica/Documenti/gianob/gianobdrs/varie/commissioning_marzo/raw'
CONFIG['BASE_RED_DIR'] = os.path.join(CONFIG['APP_DIR'],'reduced')
#CONFIG['BASE_RED_DIR'] = '/mnt/nfs/REDUCED'

CONFIG['BASE_RAMP'] = '/home/avet/gianorp/databases'


CONFIG['RAW_DIR'] = os.path.join(CONFIG['BASE_RAW'],CONFIG['DATE'])
CONFIG['RED_DIR'] = os.path.join(CONFIG['BASE_RED_DIR'],CONFIG['DATE'])
CONFIG['OFFLINE_DIR'] = False
CONFIG['RED_CALIB'] = os.path.join(CONFIG['RED_DIR'],'CALIB')
CONFIG['RED_STR'] = os.path.join(CONFIG['RED_DIR'],'STR')

# Resources

CONFIG['RES_DIR']      = os.path.join(CONFIG['APP_DIR'], 'resources')
CONFIG['BADPIX_MASK']  = os.path.join(CONFIG['RES_DIR'], 'badpix_mask.fits')
CONFIG['LOGGER'] = {'TERM':True,'FILE':True} # logger writes to terminal and/or to file
CONFIG['LOG_FILE'] = os.path.join(CONFIG['RED_DIR'], 'drs.log')
CONFIG['STRAIGHT'] = os.path.join(CONFIG['RES_DIR'],'straight_giano_2D')
CONFIG['STRAIGHT_OPT'] = ['I=1'] # the option DY is computed automatically
#CONFIG['STRAIGHT_OPT'] = ['I=1','DY=-5'] # define DY only if you want to override the automatic procedure
CONFIG['BASE_CALIB_DIR']    = os.path.join(CONFIG['APP_DIR'], 'calibrations')
CONFIG['CALIB_DIR']    = os.path.join(CONFIG['BASE_CALIB_DIR'], 'calfiles')
CONFIG['CALIB_DB_DIR']    = os.path.join(CONFIG['BASE_CALIB_DIR'], 'database')
CONFIG['WEBUI_DB_DIR'] = os.path.join(CONFIG['APP_DIR'], 'webuidatabases')

# Output name

CONFIG['MERGED'] = 's1d' # suffix for merged spectra
CONFIG['UNMERGED'] = 'ms1d' # suffix for unmerged spectra

#
# Header configuration 
#

# Keywords used by the pipeline: change here if the keywords change
# If some keywords are added or removed, change varie/check_keywords accordingly.
CONFIG['KEYS'] = {'OBJECT' : 'OBJECT', 'OBSTYPE' : 'OBS-TYPE', 'OBSMODE' : 'OBSMODE' , 'IMANAME' : 'IMANAME', 'FILENAME' : 'FILENAME', 'NCOMBINE' : 'NCOMBINE', 'MJD' : 'MJD-OBS', 'EXPTIME' : 'EXPTIME', 'NODSTARE' : 'HIERARCH TNG CAT ACQTEMPL' , 'GROUPN' : 'GROUP_N', 'GROUPI' : 'GROUP_I', 'SLIT' : 'SLIT_POS' , 'STARE' : 'STAREPOS' , 'GROUPID' : 'GROUPID' , 'ID' : 'OBSID' , 'PID' : 'PAIRID' , 'NPAIRS' : 'HIERARCH TNG CAT EXP NPAIRS' ,'NREP' : 'HIERARCH TNG CAT EXP NREP' , 'EXTMODE' : 'HIERARCH TNG CAT DR SPEXTMODE' , 'RA' : 'HIERARCH TNG TEL TARG ALPHA' , 'DEC' : 'HIERARCH TNG TEL TARG DELTA' , 'PMA' : 'HIERARCH TNG TEL TARG PMA' , 'PMD' : 'HIERARCH TNG TEL TARG PMD' , 'EQUINOX' : 'HIERARCH TNG TEL TARG EQUINOX' , 'TARG_TYPE' : 'HIERARCH TNG CAT TARG TYPE' , 'AM' : 'AIRMASS' , 'RADVEL' : 'HIERARCH TNG TEL TARG RADVEL' }


# Values of the keyword:
# CONFIG['OBSTYPE'] keyword values to determine the nature of the files
CONFIG['DARK'] = 'DARK'
CONFIG['FLAT'] = 'FLAT'
CONFIG['WCAL_UNE'] = 'WCAL_UNE'
CONFIG['WCAL_FP'] = 'WCAL_FP'
#CONFIG['WCAL_FP'] = 'WCAL_LFC'
CONFIG['SCIENCE'] = 'SCIENCE'
# CONFIG['NODSTARE'] keyword values to determine if stare or nodding
CONFIG['NODVALUE'] = 'GIANO_sci_nodding'
CONFIG['STAREVALUE'] = 'GIANO_sci_stare'
# CONFIG['SLIT'] keyword values to determine the slit position
CONFIG['A'] = 'A' # value of CONFIG['SLIT'] for A position
CONFIG['B'] = 'B' # value of CONFIG['SLIT'] for B position
CONFIG['C'] = 'C' # value of CONFIG['SLIT'] for C position
# CONFIG['STARE'] keyword values to determine the Obj-Sky position
CONFIG['OBJ'] = 'OBJ'
CONFIG['SKY'] = 'SKY'
# CONFIG['EXTMODE'] keyword values to determine to extraction mode
CONFIG['EXTPAIR'] = 'PAIR_EXT'
CONFIG['EXTAVG'] = 'GRPAVG_EXT'
CONFIG['EXTDEFAULT'] = CONFIG['EXTAVG']
# CONFIG['TARG_TYPE'] keyword values to determine type of object (science, telluric, ...) 
CONFIG['TELLURIC'] = 'TELLURIC'
CONFIG['FASTROT'] = 'FASTROT'
CONFIG['TYPE_SCIENCE'] = 'SCIENCE'

#
# Keywords added by the DRS, with relative comments
#
CONFIG['KEY_DRS'] = 'HIERARCH TNG DRS'
CONFIG['RON_EFF'] = (' '.join((CONFIG['KEY_DRS'],'RON')),'Effective RON after image reduction')
CONFIG['GAIN_EFF'] = (' '.join((CONFIG['KEY_DRS'],'GAIN')),'Effective gain after image reduction')
CONFIG['TEXP_EFF'] = (' '.join((CONFIG['KEY_DRS'],'EXPTIME')),'Effective exposure time after image reduction')
CONFIG['SPEC_USED'] = (' '.join((CONFIG['KEY_DRS'],'SPEC')),'Images combined')
CONFIG['SPEC_MJD'] = (' '.join((CONFIG['KEY_DRS'],'MJD')),'MJD of the relative image')
CONFIG['SNR'] = (' '.join((CONFIG['KEY_DRS'],'SNR')),'SNR in the middle of the order',)
CONFIG['STRAIGHT_PAR'] = OrderedDict([ ('P1',' '.join((CONFIG['KEY_DRS'],'STR2DP1'))), ('P2',' '.join((CONFIG['KEY_DRS'],'STR2DP2'))), ('P3',' '.join((CONFIG['KEY_DRS'],'STR2DP3'))), ('P4',' '.join((CONFIG['KEY_DRS'],'STR2DP4'))), ('P5',' '.join((CONFIG['KEY_DRS'],'STR2DP5'))), ('P6',' '.join((CONFIG['KEY_DRS'],'STR2DP6'))) ])
CONFIG['DRS_MJD'] = (' '.join((CONFIG['KEY_DRS'],'MJD')),'MJD of the combined image')
CONFIG['BERV'] = (' '.join((CONFIG['KEY_DRS'],'BERV')),'Barycentric correction [km/s]')
CONFIG['HJD'] = (' '.join((CONFIG['KEY_DRS'],'HJD')),'HJD of the combined image')
CONFIG['AIRMASS'] = (' '.join((CONFIG['KEY_DRS'],'AIRMASS')),'Airmass of the combined image')
CONFIG['MASTERFLAT'] = (' '.join((CONFIG['KEY_DRS'],'FLAT')),'Flat-field used for the reduction')
CONFIG['MASTERLAMP'] = (' '.join((CONFIG['KEY_DRS'],'LAMP')),'Calibration lamp used for the reduction')
CONFIG['KEY_WEXT'] = (' '.join((CONFIG['KEY_DRS'],'WEXT')),'Standard extraction window [pixel]')

# Wavelength calibration
CONFIG['CAL_FUNC'] = {'Oliva':True, 'Poly3':False} # function used for wavelength calibration (Tino Oliva Polynomial or 3-degree polynomial)
#CONFIG['CAL_FUNC'] = {'Oliva':False, 'Poly3':True}
CONFIG['WLFIT'] = (' '.join((CONFIG['KEY_DRS'],'CAL WLFUNC')),'Function used for wavelength calibration')

if CONFIG['CAL_FUNC']['Oliva']:
    CONFIG['WLFIT_FUNC'] = 'l0 + k1*(x-xc) + k2*(x-xc)**2 + k3*(x-xc)**3'

else:
    CONFIG['WLFIT_FUNC'] = 'c0 + c1*x + c2*x**2 + c3*x**3'

CONFIG['WLCOEFFS'] = {'k1':(' '.join((CONFIG['KEY_DRS'],'CAL K1')),'k1 coefficient of the calibration function'),'k2':(' '.join((CONFIG['KEY_DRS'],'CAL K2')),'k2 coefficient of the calibration function'),'k3':(' '.join((CONFIG['KEY_DRS'],'CAL K3')),'k3 coefficient of the calibration function'),'l0':(' '.join((CONFIG['KEY_DRS'],'CAL L0')),'l0 coefficient of the calibration function'),'xc':(' '.join((CONFIG['KEY_DRS'],'CAL XC')),'xc coefficient of the calibration function'),'rms':(' '.join((CONFIG['KEY_DRS'],'CAL RMSE')),'[m/s] RMS error of the calibration'), 'c0':(' '.join((CONFIG['KEY_DRS'],'CAL C0')),'c0 coefficient of the calibration function'),'c1':(' '.join((CONFIG['KEY_DRS'],'CAL C1')),'c1 coefficient of the calibration function'),'c2':(' '.join((CONFIG['KEY_DRS'],'CAL C2')),'c2 coefficient of the calibration function'),'c3':(' '.join((CONFIG['KEY_DRS'],'CAL C3')),'c3 coefficient of the calibration function'),'rms_poly':(' '.join((CONFIG['KEY_DRS'],'CAL RMSE')),'[m/s] RMS error of the calibration')}

#
# DB configuration 
#
# Ramp processor database
CONFIG['RAMP_NAME'] = 'ramps' + CONFIG['DATE'] + '.db'
CONFIG['DB_RAMP'] = os.path.join(CONFIG['BASE_RAMP'],CONFIG['RAMP_NAME'])
CONFIG['DB_RAMP_TBL'] = 'reducedramps'
CONFIG['DB_RAMP_COLS'] = {'fpath':'FPATH' , 'obstype':'OBSTYPE' , 'dateobs':'DATEOBS' , 'object' : 'OBJECT' , 'exptime':'EXPTIME' , 'nodstare':'NODSTARE' , 'slitpos':'SLITPOS' , 'groupi':'GROUPI' , 'groupn':'GROUPN'}

# Calibration database
CONFIG['DB_CALIB'] = 'drs_calib.db'
CONFIG['DB_CALIB_PATH'] = os.path.join(CONFIG['CALIB_DB_DIR'], CONFIG['DB_CALIB'])
CONFIG['DB_CALIB_TBL'] = 'calibrations'

CONFIG['DB_CALIB_COLS'] = OrderedDict([('01_data', 'date_calib'), ('dark10', 'masterdark10'), ('dark30', 'masterdark30'), ('dark60', 'masterdark60'), ('dark100', 'masterdark100'),  ('dark200', 'masterdark200'), ('dark300', 'masterdark300'), ('dark600', 'masterdark600'),('flat', 'masterflat'), ('flatstr', 'masterflat_str'), ('flatnor', 'masterflat_nor'), ('shiftY', 'shift_Y') ,('une', 'wl_une'), ('une_str', 'wl_une_str'), ('une_calib', 'wl_une_calib'), ('fp', 'wl_fp'), ('fp_str', 'wl_fp_str'), ('fp_calib','wl_fp_calib')])

CONFIG['DB_CALIB_DATATYPE'] = OrderedDict()
for colname in CONFIG['DB_CALIB_COLS']:
    CONFIG['DB_CALIB_DATATYPE'][colname] = 'TEXT' 
CONFIG['DB_CALIB_DATATYPE']['01_data'] = 'TEXT unique'
CONFIG['DB_CALIB_DATATYPE']['shiftY'] = 'INTEGER'

# Night reduction database

CONFIG['DB_ONLINE'] = ''.join(('db_',CONFIG['DATE'],'_online.db'))
CONFIG['DB_OFFLINE'] = ''.join(('db_',CONFIG['DATE'],'_offline.db'))
CONFIG['DB_ONLINE_PATH'] = os.path.join(CONFIG['WEBUI_DB_DIR'], CONFIG['DB_ONLINE'])
CONFIG['DB_OFFLINE_PATH'] = os.path.join(CONFIG['WEBUI_DB_DIR'], CONFIG['DB_OFFLINE'])

CONFIG['DB_2D_TBL'] = 'spec2dfiles'
CONFIG['DB_1D_TBL'] = 'spec1dfiles'
CONFIG['DB_CAL_TBL'] = 'calib'

CONFIG['DB_2D_COLS'] = OrderedDict([('names', 'spec_2d_names'), ('stamp', 'process_timestamp')])
CONFIG['DB_1D_COLS'] = OrderedDict([('path', 'spec_1d_path'), ('stamp', 'process_timestamp'), ('id', 'spec_1d_id'), ('type', 'spec_1d_type'), ('stat', 'arch_stat'), ('name', 'objname'), ('slit', 'slitpos'), ('snry', 'snr1'), ('snrj', 'snr2'), ('snrh', 'snr3'), ('snrk', 'snr4')])
CONFIG['DB_CAL_COLS'] = OrderedDict([('type', 'calib_type'), ('names', 'calib_names'), ('status', 'calib_status'), ('stamp', 'process_timestamp')])

CONFIG['DB_2D_DATATYPE'] = {'names': 'TEXT unique', 'stamp': 'REAL'}
CONFIG['DB_1D_DATATYPE'] = {'path': 'TEXT unique', 'stamp': 'REAL', 'id': 'TEXT', 'type': 'TEXT', 'stat': 'INTEGER', 'name': 'TEXT', 'slit': 'TEXT', 'snry': 'REAL', 'snrj': 'REAL', 'snrh': 'REAL', 'snrk': 'REAL'}
CONFIG['DB_CAL_DATATYPE'] = {'type': 'TEXT', 'names': 'TEXT unique', 'status': 'TEXT', 'stamp': 'REAL'}

CONFIG['DB_NIGHT'] = CONFIG['DB_ONLINE']
CONFIG['DB_NIGHT_PATH'] = CONFIG['DB_ONLINE_PATH']

#
# Extraction info
#

CONFIG['MASK_C'] = os.path.join(CONFIG['RES_DIR'], 'GIANOB_MASKC.fits')
CONFIG['A_POS'] = 8. # guess pixel position for A
CONFIG['B_POS'] = 23. # guess pixel position for B
CONFIG['C_POS'] = 15. # guess pixel position for C
CONFIG['Y_POS'] = 4 # max. pixel difference between expected and real pixel position
CONFIG['HWTM'] = 6. # hwtm limit for contamination between A and B
CONFIG['S1D'] = True # flag for creation of s1d output (True/False)
CONFIG['S1D_NORM'] = False # flag for normalization of s1d output (True/False)
CONFIG['S1D_STEP'] = 0.001 # constant step to use in s1d spectra

#
# Wavelength calibration
#

CONFIG['WAVE_SELECT'] = os.path.join(CONFIG['RES_DIR'], 'UNe_lines_GIANO_selected.txt')
CONFIG['WAVE_ALL'] = os.path.join(CONFIG['RES_DIR'], 'UNe_observed_lines_GIANOB_18nov2016.txt')
CONFIG['WAVE_FIT'] = {'drift':0.0, 'low_fwhm':1.7, 'high_fwhm':4.0, 'wrange1':10, 'confidence1':3, 'wrange2':5, 'confidence2':1.5, 'xc_range':10}
CONFIG['XC_GUESS'] = {32:987, 33:984, 34:982, 35:980, 36:978, 37:976, 38:974, 39:972, 40:970, 41:968, 42:965, 43:963, 44:960, 45:957, 46:955, 47:952, 48:949, 49:946, 50:943, 51:940, 52:937, 53:933, 54:930, 55:927, 56:924, 57:921, 58:918, 59:914, 60:910, 61:907, 62:904, 63:901, 64:898, 65:895, 66:892, 67:889, 68:886, 69:883, 70:880, 71:877, 72:874, 73:871, 74:868, 75:865, 76:862, 77:859, 78:857, 79:855, 80:853, 81:851}
CONFIG['L0_GUESS'] = {32:2398.32, 33:2325.63, 34:2257.24, 35:2192.68, 36:2131.75, 37:2074.09, 38:2019.53, 39:1967.73, 40:1918.56, 41:1871.75, 42:1827.18, 43:1784.70, 44:1744.14, 45:1705.38, 46:1668.31, 47:1632.82, 48:1598.81, 49:1566.20, 50:1534.86, 51:1504.78, 52:1475.85, 53:1448.03, 54:1421.20, 55:1395.38, 56:1370.45, 57:1346.41, 58:1323.22, 59:1300.78, 60:1279.12, 61:1258.15, 62:1237.85, 63:1218.21, 64:1199.17, 65:1180.72, 66:1162.83, 67:1145.47, 68:1128.62, 69:1112.26, 70:1096.36, 71:1080.91, 72:1065.89, 73:1051.28, 74:1037.06, 75:1023.22, 76:1003.74, 77:996.61, 78:983.81, 79:971.34, 80:959.17, 81:947.30}

#
# Misc Calibrations
#

CONFIG['DO_CALIB'] = {'dark':True, 'flat':True, 'une':True, 'fp':True, 'only_calib':False}
#CONFIG['DO_CALIB'] = {'dark':False, 'flat':False, 'une':False, 'fp':False, 'only_calib':False}

CONFIG['USE_FLAT'] = {'global':False, 'order':True, 'nor':False} # global: flat normalized by global mean value - order: flat normalized order by order by mean value - nor: flat normalized row by row by continuum fitting, removing the blaze function - No True value: no flat division

CONFIG['DARKLIST'] = {10:[],30:[],60:[],100:[],200:[],300:[],600:[]} # exptime dei dark
CONFIG['NDARK'] = len(CONFIG['DARKLIST']) # quanti tipi di dark (esempio: 10,30,60,100 sec = 4) meglio sovrastimare

CONFIG['WEXT'] = 10 # extraction half-window for wavelength calibration, it will extract 2*wext around the center of the order

#
# Detector info
#

CONFIG['RON'] = 5.0 # electrons
CONFIG['GAIN'] = 2.2 # e/ADU
CONFIG['XCCD'] = 2048
CONFIG['YCCD'] = 2048
CONFIG['N_ORD'] = 50 # number of echelle orders
CONFIG['W_ORD'] = 41 # width of straighten order in pixel
CONFIG['SHIFT_Y'] = 20 # expected bottom position of flat signal on the lowest order and the left side of the detector. DO NOT CHANGE.

#
# Quality checks
#

CONFIG['DARK_MEAN'] = {10:[10.0,10.0,10.0,10.0], 30:[25.0,25.0,25.0,25.0], 60:[50.0,50.0,50.0,50.0], 100:[80.0,80.0,80.0,80.0], 200:[800.0,800.0,800.0,800.0], 300:[800.0,800.0,800.0,800.0], 600:[800.0,800.0,800.0,800.0]} # Dark quality check: mean signal below this number (4 quadrant for 7 exposure time)
CONFIG['FLATSIGNAL'] = 300 # lowest flat signal expected to pass quality check
CONFIG['SCIENCECHECK'] = [500,540,140,160] # region x1:x2,y1:y2 for images' quality check
#CONFIG['NODSIGNAL'] = 2*CONFIG['DARK_MEAN']['quadrant'][0] # lowest image signal expected to pass quality check
CONFIG['NODSIGNAL'] = 0.0 # lowest image signal expected to pass quality check



if USRCONFIG['OFFLINE']:
    for key in USRCONFIG.keys():
        CONFIG[key] = USRCONFIG[key]

    CONFIG['RAW_DIR'] = os.path.join(CONFIG['BASE_RAW'],CONFIG['DATE'])
    CONFIG['OFFLINE_DIR'] = os.path.join(CONFIG['BASE_RED_DIR'],CONFIG['DATE'])
    CONFIG['RED_DIR'] = os.path.join(CONFIG['OFFLINE_DIR'],'offline')
    CONFIG['RED_CALIB'] = os.path.join(CONFIG['RED_DIR'],'CALIB')
    CONFIG['RED_STR'] = os.path.join(CONFIG['RED_DIR'],'STR')
    CONFIG['LOG_FILE'] = os.path.join(CONFIG['RED_DIR'], 'drs.log')
    CONFIG['RAMP_NAME'] = 'ramps' + CONFIG['DATE'] + '.db'
    CONFIG['DB_RAMP'] = os.path.join(CONFIG['BASE_RAMP'],CONFIG['RAMP_NAME'])

    CONFIG['DB_OFFLINE'] = ''.join(('db_',CONFIG['DATE'],'_offline.db'))
    CONFIG['DB_OFFLINE_PATH'] = os.path.join(CONFIG['WEBUI_DB_DIR'], CONFIG['DB_OFFLINE'])
    CONFIG['DB_NIGHT'] = CONFIG['DB_OFFLINE']
    CONFIG['DB_NIGHT_PATH'] = CONFIG['DB_OFFLINE_PATH']

    maskc = ''.join(('GIANOB_MASKC_',CONFIG['DATE'],'.fits'))
    CONFIG['MASK_C'] = os.path.join(CONFIG['RES_DIR'], maskc)