def main(night_name=None,
e2dsfile=None,
mask=None,
rv=None,
width=None,
step=None):
"""
cal_CCF_E2DS_spirou.py main function, if arguments are None uses
arguments from run time i.e.:
cal_CCF_E2DS_spirou.py [night_directory] [E2DSfilename] [mask] [RV]
[width] [step]
:param night_name: string or None, the folder within data raw directory
containing files (also reduced directory) i.e.
/data/raw/20170710 would be "20170710" but
/data/raw/AT5/20180409 would be "AT5/20180409"
:param e2dsfile: string, the E2DS file to use
:param mask: string, the mask file to use (i.e. "UrNe.mas")
:param rv: float, the target RV to use
:param width: float, the CCF width to use
:param step: float, the CCF step to use
:return ll: dictionary, containing all the local variables defined in
main
"""
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
# deal with arguments being None (i.e. get from sys.argv)
pos = [0, 1, 2, 3, 4]
fmt = [str, str, float, float, float]
name = ['e2dsfile', 'ccf_mask', 'target_rv', 'ccf_width', 'ccf_step']
lname = ['input_file', 'CCF_mask', 'RV', 'CCF_width', 'CCF_step']
req = [True, True, True, False, False]
call = [e2dsfile, mask, rv, width, step]
call_priority = [True, True, True, True, True]
# now get custom arguments
customargs = spirouStartup.GetCustomFromRuntime(p, pos, fmt, name, req,
call, call_priority, lname)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsfile='e2dsfile',
mainfitsdir='reduced')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, e2dsfilename = spirouStartup.SingleFileSetup(p, filename=p['E2DSFILE'])
# ----------------------------------------------------------------------
# Once we have checked the e2dsfile we can load calibDB
# ----------------------------------------------------------------------
# as we have custom arguments need to load the calibration database
p = spirouStartup.LoadCalibDB(p)
# ----------------------------------------------------------------------
# Deal with optional run time arguments
# ----------------------------------------------------------------------
# define default arguments (if ccf_width and ccf_step are not defined
# in function call or run time arguments
if 'ccf_width' not in p:
p['CCF_WIDTH'] = p['IC_CCF_WIDTH']
if 'ccf_step' not in p:
p['CCF_STEP'] = p['IC_CCF_STEP']
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
e2ds, hdr, nbo, nx = spirouImage.ReadData(p, e2dsfilename)
# add to loc
loc = ParamDict()
loc['E2DS'] = e2ds
loc['NUMBER_ORDERS'] = nbo
loc.set_sources(['E2DS', 'number_orders'], __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Get basic image properties for reference file
# ----------------------------------------------------------------------
# get sig det value
p = spirouImage.GetSigdet(p, hdr, name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, hdr, name='exptime')
# get gain
p = spirouImage.GetGain(p, hdr, name='gain')
# get acquisition time
p = spirouImage.GetAcqTime(p, hdr, name='acqtime', kind='julian')
# get obj name
p = spirouImage.ReadParam(p, hdr, 'KW_OBJNAME', name='OBJNAME', dtype=str)
bjdref = p['ACQTIME']
# set sigdet and conad keywords (sigdet is changed later)
p['KW_CCD_SIGDET'][1] = p['SIGDET']
p['KW_CCD_CONAD'][1] = p['GAIN']
# ----------------------------------------------------------------------
# Earth Velocity calculation
# ----------------------------------------------------------------------
if p['IC_IMAGE_TYPE'] == 'H4RG':
p, loc = spirouImage.GetEarthVelocityCorrection(p, loc, hdr)
# ----------------------------------------------------------------------
# Read wavelength solution
# ----------------------------------------------------------------------
# log
WLOG(p, '', 'Reading wavelength solution ')
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get wave image
wout = spirouImage.GetWaveSolution(p,
hdr=hdr,
return_wavemap=True,
return_filename=True,
fiber=wave_fiber)
param_ll, wave_ll, wavefile, wsource = wout
# save to storage
loc['PARAM_LL'], loc['WAVE_LL'], loc['WAVEFILE'], loc['WSOURCE'] = wout
source = __NAME__ + '/main() + spirouTHORCA.GetWaveSolution()'
loc.set_sources(['WAVE_LL', 'PARAM_LL', 'WAVEFILE', 'WSOURCE'], source)
# ----------------------------------------------------------------------
# Read Flat file
# ----------------------------------------------------------------------
# TODO We do not need to correct FLAT
# log
# WLOG(p, '', 'Reading Flat-Field ')
# get flat
# loc['FLAT'] = spirouImage.ReadFlatFile(p, hdr)
# loc.set_source('FLAT', __NAME__ + '/main() + /spirouImage.ReadFlatFile')
# get all values in flat that are zero to 1
# loc['FLAT'] = np.where(loc['FLAT'] == 0, 1.0, loc['FLAT'])
# get blaze
# p, loc['BLAZE'] = spirouImage.ReadBlazeFile(p, hdr)
p, blaze0 = spirouImage.ReadBlazeFile(p, hdr)
# ----------------------------------------------------------------------
# Preliminary set up = no flat, no blaze
# ----------------------------------------------------------------------
# reset flat to all ones
# loc['FLAT'] = np.ones((nbo, nx))
# set blaze to all ones (if not bug in correlbin !!!
# TODO Check why Blaze makes bugs in correlbin
loc['BLAZE'] = np.ones((nbo, nx))
# set sources
# loc.set_sources(['flat', 'blaze'], __NAME__ + '/main()')
loc.set_sources(['blaze'], __NAME__ + '/main()')
# Modification of E2DS array with N.A.N
if np.isnan(np.sum(e2ds)):
WLOG(p, 'warning', 'NaN values found in e2ds, converting process')
# First basic approach Replacing N.A.N by zeros
# e2ds[np.isnan(e2ds)] = 0
# Second approach replacing N.A.N by the Adjusted Blaze
e2dsb = e2ds / blaze0
for i in np.arange(len(e2ds)):
with warnings.catch_warnings(record=True) as _:
rap = np.mean(e2dsb[i][np.isfinite(e2dsb[i])])
if np.isnan(rap):
rap = 0.0
e2ds[i] = np.where(np.isfinite(e2dsb[i]), e2ds[i], blaze0[i] * rap)
# ----------------------------------------------------------------------
# correct extracted image for flat
# ----------------------------------------------------------------------
# loc['E2DSFF'] = e2ds/loc['FLAT']
# loc['E2DSFF'] = e2ds*1.
loc['E2DSFF'] = e2ds
loc.set_source('E2DSFF', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Compute photon noise uncertainty for reference file
# ----------------------------------------------------------------------
# set up the arguments for DeltaVrms2D
dargs = [loc['E2DS'], loc['WAVE_LL']]
dkwargs = dict(sigdet=p['IC_DRIFT_NOISE'],
size=p['IC_DRIFT_BOXSIZE'],
threshold=p['IC_DRIFT_MAXFLUX'])
# run DeltaVrms2D
dvrmsref, wmeanref = spirouRV.DeltaVrms2D(*dargs, **dkwargs)
# save to loc
loc['DVRMSREF'], loc['WMEANREF'] = dvrmsref, wmeanref
loc.set_sources(['dvrmsref', 'wmeanref'], __NAME__ + '/main()()')
# log the estimated RV uncertainty
# wmsg = 'On fiber {0} estimated RV uncertainty on spectrum is {1:.3f} m/s'
# WLOG(p, 'info', wmsg.format(p['FIBER'], wmeanref))
wmsg = 'On fiber estimated RV uncertainty on spectrum is {0:.3f} m/s'
WLOG(p, 'info', wmsg.format(wmeanref))
# TEST N.A.N
# loc['E2DSFF'][20:22,2000:3000]=np.nan
# e2ds[20:30,1000:3000]=np.nan
# ----------------------------------------------------------------------
# Reference plots
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive session if needed
sPlt.start_interactive_session(p)
# plot FP spectral order
sPlt.drift_plot_selected_wave_ref(p,
loc,
x=loc['WAVE_LL'],
y=loc['E2DS'])
# plot photon noise uncertainty
sPlt.drift_plot_photon_uncertainty(p, loc)
# ----------------------------------------------------------------------
# Get template RV (from ccf_mask)
# ----------------------------------------------------------------------
# get the CCF mask from file (check location of mask)
loc = spirouRV.GetCCFMask(p, loc)
# check and deal with mask in microns (should be in nm)
if np.mean(loc['LL_MASK_CTR']) < 2.0:
loc['LL_MASK_CTR'] *= 1000.0
loc['LL_MASK_D'] *= 1000.0
# ----------------------------------------------------------------------
# Do correlation
# ----------------------------------------------------------------------
# calculate and fit the CCF
loc = spirouRV.Coravelation(p, loc)
# ----------------------------------------------------------------------
# Correlation stats
# ----------------------------------------------------------------------
# get the maximum number of orders to use
nbmax = p['CCF_NUM_ORDERS_MAX']
# get the average ccf
loc['AVERAGE_CCF'] = np.nansum(loc['CCF'][:nbmax], axis=0)
# normalize the average ccf
normalized_ccf = loc['AVERAGE_CCF'] / np.max(loc['AVERAGE_CCF'])
# get the fit for the normalized average ccf
ccf_res, ccf_fit = spirouRV.FitCCF(p,
loc['RV_CCF'],
normalized_ccf,
fit_type=0)
loc['CCF_RES'] = ccf_res
loc['CCF_FIT'] = ccf_fit
# get the max cpp
loc['MAXCPP'] = np.nansum(loc['CCF_MAX']) / np.nansum(
loc['PIX_PASSED_ALL'])
# get the RV value from the normalised average ccf fit center location
loc['RV'] = float(ccf_res[1])
# get the contrast (ccf fit amplitude)
loc['CONTRAST'] = np.abs(100 * ccf_res[0])
# get the FWHM value
loc['FWHM'] = ccf_res[2] * spirouCore.spirouMath.fwhm()
# ----------------------------------------------------------------------
# set the source
keys = [
'average_ccf', 'maxcpp', 'rv', 'contrast', 'fwhm', 'ccf_res', 'ccf_fit'
]
loc.set_sources(keys, __NAME__ + '/main()')
# ----------------------------------------------------------------------
# log the stats
wmsg = ('Correlation: C={0:.1f}[%] RV={1:.5f}[km/s] '
'FWHM={2:.4f}[km/s] maxcpp={3:.1f}')
wargs = [loc['CONTRAST'], loc['RV'], loc['FWHM'], loc['MAXCPP']]
WLOG(p, 'info', wmsg.format(*wargs))
# ----------------------------------------------------------------------
# rv ccf plot
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# Plot rv vs ccf (and rv vs ccf_fit)
sPlt.ccf_rv_ccf_plot(p, loc['RV_CCF'], normalized_ccf, ccf_fit)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# TODO: Needs doing
# finally log the failed messages and set QC = 1 if we pass the
# quality control QC = 0 if we fail quality control
if passed:
WLOG(p, 'info', 'QUALITY CONTROL SUCCESSFUL - Well Done -')
p['QC'] = 1
p.set_source('QC', __NAME__ + '/main()')
else:
for farg in fail_msg:
wmsg = 'QUALITY CONTROL FAILED: {0}'
WLOG(p, 'warning', wmsg.format(farg))
p['QC'] = 0
p.set_source('QC', __NAME__ + '/main()')
# add to qc header lists
qc_values.append('None')
qc_names.append('None')
qc_logic.append('None')
qc_pass.append(1)
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ----------------------------------------------------------------------
# archive ccf to table
# ----------------------------------------------------------------------
# construct filename
res_table_file = spirouConfig.Constants.CCF_TABLE_FILE(p)
# log progress
WLOG(p, '', 'Archiving CCF on file {0}'.format(res_table_file))
# define column names
columns = ['order', 'maxcpp', 'nlines', 'contrast', 'RV', 'sig']
# define values for each column
values = [
loc['ORDERS'], loc['CCF_MAX'] / loc['PIX_PASSED_ALL'], loc['TOT_LINE'],
np.abs(100 * loc['CCF_ALL_RESULTS'][:, 0]),
loc['CCF_ALL_RESULTS'][:, 1], loc['CCF_ALL_RESULTS'][:, 2]
]
# define the format for each column
formats = ['2.0f', '5.0f', '4.0f', '4.1f', '9.4f', '7.4f']
# construct astropy table from column names, values and formats
table = spirouImage.MakeTable(p, columns, values, formats)
# save table to file
spirouImage.WriteTable(p, table, res_table_file, fmt='ascii')
# ----------------------------------------------------------------------
# archive ccf to fits file
# ----------------------------------------------------------------------
raw_infile = os.path.basename(p['E2DSFILE'])
# construct folder and filename
corfile, tag = spirouConfig.Constants.CCF_FITS_FILE(p)
corfilename = os.path.split(corfile)[-1]
# log that we are archiving the CCF on file
WLOG(p, '', 'Archiving CCF on file {0}'.format(corfilename))
# get constants from p
mask = p['CCF_MASK']
# if file exists remove it
if os.path.exists(corfile):
os.remove(corfile)
# add the average ccf to the end of ccf
data = np.vstack([loc['CCF'], loc['AVERAGE_CCF']])
# add drs keys
hdict = spirouImage.CopyOriginalKeys(hdr)
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_DATE'], value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DATE_NOW'], value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_PID'], value=p['PID'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag)
# set the input files
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBLAZE'], value=p['BLAZFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBWAVE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='file',
values=p['E2DSFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_INCCFMASK'],
value=p['CCF_MASK'])
hdict = spirouImage.AddKey(p, hdict, p['KW_INRV'], value=p['TARGET_RV'])
hdict = spirouImage.AddKey(p, hdict, p['KW_INWIDTH'], value=p['CCF_WIDTH'])
hdict = spirouImage.AddKey(p, hdict, p['KW_INSTEP'], value=p['CCF_STEP'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add CCF keys
hdict = spirouImage.AddKey(p, hdict, p['KW_CCF_CTYPE'], value='km/s')
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CCF_CRVAL'],
value=loc['RV_CCF'][0])
# the rv step
rvstep = np.abs(loc['RV_CCF'][0] - loc['RV_CCF'][1])
hdict = spirouImage.AddKey(p, hdict, p['KW_CCF_CDELT'], value=rvstep)
# add ccf stats
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CCF_RV'],
value=loc['CCF_RES'][1])
hdict = spirouImage.AddKey(p, hdict, p['KW_CCF_RVC'], value=loc['RV'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CCF_FWHM'], value=loc['FWHM'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CCF_WMREF'],
value=loc['WMEANREF'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CCF_CONTRAST'],
value=loc['CONTRAST'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CCF_MAXCPP'],
value=loc['MAXCPP'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CCF_MASK'], value=p['CCF_MASK'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CCF_LINES'],
value=np.nansum(loc['TOT_LINE']))
# add berv values
hdict = spirouImage.AddKey(p, hdict, p['KW_BERV'], value=loc['BERV'])
hdict = spirouImage.AddKey(p, hdict, p['KW_BJD'], value=loc['BJD'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_BERV_MAX'],
value=loc['BERV_MAX'])
# write image and add header keys (via hdict)
p = spirouImage.WriteImage(p, corfile, data, hdict)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def main(night_name=None, files=None, fiber_type=None, **kwargs):
"""
cal_DRIFT_E2DS_spirou.py main function, if night_name and files are
None uses arguments from run time i.e.:
cal_DRIFT_E2DS_spirou.py [night_directory] [files]
:param night_name: string or None, the folder within data raw directory
containing files (also reduced directory) i.e.
/data/raw/20170710 would be "20170710" but
/data/raw/AT5/20180409 would be "AT5/20180409"
:param files: string, list or None, the list of files to use for
arg_file_names and fitsfilename
(if None assumes arg_file_names was set from run time)
:param fiber_type: string, if None does all fiber types (defined in
constants_SPIROU FIBER_TYPES (default is AB, A, B, C
if defined then only does this fiber type (but must
be in FIBER_TYPES)
:param kwargs: any keyword to overwrite constant in param dict "p"
:return ll: dictionary, containing all the local variables defined in
main
"""
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
p = spirouStartup.LoadArguments(p, night_name, files)
p = spirouStartup.InitialFileSetup(p, calibdb=True)
# deal with fiber type
if fiber_type is None:
fiber_type = p['FIBER_TYPES']
if type(fiber_type) == str:
if fiber_type.upper() == 'ALL':
fiber_type = p['FIBER_TYPES']
elif fiber_type in p['FIBER_TYPES']:
fiber_type = [fiber_type]
else:
emsg = 'fiber_type="{0}" not understood'
WLOG(p, 'error', emsg.format(fiber_type))
# set fiber type
p['FIB_TYPE'] = fiber_type
p.set_source('FIB_TYPE', __NAME__ + '__main__()')
# Overwrite keys from source
for kwarg in kwargs:
p[kwarg] = kwargs[kwarg]
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
p, data, hdr = spirouImage.ReadImageAndCombine(p, framemath='add')
# ----------------------------------------------------------------------
# fix for un-preprocessed files
# ----------------------------------------------------------------------
data = spirouImage.FixNonPreProcess(p, data)
# ----------------------------------------------------------------------
# Get basic image properties
# ----------------------------------------------------------------------
# get sig det value
p = spirouImage.GetSigdet(p, hdr, name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, hdr, name='exptime')
# get gain
p = spirouImage.GetGain(p, hdr, name='gain')
# set sigdet and conad keywords (sigdet is changed later)
p['KW_CCD_SIGDET'][1] = p['SIGDET']
p['KW_CCD_CONAD'][1] = p['GAIN']
# now change the value of sigdet if require
if p['IC_EXT_SIGDET'] > 0:
p['SIGDET'] = float(p['IC_EXT_SIGDET'])
# get DPRTYPE from header (Will have it if valid)
p = spirouImage.ReadParam(p, hdr, 'KW_DPRTYPE', required=False, dtype=str)
# check the DPRTYPE is not None
if (p['DPRTYPE'] == 'None') or (['DPRTYPE'] is None):
emsg1 = 'Error: {0} is not set in header for file {1}'
eargs = [p['KW_DPRTYPE'][0], p['FITSFILENAME']]
emsg2 = '\tPlease run pre-processing on file.'
emsg3 = ('\tIf pre-processing fails or skips file, file is not '
'currrently as valid DRS fits file.')
WLOG(p, 'error', [emsg1.format(*eargs), emsg2, emsg3])
else:
p['DPRTYPE'] = p['DPRTYPE'].strip()
# ----------------------------------------------------------------------
# Correction of DARK
# ----------------------------------------------------------------------
p, datac = spirouImage.CorrectForDark(p, data, hdr)
# ----------------------------------------------------------------------
# Resize image
# ----------------------------------------------------------------------
# rotate the image and convert from ADU/s to ADU
data = spirouImage.ConvertToADU(spirouImage.FlipImage(p, datac), p=p)
# convert NaN to zeros
data0 = np.where(~np.isfinite(data), np.zeros_like(data), data)
# resize image
bkwargs = dict(xlow=p['IC_CCDX_LOW'],
xhigh=p['IC_CCDX_HIGH'],
ylow=p['IC_CCDY_LOW'],
yhigh=p['IC_CCDY_HIGH'],
getshape=False)
data1 = spirouImage.ResizeImage(p, data0, **bkwargs)
# log change in data size
wmsg = 'Image format changed to {1}x{0}'
WLOG(p, '', wmsg.format(*data1.shape))
# ----------------------------------------------------------------------
# Correct for the BADPIX mask (set all bad pixels to zero)
# ----------------------------------------------------------------------
p, data1 = spirouImage.CorrectForBadPix(p, data1, hdr)
# ----------------------------------------------------------------------
# Log the number of dead pixels
# ----------------------------------------------------------------------
# get the number of bad pixels
n_bad_pix = np.sum(~np.isfinite(data1))
n_bad_pix_frac = n_bad_pix * 100 / np.product(data1.shape)
# Log number
wmsg = 'Nb dead pixels = {0} / {1:.4f} %'
WLOG(p, 'info', wmsg.format(int(n_bad_pix), n_bad_pix_frac))
# ----------------------------------------------------------------------
# Get the miny, maxy and max_signal for the central column
# ----------------------------------------------------------------------
# get the central column
y = data1[p['IC_CENT_COL'], :]
# get the min max and max signal using box smoothed approach
miny, maxy, max_signal, diff_maxmin = spirouBACK.MeasureMinMaxSignal(p, y)
# Log max average flux/pixel
wmsg = 'Maximum average flux/pixel in the spectrum: {0:.1f} [ADU]'
WLOG(p, 'info', wmsg.format(max_signal / p['NBFRAMES']))
# ----------------------------------------------------------------------
# Background computation
# ----------------------------------------------------------------------
if p['IC_DO_BKGR_SUBTRACTION']:
# log that we are doing background measurement
WLOG(p, '', 'Doing background measurement on raw frame')
# get the bkgr measurement
bargs = [p, data1, hdr]
# background, xc, yc, minlevel = spirouBACK.MeasureBackgroundFF(*bargs)
p, background = spirouBACK.MeasureBackgroundMap(*bargs)
else:
background = np.zeros_like(data1)
p['BKGRDFILE'] = 'None'
p.set_source('BKGRDFILE', __NAME__ + '.main()')
# apply background correction to data (and set to zero where negative)
data1 = data1 - background
# ----------------------------------------------------------------------
# Read tilt slit angle
# ----------------------------------------------------------------------
# define loc storage parameter dictionary
loc = ParamDict()
# get tilts (if the mode requires it)
if p['IC_EXTRACT_TYPE'] not in EXTRACT_SHAPE_TYPES:
p, loc['TILT'] = spirouImage.ReadTiltFile(p, hdr)
loc.set_source('TILT',
__NAME__ + '/main() + /spirouImage.ReadTiltFile')
else:
loc['TILT'] = None
loc.set_source('TILT', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Earth Velocity calculation
# ----------------------------------------------------------------------
if p['IC_IMAGE_TYPE'] == 'H4RG':
p, loc = spirouImage.GetEarthVelocityCorrection(p, loc, hdr)
# ----------------------------------------------------------------------
# Get all fiber data (for all fibers)
# ----------------------------------------------------------------------
# TODO: This is temp solution for options 5a and 5b
loc_fibers = spirouLOCOR.GetFiberData(p, hdr)
# ------------------------------------------------------------------
# Deal with debananafication
# ------------------------------------------------------------------
# if mode 4a or 4b we need to straighten in x only
if p['IC_EXTRACT_TYPE'] in ['4a', '4b']:
# get the shape parameters
p, shapem_x = spirouImage.GetShapeX(p, hdr)
p, shape_local = spirouImage.GetShapeLocal(p, hdr)
# log progress
WLOG(p, '', 'Debananafying (straightening) image')
# apply shape transforms
targs = dict(lin_transform_vect=shape_local, dxmap=shapem_x)
data2 = spirouImage.EATransform(data1, **targs)
# if mode 5a or 5b we need to straighten in x and y using the
# polynomial fits for location
elif p['IC_EXTRACT_TYPE'] in ['5a', '5b']:
# get the shape parameters
p, shapem_x = spirouImage.GetShapeX(p, hdr)
p, shapem_y = spirouImage.GetShapeY(p, hdr)
p, shape_local = spirouImage.GetShapeLocal(p, hdr)
p, fpmaster = spirouImage.GetFPMaster(p, hdr)
# get the bad pixel map
bkwargs = dict(return_map=True, quiet=True)
p, badpix = spirouImage.CorrectForBadPix(p, data1, hdr, **bkwargs)
# log progress
WLOG(p, '', 'Cleaning image')
# clean the image
data1 = spirouEXTOR.CleanHotpix(data1, badpix)
# log progress
WLOG(p, '', 'Debananafying (straightening) image')
# apply shape transforms
targs = dict(lin_transform_vect=shape_local,
dxmap=shapem_x,
dymap=shapem_y)
data2 = spirouImage.EATransform(data1, **targs)
# in any other mode we do not straighten
else:
data2 = np.array(data1)
# ----------------------------------------------------------------------
# Fiber loop
# ----------------------------------------------------------------------
# loop around fiber types
for fiber in p['FIB_TYPE']:
# set fiber
p['FIBER'] = fiber
p.set_source('FIBER', __NAME__ + '/main()()')
# ------------------------------------------------------------------
# Read wavelength solution
# ------------------------------------------------------------------
# set source of wave file
wsource = __NAME__ + '/main() + /spirouImage.GetWaveSolution'
# Force A and B to AB solution
if fiber in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = fiber
# get wave image
wkwargs = dict(hdr=hdr,
return_wavemap=True,
return_filename=True,
return_header=True,
fiber=wave_fiber)
wout = spirouImage.GetWaveSolution(p, **wkwargs)
loc['WAVEPARAMS'], loc['WAVE'], loc['WAVEFILE'] = wout[:3]
loc['WAVEHDR'], loc['WSOURCE'] = wout[3:]
source_names = ['WAVE', 'WAVEFILE', 'WAVEPARAMS', 'WAVEHDR']
loc.set_sources(source_names, wsource)
# get dates
loc['WAVE_ACQTIMES'] = spirouDB.GetTimes(p, loc['WAVEHDR'])
loc.set_source('WAVE_ACQTIMES', __NAME__ + '.main()')
# get the recipe that produced the wave solution
if 'WAVECODE' in loc['WAVEHDR']:
loc['WAVE_CODE'] = loc['WAVEHDR']['WAVECODE']
else:
loc['WAVE_CODE'] = 'UNKNOWN'
loc.set_source('WAVE_CODE', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# Get WFP keys
# ----------------------------------------------------------------------
# Read the WFP keys - if they don't exist set to None and deal
# with later
p = spirouImage.ReadParam(p,
loc['WAVEHDR'],
'KW_WFP_DRIFT',
name='WFP_DRIFT',
required=False)
p = spirouImage.ReadParam(p,
loc['WAVEHDR'],
'KW_WFP_FWHM',
name='WFP_FWHM',
required=False)
p = spirouImage.ReadParam(p,
loc['WAVEHDR'],
'KW_WFP_CONTRAST',
name='WFP_CONTRAST',
required=False)
p = spirouImage.ReadParam(p,
loc['WAVEHDR'],
'KW_WFP_MAXCPP',
name='WFP_MAXCPP',
required=False)
p = spirouImage.ReadParam(p,
loc['WAVEHDR'],
'KW_WFP_MASK',
name='WFP_MASK',
required=False)
p = spirouImage.ReadParam(p,
loc['WAVEHDR'],
'KW_WFP_LINES',
name='WFP_LINES',
required=False)
p = spirouImage.ReadParam(p,
loc['WAVEHDR'],
'KW_WFP_TARG_RV',
name='WFP_TARG_RV',
required=False)
p = spirouImage.ReadParam(p,
loc['WAVEHDR'],
'KW_WFP_WIDTH',
name='WFP_WIDTH',
required=False)
p = spirouImage.ReadParam(p,
loc['WAVEHDR'],
'KW_WFP_STEP',
name='WFP_STEP',
required=False)
# ----------------------------------------------------------------------
# Read Flat file
# ----------------------------------------------------------------------
fout = spirouImage.ReadFlatFile(p, hdr, return_header=True)
p, loc['FLAT'], flathdr = fout
loc.set_source('FLAT',
__NAME__ + '/main() + /spirouImage.ReadFlatFile')
# get flat extraction mode
if p['KW_E2DS_EXTM'][0] in flathdr:
flat_ext_mode = flathdr[p['KW_E2DS_EXTM'][0]]
else:
flat_ext_mode = None
# ------------------------------------------------------------------
# Check extraction method is same as flat extraction method
# ------------------------------------------------------------------
# get extraction method and function
extmethod, extfunc = spirouEXTOR.GetExtMethod(p, p['IC_EXTRACT_TYPE'])
if not DEBUG:
# compare flat extraction mode to extraction mode
spirouEXTOR.CompareExtMethod(p, flat_ext_mode, extmethod, 'FLAT',
'EXTRACTION')
# ------------------------------------------------------------------
# Read Blaze file
# ------------------------------------------------------------------
p, loc['BLAZE'] = spirouImage.ReadBlazeFile(p, hdr)
blazesource = __NAME__ + '/main() + /spirouImage.ReadBlazeFile'
loc.set_source('BLAZE', blazesource)
# ------------------------------------------------------------------
# Get fiber specific parameters from loc_fibers
# ------------------------------------------------------------------
# get this fibers parameters
p = spirouImage.FiberParams(p, p['FIBER'], merge=True)
# get localisation parameters
for key in loc_fibers[fiber]:
loc[key] = loc_fibers[fiber][key]
loc.set_source(key, loc_fibers[fiber].sources[key])
# get locofile source
p['LOCOFILE'] = loc['LOCOFILE']
p.set_source('LOCOFILE', loc.sources['LOCOFILE'])
# get the order_profile
order_profile = loc_fibers[fiber]['ORDER_PROFILE']
# ------------------------------------------------------------------
# Set up Extract storage
# ------------------------------------------------------------------
# Create array to store extraction (for each order and each pixel
# along order)
loc['E2DS'] = np.zeros((loc['NUMBER_ORDERS'], data2.shape[1]))
loc['E2DSFF'] = np.zeros((loc['NUMBER_ORDERS'], data2.shape[1]))
loc['E2DSLL'] = []
loc['SPE1'] = np.zeros((loc['NUMBER_ORDERS'], data2.shape[1]))
loc['SPE3'] = np.zeros((loc['NUMBER_ORDERS'], data2.shape[1]))
loc['SPE4'] = np.zeros((loc['NUMBER_ORDERS'], data2.shape[1]))
loc['SPE5'] = np.zeros((loc['NUMBER_ORDERS'], data2.shape[1]))
# Create array to store the signal to noise ratios for each order
loc['SNR'] = np.zeros(loc['NUMBER_ORDERS'])
# ------------------------------------------------------------------
# Extract orders
# ------------------------------------------------------------------
# source for parameter dictionary
source = __NAME__ + '/main()'
# get limits of order extraction
valid_orders = spirouEXTOR.GetValidOrders(p, loc)
# loop around each order
for order_num in valid_orders:
# -------------------------------------------------------------
# IC_EXTRACT_TYPE decides the extraction routine
# -------------------------------------------------------------
eargs = [p, loc, data2, order_num]
ekwargs = dict(mode=p['IC_EXTRACT_TYPE'],
order_profile=order_profile)
with warnings.catch_warnings(record=True) as w:
eout = spirouEXTOR.Extraction(*eargs, **ekwargs)
# deal with different return
if p['IC_EXTRACT_TYPE'] in EXTRACT_LL_TYPES:
e2ds, e2dsll, cpt = eout
else:
e2ds, cpt = eout
e2dsll = None
# -------------------------------------------------------------
# calculate the noise
range1, range2 = p['IC_EXT_RANGE1'], p['IC_EXT_RANGE2']
# set the noise
noise = p['SIGDET'] * np.sqrt(range1 + range2)
# get window size
blaze_win1 = int(data2.shape[0] / 2) - p['IC_EXTFBLAZ']
blaze_win2 = int(data2.shape[0] / 2) + p['IC_EXTFBLAZ']
# get average flux per pixel
flux = np.nansum(
e2ds[blaze_win1:blaze_win2]) / (2 * p['IC_EXTFBLAZ'])
# calculate signal to noise ratio = flux/sqrt(flux + noise^2)
snr = flux / np.sqrt(flux + noise**2)
# log the SNR RMS
wmsg = 'On fiber {0} order {1}: S/N= {2:.1f} Nbcosmic= {3}'
wargs = [p['FIBER'], order_num, snr, cpt]
WLOG(p, '', wmsg.format(*wargs))
# add calculations to storage
loc['E2DS'][order_num] = e2ds
loc['E2DSFF'][order_num] = e2ds / loc['FLAT'][order_num]
loc['SNR'][order_num] = snr
# save the longfile
if p['IC_EXTRACT_TYPE'] in EXTRACT_LL_TYPES:
loc['E2DSLL'].append(e2dsll)
# set sources
loc.set_sources(['e2ds', 'SNR'], source)
# Log if saturation level reached
satvalue = (flux / p['GAIN']) / (range1 + range2)
if satvalue > (p['QC_LOC_FLUMAX'] * p['NBFRAMES']):
wmsg = 'SATURATION LEVEL REACHED on Fiber {0} order={1}'
WLOG(p, 'warning', wmsg.format(fiber, order_num))
# ------------------------------------------------------------------
# Thermal correction
# ------------------------------------------------------------------
# get fiber type
if fiber in ['AB', 'A', 'B']:
fibertype = p['DPRTYPE'].split('_')[0]
else:
fibertype = p['DPRTYPE'].split('_')[1]
# apply thermal correction based on fiber type
if fibertype in p['THERMAL_CORRECTION_TYPE1']:
# log progress
wmsg = 'Correcting thermal background for {0}={1} mode={2}'
wargs = [fiber, fibertype, 1]
WLOG(p, 'info', wmsg.format(*wargs))
# correct E2DS
tkwargs = dict(image=loc['E2DS'], mode=1, fiber=fiber, hdr=hdr)
p, loc['E2DS'] = spirouBACK.ThermalCorrect(p, **tkwargs)
# correct E2DSFF
tkwargs = dict(image=loc['E2DSFF'],
mode=1,
fiber=fiber,
hdr=hdr,
flat=loc['FLAT'])
p, loc['E2DSFF'] = spirouBACK.ThermalCorrect(p, **tkwargs)
elif fibertype in p['THERMAL_CORRECTION_TYPE2']:
# log progress
wmsg = 'Correcting thermal background for {0}={1} mode={2}'
wargs = [fiber, fibertype, 2]
WLOG(p, 'info', wmsg.format(*wargs))
# correct E2DS
tkwargs = dict(image=loc['E2DS'], mode=2, fiber=fiber, hdr=hdr)
p, loc['E2DS'] = spirouBACK.ThermalCorrect(p, **tkwargs)
# correct E2DSFF
tkwargs = dict(image=loc['E2DSFF'],
mode=2,
fiber=fiber,
hdr=hdr,
flat=loc['FLAT'])
p, loc['E2DSFF'] = spirouBACK.ThermalCorrect(p, **tkwargs)
else:
# log progress
wmsg = 'Not correcting thermal background for {0}={1}'
wargs = [fiber, fibertype]
WLOG(p, 'info', wmsg.format(*wargs))
# set filename for output
outfile = 'THERMALFILE_{0}'.format(fiber)
p[outfile] = 'None'
p.set_source(outfile, __NAME__ + '.main()')
# ------------------------------------------------------------------
# Plots
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive session if needed
sPlt.start_interactive_session(p)
# plot all orders or one order
if p['IC_FF_PLOT_ALL_ORDERS']:
# plot image with all order fits (slower)
sPlt.ext_aorder_fit(p, loc, data1, max_signal / 10.)
else:
# plot image with selected order fit and edge fit (faster)
sPlt.ext_sorder_fit(p, loc, data1, max_signal / 10.)
# plot e2ds against wavelength
sPlt.ext_spectral_order_plot(p, loc)
if p['IC_EXTRACT_TYPE'] in EXTRACT_SHAPE_TYPES:
sPlt.ext_debanana_plot(p, loc, data2, max_signal / 10.)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# if array is completely NaNs it shouldn't pass
if np.sum(np.isfinite(loc['E2DS'])) == 0:
fail_msg.append('E2DS image is all NaNs')
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append('NaN')
qc_names.append('image')
qc_logic.append('image is all NaN')
# ----------------------------------------------------------------------
# saturation check: check that the max_signal is lower than
# qc_max_signal
max_qcflux = p['QC_MAX_SIGNAL'] * p['NBFRAMES']
if max_signal > max_qcflux:
fmsg = 'Too much flux in the image ({0:.2f} > {1:.2f})'
fail_msg.append(fmsg.format(max_signal, max_qcflux))
passed = False
# Question: Why is this test ignored?
# For some reason this test is ignored in old code
passed = True
WLOG(p, 'info', fail_msg[-1])
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(max_signal)
qc_names.append('max_signal')
qc_logic.append('QC_MAX_SIGNAL > {0:.3f}'.format(max_qcflux))
# finally log the failed messages and set QC = 1 if we pass the
# quality control QC = 0 if we fail quality control
if passed:
WLOG(p, 'info', 'QUALITY CONTROL SUCCESSFUL - Well Done -')
p['QC'] = 1
p.set_source('QC', __NAME__ + '/main()')
else:
for farg in fail_msg:
wmsg = 'QUALITY CONTROL FAILED: {0}'
WLOG(p, 'warning', wmsg.format(farg))
p['QC'] = 0
p.set_source('QC', __NAME__ + '/main()')
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ------------------------------------------------------------------
# Store extraction in file(s)
# ------------------------------------------------------------------
raw_ext_file = os.path.basename(p['FITSFILENAME'])
# construct filename
e2dsfits, tag1 = spirouConfig.Constants.EXTRACT_E2DS_FILE(p)
e2dsfitsname = os.path.split(e2dsfits)[-1]
e2dsfffits, tag2 = spirouConfig.Constants.EXTRACT_E2DSFF_FILE(p)
e2dsfffitsname = os.path.split(e2dsfffits)[-1]
e2dsllfits, tag4 = spirouConfig.Constants.EXTRACT_E2DSLL_FILE(p)
e2dsfllitsname = os.path.split(e2dsllfits)[-1]
# log that we are saving E2DS spectrum
wmsg = 'Saving E2DS spectrum of Fiber {0} in {1}'
WLOG(p, '', wmsg.format(p['FIBER'], e2dsfitsname))
wmsg = 'Saving E2DSFF spectrum of Fiber {0} in {1}'
WLOG(p, '', wmsg.format(p['FIBER'], e2dsfffitsname))
# add keys from original header file
hdict = spirouImage.CopyOriginalKeys(hdr)
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DRS_DATE'],
value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DATE_NOW'],
value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_PID'], value=p['PID'])
hdict = spirouImage.AddKey(p, hdict, p['KW_FIBER'], value=p['FIBER'])
# set the input files
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBDARK'],
value=p['DARKFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBBAD'],
value=p['BADPFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBLOCO'],
value=p['LOCOFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBBACK'],
value=p['BKGRDFILE'])
if p['IC_EXTRACT_TYPE'] not in EXTRACT_SHAPE_TYPES:
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBTILT'],
value=p['TILTFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBBLAZE'],
value=p['BLAZFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBFLAT'],
value=p['FLATFILE'])
if p['IC_EXTRACT_TYPE'] in EXTRACT_SHAPE_TYPES:
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBSHAPEX'],
value=p['SHAPEXFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBSHAPEY'],
value=p['SHAPEYFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBSHAPE'],
value=p['SHAPEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBFPMASTER'],
value=p['FPMASTERFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBTHERMAL'],
value=p['THERMALFILE_{0}'.format(fiber)])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBWAVE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='file',
values=p['ARG_FILE_NAMES'])
# construct loco filename
locofile, _ = spirouConfig.Constants.EXTRACT_LOCO_FILE(p)
locofilename = os.path.basename(locofile)
# add barycentric keys to header
hdict = spirouImage.AddKey(p, hdict, p['KW_BERV'], value=loc['BERV'])
hdict = spirouImage.AddKey(p, hdict, p['KW_BJD'], value=loc['BJD'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_BERV_MAX'],
value=loc['BERV_MAX'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_B_OBS_HOUR'],
value=loc['BERVHOUR'])
# add barycentric estimate keys to header
hdict = spirouImage.AddKey(p,
hdict,
p['KW_BERV_EST'],
value=loc['BERV_EST'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_BJD_EST'],
value=loc['BJD_EST'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_BERV_MAX_EST'],
value=loc['BERV_MAX_EST'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_BERV_SOURCE'],
value=loc['BERV_SOURCE'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# copy extraction method and function to header
# (for reproducibility)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_E2DS_EXTM'],
value=extmethod)
hdict = spirouImage.AddKey(p, hdict, p['KW_E2DS_FUNC'], value=extfunc)
# add localization file name to header
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOCO_FILE'],
value=locofilename)
# add wave solution date
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME1'],
value=loc['WAVE_ACQTIMES'][0])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME2'],
value=loc['WAVE_ACQTIMES'][1])
# add wave solution number of orders
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_ORD_N'],
value=loc['WAVEPARAMS'].shape[0])
# add wave solution degree of fit
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_LL_DEG'],
value=loc['WAVEPARAMS'].shape[1] - 1)
# -------------------------------------------------------------------------
# add keys of the wave solution FP CCF
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_FILE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_DRIFT'],
value=p['WFP_DRIFT'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_FWHM'],
value=p['WFP_FWHM'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_CONTRAST'],
value=p['WFP_CONTRAST'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_MAXCPP'],
value=p['WFP_MAXCPP'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_MASK'],
value=p['WFP_MASK'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_LINES'],
value=p['WFP_LINES'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_TARG_RV'],
value=p['WFP_TARG_RV'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_WIDTH'],
value=p['WFP_WIDTH'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_STEP'],
value=p['WFP_STEP'])
# write 1D list of the SNR
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_E2DS_SNR'],
values=loc['SNR'])
# add localization file keys to header
root = p['KW_ROOT_DRS_LOC'][0]
hdict = spirouImage.CopyRootKeys(p, hdict, locofile, root=root)
# add wave solution coefficients
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_WAVE_PARAM'],
values=loc['WAVEPARAMS'])
# Save E2DS file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_EXT_TYPE'],
value=p['DPRTYPE'])
p = spirouImage.WriteImage(p, e2dsfits, loc['E2DS'], hdict)
# Save E2DSFF file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag2)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_EXT_TYPE'],
value=p['DPRTYPE'])
p = spirouImage.WriteImage(p, e2dsfffits, loc['E2DSFF'], hdict)
# Save E2DSLL file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag4)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_EXT_TYPE'],
value=p['DPRTYPE'])
if p['IC_EXTRACT_TYPE'] in EXTRACT_LL_TYPES:
llstack = np.vstack(loc['E2DSLL'])
p = spirouImage.WriteImage(p, e2dsllfits, llstack, hdict)
# ------------------------------------------------------------------
# 1-dimension spectral S1D (uniform in wavelength)
# ------------------------------------------------------------------
# get arguments for E2DS to S1D
e2dsargs = [loc['WAVE'], loc['E2DSFF'], loc['BLAZE']]
# get 1D spectrum
xs1d1, ys1d1 = spirouImage.E2DStoS1D(p, *e2dsargs, wgrid='wave')
# Plot the 1D spectrum
if p['DRS_PLOT'] > 0:
sPlt.ext_1d_spectrum_plot(p, xs1d1, ys1d1)
# construct file name
s1dfile1, tag3 = spirouConfig.Constants.EXTRACT_S1D_FILE1(p)
s1dfilename1 = os.path.basename(s1dfile1)
# add header keys
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DRS_DATE'],
value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DATE_NOW'],
value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag3)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_EXT_TYPE'],
value=p['DPRTYPE'])
# log writing to file
wmsg = 'Saving 1D spectrum (uniform in wavelength) for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(p['FIBER'], s1dfilename1))
# Write to file
columns = ['wavelength', 'flux', 'eflux']
values = [xs1d1, ys1d1, np.zeros_like(ys1d1)]
units = ['nm', None, None]
s1d1 = spirouImage.MakeTable(p, columns, values, units=units)
spirouImage.WriteTable(p, s1d1, s1dfile1, header=hdict)
# ------------------------------------------------------------------
# 1-dimension spectral S1D (uniform in velocity)
# ------------------------------------------------------------------
# get arguments for E2DS to S1D
e2dsargs = [loc['WAVE'], loc['E2DSFF'], loc['BLAZE']]
# get 1D spectrum
xs1d2, ys1d2 = spirouImage.E2DStoS1D(p, *e2dsargs, wgrid='velocity')
# Plot the 1D spectrum
if p['DRS_PLOT'] > 0:
sPlt.ext_1d_spectrum_plot(p, xs1d2, ys1d2)
# construct file name
s1dfile2, tag4 = spirouConfig.Constants.EXTRACT_S1D_FILE2(p)
s1dfilename2 = os.path.basename(s1dfile2)
# add header keys
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DRS_DATE'],
value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DATE_NOW'],
value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag4)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_EXT_TYPE'],
value=p['DPRTYPE'])
# log writing to file
wmsg = 'Saving 1D spectrum (uniform in velocity) for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(p['FIBER'], s1dfilename2))
# Write to file
columns = ['wavelength', 'flux', 'eflux']
values = [xs1d2, ys1d2, np.zeros_like(ys1d2)]
units = ['nm', None, None]
s1d2 = spirouImage.MakeTable(p, columns, values, units=units)
spirouImage.WriteTable(p, s1d2, s1dfile2, header=hdict)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def main(night_name=None, files=None):
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
# get parameters from configuration files and run time arguments
customargs = spirouStartup.GetCustomFromRuntime(p, [0], [str], ['reffile'])
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsfile='reffile',
mainfitsdir='reduced')
# setup files and get fiber
p = spirouStartup.InitialFileSetup(p, calibdb=True)
# set the fiber type
p['FIB_TYP'] = [p['FIBER']]
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
gfkwargs = dict(path=p['REDUCED_DIR'], filename=p['REFFILE'])
p['REFFILENAME'] = spirouStartup.GetFile(p, **gfkwargs)
p.set_source('REFFILENAME', __NAME__ + '/main()')
# get the fiber type
p['FIBER'] = 'AB'
e2ds, hdr, nx, ny = spirouImage.ReadImage(p)
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get wave image
_, wave, _ = spirouImage.GetWaveSolution(p,
hdr=hdr,
return_wavemap=True,
fiber=wave_fiber)
blaze = spirouImage.ReadBlazeFile(p)
# ----------------------------------------------------------------------
# Get lamp params
# ----------------------------------------------------------------------
# get lamp parameters
p = spirouTHORCA.GetLampParams(p, hdr)
# ----------------------------------------------------------------------
# Get catalogue and fitted line list
# ----------------------------------------------------------------------
# load line file (from p['IC_LL_LINE_FILE'])
ll_line_cat, ampl_line_cat = spirouImage.ReadLineList(p)
# construct fitted lines table filename
wavelltbl = spirouConfig.Constants.WAVE_LINE_FILE(p)
WLOG(p, '', wavelltbl)
# read fitted lines
ll_ord, ll_line_fit, ampl_line_fit = np.genfromtxt(wavelltbl,
skip_header=4,
skip_footer=2,
unpack=True,
usecols=(0, 1, 3))
# ----------------------------------------------------------------------
# Plots
# ----------------------------------------------------------------------
# define line colours
col = ['magenta', 'purple']
# get order parity
ll_ord_par = np.mod(ll_ord, 2)
print(ll_ord_par)
col2 = [col[int(x)] for x in ll_ord_par]
# start interactive plot
sPlt.start_interactive_session(p)
plt.figure()
for order_num in np.arange(nx):
plt.plot(wave[order_num], e2ds[order_num])
# get heights
heights = []
for line in range(len(ll_line_cat)):
heights.append(200000 + np.max([np.min(e2ds), ampl_line_cat[line]]))
# plot ll_line_cat
plt.vlines(ll_line_cat,
0,
heights,
colors='darkgreen',
linestyles='dashed')
# get heights
heights = []
for line in range(len(ll_line_fit)):
heights.append(200000 + np.max([np.min(e2ds), ampl_line_fit[line]]))
# plot ll_line_fit
plt.vlines(ll_line_fit, 0, heights, colors=col2, linestyles='dashdot')
plt.xlabel('Wavelength [nm]')
plt.ylabel('Flux e-')
plt.title(p['REFFILENAME'])
# end interactive session
# sPlt.end_interactive_session()
# old code:
# plt.ion()
# plt.figure()
#
# for order_num in np.arange(nx):
# plt.plot(wave[order_num], e2ds[order_num])
#
# for line in range(len(ll_line_cat)):
# plt.vlines(ll_line_cat[line], 0, 200000 +
# max(np.min(e2ds), ampl_line_cat[line]),
# colors='darkgreen', linestyles='dashed')
#
# for line in range(len(ll_line_fit)):
# plt.vlines(ll_line_fit[line], 0, 200000 +
# max(np.min(e2ds), ampl_line_fit[line]),
# colors='magenta', linestyles='dashdot')
#
# plt.xlabel('Wavelength [nm]')
# plt.ylabel('Flux e-')
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p, outputs=None)
# return a copy of locally defined variables in the memory
return dict(locals())
def main(night_name=None, fpfile=None, hcfiles=None):
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
if hcfiles is None or fpfile is None:
names, types = ['fpfile', 'hcfiles'], [str, str]
customargs = spirouStartup.GetCustomFromRuntime(p, [0, 1],
types,
names,
last_multi=True)
else:
customargs = dict(hcfiles=hcfiles, fpfile=fpfile)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsdir='reduced',
mainfitsfile='hcfiles')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, fpfitsfilename = spirouStartup.SingleFileSetup(p, filename=p['FPFILE'])
fiber1 = str(p['FIBER'])
p, hcfilenames = spirouStartup.MultiFileSetup(p, files=p['HCFILES'])
fiber2 = str(p['FIBER'])
# set the hcfilename to the first hcfilenames
hcfitsfilename = hcfilenames[0]
# ----------------------------------------------------------------------
# Once we have checked the e2dsfile we can load calibDB
# ----------------------------------------------------------------------
# as we have custom arguments need to load the calibration database
p = spirouStartup.LoadCalibDB(p)
# ----------------------------------------------------------------------
# Have to check that the fibers match
# ----------------------------------------------------------------------
if fiber1 == fiber2:
p['FIBER'] = fiber1
fsource = __NAME__ + '/main() & spirouStartup.GetFiberType()'
p.set_source('FIBER', fsource)
else:
emsg = 'Fiber not matching for {0} and {1}, should be the same'
eargs = [hcfitsfilename, fpfitsfilename]
WLOG(p, 'error', emsg.format(*eargs))
# set the fiber type
p['FIB_TYP'] = [p['FIBER']]
p.set_source('FIB_TYP', __NAME__ + '/main()')
# set find line mode
find_lines_mode = p['HC_FIND_LINES_MODE']
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read and combine all HC files except the first (fpfitsfilename)
rargs = [p, 'add', hcfitsfilename, hcfilenames[1:]]
p, hcdata, hchdr = spirouImage.ReadImageAndCombine(*rargs)
# read first file (fpfitsfilename)
fpdata, fphdr, _, _ = spirouImage.ReadImage(p, fpfitsfilename)
# add data and hdr to loc
loc = ParamDict()
loc['HCDATA'], loc['HCHDR'] = hcdata, hchdr
loc['FPDATA'], loc['FPHDR'] = fpdata, fphdr
# set the source
sources = ['HCDATA', 'HCHDR']
loc.set_sources(sources, 'spirouImage.ReadImageAndCombine()')
sources = ['FPDATA', 'FPHDR']
loc.set_sources(sources, 'spirouImage.ReadImage()')
# ----------------------------------------------------------------------
# Get basic image properties for reference file
# ----------------------------------------------------------------------
# get sig det value
p = spirouImage.GetSigdet(p, hchdr, name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, hchdr, name='exptime')
# get gain
p = spirouImage.GetGain(p, hchdr, name='gain')
# get acquisition time
p = spirouImage.GetAcqTime(p, hchdr, name='acqtime', kind='julian')
bjdref = p['ACQTIME']
# set sigdet and conad keywords (sigdet is changed later)
p['KW_CCD_SIGDET'][1] = p['SIGDET']
p['KW_CCD_CONAD'][1] = p['GAIN']
# get lamp parameters
p = spirouTHORCA.GetLampParams(p, hchdr)
# ----------------------------------------------------------------------
# Obtain the flat
# ----------------------------------------------------------------------
# get the flat
p, loc = spirouFLAT.GetFlat(p, loc, hchdr)
# ----------------------------------------------------------------------
# Read blaze
# ----------------------------------------------------------------------
# get tilts
p, loc['BLAZE'] = spirouImage.ReadBlazeFile(p, hchdr)
loc.set_source('BLAZE', __NAME__ + '/main() + /spirouImage.ReadBlazeFile')
# correct the data with the flat
# TODO: Should this be used?
# log
# WLOG(p, '', 'Applying flat correction')
# loc['HCDATA'] = loc['HCDATA']/loc['FLAT']
# loc['FPDATA'] = loc['FPDATA']/loc['FLAT']
# ----------------------------------------------------------------------
# Start plotting session
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive plot
sPlt.start_interactive_session(p)
# ----------------------------------------------------------------------
# loop around fiber type
# ----------------------------------------------------------------------
for fiber in p['FIB_TYP']:
# set fiber type for inside loop
p['FIBER'] = fiber
# ------------------------------------------------------------------
# Instrumental drift computation (if previous solution exists)
# ------------------------------------------------------------------
# get key
keydb = 'HCREF_{0}'.format(p['FIBER'])
# check for key in calibDB
if keydb in p['CALIBDB'].keys():
# log process
wmsg = ('Doing Instrumental drift computation from previous '
'calibration')
WLOG(p, '', wmsg)
# calculate instrument drift
loc = spirouTHORCA.CalcInstrumentDrift(p, loc)
# ------------------------------------------------------------------
# Wave solution
# ------------------------------------------------------------------
# log message for loop
wmsg = 'Processing Wavelength Calibration for Fiber {0}'
WLOG(p, 'info', wmsg.format(p['FIBER']))
# ------------------------------------------------------------------
# Part 1 of cal_HC
# ------------------------------------------------------------------
p, loc = cal_HC_E2DS_spirou.part1(p, loc, mode=find_lines_mode)
# ------------------------------------------------------------------
# FP solution
# ------------------------------------------------------------------
# log message
wmsg = 'Calculating FP wave solution'
WLOG(p, '', wmsg)
# calculate FP wave solution
# spirouTHORCA.FPWaveSolution(p, loc, mode=find_lines_mode)
spirouTHORCA.FPWaveSolutionNew(p, loc)
# ------------------------------------------------------------------
# FP solution plots
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# Plot the FP extracted spectrum against wavelength solution
sPlt.wave_plot_final_fp_order(p, loc, iteration=1)
# Plot the measured FP cavity width offset against line number
sPlt.wave_local_width_offset_plot(p, loc)
# Plot the FP line wavelength residuals
sPlt.wave_fp_wavelength_residuals(p, loc)
# ------------------------------------------------------------------
# Part 2 of cal_HC
# ------------------------------------------------------------------
# set params for part2
p['QC_RMS_LITTROW_MAX'] = p['QC_WAVE_RMS_LITTROW_MAX']
p['QC_DEV_LITTROW_MAX'] = p['QC_WAVE_DEV_LITTROW_MAX']
p['IC_HC_N_ORD_START_2'] = min(p['IC_HC_N_ORD_START_2'],
p['IC_FP_N_ORD_START'])
p['IC_HC_N_ORD_FINAL_2'] = max(p['IC_HC_N_ORD_FINAL_2'],
p['IC_FP_N_ORD_FINAL'])
# run part 2
# p, loc = part2test(p, loc)
p, loc = cal_HC_E2DS_spirou.part2(p, loc)
# ----------------------------------------------------------------------
# End plotting session
# ----------------------------------------------------------------------
# end interactive session
sPlt.end_interactive_session(p)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def main(night_name=None, files=None):
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
p = spirouStartup.LoadArguments(p,
night_name,
files,
mainfitsdir='reduced')
p = spirouStartup.InitialFileSetup(p, calibdb=True)
# set up function name
main_name = __NAME__ + '.main()'
# ------------------------------------------------------------------
# Load first file
# ------------------------------------------------------------------
loc = ParamDict()
rd = spirouImage.ReadImage(p, p['FITSFILENAME'])
loc['DATA'], loc['DATAHDR'], loc['YDIM'], loc['XDIM'] = rd
loc.set_sources(['DATA', 'DATAHDR', 'XDIM', 'YDIM'], main_name)
# ------------------------------------------------------------------
# Get the wave solution
# ------------------------------------------------------------------
masterwavefile = spirouDB.GetDatabaseMasterWave(p)
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# read master wave map
wout = spirouImage.GetWaveSolution(p,
filename=masterwavefile,
return_wavemap=True,
quiet=True,
return_header=True,
fiber=wave_fiber)
_, loc['WAVE'], loc['WAVEFILE'], _ = wout
loc.set_sources(['WAVE', 'WAVEFILE'], main_name)
# get the wave keys
loc = spirouImage.GetWaveKeys(p, loc, loc['DATAHDR'])
# ------------------------------------------------------------------
# Construct convolution kernels (used in GetMolecularTellLines)
# ------------------------------------------------------------------
loc = spirouTelluric.ConstructConvKernel1(p, loc)
# ------------------------------------------------------------------
# Get molecular telluric lines
# ------------------------------------------------------------------
loc = spirouTelluric.GetMolecularTellLines(p, loc)
# if TAPAS FNAME is not None we generated a new file so should add to tellDB
if loc['TAPAS_FNAME'] is not None:
# add to the telluric database
spirouDB.UpdateDatabaseTellConv(p, loc['TAPAS_FNAME'], loc['DATAHDR'])
# put file in telluDB
spirouDB.PutTelluFile(p, loc['TAPAS_ABSNAME'])
# ----------------------------------------------------------------------
# load the expected atmospheric transmission
# ----------------------------------------------------------------------
# read filename from telluDB
tapas_file_names = spirouDB.GetDatabaseTellConv(p)
tapas_file_name = tapas_file_names[-1]
# load atmospheric transmission
sp_tapas = np.load(tapas_file_name)
loc['TAPAS_ALL_SPECIES'] = sp_tapas
# extract the water and other line-of-sight optical depths
loc['TAPAS_WATER'] = sp_tapas[1, :]
loc['TAPAS_OTHERS'] = np.prod(sp_tapas[2:, :], axis=0)
loc.set_sources(['TAPAS_ALL_SPECIES', 'TAPAS_WATER', 'TAPAS_OTHERS'],
main_name)
# ------------------------------------------------------------------
# Get master wave solution map
# ------------------------------------------------------------------
# get master wave map
masterwavefile = spirouDB.GetDatabaseMasterWave(p)
# log process
wmsg1 = 'Shifting transmission map on to master wavelength grid'
wmsg2 = '\tFile = {0}'.format(os.path.basename(masterwavefile))
WLOG(p, '', [wmsg1, wmsg2])
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# read master wave map
mout = spirouImage.GetWaveSolution(p,
filename=masterwavefile,
return_wavemap=True,
quiet=True,
return_header=True,
fiber=wave_fiber)
masterwavep, masterwave, masterwaveheader, mwsource = mout
# get wave acqtimes
master_acqtimes = spirouDB.GetTimes(p, masterwaveheader)
# ------------------------------------------------------------------
# Loop around the files
# ------------------------------------------------------------------
# construct extension
tellu_ext = '{0}_{1}.fits'
# get current telluric maps from telluDB
# tellu_db_data = spirouDB.GetDatabaseTellMap(p, required=False)
# tellu_db_files = tellu_db_data[0]
# storage for valid output files
loc['OUTPUTFILES'] = []
# loop around the files
for basefilename in p['ARG_FILE_NAMES']:
# ------------------------------------------------------------------
# Get absolute path of filename
# ------------------------------------------------------------------
filename = os.path.join(p['ARG_FILE_DIR'], basefilename)
# ------------------------------------------------------------------
# Read obj telluric file and correct blaze (per order)
# ------------------------------------------------------------------
# get image
sp, shdr, _, _ = spirouImage.ReadImage(p, filename)
# ------------------------------------------------------------------
# check that file has valid DPRTYPE
# ------------------------------------------------------------------
# get FP_FP DPRTYPE
p = spirouImage.ReadParam(p, shdr, 'KW_DPRTYPE', 'DPRTYPE', dtype=str)
# if dprtype is incorrect skip
if p['DPRTYPE'] not in p['ALLOWED_TELLURIC_DPRTYPES']:
wmsg1 = 'Skipping file (DPRTYPE incorrect)'
wmsg2 = '\t DPRTYPE = {0}'.format(p['DPRTYPE'])
WLOG(p, 'warning', [wmsg1, wmsg2])
continue
# get blaze
p, blaze = spirouImage.ReadBlazeFile(p, shdr)
# get the blaze percentile
blaze_p = p['MKTELLU_BLAZE_PERCENTILE']
# loop through blaze orders, normalize blaze by its peak amplitude
for order_num in range(sp.shape[0]):
# normalize the spectrum
spo, bzo = sp[order_num], blaze[order_num]
sp[order_num] = spo / np.nanpercentile(spo, blaze_p)
# normalize the blaze
blaze[order_num] = bzo / np.nanpercentile(bzo, blaze_p)
# find where the blaze is bad
with warnings.catch_warnings(record=True) as _:
badblaze = blaze < p['MKTELLU_CUT_BLAZE_NORM']
# set bad blaze to NaN
blaze[badblaze] = np.nan
# set to NaN values where spectrum is zero
zeromask = sp == 0
sp[zeromask] = np.nan
# divide spectrum by blaze
with warnings.catch_warnings(record=True) as _:
sp = sp / blaze
# add sp to loc
loc['SP'] = sp
loc.set_source('SP', main_name)
# ----------------------------------------------------------------------
# Get object name, airmass and berv
# ----------------------------------------------------------------------
# Get object name
loc['OBJNAME'] = spirouImage.GetObjName(p, shdr)
# Get the airmass
loc['AIRMASS'] = spirouImage.GetAirmass(p, shdr)
# Get the Barycentric correction from header
p, loc = spirouImage.GetEarthVelocityCorrection(p, loc, shdr)
# set sources
source = main_name + '+ spirouImage.ReadParams()'
loc.set_sources(['OBJNAME', 'AIRMASS'], source)
# ------------------------------------------------------------------
# get output transmission filename
outfile, tag1 = spirouConfig.Constants.TELLU_TRANS_MAP_FILE(
p, filename)
outfilename = os.path.basename(outfile)
loc['OUTPUTFILES'].append(outfile)
# ----------------------------------------------------------------------
# Load template (if available)
# ----------------------------------------------------------------------
# read filename from telluDB
template_file = spirouDB.GetDatabaseObjTemp(p,
loc['OBJNAME'],
required=False)
# if we don't have a template flag it
if template_file is None:
loc['FLAG_TEMPLATE'] = False
loc['TEMPLATE'] = None
# construct progres string
pstring = 'No template found.'
else:
loc['FLAG_TEMPLATE'] = True
# load template
template, _, _, _ = spirouImage.ReadImage(p, template_file)
# add to loc
loc['TEMPLATE'] = template
# construct progres string
template_bfile = os.path.basename(template_file)
pstring = 'Using template {0}'.format(template_bfile)
# set the source for flag and template
loc.set_sources(['FLAG_TEMPLATE', 'TEMPLATE'], main_name)
# ------------------------------------------------------------------
# log processing file
wmsg = 'Processing file {0}. {1}'
WLOG(p, '', [wmsg.format(outfilename, pstring)])
# ------------------------------------------------------------------
# Check that basefile is not in blacklist
# ------------------------------------------------------------------
blacklist_check = spirouTelluric.CheckBlackList(loc['OBJNAME'])
if blacklist_check:
# log black list file found
wmsg = 'File {0} is blacklisted (OBJNAME={1}). Skipping'
wargs = [basefilename, loc['OBJNAME']]
WLOG(p, 'warning', wmsg.format(*wargs))
# skip this file
continue
# ------------------------------------------------------------------
# deal with applying template to spectrum
# ------------------------------------------------------------------
# Requires from loc:
# TEMPLATE (None or template loaded from file)
# FLAG_TEMPLATE
# WAVE
# SP
# BERV
#
# Returns:
# SP (modified if template was used)
# TEMPLATE
# WCONV
loc = spirouTelluric.ApplyTemplate(p, loc)
# ------------------------------------------------------------------
# calcullate telluric absorption (with a sigma clip loop)
# ------------------------------------------------------------------
# Requires from loc:
# AIRMASS
# WAVE
# SP
# WCONV
# Returns:
# PASSED [Bool] True or False
# SP_OUT
# SED_OUT
# RECOV_AIRMASS
# RECOV_WATER
loc = spirouTelluric.CalcTelluAbsorption(p, loc)
# calculate tranmission map from sp and sed
transmission_map = loc['SP_OUT'] / loc['SED_OUT']
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# if array is completely NaNs it shouldn't pass
if np.sum(np.isfinite(transmission_map)) == 0:
fail_msg.append('transmission map is all NaNs')
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append('NaN')
qc_names.append('image')
qc_logic.append('image is all NaN')
# ----------------------------------------------------------------------
# get SNR for each order from header
nbo = loc['DATA'].shape[0]
snr_order = p['QC_MK_TELLU_SNR_ORDER']
snr = spirouImage.Read1Dkey(p, shdr, p['kw_E2DS_SNR'][0], nbo)
# check that SNR is high enough
if snr[snr_order] < p['QC_MK_TELLU_SNR_MIN']:
fmsg = 'low SNR in order {0}: ({1:.2f} < {2:.2f})'
fargs = [snr_order, snr[snr_order], p['QC_MK_TELLU_SNR_MIN']]
fail_msg.append(fmsg.format(*fargs))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(snr[snr_order])
qc_name_str = 'SNR[{0}]'.format(snr_order)
qc_names.append(qc_name_str)
qc_logic.append('{0} < {1:.2f}'.format(qc_name_str,
p['QC_MK_TELLU_SNR_ORDER']))
# ----------------------------------------------------------------------
# check that the file passed the CalcTelluAbsorption sigma clip loop
if not loc['PASSED']:
fmsg = 'File {0} did not converge on a solution in function: {1}'
fargs = [basefilename, 'spirouTelluric.CalcTelluAbsorption()']
fail_msg.append(fmsg.format(*fargs))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(basefilename)
qc_names.append('FILE')
qc_logic.append('FILE did not converge')
# ----------------------------------------------------------------------
# check that the airmass is not too different from input airmass
airmass_diff = np.abs(loc['RECOV_AIRMASS'] - loc['AIRMASS'])
fargs = [
loc['RECOV_AIRMASS'], loc['AIRMASS'], p['QC_MKTELLU_AIRMASS_DIFF']
]
if airmass_diff > p['QC_MKTELLU_AIRMASS_DIFF']:
fmsg = ('Recovered airmass to de-similar than input airmass.'
'Recovered: {0:.3f}. Input: {1:.3f}. QC limit = {2}')
fail_msg.append(fmsg.format(*fargs))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(airmass_diff)
qc_names.append('airmass_diff')
qc_logic.append('airmass_diff > {0:.2f}'
''.format(p['QC_MKTELLU_AIRMASS_DIFF']))
# ----------------------------------------------------------------------
# check that the water vapor is within limits
water_cond1 = loc['RECOV_WATER'] < p['MKTELLU_TRANS_MIN_WATERCOL']
water_cond2 = loc['RECOV_WATER'] > p['MKTELLU_TRANS_MAX_WATERCOL']
fargs = [
p['MKTELLU_TRANS_MIN_WATERCOL'], p['MKTELLU_TRANS_MAX_WATERCOL']
]
if water_cond1 or water_cond2:
fmsg = ('Recovered water vapor optical depth not between {0:.3f} '
'and {1:.3f}')
fail_msg.append(fmsg.format(*fargs))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(loc['RECOV_WATER'])
qc_names.append('RECOV_WATER')
qc_logic.append('RECOV_WATER not between {0:.3f} and {1:.3f}'
''.format(*fargs))
# ----------------------------------------------------------------------
# finally log the failed messages and set QC = 1 if we pass the
# quality control QC = 0 if we fail quality control
if passed:
WLOG(p, 'info', 'QUALITY CONTROL SUCCESSFUL - Well Done -')
p['QC'] = 1
p.set_source('QC', __NAME__ + '/main()')
else:
for farg in fail_msg:
wmsg = 'QUALITY CONTROL FAILED: {0}'
WLOG(p, 'warning', wmsg.format(farg))
p['QC'] = 0
p.set_source('QC', __NAME__ + '/main()')
continue
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ------------------------------------------------------------------
# Save transmission map to file
# ------------------------------------------------------------------
# get raw file name
raw_in_file = os.path.basename(p['FITSFILENAME'])
# copy original keys
hdict = spirouImage.CopyOriginalKeys(loc['DATAHDR'])
# add version number
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DRS_DATE'],
value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DATE_NOW'],
value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_PID'], value=p['PID'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
# set the input files
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBBLAZE'],
value=p['BLAZFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBWAVE'],
value=os.path.basename(masterwavefile))
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=mwsource)
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='file',
values=p['ARG_FILE_NAMES'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add wave solution date
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME1'],
value=master_acqtimes[0])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME2'],
value=master_acqtimes[1])
# add wave solution number of orders
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_ORD_N'],
value=masterwavep.shape[0])
# add wave solution degree of fit
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_LL_DEG'],
value=masterwavep.shape[1] - 1)
# add wave solution coefficients
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_WAVE_PARAM'],
values=masterwavep)
# add telluric keys
hdict = spirouImage.AddKey(p,
hdict,
p['KW_TELLU_AIRMASS'],
value=loc['RECOV_AIRMASS'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_TELLU_WATER'],
value=loc['RECOV_WATER'])
# write to file
p = spirouImage.WriteImage(p, outfile, transmission_map, hdict)
# ------------------------------------------------------------------
# Add transmission map to telluDB
# ------------------------------------------------------------------
if p['QC']:
# copy tellu file to the telluDB folder
spirouDB.PutTelluFile(p, outfile)
# update the master tellu DB file with transmission map
targs = [
p, outfilename, loc['OBJNAME'], loc['RECOV_AIRMASS'],
loc['RECOV_WATER']
]
spirouDB.UpdateDatabaseTellMap(*targs)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def main(night_name=None, reffile=None):
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
customargs = spirouStartup.GetCustomFromRuntime(p, [0], [str], ['reffile'],
[True], [reffile])
p = spirouStartup.LoadArguments(p, night_name, customargs=customargs,
mainfitsfile='reffile',
mainfitsdir='reduced')
# load the calibDB
p = spirouStartup.LoadCalibDB(p)
# force plotting to 1
p['DRS_PLOT'] = 1
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
p, fpfitsfilename = spirouStartup.SingleFileSetup(p, filename=p['REFFILE'])
# get the fiber type
fiber1 = str(p['FIBER'])
e2ds, hdr, nx, ny = spirouImage.ReadImage(p)
p, blaze = spirouImage.ReadBlazeFile(p)
# set source of wave file
wsource = __NAME__ + '/main() + /spirouImage.GetWaveSolution'
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get wave image
_, wave, _ = spirouImage.GetWaveSolution(p, hdr=hdr, return_wavemap=True,
fiber=wave_fiber)
# ----------------------------------------------------------------------
# Get basic image properties
# ----------------------------------------------------------------------
plt.ion()
plt.figure()
for i in np.arange(nx):
plt.plot(wave[i], e2ds[i])
plt.xlabel('Wavelength [nm]')
plt.ylabel('Flux e-')
plt.title('Extracted spectra')
plt.figure()
for i in np.arange(nx):
plt.plot(wave[i], e2ds[i] / blaze[i])
plt.xlabel('Wavelength [nm]')
plt.ylabel('Relative Flux e-')
plt.title('Blaze corrected Extracted spectra')
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p, outputs=None)
# return a copy of locally defined variables in the memory
return dict(locals())
p = spirouStartup.Begin(recipe=__NAME__)
customargs = spirouStartup.GetCustomFromRuntime(p, [0], [str], ['reffile'],
[True], [reffile])
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsfile='reffile',
mainfitsdir='reduced')
p['FIBER'] = 'AB'
# load the calibDB
p = spirouStartup.LoadCalibDB(p)
# load ref spectrum
e2ds, hdr, nx, ny = spirouImage.ReadImage(p)
# get blaze
blaze = spirouImage.ReadBlazeFile(p)
# get wave image
_, wave, _ = spirouImage.GetWaveSolution(p, hdr=hdr, return_wavemap=True)
# get files
files = os.listdir('.')
fluxes = []
times = []
fig1, frame1 = plt.subplots(ncols=1, nrows=1)
# loop around files and sum flux
for filename in files:
if 'corrected.fits' not in filename:
continue
def main(night_name=None, files=None):
"""
cal_HC_E2DS.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_DARK_spirou.py [night_directory] [fitsfilename]
:param night_name: string or None, the folder within data raw directory
containing files (also reduced directory) i.e.
/data/raw/20170710 would be "20170710" but
/data/raw/AT5/20180409 would be "AT5/20180409"
:param files: string, list or None, the list of files to use for
arg_file_names and fitsfilename
(if None assumes arg_file_names was set from run time)
:return ll: dictionary, containing all the local variables defined in
main
"""
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p, night_name, files, mainfitsdir='reduced')
# setup files and get fiber
p = spirouStartup.InitialFileSetup(p, calibdb=True)
# set the fiber type
p['FIB_TYP'] = [p['FIBER']]
p.set_source('FIB_TYP', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read and combine all files
p, hcdata, hchdr = spirouImage.ReadImageAndCombine(p, 'add')
# add data and hdr to loc
loc = ParamDict()
loc['HCDATA'], loc['HCHDR'] = hcdata, hchdr
# set the source
sources = ['HCDATA', 'HCHDR']
loc.set_sources(sources, 'spirouImage.ReadImageAndCombine()')
# ----------------------------------------------------------------------
# Get basic parameters
# ----------------------------------------------------------------------
# get sig det value
p = spirouImage.GetSigdet(p, loc['HCHDR'], name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, loc['HCHDR'], name='exptime')
# get gain
p = spirouImage.GetGain(p, loc['HCHDR'], name='gain')
# get acquisition time
p = spirouImage.GetAcqTime(p, loc['HCHDR'], name='ACQTIME', kind='julian')
bjdref = p['ACQTIME']
# set sigdet and conad keywords (sigdet is changed later)
p['KW_CCD_SIGDET'][1] = p['SIGDET']
p['KW_CCD_CONAD'][1] = p['GAIN']
# get lamp parameters
p = spirouTHORCA.GetLampParams(p, loc['HCHDR'])
# get number of orders
# we always get fibre A number because AB is doubled in constants file
loc['NBO'] = p['QC_LOC_NBO_FPALL']['A']
loc.set_source('NBO', __NAME__ + '.main()')
# get number of pixels in x from hcdata size
loc['NBPIX'] = loc['HCDATA'].shape[1]
loc.set_source('NBPIX', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# Read blaze
# ----------------------------------------------------------------------
# get tilts
loc['BLAZE'] = spirouImage.ReadBlazeFile(p, hchdr)
loc.set_source('BLAZE', __NAME__ + '/main() + /spirouImage.ReadBlazeFile')
# ----------------------------------------------------------------------
# Read wave solution
# ----------------------------------------------------------------------
# wavelength file; we will use the polynomial terms in its header,
# NOT the pixel values that would need to be interpolated
# getting header info with wavelength polynomials
# set source of wave file
wsource = __NAME__ + '/main() + /spirouImage.GetWaveSolution'
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get wave image
wout = spirouImage.GetWaveSolution(p, hdr=hchdr, return_wavemap=True,
return_filename=True, fiber=wave_fiber)
loc['WAVEPARAMS'], loc['WAVE_INIT'], loc['WAVEFILE'], loc['WSOURCE'] = wout
loc.set_sources(['WAVE_INIT', 'WAVEFILE', 'WAVEPARAMS', 'WSOURCE'], wsource)
# ----------------------------------------------------------------------
# Check that wave parameters are consistent with "ic_ll_degr_fit"
# ----------------------------------------------------------------------
loc = spirouImage.CheckWaveSolConsistency(p, loc)
# ----------------------------------------------------------------------
# Read UNe solution
# ----------------------------------------------------------------------
wave_u_ne, amp_u_ne = spirouImage.ReadLineList(p)
loc['LL_LINE'], loc['AMPL_LINE'] = wave_u_ne, amp_u_ne
source = __NAME__ + '.main() + spirouImage.ReadLineList()'
loc.set_sources(['ll_line', 'ampl_line'], source)
# ----------------------------------------------------------------------
# Generate wave map from wave solution
# ----------------------------------------------------------------------
loc = spirouWAVE.generate_wave_map(p, loc)
# ----------------------------------------------------------------------
# Find Gaussian Peaks in HC spectrum
# ----------------------------------------------------------------------
loc = spirouWAVE.find_hc_gauss_peaks(p, loc)
# ----------------------------------------------------------------------
# Start plotting session
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive plot
sPlt.start_interactive_session(p)
# ----------------------------------------------------------------------
# Fit Gaussian peaks (in triplets) to
# ----------------------------------------------------------------------
loc = spirouWAVE.fit_gaussian_triplets(p, loc)
# ----------------------------------------------------------------------
# Generate Resolution map and line profiles
# ----------------------------------------------------------------------
# log progress
wmsg = 'Generating resolution map and '
# generate resolution map
loc = spirouWAVE.generate_resolution_map(p, loc)
# map line profile map
if p['DRS_PLOT'] > 0:
sPlt.wave_ea_plot_line_profiles(p, loc)
# ----------------------------------------------------------------------
# End plotting session
# ----------------------------------------------------------------------
# end interactive session
if p['DRS_PLOT'] > 0:
sPlt.end_interactive_session(p)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# quality control on sigma clip (sig1 > qc_hc_wave_sigma_max
if loc['SIG1'] > p['QC_HC_WAVE_SIGMA_MAX']:
fmsg = 'Sigma too high ({0:.5f} > {1:.5f})'
fail_msg.append(fmsg.format(loc['SIG1'], p['QC_HC_WAVE_SIGMA_MAX']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(loc['SIG1'])
qc_names.append('SIG1')
qc_logic.append('SIG1 > {0:.2f}'.format(p['QC_HC_WAVE_SIGMA_MAX']))
# ----------------------------------------------------------------------
# check the difference between consecutive orders is always positive
# get the differences
wave_diff = loc['WAVE_MAP2'][1:]-loc['WAVE_MAP2'][:-1]
if np.min(wave_diff) < 0:
fmsg = 'Negative wavelength difference between orders'
fail_msg.append(fmsg)
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(np.min(wave_diff))
qc_names.append('MIN WAVE DIFF')
qc_logic.append('MIN WAVE DIFF < 0')
# ----------------------------------------------------------------------
# finally log the failed messages and set QC = 1 if we pass the
# quality control QC = 0 if we fail quality control
if passed:
WLOG(p, 'info', 'QUALITY CONTROL SUCCESSFUL - Well Done -')
p['QC'] = 1
p.set_source('QC', __NAME__ + '/main()')
else:
for farg in fail_msg:
wmsg = 'QUALITY CONTROL FAILED: {0}'
WLOG(p, 'warning', wmsg.format(farg))
p['QC'] = 0
p.set_source('QC', __NAME__ + '/main()')
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ----------------------------------------------------------------------
# log the global stats
# ----------------------------------------------------------------------
# calculate catalog-fit residuals in km/s
res_hc =[]
sumres_hc = 0.0
sumres2_hc = 0.0
for order in range(loc['NBO']):
# get HC line wavelengths for the order
order_mask = loc['ORD_T'] == order
hc_x_ord = loc['XGAU_T'][order_mask]
hc_ll_ord = np.polyval(loc['POLY_WAVE_SOL'][order][::-1],hc_x_ord)
hc_ll_cat = loc['WAVE_CATALOG'][order_mask]
hc_ll_diff = hc_ll_ord - hc_ll_cat
res_hc.append(hc_ll_diff*speed_of_light/hc_ll_cat)
sumres_hc += np.nansum(res_hc[order])
sumres2_hc += np.nansum(res_hc[order] ** 2)
total_lines_hc = len(np.concatenate(res_hc))
final_mean_hc = sumres_hc/total_lines_hc
final_var_hc = (sumres2_hc/total_lines_hc) - (final_mean_hc ** 2)
wmsg1 = 'On fiber {0} HC fit line statistic:'.format(p['FIBER'])
wargs2 = [final_mean_hc * 1000.0, np.sqrt(final_var_hc) * 1000.0,
total_lines_hc, 1000.0 * np.sqrt(final_var_hc / total_lines_hc)]
wmsg2 = ('\tmean={0:.3f}[m/s] rms={1:.1f} {2} HC lines (error on mean '
'value:{3:.4f}[m/s])'.format(*wargs2))
WLOG(p, 'info', [wmsg1, wmsg2])
# ----------------------------------------------------------------------
# Save wave map to file
# ----------------------------------------------------------------------
# get base input filenames
bfilenames = []
for raw_file in p['ARG_FILE_NAMES']:
bfilenames.append(os.path.basename(raw_file))
# get wave filename
wavefits, tag1 = spirouConfig.Constants.WAVE_FILE_EA(p)
wavefitsname = os.path.basename(wavefits)
# log progress
WLOG(p, '', 'Saving wave map to {0}'.format(wavefitsname))
# log progress
wargs = [p['FIBER'], wavefitsname]
wmsg = 'Write wavelength solution for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(*wargs))
# write solution to fitsfilename header
# copy original keys
hdict = spirouImage.CopyOriginalKeys(loc['HCHDR'])
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_DATE'], value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DATE_NOW'], value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_PID'], value=p['PID'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
# set the input files
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBLAZE'], value=p['BLAZFILE'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add wave solution date
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVE_TIME1'],
value=p['MAX_TIME_HUMAN'])
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVE_TIME2'],
value=p['MAX_TIME_UNIX'])
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVE_CODE'], value=__NAME__)
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBWAVE'], value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
hdict = spirouImage.AddKey1DList(p, hdict, p['KW_INFILE1'], dim1name='file',
values=p['ARG_FILE_NAMES'])
# add number of orders
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVE_ORD_N'],
value=loc['POLY_WAVE_SOL'].shape[0])
# add degree of fit
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVE_LL_DEG'],
value=loc['POLY_WAVE_SOL'].shape[1]-1)
# add wave solution
hdict = spirouImage.AddKey2DList(p, hdict, p['KW_WAVE_PARAM'],
values=loc['POLY_WAVE_SOL'])
# write the wave "spectrum"
p = spirouImage.WriteImage(p, wavefits, loc['WAVE_MAP2'], hdict)
# get filename for E2DS calibDB copy of FITSFILENAME
e2dscopy_filename, tag2 = spirouConfig.Constants.WAVE_E2DS_COPY(p)
wargs = [p['FIBER'], os.path.split(e2dscopy_filename)[-1]]
wmsg = 'Write reference E2DS spectra for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(*wargs))
# make a copy of the E2DS file for the calibBD
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag2)
p = spirouImage.WriteImage(p, e2dscopy_filename, loc['HCDATA'], hdict)
# ----------------------------------------------------------------------
# Save resolution and line profiles to file
# ----------------------------------------------------------------------
raw_infile = os.path.basename(p['FITSFILENAME'])
# get wave filename
resfits, tag3 = spirouConfig.Constants.WAVE_RES_FILE_EA(p)
resfitsname = os.path.basename(resfits)
WLOG(p, '', 'Saving wave resmap to {0}'.format(resfitsname))
# make a copy of the E2DS file for the calibBD
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_DATE'], value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DATE_NOW'], value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag3)
# get res data in correct format
resdata, hdicts = spirouTHORCA.GenerateResFiles(p, loc, hdict)
# save to file
p = spirouImage.WriteImageMulti(p, resfits, resdata, hdicts=hdicts)
# ----------------------------------------------------------------------
# Update calibDB
# ----------------------------------------------------------------------
if p['QC']:
# set the wave key
keydb = 'WAVE_{0}'.format(p['FIBER'])
# copy wave file to calibDB folder
spirouDB.PutCalibFile(p, wavefits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, wavefitsname, loc['HCHDR'])
# set the hcref key
keydb = 'HCREF_{0}'.format(p['FIBER'])
# copy wave file to calibDB folder
spirouDB.PutCalibFile(p, e2dscopy_filename)
# update the master calib DB file with new key
e2dscopyfits = os.path.split(e2dscopy_filename)[-1]
spirouDB.UpdateCalibMaster(p, keydb, e2dscopyfits, loc['HCHDR'])
# ----------------------------------------------------------------------
# Update header of current files
# ----------------------------------------------------------------------
# only copy over if QC passed
if p['QC']:
rdir = os.path.dirname(wavefits)
# loop around hc files and update header with
for rawhcfile in p['ARG_FILE_NAMES']:
hcfile = os.path.join(rdir, rawhcfile)
raw_infilepath1 = os.path.join(p['ARG_FILE_DIR'], hcfile)
p = spirouImage.UpdateWaveSolutionHC(p, loc, raw_infilepath1)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def main(night_name=None, fpfile=None, hcfiles=None):
"""
cal_WAVE_E2DS.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_DARK_spirou.py [night_directory] [fpfile] [hcfiles]
:param night_name: string or None, the folder within data raw directory
containing files (also reduced directory) i.e.
/data/raw/20170710 would be "20170710" but
/data/raw/AT5/20180409 would be "AT5/20180409"
:param fpfile: string, or None, the FP file to use for
arg_file_names and fitsfilename
(if None assumes arg_file_names was set from run time)
:param hcfiles: string, list or None, the list of HC files to use for
arg_file_names and fitsfilename
(if None assumes arg_file_names was set from run time)
:return ll: dictionary, containing all the local variables defined in
main
"""
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# test files TC2
# night_name = 'AT5/AT5-12/2018-05-29_17-41-44/'
# fpfile = '2279844a_fp_fp_pp_e2dsff_AB.fits'
# hcfiles = ['2279845c_hc_pp_e2dsff_AB.fits']
# test files TC3
# night_name = 'TC3/AT5/AT5-12/2018-07-24_16-17-57/'
# fpfile = '2294108a_pp_e2dsff_AB.fits'
# hcfiles = ['2294115c_pp_e2dsff_AB.fits']
# night_name = 'TC3/AT5/AT5-12/2018-07-25_16-49-50/'
# fpfile = '2294223a_pp_e2dsff_AB.fits'
# hcfiles = ['2294230c_pp_e2dsff_AB.fits']
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
if hcfiles is None or fpfile is None:
names, types = ['fpfile', 'hcfiles'], [str, str]
customargs = spirouStartup.GetCustomFromRuntime(p, [0, 1],
types,
names,
last_multi=True)
else:
customargs = dict(hcfiles=hcfiles, fpfile=fpfile)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsdir='reduced',
mainfitsfile='hcfiles')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, fpfitsfilename = spirouStartup.SingleFileSetup(p, filename=p['FPFILE'])
fiber1 = str(p['FIBER'])
p, hcfilenames = spirouStartup.MultiFileSetup(p, files=p['HCFILES'])
fiber2 = str(p['FIBER'])
# set the hcfilename to the first hcfilenames
hcfitsfilename = hcfilenames[0]
# ----------------------------------------------------------------------
# Once we have checked the e2dsfile we can load calibDB
# ----------------------------------------------------------------------
# as we have custom arguments need to load the calibration database
p = spirouStartup.LoadCalibDB(p)
# ----------------------------------------------------------------------
# Have to check that the fibers match
# ----------------------------------------------------------------------
if fiber1 == fiber2:
p['FIBER'] = fiber1
fsource = __NAME__ + '/main() & spirouStartup.GetFiberType()'
p.set_source('FIBER', fsource)
else:
emsg = 'Fiber not matching for {0} and {1}, should be the same'
eargs = [hcfitsfilename, fpfitsfilename]
WLOG(p, 'error', emsg.format(*eargs))
# set the fiber type
p['FIB_TYP'] = [p['FIBER']]
p.set_source('FIB_TYP', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Read FP and HC files
# ----------------------------------------------------------------------
# read and combine all HC files except the first (fpfitsfilename)
rargs = [p, 'add', hcfitsfilename, hcfilenames[1:]]
p, hcdata, hchdr = spirouImage.ReadImageAndCombine(*rargs)
# read first file (fpfitsfilename)
fpdata, fphdr, _, _ = spirouImage.ReadImage(p, fpfitsfilename)
# TODO: ------------------------------------------------------------
# TODO remove to test NaNs
# TODO: ------------------------------------------------------------
# hcmask = np.isfinite(hcdata)
# fpmask = np.isfinite(fpdata)
# hcdata[~hcmask] = 0.0
# fpdata[~fpmask] = 0.0
# TODO: ------------------------------------------------------------
# add data and hdr to loc
loc = ParamDict()
loc['HCDATA'], loc['HCHDR'] = hcdata, hchdr
loc['FPDATA'], loc['FPHDR'] = fpdata, fphdr
# set the source
sources = ['HCDATA', 'HCHDR']
loc.set_sources(sources, 'spirouImage.ReadImageAndCombine()')
sources = ['FPDATA', 'FPHDR']
loc.set_sources(sources, 'spirouImage.ReadImage()')
# ----------------------------------------------------------------------
# Get basic image properties for reference file
# ----------------------------------------------------------------------
# get sig det value
p = spirouImage.GetSigdet(p, hchdr, name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, hchdr, name='exptime')
# get gain
p = spirouImage.GetGain(p, hchdr, name='gain')
# get acquisition time
p = spirouImage.GetAcqTime(p, hchdr, name='acqtime', kind='julian')
bjdref = p['ACQTIME']
# set sigdet and conad keywords (sigdet is changed later)
p['KW_CCD_SIGDET'][1] = p['SIGDET']
p['KW_CCD_CONAD'][1] = p['GAIN']
# get lamp parameters
p = spirouTHORCA.GetLampParams(p, hchdr)
# get number of orders
# we always get fibre A number because AB is doubled in constants file
loc['NBO'] = p['QC_LOC_NBO_FPALL']['A']
loc.set_source('NBO', __NAME__ + '.main()')
# get number of pixels in x from hcdata size
loc['NBPIX'] = loc['HCDATA'].shape[1]
loc.set_source('NBPIX', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# Read blaze
# ----------------------------------------------------------------------
# get tilts
p, loc['BLAZE'] = spirouImage.ReadBlazeFile(p, hchdr)
loc.set_source('BLAZE', __NAME__ + '/main() + /spirouImage.ReadBlazeFile')
# make copy of blaze (as it's overwritten later)
loc['BLAZE2'] = np.copy(loc['BLAZE'])
# ----------------------------------------------------------------------
# Read wave solution
# ----------------------------------------------------------------------
# wavelength file; we will use the polynomial terms in its header,
# NOT the pixel values that would need to be interpolated
# set source of wave file
wsource = __NAME__ + '/main() + /spirouImage.GetWaveSolution'
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get wave image
wout = spirouImage.GetWaveSolution(p,
hdr=hchdr,
return_wavemap=True,
return_filename=True,
fiber=wave_fiber)
loc['WAVEPARAMS'], loc['WAVE_INIT'], loc['WAVEFILE'], loc['WSOURCE'] = wout
loc.set_sources(['WAVE_INIT', 'WAVEFILE', 'WAVEPARAMS', 'WSOURCE'],
wsource)
poly_wave_sol = loc['WAVEPARAMS']
# ----------------------------------------------------------------------
# Check that wave parameters are consistent with "ic_ll_degr_fit"
# ----------------------------------------------------------------------
loc = spirouImage.CheckWaveSolConsistency(p, loc)
# ----------------------------------------------------------------------
# Read UNe solution
# ----------------------------------------------------------------------
wave_u_ne, amp_u_ne = spirouImage.ReadLineList(p)
loc['LL_LINE'], loc['AMPL_LINE'] = wave_u_ne, amp_u_ne
source = __NAME__ + '.main() + spirouImage.ReadLineList()'
loc.set_sources(['ll_line', 'ampl_line'], source)
# ----------------------------------------------------------------------
# Generate wave map from wave solution
# ----------------------------------------------------------------------
loc = spirouWAVE.generate_wave_map(p, loc)
# ----------------------------------------------------------------------
# Find Gaussian Peaks in HC spectrum
# ----------------------------------------------------------------------
loc = spirouWAVE.find_hc_gauss_peaks(p, loc)
# ----------------------------------------------------------------------
# Start plotting session
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive plot
sPlt.start_interactive_session(p)
# ----------------------------------------------------------------------
# Fit Gaussian peaks (in triplets) to
# ----------------------------------------------------------------------
loc = spirouWAVE.fit_gaussian_triplets(p, loc)
# ----------------------------------------------------------------------
# Generate Resolution map and line profiles
# ----------------------------------------------------------------------
# log progress
wmsg = 'Generating resolution map and '
# generate resolution map
loc = spirouWAVE.generate_resolution_map(p, loc)
# map line profile map
if p['DRS_PLOT'] > 0:
sPlt.wave_ea_plot_line_profiles(p, loc)
# ----------------------------------------------------------------------
# End plotting session
# ----------------------------------------------------------------------
# end interactive session
if p['DRS_PLOT'] > 0:
sPlt.end_interactive_session(p)
# ----------------------------------------------------------------------
# Set up all_lines storage
# ----------------------------------------------------------------------
# initialise up all_lines storage
all_lines_1 = []
# get parameters from p
n_ord_start = p['IC_HC_N_ORD_START_2']
n_ord_final = p['IC_HC_N_ORD_FINAL_2']
pixel_shift_inter = p['PIXEL_SHIFT_INTER']
pixel_shift_slope = p['PIXEL_SHIFT_SLOPE']
# get values from loc
xgau = np.array(loc['XGAU_T'])
dv = np.array(loc['DV_T'])
fit_per_order = np.array(loc['POLY_WAVE_SOL'])
ew = np.array(loc['EW_T'])
peak = np.array(loc['PEAK_T'])
amp_catalog = np.array(loc['AMP_CATALOG'])
wave_catalog = np.array(loc['WAVE_CATALOG'])
ord_t = np.array(loc['ORD_T'])
# loop through orders
for iord in range(n_ord_start, n_ord_final):
# keep relevant lines
# -> right order
# -> finite dv
gg = (ord_t == iord) & (np.isfinite(dv))
nlines = np.nansum(gg)
# put lines into ALL_LINES structure
# reminder:
# gparams[0] = output wavelengths
# gparams[1] = output sigma(gauss fit width)
# gparams[2] = output amplitude(gauss fit)
# gparams[3] = difference in input / output wavelength
# gparams[4] = input amplitudes
# gparams[5] = output pixel positions
# gparams[6] = output pixel sigma width (gauss fit width in pixels)
# gparams[7] = output weights for the pixel position
chebval = np.polynomial.chebyshev.chebval
# dummy array for weights
test = np.ones(np.shape(xgau[gg]), 'd') * 1e4
# get the final wavelength value for each peak in order
output_wave_1 = np.polyval(fit_per_order[iord][::-1], xgau[gg])
# output_wave_1 = chebval(xgau[gg], fit_per_order[iord])
# convert the pixel equivalent width to wavelength units
xgau_ew_ini = xgau[gg] - ew[gg] / 2
xgau_ew_fin = xgau[gg] + ew[gg] / 2
ew_ll_ini = np.polyval(fit_per_order[iord, :], xgau_ew_ini)
ew_ll_fin = np.polyval(fit_per_order[iord, :], xgau_ew_fin)
# ew_ll_ini = chebval(xgau_ew_ini, fit_per_order[iord])
# ew_ll_fin = chebval(xgau_ew_fin, fit_per_order[iord])
ew_ll = ew_ll_fin - ew_ll_ini
# put all lines in the order into array
gau_params = np.column_stack(
(output_wave_1, ew_ll, peak[gg], wave_catalog[gg] - output_wave_1,
amp_catalog[gg], xgau[gg], ew[gg], test))
# append the array for the order into a list
all_lines_1.append(gau_params)
# save dv in km/s and auxiliary order number
# res_1 = np.concatenate((res_1,2.997e5*(input_wave - output_wave_1)/
# output_wave_1))
# ord_save = np.concatenate((ord_save, test*iord))
# add to loc
loc['ALL_LINES_1'] = all_lines_1
loc['LL_PARAM_1'] = np.array(fit_per_order)
loc['LL_OUT_1'] = np.array(loc['WAVE_MAP2'])
loc.set_sources(['ALL_LINES_1', 'LL_PARAM_1'], __NAME__ + '/main()')
# For compatibility w/already defined functions, I need to save
# here all_lines_2
all_lines_2 = list(all_lines_1)
loc['ALL_LINES_2'] = all_lines_2
# loc['LL_PARAM_2'] = np.fliplr(fit_per_order)
# loc['LL_OUT_2'] = np.array(loc['WAVE_MAP2'])
# loc.set_sources(['ALL_LINES_2', 'LL_PARAM_2'], __NAME__ + '/main()')
# ------------------------------------------------------------------
# Littrow test
# ------------------------------------------------------------------
start = p['IC_LITTROW_ORDER_INIT_1']
end = p['IC_LITTROW_ORDER_FINAL_1']
# calculate echelle orders
o_orders = np.arange(start, end)
echelle_order = p['IC_HC_T_ORDER_START'] - o_orders
loc['ECHELLE_ORDERS'] = echelle_order
loc.set_source('ECHELLE_ORDERS', __NAME__ + '/main()')
# reset Littrow fit degree
p['IC_LITTROW_FIT_DEG_1'] = 7
# Do Littrow check
ckwargs = dict(ll=loc['LL_OUT_1'][start:end, :], iteration=1, log=True)
loc = spirouTHORCA.CalcLittrowSolution(p, loc, **ckwargs)
# Plot wave solution littrow check
if p['DRS_PLOT'] > 0:
# plot littrow x pixels against fitted wavelength solution
sPlt.wave_littrow_check_plot(p, loc, iteration=1)
# ------------------------------------------------------------------
# extrapolate Littrow solution
# ------------------------------------------------------------------
ekwargs = dict(ll=loc['LL_OUT_1'], iteration=1)
loc = spirouTHORCA.ExtrapolateLittrowSolution(p, loc, **ekwargs)
# ------------------------------------------------------------------
# Plot littrow solution
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# plot littrow x pixels against fitted wavelength solution
sPlt.wave_littrow_extrap_plot(p, loc, iteration=1)
# ------------------------------------------------------------------
# Incorporate FP into solution
# ------------------------------------------------------------------
# Copy LL_OUT_1 and LL_PARAM_1 into new constants (for FP integration)
loc['LITTROW_EXTRAP_SOL_1'] = np.array(loc['LL_OUT_1'])
loc['LITTROW_EXTRAP_PARAM_1'] = np.array(loc['LL_PARAM_1'])
# only use FP if switched on in constants file
if p['IC_WAVE_USE_FP']:
# ------------------------------------------------------------------
# Find FP lines
# ------------------------------------------------------------------
# print message to screen
wmsg = 'Identification of lines in reference file: {0}'
WLOG(p, '', wmsg.format(fpfile))
# ------------------------------------------------------------------
# Get the FP solution
# ------------------------------------------------------------------
loc = spirouTHORCA.FPWaveSolutionNew(p, loc)
# ------------------------------------------------------------------
# FP solution plots
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# Plot the FP extracted spectrum against wavelength solution
sPlt.wave_plot_final_fp_order(p, loc, iteration=1)
# Plot the measured FP cavity width offset against line number
sPlt.wave_local_width_offset_plot(p, loc)
# Plot the FP line wavelength residuals
sPlt.wave_fp_wavelength_residuals(p, loc)
# ------------------------------------------------------------------
# Create new wavelength solution
# ------------------------------------------------------------------
# TODO: Melissa fault - fix later
p['IC_HC_N_ORD_START_2'] = min(p['IC_HC_N_ORD_START_2'],
p['IC_FP_N_ORD_START'])
p['IC_HC_N_ORD_FINAL_2'] = max(p['IC_HC_N_ORD_FINAL_2'],
p['IC_FP_N_ORD_FINAL'])
start = p['IC_HC_N_ORD_START_2']
end = p['IC_HC_N_ORD_FINAL_2']
# recalculate echelle orders for Fit1DSolution
o_orders = np.arange(start, end)
echelle_order = p['IC_HC_T_ORDER_START'] - o_orders
loc['ECHELLE_ORDERS'] = echelle_order
loc.set_source('ECHELLE_ORDERS', __NAME__ + '/main()')
# select the orders to fit
lls = loc['LITTROW_EXTRAP_SOL_1'][start:end]
loc = spirouTHORCA.Fit1DSolution(p, loc, lls, iteration=2)
# from here, LL_OUT_2 wil be 0-47
# ------------------------------------------------------------------
# Repeat Littrow test
# ------------------------------------------------------------------
start = p['IC_LITTROW_ORDER_INIT_2']
end = p['IC_LITTROW_ORDER_FINAL_2']
# recalculate echelle orders for Littrow check
o_orders = np.arange(start, end)
echelle_order = p['IC_HC_T_ORDER_START'] - o_orders
loc['ECHELLE_ORDERS'] = echelle_order
loc.set_source('ECHELLE_ORDERS', __NAME__ + '/main()')
# Do Littrow check
ckwargs = dict(ll=loc['LL_OUT_2'][start:end, :], iteration=2, log=True)
loc = spirouTHORCA.CalcLittrowSolution(p, loc, **ckwargs)
# Plot wave solution littrow check
if p['DRS_PLOT'] > 0:
# plot littrow x pixels against fitted wavelength solution
sPlt.wave_littrow_check_plot(p, loc, iteration=2)
# ------------------------------------------------------------------
# extrapolate Littrow solution
# ------------------------------------------------------------------
ekwargs = dict(ll=loc['LL_OUT_2'], iteration=2)
loc = spirouTHORCA.ExtrapolateLittrowSolution(p, loc, **ekwargs)
# ------------------------------------------------------------------
# Plot littrow solution
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# plot littrow x pixels against fitted wavelength solution
sPlt.wave_littrow_extrap_plot(p, loc, iteration=2)
# ------------------------------------------------------------------
# Join 0-47 and 47-49 solutions
# ------------------------------------------------------------------
loc = spirouTHORCA.JoinOrders(p, loc)
# ------------------------------------------------------------------
# Plot single order, wavelength-calibrated, with found lines
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
sPlt.wave_ea_plot_single_order(p, loc)
# ----------------------------------------------------------------------
# Do correlation on FP spectra
# ----------------------------------------------------------------------
# ------------------------------------------------------------------
# Compute photon noise uncertainty for FP
# ------------------------------------------------------------------
# set up the arguments for DeltaVrms2D
dargs = [loc['FPDATA'], loc['LL_FINAL']]
dkwargs = dict(sigdet=p['IC_DRIFT_NOISE'],
size=p['IC_DRIFT_BOXSIZE'],
threshold=p['IC_DRIFT_MAXFLUX'])
# run DeltaVrms2D
dvrmsref, wmeanref = spirouRV.DeltaVrms2D(*dargs, **dkwargs)
# save to loc
loc['DVRMSREF'], loc['WMEANREF'] = dvrmsref, wmeanref
loc.set_sources(['dvrmsref', 'wmeanref'], __NAME__ + '/main()()')
# log the estimated RV uncertainty
wmsg = 'On fiber {0} estimated RV uncertainty on spectrum is {1:.3f} m/s'
WLOG(p, 'info', wmsg.format(p['FIBER'], wmeanref))
# Use CCF Mask function with drift constants
p['CCF_MASK'] = p['DRIFT_CCF_MASK']
p['TARGET_RV'] = p['DRIFT_TARGET_RV']
p['CCF_WIDTH'] = p['DRIFT_CCF_WIDTH']
p['CCF_STEP'] = p['DRIFT_CCF_STEP']
p['RVMIN'] = p['TARGET_RV'] - p['CCF_WIDTH']
p['RVMAX'] = p['TARGET_RV'] + p['CCF_WIDTH'] + p['CCF_STEP']
# get the CCF mask from file (check location of mask)
loc = spirouRV.GetCCFMask(p, loc)
# TODO Check why Blaze makes bugs in correlbin
loc['BLAZE'] = np.ones((loc['NBO'], loc['NBPIX']))
# set sources
# loc.set_sources(['flat', 'blaze'], __NAME__ + '/main()')
loc.set_source('blaze', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Do correlation on FP
# ----------------------------------------------------------------------
# calculate and fit the CCF
loc['E2DSFF'] = np.array(loc['FPDATA'])
loc.set_source('E2DSFF', __NAME__ + '/main()')
p['CCF_FIT_TYPE'] = 1
loc['BERV'] = 0.0
loc['BERV_MAX'] = 0.0
loc['BJD'] = 0.0
# run the RV coravelation function with these parameters
loc['WAVE_LL'] = np.array(loc['LL_FINAL'])
loc['PARAM_LL'] = np.array(loc['LL_PARAM_FINAL'])
loc = spirouRV.Coravelation(p, loc)
# ----------------------------------------------------------------------
# Update the Correlation stats with values using fiber C (FP) drift
# ----------------------------------------------------------------------
# get the maximum number of orders to use
nbmax = p['CCF_NUM_ORDERS_MAX']
# get the average ccf
loc['AVERAGE_CCF'] = np.nansum(loc['CCF'][:nbmax], axis=0)
# normalize the average ccf
normalized_ccf = loc['AVERAGE_CCF'] / np.nanmax(loc['AVERAGE_CCF'])
# get the fit for the normalized average ccf
ccf_res, ccf_fit = spirouRV.FitCCF(p,
loc['RV_CCF'],
normalized_ccf,
fit_type=1)
loc['CCF_RES'] = ccf_res
loc['CCF_FIT'] = ccf_fit
# get the max cpp
loc['MAXCPP'] = np.nansum(loc['CCF_MAX']) / np.nansum(
loc['PIX_PASSED_ALL'])
# get the RV value from the normalised average ccf fit center location
loc['RV'] = float(ccf_res[1])
# get the contrast (ccf fit amplitude)
loc['CONTRAST'] = np.abs(100 * ccf_res[0])
# get the FWHM value
loc['FWHM'] = ccf_res[2] * spirouCore.spirouMath.fwhm()
# set the source
keys = [
'AVERAGE_CCF', 'MAXCPP', 'RV', 'CONTRAST', 'FWHM', 'CCF_RES', 'CCF_FIT'
]
loc.set_sources(keys, __NAME__ + '/main()')
# ----------------------------------------------------------------------
# log the stats
wmsg = ('FP Correlation: C={0:.1f}[%] DRIFT={1:.5f}[km/s] '
'FWHM={2:.4f}[km/s] maxcpp={3:.1f}')
wargs = [loc['CONTRAST'], float(ccf_res[1]), loc['FWHM'], loc['MAXCPP']]
WLOG(p, 'info', wmsg.format(*wargs))
# ----------------------------------------------------------------------
# rv ccf plot
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# Plot rv vs ccf (and rv vs ccf_fit)
p['OBJNAME'] = 'FP'
sPlt.ccf_rv_ccf_plot(p, loc['RV_CCF'], normalized_ccf, ccf_fit)
# TODO : Add QC of the FP CCF
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# get parameters ffrom p
p['QC_RMS_LITTROW_MAX'] = p['QC_HC_RMS_LITTROW_MAX']
p['QC_DEV_LITTROW_MAX'] = p['QC_HC_DEV_LITTROW_MAX']
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# quality control on sigma clip (sig1 > qc_hc_wave_sigma_max
if loc['SIG1'] > p['QC_HC_WAVE_SIGMA_MAX']:
fmsg = 'Sigma too high ({0:.5f} > {1:.5f})'
fail_msg.append(fmsg.format(loc['SIG1'], p['QC_HC_WAVE_SIGMA_MAX']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(loc['SIG1'])
qc_names.append('SIG1')
qc_logic.append('SIG1 > {0:.2f}'.format(p['QC_HC_WAVE_SIGMA_MAX']))
# ----------------------------------------------------------------------
# check the difference between consecutive orders is always positive
# get the differences
wave_diff = loc['LL_FINAL'][1:] - loc['LL_FINAL'][:-1]
if np.min(wave_diff) < 0:
fmsg = 'Negative wavelength difference between orders'
fail_msg.append(fmsg)
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(np.min(wave_diff))
qc_names.append('MIN WAVE DIFF')
qc_logic.append('MIN WAVE DIFF < 0')
# ----------------------------------------------------------------------
# check for infinites and NaNs in mean residuals from fit
if ~np.isfinite(loc['X_MEAN_2']):
# add failed message to the fail message list
fmsg = 'NaN or Inf in X_MEAN_2'
fail_msg.append(fmsg)
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(loc['X_MEAN_2'])
qc_names.append('X_MEAN_2')
qc_logic.append('X_MEAN_2 not finite')
# ----------------------------------------------------------------------
# iterate through Littrow test cut values
lit_it = 2
# checks every other value
# TODO: This QC check (or set of QC checks needs re-writing it is
# TODO: nearly impossible to understand
for x_it in range(1, len(loc['X_CUT_POINTS_' + str(lit_it)]), 2):
# get x cut point
x_cut_point = loc['X_CUT_POINTS_' + str(lit_it)][x_it]
# get the sigma for this cut point
sig_littrow = loc['LITTROW_SIG_' + str(lit_it)][x_it]
# get the abs min and max dev littrow values
min_littrow = abs(loc['LITTROW_MINDEV_' + str(lit_it)][x_it])
max_littrow = abs(loc['LITTROW_MAXDEV_' + str(lit_it)][x_it])
# get the corresponding order
min_littrow_ord = loc['LITTROW_MINDEVORD_' + str(lit_it)][x_it]
max_littrow_ord = loc['LITTROW_MAXDEVORD_' + str(lit_it)][x_it]
# check if sig littrow is above maximum
rms_littrow_max = p['QC_RMS_LITTROW_MAX']
dev_littrow_max = p['QC_DEV_LITTROW_MAX']
if sig_littrow > rms_littrow_max:
fmsg = ('Littrow test (x={0}) failed (sig littrow = '
'{1:.2f} > {2:.2f})')
fargs = [x_cut_point, sig_littrow, rms_littrow_max]
fail_msg.append(fmsg.format(*fargs))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(sig_littrow)
qc_names.append('sig_littrow')
qc_logic.append('sig_littrow > {0:.2f}'.format(rms_littrow_max))
# ----------------------------------------------------------------------
# check if min/max littrow is out of bounds
if np.max([max_littrow, min_littrow]) > dev_littrow_max:
fmsg = ('Littrow test (x={0}) failed (min|max dev = '
'{1:.2f}|{2:.2f} > {3:.2f} for order {4}|{5})')
fargs = [
x_cut_point, min_littrow, max_littrow, dev_littrow_max,
min_littrow_ord, max_littrow_ord
]
fail_msg.append(fmsg.format(*fargs))
passed = False
qc_pass.append(0)
# TODO: Should this be the QC header values?
# TODO: it does not change the outcome of QC (i.e. passed=False)
# TODO: So what is the point?
# if sig was out of bounds, recalculate
if sig_littrow > rms_littrow_max:
# conditions
check1 = min_littrow > dev_littrow_max
check2 = max_littrow > dev_littrow_max
# get the residuals
respix = loc['LITTROW_YY_' + str(lit_it)][x_it]
# check if both are out of bounds
if check1 and check2:
# remove respective orders
worst_order = (min_littrow_ord, max_littrow_ord)
respix_2 = np.delete(respix, worst_order)
redo_sigma = True
# check if min is out of bounds
elif check1:
# remove respective order
worst_order = min_littrow_ord
respix_2 = np.delete(respix, worst_order)
redo_sigma = True
# check if max is out of bounds
elif check2:
# remove respective order
worst_order = max_littrow_ord
respix_2 = np.delete(respix, max_littrow_ord)
redo_sigma = True
# else do not recalculate sigma
else:
redo_sigma, respix_2, worst_order = False, None, None
wmsg = 'No outlying orders, sig littrow not recalculated'
fail_msg.append(wmsg.format())
# if outlying order, recalculate stats
if redo_sigma:
mean = np.nansum(respix_2) / len(respix_2)
mean2 = np.nansum(respix_2**2) / len(respix_2)
rms = np.sqrt(mean2 - mean**2)
if rms > rms_littrow_max:
fmsg = ('Littrow test (x={0}) failed (sig littrow = '
'{1:.2f} > {2:.2f} removing order {3})')
fargs = [
x_cut_point, rms, rms_littrow_max, worst_order
]
fail_msg.append(fmsg.format(*fargs))
else:
wargs = [
x_cut_point, rms, rms_littrow_max, worst_order
]
wmsg = ('Littrow test (x={0}) passed (sig littrow = '
'{1:.2f} > {2:.2f} removing order {3})')
fail_msg.append(wmsg.format(*wargs))
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(np.max([max_littrow, min_littrow]))
qc_names.append('max or min littrow')
qc_logic.append('max or min littrow > {0:.2f}'
''.format(dev_littrow_max))
# finally log the failed messages and set QC = 1 if we pass the
# quality control QC = 0 if we fail quality control
if passed:
WLOG(p, 'info', 'QUALITY CONTROL SUCCESSFUL - Well Done -')
p['QC'] = 1
p.set_source('QC', __NAME__ + '/main()')
else:
for farg in fail_msg:
wmsg = 'QUALITY CONTROL FAILED: {0}'
WLOG(p, 'warning', wmsg.format(farg))
p['QC'] = 0
p.set_source('QC', __NAME__ + '/main()')
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ------------------------------------------------------------------
# archive result in e2ds spectra
# ------------------------------------------------------------------
# get raw input file name(s)
raw_infiles1 = []
for hcfile in p['HCFILES']:
raw_infiles1.append(os.path.basename(hcfile))
raw_infile2 = os.path.basename(p['FPFILE'])
# get wave filename
wavefits, tag1 = spirouConfig.Constants.WAVE_FILE_EA_2(p)
wavefitsname = os.path.split(wavefits)[-1]
# log progress
wargs = [p['FIBER'], wavefits]
wmsg = 'Write wavelength solution for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(*wargs))
# write solution to fitsfilename header
# copy original keys
hdict = spirouImage.CopyOriginalKeys(loc['HCHDR'])
# add version number
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_DATE'], value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DATE_NOW'], value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_PID'], value=p['PID'])
# set the input files
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBLAZE'], value=p['BLAZFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBWAVE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='fpfile',
values=p['FPFILE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE2'],
dim1name='hcfile',
values=p['HCFILES'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add wave solution date
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME1'],
value=p['MAX_TIME_HUMAN'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME2'],
value=p['MAX_TIME_UNIX'])
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVE_CODE'], value=__NAME__)
# add number of orders
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_ORD_N'],
value=loc['LL_PARAM_FINAL'].shape[0])
# add degree of fit
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_LL_DEG'],
value=loc['LL_PARAM_FINAL'].shape[1] - 1)
# add wave solution
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_WAVE_PARAM'],
values=loc['LL_PARAM_FINAL'])
# add FP CCF drift
# target RV and width
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_TARG_RV'],
value=p['TARGET_RV'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_WIDTH'],
value=p['CCF_WIDTH'])
# the rv step
# rvstep = np.abs(loc['RV_CCF'][0] - loc['RV_CCF'][1])
# hdict = spirouImage.AddKey(p, hdict, p['KW_CCF_CDELT'], value=rvstep)
hdict = spirouImage.AddKey(p, hdict, p['KW_WFP_STEP'], value=p['CCF_STEP'])
# add ccf stats
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_DRIFT'],
value=loc['CCF_RES'][1])
hdict = spirouImage.AddKey(p, hdict, p['KW_WFP_FWHM'], value=loc['FWHM'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_CONTRAST'],
value=loc['CONTRAST'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_MAXCPP'],
value=loc['MAXCPP'])
hdict = spirouImage.AddKey(p, hdict, p['KW_WFP_MASK'], value=p['CCF_MASK'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_LINES'],
value=np.nansum(loc['TOT_LINE']))
# write the wave "spectrum"
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
p = spirouImage.WriteImage(p, wavefits, loc['LL_FINAL'], hdict)
# get filename for E2DS calibDB copy of FITSFILENAME
e2dscopy_filename = spirouConfig.Constants.WAVE_E2DS_COPY(p)[0]
wargs = [p['FIBER'], os.path.split(e2dscopy_filename)[-1]]
wmsg = 'Write reference E2DS spectra for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(*wargs))
# make a copy of the E2DS file for the calibBD
p = spirouImage.WriteImage(p, e2dscopy_filename, loc['HCDATA'], hdict)
# only copy over if QC passed
if p['QC']:
# loop around hc files and update header with
for hcfile in p['HCFILES']:
raw_infilepath1 = os.path.join(p['ARG_FILE_DIR'], hcfile)
p = spirouImage.UpdateWaveSolution(p, loc, raw_infilepath1)
# update fp file
raw_infilepath2 = os.path.join(p['ARG_FILE_DIR'], raw_infile2)
p = spirouImage.UpdateWaveSolution(p, loc, raw_infilepath2)
# ------------------------------------------------------------------
# Save to result table
# ------------------------------------------------------------------
# calculate stats for table
final_mean = 1000 * loc['X_MEAN_2']
final_var = 1000 * loc['X_VAR_2']
num_lines = int(np.nansum(loc['X_ITER_2'][:, 2])) # loc['X_ITER_2']
err = 1000 * np.sqrt(loc['X_VAR_2'] / num_lines)
sig_littrow = 1000 * np.array(loc['LITTROW_SIG_' + str(lit_it)])
# construct filename
wavetbl = spirouConfig.Constants.WAVE_TBL_FILE_EA(p)
wavetblname = os.path.basename(wavetbl)
# construct and write table
columnnames = [
'night_name', 'file_name', 'fiber', 'mean', 'rms', 'N_lines', 'err',
'rms_L500', 'rms_L1000', 'rms_L1500', 'rms_L2000', 'rms_L2500',
'rms_L3000', 'rms_L3500'
]
columnformats = [
'{:20s}', '{:30s}', '{:3s}', '{:7.4f}', '{:6.2f}', '{:3d}', '{:6.3f}',
'{:6.2f}', '{:6.2f}', '{:6.2f}', '{:6.2f}', '{:6.2f}', '{:6.2f}',
'{:6.2f}'
]
columnvalues = [[p['ARG_NIGHT_NAME']], [p['ARG_FILE_NAMES'][0]],
[p['FIBER']], [final_mean], [final_var],
[num_lines], [err], [sig_littrow[0]], [sig_littrow[1]],
[sig_littrow[2]], [sig_littrow[3]], [sig_littrow[4]],
[sig_littrow[5]], [sig_littrow[6]]]
# make table
table = spirouImage.MakeTable(p,
columns=columnnames,
values=columnvalues,
formats=columnformats)
# merge table
wmsg = 'Global result summary saved in {0}'
WLOG(p, '', wmsg.format(wavetblname))
spirouImage.MergeTable(p, table, wavetbl, fmt='ascii.rst')
# ----------------------------------------------------------------------
# Save resolution and line profiles to file
# ----------------------------------------------------------------------
raw_infile = os.path.basename(p['FITSFILENAME'])
# get wave filename
resfits, tag3 = spirouConfig.Constants.WAVE_RES_FILE_EA(p)
resfitsname = os.path.basename(resfits)
WLOG(p, '', 'Saving wave resmap to {0}'.format(resfitsname))
# make a copy of the E2DS file for the calibBD
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_DATE'], value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DATE_NOW'], value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag3)
# get res data in correct format
resdata, hdicts = spirouTHORCA.GenerateResFiles(p, loc, hdict)
# save to file
p = spirouImage.WriteImageMulti(p, resfits, resdata, hdicts=hdicts)
# ------------------------------------------------------------------
# Save line list table file
# ------------------------------------------------------------------
# construct filename
# TODO proper column values
wavelltbl = spirouConfig.Constants.WAVE_LINE_FILE_EA(p)
wavelltblname = os.path.split(wavelltbl)[-1]
# construct and write table
columnnames = ['order', 'll', 'dv', 'w', 'xi', 'xo', 'dvdx']
columnformats = [
'{:.0f}', '{:12.4f}', '{:13.5f}', '{:12.4f}', '{:12.4f}', '{:12.4f}',
'{:8.4f}'
]
columnvalues = []
# construct column values (flatten over orders)
for it in range(len(loc['X_DETAILS_2'])):
for jt in range(len(loc['X_DETAILS_2'][it][0])):
row = [
float(it), loc['X_DETAILS_2'][it][0][jt],
loc['LL_DETAILS_2'][it][0][jt], loc['X_DETAILS_2'][it][3][jt],
loc['X_DETAILS_2'][it][1][jt], loc['X_DETAILS_2'][it][2][jt],
loc['SCALE_2'][it][jt]
]
columnvalues.append(row)
# log saving
wmsg = 'List of lines used saved in {0}'
WLOG(p, '', wmsg.format(wavelltblname))
# make table
columnvalues = np.array(columnvalues).T
table = spirouImage.MakeTable(p,
columns=columnnames,
values=columnvalues,
formats=columnformats)
# write table
spirouImage.WriteTable(p, table, wavelltbl, fmt='ascii.rst')
# ------------------------------------------------------------------
# Move to calibDB and update calibDB
# ------------------------------------------------------------------
if p['QC']:
# set the wave key
keydb = 'WAVE_{0}'.format(p['FIBER'])
# copy wave file to calibDB folder
spirouDB.PutCalibFile(p, wavefits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, wavefitsname, loc['HCHDR'])
# set the hcref key
keydb = 'HCREF_{0}'.format(p['FIBER'])
# copy wave file to calibDB folder
spirouDB.PutCalibFile(p, e2dscopy_filename)
# update the master calib DB file with new key
e2dscopyfits = os.path.split(e2dscopy_filename)[-1]
spirouDB.UpdateCalibMaster(p, keydb, e2dscopyfits, loc['HCHDR'])
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return p and loc
return dict(locals())
def main(night_name=None, flatfile=None):
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
# deal with arguments being None (i.e. get from sys.argv)
name, lname = ['flatfile'], ['Reference file']
req, call, call_priority = [True], [flatfile], [True]
# now get custom arguments
customargs = spirouStartup.GetCustomFromRuntime(p, [0], [str], name, req,
call, call_priority, lname)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsfile='flatfile')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, reffile = spirouStartup.SingleFileSetup(p, filename=p['FLATFILE'])
# ----------------------------------------------------------------------
# Once we have checked the e2dsfile we can load calibDB
# ----------------------------------------------------------------------
# as we have custom arguments need to load the calibration database
p = spirouStartup.LoadCalibDB(p)
# ----------------------------------------------------------------------
# Get the required fiber type from the constants file
# ----------------------------------------------------------------------
# get the fiber type (set to AB)
p['FIBER'] = p['EM_FIB_TYPE']
p['FIBER_TYPES'] = [p['EM_FIB_TYPE']]
# ----------------------------------------------------------------------
# Read flat image file
# ----------------------------------------------------------------------
# read the image data (for the header only)
image, hdr, ny, nx = spirouImage.ReadData(p, reffile)
# ----------------------------------------------------------------------
# fix for un-preprocessed files
# ----------------------------------------------------------------------
image = spirouImage.FixNonPreProcess(p, image)
# ----------------------------------------------------------------------
# Get basic image properties
# ----------------------------------------------------------------------
# create loc
loc = ParamDict()
# get sig det value
p = spirouImage.GetSigdet(p, hdr, name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, hdr, name='exptime')
# get gain
p = spirouImage.GetGain(p, hdr, name='gain')
# ----------------------------------------------------------------------
# Resize flat image
# ----------------------------------------------------------------------
# rotate the image and convert from ADU/s to e-
image2 = spirouImage.ConvertToE(spirouImage.FlipImage(p, image), p=p)
# convert NaN to zeros
image2 = np.where(~np.isfinite(image2), np.zeros_like(image2), image2)
# resize image
bkwargs = dict(xlow=p['IC_CCDX_LOW'],
xhigh=p['IC_CCDX_HIGH'],
ylow=p['IC_CCDY_LOW'],
yhigh=p['IC_CCDY_HIGH'],
getshape=False)
image2 = spirouImage.ResizeImage(p, image2, **bkwargs)
# save flat to to loc and set source
loc['IMAGE'] = image2
loc.set_sources(['image'], __NAME__ + '/main()')
# log change in data size
wmsg = 'Image format changed to {0}x{1}'
WLOG(p, '', wmsg.format(*image2.shape))
# ----------------------------------------------------------------------
# Read shape or tilt slit angle
# ----------------------------------------------------------------------
# set source of tilt file
tsource = __NAME__ + '/main() + /spirouImage.ReadTiltFile'
if p['IC_EXTRACT_TYPE'] in EXTRACT_SHAPE_TYPES:
# log progress
WLOG(p, '', 'Debananafying (straightening) image')
# get the shape map
p, loc['SHAPE'] = spirouImage.ReadShapeMap(p, hdr)
loc.set_source('SHAPE', tsource)
else:
# get tilts
p, loc['TILT'] = spirouImage.ReadTiltFile(p, hdr)
loc.set_source('TILT', tsource)
# ----------------------------------------------------------------------
# Read blaze
# ----------------------------------------------------------------------
# get tilts
p, loc['BLAZE'] = spirouImage.ReadBlazeFile(p, hdr)
loc.set_source('BLAZE', __NAME__ + '/main() + /spirouImage.ReadBlazeFile')
# set number of orders from blaze file
loc['NBO'] = loc['BLAZE'].shape[0]
loc.set_source('NBO', __NAME__ + '/main()')
# ------------------------------------------------------------------
# Read wavelength solution
# ------------------------------------------------------------------
# set source of wave file
wsource = __NAME__ + '/main() + /spirouImage.GetWaveSolution'
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get wave image
wout = spirouImage.GetWaveSolution(p,
hdr=hdr,
return_wavemap=True,
return_filename=True,
fiber=wave_fiber)
loc['WAVEPARAMS'], loc['WAVE'], loc['WAVEFILE'], loc['WSOURCE'] = wout
loc.set_sources(['WAVEPARAMS', 'WAVE', 'WAVEFILE', 'WSOURCE'], wsource)
# ------------------------------------------------------------------
# Get localisation coefficients
# ------------------------------------------------------------------
# storage for fiber parameters
loc['ALL_ACC'] = OrderedDict()
loc['ALL_ASS'] = OrderedDict()
# get this fibers parameters
for fiber in p['FIBER_TYPES']:
p = spirouImage.FiberParams(p, fiber, merge=True)
# get localisation fit coefficients
p, loc = spirouLOCOR.GetCoeffs(p, hdr, loc=loc)
# save all fibers
loc['ALL_ACC'][fiber] = loc['ACC']
loc['ALL_ASS'][fiber] = loc['ASS']
# ------------------------------------------------------------------
# Get telluric and telluric mask and add to loc
# ------------------------------------------------------------------
# log process
wmsg = 'Loading telluric model and locating "good" tranmission'
WLOG(p, '', wmsg)
# load telluric and get mask (add to loc)
loc = spirouExM.get_telluric(p, loc)
# ------------------------------------------------------------------
# Make 2D map of orders
# ------------------------------------------------------------------
# log progress
WLOG(p, '', 'Making 2D map of order locations')
# make the 2D wave-image
loc = spirouExM.order_profile(p, loc)
# ------------------------------------------------------------------
# Make 2D map of wavelengths accounting for shape / tilt
# ------------------------------------------------------------------
# log progress
WLOG(p, '', 'Mapping pixels on to wavelength grid')
# make the 2D map of wavelength
loc = spirouExM.create_wavelength_image(p, loc)
# ------------------------------------------------------------------
# Use spectra wavelength to create 2D image from wave-image
# ------------------------------------------------------------------
if p['EM_SAVE_MASK_MAP'] or p['EM_SAVE_TELL_SPEC']:
# log progress
WLOG(p, '', 'Creating image from wave-image interpolation')
# create image from waveimage
wkwargs = dict(x=loc['TELL_X'], y=loc['TELL_Y'])
loc = spirouExM.create_image_from_waveimage(loc, **wkwargs)
else:
loc['SPE'] = np.zeros_like(image2).astype(float)
# ------------------------------------------------------------------
# Create 2D mask (min to max lambda + transmission threshold)
# ------------------------------------------------------------------
if p['EM_SAVE_MASK_MAP']:
# log progress
WLOG(p, '', 'Creating wavelength/tranmission mask')
# create mask
loc = spirouExM.create_mask(p, loc)
else:
loc['TELL_MASK_2D'] = np.zeros_like(image2).astype(bool)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# TODO: Needs doing
# finally log the failed messages and set QC = 1 if we pass the
# quality control QC = 0 if we fail quality control
if passed:
WLOG(p, 'info', 'QUALITY CONTROL SUCCESSFUL - Well Done -')
p['QC'] = 1
p.set_source('QC', __NAME__ + '/main()')
else:
for farg in fail_msg:
wmsg = 'QUALITY CONTROL FAILED: {0}'
WLOG(p, 'warning', wmsg.format(farg))
p['QC'] = 0
p.set_source('QC', __NAME__ + '/main()')
# add to qc header lists
qc_values.append('None')
qc_names.append('None')
qc_logic.append('None')
qc_pass.append(1)
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ------------------------------------------------------------------
# Construct parameters for header
# ------------------------------------------------------------------
hdict = OrderedDict()
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_DATE'], value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DATE_NOW'], value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_PID'], value=p['PID'])
# set the input files
if loc['SHAPE'] is not None:
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBSHAPE'],
value=p['SHAPFILE'])
else:
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBTILT'],
value=p['TILTFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBLAZE'], value=p['BLAZFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBLOCO'], value=p['LOCOFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBWAVE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='file',
values=p['FLATFILE'])
# add name of the TAPAS y data
hdict = spirouImage.AddKey(p,
hdict,
p['KW_EM_TELLY'],
value=loc['TELLSPE'])
# add name of the localisation fits file used
hfile = os.path.basename(loc['LOCO_CTR_FILE'])
hdict = spirouImage.AddKey(p, hdict, p['kw_EM_LOCFILE'], value=hfile)
# add the max and min wavelength threshold
hdict = spirouImage.AddKey(p,
hdict,
p['kw_EM_MINWAVE'],
value=p['EM_MIN_LAMBDA'])
hdict = spirouImage.AddKey(p,
hdict,
p['kw_EM_MAXWAVE'],
value=p['EM_MAX_LAMBDA'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add the transmission cut
hdict = spirouImage.AddKey(p,
hdict,
p['kw_EM_TRASCUT'],
value=p['EM_TELL_THRESHOLD'])
# ------------------------------------------------------------------
# Deal with output preferences
# ------------------------------------------------------------------
# add bad pixel map (if required)
if p['EM_COMBINED_BADPIX']:
# get bad pix mask (True where bad)
badpixmask, bhdr, badfile = spirouImage.GetBadPixMap(p, hdr)
goodpixels = badpixmask == 0
# apply mask (multiply)
loc['TELL_MASK_2D'] = loc['TELL_MASK_2D'] & goodpixels.astype(bool)
else:
badfile = 'None'
# add to hdict
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBAD'], value=badfile)
# convert waveimage mask into float array
loc['TELL_MASK_2D'] = loc['TELL_MASK_2D'].astype('float')
# check EM_OUTPUT_TYPE and deal with set to "all"
if p['EM_OUTPUT_TYPE'] not in ["drs", "raw", "preprocess", "all"]:
emsg1 = '"EM_OUTPUT_TYPE" not understood'
emsg2 = ' must be either "drs", "raw" or "preprocess"'
emsg3 = ' currently EM_OUTPUT_TYPE="{0}"'.format(p['EM_OUTPUT_TYPE'])
WLOG(p, 'error', [emsg1, emsg2, emsg3])
outputs = []
elif p['EM_OUTPUT_TYPE'] != 'all':
outputs = [str(p['EM_OUTPUT_TYPE'])]
else:
outputs = ["drs", "raw", "preprocess"]
# ----------------------------------------------------------------------
# loop around output types
# ----------------------------------------------------------------------
for output in outputs:
# log progress
WLOG(p, '', 'Processing {0} outputs'.format(output))
# change EM_OUTPUT_TYPE
p['EM_OUTPUT_TYPE'] = output
# copy arrays
out_spe = np.array(loc['SPE'])
out_wave = np.array(loc['WAVEIMAGE'])
out_mask = np.array(loc['TELL_MASK_2D'])
# change image size if needed
if output in ["raw", "preprocess"]:
kk = dict(xsize=image.shape[1], ysize=image.shape[0])
if p['EM_SAVE_TELL_SPEC']:
WLOG(p, '', 'Resizing/Flipping SPE')
out_spe = spirouExM.unresize(p, out_spe, **kk)
WLOG(p, '', 'Rescaling SPE')
out_spe = out_spe / (p['GAIN'] * p['EXPTIME'])
if p['EM_SAVE_WAVE_MAP']:
WLOG(p, '', 'Resizing/Flipping WAVEIMAGE')
out_wave = spirouExM.unresize(p, out_wave, **kk)
if p['EM_SAVE_MASK_MAP']:
WLOG(p, '', 'Resizing/Flipping TELL_MASK_2D')
out_mask = spirouExM.unresize(p, out_mask, **kk)
# if raw need to rotate (undo pre-processing)
if output == "raw":
if p['EM_SAVE_TELL_SPEC']:
WLOG(p, '', 'Rotating SPE')
out_spe = np.rot90(out_spe, 1)
if p['EM_SAVE_WAVE_MAP']:
WLOG(p, '', 'Rotating WAVEIMAGE')
out_wave = np.rot90(out_wave, 1)
if p['EM_SAVE_MASK_MAP']:
WLOG(p, '', 'Rotating TELL_MASK_2D')
out_mask = np.rot90(out_mask, 1)
# ----------------------------------------------------------------------
# save 2D spectrum, wavelength image and mask to file
# ----------------------------------------------------------------------
# save telluric spectrum
if p['EM_SAVE_TELL_SPEC']:
# construct spectrum filename
specfitsfile, tag = spirouConfig.Constants.EM_SPE_FILE(p)
specfilename = os.path.split(specfitsfile)[-1]
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DRS_DATE'],
value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DATE_NOW'],
value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag)
# log progress
wmsg = 'Writing spectrum to file {0}'
WLOG(p, '', wmsg.format(specfilename))
# write to file
p = spirouImage.WriteImage(p, specfitsfile, out_spe, hdict=hdict)
# ----------------------------------------------------------------------
# save wave map
if p['EM_SAVE_WAVE_MAP']:
# construct waveimage filename
wavefitsfile, tag = spirouConfig.Constants.EM_WAVE_FILE(p)
wavefilename = os.path.split(wavefitsfile)[-1]
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DRS_DATE'],
value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DATE_NOW'],
value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag)
# log progress
wmsg = 'Writing wave image to file {0}'
WLOG(p, '', wmsg.format(wavefilename))
# write to file
p = spirouImage.WriteImage(p, wavefitsfile, out_wave, hdict=hdict)
# ----------------------------------------------------------------------
# save mask file
if p['EM_SAVE_MASK_MAP']:
# construct tell mask 2D filename
maskfitsfile, tag = spirouConfig.Constants.EM_MASK_FILE(p)
maskfilename = os.path.split(maskfitsfile)[-1]
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DRS_DATE'],
value=p['DRS_DATE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DATE_NOW'],
value=p['DATE_NOW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag)
# log progress
wmsg = 'Writing telluric mask to file {0}'
WLOG(p, '', wmsg.format(maskfilename))
# convert boolean mask to integers
writablemask = np.array(out_mask, dtype=float)
# write to file
p = spirouImage.WriteImage(p,
maskfitsfile,
writablemask,
hdict=hdict)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def main(night_name=None, fpfile=None, hcfiles=None):
"""
cal_wave_spirou.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_wave_spirou.py [night_directory] [fpfile] [hcfiles]
:param night_name: string or None, the folder within data reduced directory
containing files (also reduced directory) i.e.
/data/reduced/20170710 would be "20170710" but
/data/reduced/AT5/20180409 is "AT5/20180409"
:param fpfile: string, or None, the FP file to use for
arg_file_names and fitsfilename
(if None assumes arg_file_names was set from run time)
:param hcfiles: string, list or None, the list of HC files to use for
arg_file_names and fitsfilename
(if None assumes arg_file_names was set from run time)
:return ll: dictionary, containing all the local variables defined in
main
"""
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
if hcfiles is None or fpfile is None:
names, types = ['fpfile', 'hcfiles'], [str, str]
customargs = spirouStartup.GetCustomFromRuntime(p, [0, 1],
types,
names,
last_multi=True)
else:
customargs = dict(hcfiles=hcfiles, fpfile=fpfile)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsdir='reduced',
mainfitsfile='hcfiles')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, fpfitsfilename = spirouStartup.SingleFileSetup(p, filename=p['FPFILE'])
fiber1 = str(p['FIBER'])
p, hcfilenames = spirouStartup.MultiFileSetup(p, files=p['HCFILES'])
fiber2 = str(p['FIBER'])
# set the hcfilename to the first hcfilenames
hcfitsfilename = hcfilenames[0]
# ----------------------------------------------------------------------
# Once we have checked the e2dsfile we can load calibDB
# ----------------------------------------------------------------------
# as we have custom arguments need to load the calibration database
p = spirouStartup.LoadCalibDB(p)
# ----------------------------------------------------------------------
# Have to check that the fibers match
# ----------------------------------------------------------------------
if fiber1 == fiber2:
p['FIBER'] = fiber1
fsource = __NAME__ + '/main() & spirouStartup.GetFiberType()'
p.set_source('FIBER', fsource)
else:
emsg = 'Fiber not matching for {0} and {1}, should be the same'
eargs = [hcfitsfilename, fpfitsfilename]
WLOG(p, 'error', emsg.format(*eargs))
# set the fiber type
p['FIB_TYP'] = [p['FIBER']]
p.set_source('FIB_TYP', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Read FP and HC files
# ----------------------------------------------------------------------
# read and combine all HC files except the first (fpfitsfilename)
rargs = [p, 'add', hcfitsfilename, hcfilenames[1:]]
p, hcdata, hchdr = spirouImage.ReadImageAndCombine(*rargs)
# read first file (fpfitsfilename)
fpdata, fphdr, _, _ = spirouImage.ReadImage(p, fpfitsfilename)
# add data and hdr to loc
loc = ParamDict()
loc['HCDATA'], loc['HCHDR'], loc['HCCDR'] = hcdata, hchdr, hchdr.comments
loc['FPDATA'], loc['FPHDR'], loc['FPCDR'] = fpdata, fphdr, fphdr.comments
# set the source
sources = ['HCDATA', 'HCHDR', 'HCCDR']
loc.set_sources(sources, 'spirouImage.ReadImageAndCombine()')
sources = ['FPDATA', 'FPHDR', 'FPCDR']
loc.set_sources(sources, 'spirouImage.ReadImage()')
# ----------------------------------------------------------------------
# Get basic image properties for reference file
# ----------------------------------------------------------------------
# get sig det value
p = spirouImage.GetSigdet(p, hchdr, name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, hchdr, name='exptime')
# get gain
p = spirouImage.GetGain(p, hchdr, name='gain')
# get acquisition time
p = spirouImage.GetAcqTime(p, hchdr, name='acqtime', kind='julian')
bjdref = p['ACQTIME']
# set sigdet and conad keywords (sigdet is changed later)
p['KW_CCD_SIGDET'][1] = p['SIGDET']
p['KW_CCD_CONAD'][1] = p['GAIN']
# get lamp parameters
p = spirouWAVE2.get_lamp_parameters(p, hchdr)
# get number of orders
# we always get fibre A number because AB is doubled in constants file
loc['NBO'] = p['QC_LOC_NBO_FPALL']['A']
loc.set_source('NBO', __NAME__ + '.main()')
# get number of pixels in x from hcdata size
loc['NBPIX'] = loc['HCDATA'].shape[1]
loc.set_source('NBPIX', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# Read blaze
# ----------------------------------------------------------------------
# get tilts
p, loc['BLAZE'] = spirouImage.ReadBlazeFile(p, hchdr)
loc.set_source('BLAZE', __NAME__ + '/main() + /spirouImage.ReadBlazeFile')
# make copy of blaze (as it's overwritten later in CCF part)
# TODO is this needed? More sensible to make and set copy in CCF?
loc['BLAZE2'] = np.copy(loc['BLAZE'])
# ----------------------------------------------------------------------
# Read wave solution
# ----------------------------------------------------------------------
# wavelength file; we will use the polynomial terms in its header,
# NOT the pixel values that would need to be interpolated
# set source of wave file
wsource = __NAME__ + '/main() + /spirouImage.GetWaveSolution'
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get wave image
wout = spirouImage.GetWaveSolution(p,
hdr=hchdr,
return_wavemap=True,
return_filename=True,
fiber=wave_fiber)
loc['WAVEPARAMS'], loc['WAVE_INIT'], loc['WAVEFILE'], loc['WSOURCE'] = wout
loc.set_sources(['WAVE_INIT', 'WAVEFILE', 'WAVEPARAMS', 'WSOURCE'],
wsource)
poly_wave_sol = loc['WAVEPARAMS']
# ----------------------------------------------------------------------
# Check that wave parameters are consistent with "ic_ll_degr_fit"
# ----------------------------------------------------------------------
loc = spirouImage.CheckWaveSolConsistency(p, loc)
# ----------------------------------------------------------------------
# HC wavelength solution
# ----------------------------------------------------------------------
# log that we are running the HC part and the mode
wmsg = 'Now running the HC solution, mode = {0}'
WLOG(p, 'info', wmsg.format(p['WAVE_MODE_HC']))
# get the solution
loc = spirouWAVE2.do_hc_wavesol(p, loc)
# ----------------------------------------------------------------------
# Quality control - HC solution
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# quality control on sigma clip (sig1 > qc_hc_wave_sigma_max
if loc['SIG1'] > p['QC_HC_WAVE_SIGMA_MAX']:
fmsg = 'Sigma too high ({0:.5f} > {1:.5f})'
fail_msg.append(fmsg.format(loc['SIG1'], p['QC_HC_WAVE_SIGMA_MAX']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(loc['SIG1'])
qc_names.append('SIG1 HC')
qc_logic.append('SIG1 > {0:.2f}'.format(p['QC_HC_WAVE_SIGMA_MAX']))
# ----------------------------------------------------------------------
# check the difference between consecutive orders is always positive
# get the differences
wave_diff = loc['WAVE_MAP2'][1:] - loc['WAVE_MAP2'][:-1]
if np.min(wave_diff) < 0:
fmsg = 'Negative wavelength difference between orders'
fail_msg.append(fmsg)
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(np.min(wave_diff))
qc_names.append('MIN WAVE DIFF HC')
qc_logic.append('MIN WAVE DIFF < 0')
# ----------------------------------------------------------------------
# check the difference between consecutive pixels along an order is
# always positive
# loop through the orders
ord_check = np.zeros((loc['NBO']), dtype=bool)
for order in range(loc['NBO']):
oc = np.all(loc['WAVE_MAP2'][order, 1:] > loc['WAVE_MAP2'][order, :-1])
ord_check[order] = oc
# TODO: Melissa Why is this here????
# ord_check[5] = False
if np.all(ord_check):
qc_pass.append(1)
qc_values.append('None')
else:
fmsg = 'Negative wavelength difference along an order'
fail_msg.append(fmsg)
passed = False
qc_pass.append(0)
qc_values.append(np.ndarray.tolist(np.where(~ord_check)[0]))
# add to qc header lists
# vale: array of orders where it fails
qc_names.append('WAVE DIFF ALONG ORDER HC')
qc_logic.append('WAVE DIFF ALONG ORDER < 0')
# ----------------------------------------------------------------------
# finally log the failed messages and set QC = 1 if we pass the
# quality control QC = 0 if we fail quality control
if passed:
WLOG(p, 'info', 'QUALITY CONTROL SUCCESSFUL - Well Done -')
p['QC'] = 1
p.set_source('QC', __NAME__ + '/main()')
else:
for farg in fail_msg:
wmsg = 'QUALITY CONTROL FAILED: {0}'
WLOG(p, 'warning', wmsg.format(farg))
p['QC'] = 0
p.set_source('QC', __NAME__ + '/main()')
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ----------------------------------------------------------------------
# log the global stats
# ----------------------------------------------------------------------
# calculate catalog-fit residuals in km/s
res_hc = []
sumres_hc = 0.0
sumres2_hc = 0.0
for order in range(loc['NBO']):
# get HC line wavelengths for the order
order_mask = loc['ORD_T'] == order
hc_x_ord = loc['XGAU_T'][order_mask]
hc_ll_ord = np.polyval(loc['POLY_WAVE_SOL'][order][::-1], hc_x_ord)
hc_ll_cat = loc['WAVE_CATALOG'][order_mask]
hc_ll_diff = hc_ll_ord - hc_ll_cat
res_hc.append(hc_ll_diff * speed_of_light / hc_ll_cat)
sumres_hc += np.nansum(res_hc[order])
sumres2_hc += np.nansum(res_hc[order]**2)
total_lines_hc = len(np.concatenate(res_hc))
final_mean_hc = sumres_hc / total_lines_hc
final_var_hc = (sumres2_hc / total_lines_hc) - (final_mean_hc**2)
wmsg1 = 'On fiber {0} HC fit line statistic:'.format(p['FIBER'])
wargs2 = [
final_mean_hc * 1000.0,
np.sqrt(final_var_hc) * 1000.0, total_lines_hc,
1000.0 * np.sqrt(final_var_hc / total_lines_hc)
]
wmsg2 = ('\tmean={0:.3f}[m/s] rms={1:.1f} {2} HC lines (error on mean '
'value:{3:.4f}[m/s])'.format(*wargs2))
WLOG(p, 'info', [wmsg1, wmsg2])
# ----------------------------------------------------------------------
# Save wave map to file
# ----------------------------------------------------------------------
# TODO single file-naming function? Ask Neil
# get base input filenames
bfilenames = []
for raw_file in p['ARG_FILE_NAMES']:
bfilenames.append(os.path.basename(raw_file))
# get wave filename
wavefits, tag1 = spirouConfig.Constants.WAVE_FILE_EA(p)
wavefitsname = os.path.basename(wavefits)
# log progress
WLOG(p, '', 'Saving wave map to {0}'.format(wavefitsname))
# log progress
wargs = [p['FIBER'], wavefitsname]
wmsg = 'Write wavelength solution for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(*wargs))
# write solution to fitsfilename header
# copy original keys
hdict = spirouImage.CopyOriginalKeys(loc['HCHDR'], loc['HCCDR'])
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
# TODO add DRS_DATE and DRS_NOW
hdict = spirouImage.AddKey(p, hdict, p['KW_PID'], value=p['PID'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
# set the input files
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBAD'], value=p['BLAZFILE'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add wave solution date
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME1'],
value=p['MAX_TIME_HUMAN'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME2'],
value=p['MAX_TIME_UNIX'])
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVE_CODE'], value=__NAME__)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBWAVE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='file',
values=p['ARG_FILE_NAMES'])
# add number of orders
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_ORD_N'],
value=loc['POLY_WAVE_SOL'].shape[0])
# add degree of fit
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_LL_DEG'],
value=loc['POLY_WAVE_SOL'].shape[1] - 1)
# add wave solution
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_WAVE_PARAM'],
values=loc['POLY_WAVE_SOL'])
# write the wave "spectrum"
p = spirouImage.WriteImage(p, wavefits, loc['WAVE_MAP2'], hdict)
# get filename for E2DS calibDB copy of FITSFILENAME
e2dscopy_filename, tag2 = spirouConfig.Constants.WAVE_E2DS_COPY(p)
wargs = [p['FIBER'], os.path.split(e2dscopy_filename)[-1]]
wmsg = 'Write reference E2DS spectra for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(*wargs))
# make a copy of the E2DS file for the calibBD
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag2)
p = spirouImage.WriteImage(p, e2dscopy_filename, loc['HCDATA'], hdict)
# ----------------------------------------------------------------------
# Save resolution and line profiles to file
# ----------------------------------------------------------------------
raw_infile = os.path.basename(p['FITSFILENAME'])
# get wave filename
resfits, tag3 = spirouConfig.Constants.WAVE_RES_FILE_EA(p)
resfitsname = os.path.basename(resfits)
WLOG(p, '', 'Saving wave resmap to {0}'.format(resfitsname))
# make a copy of the E2DS file for the calibBD
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
# TODO add DRS_DATE and DRS_NOW
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag3)
# get res data in correct format
resdata, hdicts = spirouWAVE2.generate_res_files(p, loc, hdict)
# save to file
p = spirouImage.WriteImageMulti(p, resfits, resdata, hdicts=hdicts)
# ----------------------------------------------------------------------
# Update calibDB
# ----------------------------------------------------------------------
if p['QC']:
# set the wave key
keydb = 'WAVE_{0}'.format(p['FIBER'])
# copy wave file to calibDB folder
spirouDB.PutCalibFile(p, wavefits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, wavefitsname, loc['HCHDR'])
# set the hcref key
keydb = 'HCREF_{0}'.format(p['FIBER'])
# copy wave file to calibDB folder
spirouDB.PutCalibFile(p, e2dscopy_filename)
# update the master calib DB file with new key
e2dscopyfits = os.path.split(e2dscopy_filename)[-1]
spirouDB.UpdateCalibMaster(p, keydb, e2dscopyfits, loc['HCHDR'])
# ----------------------------------------------------------------------
# Update header of current files
# ----------------------------------------------------------------------
# only copy over if QC passed
if p['QC']:
rdir = os.path.dirname(wavefits)
# loop around hc files and update header with
for rawhcfile in p['ARG_FILE_NAMES']:
hcfile = os.path.join(rdir, rawhcfile)
raw_infilepath1 = os.path.join(p['ARG_FILE_DIR'], hcfile)
p = spirouImage.UpdateWaveSolutionHC(p, loc, raw_infilepath1)
# ----------------------------------------------------------------------
# HC+FP wavelength solution
# ----------------------------------------------------------------------
# check if there's a FP input and if HC solution passed QCs
if has_fp and p['QC']:
# log that we are doing the FP solution
wmsg = 'Now running the combined FP-HC solution, mode = {}'
WLOG(p, 'info', wmsg.format(p['WAVE_MODE_FP']))
# do the wavelength solution
loc = spirouWAVE2.do_fp_wavesol(p, loc)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# get parameters ffrom p
p['QC_RMS_LITTROW_MAX'] = p['QC_HC_RMS_LITTROW_MAX']
p['QC_DEV_LITTROW_MAX'] = p['QC_HC_DEV_LITTROW_MAX']
# set passed variable and fail message list
# passed, fail_msg = True, []
# qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# check the difference between consecutive orders is always positive
# get the differences
wave_diff = loc['LL_FINAL'][1:] - loc['LL_FINAL'][:-1]
if np.min(wave_diff) < 0:
fmsg = 'Negative wavelength difference between orders'
fail_msg.append(fmsg)
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(np.min(wave_diff))
qc_names.append('MIN WAVE DIFF FP-HC')
qc_logic.append('MIN WAVE DIFF < 0')
# ----------------------------------------------------------------------
# check for infinites and NaNs in mean residuals from fit
if ~np.isfinite(loc['X_MEAN_2']):
# add failed message to the fail message list
fmsg = 'NaN or Inf in X_MEAN_2'
fail_msg.append(fmsg)
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(loc['X_MEAN_2'])
qc_names.append('X_MEAN_2')
qc_logic.append('X_MEAN_2 not finite')
# ----------------------------------------------------------------------
# iterate through Littrow test cut values
lit_it = 2
# checks every other value
# TODO: This QC check (or set of QC checks needs re-writing it is
# TODO: nearly impossible to understand
for x_it in range(1, len(loc['X_CUT_POINTS_' + str(lit_it)]), 2):
# get x cut point
x_cut_point = loc['X_CUT_POINTS_' + str(lit_it)][x_it]
# get the sigma for this cut point
sig_littrow = loc['LITTROW_SIG_' + str(lit_it)][x_it]
# get the abs min and max dev littrow values
min_littrow = abs(loc['LITTROW_MINDEV_' + str(lit_it)][x_it])
max_littrow = abs(loc['LITTROW_MAXDEV_' + str(lit_it)][x_it])
# get the corresponding order
min_littrow_ord = loc['LITTROW_MINDEVORD_' + str(lit_it)][x_it]
max_littrow_ord = loc['LITTROW_MAXDEVORD_' + str(lit_it)][x_it]
# check if sig littrow is above maximum
rms_littrow_max = p['QC_RMS_LITTROW_MAX']
dev_littrow_max = p['QC_DEV_LITTROW_MAX']
if sig_littrow > rms_littrow_max:
fmsg = ('Littrow test (x={0}) failed (sig littrow = '
'{1:.2f} > {2:.2f})')
fargs = [x_cut_point, sig_littrow, rms_littrow_max]
fail_msg.append(fmsg.format(*fargs))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(sig_littrow)
qc_names.append('sig_littrow')
qc_logic.append('sig_littrow > {0:.2f}'.format(rms_littrow_max))
# ----------------------------------------------------------------------
# check if min/max littrow is out of bounds
if np.max([max_littrow, min_littrow]) > dev_littrow_max:
fmsg = ('Littrow test (x={0}) failed (min|max dev = '
'{1:.2f}|{2:.2f} > {3:.2f} for order {4}|{5})')
fargs = [
x_cut_point, min_littrow, max_littrow, dev_littrow_max,
min_littrow_ord, max_littrow_ord
]
fail_msg.append(fmsg.format(*fargs))
passed = False
qc_pass.append(0)
# TODO: Should this be the QC header values?
# TODO: it does not change the outcome of QC (i.e. passed=False)
# TODO: So what is the point?
# if sig was out of bounds, recalculate
if sig_littrow > rms_littrow_max:
# conditions
check1 = min_littrow > dev_littrow_max
check2 = max_littrow > dev_littrow_max
# get the residuals
respix = loc['LITTROW_YY_' + str(lit_it)][x_it]
# check if both are out of bounds
if check1 and check2:
# remove respective orders
worst_order = (min_littrow_ord, max_littrow_ord)
respix_2 = np.delete(respix, worst_order)
redo_sigma = True
# check if min is out of bounds
elif check1:
# remove respective order
worst_order = min_littrow_ord
respix_2 = np.delete(respix, worst_order)
redo_sigma = True
# check if max is out of bounds
elif check2:
# remove respective order
worst_order = max_littrow_ord
respix_2 = np.delete(respix, max_littrow_ord)
redo_sigma = True
# else do not recalculate sigma
else:
redo_sigma, respix_2, worst_order = False, None, None
wmsg = 'No outlying orders, sig littrow not recalculated'
fail_msg.append(wmsg.format())
# if outlying order, recalculate stats
if redo_sigma:
mean = np.nansum(respix_2) / len(respix_2)
mean2 = np.nansum(respix_2**2) / len(respix_2)
rms = np.sqrt(mean2 - mean**2)
if rms > rms_littrow_max:
fmsg = (
'Littrow test (x={0}) failed (sig littrow = '
'{1:.2f} > {2:.2f} removing order {3})')
fargs = [
x_cut_point, rms, rms_littrow_max, worst_order
]
fail_msg.append(fmsg.format(*fargs))
else:
wargs = [
x_cut_point, rms, rms_littrow_max, worst_order
]
wmsg = (
'Littrow test (x={0}) passed (sig littrow = '
'{1:.2f} > {2:.2f} removing order {3})')
fail_msg.append(wmsg.format(*wargs))
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(np.max([max_littrow, min_littrow]))
qc_names.append('max or min littrow')
qc_logic.append('max or min littrow > {0:.2f}'
''.format(dev_littrow_max))
# finally log the failed messages and set QC = 1 if we pass the
# quality control QC = 0 if we fail quality control
if passed:
WLOG(p, 'info', 'QUALITY CONTROL SUCCESSFUL - Well Done -')
p['QC'] = 1
p.set_source('QC', __NAME__ + '/main()')
else:
for farg in fail_msg:
wmsg = 'QUALITY CONTROL FAILED: {0}'
WLOG(p, 'warning', wmsg.format(farg))
p['QC'] = 0
p.set_source('QC', __NAME__ + '/main()')
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ------------------------------------------------------------------
# archive result in e2ds spectra
# ------------------------------------------------------------------
# get raw input file name(s)
raw_infiles1 = []
for hcfile in p['HCFILES']:
raw_infiles1.append(os.path.basename(hcfile))
raw_infile2 = os.path.basename(p['FPFILE'])
# get wave filename
wavefits, tag1 = spirouConfig.Constants.WAVE_FILE_EA_2(p)
wavefitsname = os.path.split(wavefits)[-1]
# log progress
wargs = [p['FIBER'], wavefits]
wmsg = 'Write wavelength solution for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(*wargs))
# write solution to fitsfilename header
# copy original keys
hdict = spirouImage.CopyOriginalKeys(loc['HCHDR'], loc['HCCDR'])
# add version number
hdict = spirouImage.AddKey(p, hdict, p['KW_VERSION'])
hdict = spirouImage.AddKey(p, hdict, p['KW_PID'], value=p['PID'])
# set the input files
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBBAD'],
value=p['BLAZFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBWAVE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='fpfile',
values=p['FPFILE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE2'],
dim1name='hcfile',
values=p['HCFILES'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add wave solution date
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME1'],
value=p['MAX_TIME_HUMAN'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_TIME2'],
value=p['MAX_TIME_UNIX'])
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVE_CODE'], value=__NAME__)
# add number of orders
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_ORD_N'],
value=loc['LL_PARAM_FINAL'].shape[0])
# add degree of fit
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVE_LL_DEG'],
value=loc['LL_PARAM_FINAL'].shape[1] - 1)
# add wave solution
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_WAVE_PARAM'],
values=loc['LL_PARAM_FINAL'])
# add FP CCF drift
# target RV and width
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_TARG_RV'],
value=p['TARGET_RV'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_WIDTH'],
value=p['CCF_WIDTH'])
# the rv step
# rvstep = np.abs(loc['RV_CCF'][0] - loc['RV_CCF'][1])
# hdict = spirouImage.AddKey(p, hdict, p['KW_CCF_CDELT'], value=rvstep)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_STEP'],
value=p['CCF_STEP'])
# add ccf stats
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_DRIFT'],
value=loc['CCF_RES'][1])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_FWHM'],
value=loc['FWHM'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_CONTRAST'],
value=loc['CONTRAST'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_MAXCPP'],
value=loc['MAXCPP'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_MASK'],
value=p['CCF_MASK'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WFP_LINES'],
value=np.nansum(loc['TOT_LINE']))
# write the wave "spectrum"
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
p = spirouImage.WriteImage(p, wavefits, loc['LL_FINAL'], hdict)
# get filename for E2DS calibDB copy of FITSFILENAME
e2dscopy_filename = spirouConfig.Constants.WAVE_E2DS_COPY(p)[0]
wargs = [p['FIBER'], os.path.split(e2dscopy_filename)[-1]]
wmsg = 'Write reference E2DS spectra for Fiber {0} in {1}'
WLOG(p, '', wmsg.format(*wargs))
# make a copy of the E2DS file for the calibBD
p = spirouImage.WriteImage(p, e2dscopy_filename, loc['HCDATA'], hdict)
# only copy over if QC passed
if p['QC']:
# loop around hc files and update header with
for hcfile in p['HCFILES']:
raw_infilepath1 = os.path.join(p['ARG_FILE_DIR'], hcfile)
p = spirouImage.UpdateWaveSolution(p, loc, raw_infilepath1)
# update fp file
raw_infilepath2 = os.path.join(p['ARG_FILE_DIR'], raw_infile2)
p = spirouImage.UpdateWaveSolution(p, loc, raw_infilepath2)
# ------------------------------------------------------------------
# Save to result table
# ------------------------------------------------------------------
# calculate stats for table
final_mean = 1000 * loc['X_MEAN_2']
final_var = 1000 * loc['X_VAR_2']
num_lines = loc['TOTAL_LINES_2']
err = 1000 * np.sqrt(loc['X_VAR_2'] / num_lines)
sig_littrow = 1000 * np.array(loc['LITTROW_SIG_' + str(lit_it)])
# construct filename
wavetbl = spirouConfig.Constants.WAVE_TBL_FILE_EA(p)
wavetblname = os.path.basename(wavetbl)
# construct and write table
columnnames = [
'night_name', 'file_name', 'fiber', 'mean', 'rms', 'N_lines',
'err', 'rms_L500', 'rms_L1000', 'rms_L1500', 'rms_L2000',
'rms_L2500', 'rms_L3000', 'rms_L3500'
]
columnformats = [
'{:20s}', '{:30s}', '{:3s}', '{:7.4f}', '{:6.2f}', '{:3d}',
'{:6.3f}', '{:6.2f}', '{:6.2f}', '{:6.2f}', '{:6.2f}', '{:6.2f}',
'{:6.2f}', '{:6.2f}'
]
columnvalues = [[p['ARG_NIGHT_NAME']], [p['ARG_FILE_NAMES'][0]],
[p['FIBER']], [final_mean], [final_var], [num_lines],
[err], [sig_littrow[0]], [sig_littrow[1]],
[sig_littrow[2]], [sig_littrow[3]], [sig_littrow[4]],
[sig_littrow[5]], [sig_littrow[6]]]
# make table
table = spirouImage.MakeTable(p,
columns=columnnames,
values=columnvalues,
formats=columnformats)
# merge table
wmsg = 'Global result summary saved in {0}'
WLOG(p, '', wmsg.format(wavetblname))
spirouImage.MergeTable(p, table, wavetbl, fmt='ascii.rst')
# ------------------------------------------------------------------
# Save line list table file
# ------------------------------------------------------------------
# construct filename
# TODO proper column values
wavelltbl = spirouConfig.Constants.WAVE_LINE_FILE_EA(p)
wavelltblname = os.path.split(wavelltbl)[-1]
# construct and write table
columnnames = ['order', 'll', 'dv', 'w', 'xi', 'xo', 'dvdx']
columnformats = [
'{:.0f}', '{:12.4f}', '{:13.5f}', '{:12.4f}', '{:12.4f}',
'{:12.4f}', '{:8.4f}'
]
columnvalues = []
# construct column values (flatten over orders)
for it in range(len(loc['X_DETAILS_2'])):
for jt in range(len(loc['X_DETAILS_2'][it][0])):
row = [
float(it), loc['X_DETAILS_2'][it][0][jt],
loc['LL_DETAILS_2'][it][0][jt],
loc['X_DETAILS_2'][it][3][jt],
loc['X_DETAILS_2'][it][1][jt],
loc['X_DETAILS_2'][it][2][jt], loc['SCALE_2'][it][jt]
]
columnvalues.append(row)
# log saving
wmsg = 'List of lines used saved in {0}'
WLOG(p, '', wmsg.format(wavelltblname))
# make table
columnvalues = np.array(columnvalues).T
table = spirouImage.MakeTable(p,
columns=columnnames,
values=columnvalues,
formats=columnformats)
# write table
spirouImage.WriteTable(p, table, wavelltbl, fmt='ascii.rst')
# ------------------------------------------------------------------
# Move to calibDB and update calibDB
# ------------------------------------------------------------------
if p['QC']:
# set the wave key
keydb = 'WAVE_{0}'.format(p['FIBER'])
# copy wave file to calibDB folder
spirouDB.PutCalibFile(p, wavefits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, wavefitsname, loc['HCHDR'])
# set the hcref key
keydb = 'HCREF_{0}'.format(p['FIBER'])
# copy wave file to calibDB folder
spirouDB.PutCalibFile(p, e2dscopy_filename)
# update the master calib DB file with new key
e2dscopyfits = os.path.split(e2dscopy_filename)[-1]
spirouDB.UpdateCalibMaster(p, keydb, e2dscopyfits, loc['HCHDR'])
# If the HC solution failed QCs we do not compute FP-HC solution
elif has_fp and not p['QC']:
wmsg = 'HC solution failed quality controls; FP not processed'
WLOG(p, 'warning', wmsg)
# If there is no FP file we log that
elif not has_fp:
wmsg = 'No FP file given; FP-HC combined solution cannot be generated'
WLOG(p, 'warning', wmsg)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return p and loc
return dict(locals())
def main(night_name=None, files=None):
"""
cal_HC_E2DS.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_DARK_spirou.py [night_directory] [fitsfilename]
:param night_name: string or None, the folder within data raw directory
containing files (also reduced directory) i.e.
/data/raw/20170710 would be "20170710" but
/data/raw/AT5/20180409 would be "AT5/20180409"
:param files: string, list or None, the list of files to use for
arg_file_names and fitsfilename
(if None assumes arg_file_names was set from run time)
:return ll: dictionary, containing all the local variables defined in
main
"""
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
files,
mainfitsdir='reduced')
# setup files and get fiber
p = spirouStartup.InitialFileSetup(p, calibdb=True)
# set the fiber type
p['FIB_TYP'] = [p['FIBER']]
p.set_source('FIB_TYP', __NAME__ + '/main()')
# set find line mode
find_lines_mode = p['HC_FIND_LINES_MODE']
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read and combine all files
p, hcdata, hchdr = spirouImage.ReadImageAndCombine(p, 'add')
# add data and hdr to loc
loc = ParamDict()
loc['HCDATA'], loc['HCHDR'] = hcdata, hchdr
# set the source
sources = ['HCDATA', 'HCHDR']
loc.set_sources(sources, 'spirouImage.ReadImageAndCombine()')
# ----------------------------------------------------------------------
# Get basic parameters
# ----------------------------------------------------------------------
# get sig det value
p = spirouImage.GetSigdet(p, loc['HCHDR'], name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, loc['HCHDR'], name='exptime')
# get gain
p = spirouImage.GetGain(p, loc['HCHDR'], name='gain')
# get acquisition time
p = spirouImage.GetAcqTime(p, loc['HCHDR'], name='acqtime', kind='julian')
bjdref = p['ACQTIME']
# set sigdet and conad keywords (sigdet is changed later)
p['KW_CCD_SIGDET'][1] = p['SIGDET']
p['KW_CCD_CONAD'][1] = p['GAIN']
# get lamp parameters
p = spirouTHORCA.GetLampParams(p, loc['HCHDR'])
# ----------------------------------------------------------------------
# Obtain the flat
# ----------------------------------------------------------------------
# get the flat
# p, loc = spirouFLAT.GetFlat(p, loc, hchdr)
# correct the data with the flat
# TODO: Should this be used?
# log
# WLOG(p, '', 'Applying flat correction')
# loc['HCDATA'] = loc['HCDATA']/loc['FLAT']
# ----------------------------------------------------------------------
# Read blaze
# ----------------------------------------------------------------------
# get tilts
loc['BLAZE'] = spirouImage.ReadBlazeFile(p, hchdr)
loc.set_source('BLAZE', __NAME__ + '/main() + /spirouImage.ReadBlazeFile')
# ----------------------------------------------------------------------
# Start plotting session
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive plot
sPlt.start_interactive_session(p)
# ----------------------------------------------------------------------
# loop around fiber type
# ----------------------------------------------------------------------
for fiber in p['FIB_TYP']:
# set fiber type for inside loop
p['FIBER'] = fiber
# ------------------------------------------------------------------
# Wave solution
# ------------------------------------------------------------------
# log message for loop
wmsg = 'Processing Wavelength Calibration for Fiber {0}'
WLOG(p, 'info', wmsg.format(p['FIBER']))
# ------------------------------------------------------------------
# Part 1
# ------------------------------------------------------------------
p, loc = part1(p, loc, mode=find_lines_mode)
# ------------------------------------------------------------------
# Part 2
# ------------------------------------------------------------------
# set params for part2
p['QC_RMS_LITTROW_MAX'] = p['QC_HC_RMS_LITTROW_MAX']
p['QC_DEV_LITTROW_MAX'] = p['QC_HC_DEV_LITTROW_MAX']
# ------------------------------------------------------------------
# run part 2
p, loc = part2(p, loc)
# ----------------------------------------------------------------------
# End plotting session
# ----------------------------------------------------------------------
# end interactive session
if p['DRS_PLOT'] > 0:
sPlt.end_interactive_session(p)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
