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__)
# deal with reference file being None (i.e. get from sys.argv)
if reffile is None:
customargs = spirouStartup.GetCustomFromRuntime(p, [0], [str],
['reffile'])
else:
customargs = dict(reffile=reffile)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p, night_name, customargs=customargs,
mainfitsfile='reffile',
mainfitsdir='reduced')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, reffilename = spirouStartup.SingleFileSetup(p, filename=p['REFFILE'],
skipcheck=True)
p['REFFILENAME'] = reffilename
p.set_source('REFFILENAME', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
data, hdr, nbo, nx = spirouImage.ReadData(p, p['REFFILENAME'])
# ----------------------------------------------------------------------
# Add keys and save file
# ----------------------------------------------------------------------
newfilename = p['REFFILE'].replace('.fits', '_edit.fits')
newpath = os.path.join(p['ARG_FILE_DIR'], newfilename)
# add keys from original header file
hdict = spirouImage.CopyOriginalKeys(hdr)
# set the version
hdict = spirouImage.AddKey(p, hdict, HEADER_KEY, value=HEADER_VALUE)
# log saving
wmsg = 'Writing file {0} to {1}'
WLOG(p, '', wmsg.format(newfilename, p['ARG_FILE_DIR']))
# save drift values
p = spirouImage.WriteImage(p, newpath, 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):
# ----------------------------------------------------------------------
# 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 up first file
# ----------------------------------------------------------------------
# construct loc parameter dictionary for storing data
loc = ParamDict()
# read first file and assign values
rdata = spirouImage.ReadImage(p, p['FITSFILENAME'])
loc['DATA'], loc['DATAHDR'] = rdata[:2]
# Get output key
loc['OUTPUT'] = loc['DATAHDR'][p['KW_OUTPUT'][0]]
# set source
source = main_name + '+ spirouImage.ReadParams()'
loc.set_source('OUTPUT', source)
# ----------------------------------------------------------------------
# Get database files
# ----------------------------------------------------------------------
# get current telluric maps from telluDB
files, output_codes = [], []
# filter by object name (only keep OBJNAME objects) and only keep
# unique filenames
use_files = []
for it in range(len(files)):
# check that OUTPUT is correct
cond1 = p['KW_OUTPUT'] in output_codes[it]
# check that filename is not already used
cond2 = files[it] not in use_files
# append to file list if criteria correct
if cond1 and cond2:
use_files.append(files[it])
# log if we have no files
if len(use_files) == 0:
wmsg = 'No files found for OUTPUT ="{0}" skipping'
WLOG(p, 'warning', wmsg.format(loc['KW_OUTPUT']))
# End Message
wmsg = 'Recipe {0} has been successfully completed'
WLOG(p, 'info', wmsg.format(p['PROGRAM']))
# return a copy of locally defined variables in the memory
return dict(locals())
else:
# log how many found
wmsg = 'N={0} files found for OUTPUT="{1}"'
WLOG(p, '', wmsg.format(len(use_files), loc['OUTPUT']))
# ----------------------------------------------------------------------
# Set up storage for cubes (NaN arrays)
# ----------------------------------------------------------------------
# set up flat size
dims = [loc['DATA'].shape[0], loc['DATA'].shape[1], len(use_files)]
flatsize = np.product(dims)
# create NaN filled storage
big_cube = np.repeat([np.nan], flatsize).reshape(*dims)
big_cube0 = np.repeat([np.nan], flatsize).reshape(*dims)
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get master wave map
loc['MASTERWAVEFILE'] = spirouDB.GetDatabaseMasterWave(p)
# read master wave map
mout = spirouImage.GetWaveSolution(p,
filename=loc['MASTERWAVEFILE'],
return_wavemap=True,
quiet=True,
fiber=wave_fiber)
loc['MASTERWAVEPARAMS'], loc['MASTERWAVE'], loc['WSOURCE'] = mout
keys = ['MASTERWAVEPARAMS', 'MASTERWAVE', 'MASTERWAVEFILE', 'WSOURCE']
loc.set_sources(keys, main_name)
# ----------------------------------------------------------------------
# Loop through input files
# ----------------------------------------------------------------------
base_filelist, berv_list = [], []
# loop through files
for it, filename in enumerate(use_files):
# get base filenmae
basefilename = os.path.basename(filename)
# append basename to file list
base_filelist.append(basefilename)
# ------------------------------------------------------------------
# Load the data for this file
tdata, thdr, _, _ = spirouImage.ReadImage(p, filename)
# ------------------------------------------------------------------
# log stats
wmsg = 'Processing file {0} of {1} file={2}'
wargs = [it + 1, len(use_files), basefilename]
WLOG(p, '', wmsg.format(*wargs))
# ------------------------------------------------------------------
# add to cube storage
big_cube0[:, :, it] = tdata
# ----------------------------------------------------------------------
# Save cubes to file
# ----------------------------------------------------------------------
# get raw file name
raw_in_file = os.path.basename(p['FITSFILENAME'])
# construct file names
outfile = raw_in_file.replace('.fits', '_stack.fits')
tag = loc['OUTPUT'] + '_STACK'
# log big cube 1
wmsg1 = 'Saving bigcube to file {0}'.format(os.path.basename(outfile))
# hdict is first file 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=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['MASTERWAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
# add file list to header
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_OBJFILELIST'],
values=base_filelist)
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_OBJBERVLIST'],
values=berv_list)
# add wave solution coefficients
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_WAVE_PARAM'],
values=loc['MASTERWAVEPARAMS'])
# log big cube 0
wmsg = 'Saving bigcube0 to file {0}'.format(os.path.basename(outfile))
# save big cube 0
big_cube_s0 = np.swapaxes(big_cube0, 1, 2)
p = spirouImage.WriteImageMulti(p, outfile, big_cube_s0, 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, reffile=None):
"""
cal_DRIFTPEAK_E2DS_spirou.py main function, if arguments are None uses
arguments from run time i.e.:
cal_DRIFTPEAK_E2DS_spirou.py [night_directory] [reffile]
: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 reffile: string, the reference file 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 reference file being None (i.e. get from sys.argv)
if reffile is None:
customargs = spirouStartup.GetCustomFromRuntime(
p, [0], [str], ['reffile'])
else:
customargs = dict(reffile=reffile)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsfile='reffile',
mainfitsdir='reduced')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, reffilename = spirouStartup.SingleFileSetup(p, filename=p['REFFILE'])
p['REFFILENAME'] = reffilename
p.set_source('REFFILENAME', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# 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)
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
speref, hdr, nbo, nx = spirouImage.ReadData(p, p['REFFILENAME'])
# add to loc
loc = ParamDict()
loc['SPEREF'] = speref
loc['NUMBER_ORDERS'] = nbo
loc.set_sources(['SPEREF', 'NUMBER_ORDERS'], __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Get lamp type
# ----------------------------------------------------------------------
# get lamp type
if p['KW_EXT_TYPE'][0] in hdr:
ext_type = hdr[p['KW_EXT_TYPE'][0]]
drift_types = p['DRIFT_PEAK_ALLOWED_TYPES'].keys()
found = False
for kind in drift_types:
if ext_type == kind:
loc['LAMP'] = p['DRIFT_PEAK_ALLOWED_TYPES'][kind]
found = True
if not found:
eargs1 = [p['KW_EXT_TYPE'][0], ' or '.join(drift_types)]
emsg1 = (
'Wrong type of image for Drift, header key "{0}" should be'
'{1}'.format(*eargs1))
emsg2 = '\tPlease check DRIFT_PEAK_ALLOWED_TYPES'
WLOG(p, 'error', [emsg1, emsg2])
else:
emsg = 'Header key = "{0}" missing from file {1}'
eargs = [p['KW_EXT_TYPE'][0], p['REFFILENAME']]
WLOG(p, 'error', emsg.format(*eargs))
loc.set_source('LAMP', __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')
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']
# ----------------------------------------------------------------------
# Read 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
source = __NAME__ + '/main() + /spirouImage.GetWaveSolution'
wout = spirouImage.GetWaveSolution(p,
hdr=hdr,
return_wavemap=True,
return_filename=True,
fiber=wave_fiber)
_, loc['WAVE'], loc['WAVEFILE'], loc['WSOURCE'] = wout
loc.set_sources(['WAVE', 'WAVEFILE', 'WSOURCE'], source)
# ----------------------------------------------------------------------
# Read Flat file
# ----------------------------------------------------------------------
# get flat
p, 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'])
# correct for flat file
loc['SPEREF'] = loc['SPEREF'] / loc['FLAT']
# ----------------------------------------------------------------------
# Background correction
# ----------------------------------------------------------------------
# test whether we want to subtract background
if p['IC_DRIFT_BACK_CORR']:
# Loop around the orders
for order_num in range(loc['NUMBER_ORDERS']):
# get the box size from constants
bsize = p['DRIFT_PEAK_MINMAX_BOXSIZE']
# Measurethe min and max flux
miny, maxy = spirouBACK.MeasureMinMax(loc['SPEREF'][order_num],
bsize)
# subtract off the background (miny)
loc['SPEREF'][order_num] = loc['SPEREF'][order_num] - miny
# ----------------------------------------------------------------------
# Identify FP peaks in reference file
# ----------------------------------------------------------------------
# log that we are identifying peaks
wmsg = 'Identification of lines in reference file: {0}'
WLOG(p, '', wmsg.format(p['REFFILE']))
# get the position of FP peaks from reference file
loc = spirouRV.CreateDriftFile(p, loc)
# ----------------------------------------------------------------------
# Removal of suspiciously wide FP lines
# ----------------------------------------------------------------------
loc = spirouRV.RemoveWidePeaks(p, loc)
# ----------------------------------------------------------------------
# Get reference drift
# ----------------------------------------------------------------------
# are we using gaussfit?
gaussfit = p['DRIFT_PEAK_GETDRIFT_GAUSSFIT']
# get drift
loc['XREF'] = spirouRV.GetDrift(p,
loc['SPEREF'],
loc['ORDPEAK'],
loc['XPEAK'],
gaussfit=gaussfit)
loc.set_source('XREF', __NAME__ + '/main()')
# remove any drifts that are zero (i.e. peak not measured
loc = spirouRV.RemoveZeroPeaks(p, loc)
# ------------------------------------------------------------------
# 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)
# ------------------------------------------------------------------
# Get all other files that match kw_OUTPUT and kw_EXT_TYPE from
# ref file
# ------------------------------------------------------------------
# get files
listfiles, listtypes = spirouImage.GetSimilarDriftFiles(p, hdr)
# get the number of files
nfiles = len(listfiles)
# Log the number of files found
wmsgs = [
'Number of files found on directory = {0}'.format(nfiles),
'\tExtensions allowed:'
]
for listtype in listtypes:
wmsgs.append('\t\t - {0}'.format(listtype))
WLOG(p, 'info', wmsgs)
# ------------------------------------------------------------------
# Set up Extract storage for all files
# ------------------------------------------------------------------
# decide whether we need to skip (for large number of files)
if len(listfiles) >= p['DRIFT_NLARGE']:
skip = p['DRIFT_PEAK_FILE_SKIP']
nfiles = int(nfiles / skip)
else:
skip = 1
# set up storage
loc['DRIFT'] = np.zeros((nfiles, loc['NUMBER_ORDERS']))
loc['DRIFT_LEFT'] = np.zeros((nfiles, loc['NUMBER_ORDERS']))
loc['DRIFT_RIGHT'] = np.zeros((nfiles, loc['NUMBER_ORDERS']))
loc['ERRDRIFT'] = np.zeros((nfiles, loc['NUMBER_ORDERS']))
loc['DELTATIME'] = np.zeros(nfiles)
loc['MEANRV'] = np.zeros(nfiles)
loc['MEANRV_LEFT'] = np.zeros(nfiles)
loc['MEANRV_RIGHT'] = np.zeros(nfiles)
loc['MERRDRIFT'] = np.zeros(nfiles)
loc['FLUXRATIO'] = np.zeros(nfiles)
# add sources
source = __NAME__ + '/main()'
keys = [
'drift', 'drift_left', 'drift_right', 'errdrift', 'deltatime',
'meanrv', 'meanrv_left', 'meanrv_right', 'merrdrift', 'fluxratio'
]
loc.set_sources(keys, source)
# ------------------------------------------------------------------
# Loop around all files: correct for dark, reshape, extract and
# calculate dvrms and meanpond
# ------------------------------------------------------------------
# get the maximum number of orders to use
nomin = p['IC_DRIFT_PEAK_N_ORDER_MIN']
nomax = p['IC_DRIFT_PEAK_N_ORDER_MAX']
# loop around files
for i_it in range(nfiles):
# get file for this iteration
fpfile = listfiles[::skip][i_it]
# Log the file we are reading
wmsg = 'Reading file {0}'
WLOG(p, '', wmsg.format(os.path.split(fpfile)[-1]))
# ------------------------------------------------------------------
# read e2ds files and get timestamp
# ------------------------------------------------------------------
# read data
rout = spirouImage.ReadData(p, filename=fpfile, log=False)
loc['SPE'], hdri, nxi, nyi = rout
# apply flat
loc['SPE'] = loc['SPE'] / loc['FLAT']
# get acqtime
bjdspe = spirouImage.GetAcqTime(p,
hdri,
name='acqtime',
return_value=1,
kind='julian')
# ----------------------------------------------------------------------
# Background correction
# ----------------------------------------------------------------------
# test whether we want to subtract background
if p['IC_DRIFT_BACK_CORR']:
# Loop around the orders
for order_num in range(loc['NUMBER_ORDERS']):
# get the box size from constants
bsize = p['DRIFT_PEAK_MINMAX_BOXSIZE']
# Measurethe min and max flux
miny, maxy = spirouBACK.MeasureMinMax(loc['SPE'][order_num],
bsize)
# subtract off the background (miny)
loc['SPE'][order_num] = loc['SPE'][order_num] - miny
# ------------------------------------------------------------------
# calculate flux ratio
# ------------------------------------------------------------------
sorder = p['IC_DRIFT_ORDER_PLOT']
fratio = np.nansum(loc['SPE'][sorder]) / np.nansum(
loc['SPEREF'][sorder])
loc['FLUXRATIO'][i_it] = fratio
# ------------------------------------------------------------------
# Calculate delta time
# ------------------------------------------------------------------
# calculate the time from reference (in hours)
loc['DELTATIME'][i_it] = (bjdspe - bjdref) * 24
# ------------------------------------------------------------------
# Calculate PearsonR coefficient
# ------------------------------------------------------------------
pargs = [loc['NUMBER_ORDERS'], loc['SPE'], loc['SPEREF']]
correlation_coeffs = spirouRV.PearsonRtest(*pargs)
# ----------------------------------------------------------------------
# Get drift with comparison to the reference image
# ----------------------------------------------------------------------
# only calculate drift if the correlation between orders and
# reference file is above threshold
prcut = p['DRIFT_PEAK_PEARSONR_CUT']
if np.min(correlation_coeffs[nomin:nomax]) > prcut:
# get drifts for each order
dargs = [p, loc['SPE'], loc['ORDPEAK'], loc['XREF']]
x = spirouRV.GetDrift(*dargs, gaussfit=gaussfit)
# get delta v
loc['DV'] = (x - loc['XREF']) * loc['VRPEAK']
# sigma clip
loc = spirouRV.SigmaClip(loc, sigma=p['DRIFT_PEAK_SIGMACLIP'])
# work out median drifts per order
loc = spirouRV.DriftPerOrder(loc, i_it)
# work out mean drift across all orders
loc = spirouRV.DriftAllOrders(p, loc, i_it, nomin, nomax)
# log the mean drift
wmsg = ('Time from ref= {0:.2f} h - Flux Ratio= {1:.3f} '
'- Drift mean= {2:.2f} +- {3:.2f} m/s')
wargs = [
loc['DELTATIME'][i_it], loc['FLUXRATIO'][i_it],
loc['MEANRV'][i_it], loc['MERRDRIFT'][i_it]
]
WLOG(p, 'info', wmsg.format(*wargs))
# else we can't use this extract
else:
if p['DRS_PLOT'] > 0:
# start interactive session if needed
sPlt.plt.ioff()
# plot comparison between spe and ref
sPlt.drift_plot_correlation_comp(p, loc, correlation_coeffs,
i_it)
sPlt.plt.show()
sPlt.plt.close()
# turn interactive plotting back on
sPlt.plt.ion()
# log that we cannot use this extraction
wmsg1 = 'The correlation of some orders compared to the template is'
wmsg2 = ' < {0}, something went wrong in the extract.'
WLOG(p, 'warning', wmsg1)
WLOG(p, 'warning', wmsg2.format(prcut))
# ------------------------------------------------------------------
# peak to peak drift
driftptp = np.max(loc['MEANRV']) - np.min(loc['MEANRV'])
driftrms = np.std(loc['MEANRV'])
# log th etotal drift peak-to-peak and rms
wmsg = ('Total drift Peak-to-Peak={0:.3f} m/s RMS={1:.3f} m/s in '
'{2:.2f} hour')
wargs = [driftptp, driftrms, np.max(loc['DELTATIME'])]
WLOG(p, '', wmsg.format(*wargs))
# ------------------------------------------------------------------
# Plot of mean drift
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive session if needed
sPlt.start_interactive_session(p)
# plot delta time against median drift
sPlt.drift_peak_plot_dtime_against_drift(p, loc)
# ----------------------------------------------------------------------
# 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]
# ------------------------------------------------------------------
# Save drift values to file
# ------------------------------------------------------------------
# get raw input file name
raw_infile = os.path.basename(p['REFFILE'])
# construct filename
driftfits, tag = spirouConfig.Constants.DRIFTPEAK_E2DS_FITS_FILE(p)
driftfitsname = os.path.split(driftfits)[-1]
# log that we are saving drift values
wmsg = 'Saving drift values of Fiber {0} in {1}'
WLOG(p, '', wmsg.format(p['FIBER'], driftfitsname))
# 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_OUTPUT'], value=tag)
# set the input files
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBFLAT'], value=p['FLATFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_REFFILE'], value=raw_infile)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBWAVE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# save drift values
p = spirouImage.WriteImage(p, driftfits, loc['DRIFT'], hdict)
# ------------------------------------------------------------------
# print .tbl result
# ------------------------------------------------------------------
# construct filename
drifttbl = spirouConfig.Constants.DRIFTPEAK_E2DS_TBL_FILE(p)
drifttblname = os.path.split(drifttbl)[-1]
# construct and write table
columnnames = ['time', 'drift', 'drifterr', 'drift_left', 'drift_right']
columnformats = ['7.4f', '6.2f', '6.3f', '6.2f', '6.2f']
columnvalues = [
loc['DELTATIME'], loc['MEANRV'], loc['MERRDRIFT'], loc['MEANRV_LEFT'],
loc['MEANRV_RIGHT']
]
table = spirouImage.MakeTable(p,
columns=columnnames,
values=columnvalues,
formats=columnformats)
# write table
wmsg = 'Average Drift saved in {0} Saved '
WLOG(p, '', wmsg.format(drifttblname))
spirouImage.WriteTable(p, table, drifttbl, fmt='ascii.rst')
# ------------------------------------------------------------------
# Plot amp and llpeak
# ------------------------------------------------------------------
if p['DRS_PLOT'] and p['DRIFT_PEAK_PLOT_LINE_LOG_AMP']:
# start interactive session if needed
sPlt.start_interactive_session(p)
# plot delta time against median drift
sPlt.drift_peak_plot_llpeak_amps(p, loc)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def measure_background_flatfield(p, image, header):
"""
Measures the background of a flat field image - currently does not work
as need an interpolation function (see code)
:param p: parameter dictionary, ParamDict containing constants
Must contain at least:
IC_BKGR_WINDOW: int, Half-size of window for background
measurements
GAIN: float, the gain of the image (from HEADER)
SIGDET: float, the read noise of the image (from HEADER)
log_opt: string, log option, normally the program name
:param image: numpy array (2D), the image to measure the background of
:return background: numpy array (2D), the background image (currently all
zeros) as background not implemented
:return xc: numpy array (1D), the box centers (x positions) used to create
the background image
:return yc: numpy array (1D), the box centers (y positions) used to create
the background image
:return minlevel: numpy array (2D), the 2 * size -th minimum pixel value
of each box for each pixel in the image
"""
# func_name = __NAME__ + '.measure_background_flatfield()'
image1 = np.array(image)
image_med = signal.medfilt(image1, [3, 3])
# get constants
size = p['IC_BKGR_WINDOW']
percent = p['IC_BKGR_PERCENT']
# create the box centers
xc = np.arange(size, image_med.shape[0], 2 * size)
yc = np.arange(size, image_med.shape[1], 2 * size)
# min level box
minlevel = np.zeros((len(xc), len(yc)))
# loop around all boxes with centers xc and yc
for i_it in range(len(xc)):
for j_it in range(len(yc)):
xci, yci = xc[i_it], yc[j_it]
# get the pixels for this box
subframe = image_med[xci - size:xci + size,
yci - size:yci + size].ravel()
# get the (2*size)th minimum pixel
with warnings.catch_warnings(record=True) as _:
value = np.nanpercentile(subframe, percent)
if np.isfinite(value):
minlevel[i_it, j_it] = value
else:
minlevel[i_it, j_it] = 0.0
# TODO: FIX PROBLEMS: SECTION NEEDS COMMENTING!!!
gridx1, gridy1 = np.mgrid[size:image_med.shape[0]:2 * size,
size:image_med.shape[1]:2 * size]
gridx2, gridy2 = np.indices(image_med.shape)
# TODO: FIX PROBLEMS: SECTION NEEDS COMMENTING!!!
minlevel2 = np.zeros((minlevel.shape[0] + 2, minlevel.shape[1] + 2),
dtype=float)
minlevel2[1:-1, 1:-1] = minlevel
minlevel2[0, 1:-1] = minlevel[0]
minlevel2[-1, 1:-1] = minlevel[-1]
minlevel2[1:-1, 0] = minlevel[:, 0]
minlevel2[1:-1, -1] = minlevel[:, -1]
minlevel2[0, 0] = minlevel[0, 0]
minlevel2[-1, -1] = minlevel[-1, -1]
minlevel2[0, -1] = minlevel[0, -1]
minlevel2[-1, 0] = minlevel[-1, 0]
# TODO: FIX PROBLEMS: SECTION NEEDS COMMENTING!!!
gridx1c = np.zeros((gridx1.shape[0] + 2, gridx1.shape[1] + 2), dtype=float)
gridx1c[1:-1, 1:-1] = gridx1
gridx1c[0, :] = 0
gridx1c[-1, :] = np.shape(image_med)[0]
gridx1c[:, 0] = gridx1c[:, 1]
gridx1c[:, -1] = gridx1c[:, -2]
# TODO: FIX PROBLEMS: SECTION NEEDS COMMENTING!!!
gridy1c = np.zeros((gridy1.shape[0] + 2, gridy1.shape[1] + 2), dtype=float)
gridy1c[1:-1, 1:-1] = gridy1
gridy1c[:, 0] = 0
gridy1c[:, -1] = np.shape(image_med)[1]
gridy1c[0, :] = gridy1c[1, :]
gridy1c[-1, :] = gridy1c[-2, :]
# TODO: FIX PROBLEMS: SECTION NEEDS COMMENTING!!!
points = np.array([gridx1c.ravel(), gridy1c.ravel()]).T
background = griddata(points, minlevel2.ravel(), (gridx2, gridy2),
method='cubic')
# ----------------------------------------------------------------------
# Produce DEBUG plot
# ----------------------------------------------------------------------
data1 = image - background
# construct debug background file name
debug_background, tag = spirouConfig.Constants.BACKGROUND_CORRECT_FILE(p)
# construct images
dimages = [data1, background, image1, image_med]
# construct hdicts
hdict = spirouImage.CopyOriginalKeys(header)
drsname = ['DRSNAME', None, 'Extension description']
hdict1 = spirouImage.AddKey(p, hdict, drsname, value='Corrected')
hdict2 = spirouImage.AddKey(p, hdict, drsname, value='Background')
hdict3 = spirouImage.AddKey(p, hdict, drsname, value='Original')
hdict4 = spirouImage.AddKey(p, hdict, drsname, value='Median')
dheaders = [hdict1, hdict2, hdict3, hdict4]
# write debug to file
spirouImage.WriteImageMulti(p, debug_background, dimages, hdicts=dheaders)
# ----------------------------------------------------------------------
# return background, xc, yc and minlevel
return background, gridx1c, gridy1c, minlevel2
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, files=None):
"""
cal_SLIT_spirou.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_SLIT_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)
: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)
# set the fiber type
p['FIB_TYP'] = 'AB'
p.set_source('FIB_TYP', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# 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')
# ----------------------------------------------------------------------
# Correction of DARK
# ----------------------------------------------------------------------
p, datac = spirouImage.CorrectForDark(p, data, hdr)
# ----------------------------------------------------------------------
# Resize image
# ----------------------------------------------------------------------
# rotate the image and convert from ADU/s to e-
data = spirouImage.ConvertToE(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)
data2 = spirouImage.ResizeImage(p, data0, **bkwargs)
# log change in data size
WLOG(p, '', ('Image format changed to '
'{0}x{1}').format(*data2.shape))
# ----------------------------------------------------------------------
# Correct for the BADPIX mask (set all bad pixels to zero)
# ----------------------------------------------------------------------
p, data2 = spirouImage.CorrectForBadPix(p, data2, hdr)
# ----------------------------------------------------------------------
# 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, data2, hdr]
# background, xc, yc, minlevel = spirouBACK.MeasureBackgroundFF(*bargs)
p, background = spirouBACK.MeasureBackgroundMap(*bargs)
else:
background = np.zeros_like(data2)
p['BKGRDFILE'] = 'None'
p.set_source('BKGRDFILE', __NAME__ + '.main()')
# correct data2 with background
data2 = data2 - background
# ----------------------------------------------------------------------
# Log the number of dead pixels
# ----------------------------------------------------------------------
# get the number of bad pixels
n_bad_pix = np.nansum(~np.isfinite(data2))
n_bad_pix_frac = n_bad_pix * 100 / np.product(data2.shape)
# Log number
wmsg = 'Nb dead pixels = {0} / {1:.2f} %'
WLOG(p, 'info', wmsg.format(int(n_bad_pix), n_bad_pix_frac))
# ----------------------------------------------------------------------
# Log the number of dead pixels
# ----------------------------------------------------------------------
loc = ParamDict()
# ----------------------------------------------------------------------
# Loop around fiber types
# ----------------------------------------------------------------------
# set fiber
p['FIBER'] = p['FIB_TYP']
# ------------------------------------------------------------------
# Get localisation coefficients
# ------------------------------------------------------------------
# original there is a loop but it is not used --> removed
p = spirouImage.FiberParams(p, p['FIBER'], merge=True)
# get localisation fit coefficients
p, loc = spirouLOCOR.GetCoeffs(p, hdr, loc)
# ------------------------------------------------------------------
# Calculating the tilt
# ------------------------------------------------------------------
# get the tilt by extracting the AB fibers and correlating them
loc = spirouImage.GetTilt(p, loc, data2)
# fit the tilt with a polynomial
loc = spirouImage.FitTilt(p, loc)
# log the tilt dispersion
wmsg = 'Tilt dispersion = {0:.3f} deg'
WLOG(p, 'info', wmsg.format(loc['RMS_TILT']))
# ------------------------------------------------------------------
# Plotting
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# plots setup: start interactive plot
sPlt.start_interactive_session(p)
# plot image with selected order shown
sPlt.slit_sorder_plot(p, loc, data2)
# plot slit tilt angle and fit
sPlt.slit_tilt_angle_and_fit_plot(p, loc)
# end interactive section
sPlt.end_interactive_session(p)
# ------------------------------------------------------------------
# Replace tilt by the global fit
# ------------------------------------------------------------------
loc['TILT'] = loc['YFIT_TILT']
oldsource = loc.get_source('tilt')
loc.set_source('TILT', oldsource + '+{0}/main()'.format(__NAME__))
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# check that tilt rms is below required
if loc['RMS_TILT'] > p['QC_SLIT_RMS']:
# add failed message to fail message list
fmsg = 'abnormal RMS of SLIT angle ({0:.2f} > {1:.2f} deg)'
fail_msg.append(fmsg.format(loc['RMS_TILT'], p['QC_SLIT_RMS']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(loc['RMS_TILT'])
qc_names.append('RMS_TILT')
qc_logic.append('RMS_TILT > {0:.2f}'.format(p['QC_SLIT_RMS']))
# ----------------------------------------------------------------------
# check that tilt is less than max tilt required
max_tilt = np.max(loc['TILT'])
if max_tilt > p['QC_SLIT_MAX']:
# add failed message to fail message list
fmsg = 'abnormal SLIT angle ({0:.2f} > {1:.2f} deg)'
fail_msg.append(fmsg.format(max_tilt, p['QC_SLIT_MAX']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(max_tilt)
qc_names.append('max_tilt')
qc_logic.append('max_tilt > {0:.2f}'.format(p['QC_SLIT_MAX']))
# ----------------------------------------------------------------------
# check that tilt is greater than min tilt required
min_tilt = np.min(loc['TILT'])
if min_tilt < p['QC_SLIT_MIN']:
# add failed message to fail message list
fmsg = 'abnormal SLIT angle ({0:.2f} < {1:.2f} deg)'
fail_msg.append(fmsg.format(max_tilt, p['QC_SLIT_MIN']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(min_tilt)
qc_names.append('min_tilt')
qc_logic.append('min_tilt > {0:.2f}'.format(p['QC_SLIT_MIN']))
# ----------------------------------------------------------------------
# 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]
# ----------------------------------------------------------------------
# Save and record of tilt table
# ----------------------------------------------------------------------
# copy the tilt along the orders
tiltima = np.ones((int(loc['NUMBER_ORDERS']/2), data2.shape[1]))
tiltima *= loc['TILT'][:, None]
# get the raw tilt file name
raw_tilt_file = os.path.basename(p['FITSFILENAME'])
# construct file name and path
tiltfits, tag = spirouConfig.Constants.SLIT_TILT_FILE(p)
tiltfitsname = os.path.basename(tiltfits)
# Log that we are saving tilt file
wmsg = 'Saving tilt information in file: {0}'
WLOG(p, '', wmsg.format(tiltfitsname))
# Copy keys from fits file
hdict = spirouImage.CopyOriginalKeys(hdr)
# 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=tag)
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'])
hdict = spirouImage.AddKey1DList(p, hdict, p['KW_INFILE1'], dim1name='file',
values=p['ARG_FILE_NAMES'])
# add qc parameters
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add tilt parameters as 1d list
hdict = spirouImage.AddKey1DList(p, hdict, p['KW_TILT'], values=loc['TILT'])
# write tilt file to file
p = spirouImage.WriteImage(p, tiltfits, tiltima, hdict)
# ----------------------------------------------------------------------
# Update the calibration data base
# ----------------------------------------------------------------------
if p['QC']:
keydb = 'TILT'
# copy localisation file to the calibDB folder
spirouDB.PutCalibFile(p, tiltfits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, tiltfitsname, hdr)
# ----------------------------------------------------------------------
# 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):
"""
cal_DARK_spirou.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__)
p = spirouStartup.LoadArguments(p, night_name, files)
p = spirouStartup.InitialFileSetup(p)
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
p, data, hdr = spirouImage.ReadImageAndCombine(p, framemath='average')
# ----------------------------------------------------------------------
# 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')
# ----------------------------------------------------------------------
# Dark exposure time check
# ----------------------------------------------------------------------
# log the Dark exposure time
WLOG(p, 'info', 'Dark Time = {0:.3f} s'.format(p['EXPTIME']))
# Quality control: make sure the exposure time is longer than qc_dark_time
if p['EXPTIME'] < p['QC_DARK_TIME']:
emsg = 'Dark exposure time too short (< {0:.1f} s)'
WLOG(p, 'error', emsg.format(p['QC_DARK_TIME']))
# ----------------------------------------------------------------------
# Resize image
# ----------------------------------------------------------------------
# # rotate the image and conver from ADU/s to e-
# data = data[::-1, ::-1] * p['exptime'] * p['gain']
# convert NaN to zeros
nanmask = ~np.isfinite(data)
data0 = np.where(nanmask, np.zeros_like(data), data)
# resize blue image
bkwargs = dict(xlow=p['IC_CCDX_BLUE_LOW'],
xhigh=p['IC_CCDX_BLUE_HIGH'],
ylow=p['IC_CCDY_BLUE_LOW'],
yhigh=p['IC_CCDY_BLUE_HIGH'])
datablue, nx2, ny2 = spirouImage.ResizeImage(p, data, **bkwargs)
# Make sure we have data in the blue image
if nx2 == 0 or ny2 == 0:
WLOG(p, 'error', ('IC_CCD(X/Y)_BLUE_(LOW/HIGH) remove '
'all pixels from image.'))
# resize red image
rkwargs = dict(xlow=p['IC_CCDX_RED_LOW'],
xhigh=p['IC_CCDX_RED_HIGH'],
ylow=p['IC_CCDY_RED_LOW'],
yhigh=p['IC_CCDY_RED_HIGH'])
datared, nx3, ny3 = spirouImage.ResizeImage(p, data, **rkwargs)
# Make sure we have data in the red image
if nx3 == 0 or ny3 == 0:
WLOG(p, 'error', ('IC_CCD(X/Y)_RED_(LOW/HIGH) remove '
'all pixels from image.'))
# ----------------------------------------------------------------------
# Dark Measurement
# ----------------------------------------------------------------------
# Log that we are doing dark measurement
WLOG(p, '', 'Doing Dark measurement')
# measure dark for whole frame
p = spirouImage.MeasureDark(p, data, 'Whole det', 'full')
# measure dark for blue part
p = spirouImage.MeasureDark(p, datablue, 'Blue part', 'blue')
# measure dark for rede part
p = spirouImage.MeasureDark(p, datared, 'Red part', 'red')
# ----------------------------------------------------------------------
# Identification of bad pixels
# ----------------------------------------------------------------------
# get number of bad dark pixels (as a fraction of total pixels)
with warnings.catch_warnings(record=True) as w:
baddark = 100.0 * np.sum(data0 > p['DARK_CUTLIMIT'])
baddark /= np.product(data0.shape)
# log the fraction of bad dark pixels
wmsg = 'Frac pixels with DARK > {0:.2f} ADU/s = {1:.3f} %'
WLOG(p, 'info', wmsg.format(p['DARK_CUTLIMIT'], baddark))
# define mask for values above cut limit or NaN
with warnings.catch_warnings(record=True) as w:
datacutmask = ~((data0 > p['DARK_CUTLIMIT']) | (~np.isfinite(data)))
spirouCore.spirouLog.warninglogger(p, w)
# get number of pixels above cut limit or NaN
n_bad_pix = np.product(data.shape) - np.nansum(datacutmask)
# work out fraction of dead pixels + dark > cut, as percentage
p['DADEADALL'] = n_bad_pix * 100 / np.product(data.shape)
p.set_source('DADEADALL', __NAME__ + '/main()')
# log fraction of dead pixels + dark > cut
logargs = [p['DARK_CUTLIMIT'], p['DADEADALL']]
WLOG(p, 'info', ('Total Frac dead pixels (N.A.N) + DARK > '
'{0:.2f} ADU/s = {1:.3f} %').format(*logargs))
# ----------------------------------------------------------------------
# Plots
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive plot
sPlt.start_interactive_session(p)
# plot the image with blue and red regions
sPlt.darkplot_image_and_regions(p, data)
# plot histograms
sPlt.darkplot_histograms(p)
# end interactive session
sPlt.end_interactive_session(p)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# check that med < qc_max_darklevel
if p['MED_FULL'] > p['QC_MAX_DARKLEVEL']:
# add failed message to fail message list
fmsg = 'Unexpected Median Dark level ({0:5.2f} > {1:5.2f} ADU/s)'
fail_msg.append(fmsg.format(p['MED_FULL'], p['QC_MAX_DARKLEVEL']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(p['MED_FULL'])
qc_names.append('MED_FULL')
qc_logic.append('MED_FULL > {0:.2f}'.format(p['QC_MAX_DARKLEVEL']))
# ----------------------------------------------------------------------
# check that fraction of dead pixels < qc_max_dead
if p['DADEADALL'] > p['QC_MAX_DEAD']:
# add failed message to fail message list
fmsg = 'Unexpected Fraction of dead pixels ({0:5.2f} > {1:5.2f} %)'
fail_msg.append(fmsg.format(p['DADEADALL'], p['QC_MAX_DEAD']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(p['DADEADALL'])
qc_names.append('DADEADALL')
qc_logic.append('DADEADALL > {0:.2f}'.format(p['QC_MAX_DEAD']))
# ----------------------------------------------------------------------
# checl that the precentage of dark pixels < qc_max_dark
if baddark > p['QC_MAX_DARK']:
fmsg = ('Unexpected Fraction of dark pixels > {0:.2f} ADU/s '
'({1:.2f} > {2:.2f}')
fail_msg.append(
fmsg.format(p['DARK_CUTLIMIT'], baddark, p['QC_MAX_DARK']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(baddark)
qc_names.append('baddark')
qc_logic.append('baddark > {0:.2f}'.format(p['QC_MAX_DARK']))
# ----------------------------------------------------------------------
# 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]
# ----------------------------------------------------------------------
# Save dark to file
# ----------------------------------------------------------------------
# get raw dark filename
rawdarkfile = os.path.basename(p['FITSFILENAME'])
# construct folder and filename
darkfits, tag = spirouConfig.Constants.DARK_FILE(p)
darkfitsname = os.path.basename(darkfits)
# log saving dark frame
WLOG(p, '', 'Saving Dark frame in ' + darkfitsname)
# add keys from original header file
hdict = spirouImage.CopyOriginalKeys(hdr)
# define new keys to add
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)
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='file',
values=p['ARG_FILE_NAMES'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DARK_DEAD'],
value=p['DADEAD_FULL'])
hdict = spirouImage.AddKey(p, hdict, p['KW_DARK_MED'], value=p['MED_FULL'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DARK_B_DEAD'],
value=p['DADEAD_BLUE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DARK_B_MED'],
value=p['MED_BLUE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DARK_R_DEAD'],
value=p['DADEAD_RED'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DARK_R_MED'],
value=p['MED_RED'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_DARK_CUT'],
value=p['DARK_CUTLIMIT'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# Set to zero dark value > dark_cutlimit
cutmask = data0 > p['DARK_CUTLIMIT']
data0c = np.where(cutmask, np.zeros_like(data0), data0)
# write image and add header keys (via hdict)
p = spirouImage.WriteImage(p, darkfits, data0c, hdict)
# ----------------------------------------------------------------------
# Save bad pixel mask
# ----------------------------------------------------------------------
# construct bad pixel file name
badpixelfits, tag = spirouConfig.Constants.DARK_BADPIX_FILE(p)
badpixelfitsname = os.path.split(badpixelfits)[-1]
# log that we are saving bad pixel map in dir
WLOG(p, '', 'Saving Bad Pixel Map in ' + badpixelfitsname)
# add keys from original header file
hdict = spirouImage.CopyOriginalKeys(hdr)
# define new keys to add
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)
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
hdict['DACUT'] = (p['DARK_CUTLIMIT'],
'Threshold of dark level retain [ADU/s]')
# write to file
datacutmask = np.array(datacutmask, dtype=float)
p = spirouImage.WriteImage(p,
badpixelfits,
datacutmask,
hdict,
dtype='float64')
# ----------------------------------------------------------------------
# Move to calibDB and update calibDB
# ----------------------------------------------------------------------
if p['QC']:
# set dark key
if p['DPRTYPE'] == 'DARK_DARK':
keydb = 'DARK'
elif p['USE_SKYDARK_CORRECTION']:
keydb = 'SKYDARK'
else:
emsg = 'Error: Currently {0} only supports DARK_DARK and OBJ_DARK'
WLOG(p, 'error', emsg.format(__NAME__))
# copy dark fits file to the calibDB folder
spirouDB.PutCalibFile(p, darkfits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, darkfitsname, hdr)
# # set badpix key
# keydb = 'BADPIX_OLD'
# # copy badpix fits file to calibDB folder
# spirouDB.PutCalibFile(p, badpixelfits)
# # update the master calib DB file with new key
# spirouDB.UpdateCalibMaster(p, keydb, badpixelfitsname, hdr)
# ----------------------------------------------------------------------
# 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):
"""
cal_SLIT_spirou.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_SLIT_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)
: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)
# set the fiber type
p['FIBER'] = 'AB'
p.set_source('FIBER', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# 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')
# ----------------------------------------------------------------------
# Correction of DARK
# ----------------------------------------------------------------------
p, datac = spirouImage.CorrectForDark(p, data, hdr)
datac = data
# ----------------------------------------------------------------------
# Resize image
# ----------------------------------------------------------------------
# rotate the image and convert from ADU/s to e-
data = spirouImage.ConvertToE(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)
data2 = spirouImage.ResizeImage(p, data0, **bkwargs)
# log change in data size
WLOG(p, '', ('Image format changed to '
'{0}x{1}').format(*data2.shape))
# ----------------------------------------------------------------------
# Correct for the BADPIX mask (set all bad pixels to zero)
# ----------------------------------------------------------------------
p, data2 = spirouImage.CorrectForBadPix(p, data2, hdr)
p, badpixmap = spirouImage.CorrectForBadPix(p, data2, hdr, return_map=True)
# ----------------------------------------------------------------------
# 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, data2, hdr, badpixmap]
# background, xc, yc, minlevel = spirouBACK.MeasureBackgroundFF(*bargs)
p, background = spirouBACK.MeasureBackgroundMap(*bargs)
else:
background = np.zeros_like(data2)
p['BKGRDFILE'] = 'None'
p.set_source('BKGRDFILE', __NAME__ + '.main()')
# apply background correction to data
data2 = data2 - background
# save data to loc
loc = ParamDict()
loc['DATA'] = data2
loc.set_source('DATA', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Log the number of dead pixels
# ----------------------------------------------------------------------
# get the number of bad pixels
n_bad_pix = np.nansum(data2 <= 0)
n_bad_pix_frac = n_bad_pix * 100 / np.product(data2.shape)
# Log number
wmsg = 'Nb dead pixels = {0} / {1:.2f} %'
WLOG(p, 'info', wmsg.format(int(n_bad_pix), n_bad_pix_frac))
# ------------------------------------------------------------------
# Get localisation coefficients
# ------------------------------------------------------------------
# original there is a loop but it is not used --> removed
p = spirouImage.FiberParams(p, p['FIBER'], merge=True)
# get localisation fit coefficients
p, loc = spirouLOCOR.GetCoeffs(p, hdr, loc)
# ------------------------------------------------------------------
# Calculate shape map
# ------------------------------------------------------------------
loc = spirouImage.GetShapeMap(p, loc)
# ------------------------------------------------------------------
# Plotting
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# plots setup: start interactive plot
sPlt.start_interactive_session(p)
# plot the shape process for each order
sPlt.slit_shape_angle_plot(p, loc)
# end interactive section
sPlt.end_interactive_session(p)
# ------------------------------------------------------------------
# Writing to file
# ------------------------------------------------------------------
# get the raw tilt file name
raw_shape_file = os.path.basename(p['FITSFILENAME'])
# construct file name and path
shapefits, tag = spirouConfig.Constants.SLIT_XSHAPE_FILE(p)
shapefitsname = os.path.basename(shapefits)
# Log that we are saving tilt file
wmsg = 'Saving shape information in file: {0}'
WLOG(p, '', wmsg.format(shapefitsname))
# Copy keys from fits file
# Copy keys from fits file
hdict = spirouImage.CopyOriginalKeys(hdr)
# 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_OUTPUT'], value=tag)
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_CDBSHAPE'], value=raw_shape_file)
# write tilt file to file
p = spirouImage.WriteImage(p, shapefits, loc['DXMAP'], hdict)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# TODO: Decide on some quality control criteria?
# set passed variable and fail message list
passed, fail_msg = True, []
# 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()')
# ----------------------------------------------------------------------
# Move to calibDB and update calibDB
# ----------------------------------------------------------------------
if p['QC']:
keydb = 'SHAPE'
# copy shape file to the calibDB folder
spirouDB.PutCalibFile(p, shapefits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, shapefitsname, hdr)
# ----------------------------------------------------------------------
# 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 output_lsd_image(p, loc, hdict):
"""
Function to set up and save output FITS image to store LSD analyis.
:param p: parameter dictionary, ParamDict containing constants
:param loc: parameter dictionary, ParamDict to store data
Must contain at least:
loc['LSDDATA']: numpy array (2D), LSD analysis data
:param hdict: dictionary, header dictionary of keywordstores
each key is the HEADER key and each value is a list of
two values: [HEADER value, HEADER comment]
:return lsdfits, lsdfitsfitsname:
lsdfits: string, output full path
lsdfitsfitsname: string, output filename
"""
# construct file names
lsdfits, tag = spirouConfig.Constants.LSD_POL_FILE(p, loc)
lsdfitsfitsname = os.path.split(lsdfits)[-1]
columns = ['velocities', 'stokesI', 'stokesI_model', 'stokesVQU', 'Null']
values = [loc['LSD_VELOCITIES'], loc['LSD_STOKESI'],
loc['LSD_STOKESI_MODEL'], loc['LSD_STOKESVQU'],
loc['LSD_NULL']]
# save all data into a single array for output FITS
loc['LSDDATA'] = []
loc['LSDDATA'] = np.append(loc['LSDDATA'], loc['LSD_VELOCITIES'])
loc['LSDDATA'] = np.append(loc['LSDDATA'], loc['LSD_STOKESI'])
loc['LSDDATA'] = np.append(loc['LSDDATA'], loc['LSD_STOKESI_MODEL'])
loc['LSDDATA'] = np.append(loc['LSDDATA'], loc['LSD_STOKESVQU'])
loc['LSDDATA'] = np.append(loc['LSDDATA'], loc['LSD_NULL'])
# add LSD parameters keywords to header
# add input parameters for LSD analysis
hdict = spirouImage.AddKey(p, hdict, p['KW_POL_STOKES'], value=loc['STOKES'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_MASK'],
value=loc['SELECTED_FILE_CCFLINES'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_V0'],
value=p['IC_POLAR_LSD_V0'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_VF'],
value=p['IC_POLAR_LSD_VF'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_NP'],
value=p['IC_POLAR_LSD_NP'])
# add fitted values from gaussian fit to Stokes I LSD
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_FIT_RV'],
value=loc['LSD_FIT_RV'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_FIT_RESOL'],
value=loc['LSD_FIT_RESOL'])
# add statistical quantities from LSD analysis
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_MEANPOL'],
value=loc['LSD_POL_MEAN'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_STDDEVPOL'],
value=loc['LSD_POL_STDDEV'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_MEDIANPOL'],
value=loc['LSD_POL_MEDIAN'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_MEDABSDEVPOL'],
value=loc['LSD_POL_MEDABSDEV'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_STOKESVQU_MEAN'],
value=loc['LSD_STOKESVQU_MEAN'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_STOKESVQU_STDDEV'],
value=loc['LSD_STOKESVQU_STDDEV'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_NULL_MEAN'],
value=loc['LSD_NULL_MEAN'])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_NULL_STDDEV'],
value=loc['LSD_NULL_STDDEV'])
# add information about the meaning of data columns
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_COL1'],
value=p['IC_POLAR_LSD_DATAINFO'][0])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_COL2'],
value=p['IC_POLAR_LSD_DATAINFO'][1])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_COL3'],
value=p['IC_POLAR_LSD_DATAINFO'][2])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_COL4'],
value=p['IC_POLAR_LSD_DATAINFO'][3])
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_LSD_COL5'],
value=p['IC_POLAR_LSD_DATAINFO'][4])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag)
# Store LSD analysis data in FITS TABLE
table = spirouImage.MakeTable(p, columns, values)
spirouImage.WriteTable(p, table, lsdfits, fmt='fits', header=hdict)
# deal with output onto index.fits
p = spirouImage.spirouFITS.write_output_dict(p, lsdfits, hdict)
# Store LSD analysis data in file
#p = spirouImage.WriteImage(p, lsdfits, loc['LSDDATA'], hdict)
# return p, lsdfits and lsdfitsname
return p, lsdfits, lsdfitsfitsname
def main(night_name=None):
# ----------------------------------------------------------------------
# Set up
# ----------------------------------------------------------------------
main_name = __NAME__ + '.main()'
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
p = spirouStartup.LoadArguments(p, night_name, require_night_name=False)
# ----------------------------------------------------------------------
# find all directories if night name was None (ARG_NIGHT_NAME = '')
files, dirs = find_all_reduced_files(p)
# ----------------------------------------------------------------------
# loop around each file
# ----------------------------------------------------------------------
for it in range(len(files)):
# get file name for this iteration
basefilename = os.path.basename(files[it])
# Log process
wmsg = 'Processing file {0} ({1}/{2})'
wargs = [basefilename, it + 1, len(files)]
WLOG(p, 'info', wmsg.format(*wargs))
# get this iteration values
p['FITSFILENAME'] = files[it]
p['ARG_NIGHT_NAME'] = dirs[it]
p['REDUCED_DIR'] = os.path.join(p['DRS_DATA_REDUC'], dirs[it])
p['ARG_FILE_NAMES'] = [basefilename]
p['DRS_TYPE'] = "REDUCED"
# identify fiber
if '_AB.fits' in os.path.basename(files[it]):
p['FIBER'] = 'AB'
elif '_AB.fits' in os.path.basename(files[it]):
p['FIBER'] = 'A'
elif '_AB.fits' in os.path.basename(files[it]):
p['FIBER'] = 'B'
elif '_C.fits' in os.path.basename(files[it]):
p['FIBER'] = 'C'
else:
wmsg1 = 'Wrong fiber type found. This should happen. Skipping'
wmsg2 = '\tFile = {0}'.format(files[it])
WLOG(p, 'warning', [wmsg1, wmsg2])
# skip
continue
# set sources
source = ['FITSFILENAME', 'ARG_NIGHT_NAME', 'REDUCED_DIR', 'FIBER',
'ARG_FILE_NAMES']
p.set_sources(source, main_name)
# define loc storage parameter dictionary
loc = ParamDict()
# ---------------------------------------------------------------------
# Read image file
# ---------------------------------------------------------------------
# read the image data
p, data, hdr = spirouImage.ReadImageAndCombine(p, framemath='add')
# ---------------------------------------------------------------------
# Load calibDB for this file
# ---------------------------------------------------------------------
# as we need a different calibDB for each file
p = spirouStartup.LoadCalibDB(p, header=hdr)
# ------------------------------------------------------------------
# Read wavelength solution
# ------------------------------------------------------------------
# force reading from calibDB
p['CALIB_DB_FORCE_WAVESOL'] = True
p.set_source('CALIB_DB_FORCE_WAVESOL', main_name)
# 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,
return_header=True, fiber=wave_fiber)
loc['WAVEPARAMS'], loc['WAVE'], loc['WAVEFILE'] = wout[:3]
loc['WAVEHDR'], loc['WSOURCE'] = wout[3:]
source_names = ['WAVE', 'WAVEFILE', 'WAVEPARAMS', 'WAVEHDR', 'WSOURCE']
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()')
# ------------------------------------------------------------------
# Save file with new header
# ------------------------------------------------------------------
# log that we are saving E2DS spectrum
wmsg = 'Saving E2DS spectrum of Fiber {0} in {1}'
WLOG(p, '', wmsg.format(p['FIBER'], basefilename))
# 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'])
# set the input files
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBWAVE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
# 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 wave solution coefficients
hdict = spirouImage.AddKey2DList(p, hdict, p['KW_WAVE_PARAM'],
values=loc['WAVEPARAMS'])
# write to file
p = spirouImage.WriteImage(p, p['FITSFILENAME'], data, hdict)
# ----------------------------------------------------------------------
# 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, files=None):
"""
pol_spirou.py main function, if night_name and files are None uses
arguments from run time i.e.:
pol_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 process
(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')
p = spirouStartup.InitialFileSetup(p, calibdb=True)
# ----------------------------------------------------------------------
# Loop through files, identify and sort files and identify fiber types
# ----------------------------------------------------------------------
# set up polar storage
polardict = ParamDict()
# sort files
polardict = spirouPOLAR.SortPolarFiles(p, polardict)
# ----------------------------------------------------------------------
# Load the input polarimetry data and check if provided data are
# sufficient for polarimetry calculation
# ----------------------------------------------------------------------
# set up data storage
loc = ParamDict()
# load files
p, loc = spirouPOLAR.LoadPolarData(p, polardict, loc)
# ------------------------------------------------------------------
# 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=loc['HDR'],
return_wavemap=True,
return_filename=True,
fiber=wave_fiber)
_, loc['WAVE'], loc['WAVEFILE'], loc['WSOURCE'] = wout
loc.set_sources(['WAVE', 'WAVEFILE', 'WSOURCE'], wsource)
# ----------------------------------------------------------------------
# Polarimetry computation
# ----------------------------------------------------------------------
loc = spirouPOLAR.CalculatePolarimetry(p, loc)
# ----------------------------------------------------------------------
# Stokes I computation
# ----------------------------------------------------------------------
loc = spirouPOLAR.CalculateStokesI(p, loc)
# ----------------------------------------------------------------------
# Calculate continuum (for plotting)
# ----------------------------------------------------------------------
loc = spirouPOLAR.CalculateContinuum(p, loc)
# ----------------------------------------------------------------------
# Plots
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive plot
sPlt.start_interactive_session(p)
# plot continuum plots
sPlt.polar_continuum_plot(p, loc)
# plot polarimetry results
sPlt.polar_result_plot(p, loc)
# plot total flux (Stokes I)
sPlt.polar_stokes_i_plot(p, loc)
# end interactive session
sPlt.end_interactive_session(p)
# ----------------------------------------------------------------------
# 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)
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ------------------------------------------------------------------
# Store polarimetry in file(s)
# ------------------------------------------------------------------
# construct file names
degpolfits, tag1 = spirouConfig.Constants.DEG_POL_FILE(p, loc)
degpolfitsname = os.path.split(degpolfits)[-1]
stokes_ifits, tag2 = spirouConfig.Constants.STOKESI_POL_FILE(p, loc)
stokes_ifitsname = os.path.split(stokes_ifits)[-1]
nullpol1fits, tag3 = spirouConfig.Constants.NULL_POL1_FILE(p, loc)
nullpol1fitsname = os.path.split(nullpol1fits)[-1]
nullpol2fits, tag4 = spirouConfig.Constants.NULL_POL2_FILE(p, loc)
nullpol2fitsname = os.path.split(nullpol2fits)[-1]
# log that we are saving POL spectrum
wmsg = 'Saving POL, STOKESI, NULL1, and NULL2 to {0}, {1}, {2}, {3}'
wargs = [
degpolfitsname, stokes_ifitsname, nullpol1fitsname, nullpol2fitsname
]
WLOG(p, '', wmsg.format(*wargs))
# construct header keywords for output products
hdict, loc = spirouPOLAR.PolarHeader(p, loc, polardict, qc_params)
# save POL data to file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
p = spirouImage.WriteImageMulti(p, degpolfits, [loc['POL'], loc['POLERR']],
hdict)
# save NULL1 data to file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag3)
p = spirouImage.WriteImage(p, nullpol1fits, loc['NULL1'], hdict)
# save NULL2 data to file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag4)
p = spirouImage.WriteImage(p, nullpol2fits, loc['NULL2'], hdict)
# add stokes parameter keyword to header
hdict = spirouImage.AddKey(p, hdict, p['KW_POL_STOKES'], value="I")
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag2)
# save STOKESI data to file
multi_image = [loc['STOKESI'], loc['STOKESIERR']]
p = spirouImage.WriteImageMulti(p, stokes_ifits, multi_image, hdict)
# ------------------------------------------------------------------
if p['IC_POLAR_LSD_ANALYSIS']:
# ------------------------------------------------------------------
# LSD Analysis
# ------------------------------------------------------------------
loc = spirouPOLAR.LSDAnalysis(p, loc)
if p['DRS_PLOT'] > 0:
# plot LSD analysis
sPlt.polar_lsd_plot(p, loc)
# save LSD analysis data to file
p, lsdfits, lsdfitsfitsname = spirouPOLAR.OutputLSDimage(p, loc, hdict)
# log that we are saving LSD analysis data
wmsg = 'Saving LSD analysis data to {0}'.format(lsdfitsfitsname)
WLOG(p, '', wmsg)
# ----------------------------------------------------------------------
# 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):
"""
cal_DRIFT_E2DS_spirou.py main function, if arguments are None uses
arguments from run time i.e.:
cal_DRIFT_E2DS_spirou.py [night_directory] [reffile]
: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 reffile: string, the reference file 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 reference file being None (i.e. get from sys.argv)
if reffile is None:
customargs = spirouStartup.GetCustomFromRuntime(
p, [0], [str], ['reffile'])
else:
customargs = dict(reffile=reffile)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsfile='reffile',
mainfitsdir='reduced')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, reffilename = spirouStartup.SingleFileSetup(p, filename=p['REFFILE'])
p['REFFILENAME'] = reffilename
p.set_source('REFFILENAME', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# 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)
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
speref, hdr, nbo, nx = spirouImage.ReadData(p, reffilename)
# add to loc
loc = ParamDict()
loc['SPEREF'] = speref
loc['NUMBER_ORDERS'] = nbo
loc.set_sources(['speref', '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')
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']
# ----------------------------------------------------------------------
# Read 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,
fiber=wave_fiber,
return_wavemap=True,
return_filename=True)
_, loc['WAVE'], loc['WAVEFILE'], loc['WSOURCE'] = wout
source = __NAME__ + '/main() + /spirouImage.GetWaveSolution'
loc.set_sources(['WAVE', 'WAVEFILE', 'WSOURCE'], source)
# ----------------------------------------------------------------------
# Read Flat file
# ----------------------------------------------------------------------
# get flat
p, 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'])
# ----------------------------------------------------------------------
# Background correction
# ----------------------------------------------------------------------
# log that we are performing background correction
if p['IC_DRIFT_BACK_CORR']:
WLOG(p, '', 'Perform background correction')
# get the box size from constants
bsize = p['DRIFT_PEAK_MINMAX_BOXSIZE']
# Loop around the orders
for order_num in range(loc['NUMBER_ORDERS']):
miny, maxy = spirouBACK.MeasureMinMax(loc['SPEREF'][order_num],
bsize)
loc['SPEREF'][order_num] = loc['SPEREF'][order_num] - miny
# ------------------------------------------------------------------
# Compute photon noise uncertainty for reference file
# ------------------------------------------------------------------
# set up the arguments for DeltaVrms2D
dargs = [loc['SPEREF'], loc['WAVE']]
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))
# ------------------------------------------------------------------
# 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)
# plot photon noise uncertainty
sPlt.drift_plot_photon_uncertainty(p, loc)
# ------------------------------------------------------------------
# Get all other files that match kw_OUTPUT and kw_EXT_TYPE from
# ref file
# ------------------------------------------------------------------
# get files
listfiles, listtypes = spirouImage.GetSimilarDriftFiles(p, hdr)
# get the number of files
nfiles = len(listfiles)
# Log the number of files found
wmsgs = [
'Number of files found on directory = {0}'.format(nfiles),
'\tExtensions allowed:'
]
for listtype in listtypes:
wmsgs.append('\t\t - {0}'.format(listtype))
WLOG(p, 'info', wmsgs)
# ------------------------------------------------------------------
# Set up Extract storage for all files
# ------------------------------------------------------------------
# decide whether we need to skip (for large number of files)
if len(listfiles) >= p['DRIFT_NLARGE']:
skip = p['DRIFT_E2DS_FILE_SKIP']
nfiles = int(nfiles / skip)
else:
skip = 1
# set up storage
loc['DRIFT'] = np.zeros((nfiles, loc['NUMBER_ORDERS']))
loc['ERRDRIFT'] = np.zeros((nfiles, loc['NUMBER_ORDERS']))
loc['DELTATIME'] = np.zeros(nfiles)
# set loc sources
keys = ['drift', 'errdrift', 'deltatime']
loc.set_sources(keys, __NAME__ + '/main()()')
# ------------------------------------------------------------------
# Loop around all files: correct for dark, reshape, extract and
# calculate dvrms and meanpond
# ------------------------------------------------------------------
wref = 1
for i_it in range(nfiles):
# get file for this iteration
fpfile = listfiles[::skip][i_it]
# Log the file we are reading
wmsg = 'Reading file {0}'
WLOG(p, '', wmsg.format(os.path.split(fpfile)[-1]))
# ------------------------------------------------------------------
# read e2ds files and get timestamp
# ------------------------------------------------------------------
# read data
rout = spirouImage.ReadData(p, filename=fpfile, log=False)
loc['SPE'], hdri, nxi, nyi = rout
# get acqtime
bjdspe = spirouImage.GetAcqTime(p,
hdri,
name='acqtime',
return_value=1,
kind='julian')
# test whether we want to subtract background
if p['IC_DRIFT_BACK_CORR']:
# Loop around the orders
for order_num in range(loc['NUMBER_ORDERS']):
# get the box size from constants
bsize = p['DRIFT_PEAK_MINMAX_BOXSIZE']
# Measurethe min and max flux
miny, maxy = spirouBACK.MeasureMinMax(loc['SPE'][order_num],
bsize)
# subtract off the background (miny)
loc['SPE'][order_num] = loc['SPE'][order_num] - miny
# ------------------------------------------------------------------
# Compute photon noise uncertainty for iteration file
# ------------------------------------------------------------------
# set up the arguments for DeltaVrms2D
dargs = [loc['SPE'], loc['WAVE']]
dkwargs = dict(sigdet=p['IC_DRIFT_NOISE'],
size=p['IC_DRIFT_BOXSIZE'],
threshold=p['IC_DRIFT_MAXFLUX'])
# run DeltaVrms2D
dvrmsspe, wmodespe = spirouRV.DeltaVrms2D(*dargs, **dkwargs)
# ------------------------------------------------------------------
# Compute the correction of the cosmics and re-normalisation by
# comparison with the reference spectrum
# ------------------------------------------------------------------
# correction of the cosmics and renomalisation by comparison with
# the reference spectrum
dargs = [p, loc['SPEREF'], loc['SPE']]
dkwargs = dict(threshold=p['IC_DRIFT_MAXFLUX'],
size=p['IC_DRIFT_BOXSIZE'],
cut=p['IC_DRIFT_CUT_E2DS'])
spen, cfluxr, cpt = spirouRV.ReNormCosmic2D(*dargs, **dkwargs)
# ------------------------------------------------------------------
# Calculate the RV drift
# ------------------------------------------------------------------
dargs = [loc['SPEREF'], spen, loc['WAVE']]
dkwargs = dict(sigdet=p['IC_DRIFT_NOISE'],
threshold=p['IC_DRIFT_MAXFLUX'],
size=p['IC_DRIFT_BOXSIZE'])
rv = spirouRV.CalcRVdrift2D(*dargs, **dkwargs)
# ------------------------------------------------------------------
# Calculate delta time
# ------------------------------------------------------------------
# calculate the time from reference (in hours)
deltatime = (bjdspe - bjdref) * 24
# ------------------------------------------------------------------
# Calculate RV properties
# ------------------------------------------------------------------
# calculate the mean flux ratio
meanfratio = np.nanmean(cfluxr)
# calculate the weighted mean radial velocity
wref = 1.0 / dvrmsref
meanrv = -1.0 * np.nansum(rv * wref) / np.nansum(wref)
err_meanrv = np.sqrt(dvrmsref + dvrmsspe)
merr = 1. / np.sqrt(np.nansum((1. / err_meanrv)**2))
# Log the RV properties
wmsg = (
'Time from ref={0:.2f} h - Drift mean= {1:.2f} +- {2:.3f} m/s '
'- Flux ratio= {3:.3f} - Nb Comsic= {4}')
WLOG(p, '', wmsg.format(deltatime, meanrv, merr, meanfratio, cpt))
# add this iteration to storage
loc['DRIFT'][i_it] = -1.0 * rv
loc['ERRDRIFT'][i_it] = err_meanrv
loc['DELTATIME'][i_it] = deltatime
# ------------------------------------------------------------------
# Calculate drift properties
# ------------------------------------------------------------------
# get the maximum number of orders to use
nomax = nbo # p['IC_DRIFT_N_ORDER_MAX']
# ------------------------------------------------------------------
# if use mean
if p['DRIFT_TYPE_E2DS'].upper() == 'WEIGHTED MEAN':
# mean radial velocity
sumwref = np.nansum(wref[:nomax])
meanrv = np.nansum(loc['DRIFT'][:, :nomax] * wref[:nomax], 1) / sumwref
# error in mean radial velocity
errdrift2 = loc['ERRDRIFT'][:, :nomax]**2
meanerr = 1.0 / np.sqrt(np.nansum(1.0 / errdrift2, 1))
# add to loc
loc['MDRIFT'] = meanrv
loc['MERRDRIFT'] = meanerr
# else use median
else:
# median drift
loc['MDRIFT'] = np.nanmedian(loc['DRIFT'][:, :nomax], 1)
# median err drift
loc['MERRDRIFT'] = np.nanmedian(loc['ERRDRIFT'][:, :nomax], 1)
# ------------------------------------------------------------------
# set source
loc.set_sources(['mdrift', 'merrdrift'], __NAME__ + '/main()()')
# ------------------------------------------------------------------
# peak to peak drift
driftptp = np.max(loc['MDRIFT']) - np.min(loc['MDRIFT'])
driftrms = np.std(loc['MDRIFT'])
# log th etotal drift peak-to-peak and rms
wmsg = ('Total drift Peak-to-Peak={0:.3f} m/s RMS={1:.3f} m/s in '
'{2:.2f} hour')
wargs = [driftptp, driftrms, np.max(loc['DELTATIME'])]
WLOG(p, '', wmsg.format(*wargs))
# ------------------------------------------------------------------
# Plot of mean drift
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive session if needed
sPlt.start_interactive_session(p)
# plot delta time against median drift
sPlt.drift_plot_dtime_against_mdrift(p, loc, kind='e2ds')
# ----------------------------------------------------------------------
# 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]
# ------------------------------------------------------------------
# Save drift values to file
# ------------------------------------------------------------------
# get raw input file name
raw_infile = os.path.basename(p['REFFILE'])
# construct filename
driftfits, tag = spirouConfig.Constants.DRIFT_E2DS_FITS_FILE(p)
driftfitsname = os.path.split(driftfits)[-1]
# log that we are saving drift values
wmsg = 'Saving drift values of Fiber {0} in {1}'
WLOG(p, '', wmsg.format(p['FIBER'], driftfitsname))
# 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_OUTPUT'], value=tag)
# set the input files
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBFLAT'], value=p['FLATFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_REFFILE'], value=raw_infile)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBWAVE'],
value=loc['WAVEFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_WAVESOURCE'],
value=loc['WSOURCE'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# save drift values
p = spirouImage.WriteImage(p, driftfits, loc['DRIFT'], hdict)
# ------------------------------------------------------------------
# print .tbl result
# ------------------------------------------------------------------
# construct filename
drifttbl = spirouConfig.Constants.DRIFT_E2DS_TBL_FILE(p)
drifttblname = os.path.split(drifttbl)[-1]
# construct and write table
columnnames = ['time', 'drift', 'drifterr']
columnformats = ['7.4f', '6.2f', '6.3f']
columnvalues = [loc['DELTATIME'], loc['MDRIFT'], loc['MERRDRIFT']]
table = spirouImage.MakeTable(p,
columns=columnnames,
values=columnvalues,
formats=columnformats)
# write table
wmsg = 'Average Drift saved in {0} Saved '
WLOG(p, '', wmsg.format(drifttblname))
spirouImage.WriteTable(p, table, drifttbl, fmt='ascii.rst')
# ----------------------------------------------------------------------
# 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['XDIM'], loc['YDIM'] = rd
loc.set_sources(['DATA', 'DATAHDR', 'XDIM', 'YDIM'], main_name)
# ----------------------------------------------------------------------
# Get object name, airmass and berv
# ----------------------------------------------------------------------
# Get object name
loc['OBJNAME'] = spirouImage.GetObjName(p, loc['DATAHDR'])
# Get the airmass
loc['AIRMASS'] = spirouImage.GetAirmass(p, loc['DATAHDR'])
# Get the Barycentric correction from header
p, loc = spirouImage.GetEarthVelocityCorrection(p, loc, loc['DATAHDR'])
# set sources
source = main_name + '+ spirouImage.ReadParams()'
loc.set_sources(['OBJNAME', 'AIRMASS'], source)
loc.set_sources(['OBJNAME', 'AIRMASS'], source)
# ----------------------------------------------------------------------
# Read wavelength solution
# ----------------------------------------------------------------------
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# used for plotting only
wout = spirouImage.GetWaveSolution(p,
image=loc['DATA'],
hdr=loc['DATAHDR'],
return_wavemap=True,
fiber=wave_fiber)
_, loc['WAVE'], _ = wout
loc.set_source('WAVE', main_name)
# ----------------------------------------------------------------------
# Get and Normalise the blaze
# ----------------------------------------------------------------------
p, loc = spirouTelluric.GetNormalizedBlaze(p, loc, loc['DATAHDR'])
# ----------------------------------------------------------------------
# Load transmission files
# ----------------------------------------------------------------------
transdata = spirouDB.GetDatabaseTellMap(p)
trans_files = transdata[0]
# make sure we have unique filenames for trans_files
trans_files = np.unique(trans_files)
# ----------------------------------------------------------------------
# Start plotting
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# start interactive plot
sPlt.start_interactive_session(p)
# ----------------------------------------------------------------------
# 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
else:
loc['FLAG_TEMPLATE'] = True
# load template
template, _, _, _ = spirouImage.ReadImage(p, template_file)
# add to loc
loc['TEMPLATE'] = template
# set the source for flag and template
loc.set_sources(['FLAG_TEMPLATE', 'TEMPLATE'], main_name)
# ----------------------------------------------------------------------
# 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
loc['TAPAS_ALL_SPECIES'] = np.load(tapas_file_name)
loc.set_source('TAPAS_ALL_SPECIES', main_name)
# ----------------------------------------------------------------------
# Generate the absorption map
# ----------------------------------------------------------------------
# get number of files
nfiles = len(trans_files)
npc = p['TELLU_NUMBER_OF_PRINCIPLE_COMP']
# check that we have enough files (greater than number of principle
# components)
if nfiles <= npc:
emsg1 = 'Not enough "TELL_MAP" files in telluDB to run PCA analysis'
emsg2 = '\tNumber of files = {0}, number of PCA components = {1}'
emsg3 = '\tNumber of files > number of PCA components'
emsg4 = '\tAdd more files or reduce number of PCA components'
WLOG(p, 'error', [emsg1, emsg2.format(nfiles, npc), emsg3, emsg4])
# check whether we can used pre-saved abso
filetime = spirouImage.GetMostRecent(trans_files)
tout = spirouConfig.Constants.TELLU_ABSO_SAVE(p, filetime)
abso_save_file, absoprefix = tout
use_saved = os.path.exists(abso_save_file)
# noinspection PyBroadException
try:
# try loading from file
abso = np.load(abso_save_file)
# log progress
wmsg = 'Loaded abso from file {0}'.format(abso_save_file)
WLOG(p, '', wmsg)
except:
# set up storage for the absorption
abso = np.zeros([nfiles, np.product(loc['DATA'].shape)])
# loop around outputfiles and add them to abso
for it, filename in enumerate(trans_files):
# load data
data_it, _, _, _ = spirouImage.ReadImage(p, filename=filename)
# push data into array
abso[it, :] = data_it.reshape(np.product(loc['DATA'].shape))
# log progres
wmsg = 'Saving abso to file {0}'.format(abso_save_file)
WLOG(p, '', wmsg)
# remove all abso save files (only need most recent one)
afolder = os.path.dirname(abso_save_file)
afilelist = os.listdir(afolder)
for afile in afilelist:
if afile.startswith(absoprefix):
os.remove(os.path.join(afolder, afile))
# save to file for later use
np.save(abso_save_file, abso)
# filter out rows of all NaNs
# TODO: Why are we getting all NaN e2ds files?
abso_filtered = []
for row in range(len(abso)):
if np.sum(np.isnan(abso[row])) != len(abso[row]):
abso_filtered.append(abso[row])
else:
wargs = [trans_files[row]]
WLOG(p, '', 'Removing trans file {0} (all NaN)'.format(*wargs))
abso = np.array(abso_filtered)
# log the absorption cube
with warnings.catch_warnings(record=True) as w:
log_abso = np.log(abso)
# ----------------------------------------------------------------------
# Locate valid pixels for PCA
# ----------------------------------------------------------------------
# determining the pixels relevant for PCA construction
keep = np.isfinite(np.sum(abso, axis=0))
# log fraction of valid (non NaN) pixels
fraction = np.nansum(keep) / len(keep)
wmsg = 'Fraction of valid pixels (not NaNs) for PCA construction = {0:.3f}'
WLOG(p, '', wmsg.format(fraction))
# log fraction of valid pixels > 1 - (1/e)
with warnings.catch_warnings(record=True) as w:
keep &= np.min(log_abso, axis=0) > -1
fraction = np.nansum(keep) / len(keep)
wmsg = 'Fraction of valid pixels with transmission > 1 - (1/e) = {0:.3f}'
WLOG(p, '', wmsg.format(fraction))
# ----------------------------------------------------------------------
# Perform PCA analysis on the log of the telluric absorption map
# ----------------------------------------------------------------------
# Requires p:
# TELLU_NUMBER_OF_PRINCIPLE_COMP
# ADD_DERIV_PC
# FIT_DERIV_PC
# Requires loc:
# DATA
# Returns loc:
# PC
# NPC
# FIT_PC
loc = spirouTelluric.CalculateAbsorptionPCA(p, loc, log_abso, keep)
# Plot PCA components
# debug plot
if p['DRS_PLOT'] and (p['DRS_DEBUG'] > 1):
# plot the transmission map plot
sPlt.tellu_pca_comp_plot(p, loc)
# ----------------------------------------------------------------------
# Get master wavelength grid for shifting
# ----------------------------------------------------------------------
# get master wave map
loc['MASTERWAVEFILE'] = spirouDB.GetDatabaseMasterWave(p)
loc.set_source('MASTERWAVEFILE', main_name)
# log progress
wmsg1 = 'Getting master wavelength grid'
wmsg2 = '\tFile = {0}'.format(os.path.basename(loc['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=loc['MASTERWAVEFILE'],
return_wavemap=True,
quiet=True,
fiber=wave_fiber)
_, loc['MASTERWAVE'], _ = mout
loc.set_source('MASTERWAVE', main_name)
# ----------------------------------------------------------------------
# Loop around telluric files
# ----------------------------------------------------------------------
for basefilename in p['ARG_FILE_NAMES']:
# ------------------------------------------------------------------
# Construct absolute file path
# ------------------------------------------------------------------
filename = os.path.join(p['ARG_FILE_DIR'], basefilename)
# ------------------------------------------------------------------
# Construct output file names
# ------------------------------------------------------------------
outfile1, tag1 = CONSTANTS.TELLU_FIT_OUT_FILE(p, filename)
outfilename1 = os.path.basename(outfile1)
outfile2, tag2 = CONSTANTS.TELLU_FIT_RECON_FILE(p, filename)
outfilename2 = os.path.basename(outfile2)
# ------------------------------------------------------------------
# Read filename
# ------------------------------------------------------------------
# read image
tdata, thdr, _, _ = spirouImage.ReadImage(p, filename)
# normalise with blaze function
loc['SP'] = tdata / loc['NBLAZE']
loc.set_source('SP', main_name)
# ------------------------------------------------------------------
# check that file has valid DPRTYPE
# ------------------------------------------------------------------
# get FP_FP DPRTYPE
p = spirouImage.ReadParam(p, thdr, '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
# ------------------------------------------------------------------
# Set storage
# ------------------------------------------------------------------
loc['RECON_ABSO'] = np.ones(np.product(loc['DATA'].shape))
loc['AMPS_ABSOL_TOTAL'] = np.zeros(loc['NPC'])
loc.set_sources(['RECON_ABSO', 'AMPS_ABSOL_TOTAL'], main_name)
# ------------------------------------------------------------------
# Read wavelength solution
# ------------------------------------------------------------------
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get wavelength solution
wout = spirouImage.GetWaveSolution(p,
image=tdata,
hdr=thdr,
return_wavemap=True,
return_filename=True,
fiber=wave_fiber)
_, loc['WAVE_IT'], loc['WAVEFILE'], loc['WSOURCE'] = wout
loc.set_sources(['WAVE_IT', 'WAVEFILE', 'WSOURCE'], main_name)
# load wave keys
loc = spirouImage.GetWaveKeys(p, loc, thdr)
# ------------------------------------------------------------------
# Interpolate at shifted wavelengths (if we have a template)
# ------------------------------------------------------------------
if loc['FLAG_TEMPLATE']:
# Requires p:
# TELLU_FIT_KEEP_FRAC
# Requires loc:
# DATA
# TEMPLATE
# WAVE_IT
# Returns:
# TEMPLATE2
loc = spirouTelluric.BervCorrectTemplate(p, loc, thdr)
# debug plot
if p['DRS_PLOT'] and (p['DRS_DEBUG'] > 1):
# plot the transmission map plot
sPlt.tellu_fit_tellu_spline_plot(p, loc)
# store PC and TAPAS_ALL_SPECIES before shift
loc['PC_PRESHIFT'] = np.array(loc['PC'])
loc['TAPAS_ALL_PRESHIFT'] = np.array(loc['TAPAS_ALL_SPECIES'])
loc.set_sources(['PC_PRESHIFT', 'TAPAS_ALL_PRESHIFT'], main_name)
# ------------------------------------------------------------------
# Shift the pca components to correct frame
# ------------------------------------------------------------------
# log process
wmsg1 = 'Shifting PCA components from master wavelength grid'
wmsg2 = '\tFile = {0}'.format(os.path.basename(loc['MASTERWAVEFILE']))
WLOG(p, '', [wmsg1, wmsg2])
# shift pca components (one by one)
for comp in range(loc['NPC']):
wargs = [p, loc['PC'][:, comp], loc['MASTERWAVE'], loc['WAVE_IT']]
shift_pc = spirouTelluric.Wave2Wave(*wargs, reshape=True)
loc['PC'][:, comp] = shift_pc.reshape(wargs[1].shape)
wargs = [
p, loc['FIT_PC'][:, comp], loc['MASTERWAVE'], loc['WAVE_IT']
]
shift_fpc = spirouTelluric.Wave2Wave(*wargs, reshape=True)
loc['FIT_PC'][:, comp] = shift_fpc.reshape(wargs[1].shape)
# ------------------------------------------------------------------
# Shift the tapas spectrum to correct frame
# ------------------------------------------------------------------
# log process
wmsg1 = 'Shifting TAPAS spectrum from master wavelength grid'
wmsg2 = '\tFile = {0}'.format(os.path.basename(loc['MASTERWAVEFILE']))
WLOG(p, '', [wmsg1, wmsg2])
# shift tapas
for comp in range(len(loc['TAPAS_ALL_SPECIES'])):
wargs = [
p, loc['TAPAS_ALL_SPECIES'][comp], loc['MASTERWAVE'],
loc['WAVE_IT']
]
stapas = spirouTelluric.Wave2Wave(*wargs, reshape=True)
loc['TAPAS_ALL_SPECIES'][comp] = stapas.reshape(wargs[1].shape)
# Debug plot to test shifting
if p['DRS_PLOT'] and p['DRS_DEBUG'] > 1:
sPlt.tellu_fit_debug_shift_plot(p, loc)
# ------------------------------------------------------------------
# Calculate reconstructed absorption
# ------------------------------------------------------------------
# Requires p:
# TELLU_FIT_MIN_TRANSMISSION
# TELLU_FIT_NITER
# TELLU_LAMBDA_MIN
# TELLU_LAMBDA_MAX
# TELLU_FIT_VSINI
# TRANSMISSION_CUT
# FIT_DERIV_PC
# LOG_OPT
# Requires loc:
# FLAG_TEMPLATE
# TAPAS_ALL_SPECIES
# AMPS_ABSOL_TOTAL
# WAVE_IT
# TEMPLATE2
# FIT_PC
# NPC
# PC
# Returns loc:
# SP2
# TEMPLATE2
# RECON_ABSO
# AMPS_ABSOL_TOTAL
loc = spirouTelluric.CalcReconAbso(p, loc)
# debug plot
if p['DRS_PLOT'] > 0:
# plot the recon abso plot
sPlt.tellu_fit_recon_abso_plot(p, loc)
# ------------------------------------------------------------------
# Get molecular absorption
# ------------------------------------------------------------------
# Requires p:
# TELLU_FIT_LOG_LIMIT
# Requeres loc:
# RECON_ABSO
# TAPAS_ALL_SPECIES
# Returns loc:
# TAPAS_{molecule}
loc = spirouTelluric.CalcMolecularAbsorption(p, loc)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# get SNR for each order from header
nbo = loc['DATA'].shape[0]
snr_order = p['QC_FIT_TELLU_SNR_ORDER']
snr = spirouImage.Read1Dkey(p, thdr, p['kw_E2DS_SNR'][0], nbo)
# check that SNR is high enough
if snr[snr_order] < p['QC_FIT_TELLU_SNR_MIN']:
fmsg = 'low SNR in order {0}: ({1:.2f} < {2:.2f})'
fargs = [snr_order, snr[snr_order], p['QC_FIT_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_FIT_TELLU_SNR_ORDER']))
# ----------------------------------------------------------------------
# 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]
# ------------------------------------------------------------------
# Get components amplitudes for header
# ------------------------------------------------------------------
# get raw file name
raw_in_file = os.path.basename(p['FITSFILENAME'])
# copy original keys
hdict = spirouImage.CopyOriginalKeys(thdr)
# 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='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)
# set tellu keys
npc = loc['NPC']
hdict = spirouImage.AddKey(p, hdict, p['KW_TELLU_NPC'], value=npc)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_TELLU_FIT_DPC'],
value=p['FIT_DERIV_PC'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_TELLU_ADD_DPC'],
value=p['ADD_DERIV_PC'])
if p['ADD_DERIV_PC']:
values = loc['AMPS_ABSOL_TOTAL'][:npc - 2]
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_TELLU_AMP_PC'],
values=values,
dim1name='amp')
hdict = spirouImage.AddKey(p,
hdict,
p['KW_TELLU_DV_TELL1'],
value=loc['AMPS_ABSOL_TOTAL'][npc - 2])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_TELLU_DV_TELL2'],
value=loc['AMPS_ABSOL_TOTAL'][npc - 1])
else:
values = loc['AMPS_ABSOL_TOTAL'][:npc]
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_TELLU_AMP_PC'],
values=values,
dim1name='PC')
# ------------------------------------------------------------------
# Write corrected spectrum to E2DS
# ------------------------------------------------------------------
# reform the E2DS
sp_out = loc['SP2'] / loc['RECON_ABSO']
sp_out = sp_out.reshape(loc['DATA'].shape)
# multiply by blaze
sp_out = sp_out * loc['NBLAZE']
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
# log progress
wmsg = 'Saving {0} to file'.format(outfilename1)
WLOG(p, '', wmsg)
# write sp_out to file
p = spirouImage.WriteImage(p, outfile1, sp_out, hdict)
# ------------------------------------------------------------------
# 1-dimension spectral S1D (uniform in wavelength)
# ------------------------------------------------------------------
# get arguments for E2DS to S1D
e2dsargs = [loc['WAVE'], sp_out, 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
targs = [p, raw_in_file]
s1dfile1, tag3 = spirouConfig.Constants.TELLU_FIT_S1D_FILE1(*targs)
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) in {0}'
WLOG(p, '', wmsg.format(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'], sp_out, 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
targs = [p, raw_in_file]
s1dfile2, tag4 = spirouConfig.Constants.TELLU_FIT_S1D_FILE2(*targs)
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) in {0}'
WLOG(p, '', wmsg.format(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)
# ------------------------------------------------------------------
# Write reconstructed absorption to E2DS
# ------------------------------------------------------------------
# set up empty storage
recon_abso2 = np.zeros_like(loc['DATA'])
# get dimensions of data
ydim, xdim = loc['DATA'].shape
# loop around orders
for order_num in range(ydim):
# get start and end points
start, end = xdim * order_num, xdim * order_num + xdim
# save to storage
recon_abso2[order_num, :] = loc['RECON_ABSO'][start:end]
# add molecular absorption to file
for it, molecule in enumerate(p['TELLU_ABSORBERS'][1:]):
# get molecule keyword store and key
molkey = '{0}_{1}'.format(p['KW_TELLU_ABSO'][0], molecule.upper())
molkws = [molkey, 0, 'Absorption in {0}'.format(molecule.upper())]
# load into hdict
hdict = spirouImage.AddKey(p, hdict, molkws, value=loc[molkey])
# add water col
if molecule == 'h2o':
loc['WATERCOL'] = loc[molkey]
# set source
loc.set_source('WATERCOL', main_name)
# add the tau keys
hdict = spirouImage.AddKey(p,
hdict,
p['KW_TAU_H2O'],
value=loc['TAU_H2O'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_TAU_REST'],
value=loc['TAU_REST'])
# log progress
wmsg = 'Saving {0} to file'.format(outfilename2)
WLOG(p, '', wmsg)
# write recon_abso to file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag2)
p = spirouImage.WriteImage(p, outfile2, recon_abso2, hdict)
# ------------------------------------------------------------------
# Update the Telluric database
# ------------------------------------------------------------------
if p['QC']:
# add TELLU_OBJ to telluric database
oparams = dict(objname=loc['OBJNAME'],
berv=loc['BERV'],
airmass=loc['AIRMASS'],
watercol=loc['WATERCOL'])
spirouDB.UpdateDatabaseTellObj(p, outfilename1, **oparams)
# copy file to database
spirouDB.PutTelluFile(p, outfile1)
# add TELLU_RECON to telluric database
# add TELLU_OBJ to telluric database
oparams = dict(objname=loc['OBJNAME'],
berv=loc['BERV'],
airmass=loc['AIRMASS'],
watercol=loc['WATERCOL'])
spirouDB.UpdateDatabaseTellRecon(p, outfilename2, **oparams)
# copy file to database
spirouDB.PutTelluFile(p, outfile2)
# ----------------------------------------------------------------------
# End plotting
# ----------------------------------------------------------------------
# debug plot
if p['DRS_PLOT'] > 0:
# 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, 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, hcfile=None, fpfiles=None):
"""
cal_SLIT_spirou.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_SLIT_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)
: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 hcfile is None or fpfiles is None:
names, types = ['hcfile', 'fpfiles'], [str, str]
customargs = spirouStartup.GetCustomFromRuntime(p, [0, 1],
types,
names,
last_multi=True)
else:
customargs = dict(hcfile=hcfile, fpfiles=fpfiles)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsfile='fpfiles')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, hcfitsfilename = spirouStartup.SingleFileSetup(p, filename=p['HCFILE'])
p, fpfilenames = spirouStartup.MultiFileSetup(p, files=p['FPFILES'])
# set fiber (it doesn't matter with the 2D image but we need this to get
# the lamp type for FPFILES and HCFILES, AB == C
p['FIBER'] = 'AB'
p['FIB_TYP'] = [p['FIBER']]
fsource = __NAME__ + '/main()'
p.set_sources(['FIBER', 'FIB_TYP'], fsource)
# set the hcfilename to the first hcfilenames
fpfitsfilename = fpfilenames[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)
# add a force plot off
p['PLOT_PER_ORDER'] = PLOT_PER_ORDER
p.set_source('PLOT_PER_ORDER', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# Read FP and HC files
# ----------------------------------------------------------------------
# read and combine all FP files except the first (fpfitsfilename)
rargs = [p, 'add', fpfitsfilename, fpfilenames[1:]]
p, fpdata, fphdr = spirouImage.ReadImageAndCombine(*rargs)
# read first file (hcfitsfilename)
hcdata, hchdr, _, _ = spirouImage.ReadImage(p, hcfitsfilename)
# 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()')
# ---------------------------------------------------------------------
# fix for un-preprocessed files
# ----------------------------------------------------------------------
hcdata = spirouImage.FixNonPreProcess(p, hcdata)
fpdata = spirouImage.FixNonPreProcess(p, fpdata)
# ----------------------------------------------------------------------
# Get basic image properties for reference file
# ----------------------------------------------------------------------
# get sig det value
p = spirouImage.GetSigdet(p, fphdr, name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, fphdr, name='exptime')
# get gain
p = spirouImage.GetGain(p, fphdr, name='gain')
# get lamp parameters
p = spirouTHORCA.GetLampParams(p, hchdr)
# ----------------------------------------------------------------------
# Correction of DARK
# ----------------------------------------------------------------------
# p, hcdatac = spirouImage.CorrectForDark(p, hcdata, hchdr)
hcdatac = hcdata
p['DARKFILE'] = 'None'
# p, fpdatac = spirouImage.CorrectForDark(p, fpdata, fphdr)
fpdatac = fpdata
# ----------------------------------------------------------------------
# Resize hc data
# ----------------------------------------------------------------------
# rotate the image and convert from ADU/s to e-
hcdata = spirouImage.ConvertToE(spirouImage.FlipImage(p, hcdatac), p=p)
# convert NaN to zeros
hcdata0 = np.where(~np.isfinite(hcdata), np.zeros_like(hcdata), hcdata)
# 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)
hcdata2 = spirouImage.ResizeImage(p, hcdata0, **bkwargs)
# log change in data size
WLOG(p, '', ('HC Image format changed to '
'{0}x{1}').format(*hcdata2.shape))
# ----------------------------------------------------------------------
# Resize fp data
# ----------------------------------------------------------------------
# rotate the image and convert from ADU/s to e-
fpdata = spirouImage.ConvertToE(spirouImage.FlipImage(p, fpdatac), p=p)
# convert NaN to zeros
fpdata0 = np.where(~np.isfinite(fpdata), np.zeros_like(fpdata), fpdata)
# 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)
fpdata2 = spirouImage.ResizeImage(p, fpdata0, **bkwargs)
# log change in data size
WLOG(p, '', ('FP Image format changed to '
'{0}x{1}').format(*fpdata2.shape))
# ----------------------------------------------------------------------
# Correct for the BADPIX mask (set all bad pixels to zero)
# ----------------------------------------------------------------------
# p, hcdata2 = spirouImage.CorrectForBadPix(p, hcdata2, hchdr)
# p, fpdata2 = spirouImage.CorrectForBadPix(p, fpdata2, fphdr)
p['BADPFILE'] = 'None'
# save data to loc
loc['HCDATA'] = hcdata2
loc.set_source('HCDATA', __NAME__ + '/main()')
# save data to loc
loc['FPDATA'] = fpdata2
loc.set_source('FPDATA', __NAME__ + '/main()')
# ----------------------------------------------------------------------
# Log the number of dead pixels
# ----------------------------------------------------------------------
# get the number of bad pixels
n_bad_pix = np.nansum(hcdata2 <= 0)
n_bad_pix_frac = n_bad_pix * 100 / np.product(hcdata2.shape)
# Log number
wmsg = 'Nb HC dead pixels = {0} / {1:.2f} %'
WLOG(p, 'info', wmsg.format(int(n_bad_pix), n_bad_pix_frac))
# ----------------------------------------------------------------------
# Log the number of dead pixels
# ----------------------------------------------------------------------
# get the number of bad pixels
n_bad_pix = np.nansum(fpdata2 <= 0)
n_bad_pix_frac = n_bad_pix * 100 / np.product(fpdata2.shape)
# Log number
wmsg = 'Nb FP dead pixels = {0} / {1:.2f} %'
WLOG(p, 'info', wmsg.format(int(n_bad_pix), n_bad_pix_frac))
# ------------------------------------------------------------------
# Get localisation coefficients
# ------------------------------------------------------------------
# original there is a loop but it is not used --> removed
p = spirouImage.FiberParams(p, p['FIBER'], merge=True)
# get localisation fit coefficients
p, loc = spirouLOCOR.GetCoeffs(p, fphdr, loc)
# ------------------------------------------------------------------
# Get master wave solution map
# ------------------------------------------------------------------
# get master wave map
masterwavefile = spirouDB.GetDatabaseMasterWave(p)
# log process
wmsg1 = 'Getting 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
wout = spirouImage.GetWaveSolution(p,
filename=masterwavefile,
return_wavemap=True,
quiet=True,
return_header=True,
fiber=wave_fiber)
loc['MASTERWAVEP'], loc['MASTERWAVE'] = wout[:2]
loc['MASTERWAVEHDR'], loc['WSOURCE'] = wout[2:]
# set sources
wsource = ['MASTERWAVEP', 'MASTERWAVE', 'MASTERWAVEHDR']
loc.set_sources(wsource, 'spirouImage.GetWaveSolution()')
# ----------------------------------------------------------------------
# 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)
# ----------------------------------------------------------------------
# Read cavity length file
# ----------------------------------------------------------------------
loc['CAVITY_LEN_COEFFS'] = spirouImage.ReadCavityLength(p)
source = __NAME__ + '.main() + spirouImage.ReadCavityLength()'
loc.set_source('CAVITY_LEN_COEFFS', source)
# ------------------------------------------------------------------
# Calculate shape map
# ------------------------------------------------------------------
loc = spirouImage.GetShapeMap(p, loc)
# ------------------------------------------------------------------
# Plotting
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# plots setup: start interactive plot
sPlt.start_interactive_session(p)
# plot the shape process for one order
sPlt.slit_shape_angle_plot(p, loc)
# end interactive section
sPlt.end_interactive_session(p)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# TODO: Decide on some quality control criteria?
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# 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]
# ------------------------------------------------------------------
# Writing DXMAP to file
# ------------------------------------------------------------------
# get the raw tilt file name
raw_shape_file = os.path.basename(p['FITSFILENAME'])
# construct file name and path
shapefits, tag = spirouConfig.Constants.SLIT_XSHAPE_FILE(p)
shapefitsname = os.path.basename(shapefits)
# Log that we are saving tilt file
wmsg = 'Saving shape information in file: {0}'
WLOG(p, '', wmsg.format(shapefitsname))
# Copy keys from fits file
hdict = spirouImage.CopyOriginalKeys(fphdr)
# 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=tag)
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.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='hcfile',
values=p['HCFILE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE2'],
dim1name='fpfile',
values=p['FPFILES'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# write tilt file to file
p = spirouImage.WriteImage(p, shapefits, loc['DXMAP'], hdict)
# ------------------------------------------------------------------
# Writing sanity check files
# ------------------------------------------------------------------
if p['SHAPE_DEBUG_OUTPUTS']:
# log
WLOG(p, '', 'Saving debug sanity check files')
# construct file names
input_fp_file, tag1 = spirouConfig.Constants.SLIT_SHAPE_IN_FP_FILE(p)
output_fp_file, tag2 = spirouConfig.Constants.SLIT_SHAPE_OUT_FP_FILE(p)
input_hc_file, tag3 = spirouConfig.Constants.SLIT_SHAPE_IN_HC_FILE(p)
output_hc_file, tag4 = spirouConfig.Constants.SLIT_SHAPE_OUT_HC_FILE(p)
overlap_file, tag5 = spirouConfig.Constants.SLIT_SHAPE_OVERLAP_FILE(p)
# write input fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
p = spirouImage.WriteImage(p, input_fp_file, loc['FPDATA'], hdict)
# write output fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag2)
p = spirouImage.WriteImage(p, output_fp_file, loc['FPDATA2'], hdict)
# write input fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag3)
p = spirouImage.WriteImage(p, input_hc_file, loc['HCDATA'], hdict)
# write output fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag4)
p = spirouImage.WriteImage(p, output_hc_file, loc['HCDATA2'], hdict)
# write overlap file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag5)
p = spirouImage.WriteImage(p, overlap_file, loc['ORDER_OVERLAP'],
hdict)
# ----------------------------------------------------------------------
# Move to calibDB and update calibDB
# ----------------------------------------------------------------------
if p['QC']:
keydb = 'SHAPE'
# copy shape file to the calibDB folder
spirouDB.PutCalibFile(p, shapefits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, shapefitsname, fphdr)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def main(night_name=None, ufiles=None):
"""
cal_preprocess_spirou.py main function, if night_name and files are
None uses arguments from run time i.e.:
cal_preprocess_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 ufiles: string, list or None, the list of files to process
Note can include wildcard i.e. "*.fits"
(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__)
# need custom args (to accept full path or wild card
if ufiles is None:
names, types = ['ufiles'], [str]
customargs = spirouStartup.GetCustomFromRuntime(p, [0], types, names,
last_multi=True)
else:
customargs = dict(ufiles=ufiles)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p, night_name, customargs=customargs,
mainfitsdir='raw')
# ----------------------------------------------------------------------
# Get hot pixels for corruption check
# ----------------------------------------------------------------------
hotpixels = spirouImage.PPGetHotPixels(p)
# ----------------------------------------------------------------------
# Process files (including wildcards)
# ----------------------------------------------------------------------
# get raw folder (assume all files are in the root directory)
rawdir = spirouConfig.Constants.RAW_DIR(p)
try:
ufiles = spirouFile.Paths(p['UFILES'], root=rawdir).abs_paths
except PathException as e:
WLOG(p, 'error', e)
# log how many files were found
wmsg = '{0} files found'
WLOG(p, '', wmsg.format(len(ufiles)))
# storage for output files
p['OUTPUT_NAMES'] = []
p.set_source('OUTPUT_NAMES', __NAME__ + '.main()')
# loop around files
for u_it, ufile in enumerate(ufiles):
# log the file process
wmsg = 'Processing file {0} ({1} of {2})'
WLOG(p, '', spirouStartup.spirouStartup.HEADER)
bfilename = os.path.basename(ufile)
WLOG(p, 'info', wmsg.format(bfilename, u_it+1, len(ufiles)))
WLOG(p, '', spirouStartup.spirouStartup.HEADER)
# ------------------------------------------------------------------
# Check that we can process file
# ------------------------------------------------------------------
# check if ufile exists
if not os.path.exists(ufile):
wmsg = 'File {0} does not exist... skipping'
WLOG(p, 'warning', wmsg.format(ufile))
continue
# skip processed files
elif p['PROCESSED_SUFFIX'] in bfilename:
wmsg = 'File {0} has been processed... skipping'
WLOG(p, 'warning', wmsg.format(ufile))
continue
# skip non-fits files
elif '.fits' not in bfilename:
wmsg = 'File {0} not a fits file... skipping'
WLOG(p, 'warning', wmsg.format(ufile))
continue
# skip index file
elif bfilename == spirouConfig.Constants.INDEX_OUTPUT_FILENAME():
wmsg = 'Skipping index fits file'
WLOG(p, 'warning', wmsg.format(ufile))
continue
# ------------------------------------------------------------------
# Read image file
# ------------------------------------------------------------------
# read the image data
rout = spirouImage.ReadImage(p, filename=ufile)
image, hdr, nx, ny = rout
# ------------------------------------------------------------------
# Identify file (and update filename, header and comments)
# ------------------------------------------------------------------
ufile, hdr = spirouImage.IdentifyUnProFile(p, ufile, hdr)
# ------------------------------------------------------------------
# correct image
# ------------------------------------------------------------------
# correct for the top and bottom reference pixels
WLOG(p, '', 'Correcting for top and bottom pixels')
image = spirouImage.PPCorrectTopBottom(p, image)
# correct by a median filter from the dark amplifiers
wmsg = 'Correcting by the median filter from dark amplifiers'
WLOG(p, '', wmsg)
image = spirouImage.PPMedianFilterDarkAmps(p, image)
# correct for the 1/f noise
wmsg = 'Correcting for the 1/f noise'
WLOG(p, '', wmsg)
image = spirouImage.PPMedianOneOverfNoise2(p, image)
# ------------------------------------------------------------------
# Quality control to check for corrupt files
# ------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# get pass condition
cout = spirouImage.PPTestForCorruptFile(p, image, hotpixels)
snr_hotpix, rms_list = cout
# print out SNR hotpix value
wmsg = 'Corruption check: SNR Hotpix value = {0:.5e}'
WLOG(p, '', wmsg.format(snr_hotpix))
#deal with printing corruption message
if snr_hotpix < p['PP_CORRUPT_SNR_HOTPIX']:
# add failed message to fail message list
fargs = [snr_hotpix, p['PP_CORRUPT_SNR_HOTPIX'],ufile ]
fmsg = ('File was found to be corrupted. (SNR_HOTPIX < threshold, '
'{0:.4e} < {1:.4e}). File will not be saved. '
'File = {2}'.format(*fargs))
fail_msg.append(fmsg)
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(snr_hotpix)
qc_names.append('snr_hotpix')
qc_logic.append('snr_hotpix < {0:.5e}'
''.format(p['PP_CORRUPT_SNR_HOTPIX']))
# ----------------------------------------------------------------------
if np.max(rms_list) > p['PP_CORRUPT_RMS_THRES']:
# add failed message to fail message list
fargs = [np.max(rms_list), p['PP_CORRUPT_RMS_THRES'], ufile]
fmsg = ('File was found to be corrupted. (RMS < threshold, '
'{0:.4e} > {1:.4e}). File will not be saved. '
'File = {0}'.format(*fargs))
fail_msg.append(fmsg)
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(np.max(rms_list))
qc_names.append('max(rms_list)')
qc_logic.append('max(rms_list) > {0:.4e}'
''.format(p['PP_CORRUPT_RMS_THRES']))
# ----------------------------------------------------------------------
# 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()')
WLOG(p, 'warning', '\tFile not written')
continue
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ------------------------------------------------------------------
# rotate image
# ------------------------------------------------------------------
# rotation to match HARPS orientation (expected by DRS)
image = spirouImage.RotateImage(image, p['RAW_TO_PP_ROTATION'])
# ------------------------------------------------------------------
# Save rotated image
# ------------------------------------------------------------------
# construct rotated file name
outfits = spirouConfig.Constants.PP_FILE(p, bfilename)
outfitsname = os.path.basename(outfits)
# log that we are saving rotated image
WLOG(p, '', 'Saving Rotated Image in ' + outfitsname)
# add keys from original header file
hdict = spirouImage.CopyOriginalKeys(hdr)
# set the version
hdict = spirouImage.AddKey(p, hdict, p['KW_PPVERSION'])
hdict = spirouImage.AddKey(p, hdict, p['KW_PID'], value=p['PID'])
# set the inputs
hdict = spirouImage.AddKey1DList(p, hdict, p['KW_INFILE1'],
dim1name='file',
values=[os.path.basename(ufile)])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddKey1DList(p, hdict, p['KW_DRS_QC_NAME'],
values=qc_names)
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# set the DRS type (for file indexing)
p['DRS_TYPE'] = 'RAW'
p.set_source('DRS_TYPE', __NAME__ + '.main()')
# write to file
p = spirouImage.WriteImage(p, outfits, image, hdict)
# index this file
p = spirouStartup.End(p, outputs='pp', end=False)
# ------------------------------------------------------------------
# append to output storage in p
# ------------------------------------------------------------------
p['OUTPUT_NAMES'].append(outfitsname)
# ----------------------------------------------------------------------
# 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, hcfile=None, fpfiles=None):
"""
cal_SLIT_spirou.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_SLIT_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)
: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 hcfile is None or fpfiles is None:
names, types = ['hcfile', 'fpfiles'], [str, str]
customargs = spirouStartup.GetCustomFromRuntime(p, [0, 1],
types,
names,
last_multi=True)
else:
customargs = dict(hcfile=hcfile, fpfile=fpfiles)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsfile='fpfiles')
# ----------------------------------------------------------------------
# Construct reference filename and get fiber type
# ----------------------------------------------------------------------
p, hcfitsfilename = spirouStartup.SingleFileSetup(p, filename=p['HCFILE'])
p, fpfitsfiles = spirouStartup.MultiFileSetup(p, files=p['FPFILES'])
# set fiber (it doesn't matter with the 2D image but we need this to get
# the lamp type for FPFILES and HCFILES, AB == C
p['FIBER'] = 'AB'
p['FIB_TYP'] = [p['FIBER']]
fsource = __NAME__ + '/main()'
p.set_sources(['FIBER', 'FIB_TYP'], fsource)
# ----------------------------------------------------------------------
# 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)
# add a force plot off
p['PLOT_PER_ORDER'] = PLOT_PER_ORDER
p.set_source('PLOT_PER_ORDER', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# Read FP and HC files
# ----------------------------------------------------------------------
# read input fp and hc data
rkwargs = dict(filename=fpfitsfiles[0],
filenames=fpfitsfiles[1:],
framemath='add')
p, fpdata, fphdr = spirouImage.ReadImageAndCombine(p, **rkwargs)
hcdata, hchdr, _, _ = spirouImage.ReadImage(p, hcfitsfilename)
# 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.ReadImage()')
sources = ['FPDATA', 'FPHDR']
loc.set_sources(sources, 'spirouImage.ReadImage()')
# ---------------------------------------------------------------------
# fix for un-preprocessed files
# ----------------------------------------------------------------------
hcdata = spirouImage.FixNonPreProcess(p, hcdata)
fpdata = spirouImage.FixNonPreProcess(p, fpdata)
# ----------------------------------------------------------------------
# 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)
# add a force plot off
p['PLOT_PER_ORDER'] = PLOT_PER_ORDER
p.set_source('PLOT_PER_ORDER', __NAME__ + '.main()')
# ----------------------------------------------------------------------
# Get basic image properties for reference file
# ----------------------------------------------------------------------
# get sig det value
p = spirouImage.GetSigdet(p, fphdr, name='sigdet')
# get exposure time
p = spirouImage.GetExpTime(p, fphdr, name='exptime')
# get gain
p = spirouImage.GetGain(p, fphdr, name='gain')
# get lamp parameters
p = spirouTHORCA.GetLampParams(p, hchdr)
# get FP_FP DPRTYPE
p = spirouImage.ReadParam(p, fphdr, 'KW_DPRTYPE', 'DPRTYPE', dtype=str)
# ----------------------------------------------------------------------
# Correction of reference FP
# ----------------------------------------------------------------------
# set the number of frames
p['NBFRAMES'] = len(fpfitsfiles)
p.set_source('NBFRAMES', __NAME__ + '.main()')
# Correction of DARK
p, fpdatac = spirouImage.CorrectForDark(p, fpdata, fphdr)
# Resize hc data
# rotate the image and convert from ADU/s to e-
fpdata = spirouImage.ConvertToE(spirouImage.FlipImage(p, fpdatac), p=p)
# 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)
fpdata1 = spirouImage.ResizeImage(p, fpdata, **bkwargs)
# log change in data size
WLOG(p, '',
('FPref Image format changed to {0}x{1}').format(*fpdata1.shape))
# Correct for the BADPIX mask (set all bad pixels to zero)
bargs = [p, fpdata1, fphdr]
p, fpdata1 = spirouImage.CorrectForBadPix(*bargs)
p, badpixmask = spirouImage.CorrectForBadPix(*bargs, return_map=True)
# log progress
WLOG(p, '', 'Cleaning FPref hot pixels')
# correct hot pixels
fpdata1 = spirouEXTOR.CleanHotpix(fpdata1, badpixmask)
# add to loc
loc['FPDATA1'] = fpdata1
loc.set_source('FPDATA1', __NAME__ + '.main()')
# Log the number of dead pixels
# get the number of bad pixels
with warnings.catch_warnings(record=True) as _:
n_bad_pix = np.nansum(fpdata1 <= 0)
n_bad_pix_frac = n_bad_pix * 100 / np.product(fpdata1.shape)
# Log number
wmsg = 'Nb FPref dead pixels = {0} / {1:.2f} %'
WLOG(p, 'info', wmsg.format(int(n_bad_pix), n_bad_pix_frac))
# ----------------------------------------------------------------------
# Correction of HC
# ----------------------------------------------------------------------
# set the number of frames
p['NBFRAMES'] = 1
p.set_source('NBFRAMES', __NAME__ + '.main()')
# Correction of DARK
p, hcdatac = spirouImage.CorrectForDark(p, hcdata, hchdr)
# Resize hc data
# rotate the image and convert from ADU/s to e-
hcdata = spirouImage.ConvertToE(spirouImage.FlipImage(p, hcdatac), p=p)
# 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)
hcdata1 = spirouImage.ResizeImage(p, hcdata, **bkwargs)
# log change in data size
WLOG(p, '', ('HC Image format changed to {0}x{1}').format(*hcdata1.shape))
# Correct for the BADPIX mask (set all bad pixels to zero)
bargs = [p, hcdata1, hchdr]
p, hcdata1 = spirouImage.CorrectForBadPix(*bargs)
p, badpixmask = spirouImage.CorrectForBadPix(*bargs, return_map=True)
# log progress
WLOG(p, '', 'Cleaning HC hot pixels')
# correct hot pixels
hcdata1 = spirouEXTOR.CleanHotpix(hcdata1, badpixmask)
# add to loc
loc['HCDATA1'] = hcdata1
loc.set_source('HCDATA1', __NAME__ + '.main()')
# Log the number of dead pixels
# get the number of bad pixels
with warnings.catch_warnings(record=True) as _:
n_bad_pix = np.nansum(hcdata1 <= 0)
n_bad_pix_frac = n_bad_pix * 100 / np.product(hcdata1.shape)
# Log number
wmsg = 'Nb HC dead pixels = {0} / {1:.2f} %'
WLOG(p, 'info', wmsg.format(int(n_bad_pix), n_bad_pix_frac))
# -------------------------------------------------------------------------
# get all FP_FP files
# -------------------------------------------------------------------------
fpfilenames = spirouImage.FindFiles(p,
filetype=p['DPRTYPE'],
allowedtypes=p['ALLOWED_FP_TYPES'])
# convert filenames to a numpy array
fpfilenames = np.array(fpfilenames)
# julian date to know which file we need to
# process together
fp_time = np.zeros(len(fpfilenames))
basenames, fp_exp, fp_pp_version, nightnames = [], [], [], []
# log progress
WLOG(p, '', 'Reading all fp file headers')
# looping through the file headers
for it in range(len(fpfilenames)):
# log progress
wmsg = '\tReading file {0} / {1}'
WLOG(p, 'info', wmsg.format(it + 1, len(fpfilenames)))
# get fp filename
fpfilename = fpfilenames[it]
# get night name
night_name = os.path.dirname(fpfilenames[it]).split(p['TMP_DIR'])[-1]
# read data
data_it, hdr_it, _, _ = spirouImage.ReadImage(p, fpfilename)
# get header
hdr = spirouImage.ReadHeader(p, filepath=fpfilenames[it])
# add MJDATE to dark times
fp_time[it] = float(hdr[p['KW_ACQTIME'][0]])
# add other keys (for tabular output)
basenames.append(os.path.basename(fpfilenames[it]))
nightnames.append(night_name)
fp_exp.append(float(hdr[p['KW_EXPTIME'][0]]))
fp_pp_version.append(hdr[p['KW_PPVERSION'][0]])
# -------------------------------------------------------------------------
# match files by date
# -------------------------------------------------------------------------
# log progress
wmsg = 'Matching FP files by observation time (+/- {0} hrs)'
WLOG(p, '', wmsg.format(p['DARK_MASTER_MATCH_TIME']))
# get the time threshold
time_thres = p['FP_MASTER_MATCH_TIME']
# get items grouped by time
matched_id = spirouImage.GroupFilesByTime(p, fp_time, time_thres)
# -------------------------------------------------------------------------
# construct the master fp file (+ correct for dark/badpix)
# -------------------------------------------------------------------------
cargs = [fpdata1, fpfilenames, matched_id]
fpcube, transforms = spirouImage.ConstructMasterFP(p, *cargs)
# log process
wmsg1 = 'Master FP construction complete.'
wmsg2 = '\tAdding {0} group images to form FP master image'
WLOG(p, 'info', [wmsg1, wmsg2.format(len(fpcube))])
# sum the cube to make fp data
masterfp = np.sum(fpcube, axis=0)
# add to loc
loc['MASTERFP'] = masterfp
loc.set_source('MASTERFP', __NAME__ + '.main()')
# ------------------------------------------------------------------
# Get localisation coefficients
# ------------------------------------------------------------------
# original there is a loop but it is not used --> removed
p = spirouImage.FiberParams(p, p['FIBER'], merge=True)
# get localisation fit coefficients
p, loc = spirouLOCOR.GetCoeffs(p, fphdr, loc)
# ------------------------------------------------------------------
# Get master wave solution map
# ------------------------------------------------------------------
# get master wave map
masterwavefile = spirouDB.GetDatabaseMasterWave(p)
# log process
wmsg1 = 'Getting 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
wout = spirouImage.GetWaveSolution(p,
filename=masterwavefile,
return_wavemap=True,
quiet=True,
return_header=True,
fiber=wave_fiber)
loc['MASTERWAVEP'], loc['MASTERWAVE'] = wout[:2]
loc['MASTERWAVEHDR'], loc['WSOURCE'] = wout[2:]
# set sources
wsource = ['MASTERWAVEP', 'MASTERWAVE', 'MASTERWAVEHDR']
loc.set_sources(wsource, 'spirouImage.GetWaveSolution()')
# ----------------------------------------------------------------------
# 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)
# ----------------------------------------------------------------------
# Read cavity length file
# ----------------------------------------------------------------------
loc['CAVITY_LEN_COEFFS'] = spirouImage.ReadCavityLength(p)
source = __NAME__ + '.main() + spirouImage.ReadCavityLength()'
loc.set_source('CAVITY_LEN_COEFFS', source)
# ----------------------------------------------------------------------
# Calculate shape map
# ----------------------------------------------------------------------
# calculate dx map
loc = spirouImage.GetXShapeMap(p, loc)
# if dx map is None we shouldn't continue
if loc['DXMAP'] is None:
fargs = [
loc['MAXDXMAPINFO'][0], loc['MAXDXMAPINFO'][1], loc['MAXDXMAPSTD'],
p['SHAPE_QC_DXMAP_STD']
]
fmsg = ('The std of the dxmap for order {0} y-pixel {1} is too large.'
' std = {2} (limit = {3})'.format(*fargs))
wmsg = 'QUALITY CONTROL FAILED: {0}'
WLOG(p, 'warning', wmsg.format(fmsg))
WLOG(p, 'warning', 'Cannot continue. Exiting.')
# End Message
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
# calculate dymap
loc = spirouImage.GetYShapeMap(p, loc, fphdr)
# ------------------------------------------------------------------
# Need to straighten the dxmap
# ------------------------------------------------------------------
# copy it first
loc['DXMAP0'] = np.array(loc['DXMAP'])
# straighten it
loc['DXMAP'] = spirouImage.EATransform(loc['DXMAP'], dymap=loc['DYMAP'])
# ------------------------------------------------------------------
# Need to straighten the hc data and fp data for debug
# ------------------------------------------------------------------
# log progress
WLOG(p, '', 'Shape finding complete. Applying transforms.')
# apply very last update of the debananafication
tkwargs = dict(dxmap=loc['DXMAP'], dymap=loc['DYMAP'])
loc['HCDATA2'] = spirouImage.EATransform(loc['HCDATA1'], **tkwargs)
loc['FPDATA2'] = spirouImage.EATransform(loc['FPDATA1'], **tkwargs)
loc.set_sources(['HCDATA2', 'FPDATA2'], __NAME__ + '.main()')
# ------------------------------------------------------------------
# Plotting
# ------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
# plots setup: start interactive plot
sPlt.start_interactive_session(p)
# plot the shape process for one order
sPlt.slit_shape_angle_plot(p, loc)
# end interactive section
sPlt.end_interactive_session(p)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# TODO: Decide on some quality control criteria?
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# 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(loc['MAXDXMAPSTD'])
qc_names.append('DXMAP STD')
qc_logic.append('DXMAP STD < {0}'.format(p['SHAPE_QC_DXMAP_STD']))
qc_pass.append(1)
# store in qc_params
qc_params = [qc_names, qc_values, qc_logic, qc_pass]
# ------------------------------------------------------------------
# Writing FP big table
# ------------------------------------------------------------------
# construct big fp table
colnames = [
'FILENAME', 'NIGHT', 'MJDATE', 'EXPTIME', 'PVERSION', 'GROUPID',
'DXREF', 'DYREF', 'A', 'B', 'C', 'D'
]
values = [
basenames, nightnames, fp_time, fp_exp, fp_pp_version, matched_id,
transforms[:, 0], transforms[:, 1], transforms[:, 2], transforms[:, 3],
transforms[:, 4], transforms[:, 5]
]
fptable = spirouImage.MakeTable(p, colnames, values)
# ------------------------------------------------------------------
# Writing DXMAP to file
# ------------------------------------------------------------------
# get the raw tilt file name
raw_shape_file = os.path.basename(p['FITSFILENAME'])
# construct file name and path
shapexfits, tag = spirouConfig.Constants.SLIT_XSHAPE_FILE(p)
shapexfitsname = os.path.basename(shapexfits)
# Log that we are saving tilt file
wmsg = 'Saving shape x information in file: {0}'
WLOG(p, '', wmsg.format(shapexfitsname))
# Copy keys from fits file
hdict = spirouImage.CopyOriginalKeys(fphdr)
# 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=tag)
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.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='hcfile',
values=p['HCFILE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE2'],
dim1name='fpfile',
values=p['FPFILES'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# write tilt file to file
p = spirouImage.WriteImageTable(p,
shapexfits,
image=loc['DXMAP'],
table=fptable,
hdict=hdict)
# ------------------------------------------------------------------
# Writing DYMAP to file
# ------------------------------------------------------------------
# get the raw tilt file name
raw_shape_file = os.path.basename(p['FITSFILENAME'])
# construct file name and path
shapeyfits, tag = spirouConfig.Constants.SLIT_YSHAPE_FILE(p)
shapeyfitsname = os.path.basename(shapeyfits)
# Log that we are saving tilt file
wmsg = 'Saving shape y information in file: {0}'
WLOG(p, '', wmsg.format(shapeyfitsname))
# Copy keys from fits file
hdict = spirouImage.CopyOriginalKeys(fphdr)
# 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=tag)
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.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='hcfile',
values=p['HCFILE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE2'],
dim1name='fpfile',
values=p['FPFILES'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# write tilt file to file
p = spirouImage.WriteImageTable(p,
shapeyfits,
image=loc['DYMAP'],
table=fptable,
hdict=hdict)
# ------------------------------------------------------------------
# Writing Master FP to file
# ------------------------------------------------------------------
# get the raw tilt file name
raw_shape_file = os.path.basename(p['FITSFILENAME'])
# construct file name and path
fpmasterfits, tag = spirouConfig.Constants.SLIT_MASTER_FP_FILE(p)
fpmasterfitsname = os.path.basename(fpmasterfits)
# Log that we are saving tilt file
wmsg = 'Saving master FP file: {0}'
WLOG(p, '', wmsg.format(fpmasterfitsname))
# Copy keys from fits file
hdict = spirouImage.CopyOriginalKeys(fphdr)
# 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=tag)
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.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='hcfile',
values=p['HCFILE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE2'],
dim1name='fpfile',
values=p['FPFILES'])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# write tilt file to file
p = spirouImage.WriteImageTable(p,
fpmasterfits,
image=masterfp,
table=fptable,
hdict=hdict)
# ------------------------------------------------------------------
# Writing sanity check files
# ------------------------------------------------------------------
if p['SHAPE_DEBUG_OUTPUTS']:
# log
WLOG(p, '', 'Saving debug sanity check files')
# construct file names
input_fp_file, tag1 = spirouConfig.Constants.SLIT_SHAPE_IN_FP_FILE(p)
output_fp_file, tag2 = spirouConfig.Constants.SLIT_SHAPE_OUT_FP_FILE(p)
input_hc_file, tag3 = spirouConfig.Constants.SLIT_SHAPE_IN_HC_FILE(p)
output_hc_file, tag4 = spirouConfig.Constants.SLIT_SHAPE_OUT_HC_FILE(p)
bdxmap_file, tag5 = spirouConfig.Constants.SLIT_SHAPE_BDXMAP_FILE(p)
# write input fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
p = spirouImage.WriteImage(p, input_fp_file, loc['FPDATA1'], hdict)
# write output fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag2)
p = spirouImage.WriteImage(p, output_fp_file, loc['FPDATA2'], hdict)
# write input fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag3)
p = spirouImage.WriteImage(p, input_hc_file, loc['HCDATA1'], hdict)
# write output fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag4)
p = spirouImage.WriteImage(p, output_hc_file, loc['HCDATA2'], hdict)
# write overlap file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag5)
p = spirouImage.WriteImage(p, bdxmap_file, loc['DXMAP0'], hdict)
# ----------------------------------------------------------------------
# Move to calibDB and update calibDB
# ----------------------------------------------------------------------
if p['QC']:
# add shape x
keydb = 'SHAPEX'
# copy shape file to the calibDB folder
spirouDB.PutCalibFile(p, shapexfits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, shapexfitsname, fphdr)
# add shape y
keydb = 'SHAPEY'
# copy shape file to the calibDB folder
spirouDB.PutCalibFile(p, shapeyfits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, shapeyfitsname, fphdr)
# add fp master
keydb = 'FPMASTER'
# copy shape file to the calibDB folder
spirouDB.PutCalibFile(p, fpmasterfits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, fpmasterfitsname, fphdr)
# ----------------------------------------------------------------------
# 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):
"""
cal_shape_spirou.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_shape_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__)
p = spirouStartup.LoadArguments(p, night_name, files)
p = spirouStartup.InitialFileSetup(p)
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
p, data, hdr = spirouImage.ReadImageAndCombine(p, framemath='add')
# ----------------------------------------------------------------------
# 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 basic image properties for FP 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')
# ----------------------------------------------------------------------
# Correction of reference FP
# ----------------------------------------------------------------------
# set the number of frames
p['NBFRAMES'] = 1
p.set_source('NBFRAMES', __NAME__ + '.main()')
# Correction of DARK
p, datac = spirouImage.CorrectForDark(p, data, hdr)
# Resize hc data
# rotate the image and convert from ADU/s to e-
data = spirouImage.ConvertToE(spirouImage.FlipImage(p, datac), p=p)
# 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, data, **bkwargs)
# log change in data size
WLOG(p, '',
('FPref Image format changed to {0}x{1}').format(*data1.shape))
# Correct for the BADPIX mask (set all bad pixels to zero)
bargs = [p, data1, hdr]
p, data1 = spirouImage.CorrectForBadPix(*bargs)
p, badpixmask = spirouImage.CorrectForBadPix(*bargs, return_map=True)
# log progress
WLOG(p, '', 'Cleaning FPref hot pixels')
# correct hot pixels
data1 = spirouEXTOR.CleanHotpix(data1, badpixmask)
# Log the number of dead pixels
# get the number of bad pixels
with warnings.catch_warnings(record=True) as _:
n_bad_pix = np.nansum(data1 <= 0)
n_bad_pix_frac = n_bad_pix * 100 / np.product(data1.shape)
# Log number
wmsg = 'Nb FPref dead pixels = {0} / {1:.2f} %'
WLOG(p, 'info', wmsg.format(int(n_bad_pix), n_bad_pix_frac))
# ----------------------------------------------------------------------
# Get master FP file
# ----------------------------------------------------------------------
# log progress
WLOG(p, '', 'Getting FP Master from calibDB')
# get master fp
p, masterfp = spirouImage.GetFPMaster(p, hdr)
# ----------------------------------------------------------------------
# Get transform parameters
# ----------------------------------------------------------------------
# log progress
wargs = [p['ARG_FILE_NAMES'][0], p['FPMASTERFILE']]
WLOG(p, 'info', 'Calculating transforming for {0} onto {1}'.format(*wargs))
gout = spirouImage.GetLinearTransformParams(p, masterfp, data1)
transform, xres, yres = gout
# ------------------------------------------------------------------
# Need to straighten the fp data for debug
# ------------------------------------------------------------------
p, shapem_x = spirouImage.GetShapeX(p, hdr)
p, shapem_y = spirouImage.GetShapeY(p, hdr)
data2 = spirouImage.EATransform(data1, transform, dxmap=shapem_x,
dymap=shapem_y)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# if transform is None means the fp image quality was too poor
if transform is None:
fail_msg.append('FP Image quality too poor (sigma clip failed)')
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
qc_values.append('None')
qc_names.append('Image Quality')
qc_logic.append('Image too poor')
# ----------------------------------------------------------------------
# get residual qc parameter
qc_res = p['SHAPE_QC_LINEAR_TRANS_RES_THRES']
# assess quality of x residuals
if xres > qc_res:
fail_msg.append('x-resdiuals too high {0} > {1}'.format(xres, qc_res))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
qc_values.append(xres)
qc_names.append('XRES')
qc_logic.append('XRES > {0}'.format(qc_res))
# assess quality of x residuals
if yres > qc_res:
fail_msg.append('y-resdiuals too high {0} > {1}'.format(yres, qc_res))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
qc_values.append(yres)
qc_names.append('YRES')
qc_logic.append('YRES > {0}'.format(qc_res))
# ----------------------------------------------------------------------
# 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]
# ------------------------------------------------------------------
# Writing shape to file
# ------------------------------------------------------------------
# get the raw tilt file name
raw_shape_file = os.path.basename(p['FITSFILENAME'])
# construct file name and path
shapefits, tag = spirouConfig.Constants.SLIT_SHAPE_LOCAL_FILE(p)
shapefitsname = os.path.basename(shapefits)
# Log that we are saving tilt file
wmsg = 'Saving shape information in file: {0}'
WLOG(p, '', wmsg.format(shapefitsname))
# Copy keys from fits file
hdict = spirouImage.CopyOriginalKeys(hdr)
# 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=tag)
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_CDBSHAPEX'],
value=p['SHAPEXFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBSHAPEY'],
value=p['SHAPEYFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBFPMASTER'],
value=p['FPMASTERFILE'])
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 the transform parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_SHAPE_DX'], value=transform[0])
hdict = spirouImage.AddKey(p, hdict, p['KW_SHAPE_DY'], value=transform[1])
hdict = spirouImage.AddKey(p, hdict, p['KW_SHAPE_A'], value=transform[2])
hdict = spirouImage.AddKey(p, hdict, p['KW_SHAPE_B'], value=transform[3])
hdict = spirouImage.AddKey(p, hdict, p['KW_SHAPE_C'], value=transform[4])
hdict = spirouImage.AddKey(p, hdict, p['KW_SHAPE_D'], value=transform[5])
# write tilt file to file
p = spirouImage.WriteImage(p, shapefits, [transform], hdict)
# ----------------------------------------------------------------------
# Move to calibDB and update calibDB
# ----------------------------------------------------------------------
if p['QC']:
# add shape
keydb = 'SHAPE'
# copy shape file to the calibDB folder
spirouDB.PutCalibFile(p, shapefits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, shapefitsname, hdr)
# ------------------------------------------------------------------
# Writing sanity check files
# ------------------------------------------------------------------
if p['SHAPE_DEBUG_OUTPUTS']:
# log
WLOG(p, '', 'Saving debug sanity check files')
# construct file names
dargs = [p, p['ARG_FILE_NAMES'][0]]
out1 = spirouConfig.Constants.SLIT_SHAPE_IN_FP_FILE(*dargs)
input_fp_file, tag1= out1
out2 = spirouConfig.Constants.SLIT_SHAPE_OUT_FP_FILE(*dargs)
output_fp_file, tag2 = out2
# write input fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
p = spirouImage.WriteImage(p, input_fp_file, data1, hdict)
# write output fp file
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag2)
p = spirouImage.WriteImage(p, output_fp_file, data2, 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):
"""
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, files=None):
"""
cal_loc_RAW_spirou.py main function, if night_name and files are None uses
arguments from run time i.e.:
cal_loc_RAW_spirou.py [night_name] [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)
: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)
# ----------------------------------------------------------------------
# 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')
# ----------------------------------------------------------------------
# Correction of DARK
# ----------------------------------------------------------------------
p, datac = spirouImage.CorrectForDark(p, data, hdr)
# ----------------------------------------------------------------------
# Interpolation over bad regions (to fill in the holes)
# ----------------------------------------------------------------------
# log process
# wmsg = 'Interpolating over bad regions'
# WLOG(p, '', wmsg)
# run interpolation
# datac = spirouImage.InterpolateBadRegions(p, datac)
# ----------------------------------------------------------------------
# Resize image
# ----------------------------------------------------------------------
# rotate the image and convert from ADU/s to e-
data = spirouImage.ConvertToE(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)
data2 = spirouImage.ResizeImage(p, data0, **bkwargs)
# log change in data size
WLOG(p, '', ('Image format changed to ' '{0}x{1}').format(*data2.shape))
# ----------------------------------------------------------------------
# Correct for the BADPIX mask (set all bad pixels to zero)
# ----------------------------------------------------------------------
p, data2 = spirouImage.CorrectForBadPix(p, data2, hdr)
# ----------------------------------------------------------------------
# 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, data2, hdr]
# background, xc, yc, minlevel = spirouBACK.MeasureBackgroundFF(*bargs)
p, background = spirouBACK.MeasureBackgroundMap(*bargs)
else:
background = np.zeros_like(data2)
p['BKGRDFILE'] = 'None'
p.set_source('BKGRDFILE', __NAME__ + '.main()')
# apply background correction to data
data2 = data2 - background
# ----------------------------------------------------------------------
# Construct image order_profile
# ----------------------------------------------------------------------
# log that we are doing background measurement
WLOG(p, '', 'Creating Order Profile')
order_profile = spirouLOCOR.BoxSmoothedImage(data2, p['LOC_BOX_SIZE'])
# data 2 is now set to the order profile
data2o = data2.copy()
data2 = order_profile.copy()
# ----------------------------------------------------------------------
# Write image order_profile to file
# ----------------------------------------------------------------------
# Construct folder and filename
rawfits, tag1 = spirouConfig.Constants.LOC_ORDER_PROFILE_FILE(p)
rawfitsname = os.path.split(rawfits)[-1]
# log saving order profile
wmsg = 'Saving processed raw frame in {0}'
WLOG(p, '', wmsg.format(rawfitsname))
# add keys from original header file
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_OUTPUT'], value=tag1)
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBDARK'], value=p['DARKFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBAD'], value=p['BADPFILE'])
# write to file
p = spirouImage.WriteImage(p, rawfits, order_profile, hdict)
# ----------------------------------------------------------------------
# Move order_profile to calibDB and update calibDB
# ----------------------------------------------------------------------
# set key for calibDB
keydb = 'ORDER_PROFILE_{0}'.format(p['FIBER'])
# copy dark fits file to the calibDB folder
spirouDB.PutCalibFile(p, rawfits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, rawfitsname, hdr)
# ######################################################################
# Localization of orders on central column
# ######################################################################
# storage dictionary for localization parameters
loc = ParamDict()
# Plots setup: start interactive plot
if p['DRS_PLOT'] > 0:
sPlt.start_interactive_session(p)
# ----------------------------------------------------------------------
# Measurement and correction of background on the central column
# ----------------------------------------------------------------------
loc = spirouBACK.MeasureBkgrdGetCentPixs(p, loc, data2)
# ----------------------------------------------------------------------
# Search for order center on the central column - quick estimation
# ----------------------------------------------------------------------
# log progress
WLOG(p, '', 'Searching order center on central column')
# plot the minimum of ycc and ic_locseuil if in debug and plot mode
if p['DRS_DEBUG'] > 0 and p['DRS_PLOT']:
sPlt.debug_locplot_min_ycc_loc_threshold(p, loc['YCC'])
# find the central positions of the orders in the central
posc_all = spirouLOCOR.FindPosCentCol(loc['YCC'], p['IC_LOCSEUIL'])
# depending on the fiber type we may need to skip some pixels and also
# we need to add back on the ic_offset applied
start = p['IC_FIRST_ORDER_JUMP']
posc = posc_all[start:] + p['IC_OFFSET']
# work out the number of orders to use (minimum of ic_locnbmaxo and number
# of orders found in 'LocateCentralOrderPositions')
number_of_orders = np.min([p['IC_LOCNBMAXO'], len(posc)])
# log the number of orders than have been detected
wargs = [p['FIBER'], int(number_of_orders / p['NBFIB']), p['NBFIB']]
WLOG(p, 'info', ('On fiber {0} {1} orders have been detected '
'on {2} fiber(s)').format(*wargs))
# ----------------------------------------------------------------------
# Search for order center and profile on specific columns
# ----------------------------------------------------------------------
# get fit polynomial orders for position and width
fitpos, fitwid = p['IC_LOCDFITC'], p['IC_LOCDFITW']
# Create arrays to store position and width of order for each order
loc['CTRO'] = np.zeros((number_of_orders, data2.shape[1]), dtype=float)
loc['SIGO'] = np.zeros((number_of_orders, data2.shape[1]), dtype=float)
# Create arrays to store coefficients for position and width
loc['ACC'] = np.zeros((number_of_orders, fitpos + 1))
loc['ASS'] = np.zeros((number_of_orders, fitpos + 1))
# Create arrays to store rms values for position and width
loc['RMS_CENTER'] = np.zeros(number_of_orders)
loc['RMS_FWHM'] = np.zeros(number_of_orders)
# Create arrays to store point to point max value for position and width
loc['MAX_PTP_CENTER'] = np.zeros(number_of_orders)
loc['MAX_PTP_FRACCENTER'] = np.zeros(number_of_orders)
loc['MAX_PTP_FWHM'] = np.zeros(number_of_orders)
loc['MAX_PTP_FRACFWHM'] = np.zeros(number_of_orders)
# Create arrays to store rejected points
loc['MAX_RMPTS_POS'] = np.zeros(number_of_orders)
loc['MAX_RMPTS_WID'] = np.zeros(number_of_orders)
# set the central col centers in the cpos_orders array
loc['CTRO'][:, p['IC_CENT_COL']] = posc[0:number_of_orders]
# set source for all locs
loc.set_all_sources(__NAME__ + '/main()')
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# storage for plotting
loc['XPLOT'], loc['YPLOT'] = [], []
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# loop around each order
rorder_num = 0
for order_num in range(number_of_orders):
# find the row centers of the columns
loc = spirouLOCOR.FindOrderCtrs(p, data2, loc, order_num)
# only keep the orders with non-zero width
mask = loc['SIGO'][order_num, :] != 0
loc['X'] = np.arange(data2.shape[1])[mask]
loc.set_source('X', __NAME__ + '/main()')
# check that we have enough data points to fit data
if len(loc['X']) > (fitpos + 1):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# initial fit params
iofargs = [p, loc, mask, rorder_num]
# initial fit for center positions for this order
loc, cf_data = spirouLOCOR.InitialOrderFit(*iofargs, kind='center')
# initial fit for widths for this order
loc, wf_data = spirouLOCOR.InitialOrderFit(*iofargs, kind='fwhm')
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Log order number and fit at central pixel and width and rms
wargs = [
rorder_num, cf_data['cfitval'], wf_data['cfitval'],
cf_data['rms']
]
WLOG(p, '', ('ORDER: {0} center at pixel {1:.1f} width '
'{2:.1f} rms {3:.3f}').format(*wargs))
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# sigma fit params
sigfargs = [p, loc, cf_data, mask, order_num, rorder_num]
# sigma clip fit for center positions for this order
cf_data = spirouLOCOR.SigClipOrderFit(*sigfargs, kind='center')
# load results into storage arrags for this order
loc['ACC'][rorder_num] = cf_data['a']
loc['RMS_CENTER'][rorder_num] = cf_data['rms']
loc['MAX_PTP_CENTER'][rorder_num] = cf_data['max_ptp']
loc['MAX_PTP_FRACCENTER'][rorder_num] = cf_data['max_ptp_frac']
loc['MAX_RMPTS_POS'][rorder_num] = cf_data['max_rmpts']
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# sigma fit params
sigfargs = [p, loc, wf_data, mask, order_num, rorder_num]
# sigma clip fit for width positions for this order
wf_data = spirouLOCOR.SigClipOrderFit(*sigfargs, kind='fwhm')
# load results into storage arrags for this order
loc['ASS'][rorder_num] = wf_data['a']
loc['RMS_FWHM'][rorder_num] = wf_data['rms']
loc['MAX_PTP_FWHM'][rorder_num] = wf_data['max_ptp']
loc['MAX_PTP_FRACFWHM'][rorder_num] = wf_data['max_ptp_frac']
loc['MAX_RMPTS_WID'][rorder_num] = wf_data['max_rmpts']
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# increase the roder_num iterator
rorder_num += 1
# else log that the order is unusable
else:
WLOG(p, '', 'Order found too much incomplete, discarded')
# ----------------------------------------------------------------------
# Plot the image (ready for fit points to be overplotted later)
if p['DRS_PLOT'] > 0:
# get saturation threshold
satseuil = p['IC_SATSEUIL'] * p['GAIN'] * p['NBFRAMES']
# plot image above saturation threshold
sPlt.locplot_im_sat_threshold(p, loc, data2, satseuil)
# ----------------------------------------------------------------------
# Log that order geometry has been measured
WLOG(p, 'info', ('On fiber {0} {1} orders geometry have been '
'measured').format(p['FIBER'], rorder_num))
# Get mean rms
mean_rms_center = np.nansum(
loc['RMS_CENTER'][:rorder_num]) * 1000 / rorder_num
mean_rms_fwhm = np.nansum(loc['RMS_FWHM'][:rorder_num]) * 1000 / rorder_num
# Log mean rms values
wmsg = 'Average uncertainty on {0}: {1:.2f} [mpix]'
WLOG(p, 'info', wmsg.format('position', mean_rms_center))
WLOG(p, 'info', wmsg.format('width', mean_rms_fwhm))
# ----------------------------------------------------------------------
# Plot of RMS for positions and widths
# ----------------------------------------------------------------------
if p['DRS_PLOT'] > 0:
sPlt.locplot_order_number_against_rms(p, loc, rorder_num)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# check that max number of points rejected in center fit is below threshold
if np.nansum(loc['MAX_RMPTS_POS']) > p['QC_LOC_MAXLOCFIT_REMOVED_CTR']:
fmsg = 'abnormal points rejection during ctr fit ({0:.2f} > {1:.2f})'
fail_msg.append(
fmsg.format(np.nansum(loc['MAX_RMPTS_POS']),
p['QC_LOC_MAXLOCFIT_REMOVED_CTR']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(np.nansum(loc['MAX_RMPTS_POS']))
qc_names.append('sum(MAX_RMPTS_POS)')
qc_logic.append('sum(MAX_RMPTS_POS) > {0:.2f}'
''.format(p['QC_LOC_MAXLOCFIT_REMOVED_CTR']))
# ----------------------------------------------------------------------
# check that max number of points rejected in width fit is below threshold
if np.nansum(loc['MAX_RMPTS_WID']) > p['QC_LOC_MAXLOCFIT_REMOVED_WID']:
fmsg = 'abnormal points rejection during width fit ({0:.2f} > {1:.2f})'
fail_msg.append(
fmsg.format(np.nansum(loc['MAX_RMPTS_WID']),
p['QC_LOC_MAXLOCFIT_REMOVED_WID']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(np.nansum(loc['MAX_RMPTS_WID']))
qc_names.append('sum(MAX_RMPTS_WID)')
qc_logic.append('sum(MAX_RMPTS_WID) > {0:.2f}'
''.format(p['QC_LOC_MAXLOCFIT_REMOVED_WID']))
# ----------------------------------------------------------------------
# check that the rms in center fit is lower than qc threshold
if mean_rms_center > p['QC_LOC_RMSMAX_CENTER']:
fmsg = 'too high rms on center fitting ({0:.2f} > {1:.2f})'
fail_msg.append(fmsg.format(mean_rms_center,
p['QC_LOC_RMSMAX_CENTER']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(mean_rms_center)
qc_names.append('mean_rms_center')
qc_logic.append('mean_rms_center > {0:.2f}'
''.format(p['QC_LOC_RMSMAX_CENTER']))
# ----------------------------------------------------------------------
# check that the rms in center fit is lower than qc threshold
if mean_rms_fwhm > p['QC_LOC_RMSMAX_FWHM']:
fmsg = 'too high rms on profile fwhm fitting ({0:.2f} > {1:.2f})'
fail_msg.append(fmsg.format(mean_rms_fwhm, p['QC_LOC_RMSMAX_CENTER']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(mean_rms_fwhm)
qc_names.append('mean_rms_fwhm')
qc_logic.append('mean_rms_fwhm > {0:.2f}'
''.format(p['QC_LOC_RMSMAX_CENTER']))
# ----------------------------------------------------------------------
# check for abnormal number of identified orders
if rorder_num != p['QC_LOC_NBO']:
fmsg = ('abnormal number of identified orders (found {0:.2f} '
'expected {1:.2f})')
fail_msg.append(fmsg.format(rorder_num, p['QC_LOC_NBO']))
passed = False
qc_pass.append(0)
else:
qc_pass.append(1)
# add to qc header lists
qc_values.append(rorder_num)
qc_names.append('rorder_num')
qc_logic.append('rorder_num != {0:.2f}'.format(p['QC_LOC_NBO']))
# ----------------------------------------------------------------------
# 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]
# ----------------------------------------------------------------------
# Save and record of image of localization with order center and keywords
# ----------------------------------------------------------------------
raw_loco_file = os.path.basename(p['FITSFILENAME'])
# construct filename
locofits, tag2 = spirouConfig.Constants.LOC_LOCO_FILE(p)
locofitsname = os.path.split(locofits)[-1]
# log that we are saving localization file
WLOG(p, '', ('Saving localization information '
'in file: {0}').format(locofitsname))
# add keys from original header file
hdict = spirouImage.CopyOriginalKeys(hdr)
# define new keys to add
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=tag2)
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=raw_loco_file)
hdict = spirouImage.AddKey(p, hdict, p['KW_CCD_SIGDET'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CCD_CONAD'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOCO_BCKGRD'],
value=loc['MEAN_BACKGRD'])
hdict = spirouImage.AddKey(p, hdict, p['KW_LOCO_NBO'], value=rorder_num)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOCO_DEG_C'],
value=p['IC_LOCDFITC'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOCO_DEG_W'],
value=p['IC_LOCDFITW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_LOCO_DEG_E'])
hdict = spirouImage.AddKey(p, hdict, p['KW_LOCO_DELTA'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_MAXFLX'],
value=float(loc['MAX_SIGNAL']))
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_SMAXPTS_CTR'],
value=np.nansum(loc['MAX_RMPTS_POS']))
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_SMAXPTS_WID'],
value=np.nansum(loc['MAX_RMPTS_WID']))
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_RMS_CTR'],
value=mean_rms_center)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_RMS_WID'],
value=mean_rms_fwhm)
# write 2D list of position fit coefficients
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_LOCO_CTR_COEFF'],
values=loc['ACC'][0:rorder_num])
# write 2D list of width fit coefficients
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_LOCO_FWHM_COEFF'],
values=loc['ASS'][0:rorder_num])
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# write center fits and add header keys (via hdict)
center_fits = spirouLOCOR.CalcLocoFits(loc['ACC'], data2.shape[1])
p = spirouImage.WriteImage(p, locofits, center_fits, hdict)
# ----------------------------------------------------------------------
# Save and record of image of sigma
# ----------------------------------------------------------------------
# construct filename
locofits2, tag3 = spirouConfig.Constants.LOC_LOCO_FILE2(p)
locofits2name = os.path.split(locofits2)[-1]
# log that we are saving localization file
wmsg = 'Saving FWHM information in file: {0}'
WLOG(p, '', wmsg.format(locofits2name))
# add keys from original header file
hdict = spirouImage.CopyOriginalKeys(hdr)
# define new keys to add
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_CDBDARK'], value=p['DARKFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBAD'], value=p['BADPFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBACK'], value=p['BKGRDFILE'])
hdict = spirouImage.AddKey1DList(p,
hdict,
p['KW_INFILE1'],
dim1name='file',
values=p['ARG_FILE_NAMES'])
# add outputs
hdict = spirouImage.AddKey(p, hdict, p['KW_CCD_SIGDET'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CCD_CONAD'])
hdict = spirouImage.AddKey(p, hdict, p['KW_LOCO_NBO'], value=rorder_num)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOCO_DEG_C'],
value=p['IC_LOCDFITC'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOCO_DEG_W'],
value=p['IC_LOCDFITW'])
hdict = spirouImage.AddKey(p, hdict, p['KW_LOCO_DEG_E'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_MAXFLX'],
value=float(loc['MAX_SIGNAL']))
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_SMAXPTS_CTR'],
value=np.nansum(loc['MAX_RMPTS_POS']))
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_SMAXPTS_WID'],
value=np.nansum(loc['MAX_RMPTS_WID']))
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_RMS_CTR'],
value=mean_rms_center)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_LOC_RMS_WID'],
value=mean_rms_fwhm)
# write 2D list of position fit coefficients
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_LOCO_CTR_COEFF'],
values=loc['ACC'][0:rorder_num])
# write 2D list of width fit coefficients
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_LOCO_FWHM_COEFF'],
values=loc['ASS'][0:rorder_num])
# add quality control
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
# write image and add header keys (via hdict)
width_fits = spirouLOCOR.CalcLocoFits(loc['ASS'], data2.shape[1])
p = spirouImage.WriteImage(p, locofits2, width_fits, hdict)
# ----------------------------------------------------------------------
# Save and Record of image of localization
# ----------------------------------------------------------------------
if p['IC_LOCOPT1']:
# construct filename
locofits3, tag4 = spirouConfig.Constants.LOC_LOCO_FILE3(p)
locofits3name = os.path.split(locofits3)[-1]
# log that we are saving localization file
wmsg1 = 'Saving localization image with superposition of orders in '
wmsg2 = 'file: {0}'.format(locofits3name)
WLOG(p, '', [wmsg1, wmsg2])
# superpose zeros over the fit in the image
data4 = spirouLOCOR.ImageLocSuperimp(data2o, loc['ACC'][0:rorder_num])
# save this image to file
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_FIBER'], value=p['FIBER'])
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag4)
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBDARK'],
value=p['DARKFILE'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_CDBBAD'],
value=p['BADPFILE'])
p = spirouImage.WriteImage(p, locofits3, data4, hdict)
# ----------------------------------------------------------------------
# Update the calibration database
# ----------------------------------------------------------------------
if p['QC'] == 1:
keydb = 'LOC_' + p['FIBER']
# copy localisation file to the calibDB folder
spirouDB.PutCalibFile(p, locofits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, locofitsname, hdr)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def main(filetype='DARK_DARK'):
"""
cal_DARK_spirou.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
# ----------------------------------------------------------------------
# set up function name
main_name = __NAME__ + '.main()'
# get parameters from config files/run time args/load paths + calibdb
p = spirouStartup.Begin(recipe=__NAME__)
# now get custom arguments
pos, fmt = [0], [str]
names, call = ['filetype'], [filetype]
customargs = spirouStartup.GetCustomFromRuntime(p, pos, fmt, names,
calls=call,
require_night_name=False)
p = spirouStartup.LoadArguments(p, None, customargs=customargs,
mainfitsdir='tmp',
require_night_name=False)
# set the DRS type (for file indexing)
p['DRS_TYPE'] = 'RAW'
p.set_source('DRS_TYPE', __NAME__ + '.main()')
# -------------------------------------------------------------------------
# find all "filetype" objects
filenames = spirouImage.FindFiles(p, filetype=p['FILETYPE'],
allowedtypes=p['ALLOWED_DARK_TYPES'])
# convert filenames to a numpy array
filenames = np.array(filenames)
# -------------------------------------------------------------------------
# julian date to know which file we need to
# process together
dark_time = np.zeros(len(filenames))
dark_exp, dark_pp_version, dark_wt_temp = [], [], []
basenames, nightnames, dark_cass_temp, dark_humidity = [], [], [], []
# log progress
WLOG(p, '', 'Reading all dark file headers')
# looping through the file headers
for it in range(len(filenames)):
# get night name
night_name = os.path.dirname(filenames[it]).split(p['TMP_DIR'])[-1]
# get header
hdr = spirouImage.ReadHeader(p, filepath=filenames[it])
# add MJDATE to dark times
dark_time[it] = float(hdr[p['KW_ACQTIME'][0]])
# add other keys (for tabular output)
basenames.append(os.path.basename(filenames[it]))
nightnames.append(night_name)
dark_exp.append(float(hdr[p['KW_EXPTIME'][0]]))
dark_pp_version.append(hdr[p['KW_PPVERSION'][0]])
dark_wt_temp.append(float(hdr[p['KW_WEATHER_TOWER_TEMP'][0]]))
dark_cass_temp.append(float(hdr[p['KW_CASS_TEMP'][0]]))
dark_humidity.append(float(hdr[p['KW_HUMIDITY'][0]]))
# -------------------------------------------------------------------------
# match files by date
# -------------------------------------------------------------------------
# log progress
wmsg = 'Matching dark files by observation time (+/- {0} hrs)'
WLOG(p, '', wmsg.format(p['DARK_MASTER_MATCH_TIME']))
# get the time threshold
time_thres = p['DARK_MASTER_MATCH_TIME']
# get items grouped by time
matched_id = spirouImage.GroupFilesByTime(p, dark_time, time_thres)
# -------------------------------------------------------------------------
# get the most recent position
lastpos = np.argmax(dark_time)
# load up the most recent dark
rout = spirouImage.ReadImage(p, filenames[lastpos], log=False)
data_ref, hdr_ref, nx, ny = rout
# set the night name and update the reduced directory
p['ARG_NIGHT_NAME'] = nightnames[lastpos]
p.set_source('ARG_NIGHT_NAME', __NAME__ + '.main()')
p['REDUCED_DIR'] = spirouConfig.Constants.REDUCED_DIR(p)
p.set_source('REDUCED_DIR', __NAME__ + '.main()')
# -------------------------------------------------------------------------
# Read individual files and sum groups
# -------------------------------------------------------------------------
# log process
WLOG(p, '', 'Reading Dark files and combining groups')
# Find all unique groups
u_groups = np.unique(matched_id)
# currently number of bins == number of groups
num_bins = len(u_groups)
# storage of dark cube
dark_cube = np.zeros([num_bins, ny, nx])
bin_cube = np.zeros(num_bins)
# loop through groups
for g_it, group_num in enumerate(u_groups):
# log progress
WLOG(p, '', '\tGroup {0} of {1}'.format(g_it + 1, len(u_groups)))
# find all files for this group
dark_ids = filenames[matched_id == group_num]
# load this groups files into a cube
cube = []
for filename in dark_ids:
# read data
data_it, _, _, _ = spirouImage.ReadImage(p, filename, log=False)
# add to cube
cube.append(data_it)
# median dark cube
groupdark = np.nanmedian(cube, axis=0)
# sum within each bin
dark_cube[g_it % num_bins] += groupdark
# record the number of cubes that are going into this bin
bin_cube[g_it % num_bins] += 1
# need to normalize if we have more than 1 cube per bin
for bin_it in range(num_bins):
dark_cube[bin_it] /= bin_cube[bin_it]
# -------------------------------------------------------------------------
# we perform a median filter over a +/- "med_size" pixel box
# -------------------------------------------------------------------------
# log process
WLOG(p, '', 'Performing median filter for {0} bins'.format(num_bins))
# get med_size from p
med_size = p['DARK_MASTER_MED_SIZE']
# storage of output dark cube
dark_cube1 = np.zeros([num_bins, ny, nx])
# loop around the bins
for bin_it in range(num_bins):
# get the dark for this bin
bindark = dark_cube[bin_it]
# performing a median filter of the image with [-med_size, med_size]
# box in x and 1 pixel wide in y. Skips the pixel considered,
# so this is equivalent of a 2*med_size boxcar
tmp = []
for jt in range(-med_size, med_size + 1):
if jt != 0:
tmp.append(np.roll(bindark, [0, jt]))
# low frequency image
lf_dark = np.nanmedian(tmp, axis=0)
# high frequency image
dark_cube1[bin_it] = bindark - lf_dark
# -------------------------------------------------------------------------
# median the dark cube to create the master dark
master_dark = np.nanmedian(dark_cube1, axis=0)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# 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]
# ----------------------------------------------------------------------
# Save master dark to file
# ----------------------------------------------------------------------
# set reference filename
reffile = filenames[lastpos]
# construct folder and filename
darkmasterfits, tag = spirouConfig.Constants.DARK_FILE_MASTER(p, reffile)
darkmasterfitsname = os.path.basename(darkmasterfits)
# log writing of file
WLOG(p, '', 'Saving master dark to {0}'.format(darkmasterfitsname))
# construct big dark table
colnames = ['FILENAME', 'NIGHT', 'MJDATE', 'EXPTIME', 'WEATHER_TEMP',
'CASS_TEMP', 'RELHUMID', 'PVERSION', 'GROUPID']
values = [basenames, nightnames, dark_time, dark_exp, dark_wt_temp,
dark_cass_temp, dark_humidity, dark_pp_version, matched_id]
darktable = spirouImage.MakeTable(p, colnames, values)
# add keys from original header file
hdict = spirouImage.CopyOriginalKeys(hdr_ref)
# define new keys to add
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)
# add qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# write master dark + dark table to file
p = spirouImage.WriteImageTable(p, darkmasterfits, image=master_dark,
table=darktable, hdict=hdict)
# ----------------------------------------------------------------------
# Move to calibDB and update calibDB
# ----------------------------------------------------------------------
if p['QC']:
# set dark master key
keydb = 'DARKM'
# copy dark fits file to the calibDB folder
spirouDB.PutCalibFile(p, darkmasterfits)
# update the master calib DB file with new key
spirouDB.UpdateCalibMaster(p, keydb, darkmasterfitsname, hdr_ref)
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def part2test(p, loc):
# ------------------------------------------------------------------
# Fit wavelength solution on identified lines (using Littrow)
# ------------------------------------------------------------------
# log message
wmsg = ('On fiber {0} fitting wavelength solution on identified '
'lines: (second pass)')
WLOG(p, '', wmsg.format(p['FIBER']))
# fit lines
start, end = p['IC_HC_N_ORD_START_2'], p['IC_HC_N_ORD_FINAL_2']
lls = loc['LITTROW_EXTRAP_SOL_1'][start:end]
loc = spirouTHORCA.Fit1DSolution(p, loc, lls, iteration=2)
# ------------------------------------------------------------------
# Littrow test
# ------------------------------------------------------------------
ckwargs = dict(ll=loc['LL_OUT_2'], 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 0-24 and 25-36 solutions
# ------------------------------------------------------------------
loc = spirouTHORCA.JoinOrders(p, loc)
# ----------------------------------------------------------------------
# Quality control
# ----------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
# check for infinites and NaNs in X_MEAN_2
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
# iterate through Littrow test cut values
# for x_it in range(len(loc['X_CUT_POINTS_2'])):
for x_it in range(1, len(loc['X_CUT_POINTS_2']), 2):
# get x cut point
x_cut_point = loc['X_CUT_POINTS_2'][x_it]
# get the sigma for this cut point
sig_littrow = loc['LITTROW_SIG_2'][x_it]
# get the abs min and max dev littrow values
min_littrow = abs(loc['LITTROW_MINDEV_2'][x_it])
max_littrow = abs(loc['LITTROW_MAXDEV_2'][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
# 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})')
fargs = [x_cut_point, min_littrow, max_littrow, dev_littrow_max]
fail_msg.append(fmsg.format(*fargs))
passed = False
# 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()')
# ------------------------------------------------------------------
# archive result in e2ds spectra
# ------------------------------------------------------------------
# get raw input file name
raw_infile1 = os.path.basename(p['HCFILES'][0])
raw_infile2 = os.path.basename(p['FPFILE'])
# get wave filename
wavefits, tag1 = spirouConfig.Constants.WAVE_FILE_FP(p)
wavefitsname = os.path.split(wavefits)[-1]
WLOG(p, '', wavefits)
# 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'])
# 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_OUTPUT'], value=tag1)
# set the input files
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBFLAT'], value=p['FLATFILE'])
hdict = spirouImage.AddKey(p, hdict, p['KW_CDBBLAZE'], value=p['BLAZFILE'])
# add quality control
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
# 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'])
# write original E2DS file and add header keys (via hdict)
# spirouImage.WriteImage(p['FITSFILENAME'], loc['HCDATA'], hdict)
# write the wave "spectrum"
p = spirouImage.WriteImage(p, wavefits, loc['LL_FINAL'], 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 to result table
# ------------------------------------------------------------------
# calculate stats for table
final_mean = 1000 * loc['X_MEAN_2']
final_var = 1000 * loc['X_VAR_2']
num_iterations = int(np.nansum(loc['X_ITER_2'][:, 2]))
err = 1000 * np.sqrt(final_var / num_iterations)
sig_littrow = 1000 * np.array(loc['LITTROW_SIG_2'])
# construct filename
wavetbl = spirouConfig.Constants.WAVE_TBL_FILE_FP(p)
wavetblname = os.path.split(wavetbl)[-1]
# construct and write table
columnnames = [
'night_name', 'file_name', 'fiber', 'mean', 'rms', 'N_lines', 'err',
'rms_L0', 'rms_L1', 'rms_L2'
]
columnformats = [
'{:20s}', '{:30s}', '{:3s}', '{:7.4f}', '{:6.2f}', '{:3d}', '{:6.3f}',
'{:6.2f}', '{:6.2f}', '{:6.2f}'
]
columnvalues = [[p['ARG_NIGHT_NAME']], [p['ARG_FILE_NAMES'][0]],
[p['FIBER']], [final_mean], [final_var], [num_iterations],
[err], [sig_littrow[0]], [sig_littrow[1]],
[sig_littrow[2]]]
# 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
wavelltbl = spirouConfig.Constants.WAVE_LINE_FILE(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.PutFile(p, wavefits)
# # update the master calib DB file with new key
# spirouDB.UpdateMaster(p, keydb, wavefitsname, loc['HCHDR'])
#
# # set the hcref key
# keydb = 'HCREF_{0}'.format(p['FIBER'])
# # copy wave file to calibDB folder
# spirouDB.PutFile(p, e2dscopy_filename)
# # update the master calib DB file with new key
# e2dscopyfits = os.path.split(e2dscopy_filename)[-1]
# spirouDB.UpdateMaster(p, keydb, e2dscopyfits, loc['HCHDR'])
# return p and loc
return p, loc
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 up first file
# ----------------------------------------------------------------------
# construct loc parameter dictionary for storing data
loc = ParamDict()
# read first file and assign values
rdata = spirouImage.ReadImage(p, p['FITSFILENAME'])
loc['DATA'], loc['DATAHDR'] = rdata[:2]
# Get object name and airmass
loc['OBJNAME'] = spirouImage.GetObjName(p, loc['DATAHDR'])
loc.set_source('OBJNAME', main_name)
loc['AIRMASS'] = spirouImage.GetAirmass(p, loc['DATAHDR'])
# set source
source = main_name + '+ spirouImage.ReadParams()'
loc.set_sources(['OBJNAME', 'AIRMASS'], source)
# ----------------------------------------------------------------------
# Get and Normalise the blaze
# ----------------------------------------------------------------------
p, loc = spirouTelluric.GetNormalizedBlaze(p, loc, loc['DATAHDR'])
# ----------------------------------------------------------------------
# Get database files
# ----------------------------------------------------------------------
# get current telluric maps from telluDB
tellu_db_data = spirouDB.GetDatabaseTellObj(p, required=False)
tellu_db_files, tellu_db_names = tellu_db_data[0], tellu_db_data[1]
# sort files by name
# sortmask = spirouImage.SortByName(tellu_db_files)
# tellu_db_files = np.array(tellu_db_files)[sortmask]
# tellu_db_names = np.array(tellu_db_names)[sortmask]
# filter by object name (only keep OBJNAME objects) and only keep
# unique filenames
tell_files, tell_names = [], []
for it in range(len(tellu_db_files)):
# check that objname is correct
cond1 = loc['OBJNAME'] in tellu_db_names[it]
# check that filename is not already used
cond2 = tellu_db_files[it] not in tell_files
# append to file list if criteria correct
if cond1 and cond2:
tell_files.append(tellu_db_files[it])
tell_names.append(tellu_db_names[it])
# log if we have no files
if len(tell_files) == 0:
wmsg = 'No "TELL_OBJ" files found for object ="{0}" skipping'
WLOG(p, 'warning', wmsg.format(loc['OBJNAME']))
# End Message
wmsg = 'Recipe {0} has been successfully completed'
WLOG(p, 'info', wmsg.format(p['PROGRAM']))
# return a copy of locally defined variables in the memory
return dict(locals())
else:
# log how many found
wmsg = 'N={0} "TELL_OBJ" files found for object ="{1}"'
WLOG(p, 'info', wmsg.format(len(tell_files), loc['OBJNAME']))
# ----------------------------------------------------------------------
# Set up storage for cubes (NaN arrays)
# ----------------------------------------------------------------------
# set up flat size
dims = [loc['DATA'].shape[0], loc['DATA'].shape[1], len(tell_files)]
flatsize = np.product(dims)
# create NaN filled storage
big_cube = np.repeat([np.nan], flatsize).reshape(*dims)
big_cube0 = np.repeat([np.nan], flatsize).reshape(*dims)
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# get master wave map
loc['MASTERWAVEFILE'] = spirouDB.GetDatabaseMasterWave(p)
# read master wave map
mout = spirouImage.GetWaveSolution(p,
filename=loc['MASTERWAVEFILE'],
return_wavemap=True,
quiet=True,
fiber=wave_fiber)
loc['MASTERWAVEPARAMS'], loc['MASTERWAVE'], loc['WSOURCE'] = mout
keys = ['MASTERWAVEPARAMS', 'MASTERWAVE', 'MASTERWAVEFILE', 'WSOURCE']
loc.set_sources(keys, main_name)
# ----------------------------------------------------------------------
# Compile a median SNR for rejection of bad files
# ----------------------------------------------------------------------
snr_all = []
# choose snr to check
snr_order = p['QC_FIT_TELLU_SNR_ORDER']
# loop through files
for it, filename in enumerate(tell_files):
header = spirouImage.ReadHeader(p, filename)
# get the SNR from header
nbo = spirouImage.ReadParam(p,
header,
'KW_WAVE_ORD_N',
dtype=int,
return_value=True)
snr = spirouImage.Read1Dkey(p, header, p['kw_E2DS_SNR'][0], nbo)
# append snr_all
snr_all.append(snr[snr_order])
# work our bad snr (less than half the median SNR)
snr_thres = np.nanmedian(snr_all) / 2.0
bad_snr_objects = np.where(snr_all < snr_thres)[0]
# ----------------------------------------------------------------------
# Loop through input files
# ----------------------------------------------------------------------
# empty lists for storage
loc['BASE_ROWNUM'], loc['BASE_FILELIST'] = [], []
loc['BASE_OBJNAME'], loc['BASE_OBJECT'] = [], []
loc['BASE_BERVLIST'], loc['BASE_WAVELIST'] = [], []
loc['BASE_SNRLIST_{0}'.format(snr_order)] = []
loc['BASE_DATELIST'], loc['BASE_VERSION'] = [], []
loc['BASE_DARKFILE'], loc['BASE_BADFILE'] = [], []
loc['BASE_LOCOFILE'], loc['BASE_BLAZFILE'] = [], []
loc['BASE_FLATFILE'], loc['BASE_SHAPEFILE'] = [], []
# loop through files
for it, filename in enumerate(tell_files):
# get base filenmae
basefilename = os.path.basename(filename)
# ------------------------------------------------------------------
# skip if in bad snr objects
if it in bad_snr_objects:
wargs = [it + 1, len(tell_files), snr_all[it], snr_thres]
wmsg1 = ('Skipping file {0} of {1} due to bad SNR ({2:.3f} < '
'{3:.3f})'.format(*wargs))
wmsg2 = '\tFile = {0}'.format(basefilename)
WLOG(p, 'warning', [wmsg1, wmsg2])
continue
# ------------------------------------------------------------------
# append basename to file list
loc['BASE_FILELIST'].append(basefilename)
# ------------------------------------------------------------------
# create image for storage
image = np.repeat([np.nan], np.product(loc['DATA'].shape))
image = image.reshape(loc['DATA'].shape)
# ------------------------------------------------------------------
# Load the data for this file
tdata0, thdr, _, _ = spirouImage.ReadImage(p, filename)
nbo, npix = tdata0.shape
# Correct for the blaze
tdata = tdata0 / loc['NBLAZE']
# get berv and add to list
if p['KW_BERV'][0] in thdr:
loc['BASE_BERVLIST'].append('{0}'.format(thdr[p['KW_BERV'][0]]))
else:
loc['BASE_BERVLIST'].append('UNKNOWN')
# ------------------------------------------------------------------
# Get parameters from header
snr = snr_all[it]
dateobs = spirouImage.ReadParam(p,
thdr,
'KW_DATE_OBS',
dtype=str,
return_value=True)
utcobs = spirouImage.ReadParam(p,
thdr,
'KW_UTC_OBS',
dtype=str,
return_value=True)
tobjname = spirouImage.ReadParam(p,
thdr,
'KW_OBJNAME',
dtype=str,
return_value=True)
tobject = spirouImage.ReadParam(p,
thdr,
'KW_OBJECT',
dtype=str,
return_value=True)
tversion = spirouImage.ReadParam(p,
thdr,
'KW_version',
dtype=str,
return_value=True)
tdarkfile = spirouImage.ReadParam(p,
thdr,
'KW_CDBDARK',
dtype=str,
return_value=True)
tbadfile = spirouImage.ReadParam(p,
thdr,
'KW_CDBBAD',
dtype=str,
return_value=True)
tlocofile = spirouImage.ReadParam(p,
thdr,
'KW_CDBLOCO',
dtype=str,
return_value=True)
tblazfile = spirouImage.ReadParam(p,
thdr,
'KW_CDBBLAZE',
dtype=str,
return_value=True)
tflatfile = spirouImage.ReadParam(p,
thdr,
'KW_CDBFLAT',
dtype=str,
return_value=True)
tshapfile = spirouImage.ReadParam(p,
thdr,
'KW_CDBSHAPE',
dtype=str,
return_value=True)
# append to lists
loc['BASE_ROWNUM'].append(it)
loc['BASE_SNRLIST_{0}'.format(snr_order)].append(snr_all[it])
loc['BASE_DATELIST'].append('{0}_{1}'.format(dateobs, utcobs))
loc['BASE_OBJNAME'].append(tobjname)
loc['BASE_OBJECT'].append(tobject)
loc['BASE_VERSION'].append(tversion)
loc['BASE_DARKFILE'].append(tdarkfile)
loc['BASE_BADFILE'].append(tbadfile)
loc['BASE_LOCOFILE'].append(tlocofile)
loc['BASE_BLAZFILE'].append(tblazfile)
loc['BASE_FLATFILE'].append(tflatfile)
loc['BASE_SHAPEFILE'].append(tshapfile)
# ------------------------------------------------------------------
# Get the wave solution for this file
# ------------------------------------------------------------------
# Force A and B to AB solution
if p['FIBER'] in ['A', 'B']:
wave_fiber = 'AB'
else:
wave_fiber = p['FIBER']
# need to reload calibDB
# as we have custom arguments need to load the calibration database
calib_db = dict(p['CALIBDB'])
del p['CALIBDB']
p = spirouStartup.LoadCalibDB(p, header=thdr)
# get wave solution
wout = spirouImage.GetWaveSolution(p,
image=tdata,
hdr=thdr,
return_wavemap=True,
fiber=wave_fiber,
return_filename=True)
_, loc['WAVE'], loc['WAVEFILE'], _ = wout
loc.set_sources(['WAVE', 'WAVEFILE'], main_name)
# add wave to wave list
loc['BASE_WAVELIST'].append(loc['WAVEFILE'])
# readd original calibDB to p
p['CALIBDB'] = dict(calib_db)
# ------------------------------------------------------------------
# Get the Barycentric correction from header
dv, _, _ = spirouImage.GetBERV(p, thdr)
# ------------------------------------------------------------------
# log stats
wmsg = 'Processing file {0} of {1} file={2} dv={3}'
wargs = [it + 1, len(tell_files), basefilename, dv]
WLOG(p, 'info', wmsg.format(*wargs))
# ------------------------------------------------------------------
# shift to correct berv
dvshift = spirouMath.relativistic_waveshift(dv, units='km/s')
image = spirouTelluric.Wave2Wave(p, tdata, loc['WAVE'] * dvshift,
loc['MASTERWAVE'])
# ------------------------------------------------------------------
# loop around orders
for order_num in range(loc['DATA'].shape[0]):
# normalise the tdata
tdata[order_num, :] /= np.nanmedian(tdata[order_num, :])
image[order_num, :] /= np.nanmedian(image[order_num, :])
# ------------------------------------------------------------------
# add to cube storage
big_cube[:, :, it] = image
big_cube0[:, :, it] = tdata
# ----------------------------------------------------------------------
# log if we have no files
if len(loc['BASE_FILELIST']) == 0:
wmsg = 'No good files found for object ="{0}" skipping'
WLOG(p, 'warning', wmsg.format(loc['OBJNAME']))
# End Message
wmsg = 'Recipe {0} has been successfully completed'
WLOG(p, 'info', wmsg.format(p['PROGRAM']))
# return a copy of locally defined variables in the memory
return dict(locals())
# ----------------------------------------------------------------------
# make median image
with warnings.catch_warnings(record=True) as _:
big_cube_med = np.nanmedian(big_cube, axis=2)
# ----------------------------------------------------------------------
# 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]
# ----------------------------------------------------------------------
# Write Cube median (the template) to file
# ----------------------------------------------------------------------
# get raw file name
raw_in_file = os.path.basename(p['FITSFILENAME'])
# construct filename
outfile, tag = spirouConfig.Constants.OBJTELLU_TEMPLATE_FILE(p, loc)
outfilename = os.path.basename(outfile)
# hdict is first file 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=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['MASTERWAVEFILE'])
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 qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add wave solution coefficients
hdict = spirouImage.AddKey2DList(p,
hdict,
p['KW_WAVE_PARAM'],
values=loc['MASTERWAVEPARAMS'])
# write to file
p = spirouImage.WriteImage(p, outfile, big_cube_med, hdict)
# ----------------------------------------------------------------------
# Update the telluric database with the template
# ----------------------------------------------------------------------
spirouDB.UpdateDatabaseObjTemp(p, outfilename, loc['OBJNAME'],
loc['DATAHDR'])
# put file in telluDB
spirouDB.PutTelluFile(p, outfile)
# ----------------------------------------------------------------------
# Save cubes to file
# ----------------------------------------------------------------------
# make big cube table
big_table = spirouTelluric.ConstructBigTable(p, loc)
# construct file names
outfile1, tag1 = spirouConfig.Constants.OBJTELLU_TEMPLATE_CUBE_FILE1(
p, loc)
outfile2, tag2 = spirouConfig.Constants.OBJTELLU_TEMPLATE_CUBE_FILE2(
p, loc)
# log big cube 1
wmsg1 = 'Saving bigcube to file {0}'.format(os.path.basename(outfile1))
# save big cube 1
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag1)
big_cube_s = np.swapaxes(big_cube, 1, 2)
p = spirouImage.WriteImageTable(p,
outfile1,
image=big_cube_s,
table=big_table,
hdict=hdict)
# log big cube 0
wmsg = 'Saving bigcube0 to file {0}'.format(os.path.basename(outfile2))
# save big cube 0
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag2)
big_cube_s0 = np.swapaxes(big_cube0, 1, 2)
p = spirouImage.WriteImageTable(p,
outfile2,
image=big_cube_s0,
table=big_table,
hdict=hdict)
# # mega plot
# nfiles = big_cube_s0.shape[1]
# ncols = int(np.ceil(np.sqrt(nfiles)))
# nrows = int(np.ceil(nfiles/ncols))
# fig, frames = plt.subplots(ncols=ncols, nrows=nrows)
# for it in range(big_cube_s0.shape[1]):
# jt, kt = it // ncols, it % ncols
# frame = frames[jt][kt]
# frame.imshow(big_cube_s0[:, it, :], origin='lower')
# frame.set(xlim=(2030, 2060))
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
def measure_background_from_map(p, image, header):
func_name = __NAME__ + '.measure_background_from_map()'
# get constants from parameter dictionary
width = p['IC_BKGR_BOXSIZE']
amp_ker = p['IC_BKGR_KER_AMP']
# ------------------------------------------------------------------------
# measure local background
scattered_light = measure_local_background(p, image)
# we extract a median order profile for the center of the image
local_background_correction = scattered_light / amp_ker
# correct the image for local background
image1 = image - local_background_correction
# -------------------------------------------------------------------------
# get badpixmask
p, bmap, bhdr = spirouImage.GetBackgroundMap(p, header)
# create mask from badpixmask
bmap = np.array(bmap, dtype=bool)
# copy image
image2 = np.array(image1)
# set to NAN all "illuminated" (non-background) pixels
image2[~bmap] = np.nan
# -------------------------------------------------------------------------
# create the box centers
# we construct a binned-down version of the full image with the estimate
# of the background for each x+y "center". This image will be up-scaled to
# the size of the full science image and subtracted
# x and y centers for each background calculation
xc = np.arange(width, image2.shape[0], width)
yc = np.arange(width, image2.shape[1], width)
# background map (binned-down for now)
background_image = np.zeros((len(xc), len(yc)))
# loop around all boxes with centers xc and yc
# and find pixels within a given widths
# around these centers in the full image
for i_it in range(len(xc)):
for j_it in range(len(yc)):
xci, yci = xc[i_it], yc[j_it]
# get the pixels for this box
subframe = image2[xci - width:xci + width, yci - width:yci + width]
subframe = subframe.ravel()
# get the (2*size)th minimum pixel
with warnings.catch_warnings(record=True) as _:
# do not use the nanpercentile, just a median
# as we masked non-background pixels with NaNs
value = np.nanmedian(subframe)
if np.isfinite(value):
background_image[i_it, j_it] = value
else:
background_image[i_it, j_it] = 0.0
# define a mapping grid from size of background_image (image1[0]/width) by
# (image1[1]/width)
# get shapes
gridshape = background_image.shape
imageshape = image2.shape
# get fractional positions of the full image
indices = np.indices(imageshape)
fypix = indices[0]/imageshape[0]
fxpix = indices[1]/imageshape[1]
# scalge fraction positions to size of background image
sypix = (gridshape[0]-1) * fypix
sxpix = (gridshape[1]-1) * fxpix
# coords for mapping
coords = np.array([sypix, sxpix])
# expand image onto the grid that matches the size of the input image
background_image_full = mapc(background_image, coords,
order=2, cval=np.nan, output=float,
mode='constant')
# ----------------------------------------------------------------------
# Produce DEBUG plot
# ----------------------------------------------------------------------
data1 = image - background_image_full
# construct debug background file name
debug_background, tag = spirouConfig.Constants.BACKGROUND_CORRECT_FILE(p)
# construct images
dimages = [data1, image, image1, image2, local_background_correction,
background_image_full, background_image]
# construct hdicts
hdict = spirouImage.CopyOriginalKeys(header)
drsname = ['EXTDESC', None, 'Extension description']
hdict1 = spirouImage.AddKey(p, hdict, drsname, value='Corrected')
hdict2 = spirouImage.AddKey(p, hdict, drsname, value='Original')
hdict3 = spirouImage.AddKey(p, hdict, drsname, value='Locally corrected')
hdict4 = spirouImage.AddKey(p, hdict, drsname, value='LC NaN filled')
hdict5 = spirouImage.AddKey(p, hdict, drsname, value='Local Background')
hdict6 = spirouImage.AddKey(p, hdict, drsname, value='Global Background')
hdict7 = spirouImage.AddKey(p, hdict, drsname,
value='Global Background Binned')
dheaders = [hdict1, hdict2, hdict3, hdict4, hdict5, hdict6, hdict7]
# write debug to file
_ = spirouImage.WriteImageMulti(p, debug_background, dimages,
hdicts=dheaders)
# ----------------------------------------------------------------------
return p, background_image_full
def main(night_name=None, e2dsfiles=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 e2dsfiles: list of string, the E2DS files 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__)
# need custom args (to accept full path or wild card
if e2dsfiles is None:
names, types = ['e2dsfiles'], [str]
customargs = spirouStartup.GetCustomFromRuntime(p, [0],
types,
names,
last_multi=True)
else:
customargs = dict(e2dsfiles=e2dsfiles)
# get parameters from configuration files and run time arguments
p = spirouStartup.LoadArguments(p,
night_name,
customargs=customargs,
mainfitsdir='reduced')
# ----------------------------------------------------------------------
# Process files (including wildcards)
# ----------------------------------------------------------------------
try:
e2dsfiles = spirouFile.Paths(p['E2DSFILES'],
root=p['ARG_FILE_DIR']).abs_paths
except PathException as e:
WLOG(p, 'error', e)
# loop around files
for it, e2dsfile in enumerate(e2dsfiles):
# get the base file name
e2dsfilename = os.path.basename(e2dsfile)
# log the file process
wargs = [e2dsfilename, it + 1, len(e2dsfiles)]
wmsg = ' * Processing file {0} ({1} of {2})'.format(*wargs)
WLOG(p, '', spirouStartup.spirouStartup.HEADER)
WLOG(p, '', wmsg)
WLOG(p, '', spirouStartup.spirouStartup.HEADER)
# ------------------------------------------------------------------
# Check that we can process file
# ------------------------------------------------------------------
# check if ufile exists
if not os.path.exists(e2dsfile):
wmsg = 'File {0} does not exist... skipping'
WLOG(p, 'warning', wmsg.format(e2dsfilename))
continue
elif ('e2ds' not in e2dsfilename) and ('e2dsff' not in e2dsfilename):
wmsg = 'File {0} not a valid E2DS or E2DSFF file'
WLOG(p, 'warning', wmsg.format(e2dsfilename))
continue
elif '.fits' not in e2dsfilename:
wmsg = 'File {0} not a fits file... skipping'
WLOG(p, 'warning', wmsg.format(e2dsfilename))
continue
# ----------------------------------------------------------------------
# Read image file
# ----------------------------------------------------------------------
# read the image data
e2ds, hdr, nbo, nx = spirouImage.ReadData(p, e2dsfile)
# 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')
# ----------------------------------------------------------------------
# Read star parameters
# ----------------------------------------------------------------------
p = spirouImage.ReadParam(p, hdr, 'KW_OBJRA', dtype=str)
p = spirouImage.ReadParam(p, hdr, 'KW_OBJDEC', dtype=str)
p = spirouImage.ReadParam(p, hdr, 'KW_OBJEQUIN')
p = spirouImage.ReadParam(p, hdr, 'KW_OBJRAPM')
p = spirouImage.ReadParam(p, hdr, 'KW_OBJDECPM')
p = spirouImage.ReadParam(p, hdr, 'KW_DATE_OBS', dtype=str)
p = spirouImage.ReadParam(p, hdr, 'KW_UTC_OBS', dtype=str)
# -----------------------------------------------------------------------
# Earth Velocity calculation
# -----------------------------------------------------------------------
if p['IC_IMAGE_TYPE'] == 'H4RG':
loc = spirouImage.EarthVelocityCorrection(p,
loc,
method=p['CCF_BERVMODE'])
else:
loc['BERV'], loc['BJD'] = 0.0, 0.0
loc['BERV_MAX'], loc['BERV_SOURCE'] = 0.0, 'None'
loc.set_sources(['BERV', 'BJD', 'BERV_MAX'], __NAME__ + '.main()')
# ----------------------------------------------------------------------
# archive ccf to fits file
# ----------------------------------------------------------------------
outfilename = str(e2dsfile)
# add keys
hdict = spirouImage.CopyOriginalKeys(hdr)
# 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'])
hdict = spirouImage.AddKey(p,
hdict,
p['KW_BERV_SOURCE'],
value=loc['BERV_SOURCE'])
# write image and add header keys (via hdict)
p = spirouImage.WriteImage(p, outfilename, e2ds, 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__)
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
# ------------------------------------------------------------------
wout = spirouImage.GetWaveSolution(p, image=loc['DATA'], hdr=loc['DATAHDR'],
return_wavemap=True,
return_filename=True)
_, loc['WAVE'], loc['WAVEFILE'], _ = wout
loc.set_sources(['WAVE', 'WAVEFILE'], main_name)
# get the wave keys
loc = spirouImage.GetWaveKeys(p, loc, loc['DATAHDR'])
# ------------------------------------------------------------------
# Get and Normalise the blaze
# ------------------------------------------------------------------
p, loc = spirouTelluric.GetNormalizedBlaze(p, loc, loc['DATAHDR'])
# ------------------------------------------------------------------
# Construct convolution kernels
# ------------------------------------------------------------------
loc = spirouTelluric.ConstructConvKernel1(p, loc)
loc = spirouTelluric.ConstructConvKernel2(p, loc, vsini=p['TELLU_VSINI'])
# ------------------------------------------------------------------
# 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'])
# ------------------------------------------------------------------
# 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 for blaze
# ------------------------------------------------------------------
# get image
sp, shdr, _, _ = spirouImage.ReadImage(p, filename)
# divide my blaze
sp = sp / loc['BLAZE']
# ------------------------------------------------------------------
# Get the wave solution
# ------------------------------------------------------------------
wout = spirouImage.GetWaveSolution(p, image=sp, hdr=shdr,
return_wavemap=True,
return_filename=True)
_, loc['WAVE_IT'], loc['WAVEFILE_IT'], _ = wout
loc.set_sources(['WAVE_IT', 'WAVEFILE_IT'], main_name)
# ------------------------------------------------------------------
# Shift data to master wave file
# ------------------------------------------------------------------
# shift map
wargs = [p, sp, loc['WAVE_IT'], masterwave]
sp = spirouTelluric.Wave2Wave(*wargs)
loc['SP'] = np.array(sp)
loc.set_source('SP', main_name)
# ------------------------------------------------------------------
# get output transmission filename
outfile, tag1 = spirouConfig.Constants.TELLU_TRANS_MAP_FILE(p, filename)
outfilename = os.path.basename(outfile)
loc['OUTPUTFILES'].append(outfile)
# if we already have the file skip it
if outfile in tellu_db_files:
wmsg = 'File {0} exists in telluDB, skipping'
WLOG(p, '', wmsg.format(outfilename))
continue
else:
# log processing file
wmsg = 'Processing file {0}'
WLOG(p, '', wmsg.format(outfilename))
# Get object name and airmass
loc['OBJNAME'] = spirouImage.GetObjName(p, shdr)
loc['AIRMASS'] = spirouImage.GetAirmass(p, shdr)
# set source
source = main_name + '+ spirouImage.ReadParams()'
loc.set_sources(['OBJNAME', 'AIRMASS'], source)
# ------------------------------------------------------------------
# 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
# ------------------------------------------------------------------
# loop around the orders
# ------------------------------------------------------------------
# define storage for the transmission map
transmission_map = np.zeros_like(loc['DATA'])
# define storage for measured rms within expected clean domains
exp_clean_rms = np.zeros(loc['DATA'].shape[0])
# loop around the orders
for order_num in range(loc['DATA'].shape[0]):
# start and end
start = order_num * loc['XDIM']
end = (order_num * loc['XDIM']) + loc['XDIM']
# get this orders combined tapas transmission
trans = loc['TAPAS_ALL_SPECIES'][0, start:end]
# keep track of the pixels that are considered valid for the SED
# determination
mask1 = trans > p['TRANSMISSION_CUT']
mask1 &= np.isfinite(loc['NBLAZE'][order_num, :])
# normalise the spectrum
sp[order_num, :] /= np.nanmedian(sp[order_num, :])
# create a float mask
fmask = np.array(mask1, dtype=float)
# set up an SED to fill
sed = np.ones(loc['XDIM'])
# sigma clip until limit
ww = None
for it in range(p['N_ITER_SED_HOTSTAR']):
# copy the spectrum
sp2 = np.array(sp[order_num, :])
# flag Nans
nanmask = ~np.isfinite(sp2)
# set all NaNs to zero so that it does not propagate when
# we convlve by KER2 - must set sp2[bad] to zero as
# NaN * 0.0 = NaN and we want 0.0!
sp2[nanmask] = 0.0
# trace the invalid points
fmask[nanmask] = 0.0
# multiple by the float mask
sp2 *= fmask
# convolve with the second kernel
sp2b = np.convolve(sp2 / sed, loc['KER2'], mode='same')
# convolve with mask to get weights
ww = np.convolve(fmask, loc['KER2'], mode='same')
# normalise the spectrum by the weights
with warnings.catch_warnings(record=True) as w:
sp2bw = sp2b / ww
# set zero pixels to 1
sp2bw[sp2b == 0] = 1
# recalculate the mask using the deviation from original
with warnings.catch_warnings(record=True) as _:
dev = (sp2bw - sp[order_num, :] / sed)
dev /= np.nanmedian(np.abs(dev))
mask = mask1 * (np.abs(dev) < p['TELLU_SIGMA_DEV'])
# update the SED with the corrected spectrum
sed *= sp2bw
# identify bad pixels
with warnings.catch_warnings(record=True) as _:
bad = (sp[order_num, :] / sed[:] > 1.2)
sed[bad] = np.nan
# debug plot
if p['DRS_PLOT'] and (p['DRS_DEBUG'] > 1) and FORCE_PLOT_ON:
# start non-interactive plot
sPlt.plt.ioff()
# plot the transmission map plot
pargs = [order_num, mask1, sed, trans, sp, ww, outfilename]
sPlt.tellu_trans_map_plot(p, loc, *pargs)
# show and close
sPlt.plt.show()
sPlt.plt.close()
# set all values below a threshold to NaN
sed[ww < p['TELLU_NAN_THRESHOLD']] = np.nan
# save the spectrum (normalised by the SED) to the tranmission map
transmission_map[order_num, :] = sp[order_num, :] / sed
# get expected clean rms
fmaskb = np.array(fmask).astype(bool)
with warnings.catch_warnings(record=True):
zerotrans = np.abs(transmission_map[order_num, fmaskb]-1)
ec_rms = np.nanmedian(zerotrans)
exp_clean_rms[order_num] = ec_rms
# log the rms
wmsg = 'Order {0}: Fractional RMS in telluric free domain = {1:.3f}'
wargs = [order_num, ec_rms]
WLOG(p, '', wmsg.format(*wargs))
# ---------------------------------------------------------------------
# Quality control
# ---------------------------------------------------------------------
# set passed variable and fail message list
passed, fail_msg = True, []
qc_values, qc_names, qc_logic, qc_pass = [], [], [], []
# ----------------------------------------------------------------------
# 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
# 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']))
qc_pass.append(0)
else:
qc_pass.append(1)
# ----------------------------------------------------------------------
# check that the RMS is not too low
if exp_clean_rms[snr_order] > p['QC_TELLU_CLEAN_RMS_MAX']:
fmsg = ('Expected clean RMS is too high in order {0} '
'({1:.3f} > {2:.3f})')
fargs = [snr_order, exp_clean_rms[snr_order],
p['QC_TELLU_CLEAN_RMS_MAX']]
fail_msg.append(fmsg.format(*fargs))
passed = False
# add to qc header lists
qc_values.append(exp_clean_rms[snr_order])
qc_name_str = 'exp_clean_rms[{0}]'.format(snr_order)
qc_names.append(qc_name_str)
qc_logic.append('{0} > {1:.2f}'.format(qc_name_str,
p['QC_TELLU_CLEAN_RMS_MAX']))
qc_pass.append(0)
else:
qc_pass.append(1)
# ----------------------------------------------------------------------
# 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]
# ------------------------------------------------------------------
# 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)
# write to file
p = spirouImage.WriteImage(p, outfile, transmission_map, hdict)
# ------------------------------------------------------------------
# Generate the absorption map
# ------------------------------------------------------------------
# set up storage for the absorption
abso = np.array(transmission_map)
# set values less than low threshold to low threshold
# set values higher than high threshold to 1
low, high = p['TELLU_ABSO_LOW_THRES'], p['TELLU_ABSO_HIGH_THRES']
with warnings.catch_warnings(record=True) as w:
abso[abso < low] = low
abso[abso > high] = 1.0
# write to loc
loc['RECON_ABSO'] = abso.reshape(np.product(loc['DATA'].shape))
loc.set_source('RECON_ABSO', main_name)
# ------------------------------------------------------------------
# Get molecular absorption
# ------------------------------------------------------------------
loc = spirouTelluric.CalcMolecularAbsorption(p, loc)
# add molecular absorption to file
for it, molecule in enumerate(p['TELLU_ABSORBERS'][1:]):
# get molecule keyword store and key
molkey = '{0}_{1}'.format(p['KW_TELLU_ABSO'][0], molecule.upper())
# add water col
if molecule == 'h2o':
loc['WATERCOL'] = loc[molkey]
# set source
loc.set_source('WATERCOL', main_name)
# ------------------------------------------------------------------
# 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['AIRMASS'],
loc['WATERCOL']]
spirouDB.UpdateDatabaseTellMap(*targs)
# ----------------------------------------------------------------------
# Optional Absorption maps
# ----------------------------------------------------------------------
if p['TELLU_ABSO_MAPS']:
# ------------------------------------------------------------------
# Generate the absorption map
# ------------------------------------------------------------------
# get number of files
nfiles = len(p['OUTPUTFILES'])
# set up storage for the absorption
abso = np.zeros([nfiles, np.product(loc['DATA'].shape)])
# loop around outputfiles and add them to abso
for it, filename in enumerate(p['OUTPUTFILES']):
# push data into array
data_it, _, _, _ = spirouImage.ReadImage(p, filename)
abso[it, :] = data_it.reshape(np.product(loc['DATA'].shape))
# set values less than low threshold to low threshold
# set values higher than high threshold to 1
low, high = p['TELLU_ABSO_LOW_THRES'], p['TELLU_ABSO_HIGH_THRES']
abso[abso < low] = low
abso[abso > high] = 1.0
# set values less than TELLU_CUT_BLAZE_NORM threshold to NaN
abso[loc['NBLAZE'] < p['TELLU_CUT_BLAZE_NORM']] = np.nan
# reshape data (back to E2DS)
abso_e2ds = abso.reshape(nfiles, loc['YDIM'], loc['XDIM'])
# get file name
abso_map_file, tag2 = spirouConfig.Constants.TELLU_ABSO_MAP_FILE(p)
# get raw file name
raw_in_file = os.path.basename(p['FITSFILENAME'])
# write the map to file
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_OUTPUT'], value=tag2)
# 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'])
# write to file
p = spirouImage.WriteImage(p, abso_map_file, abso_e2ds, hdict)
# ------------------------------------------------------------------
# Generate the median and normalized absorption maps
# ------------------------------------------------------------------
# copy the absorption cube
abso2 = np.array(abso)
# log the absorption cube
log_abso = np.log(abso)
# get the threshold from p
threshold = p['TELLU_ABSO_SIG_THRESH']
# calculate the abso_med
abso_med = np.nanmedian(log_abso, axis=0)
# sigma clip around the median
for it in range(p['TELLU_ABSO_SIG_N_ITER']):
# recalculate the abso_med
abso_med = np.nanmedian(log_abso, axis=0)
# loop around each file
for jt in range(nfiles):
# get this iterations row
rowvalue = log_abso[jt, :]
# get the mask of those values above threshold
goodpix = (rowvalue > threshold) & (abso_med > threshold)
# apply the mask of good pixels to work out ratio
part1 = np.nansum(rowvalue[goodpix] * abso_med[goodpix])
part2 = np.nansum(abso_med[goodpix] ** 2)
ratio = part1 / part2
# store normalised absol back on to log_abso
log_abso[jt, :] = log_abso[jt, :] / ratio
# unlog log_abso
abso_out = np.exp(log_abso)
# calculate the median of the log_abso
abso_med_out = np.exp(np.nanmedian(log_abso, axis=0))
# reshape the median
abso_map_n = abso_med_out.reshape(loc['DATA'].shape)
# save the median absorption map to file
abso_med_file, tag3 = spirouConfig.Constants.TELLU_ABSO_MEDIAN_FILE(p)
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag3)
p = spirouImage.WriteImage(p, abso_med_file, abso_med_out, hdict)
# save the normalized absorption map to file
abso_map_file, tag4 = spirouConfig.Constants.TELLU_ABSO_NORM_MAP_FILE(p)
hdict = spirouImage.AddKey(p, hdict, p['KW_OUTPUT'], value=tag4)
p = spirouImage.WriteImage(p, abso_map_file, abso_map_n, hdict)
# ------------------------------------------------------------------
# calculate dv statistic
# ------------------------------------------------------------------
# get the order for dv calculation
dvselect = p['TELLU_ABSO_DV_ORDER']
size = p['TELLU_ABSO_DV_SIZE']
threshold2 = p['TELLU_ABSO_DV_GOOD_THRES']
fitdeg = p['TELLU_ABSO_FIT_DEG']
ydim, xdim = loc['DATA'].shape
# get the start and end points of this order
start, end = xdim * dvselect + size, xdim * dvselect - size + xdim
# get the median for selected order
abso_med2 = np.exp(abso_med[start:end])
# get the dv pixels to extract
dvpixels = np.arange(-np.floor(size / 2), np.ceil(size / 2), 1)
# loop around files
for it, filename in enumerate(p['OUTPUTFILES']):
# storage for the extracted abso ratios for this file
cc = np.zeros(size)
# loop around a box of size="size"
for jt, dv in dvpixels:
# get the start and end position
start = xdim * dvselect + size + dv
end = xdim * dvselect + xdim - size + dv
# get the log abso for this iteration
rowvalue = np.exp(log_abso[it, start:end])
# find the good pixels
goodpix = (rowvalue > threshold2) & (abso_med2 > threshold2)
# get the ratio
part1 = np.nansum(rowvalue[goodpix] * abso_med2[goodpix])
part2 = np.nansum(abso_med2[goodpix] ** 2)
cc[jt] = part1 / part2
# fit the ratio across the points
cfit = nanpolyfit(dvpixels, cc, fitdeg)
# work out the dv pix
dvpix = -0.5 * (cfit[1] / cfit[0])
# log stats
wmsg = 'File: "{0}", dv={1}'
WLOG(p, '', wmsg.format(filename, dvpix))
# ----------------------------------------------------------------------
# End Message
# ----------------------------------------------------------------------
p = spirouStartup.End(p)
# return a copy of locally defined variables in the memory
return dict(locals())
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 polar_products_header(p, loc, polardict, qc_params):
"""
Function to construct header keywords to be saved in the polar products
:param p: parameter dictionary, ParamDict containing constants
:param loc: parameter dictionary, ParamDict containing data
:param polardict: dictionary, ParamDict containing information on the
input data
:return hdict, loc: ParamDict, ParamDict: the header parameter
dictionary and the updated loc parameter dictionary
"""
# add keys from original header of base file
hdict = spirouImage.CopyOriginalKeys(loc['HDR'])
# 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'])
# add in file
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 qc parameters
hdict = spirouImage.AddKey(p, hdict, p['KW_DRS_QC'], value=p['QC'])
hdict = spirouImage.AddQCKeys(p, hdict, qc_params)
# add stokes parameter keyword to header
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_STOKES'],
value=loc['STOKES'])
# add number of exposures parameter keyword to header
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_NEXP'],
value=loc['NEXPOSURES'])
# add the polarimetry method parameter keyword to header
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_METHOD'],
value=loc['METHOD'])
mjd_first, mjd_last = 0.0, 0.0
meanbjd, tot_exptime = 0.0, 0.0
bjd_first, bjd_last, exptime_last = 0.0, 0.0, 0.0
berv_first, berv_last = 0.0, 0.0
bervmaxs = []
# loop over files in polar sequence to add keywords to header of products
for filename in polardict.keys():
# get this entry
entry = polardict[filename]
# get expnum, fiber, and header
expnum, fiber, hdr = entry['exposure'], entry['fiber'], entry['hdr']
# Add only times from fiber A
if fiber == 'A':
# calcualte total exposure time
tot_exptime += float(hdr[p['KW_EXPTIME'][0]])
# get values for BJDCEN calculation
if expnum == 1:
mjd_first = float(hdr[p['KW_ACQTIME'][0]])
bjd_first = float(hdr[p['KW_BJD'][0]])
berv_first = float(hdr[p['KW_BERV'][0]])
elif expnum == loc['NEXPOSURES']:
mjd_last = float(hdr[p['KW_ACQTIME'][0]])
bjd_last = float(hdr[p['KW_BJD'][0]])
berv_last = float(hdr[p['KW_BERV'][0]])
exptime_last = float(hdr[p['KW_EXPTIME'][0]])
meanbjd += float(hdr[p['KW_BJD'][0]])
# add exposure file name
fileexp = p['kw_POL_FILENAM{0}'.format(expnum)]
hdict = spirouImage.AddKey(p, hdict, fileexp, value=hdr['FILENAME'])
# add EXPTIME for each exposure
exptimeexp = p['kw_POL_EXPTIME{0}'.format(expnum)]
hdict = spirouImage.AddKey(p, hdict, exptimeexp,
value=hdr[p['KW_EXPTIME'][0]])
# add MJDATE for each exposure
mjdexp = p['kw_POL_MJDATE{0}'.format(expnum)]
hdict = spirouImage.AddKey(p, hdict, mjdexp,
value=hdr[p['KW_ACQTIME'][0]])
# add MJDEND for each exposure
mjdendexp = p['kw_POL_MJDEND{0}'.format(expnum)]
hdict = spirouImage.AddKey(p, hdict, mjdendexp,
value=hdr[p['KW_MJDEND'][0]])
# add BJD for each exposure
bjdexp = p['kw_POL_BJD{0}'.format(expnum)]
hdict = spirouImage.AddKey(p, hdict, bjdexp,
value=hdr[p['KW_BJD'][0]])
# add BERV for each exposure
bervexp = p['kw_POL_BERV{0}'.format(expnum)]
hdict = spirouImage.AddKey(p, hdict, bervexp,
value=hdr[p['KW_BERV'][0]])
# append BERVMAX value of each exposure
bervmaxs.append(float(hdr[p['KW_BERV_MAX'][0]]))
# add total exposure time parameter keyword to header
hdict = spirouImage.AddKey(p, hdict, p['KW_POL_EXPTIME'], value=tot_exptime)
# update existing EXPTIME keyword
hdict = spirouImage.AddKey(p, hdict, p['KW_EXPTIME'], value=tot_exptime)
# add elapsed time parameter keyword to header
elapsed_time = (bjd_last - bjd_first) * 86400. + exptime_last
hdict = spirouImage.AddKey(p, hdict, p['KW_POL_ELAPTIME'], value=elapsed_time)
# calculate MJD at center of polarimetric sequence
mjdcen = mjd_first + (mjd_last - mjd_first + exptime_last/86400.)/2.0
# add central MJD
hdict = spirouImage.AddKey(p, hdict, p['KW_POL_MJDCEN'], value=mjdcen)
# update existing MJD keyword
hdict = spirouImage.AddKey(p, hdict, p['KW_ACQTIME'], value=mjdcen)
# calculate BJD at center of polarimetric sequence
bjdcen = bjd_first + (bjd_last - bjd_first + exptime_last/86400.)/2.0
# add central BJD
hdict = spirouImage.AddKey(p, hdict, p['KW_POL_BJDCEN'], value=bjdcen)
# update existing BJD keyword
hdict = spirouImage.AddKey(p, hdict, p['KW_BJD'], value=bjdcen)
# calculate BERV at center by linear interpolation
berv_slope = (berv_last - berv_first) / (bjd_last - bjd_first)
berv_intercept = berv_first - berv_slope * bjd_first
loc['BERVCEN'] = berv_intercept + berv_slope * bjdcen
# add central BERV
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_BERVCEN'], value=loc['BERVCEN'])
# update existing BERV keyword
hdict = spirouImage.AddKey(p, hdict, p['kw_BERV'], value=loc['BERVCEN'])
# calculate maximum bervmax
bervmax = np.max(bervmaxs)
# update existing BERVMAX keyword
hdict = spirouImage.AddKey(p, hdict, p['kw_BERV_MAX'], value=bervmax)
# add mean BJD
meanbjd = meanbjd / loc['NEXPOSURES']
hdict = spirouImage.AddKey(p, hdict, p['kw_POL_MEANBJD'], value=meanbjd)
return hdict, loc
