S4_wasp39b.ecf

# Eureka! Control File for Stage 4: Generate Lightcurves 

# Number of spectroscopic channels spread evenly over given wavelength range
nspecchan   1          # Number of spectroscopic channels
wave_min    2.44         # Minimum wavelength
wave_max    4.00         # Maximum wavelength
allapers	True		# Run S4 on all of the apertures considered in S3? Otherwise will use newest output in the inputdir

# Parameters for drift correction of 1D spectra
correctDrift    False   # Set True to correct drift/jitter in 1D spectra (not recommended for simulated data)
drift_preclip   0       # Ignore first drift_preclip points of spectrum
drift_postclip  100     # Ignore last drift_postclip points of spectrum, None = no clipping
drift_range     11      # Trim spectra by +/-X pixels to compute valid region of cross correlation
drift_hw        5       # Half-width in pixels used when fitting Gaussian, must be smaller than drift_range
drift_iref      -1      # Index of reference spectrum used for cross correlation, -1 = last spectrum
sub_mean        True    # Set True to subtract spectrum mean during cross correlation
sub_continuum	True	# Set True to subtract the continuum from the spectra using a highpass filter
highpassWidth	10		# The integer width of the highpass filter when subtracting the continuum

# Parameters for sigma clipping
sigma_clip		True	# Whether or not sigma clipping should be performed on the 1D time series
sigma			10		# The number of sigmas a point must be from the rolling median to be considered an outlier
box_width		10		# The width of the box-car filter (used to calculated the rolling median) in units of number of data points
maxiters		5		# The number of iterations of sigma clipping that should be performed.
fill_value		mask	# Either the string 'mask' to mask the outlier values (recommended), 'boxcar' to replace data with the mean from the box-car filter, or a constant float-type fill value.

# Diagnostics
isplots_S4  3           # Generate few (1), some (3), or many (5) figures (Options: 1 - 5)
hide_plots	False		# If True, plots will automatically be closed rather than popping up
verbose		True		# If True, more details will be printed about steps in Stage 4

# Project directory
topdir      /Users/catrionamurray/Documents/Postdoc/CUBoulder/JWST_hackathon/Spectra_to_Transit/

# Directories relative to project dir
inputdir    NIRCam/Stage_3_Output_Eureka/	# The folder containing the outputs from Eureka!'s S3 or JWST's S3 pipeline (will be overwritten if calling S3 and S4 sequentially)
outputdir	NIRCam/Stage_4_Output_Eureka/