# Eureka! Control File for Stage 3: Data Reduction

ncpu			16			# Number of CPUs
nfiles			100			# The number of data files to analyze simultaneously
max_memory		0.5			# The maximum fraction of memory you want utilized by read-in frames (note that calculations like sigma clipping will push memory usage above this limit)
suffix			calints		# Data file suffix

gain			3.1			# A custom gain array or float

# Subarray region of interest
ywindow			[140, 393]	# Vertical axis as seen in DS9
xwindow			[11, 61]	# Horizontal axis as seen in DS9
src_pos_type	gaussian	# Determine source position when not given in header (Options: gaussian, weighted, or max)
record_ypos		True		# Option to record the y position and width for each integration (only records if src_pos_type is gaussian)
dqmask			True		# Mask pixels with an odd entry in the DQ array

# Background parameters
bg_hw			11			# Half-width of exclusion region for BG subtraction (relative to source position)
bg_thresh		[5,5]		# Double-iteration X-sigma threshold for outlier rejection along time axis
bg_deg			0			# Polynomial order for column-by-column background subtraction, -1 for median of entire frame
p3thresh		5			# X-sigma threshold for outlier rejection during background subtraction

# Spectral extraction parameters
spec_hw			5			# Half-width of aperture region for spectral extraction (relative to source position)
fittype			meddata		# Method for constructing spatial profile (Options: smooth, meddata, poly, gauss, wavelet, or wavelet2D)
window_len		7			# Smoothing window length, when fittype = smooth or meddata (when computing median frame)
median_thresh	5			# Sigma threshold when flagging outliers in median frame, when fittype=meddata and window_len > 1
prof_deg		3			# Polynomial degree, when fittype = poly
p5thresh		10			# X-sigma threshold for outlier rejection while constructing spatial profile
p7thresh		10			# X-sigma threshold for outlier rejection during optimal spectral extraction

# Diagnostics
isplots_S3		4			# Generate few (1), some (3), or many (5) figures (Options: 1 - 5)
nplots			5			# How many of each type of figure do you want to make per file?
vmin			0.98		# Sets the vmin of the color bar for Figure 3101.
vmax			1.01		# Sets the vmax of the color bar for Figure 3101.
time_axis		'y'			# Determines whether the time axis in Figure 3101 is along the y-axis ('y') or the x-axis ('x')
testing_S3		False		# Boolean, set True to only use last file and generate select figures
hide_plots		True		# If True, plots will automatically be closed rather than popping up
save_output		True		# Save outputs for use in S4
save_fluxdata	False		# Save FluxData outputs for debugging or use with other tools (can be quite large files)
verbose			True		# If True, more details will be printed about steps

# Project directory
topdir			/Volumes/DataDrive/WASP43b_Phasecurve

# Directories relative to project dir
inputdir		Stage2
outputdir		Stage3