Step Arguments
The reference pixel correction step has seven step-specific arguments:
--odd_even_columns
If the odd_even_columns
argument is given, the top/bottom reference
signal is calculated and applied separately for even- and odd-numbered
columns. The default value is True, and this argument applies to NIR
data only.
--use_side_ref_pixels
If the use_side_ref_pixels
argument is given, the side reference pixels
are used to calculate a reference signal for each row, which is subtracted
from the data. The default value is True, and this argument applies to NIR
data only.
--side_smoothing_length
The side_smoothing_length
argument is used to specify the height of
the window used in calculating the running median when calculating the side
reference signal. The default value is 11, and this argument applies to NIR
data only when the --use_side_ref_pixels
option is selected.
--side_gain
The side_gain
argument is used to specify the factor that the side
reference signal is multiplied by before subtracting from the group
row-by-row. The default value is 1.0, and this argument applies to NIR
data only when the --use_side_ref_pixels
option is selected.
--odd_even_rows
If the odd_even_rows
argument is selected, the reference signal is
calculated and applied separately for even- and odd-numbered rows. The
default value is True, and this argument applies to MIR data only.
--ovr_corr_mitigation_ftr
This is a factor to avoid overcorrection of intermittently bad reference pixels in the IRS2 algorithm. This factor is the number of sigmas away from the mean. The default value is 3.0, and this argument applies only to NIRSpec data taken with IRS2 mode.
--preserve_irs2_refpix
If the preserve_irs2_refpix
argument is set, interleaved reference pixels
in IRS2 mode will be processed along with the normal pixels and preserved
in the output. This option is intended for calibration or diagnostic reductions
only. For normal science operation, this argument should always be False,
so that interleaved pixels are stripped before continuing processing.
--refpix_algorithm
The refpix_algorithm
argument is only relevant for all NIR full-frame
data, and can be set to ‘median’ (default) to use the running median or
‘sirs’ to use the Simple Improved Reference Subtraction (SIRS).
--sigreject
The sigreject
argument is the number of sigmas to reject as outliers in the
SIRS algorithm. The value is expected to be a float.
--gaussmooth
The gaussmooth
argument is the width of Gaussian smoothing kernel to use as
a low-pass filter. The numerical value is expected to be a float.
--halfwidth
The halfwidth
argument is the half-width of convolution kernel to build. The
numerical value is expected to be an integer.