Step Arguments

The refpix step has the following step-specific arguments.

--odd_even_columns (bool, default=True)

The top/bottom reference signal is calculated and applied separately for even and odd-numbered columns. This applies to NIR data only.

--use_side_ref_pixels (bool, default=True)

The side reference pixels are used to calculate a reference signal for each row, which is subtracted from the data. This applies to NIR data only.

--side_smoothing_length (int, default=11)

Height of the window used in calculating the running median when calculating the side reference signal. This applies to NIR data only when the --use_side_ref_pixels option is selected.

--side_gain (float, default=1.0)

The factor that the side reference signal is multiplied by before subtracting from the group row-by-row. This applies to NIR data only when the --use_side_ref_pixels option is selected.

--odd_even_rows (bool, default=True)

The reference signal is calculated and applied separately for even- and odd-numbered rows. This applies to MIR data only.

--ovr_corr_mitigation_ftr (float, default=3.0)

The factor to avoid overcorrection of intermittently bad reference pixels in the IRS2 algorithm. This is the number of sigmas away from the mean. This applies only to NIRSpec data taken with IRS2 mode.

--preserve_irs2_refpix (bool, default=False)

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.

--irs2_mean_subtraction (bool, default=False)

Apply or skip a mean offset subtraction before IRS2 correction. Mean values are computed across reference pixels sorted by amplifier and detector column parity. Setting this to True may help reduce alternating column noise in some exposures.

--refpix_algorithm (str, default=’median’)

This is only relevant for all NIR full-frame data, and can be set to 'median' to use the running median or 'sirs' to use the Simple Improved Reference Subtraction (SIRS).

--sigreject (float, default=4.0)

The number of sigmas to reject as outliers in the SIRS algorithm.

--gaussmooth (float, default=1.0)

The width of Gaussian smoothing kernel to use as a low-pass filter.

--halfwidth (int, default=30)

The half-width of convolution kernel to build.

--siglimit (float, default=3.0)

The number of standard deviations to use in the iterative sigma clipping algorithm that calculates the mean of the reference pixels. The value is used as both the lower and upper bounds in the sigma clipping algorithm.