Step Arguments

The jump step has many optional arguments that can be set by the user. The details for each are listed below.

Parameters for Baseline Cosmic Ray Jump Detection

--rejection_threshold

A floating-point value that sets the sigma threshold for jump detection. In the code, sigma is determined using the read noise from the read noise reference file and the Poisson noise (based on the median difference between samples and the gain reference file). Note that any noise source beyond these two that may be present in the data will lead to an increase in the false positive rate and thus may require an increase in the value of this parameter. The default value of 4.0 for the rejection threshold will yield 6200 false positives for every million pixels, if the noise model is correct.

--three_group_rejection_threshold

Cosmic ray sigma rejection threshold for ramps having 3 groups. This is a floating-point value with default value of 6.0, and minimum of 0.0.

--four_group_rejection_threshold

Cosmic ray sigma rejection threshold for ramps having 4 groups. This is a floating-point value with default value of 5.0, and minimum of 0.0.

--maximum_cores

The number of available cores that will be used for multi-processing in this step. The default value is ‘1’, which does not use multi-processing. The other options are either an integer, ‘quarter’, ‘half’, or ‘all’. Note that these fractions refer to the total available cores and on most CPUs these include physical and virtual cores. Multiprocessing only occurs during the two point difference calculation, which does not include finding snowballs, nor finding showers. The reduction in clock time is linear for only the two point difference portion of the jump step, but will not be linear with the number of cores used for the totality of running the jump step. If the time needed to compute snowballs and/or showers is significant, the reduction in processing time for the jump step when using multiprocessing may not be as significant as expected.

--flag_4_neighbors

If set to True (default is True) it will cause the four perpendicular neighbors of all detected jumps to also be flagged as a jump. This is needed because of the inter-pixel capacitance (IPC), which causes a small jump in the neighbors. The small jump might be below the rejection threshold, but will affect the slope determination of the pixel. The step will take about 40% longer to run when this is set to True.

--max_jump_to_flag_neighbors

A floating point value in units of sigma that limits the flagging of neighbors. Any jump above this cutoff will not have its neighbors flagged. The concept is that the jumps in neighbors will be above the rejection threshold and thus be flagged as primary jumps. The default value is 200.

--min_jump_to_flag_neighbors

A floating point value in units of sigma that limits the flagging of neighbors of marginal detections. Any primary jump below this value will not have its neighbors flagged. The goal is to prevent flagging jumps that would be too small to significantly affect the slope determination. The default value is 10.

Parameters that affect after jump Flagging

After a jump of at least after_jump_flag_dn1 DN, groups up to after_jump_flag_time1 seconds will also be flagged as jumps. That pair of arguments is defined as:

--after_jump_flag_dn1

A floating point value in units of DN

--after_jump_flag_time1

A floating point value in units of seconds

A second threshold and time can also be set: after a jump of at least after_jump_flag_dn2 DN, groups up to after_jump_flag_time2 seconds will also be flagged as jumps. That pair of arguments is defined as:

--after_jump_flag_dn2

A floating point value in units of DN

--after_jump_flag_time2

A floating point value in units of seconds

Parameters that affect Near-IR Snowball Flagging

--expand_large_events

A boolean parameter that controls whether the jump step will expand the number of pixels that are flagged around large cosmic ray events. These are know as “snowballs” in the near-infrared detectors and “showers” for the MIRI detectors. In general, this should be set to True.

--min_jump_area

The minimum number of contiguous pixels needed to trigger the expanded flagging of large cosmic rays events.

--min_sat_area

The minimum number of saturated pixels required to meet sat_required_snowball.

--expand_factor

A multiplicative factor applied to the enclosing ellipse for snowballs. This larger area will have all pixels flagged as having a jump.

--sat_required_snowball

A boolean value that if True requires that there are saturated pixels within the enclosed jump circle.

--min_sat_radius_extend

The minimum radius of the saturated core of a snowball required for the radius of the saturated core to be extended.

--sat_expand

Number of pixels to add to the radius of the saturated core of snowballs

--edge_size

The distance from the edge of the detector where saturated cores are not required for snowball detection

--mask_snowball_core_next_int

Turns on/off the flagging of saturated cores of snowballs in the next integration

--snowball_time_masked_next_int

Controls the total time that the saturated cores of snowballs are flagged in the next integration.

Parameters that affect MIRI Shower Flagging

--find_showers

Turn on the detection of showers for the MIRI detectors

--extend_snr_threshold

The SNR minimum for the detection of faint extended showers in MIRI

--extend_min_area

The required minimum area of extended emission after convolution for the detection of showers in MIRI

--extend_inner_radius

The inner radius of the Ring2DKernel that is used for the detection of extended emission in showers

--extend_outer_radius

The outer radius of the Ring2DKernel that is used for the detection of extended emission in showers

--extend_ellipse_expand_ratio

Multiplicative factor to expand the radius of the ellipse fit to the detected extended emission in MIRI showers

--time_masked_after_shower

Number of seconds to flag groups as jump after a detected extended emission in MIRI showers

--min_diffs_single_pass

The minimum number of differences to switch to flagging all outliers at once

--max_shower_amplitude

The maximum allowable amplitude for MIRI showers in DN/s

Parameter that affects both Snowball and Shower flagging

--max_extended_radius

The maximum extension of the jump and saturation that will be flagged for showers or snowballs

Parameters that affect Sigma Clipping

--minimum_groups

The minimum number of groups to run the jump step with sigma clipping

--minimum_sigclip_groups

The minimum number of groups to switch the jump detection to use sigma clipping

--only_use_ints

If True the sigma clipping is applied only for a given group across all integrations. If not, all groups from all integrations are used for the sigma clipping.