Arguments

The jump step has five optional arguments that can be set by the user:

  • --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.

  • --maximum_cores: The fraction of available cores that will be used for multi-processing in this step. The default value is ‘none’ which does not use multi-processing. The other options are ‘quarter’, ‘half’, and ‘all’. Note that these fractions refer to the total available cores and on most CPUs these include physical and virtual cores. The clock time for the step is reduced almost linearly by the number of physical cores used on all machines. For example, on an Intel CPU with six real cores and 6 virtual cores setting maximum_cores to ‘half’ results in a decrease of a factor of six in the clock time for the step to run. Depending on the system the clock time can also decrease even more with maximum_cores is set to ‘all’.

  • --flag_4_neighbors: If set to True (default is True) it will cause the four perpendicular neighbors of all detected jumps to be flagged as a jump. This is needed because of the inter-pixel capacitance (IPC) causing 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.