6.11. rejectCosmicRays¶

6.11.1. Purpose¶

This primitive will mask cosmic rays in a GHOST data frame by updating the data mask.

Warning

The algorithm seems to work, but isn’t managing to update the DQ plane. I’m working on the issue. -MCW

6.11.2. Inputs and Outputs¶

The following options can be passed to rejectCosmicRays via the RecipeSystem, or overridden with a user configuration file, as marked:

Parameter	Type	Default	Override?		Description
Parameter	Type	Default	Recipe	User	Description
suffix	str	_cosmicRaysRejected	Y	Y	Suffix affixed to modified file.
subsampling	int	2	Y	Y	The number of pixels to subsample in each direction of each pixel.
sigma_lim	float	5.0	Y	Y	Sigma clipping value.
f_lim	float	6.0	Y	Y	Fine-structure clipping limit.
n_passes	int	2	Y	Y	Number of iterations to perform.

6.11.3. Algorithm¶

This primitive is a first-principles implementation of the LACosmic algorithm. NumPy array operations are used for maximum efficiency. For a full-discussion of the algorithm, see van Dokkum 2001, PASP 113, 1420-1427 (ADS). In summary (where the symbol $\ast$ denotes convolution):

Create a Laplacian, , of the input data frame, .
- Subsample the image by a factor of subsampling and apply the Laplacian transformation;
- Set any negative sub-pixels to have value 0 instead;
- Re-sample the image back to its original resolution.
Generate the ‘sigma map’, , of the frame.
- Form a ‘noise image’ of the data, $N=g^{-1}\sqrt{g(M_5\ast I)+\sigma_{rn}^2}$ , where $g$ and $\sigma_{rn}$ are the data gain and read noise respectively. $M_5$ is a $5\times 5$ median filter used to smooth the data.
- The sigma map is then generated as $S=\mathcal{L}^+ /f_S N$ , where $f_S$ is the subsampling factor used.
- Smooth the sigma map to help remove sampling flux, resulting in $S^\prime = S - (S\ast M_5)$ .
Generate the ‘fine-structure image’ of the frame, $\mathcal{F}=(M_3\ast I) - ((M_3\ast I) \ast M_7)$ , where $M_3$ and $M_7$ are $3\times 3$ and $7\times 7$ median filters,
Mark pixels as cosmic rays (via the image quality plane) if:
- $S^\prime >$ sigma_lim, and
- $\mathcal{L}^+ /\mathcal{F} >$ f_lim.
For the purposes of the algorithm (i.e. not in the data to be returned), replace cosmic rays pixels with the median value of surrounding pixels.
Iterate over steps 1-5 until n_passes is reached, or the number of cosmic rays detected falls to 0.

6.11.4. Issues and Limitations¶

Both strong spectral features and, in high-resolution mode, the ThXe calibration output may be incorrectly flagged as cosmic rays. Therefore, this primitive will trigger a call to need to add more here once this actually works

Note

The current preset values of sigma_lim (15.0, 5.0), f_lim (5.0) and n_passes (5) are a first-pass guess at what seems to flag roughly the correct number of cosmic rays. More complete testing, and the possible implementation of a table of preset values on a case-by-case basis, will need to wait until the findApertures routine (and related routines) are finalized and mixed in with the cosmic ray finding.