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Update README.md
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jdavies-st authored Jul 9, 2024
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Expand Up @@ -3,7 +3,7 @@ Algorithms for cleaning JWST data.
- `SnowblindStep`: mask cosmic ray showers and snowballs
- `JumpPlusStep`: Propagate JUMP_DET and SATURATED flags in GROUPDQ properly for frame-averaged groups
- `PersistenceFlagStep`: flag pixels effected by persistence exposure-to-exposure
- `OpenPixelStep`: flag new open pixels, hot pixels, or open adjacent pixels
- `OpenPixelStep`: flag new open pixels, hot pixels, or open adjacent pixels via self-cal


## Installation
Expand All @@ -14,13 +14,13 @@ Algorithms for cleaning JWST data.

## Usage

The steps in snowblind run like any other pipeline steps. From the command line you can run the step on the result file from JumpStep:
The steps in snowblind run like any other pipeline steps. From the command line you can run `SnowblindStep` (aliased as `snowblind`) on the result file from JumpStep:

strun snowblind jw001234_010203_00001_nrcalong_jump.fits --suffix=snowblind

Or you can run it as a post-hook in a full pipeline
Or you can run `SnowblindStep` and `JumpPlusStep` as post-hooks after `JumpStep` in a full pipeline, remembering to turn off the default snowball flagging.

strun calwebb_detector1 jw001234_010203_00001_nrcalong_uncal.fits --steps.jump.post_hooks="snowblind.SnowblindStep","snowblind.JumpPlusStep"
strun calwebb_detector1 jw001234_010203_00001_nrcalong_uncal.fits --steps.jump.post_hooks="snowblind.SnowblindStep","snowblind.JumpPlusStep" --steps.jump.flag_large_events=False

In Python, we can insert `SnowblindStep` and `JumpPlusStep` after `JumpStep` as a post-hook:

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