This calls the wf3rej executable. Use this function to facilitate batch runs or for the TEAL interface.

Running wf3rej from a python terminal

In Python without TEAL:

from wfc3tools import wf3rej

In Python with TEAL:

from import teal
from wfc3tools import wf3rej

In Pyraf:

import wfc3tools
epar wf3rej

Displaying output from wf3rej in a Jupyter Notebook

When calling wf3rej from a Jupyter notebook, informational text output from the underlying wf3rej.e program will be passed through print as the calibration runs by default, and show up in the user’s cell. This behavior can be customized by passing your own function as the log_func keyword argument to wf3rej. As output is read from the underlying program, the wf3rej Python wrapper will call log_func with the contents of each line. (print is an obvious choice for a log function, but this also provides a way to connect wf3rej to the Python logging system by passing the logging.debug function or similar.)

If log_func=None is passed, informational text output from the underlying program will be ignored, but the program’s exit code will still be checked for successful completion.

Input Parameters for the Python interface

input : str, Name of input files

  • a single filename (iaa012wdq_raw.fits)
  • a Python list of filenames
  • a partial filename with wildcards (\*raw.fits)
  • filename of an ASN table (\*asn.fits)
  • an at-file (@input)
output: string
Name of the output FITS file.
crrejtab: string
reference file name
scalense: string
scale factor applied to noise
initgues: string
intial value estimate scheme (min|med)
skysub: string
how to compute the sky (none|mode|mean)
crsigmas: string
rejection levels in each iteration
crradius: float
cosmic ray expansion radius in pixels
crthresh: float
rejection propagation threshold
badinpdq: int
data quality flag bits to reject
crmask: bool
flag CR in input DQ imageS?
shadcorr: bool
perform shading shutter correction?
verbose: bool, optional
Print verbose time stamps?

Command Line Options for the wf3rej executable

wf3rej.e input output [-options]

Input can be a single file

Where the options include:

  • t: print the timestamps
  • v: verbose
  • shadcorr: perform shading shutter correction?
  • crmask: flag CR in input DQ images?
  • table <filename>: the crrejtab filename
  • scale <number>: scale factor for noise
  • init <med|min>: initial value estimate scheme
  • sky <none|median|mode>: how to compute sky
  • sigmas: rejection leves for each iteration
  • radius <number>: CR expansion radius
  • thresh <number> : rejection propagation threshold
  • pdq <number>: data quality flag bits to reject