Lv3Step

This is a light wrapper around the level 3 pipeline stage of the official pipeline. For more details, see the official documentation.

If you have background observations, you should ensure these are being correctly picked up by using bgr_check_type and bgr_background_name.

After the main pipeline run, two optional post-processing steps are available. These are independent of each other and can be enabled separately:

  • do_drizzle: Drizzle individual exposures onto the mosaic WCS, producing one *_i2d_single.fits file per exposure. Resample parameters are read from jwst_parameters["resample"].

  • do_blot: Blot the final i2d mosaic back to each exposure’s detector frame, producing one *_i2d_blot.fits file per exposure. The fill value for pixels outside the blotted footprint is controlled by blot_fillval.

Example 1 – Drizzle individual exposures onto the mosaic WCS only:

[parameters.lv3]
do_drizzle = true

Example 2 – Blot the mosaic to every exposure’s detector frame only:

[parameters.lv3]
do_blot = true
blot_fillval = "nan"

Example 3 – Both drizzle and blot:

[parameters.lv3]
do_drizzle = true
do_blot = true

API

class pjpipe.Lv3Step(target, band, in_dir, out_dir, dr_version, is_bgr, step_ext, procs, tweakreg_degroup_nircam_modules=False, tweakreg_degroup_nircam_short_chips=False, tweakreg_group_dithers=None, tweakreg_degroup_dithers=None, skymatch_group_dithers=None, skymatch_degroup_dithers=None, bgr_check_type='parallel_off', bgr_background_name='off', process_bgr_like_science=False, jwst_parameters=None, do_drizzle=False, do_blot=False, blot_fillval=nan, overwrite=False)[source]

Wrapper around the level 3 JWST pipeline

Parameters:

  • target – Target to consider

  • band – Band to consider

  • in_dir – Input directory

  • out_dir – Output directory

  • dr_version – Data processing version

  • is_bgr – Whether we’re processing background observations or not

  • step_ext – .fits extension for the files going into the step

  • procs – Number of processes to run in parallel

  • tweakreg_degroup_nircam_modules – Whether to degroup NIRCam A and B modules. Currently, the WCS is inconsistent between the two, so should probably be set to True if you see “ghosting” in the final mosaic. Defaults to False

  • tweakreg_degroup_nircam_short_chips – Whether to degroup NIRCam short 1/2/3/4 chips. There may be some shifts between these, so should ideally find a shift for each chip. Defaults to False

  • tweakreg_group_dithers – List of ‘miri’, ‘nircam_long’, ‘nircam_short’ of whether to group up dithers for tweakreg. Defaults to None, which will keep at default

  • tweakreg_degroup_dithers – List of ‘miri’, ‘nircam_long’, ‘nircam_short’ of whether to degroup dithers for tweakreg. Defaults to None, which will keep at default.

  • skymatch_group_dithers – List of ‘miri’, ‘nircam_long’, ‘nircam_short’ of whether to group up dithers for skymatch. Defaults to None, which will keep at default

  • skymatch_degroup_dithers – List of ‘miri’, ‘nircam_long’, ‘nircam_short’ of whether to degroup dithers for skymatch. Defaults to None, which will keep at default.

  • bgr_check_type – Method to check if obs is science or background. Options are given by BGR_CHECK_TYPES. Defaults to ‘parallel_off’

  • bgr_background_name – If bgr_check_type is ‘check_in_name’ or ‘filename’, this is the string to match

  • process_bgr_like_science – If True, will process background images as if they are science images. Defaults to False

  • jwst_parameters – Parameter dictionary to pass to the level 2 pipeline. Defaults to None, which will run the observatory defaults

  • do_drizzle – If True, drizzle individual frames to the i2d mosaic WCS after the main pipeline run. Note: creates a lot of files. Defaults to False.

  • do_blot – If True, blot the final i2d mosaic to the detector frame of each exposure, producing one *_i2d_blot.fits file per exposure. Independent of do_drizzle. Defaults to False.

  • blot_fillval – Fill value for pixels outside the blotted footprint. Defaults to np.nan

  • overwrite – Whether to overwrite or not. Defaults to False

create_asn_file(files)[source]

Setup asn lv3 file

do_step()[source]

Run the level 3 pipeline

propagate_metadata(files)[source]

Propagate metadata through to the output files

Parameters:

files – List of files to loop over

run_step(asn_file)[source]

Run the level 3 step

Parameters:

asn_file – Path to association JSON file