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added ability to skip skymatch #83

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added ability to skip skymatch #83

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ef51402
added ability to skip skymatch
Jun 4, 2025
8743f55
separate bkg and sci skymatch off-switch
Jun 9, 2025
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41 changes: 33 additions & 8 deletions pjpipe/lv3/lv3_step.py
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Original file line number Diff line number Diff line change
Expand Up @@ -550,7 +550,20 @@ def run_step(
model.meta.observation.exposure_number = str(i)
model.meta.group_id = ""

asn_file = skymatch.run(asn_file)
# Add ability to skip skymatch if requested
# By default, skymatch is run on both science and background observations
# To disable skymatch for background observations,
# set lv3_step.jwst_parameters["skymatch"]["skip_bgr"] = True in config.toml
# To disable skymatch for science observations,
# set lv3_step.jwst_parameters["skymatch"]["skip"] = True in config.toml
skip_skymatch = False
if self.jwst_parameters:
skymatch_params = self.jwst_parameters.get("skymatch", {})
key = "skip_bgr" if self.is_bgr else "skip"
skip_skymatch = skymatch_params.get(key, False)

if not skip_skymatch:
asn_file = skymatch.run(asn_file)

del skymatch
gc.collect()
Expand Down Expand Up @@ -591,14 +604,26 @@ def run_step(

# Run the rest of the level 3 pipeline

if use_model_library:
# Re-instantiate the ModelLibrary, to wipe out any weirdness we might have performed
# along the way
asn_file = ModelContainer([models[m] for m in models])
asn_file = ModelLibrary(asn_file, on_disk=False)
if "name" not in asn_file._asn["products"][0]:
name = f"{self.target.lower()}_{self.band_type}_lv3_{band_short.lower()}{self.bgr_ext}"
# Ensure product name is set correctly whether skymatch is run or not
# This prevents the default "step" name from being used
if isinstance(asn_file, ModelLibrary) and hasattr(asn_file, "_asn"):
name = f"{self.target.lower()}_{self.band_type}_lv3_{self.band.lower()}{self.bgr_ext}"
if "products" in asn_file._asn and len(asn_file._asn["products"]) > 0:
asn_file._asn["products"][0]["name"] = copy.deepcopy(name)
log.info(f"Setting product name to {name}")

# Set the output_dir and output_file for im3 to ensure correct file naming
im3.output_file = f"{self.target.lower()}_{self.band_type}_lv3_{self.band.lower()}{self.bgr_ext}"
log.info(f"Setting output_file to {im3.output_file}")

# if use_model_library:
# # Re-instantiate the ModelLibrary, to wipe out any weirdness we might have performed
# # along the way
# asn_file = ModelContainer([models[m] for m in models])
# asn_file = ModelLibrary(asn_file, on_disk=False)
# if "name" not in asn_file._asn["products"][0]:
# name = f"{self.target.lower()}_{self.band_type}_lv3_{band_short.lower()}{self.bgr_ext}"
# asn_file._asn["products"][0]["name"] = copy.deepcopy(name)

im3.run(asn_file)

Expand Down