#! /usr/bin/env python
from stdatamodels.jwst import datamodels
from ..stpipe import Step
from . import persistence
__all__ = ["PersistenceStep"]
[docs]
class PersistenceStep(Step):
"""
PersistenceStep: Correct a science image for persistence.
"""
class_alias = "persistence"
spec = """
input_trapsfilled = string(default="") # Name of the most recent trapsfilled file for the current detector
flag_pers_cutoff = float(default=40.) # Pixels with persistence correction >= this value in DN will be flagged in the DQ
save_persistence = boolean(default=False) # Save subtracted persistence to an output file with suffix '_output_pers'
save_trapsfilled = boolean(default=True) # Save updated trapsfilled file with suffix '_trapsfilled'
"""
reference_file_types = ["trapdensity", "trappars", "persat"]
[docs]
def process(self, input):
if self.input_trapsfilled is not None:
if (self.input_trapsfilled == "None" or
len(self.input_trapsfilled) == 0):
self.input_trapsfilled = None
output_obj = datamodels.RampModel(input).copy()
self.trap_density_filename = self.get_reference_file(output_obj,
"trapdensity")
self.trappars_filename = self.get_reference_file(output_obj,
"trappars")
self.persat_filename = self.get_reference_file(output_obj, "persat")
# Is any reference file missing?
missing = False
missing_reftypes = []
if self.persat_filename == "N/A":
missing = True
missing_reftypes.append("PERSAT")
if self.trap_density_filename == "N/A":
missing = True
missing_reftypes.append("TRAPDENSITY")
if self.trappars_filename == "N/A":
missing = True
missing_reftypes.append("TRAPPARS")
if missing:
if len(missing_reftypes) == 1:
msg = "Missing reference file type: " + missing_reftypes[0]
else:
msg = "Missing reference file types: "
for name in missing_reftypes:
msg += (" " + name)
self.log.warning("%s", msg)
output_obj.meta.cal_step.persistence = "SKIPPED"
return output_obj
if self.input_trapsfilled is None:
traps_filled_model = None
else:
traps_filled_model = datamodels.TrapsFilledModel(
self.input_trapsfilled)
trap_density_model = datamodels.TrapDensityModel(
self.trap_density_filename)
trappars_model = datamodels.TrapParsModel(self.trappars_filename)
persat_model = datamodels.PersistenceSatModel(self.persat_filename)
pers_a = persistence.DataSet(output_obj, traps_filled_model,
self.flag_pers_cutoff,
self.save_persistence,
trap_density_model, trappars_model,
persat_model)
(output_obj, traps_filled, output_pers, skipped) = pers_a.do_all()
if skipped:
output_obj.meta.cal_step.persistence = 'SKIPPED'
else:
output_obj.meta.cal_step.persistence = 'COMPLETE'
if traps_filled_model is not None: # input traps_filled
traps_filled_model.close()
if traps_filled is not None: # output traps_filled
# Save the traps_filled image with suffix 'trapsfilled'.
self.save_model(
traps_filled, suffix='trapsfilled', force=self.save_trapsfilled
)
traps_filled.close()
if output_pers is not None: # output file of persistence
self.save_model(output_pers, suffix='output_pers')
output_pers.close()
# Close reference files.
trap_density_model.close()
trappars_model.close()
persat_model.close()
return output_obj