Executing a pipeline via run()

When calling a pipeline or step instance using the run method, you can specify individual parameter values manually. In this case, parameter files are not used. If you use run after instantiating with a parameter file (as is done when using the call method), the parameter file will be ignored:

# Instantiate the class. Do not provide a parameter file.
pipe = Detector1Pipeline()

# Manually set any desired non-default parameter values
pipe.refpix.skip = True
pipe.jump.rejection_threshold = 5
pipe.ramp_fit.override_gain = 'my_gain_file.fits'
pipe.save_result = True
pipe.output_dir = '/my/data/pipeline_outputs'

# Execute the pipeline using the run method
result = pipe.run('jw00017001001_01101_00001_nrca1_uncal.fits')

To run a single step:

from jwst.jump import JumpStep

# Instantiate the step
step = JumpStep()

# Set parameter values
step.rejection_threshold = 5
step.save_results = True
step.output_dir = '/my/data/jump_data'

# Execute using the run method
result = step.run('jw00017001001_01101_00001_nrca1_linearity.fits')