Executing a pipeline or pipeline step directly, or via run()

When calling a pipeline or step instance directly, or 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'

# Run the pipeline
result = pipe('jw00017001001_01101_00001_nrca1_uncal.fits')

# Or, 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 by calling the instance directly
result = step('jw00017001001_01101_00001_nrca1_linearity.fits')

# Or, execute using the run method
result = step.run('jw00017001001_01101_00001_nrca1_linearity.fits')