JP-2173: Add wfss_contam step to calwebb_spec2

CHANGES.rst

@@ -24,6 +24,11 @@ outlier_detection
   The bug in the implimentation of the bilinear interpolator in the ``drizzle``
   package is now fixed. [#6146]
 
+pipeline
+--------
+
+- Added wfss_contam step to `calwebb_spec2` pipeline flow for WFSS modes [#6207]
+
 wfss_contam
 -----------
 

docs/conf.py

@@ -35,7 +35,7 @@ def setup(app):
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('../'))
+# sys.path.insert(0, os.path.abspath('../'))
 sys.path.insert(0, os.path.abspath('jwst/'))
 sys.path.insert(0, os.path.abspath('exts/'))
 

jwst/pipeline/calwebb_spec2.py

@@ -26,6 +26,7 @@
 from ..srctype import srctype_step
 from ..straylight import straylight_step
 from ..wavecorr import wavecorr_step
+from ..wfss_contam import wfss_contam_step
 
 __all__ = ['Spec2Pipeline']
 
@@ -70,6 +71,7 @@ class Spec2Pipeline(Pipeline):
         'fringe': fringe_step.FringeStep,
         'pathloss': pathloss_step.PathLossStep,
         'barshadow': barshadow_step.BarShadowStep,
+        'wfss_contam': wfss_contam_step.WfssContamStep,
         'photom': photom_step.PhotomStep,
         'resample_spec': resample_spec_step.ResampleSpecStep,
         'cube_build': cube_build_step.CubeBuildStep,
@@ -367,6 +369,11 @@ def _step_verification(self, exp_type, members_by_type, multi_int):
             self.log.debug('Science data does not allow master background correction. Skipping "master_background".')
             self.master_background.skip = True
 
+        # Apply WFSS contamination correction only to WFSS exposures
+        if not self.wfss_contam.skip and exp_type not in WFSS_TYPES:
+            self.log.debug('Science data does not allow WFSS contamination correction. Skipping "wfss_contam".')
+            self.wfss_contam.skip = True
+
     def _process_grism(self, data):
         """WFSS & Grism processing
 
@@ -379,6 +386,7 @@ def _process_grism(self, data):
         calibrated = self.fringe(calibrated)
         calibrated = self.pathloss(calibrated)
         calibrated = self.barshadow(calibrated)
+        calibrated = self.wfss_contam(calibrated)
         calibrated = self.photom(calibrated)
 
         return calibrated

jwst/wfss_contam/wfss_contam_step.py

@@ -17,6 +17,7 @@ class WfssContamStep(Step):
         save_simulated_image = boolean(default=False)  # Save full-frame simulated image
         save_contam_images = boolean(default=False)  # Save source contam estimates
         maximum_cores = option('none', 'quarter', 'half', 'all', default='none')
+        skip = boolean(default=True)
     """
 
     reference_file_types = ['photom', 'wavelengthrange']