JP-3598: The ResampleSpecStep and Extract1DStep within MasterBackgroundMosStep are inaccessible

changes/8847.refpix.rst

@@ -0,0 +1 @@
+Include resample, pixel_replace, extract_1d, and combine_1d into MOS background pipeline

jwst/master_background/master_background_mos_step.py

@@ -9,6 +9,10 @@
 from ..flatfield import flat_field_step
 from ..pathloss import pathloss_step
 from ..photom import photom_step
+from ..pixel_replace import pixel_replace_step
+from ..resample import resample_spec_step
+from ..extract_1d import extract_1d_step
+from ..combine_1d import combine_1d_step
 from ..stpipe import Pipeline
 
 __all__ = ['MasterBackgroundMosStep']
@@ -60,6 +64,10 @@
         'pathloss': pathloss_step.PathLossStep,
         'barshadow': barshadow_step.BarShadowStep,
         'photom': photom_step.PhotomStep,
+        'pixel_replace': pixel_replace_step.PixelReplaceStep,
+        'resample_spec': resample_spec_step.ResampleSpecStep,
+        'extract_1d': extract_1d_step.Extract1dStep,
+        'combine_1d': combine_1d_step.Combine1dStep
     }
 
     # No need to prefetch. This will have been done by the parent step.
@@ -156,11 +164,12 @@
         return result
 
     def set_pars_from_parent(self):
-        """Set substep parameters from the parents substeps"""
+        """Set substep parameters from the parents substeps when needed"""
         if not self.parent:
             return
 
-        steps = ['barshadow', 'flat_field', 'pathloss', 'photom']
+        steps = ['barshadow', 'flat_field', 'pathloss', 'photom',
+                 'pixel_replace', 'resample_spec', 'extract_1d', 'combine_1d']
         pars_to_ignore = {
             'barshadow': ['source_type'],
             'flat_field': ['save_interpolated_flat'],
@@ -169,11 +178,29 @@
         }
 
         for step in steps:
-            pars = getattr(self.parent, step).get_pars()
-            for par in pars_to_ignore[step] + GLOBAL_PARS_TO_IGNORE:
-                del pars[par]
+            if step in pars_to_ignore:
+                pars = getattr(self.parent, step).get_pars()
+                for par in pars_to_ignore[step] + GLOBAL_PARS_TO_IGNORE:
+                    del pars[par]
+            else:
+                pars = getattr(self, step).get_pars()
             getattr(self, step).update_pars(pars)
 
+    def _extend_bg_slits(self, pre_calibrated):
+        # Copy dedicated background slitlets to a temporary model
+        bkg_model = datamodels.MultiSlitModel()
+        bkg_model.update(pre_calibrated)
+        slits = []
+        for slit in pre_calibrated.slits:
+            if nirspec_utils.is_background_msa_slit(slit):
+                self.log.info(f'Using background slitlet {slit.source_name}')
+                slits.append(slit)
+        if len(slits) == 0:
+            self.log.warning('No background slitlets found; skipping master bkg correction')
+            return None
+        bkg_model.slits.extend(slits)
+        return bkg_model
+
     def _classify_slits(self, data):
         """Determine how many Slits are background and source types
 
@@ -245,8 +272,16 @@
                 self.log.debug(f'User background provided {user_background}')
                 master_background = user_background
             else:
-                self.log.debug('Calculating 1D master background')
-                master_background = nirspec_utils.create_background_from_multislit(pre_calibrated)
+                self.log.info('Creating MOS master background from background slitlets')
+                bkg_model = self._extend_bg_slits(pre_calibrated)
+                if bkg_model is not None:
+                    bkg_model = self.pixel_replace(bkg_model)
+                    bkg_model = self.resample_spec(bkg_model)
+                    bkg_model = self.extract_1d(bkg_model)
+                    master_background = self.combine_1d(bkg_model)
+                    del bkg_model
+                else:
+                    master_background = None
             if master_background is None:
                 self.log.debug('No master background could be calculated. Returning None')
                 return None, None

jwst/master_background/nirspec_utils.py

@@ -1,8 +1,6 @@
 import logging
 import warnings
 
-from stdatamodels.jwst import datamodels
-
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
 
@@ -76,58 +74,6 @@ def map_to_science_slits(input_model, master_bkg):
     return output_model
 
 
-def create_background_from_multislit(input_model):
-    """Create a 1D master background spectrum from a set of
-    calibrated background MOS slitlets in the input
-    MultiSlitModel.
-
-    Parameters
-    ----------
-    input_model : `~jwst.datamodels.MultiSlitModel`
-        The input data model containing all slit instances.
-
-    Returns
-    -------
-    master_bkg: `~jwst.datamodels.CombinedSpecModel`
-        The 1D master background spectrum created from the inputs.
-    """
-    from ..resample import resample_spec_step
-    from ..extract_1d import extract_1d_step
-    from ..combine_1d.combine1d import combine_1d_spectra
-
-    log.info('Creating MOS master background from background slitlets')
-
-    # Copy dedicated background slitlets to a temporary model
-    bkg_model = datamodels.MultiSlitModel()
-    bkg_model.update(input_model)
-    slits = []
-    for slit in input_model.slits:
-        if is_background_msa_slit(slit):
-            log.info(f'Using background slitlet {slit.source_name}')
-            slits.append(slit)
-
-    if len(slits) == 0:
-        log.warning('No background slitlets found; skipping master bkg correction')
-        return None
-
-    bkg_model.slits.extend(slits)
-
-    # Apply resample_spec and extract_1d to all background slitlets
-    log.info('Applying resampling and 1D extraction to background slits')
-    resamp = resample_spec_step.ResampleSpecStep.call(bkg_model)
-    x1d = extract_1d_step.Extract1dStep.call(resamp)
-
-    # Call combine_1d to combine the 1D background spectra
-    log.info('Combining 1D background spectra into master background')
-    master_bkg = combine_1d_spectra(x1d, exptime_key='exposure_time')
-
-    del bkg_model
-    del resamp
-    del x1d
-
-    return master_bkg
-
-
 def correct_nrs_ifu_bkg(input_model):
     """Apply point source vs. uniform source pathloss adjustments
     to a NIRSpec IFU 2D master background array.