JP-3598: The ResampleSpecStep and Extract1DStep within MasterBackgrou…

…ndMosStep are inaccessible (#8847)

changes/8847.master_background.rst

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

docs/jwst/master_background/description.rst

@@ -376,6 +376,7 @@ as follows:
    extended sources (appropriate for background signal), and saving the extended
    source correction arrays for each slit in an internal copy of the data model
 #. If a user-supplied master background spectrum is **not** given, the
+   :ref:`pixel_replace <pixel_replace_step>`,
    :ref:`resample_spec <resample_spec_step>` and :ref:`extract_1d <extract_1d_step>`
    steps are applied to the calibrated background slits, resulting
    in extracted 1D background spectra

jwst/master_background/master_background_mos_step.py

@@ -9,6 +9,9 @@
 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 ..stpipe import Pipeline
 
 __all__ = ['MasterBackgroundMosStep']
@@ -62,6 +65,9 @@ class MasterBackgroundMosStep(Pipeline):
         '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,
     }
 
     # No need to prefetch. This will have been done by the parent step.
@@ -170,7 +176,7 @@ def process(self, data):
         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
 
@@ -188,6 +194,21 @@ def set_pars_from_parent(self):
                 del pars[par]
             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
 
@@ -269,9 +290,16 @@ def _calc_master_background(
                 master_background = user_background
                 bkg_x1d_spectra = None
             else:
-                self.log.debug('Calculating 1D master background')
-                master_background, bkg_x1d_spectra = nirspec_utils.create_background_from_multislit(
-                    pre_calibrated, sigma_clip=sigma_clip, median_kernel=median_kernel)
+                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.run(bkg_model)
+                    bkg_model = self.resample_spec.run(bkg_model)
+                    bkg_x1d_spectra = self.extract_1d.run(bkg_model)
+                    master_background = nirspec_utils.create_background_from_multispec(
+                                      bkg_x1d_spectra, sigma_clip=sigma_clip, median_kernel=median_kernel)
+                else:
+                    master_background = None
             if master_background is None:
                 self.log.debug('No master background could be calculated. Returning None')
                 return None, None, None

jwst/master_background/nirspec_utils.py

@@ -3,7 +3,6 @@
 
 from scipy.signal import medfilt
 
-from stdatamodels.jwst import datamodels
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -78,14 +77,14 @@ def map_to_science_slits(input_model, master_bkg):
     return output_model
 
 
-def create_background_from_multislit(input_model, sigma_clip=3, median_kernel=1):
+def create_background_from_multispec(bkg_model, sigma_clip=3, median_kernel=1):
     """Create a 1D master background spectrum from a set of
     calibrated background MOS slitlets in the input
-    MultiSlitModel.
+    MultiSpecModel.
 
     Parameters
     ----------
-    input_model : `~jwst.datamodels.MultiSlitModel`
+    bkg_model : `~jwst.datamodels.MultiSpecModel`
         The input data model containing all slit instances.
     sigma_clip : None or float, optional
         Optional factor for sigma clipping outliers when combining background spectra.
@@ -101,36 +100,11 @@ def create_background_from_multislit(input_model, sigma_clip=3, median_kernel=1)
     x1d: `jwst.datamodels.MultiSpecModel`
         The 1D extracted background spectra of 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', sigma_clip=sigma_clip)
+    master_bkg = combine_1d_spectra(bkg_model, exptime_key='exposure_time', sigma_clip=sigma_clip)
 
     # If requested, apply a moving-median boxcar filter to the master background spectrum
     # Round down even kernel sizes because only odd kernel sizes are supported.
@@ -150,10 +124,7 @@ def create_background_from_multislit(input_model, sigma_clip=3, median_kernel=1)
             kernel_size=[median_kernel]
         )
 
-    del bkg_model
-    del resamp
-
-    return master_bkg, x1d
+    return master_bkg
 
 
 def correct_nrs_ifu_bkg(input_model):

jwst/master_background/tests/test_master_background_mos.py

@@ -2,14 +2,17 @@
 import pytest
 from astropy.io import fits
 from astropy.table import Table
-from stdatamodels.jwst.datamodels import ImageModel
+from stdatamodels.jwst.datamodels import ImageModel, MultiSlitModel
 
 from jwst.stpipe import query_step_status
 from jwst.assign_wcs import AssignWcsStep
 from jwst.extract_2d.extract_2d_step import Extract2dStep
 from jwst.extract_2d.tests.test_nirspec import create_nirspec_hdul
 from jwst.master_background import MasterBackgroundMosStep
 from jwst.master_background import nirspec_utils
+from jwst.pixel_replace import PixelReplaceStep
+from jwst.resample import ResampleSpecStep
+from jwst.extract_1d import Extract1dStep
 
 
 def create_msa_hdul():
@@ -74,6 +77,7 @@ def nirspec_msa_metfl(tmp_path):
     hdul.close()
     return filename
 
+
 @pytest.fixture
 def nirspec_msa_extracted2d(nirspec_msa_rate, nirspec_msa_metfl):
     model = ImageModel(nirspec_msa_rate)
@@ -82,6 +86,20 @@ def nirspec_msa_extracted2d(nirspec_msa_rate, nirspec_msa_metfl):
     return model
 
 
+def mk_multispec(model):
+    specs_model = MultiSlitModel()
+    specs_model.update(model)
+    slits = []
+    for slit in model.slits:
+        if nirspec_utils.is_background_msa_slit(slit):
+            slits.append(slit)
+    specs_model.slits.extend(slits)
+    specs_model = PixelReplaceStep.call(specs_model)
+    specs_model = ResampleSpecStep.call(specs_model)
+    specs_model = Extract1dStep.call(specs_model)
+    return specs_model
+
+
 def test_master_background_mos(nirspec_msa_extracted2d):
     model = nirspec_msa_extracted2d
 
@@ -97,43 +115,47 @@ def test_master_background_mos(nirspec_msa_extracted2d):
     # Check that a background was subtracted from the science data
     assert not np.allclose(sci_orig, sci_bkgsub)
 
-    model.close()
-    result.close()
+    del model
+    del result
 
 
-def test_create_background_from_multislit(nirspec_msa_extracted2d):
+def test_create_background_from_multispec(nirspec_msa_extracted2d):
     model = nirspec_msa_extracted2d
 
-    # Insert a outliers into one of the background spectra
+    # Insert outliers into one of the background spectra
     nypix = len(model.slits[0].data)
     nxpix = len(model.slits[0].data)
-    model.slits[0].data[nypix//2,nxpix//2-1:nxpix//2+1] = 10
+    model.slits[0].data[nypix//2, nxpix//2-1:nxpix//2+1] = 10
+
+    specs_model = mk_multispec(model)
 
     # First check that we can make a master background from the inputs
 
     # Check that with sigma_clip=None, the outlier is retained
-    master_background, _ = nirspec_utils.create_background_from_multislit(
-        model, sigma_clip=None)
+    master_background = nirspec_utils.create_background_from_multispec(
+        specs_model, sigma_clip=None)
     assert np.any(master_background.spec[0].spec_table['surf_bright'] > 1)
 
     # Confirm that using a median_filter will filter out the outlier
-    master_background, _ = nirspec_utils.create_background_from_multislit(
-        model, median_kernel=4)
+    master_background = nirspec_utils.create_background_from_multispec(
+        specs_model, median_kernel=4)
     assert np.allclose(master_background.spec[0].spec_table['surf_bright'], 1)
 
     # Confirm that using a sigma clipping when combining background spectra
     # removes the outlier
-    master_background, _ = nirspec_utils.create_background_from_multislit(
-        model, sigma_clip=3)
+    master_background = nirspec_utils.create_background_from_multispec(
+        specs_model, sigma_clip=3)
     assert np.allclose(master_background.spec[0].spec_table['surf_bright'], 1)
 
-    model.close()
+    del model
+    del specs_model
+
 
 def test_map_to_science_slits(nirspec_msa_extracted2d):
     model = nirspec_msa_extracted2d
+    specs_model = mk_multispec(model)
 
-    master_background, _ = nirspec_utils.create_background_from_multislit(
-        model)
+    master_background = nirspec_utils.create_background_from_multispec(specs_model)
 
     # Check that the master background is expanded to the shape of the input slits
     mb_multislit = nirspec_utils.map_to_science_slits(model, master_background)
@@ -145,13 +167,15 @@ def test_map_to_science_slits(nirspec_msa_extracted2d):
     nonzero = slit_data != 0
     assert np.allclose(slit_data[nonzero], 1)
 
-    model.close()
+    del model
+    del specs_model
+
 
 def test_apply_master_background(nirspec_msa_extracted2d):
     model = nirspec_msa_extracted2d
+    specs_model = mk_multispec(model)
 
-    master_background, _ = nirspec_utils.create_background_from_multislit(
-    model)
+    master_background = nirspec_utils.create_background_from_multispec(specs_model)
     mb_multislit = nirspec_utils.map_to_science_slits(model, master_background)
 
     result = nirspec_utils.apply_master_background(model, mb_multislit, inverse=False)
@@ -175,7 +199,8 @@ def test_apply_master_background(nirspec_msa_extracted2d):
     assert np.any(diff != 0)
     assert np.allclose(diff[diff != 0], -1)
 
-    model.close()
-    result.close()
+    del model
+    del result
+    del specs_model