Clarify docs, add log messages

docs/jwst/extract_1d/description.rst

@@ -343,7 +343,7 @@ are used instead:
   residuals of the scene modeled by the PSF at that location.  This option is
   strongly recommended if `model_nod_pair` is True, since the negative nod location is less
   reliably estimated than the positive trace location.
-* `subtract_background`: Unlike box extraction, the background levels can be modeled and removed
+* `subtract_background`: Unlike during box extraction, the background levels can be modeled and removed
   during optimal extraction without explicitly setting a background region.  It is recommended to
   set this parameter to True if background subtraction was skipped prior to extraction. Set this
   parameter to False if a negative nod trace is present but not modeled (`model_nod_pair = False`).

jwst/extract_1d/extract.py

@@ -371,15 +371,19 @@ def get_extract_parameters(ref_dict, input_model, slitname, sp_order, meta,
                     extract_params['model_nod_pair'] = model_nod_pair
 
                     # Check for a valid PSF file
-                    if extract_params['psf'] == 'N/A':
+                    extraction_type = str(extraction_type).lower()
+                    if extract_params['psf'] == 'N/A' and extraction_type != 'box':
+                        log.warning("No PSF file available. Setting extraction type to 'box'.")
                         extraction_type = 'box'
 
                     # Set the extraction type to 'box' or 'optimal'
-                    if str(extraction_type).lower() == 'none':
+                    if extraction_type == 'none':
                         if extract_params['use_source_posn']:
                             extract_params['extraction_type'] = 'optimal'
                         else:
                             extract_params['extraction_type'] = 'box'
+                        log.info(f"Using extraction type '{extract_params['extraction_type']}' "
+                                 f"for use_source_posn = {extract_params['use_source_posn']}")
                     else:
                         extract_params['extraction_type'] = extraction_type
 

jwst/extract_1d/psf_profile.py

@@ -129,15 +129,16 @@ def _make_cutout_profile(xidx, yidx, psf_subpix, psf_data, dispaxis,
     return [sprofile, nod_profile * -1]
 
 
-def _profile_residual(param, cutout, cutout_var, xidx, yidx, psf_subpix, psf_data,
-                      dispaxis, fit_bkg=True):
+def _profile_residual(shifts_to_optimize, cutout, cutout_var, xidx, yidx,
+                      psf_subpix, psf_data, dispaxis, fit_bkg=True):
     """Residual function to minimize for optimizing trace locations."""
-    if len(param) > 1:
-        nod_offset = param[1]
+    if len(shifts_to_optimize) > 1:
+        nod_offset = shifts_to_optimize[1]
     else:
         nod_offset = None
     sprofiles = _make_cutout_profile(xidx, yidx, psf_subpix, psf_data, dispaxis,
-                                     extra_shift=param[0], nod_offset=nod_offset)
+                                     extra_shift=shifts_to_optimize[0],
+                                     nod_offset=nod_offset)
     extract_kwargs = {'extraction_type': 'optimal',
                       'fit_bkg': fit_bkg,
                       'bkg_fit_type': 'poly',
@@ -160,14 +161,13 @@ def psf_profile(input_model, trace, wl_array, psf_ref_name,
                 optimize_shifts=True, model_nod_pair=True):
     """Create a spatial profile from a PSF reference.
 
-    This is intended to provide PSF-based profiles for point sources,
-    for slit-like data containing one positive trace and, optionally,
-    one negative trace resulting from nod subtraction.  The location of
-    the positive trace should be provided in the `trace` input parameter;
-    the negative trace location will be guessed from the input metadata.
-    If a negative trace is modeled, it is recommended that `optimize_shifts`
-    also be set to True, to improve the initial guess for the trace
-    location.
+    Provides PSF-based profiles for point sources in slit-like data containing
+    one positive trace and, optionally, one negative trace resulting from nod
+    subtraction.  The location of the positive trace should be provided in the
+    `trace` input parameter; the negative trace location will be guessed from
+    the input metadata. If a negative trace is modeled, it is recommended that
+    `optimize_shifts` also be set to True, to improve the initial guess for the
+    trace location.
 
     Parameters
     ----------
@@ -184,7 +184,7 @@ def psf_profile(input_model, trace, wl_array, psf_ref_name,
     psf_ref_name : str
         PSF reference filename.
     optimize_shifts : bool, optional
-        If True, the spatial location of the trace will be optimized via
+        If True, the spatial location of the trace will be optimized by
         minimizing the residuals in a scene model compared to the data in
         the first integration of `input_model`.
     model_nod_pair : bool, optional

jwst/extract_1d/tests/test_extract.py

@@ -242,11 +242,14 @@ def test_get_extract_parameters_smoothing_bad_value(
 
 @pytest.mark.parametrize('use_source', [None, True, False])
 def test_get_extract_parameters_extraction_type_none(
-        mock_nirspec_fs_one_slit, extract1d_ref_dict, use_source):
+        mock_nirspec_fs_one_slit, extract1d_ref_dict, use_source, log_watcher):
     input_model = mock_nirspec_fs_one_slit
+
+    log_watcher.message = "Using extraction type"
     params = ex.get_extract_parameters(
         extract1d_ref_dict, input_model, 'slit1', 1, input_model.meta,
         extraction_type=None, use_source_posn=use_source, psf_ref_name='available')
+    log_watcher.assert_seen()
 
     # Extraction type is set to optimal if use_source_posn is True
     if use_source is None or use_source is True:
@@ -259,12 +262,18 @@ def test_get_extract_parameters_extraction_type_none(
 
 @pytest.mark.parametrize('extraction_type', [None, 'box', 'optimal'])
 def test_get_extract_parameters_no_psf(
-        mock_nirspec_fs_one_slit, extract1d_ref_dict, extraction_type):
+        mock_nirspec_fs_one_slit, extract1d_ref_dict, extraction_type, log_watcher):
     input_model = mock_nirspec_fs_one_slit
+
+    log_watcher.message = "Setting extraction type to 'box'"
     params = ex.get_extract_parameters(
         extract1d_ref_dict, input_model, 'slit1', 1, input_model.meta,
         extraction_type=extraction_type, psf_ref_name='N/A')
 
+    # Warning message issued if extraction type was not already 'box'
+    if extraction_type != 'box':
+        log_watcher.assert_seen()
+
     # Extraction type is always box if no psf is available
     assert params['extraction_type'] == 'box'