Merge branch 'main' of https://github.com/spacetelescope/jwst into JP-3931-test-followup

Author: emolter

changes/9533.background.rst

@@ -0,0 +1 @@
+Change background alias to "bkg_subtract" to fix conflicting aliases for the step. The new alias is the one currently used for running the step or changing parameters from the stage2 pipelines.

docs/jwst/background_step/description.rst

@@ -2,7 +2,7 @@ Description
 ===========
 
 :Class: `jwst.background.BackgroundStep`
-:Alias: background
+:Alias: bkg_subtract
 
 The background subtraction step performs
 image-from-image subtraction in order to accomplish subtraction of background

jwst/background/background_step.py

@@ -16,7 +16,7 @@
 class BackgroundStep(Step):
     """Subtract background exposures from target exposures."""
 
-    class_alias = "background"
+    class_alias = "bkg_subtract"
 
     spec = """
         bkg_list = force_list(default=None)  # List of background files. Ignored for WFSS or if asn is provided
@@ -80,9 +80,9 @@ def process(self, step_input, input_bkg_list=None):
             )
             if result is None:
                 result = input_model.copy()
-                result.meta.cal_step.back_sub = "SKIPPED"
+                result.meta.cal_step.bkg_subtract = "SKIPPED"
             else:
-                result.meta.cal_step.back_sub = "COMPLETE"
+                result.meta.cal_step.bkg_subtract = "COMPLETE"
 
         elif input_model.meta.exposure.type == "NIS_SOSS":
             # Fetch the background reference filename
@@ -126,7 +126,7 @@ def process(self, step_input, input_bkg_list=None):
             # or report and skip the step
             if bkg_list is None or len(bkg_list) == 0:
                 self.log.warning("* No background list provided * Skipping step.")
-                result.meta.cal_step.back_sub = "SKIPPED"
+                result.meta.cal_step.bkg_subtract = "SKIPPED"
                 return result
 
             # check if input data is NRS_IFU
@@ -154,13 +154,13 @@ def process(self, step_input, input_bkg_list=None):
             # Do the background subtraction
             if do_sub:
                 bkg_model, result = background_sub(result, bkg_list, self.sigma, self.maxiters)
-                result.meta.cal_step.back_sub = "COMPLETE"
+                result.meta.cal_step.bkg_subtract = "COMPLETE"
                 if self.save_combined_background:
                     comb_bkg_path = self.save_model(bkg_model, suffix=self.bkg_suffix, force=True)
                     self.log.info(f"Combined background written to {comb_bkg_path}.")
 
             else:
-                result.meta.cal_step.back_sub = "SKIPPED"
+                result.meta.cal_step.bkg_subtract = "SKIPPED"
                 self.log.warning("Skipping background subtraction")
                 self.log.warning(
                     "GWA_XTIL and GWA_YTIL source values are not the same as bkg values"

jwst/background/tests/test_background.py

@@ -177,7 +177,7 @@ def test_nirspec_gwa(tmp_cwd, background, science_image):
     test = science_image.data - back_image.data
     assert_allclose(result.data, test)
     assert type(result) is type(science_image)
-    assert result.meta.cal_step.back_sub == 'COMPLETE'
+    assert result.meta.cal_step.bkg_subtract == 'COMPLETE'
     back_image.close()
 
 
@@ -199,7 +199,7 @@ def test_nirspec_gwa_xtilt(tmp_cwd, background, science_image):
     result = BackgroundStep.call(science_image, bkg)
 
     assert type(result) is type(science_image)
-    assert result.meta.cal_step.back_sub == 'SKIPPED'
+    assert result.meta.cal_step.bkg_subtract == 'SKIPPED'
     back_image.close()
 
 
@@ -221,7 +221,7 @@ def test_nirspec_gwa_ytilt(tmp_cwd, background, science_image):
     result = BackgroundStep.call(science_image, bkg)
 
     assert type(result) is type(science_image)
-    assert result.meta.cal_step.back_sub == 'SKIPPED'
+    assert result.meta.cal_step.bkg_subtract == 'SKIPPED'
 
     back_image.close()
 
@@ -245,7 +245,7 @@ def test_miri_subarray_full_overlap(data_shape, background_shape):
 
     assert_allclose(result.data, image_value - background_value)
     assert type(result) is type(image)
-    assert result.meta.cal_step.back_sub == 'COMPLETE'
+    assert result.meta.cal_step.bkg_subtract == 'COMPLETE'
 
     image.close()
     background.close()
@@ -269,7 +269,7 @@ def test_miri_subarray_partial_overlap(data_shape, background_shape):
     assert_allclose(result.data[..., background_shape[-2]:, :], image_value)
     assert_allclose(result.data[..., :, background_shape[-1]:], image_value)
     assert type(result) is type(image)
-    assert result.meta.cal_step.back_sub == 'COMPLETE'
+    assert result.meta.cal_step.bkg_subtract == 'COMPLETE'
 
     image.close()
     background.close()
@@ -283,7 +283,7 @@ def test_asn_input(mk_asn):
     bgs = datamodels.open(bg_subtracted)
 
     assert_allclose(result.data, bgs.data)
-    assert result.meta.cal_step.back_sub == 'COMPLETE'
+    assert result.meta.cal_step.bkg_subtract == 'COMPLETE'
 
     result.close()
     bgs.close()
@@ -304,11 +304,11 @@ def test_bg_file_list(mk_asn):
     assert_allclose(result1.data, bgs.data)
     assert_allclose(result2.data, bgs.data)
     assert_allclose(result3.data, bgs.data)
-    assert result1.meta.cal_step.back_sub == 'COMPLETE'
-    assert result2.meta.cal_step.back_sub == 'COMPLETE'
-    assert result3.meta.cal_step.back_sub == 'COMPLETE'
-    assert result4.meta.cal_step.back_sub == 'SKIPPED'
-    assert result5.meta.cal_step.back_sub == 'SKIPPED'
+    assert result1.meta.cal_step.bkg_subtract == 'COMPLETE'
+    assert result2.meta.cal_step.bkg_subtract == 'COMPLETE'
+    assert result3.meta.cal_step.bkg_subtract == 'COMPLETE'
+    assert result4.meta.cal_step.bkg_subtract == 'SKIPPED'
+    assert result5.meta.cal_step.bkg_subtract == 'SKIPPED'
 
     result1.close()
     result2.close()

jwst/background/tests/test_background_wfss.py

@@ -458,5 +458,5 @@ def test_wfss_asn_input(mock_asn_and_data):
     assert result.meta.source_catalog == "test_cat.ecsv"
     assert result.meta.direct_image == i2dfile.name
     assert result.meta.segmentation_map == segmfile.name
-    assert result.meta.cal_step.back_sub == "COMPLETE"
+    assert result.meta.cal_step.bkg_subtract == "COMPLETE"
 

jwst/extract_1d/psf_profile.py

@@ -319,7 +319,7 @@ def psf_profile(
     # Check if we need to add a negative nod pair trace
     nod_offset = None
     if model_nod_pair:
-        nod_subtracted = str(input_model.meta.cal_step.back_sub) == "COMPLETE"
+        nod_subtracted = str(input_model.meta.cal_step.bkg_subtract) == "COMPLETE"
         pattype_ok = str(input_model.meta.dither.primary_type) in NOD_PAIR_PATTERN
         if not nod_subtracted:
             log.info("Input data was not nod-subtracted. A negative trace will not be modeled.")

jwst/extract_1d/tests/test_extract.py

@@ -1174,7 +1174,7 @@ def test_define_aperture_optimal_with_nod(
     exptype = "MIR_LRS-FIXEDSLIT"
 
     # mock nod subtraction
-    mock_miri_lrs_fs.meta.cal_step.back_sub = "COMPLETE"
+    mock_miri_lrs_fs.meta.cal_step.bkg_subtract = "COMPLETE"
     mock_miri_lrs_fs.meta.dither.primary_type = "ALONG-SLIT-NOD"
 
     # mock a nod position at the opposite end of the array
@@ -1607,7 +1607,7 @@ def test_create_extraction_optimal(monkeypatch, create_extraction_inputs, psf_re
     model = create_extraction_inputs[0]
 
     # mock nod subtraction
-    model.meta.cal_step.back_sub = "COMPLETE"
+    model.meta.cal_step.bkg_subtract = "COMPLETE"
     model.meta.dither.primary_type = "2-POINT-NOD"
 
     # mock a nod position at the opposite end of the array

jwst/extract_1d/tests/test_psf_profile.py

@@ -248,7 +248,7 @@ def test_psf_profile_model_nod(monkeypatch, mock_miri_lrs_fs, psf_reference_file
     _, _, wl_array = model.meta.wcs(xidx, yidx)
 
     # mock nod subtraction
-    model.meta.cal_step.back_sub = "COMPLETE"
+    model.meta.cal_step.bkg_subtract = "COMPLETE"
     model.meta.dither.primary_type = "2-POINT-NOD"
 
     # mock a nod position at the opposite end of the array
@@ -316,7 +316,7 @@ def test_psf_profile_model_nod_wrong_pattern(mock_miri_lrs_fs, psf_reference_fil
     model = mock_miri_lrs_fs
     data_shape = model.data.shape
     trace = np.full(data_shape[0], (data_shape[1] - 1) / 2.0)
-    model.meta.cal_step.back_sub = "COMPLETE"
+    model.meta.cal_step.bkg_subtract = "COMPLETE"
 
     yidx, xidx = np.mgrid[: data_shape[0], : data_shape[1]]
     _, _, wl_array = model.meta.wcs(xidx, yidx)
@@ -335,7 +335,7 @@ def test_psf_profile_model_nod_bad_position(mock_miri_lrs_fs, psf_reference_file
     model = mock_miri_lrs_fs
     data_shape = model.data.shape
     trace = np.full(data_shape[0], (data_shape[1] - 1) / 2.0)
-    model.meta.cal_step.back_sub = "COMPLETE"
+    model.meta.cal_step.bkg_subtract = "COMPLETE"
     model.meta.dither.primary_type = "2-POINT-NOD"
 
     yidx, xidx = np.mgrid[: data_shape[0], : data_shape[1]]
@@ -394,7 +394,7 @@ def test_psf_profile_optimize_with_nod(
     data_shape = model.data.shape
 
     # mock nod subtraction
-    model.meta.cal_step.back_sub = "COMPLETE"
+    model.meta.cal_step.bkg_subtract = "COMPLETE"
     model.meta.dither.primary_type = "2-POINT-NOD"
 
     # trace at pixel 9.5

jwst/lib/suffix.py

@@ -95,7 +95,7 @@
     "extract2dstep",
     "guider_cds",
     "gain_scale",
-    "background",
+    "bkg_subtract",
     "resetstep",
     "imprintstep",
     "extract1dstep",

jwst/master_background/master_background_mos_step.py

@@ -131,7 +131,7 @@ def process(self, data):
             # If some type of background processing had already been done. Abort.
             # UNLESS forcing is enacted.
             if not self.force_subtract and "COMPLETE" in [
-                data_model.meta.cal_step.back_sub,
+                data_model.meta.cal_step.bkg_subtract,
                 data_model.meta.cal_step.master_background,
             ]:
                 self.log.info("Background subtraction has already occurred. Skipping.")