[pre-commit.ci] auto fixes from pre-commit.com hooks

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Author: pre-commit-ci[bot]

jwst/assign_wcs/util.py

@@ -398,7 +398,7 @@ def create_grism_bbox(
                 extract_orders = [x[1] for x in ref_extract_orders if x[0] == filter_name].pop()
 
             wavelength_range = f.get_wfss_wavelength_range(filter_name, extract_orders)
-            print('Wavelength range', wavelength_range)
+            print("Wavelength range", wavelength_range)
     if mmag_extract is None:
         mmag_extract = 999.0  # extract all objects, regardless of magnitude
     else:
@@ -431,7 +431,7 @@ def _create_grism_bbox(
     # this contains the pure information from the catalog with no translations
     skyobject_list = get_object_info(input_model.meta.source_catalog)
 
-    print('sky object list', skyobject_list)
+    print("sky object list", skyobject_list)
     # get the imaging transform to record the center of the object in the image
     # here, image is in the imaging reference frame, before going through the
     # dispersion coefficients
@@ -451,9 +451,16 @@ def _create_grism_bbox(
         # takes in ra, dec, wavelength, order but wave and order
         # don't get used until the detector->grism_detector transform
         xcenter, ycenter, _, _ = sky_to_detector(
-            obj.sky_centroid.icrs.ra.value, obj.sky_centroid.icrs.dec.value, 1, 1)
+            obj.sky_centroid.icrs.ra.value, obj.sky_centroid.icrs.dec.value, 1, 1
+        )
 
-        print('X and Y center', xcenter, ycenter, obj.sky_centroid.icrs.ra.value, obj.sky_centroid.icrs.dec.value)
+        print(
+            "X and Y center",
+            xcenter,
+            ycenter,
+            obj.sky_centroid.icrs.ra.value,
+            obj.sky_centroid.icrs.dec.value,
+        )
         order_bounding = {}
         waverange = {}
         partial_order = {}
@@ -483,11 +490,11 @@ def _create_grism_bbox(
                 ]
             )
             if input_model.meta.exposure.type.upper() == "MIR_WFSS":
-                print('lmin lmax order', lmin,lmax,order)
-                x1, y1, _, _, _ = sky_to_grism(ra, dec, [lmin] , [order] )
-                x2, y2,_, _ , _ = sky_to_grism(ra, dec, [lmax] , [order] )
-                #y1 = ycenter + y1
-                #y2 = ycenter + y2
+                print("lmin lmax order", lmin, lmax, order)
+                x1, y1, _, _, _ = sky_to_grism(ra, dec, [lmin], [order])
+                x2, y2, _, _, _ = sky_to_grism(ra, dec, [lmax], [order])
+                # y1 = ycenter + y1
+                # y2 = ycenter + y2
                 print("+++++++++++++++++++++++++assign_wcs util.py x1,y1,x2,y2", x1, y1, x2, y2)
             else:
                 x1, y1, _, _, _ = sky_to_grism(ra, dec, [lmin] * 4, [order] * 4)
@@ -520,17 +527,17 @@ def _create_grism_bbox(
                 input_model.meta.wcsinfo.dispersion_direction,
             )
 
-            print('object is extended', obj.is_extended)
-            
+            print("object is extended", obj.is_extended)
+
             if wfss_extract_half_height is not None and not obj.is_extended:
                 if input_model.meta.wcsinfo.dispersion_direction == 2:
                     ra_center, dec_center = (
                         obj.sky_centroid.ra.value,
                         obj.sky_centroid.dec.value,
                     )
                     center, _, _, _, _ = sky_to_grism(
-                       ra_center, dec_center, (lmin + lmax) / 2, order
-                   )
+                        ra_center, dec_center, (lmin + lmax) / 2, order
+                    )
                     xmin = center - wfss_extract_half_height
                     xmax = center + wfss_extract_half_height
                 elif input_model.meta.wcsinfo.dispersion_direction == 1:
@@ -546,13 +553,13 @@ def _create_grism_bbox(
                 else:
                     raise ValueError("Cannot determine dispersion direction.")
 
-            print('xmin  xmax', xmin, xmax)
+            print("xmin  xmax", xmin, xmax)
             # Convert floating-point corner values to whole pixel indexes
             xmin = gwutils._toindex(xmin)  # noqa: SLF001
             xmax = gwutils._toindex(xmax)  # noqa: SLF001
             ymin = gwutils._toindex(ymin)  # noqa: SLF001
             ymax = gwutils._toindex(ymax)  # noqa: SLF001
-            print('ymin ymax', ymin, ymax)
+            print("ymin ymax", ymin, ymax)
             # Don't add objects and orders that are entirely off the detector.
             # "partial_order" marks objects that are near enough to the detector
             # edge to have some spectrum on the detector.

jwst/extract_1d/extract.py

@@ -1187,10 +1187,10 @@ def define_aperture(input_model, slit, extract_params, exp_type):
     data_shape = data_model.data.shape[-2:]
 
     # Get a wavelength array for the data
-    
+
     wl_array = get_wavelengths(data_model, exp_type, extract_params["spectral_order"])
 
-    print('result of get_wavelengths', wl_array)
+    print("result of get_wavelengths", wl_array)
     # Shift aperture definitions by source position if needed
     # Extract parameters are updated in place
     if extract_params["use_source_posn"]:
@@ -1620,7 +1620,7 @@ def create_extraction(
     extract_params = get_extract_parameters(
         extract_ref_dict, data_model, slitname, sp_order, input_model.meta, **kwargs
     )
-    print('in extract.py extraction parameters', extract_params["match"])
+    print("in extract.py extraction parameters", extract_params["match"])
 
     if extract_params["match"] == NO_MATCH:
         log.critical("Missing extraction parameters.")
@@ -1630,8 +1630,8 @@ def create_extraction(
         raise ContinueError()
 
     extract_params["dispaxis"] = data_model.meta.wcsinfo.dispersion_direction
-    print('extract params', extract_params["dispaxis"])
-    
+    print("extract params", extract_params["dispaxis"])
+
     if extract_params["dispaxis"] is None:
         log.warning("The dispersion direction information is missing, so skipping ...")
         raise ContinueError()
@@ -1645,7 +1645,7 @@ def create_extraction(
 
     valid = np.isfinite(wavelength)
     wavelength = wavelength[valid]
-    print('wavelength',wavelength)
+    print("wavelength", wavelength)
     if np.sum(valid) == 0:
         log.error("Spectrum is empty; no valid data.")
         raise ContinueError()
@@ -1663,7 +1663,7 @@ def create_extraction(
 
     # Set up aperture correction, to be used for every integration
     apcorr_available = False
-    print('Source type', source_type)
+    print("Source type", source_type)
     if source_type is not None and source_type.upper() == "POINT" and apcorr_ref_model is not None:
         log.info("Creating aperture correction.")
         # NIRSpec needs to use a wavelength in the middle of the
@@ -1687,7 +1687,7 @@ def create_extraction(
         )
     else:
         apcorr = None
-    print('in extract.py apcorr',apcorr)
+    print("in extract.py apcorr", apcorr)
 
     # Log the parameters before extracting
     log_initial_parameters(extract_params)
@@ -1726,7 +1726,7 @@ def create_extraction(
 
     # Extract each integration
     spec_list = []
-    print('integrations', integrations) 
+    print("integrations", integrations)
     for integ in integrations:
         (
             sum_flux,
@@ -1741,8 +1741,8 @@ def create_extraction(
             scene_model_2d,
             residual_2d,
         ) = extract_one_slit(data_model, integ, profile, bg_profile, nod_profile, extract_params)
-        print('Got here')
-                
+        print("Got here")
+
         # Save the scene model and residual
         if save_scene_model:
             if isinstance(scene_model, datamodels.CubeModel):
@@ -1808,7 +1808,7 @@ def create_extraction(
 
         del sum_flux
 
-        print('flux', flux)
+        print("flux", flux)
         error = np.sqrt(f_var_poisson + f_var_rnoise + f_var_flat)
         sb_error = np.sqrt(sb_var_poisson + sb_var_rnoise + sb_var_flat)
         berror = np.sqrt(b_var_poisson + b_var_rnoise + b_var_flat)
@@ -1886,7 +1886,7 @@ def create_extraction(
 
         if exp_type in WFSS_EXPTYPES:
             spectral_order = data_model.meta.wcsinfo.spectral_order
-            print('spectral order', spectral_order)
+            print("spectral order", spectral_order)
             if hasattr(data_model.meta, "filename"):
                 # calwebb_spec3 case: no separate slit input to function
                 spec.meta.filename = data_model.meta.filename
@@ -2143,8 +2143,8 @@ def run_extract1d(
         else:
             apcorr_ref_model = read_apcorr_ref(apcorr_ref_name, exp_type)
 
-    print('in extract.py', apcorr_ref_model)
-    
+    print("in extract.py", apcorr_ref_model)
+
     # This will be relevant if we're asked to extract a spectrum
     # and the spectral order is zero.
     # That's only OK if the disperser is a prism.
@@ -2154,7 +2154,7 @@ def run_extract1d(
     profile_model = None
     scene_model = None
     residual = None
-    print('is this true', isinstance(input_model, (ModelContainer, datamodels.MultiSlitModel)))
+    print("is this true", isinstance(input_model, (ModelContainer, datamodels.MultiSlitModel)))
     if isinstance(input_model, (ModelContainer, datamodels.MultiSlitModel)):
         if isinstance(input_model, ModelContainer):
             slits = input_model
@@ -2176,7 +2176,7 @@ def run_extract1d(
         # Set up the output model
         output_model = _make_output_model(slits[0], meta_source)
 
-        print('in extract.py number of slits', len(slits))
+        print("in extract.py number of slits", len(slits))
         for slit in slits:  # Loop over the slits in the input model
             log.info(f"Working on slit {slit.name}")
             log.debug(f"Slit is of type {type(slit)}")

jwst/extract_1d/extract_1d_step.py

@@ -94,8 +94,8 @@ def _get_extract_reference_files_by_mode(self, model, exp_type):
         if apcorr_ref != "N/A":
             self.log.info(f"Using APCORR file {apcorr_ref}")
 
-        print('************************',apcorr_ref)
-            
+        print("************************", apcorr_ref)
+
         try:
             psf_ref = self.get_reference_file(model, "psf")
         except crds.core.exceptions.CrdsLookupError:
@@ -416,8 +416,8 @@ def process(self, input_data):
                 profile = None
                 scene_model = None
                 residual = None
-                print('The returned reference files', extract_ref, apcorr_ref, psf_ref)
-              
+                print("The returned reference files", extract_ref, apcorr_ref, psf_ref)
+
                 if isinstance(model, datamodels.IFUCubeModel):
                     # Call the IFU specific extraction routine
                     extracted = self._extract_ifu(model, exp_type, extract_ref, apcorr_ref)

jwst/extract_2d/extract_2d.py

@@ -7,7 +7,7 @@
 from jwst.extract_2d.grisms import extract_grism_objects, extract_tso_object
 from jwst.extract_2d.nirspec import nrs_extract2d
 
-#from jwst.miri import extract_wfss_objects
+# from jwst.miri import extract_wfss_objects
 
 log = logging.getLogger(__name__)
 
@@ -98,7 +98,7 @@ def extract2d(
                 extract_orders=extract_orders,
             )
 
-        #elif exp_type == "MIR_WFSS":
+        # elif exp_type == "MIR_WFSS":
         #    print("extract 2d WFSS")
         #    output_model = extract_grism_objects(
         #        input_model,

jwst/extract_2d/extract_2d_step.py

@@ -42,14 +42,14 @@ def process(self, input_model):
         reference_file_names = {}
 
         if input_model.meta.exposure.type in extract_2d.slitless_modes:
-            print('Going to read in wavelength reference file')
+            print("Going to read in wavelength reference file")
             # The wavelengthrange file is used only by the WFSS modes.
             # If retrieved by a Nirspec mode, it would override the name of
             # the file in meta.ref_file if a custom file was used.
             for reftype in self.reference_file_types:
                 reffile = self.get_reference_file(input_model, reftype)
                 reference_file_names[reftype] = reffile if reffile else ""
-        print('refrence file names',reference_file_names)
+        print("reference file names", reference_file_names)
         with datamodels.open(input_model) as dm:
             output_model = extract_2d.extract2d(
                 dm,

jwst/extract_2d/grisms.py

@@ -394,7 +394,7 @@ def extract_grism_objects(
         ]:
             raise ValueError("Expected name of wavelengthrange reference file")
         else:
-            print(' mag limits', mmag_extract, nbright)
+            print(" mag limits", mmag_extract, nbright)
             grism_objects = util.create_grism_bbox(
                 input_model,
                 reference_files,
@@ -479,7 +479,7 @@ def extract_grism_objects(
                 order_model = Const1D(order)
                 order_model.inverse = Const1D(order)
 
-                print('WHAT ARE THESE', xmin, ymin, xcenter_model, ycenter_model, order_model)
+                print("WHAT ARE THESE", xmin, ymin, xcenter_model, ycenter_model, order_model)
                 if input_model.meta.exposure.type.upper() == "MIR_WFSS":
                     tr = inwcs.get_transform("dispersed_detector", "detector")
                 else:

jwst/lib/dispaxis.py

@@ -76,7 +76,7 @@ def get_dispersion_direction(exposure_type, grating="ANY", filter_wh="ANY", pupi
         "MIR_IMAGE": None,
         "MIR_LRS-FIXEDSLIT": 2,
         "MIR_LRS-SLITLESS": 2,
-        "MIR_WFSS":2,
+        "MIR_WFSS": 2,
         "MIR_LYOT": None,
         "MIR_MRS": 2,
         "MIR_TACQ": None,

jwst/lib/wcs_utils.py

@@ -40,7 +40,7 @@ def get_wavelengths(model, exp_type="", order=None, use_wavecorr=None):
     else:
         wl_array = None
 
-    print(' lib wcs_utils', wl_array)
+    print(" lib wcs_utils", wl_array)
     # Check for a present but empty wavelength array
     with warnings.catch_warnings():
         warnings.filterwarnings("ignore", message="All-NaN slice", category=RuntimeWarning)

jwst/pipeline/calwebb_spec2.py

@@ -48,6 +48,8 @@
 EXP_TYPES_USING_REFBKGDS = WFSS_TYPES + ["NIS_SOSS"]
 
 WFSS_TYPES = WFSS_TYPES + ["MIR_WFSS"]
+
+
 class Spec2Pipeline(Pipeline):
     """
     Process JWST spectroscopic exposures from Level 2a to 2b.
@@ -223,9 +225,9 @@ def process_exposure_product(
 
             # Check the datamodel to see if it's a grism image/direct image, if so get the catalog
             # name from the asn and record it to the meta
-            print('WFSS_TYPES', WFSS_TYPES, exp_type) 
+            print("WFSS_TYPES", WFSS_TYPES, exp_type)
             if exp_type in WFSS_TYPES:
-                print('In calwebb_spec2 we are in WFSS_TYPES')
+                print("In calwebb_spec2 we are in WFSS_TYPES")
                 try:
                     science.meta.source_catalog = Path(members_by_type["sourcecat"][0]).name
                     self.log.info(f"Using sourcecat file {science.meta.source_catalog}")
@@ -348,7 +350,7 @@ def process_exposure_product(
         elif exp_type == "NRS_MSASPEC":
             calibrated = self._process_nirspec_msa_slits(calibrated)
         elif exp_type == "MIR_WFSS":
-            print('in calspec2 Calling process_miri_wfss')
+            print("in calspec2 Calling process_miri_wfss")
             calibrated = self._process_miri_wfss(calibrated)
         elif exp_type in NRS_SLIT_TYPES:
             calibrated = self._process_nirspec_slits(calibrated)
@@ -588,9 +590,8 @@ def _step_verification(self, exp_type, science, members_by_type, multi_int):
                 'Science data does not allow WFSS contamination correction. Skipping "wfss_contam".'
             )
             self.wfss_contam.skip = True
-        if exp_type == 'MIR_WFSS':
+        if exp_type == "MIR_WFSS":
             self.wfss_contam.skip = True
-            
 
     def _process_grism(self, data):
         """
@@ -659,7 +660,6 @@ def _process_grism(self, data):
         calibrated = self.photom.run(calibrated)
         return calibrated
 
-    
     def _process_miri_wfss(self, data):
         """
         Calibrate MIRI WFSS  data.
@@ -716,15 +716,15 @@ def _process_miri_wfss(self, data):
 
         # Continue with remaining calibration steps, using the original
         # DN/sec image
-        print('*** run extracted_2d')
+        print("*** run extracted_2d")
         calibrated = self.extract_2d.run(calibrated)
-        print('*** src type')
+        print("*** src type")
         calibrated = self.srctype.run(calibrated)
-        #calibrated = self.straylight.run(calibrated)
-        #calibrated = self.fringe.run(calibrated)
-        #calibrated = self.pathloss.run(calibrated)
-        #calibrated = self.barshadow.run(calibrated)
-        #calibrated = self.wfss_contam.run(calibrated)
+        # calibrated = self.straylight.run(calibrated)
+        # calibrated = self.fringe.run(calibrated)
+        # calibrated = self.pathloss.run(calibrated)
+        # calibrated = self.barshadow.run(calibrated)
+        # calibrated = self.wfss_contam.run(calibrated)
         calibrated = self.photom.run(calibrated)
         return calibrated