Merge branch 'master' into abs-sep-tol-check

CHANGES.rst

@@ -129,6 +129,12 @@ ramp_fitting
   fitting or "OLS_C" to use the C extension implementation of
   ramp fitting. [#8503]
 
+refpix
+------
+
+- Use ``double`` for fft filter coefficients to improve compatibility
+  across system. [#8512]
+
 resample
 --------
 
@@ -138,11 +144,15 @@ resample
 - Update variance handling to propagate resampled variance components with
   weights that match the science `weight_type`. [#8437]
 
+- Change `fillval` parameter default from INDEF to NaN [#8488]
+
 resample_spec
 -------------
 
 - Populate the wavelength array in resampled `Slit` and `MultiSlit` models. [#8374]
 
+- Change `fillval` parameter default from INDEF to NaN [#8488]
+
 residual_fringe
 ---------------
 

docs/jwst/resample/arguments.rst

@@ -85,7 +85,7 @@ image.
         ``pixel_scale_ratio``, ``pixel_scale``, ``rotation``, ``crpix``,
         and ``crval`` will be ignored.
 
-``--fillval`` (str, default='INDEF')
+``--fillval`` (str, default='NAN')
     The value to assign to output pixels that have zero weight or do not
     receive any flux from any input pixels during drizzling.
 

jwst/refpix/irs2_subtract_reference.py

@@ -1082,19 +1082,19 @@ def fill_bad_regions(data0, ngroups, ny, nx, row, scipix_n, refpix_r, pad, hnorm
            (scipix_n + refpix_r + 2) * ny // 2 - elen // 2
 
     # Construct the filter [1, cos, 0, cos, 1].
-    temp_a1 = (np.cos(np.arange(elen, dtype=np.float32) *
+    temp_a1 = (np.cos(np.arange(elen, dtype=np.float64) *
                       np.pi / float(elen)) + 1.) / 2.
 
     # elen = 5000
     # blen = 30268
     # row * ny // 2 - 2 * blen - 2 * elen = 658552
     # len(temp_a2) = 729088
-    temp_a2 = np.concatenate((np.ones(blen, dtype=np.float32),
+    temp_a2 = np.concatenate((np.ones(blen, dtype=np.float64),
                               temp_a1.copy(),
                               np.zeros(row * ny // 2 - 2 * blen - 2 * elen,
-                                       dtype=np.float32),
+                                       dtype=np.float64),
                               temp_a1[::-1].copy(),
-                              np.ones(blen, dtype=np.float32)))
+                              np.ones(blen, dtype=np.float64)))
 
     roll_a2 = np.roll(temp_a2, -1)
     aa = np.concatenate((temp_a2, roll_a2[::-1]))

jwst/regtest/test_nirspec_lamp_ifu_spec2.py

@@ -20,9 +20,7 @@ def run_pipeline(rtdata_module):
     args = ["jwst.pipeline.Spec2Pipeline", rtdata.input,
             "--steps.assign_wcs.save_results=true",
             "--steps.msa_flagging.save_results=true",
-            "--steps.flat_field.save_results=true",
-            # Hardwire extract1d ref file selection until CRDS-525 is implemented
-            "--steps.extract_1d.override_extract1d=/grp/crds/jwst/references/jwst/jwst_nirspec_extract1d_0001.asdf"]
+            "--steps.flat_field.save_results=true"]
     Step.from_cmdline(args)
 
     return rtdata

jwst/resample/gwcs_drizzle.py

@@ -15,7 +15,7 @@ class GWCSDrizzle:
     """
 
     def __init__(self, product, outwcs=None, wt_scl=None,
-                 pixfrac=1.0, kernel="square", fillval="INDEF"):
+                 pixfrac=1.0, kernel="square", fillval="NAN"):
         """
         Create a new Drizzle output object and set the drizzle parameters.
 
@@ -53,7 +53,7 @@ def __init__(self, product, outwcs=None, wt_scl=None,
 
         fillval : str, optional
             The value a pixel is set to in the output if the input image does
-            not overlap it. The default value of INDEF does not set a value.
+            not overlap it. The default value of NAN sets NaN values.
         """
 
         # Initialize the object fields
@@ -231,7 +231,7 @@ def increment_id(self):
 
 def dodrizzle(insci, input_wcs, inwht, output_wcs, outsci, outwht, outcon,
               expin, in_units, wt_scl, uniqid=1, xmin=0, xmax=0, ymin=0, ymax=0,
-              iscale=1.0, pixfrac=1.0, kernel='square', fillval="INDEF"):
+              iscale=1.0, pixfrac=1.0, kernel='square', fillval="NAN"):
     """
     Low level routine for performing 'drizzle' operation on one image.
 
@@ -326,7 +326,7 @@ def dodrizzle(insci, input_wcs, inwht, output_wcs, outsci, outwht, outcon,
 
     fillval: str, optional
         The value a pixel is set to in the output if the input image does
-        not overlap it. The default value of INDEF does not set a value.
+        not overlap it. The default value of NAN sets NaN values.
 
     Returns
     -------
@@ -339,7 +339,7 @@ def dodrizzle(insci, input_wcs, inwht, output_wcs, outsci, outwht, outcon,
 
     # Insure that the fillval parameter gets properly interpreted for use with tdriz
     if util.is_blank(str(fillval)):
-        fillval = 'INDEF'
+        fillval = 'NAN'
     else:
         fillval = str(fillval)
 

jwst/resample/resample.py

@@ -45,7 +45,7 @@ class ResampleData:
     """
 
     def __init__(self, input_models, output=None, single=False, blendheaders=True,
-                 pixfrac=1.0, kernel="square", fillval="INDEF", wht_type="ivm",
+                 pixfrac=1.0, kernel="square", fillval="NAN", wht_type="ivm",
                  good_bits=0, pscale_ratio=1.0, pscale=None, **kwargs):
         """
         Parameters
@@ -595,7 +595,7 @@ def update_exposure_times(self, output_model):
     def drizzle_arrays(insci, inwht, input_wcs, output_wcs, outsci, outwht,
                        outcon, uniqid=1, xmin=0, xmax=0, ymin=0, ymax=0,
                        iscale=1.0, pixfrac=1.0, kernel='square',
-                       fillval="INDEF", wtscale=1.0):
+                       fillval="NAN", wtscale=1.0):
         """
         Low level routine for performing 'drizzle' operation on one image.
 
@@ -685,7 +685,7 @@ def drizzle_arrays(insci, inwht, input_wcs, output_wcs, outsci, outwht,
 
         fillval: str, optional
             The value a pixel is set to in the output if the input image does
-            not overlap it. The default value of INDEF does not set a value.
+            not overlap it. The default value of NAN sets NaN values.
 
         Returns
         -------
@@ -698,7 +698,7 @@ def drizzle_arrays(insci, inwht, input_wcs, output_wcs, outsci, outwht,
 
         # Insure that the fillval parameter gets properly interpreted for use with tdriz
         if util.is_blank(str(fillval)):
-            fillval = 'INDEF'
+            fillval = 'NAN'
         else:
             fillval = str(fillval)
 

jwst/resample/resample_step.py

@@ -45,7 +45,7 @@ class ResampleStep(Step):
     spec = """
         pixfrac = float(default=1.0) # change back to None when drizpar reference files are updated
         kernel = string(default='square') # change back to None when drizpar reference files are updated
-        fillval = string(default='INDEF' ) # change back to None when drizpar reference files are updated
+        fillval = string(default='NAN' )
         weight_type = option('ivm', 'exptime', None, default='ivm')  # change back to None when drizpar ref update
         output_shape = int_list(min=2, max=2, default=None)  # [x, y] order
         crpix = float_list(min=2, max=2, default=None)
@@ -304,7 +304,7 @@ def _set_spec_defaults(self):
         if self.kernel is None:
             self.kernel = 'square'
         if self.fillval is None:
-            self.fillval = 'INDEF'
+            self.fillval = 'NAN'
         # Force definition of good bits
         kwargs['good_bits'] = GOOD_BITS
         kwargs['pixfrac'] = self.pixfrac

jwst/resample/tests/test_resample_step.py

@@ -545,6 +545,7 @@ def test_custom_wcs_resample_imaging(nircam_rate, ratio, rotation, crpix, crval,
     'output_shape2, match',
     [((1205, 1100), True), ((1222, 1111), False), (None, True)]
 )
+@pytest.mark.xfail(reason="Empty output region, unclear what this is meant to test.")
 def test_custom_refwcs_resample_imaging(nircam_rate, output_shape2, match,
                                         tmp_path):
     crpix = (600, 550)