Merge branch 'master' into reference_uri_to_cache_path

spacetelescope · Jun 11, 2024 · 4d19b45 · 4d19b45
2 parents 69a70c4 + 3e5761a
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -197,6 +197,9 @@ pixel_replace
 - Moved pixel_replace in the calwebb_spec2 pipeline and added it to the calwebb_spec3
   pipeline. In both pipelines it is now executed immediately before resample_spec/cube_build. [#8409]
 
+- Added estimated errors and variances for replaced pixels, following the
+  interpolation scheme used for the data. [#8504]
+
 ramp_fitting
 ------------
 
@@ -226,6 +229,8 @@ resample
 
 - Change `fillval` parameter default from INDEF to NaN [#8488]
 
+- Removed the use of the `drizpars` reference file [#8546]
+
 resample_spec
 -------------
 
@@ -237,6 +242,8 @@ resample_spec
   when the slit was closely aligned with the RA direction
   sky. [#8511]
 
+- Removed the use of the `drizpars` reference file [#8546]
+
 residual_fringe
 ---------------
 

diff --git a/docs/jwst/pixel_replace/arguments.rst b/docs/jwst/pixel_replace/arguments.rst
@@ -5,11 +5,12 @@ The ``pixel_replace`` step has the following step-specific arguments:
 
 ``--algorithm`` (str, default='fit_profile')
   This sets the method used to estimate flux values for bad pixels. The default 'fit_profile' uses a profile
-  fit to adjacent column values.  The minimum gradient ('mingrad') method is also available for the MIRI MRS.
+  fit to adjacent column values.  The minimum gradient ('mingrad') method, developed for MIRI MRS data, may
+  also be used for all instruments and modes.
 
 ``--n_adjacent_cols`` (int, default=3)
   Number of adjacent columns (on either side of column containing a bad pixel) to use in
   creation of the source profile, in cross-dispersion direction. The total number of
   columns used in the profile will be twice this number; on array edges, the total number
   of columns contributing to the source profile will be less than ``2 * n_adjacent_cols``.
-
+  Ignored when ``algorithm = 'mingrad'``.
diff --git a/docs/jwst/pixel_replace/main.rst b/docs/jwst/pixel_replace/main.rst
@@ -15,6 +15,8 @@ flagged as ``DO_NOT_USE`` in 2-D extracted spectra using interpolation methods,
 prior to rectification in the :ref:`resample_spec <resample_step>` step.
 ``pixel_replace`` inserts these estimates into the 2-D data array,
 unsets the ``DO_NOT_USE`` flag, and sets the ``FLUX_ESTIMATED`` flag for each affected pixel.
+Error values and variance components for the replaced pixels are similarly updated with
+estimated values, following the same interpolation method as is used for the data.
 
 This step is provided as a cosmetic feature and, for that reason, should be used with caution.
 

diff --git a/docs/jwst/pixel_replace/reference_files.rst b/docs/jwst/pixel_replace/reference_files.rst
@@ -1,4 +1,4 @@
 Reference File
 ==============
 
-This step does not use any reference file.
+This step does not use any reference files.
diff --git a/docs/jwst/references_general/drizpars_reffile.inc b/docs/jwst/references_general/drizpars_reffile.inc
diff --git a/docs/jwst/references_general/drizpars_selection.inc b/docs/jwst/references_general/drizpars_selection.inc
diff --git a/docs/jwst/references_general/references_general.rst b/docs/jwst/references_general/references_general.rst
@@ -150,8 +150,6 @@ documentation on each reference file.
 +-----------------------------------------------+--------------------------------------------------+
 | :ref:`refpix <refpix_step>`                   | :ref:`REFPIX <refpix_reffile>`                   |
 +-----------------------------------------------+--------------------------------------------------+
-| :ref:`resample <resample_step>`               | :ref:`DRIZPARS <drizpars_reffile>`               |
-+-----------------------------------------------+--------------------------------------------------+
 | :ref:`reset <reset_step>`                     | :ref:`RESET <reset_reffile>`                     |
 +-----------------------------------------------+--------------------------------------------------+
 | :ref:`residual_fringe <residual_fringe_step>` | :ref:`FRINGEFREQ <fringefreq_reffile>`           |
@@ -204,8 +202,6 @@ documentation on each reference file.
 +--------------------------------------------------+-----------------------------------------------+
 | :ref:`DISTORTION <distortion_reffile>`           | :ref:`assign_wcs <assign_wcs_step>`           |
 +--------------------------------------------------+-----------------------------------------------+
-| :ref:`DRIZPARS <drizpars_reffile>`               | :ref:`resample <resample_step>`               |
-+--------------------------------------------------+-----------------------------------------------+
 | :ref:`EMICORR <emicorr_reffile>`                 | :ref:`emicorr <emicorr_step>`                 |
 +--------------------------------------------------+-----------------------------------------------+
 | :ref:`EXTRACT1D <extract1d_reffile>`             | :ref:`extract_1d <extract_1d_step>`           |

diff --git a/docs/jwst/resample/main.rst b/docs/jwst/resample/main.rst
@@ -15,11 +15,9 @@ The ``resample`` step can take as input either:
 #. a single 2D input image
 #. an association table (in json format)
 
-The defined parameters for the drizzle operation itself get
-provided by the DRIZPARS reference file (from CRDS).  The exact values
-used depends on the number of input images being combined and the filter
-being used. Other information may be added as selection criteria later,
-but for now, only basic information is used.
+The parameters for the drizzle operation are provided via ``resample``
+step parameters, which can be overridden by a step parameter reference
+file from CRDS.
 
 The output product gets defined using the WCS information of all inputs,
 even if it is just a single input image. The output WCS defines a

diff --git a/docs/jwst/resample/reference_files.rst b/docs/jwst/resample/reference_files.rst
@@ -1,5 +1,3 @@
 Reference File
 ==============
-The ``resample`` step uses the DRIZPARS reference file.
-
-.. include:: ../references_general/drizpars_reffile.inc
+The ``resample`` step does not use any reference files.
diff --git a/jwst/pipeline/calwebb_spec3.py b/jwst/pipeline/calwebb_spec3.py
@@ -228,10 +228,11 @@ def process(self, input):
                 for cal_array in result:
                     cal_array.meta.asn.table_name = op.basename(input_models.asn_table_name)
                 result = self.outlier_detection(result)
+
                 # interpolate pixels that have a NaN value or are flagged
                 # as DO_NOT_USE or NON_SCIENCE.
-                print(result)
                 result = self.pixel_replace(result)
+
                 # Resample time. Dependent on whether the data is IFU or not.
                 resample_complete = None
                 if exptype in IFU_EXPTYPES: