Merge branch 'master' into release_metadata

CHANGES.rst

@@ -63,6 +63,11 @@ calwebb_detector1
 - Added the optional ``clean_flicker_noise`` step between ``jump`` and
   ``ramp_fit``. [#8669]
 
+change_migration
+----------------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 clean_flicker_noise
 -------------------
 
@@ -82,12 +87,20 @@ cube_build
 
 - Replaced deep copies of NIRSpec WCS objects within most loops. [#8793]
 
+- Allow the user to provide ra and dec shifts to apply for each file to fine
+  tune the WCS. [#8720]
+
 datamodels
 ----------
 
 - Added `ModelLibrary` class to allow passing on-disk models between steps in the
   image3 pipeline. [#8683]
 
+dark_current
+------------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 documentation
 -------------
 
@@ -96,12 +109,30 @@ documentation
 - Updated description of association keyword `expname`: including path information
   in addition to the filename is discouraged, but allowed. [#8789]
 
+dq_init
+--------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 emicorr
 -------
 
 - Fixed a bug where MIRI EMI correction step would return NaNs when it was unable
   to compute a correction. [#8675]
 
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+extract_1d
+----------
+
+- Updated NIRISS SOSS extraction to utilize ``pastasoss``
+  rotation solution. [#8763]
+
+first_frame
+-----------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 flat_field
 ----------
 
@@ -110,6 +141,11 @@ flat_field
 
 - Replaced deep copies of NIRSpec WCS objects within most loops [#8793]
 
+gain_scale
+----------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 general
 -------
 
@@ -123,12 +159,37 @@ general
 
 - bump dependency to use ``stcal 1.9.0`` [#8808]
 
+group_scale
+-----------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+ipc
+---
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+jump
+----
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 klip
 ----
 
 - Allowed klip to ingest a single shifted 3-D PSF model instead of a 4-D structure
   containing one shifted PSF per science integration. [#8747]
 
+lastframe
+---------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+linearity
+---------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 master_background
 -----------------
 
@@ -193,6 +254,11 @@ pathloss
 
 - Replaced deep copies of NIRSpec WCS objects within most loops [#8793]
 
+persistence
+-----------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 photom
 ------
 
@@ -229,6 +295,18 @@ ramp_fitting
 - Updated the flow of the detector 1 pipeline when selecting the ``LIKELY`` algorithm
   for ramp fitting.  The ramps must contain a minimum number of groups (4).[#8631]
 
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+refpix
+------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+regtest
+-------
+
+- Added memory usage test for Detector1 pipeline. [#8676]
+
 resample
 --------
 
@@ -242,6 +320,11 @@ resample
 - Ensure that NaNs and DO_NOT_USE flags match up in all input data before
   resampling. [#8557]
 
+reset
+-----
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 resample_spec
 -------------
 
@@ -266,12 +349,19 @@ resample_spec
 - Ensure that NaNs and DO_NOT_USE flags match up in all input data before
   resampling. [#8557]
 
+rscd
+----
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 saturation
 ----------
 
 - Add option for using the readout pattern information to improve saturation flagging
   in grouped data. [#8731]
-
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 scripts
 -------
 
@@ -298,6 +388,11 @@ stpipe
 
 - Log jwst version at end of `Step.run`. [#8769]
 
+superbias
+---------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 tso_photometry
 --------------
 

docs/jwst/cube_build/arguments.rst

@@ -91,6 +91,12 @@ The following arguments control the size and sampling characteristics of the out
 ``nspax_y``
   The odd integer number of spaxels to use in the y dimension of the tangent plane.
 
+``offset_file [string]``
+  The string contains the name of the file holding RA and Dec offsets to apply to each input file. This file
+  must be an asdf file with a specific format. For details on how to construct the offset file see
+  :ref:`offsets`. 
+
+
 ``coord_system [string]``
   The default IFU cubes are built on the ra-dec coordinate system (``coord_system=skyalign``). In these cubes north is up 
   and east is left. There are two other coordinate systems an IFU cube can be built on:
@@ -122,3 +128,42 @@ A parameter only used for investigating which detector pixels contributed to a c
 
   The string is the x,y,z value of the cube spaxel that is being investigated. The  numbering starts counting at 0.
   To print information to the screeen about the x = 10, y = 20, z = 35 spaxel the parameter string value is '10 20 35'.
+
+.. _offsets:
+
+Creating an offset file
+-----------------------
+
+The offset file is an ASDF formatted file :`<https://asdf-standard.readthedocs.io/>`_ stands for "Advanced Scientific Data.
+For each input file in the spec3 association used to build the IFU cubes, the offset file needs to have a
+corresponding right ascension and declination offset given in arc seconds.
+
+Below is an example of how to make an ASDF offset file. It is assumed the user has determined the
+offsets to apply to the data in each file. The offsets information is stored in three lists:
+`filename`, `raoffset` and `decoffset`.  The units of the Ra and Dec offsets 
+are required to be in the offset file and only the unit, `arcsec`, is allowed. The file names should
+not contain the directory path. The offset file can have any name, but it must have the `asdf` extension.
+
+An example of making an offset file for an association containing three files is:
+
+.. code-block:: python
+		
+   import asdf
+   import astropy.units as u
+   
+   filename = ['file1.fits', 'file2.fits', 'file3.fits']
+   raoffset = [0.0, -1.0, 1.0]
+   decoffset = [0.0, 1.0, -1.0]
+
+   tree = {
+    "units": str(u.arcsec),
+    "filename": filename,
+    "raoffset": raoffset,
+    "decoffset": decoffset
+    }
+    af = asdf.AsdfFile(tree)
+    af.write_to('offsets.asdf')
+    af.close()
+    
+
+

docs/jwst/emicorr/arguments.rst

@@ -12,9 +12,6 @@ The ``emicorr`` step has the following step-specific arguments.
     If True, the reference wavelength will be scaled to the
     data's phase amplitude.
 
-``--user_supplied_reffile`` (boolean, default=None)
-    This is to specify an ASDF-format user-created reference file.
-
 ``--save_intermediate_results``  (string, default=False)
     This is a boolean flag to specify whether to write a step output
     file with the EMI correction, and a reference file with all the

docs/jwst/extract_1d/arguments.rst

@@ -169,11 +169,6 @@ The ``extract_1d`` step has the following step-specific arguments.
   used when soss_wave_grid is not provided to make sure the computation time or the memory
   used stays reasonable. Default value is 20000.
 
-``--soss_transform``
-  This is a NIRISS-SOSS algorithm-specific parameter; this defines a rotation to
-  apply to the reference files to match the observation. It should be specified as
-  a list of three floats, with default values of None.
-
 ``--soss_tikfac``
   This is a NIRISS-SOSS algorithm-specific parameter; this is the regularization
   factor used in the SOSS extraction. If not specified, ATOCA will calculate a

jwst/charge_migration/charge_migration.py

@@ -16,13 +16,13 @@
 CHLO_DNU = CHLO + DNU
 
 
-def charge_migration(input_model, signal_threshold):
+def charge_migration(output_model, signal_threshold):
     """
     Correct for chargemigration
 
     Parameters
     ----------
-    input_model : `~jwst.datamodels.RampModel`
+    output_model : `~jwst.datamodels.RampModel`
         The input science data to be corrected
 
     signal_threshold : float
@@ -35,11 +35,8 @@ def charge_migration(input_model, signal_threshold):
 
         DO_NOT_USE flags to groups exceeding signal_threshold
     """
-    data = input_model.data
-    gdq = input_model.groupdq
-
-    # Create the output model as a copy of the input
-    output_model = input_model.copy()
+    data = output_model.data
+    gdq = output_model.groupdq
 
     log.info('Using signal_threshold: %.2f', signal_threshold)
 

jwst/charge_migration/charge_migration_step.py

@@ -1,9 +1,8 @@
 #! /usr/bin/env python
 import logging
 
-from ..stpipe import Step
-
 from stdatamodels.jwst import datamodels
+from ..stpipe import Step
 
 from . import charge_migration
 
@@ -25,22 +24,24 @@ class ChargeMigrationStep(Step):
         skip = boolean(default=True)
     """
 
-    def process(self, input):
+    def process(self, step_input):
 
         # Open the input data model
-        with datamodels.RampModel(input) as input_model:
+        with datamodels.RampModel(step_input) as input_model:
+
             if (input_model.data.shape[1] < 3):  # skip step if only 1 or 2 groups/integration
                 log.info('Too few groups per integration; skipping charge_migration')
-
-                result = input_model
-                result.meta.cal_step.charge_migration = 'SKIPPED'
 
-                return result
+                input_model.meta.cal_step.charge_migration = 'SKIPPED'
+                return input_model
+
+            # Work on a copy
+            result = input_model.copy()
 
             # Retrieve the parameter value(s)
             signal_threshold = self.signal_threshold
 
-            result = charge_migration.charge_migration(input_model, signal_threshold)
+            result = charge_migration.charge_migration(result, signal_threshold)
             result.meta.cal_step.charge_migration = 'COMPLETE'
 
         return result