Merge branch 'main' of https://github.com/spacetelescope/jwst into JP-4151

emolter · emolter · commit 618096fdbc90 · 2025-10-20T09:45:52.000-04:00
diff --git a/README.md b/README.md
@@ -263,6 +263,7 @@ the specified context and less than the context for the next release.
 
 | jwst tag            | DMS build | SDP_VER  | CRDS_CONTEXT | Released   | Ops Install | Notes                                         |
 |---------------------|-----------|----------|--------------|------------|-------------|-----------------------------------------------|
+| 1.20.0              | B12.0.3   | 2025.4.0 | 1439         | 2025-09-23 |             | First release candidate for B12.0.3           |
 | 1.19.2              | B12.0.2   | 2025.3.0 | 1408         | 2025-09-11 |             | Patch release for B12.0.2                     |
 | 1.19.1              | B12.0.1   | 2025.3.0 | 1408         | 2025-07-21 |             | Patch release for B12.0.1                     |
 | 1.19.0              | B12.0     | 2025.3.0 | 1408         | 2025-06-26 |             | First release candidate for B12.0             |
diff --git a/changes/9878.stpipe.rst b/changes/9878.stpipe.rst
@@ -0,0 +1 @@
+Remove ``kwargs`` from the ``JwstStep.run`` signature to match the parent method (``Step.run``).
diff --git a/changes/9879.assign_wcs.rst b/changes/9879.assign_wcs.rst
@@ -0,0 +1 @@
+Remove legacy support for the old-style NIRSpec WCS. All processed data should now have a full slit-based WCS implementation.
diff --git a/changes/9879.clean_flicker_noise.rst b/changes/9879.clean_flicker_noise.rst
@@ -0,0 +1 @@
+Simplify WCS access for NIRSpec FS and MOS data processed with the ``mask_science_regions`` option.
diff --git a/changes/9879.msaflagopen.rst b/changes/9879.msaflagopen.rst
@@ -0,0 +1 @@
+Simplify WCS access for flagging open MSA shutters and remove unnecessary data copies.
diff --git a/changes/9903.pipeline.rst b/changes/9903.pipeline.rst
@@ -0,0 +1 @@
+Use ``Step.prepare_output`` in pipeline steps to open input models and make copies only when necessary.
diff --git a/changes/9903.stpipe.rst b/changes/9903.stpipe.rst
@@ -0,0 +1 @@
+Add an option to ``Step.prepare_output`` to open the input with a specific datamodel class.
diff --git a/docs/jwst/data_products/msa_metadata.rst b/docs/jwst/data_products/msa_metadata.rst
@@ -7,7 +7,7 @@ a crucial component of calibration processing for NIRSpec MOS exposures.
 It contains all the slitlet, shutter, and source configuration information that's needed
 by the :ref:`calwebb_spec2 <calwebb_spec2>` pipeline to process a MOS exposure.
 These metadata are originally generated by the
-`MSA Planning Tool <https://jwst-docs.stsci.edu/display/JDOX/.NIRSpec+MSA+Planning+Tool%2C+MPT+v2.0>`_
+`MSA Planning Tool <https://jwst-docs.stsci.edu/jwst-near-infrared-spectrograph/nirspec-apt-templates/nirspec-multi-object-spectroscopy-apt-template/nirspec-msa-planning-tool-mpt>`_
 (MPT) in APT and passed through the ground system to populate the
 FITS metafile. Details of the metadata and how it is used in calibration processing
 are given below.
diff --git a/docs/jwst/references_general/apcorr_reffile.inc b/docs/jwst/references_general/apcorr_reffile.inc
@@ -283,7 +283,7 @@ corrections for different radii.
 +------------+-------+-------------+-----------+------------+----------+
 | Instrument | Mode  | Column name | Data type | Dimensions | Units    |
 +============+=======+=============+===========+============+==========+
-| NIRSpec    | MOS   | filter      | string    | 12         | N/A      |
+| NIRSpec    | IFU   | filter      | string    | 12         | N/A      |
 +            +       +-------------+-----------+------------+----------+
 |            |       | grating     | string    | 15         | N/A      |
 +            +       +-------------+-----------+------------+----------+
diff --git a/jwst/assign_wcs/nirspec.py b/jwst/assign_wcs/nirspec.py
@@ -6,7 +6,6 @@
 
 import copy
 import logging
-import warnings
 
 import gwcs
 import numpy as np
@@ -41,7 +40,6 @@
     Rotation3DToGWA,
     Slit,
     Slit2Msa,
-    Slit2MsaLegacy,
     Snell,
     Unitless2DirCos,
     WavelengthFromGratingEquation,
@@ -2282,109 +2280,6 @@ def gwa_to_ymsa(msa2gwa_model, lam_cen=None, slit=None, slit_y_range=None):
     return tab
 
 
-def _nrs_wcs_set_slit_input_legacy(input_model, slit_name):
-    """
-    Return a WCS object for a specific slit, slice or shutter.
-
-    Does not compute the bounding box.
-
-    Parameters
-    ----------
-    input_model : JwstDataModel
-        A WCS object for the all open slitlets in an observation.
-    slit_name : int or str
-        Slit.name of an open slit.
-
-    Returns
-    -------
-    wcsobj : `~gwcs.wcs.WCS`
-        WCS object for this slit.
-    """
-    wcsobj = input_model.meta.wcs
-
-    slit_wcs = copy.deepcopy(wcsobj)
-    slit_wcs.set_transform("sca", "gwa", wcsobj.pipeline[1].transform[1:])
-    g2s = slit_wcs.pipeline[2].transform
-    slit_wcs.set_transform("gwa", "slit_frame", g2s.get_model(slit_name))
-
-    exp_type = input_model.meta.exposure.type
-    is_nirspec_ifu = is_nrs_ifu_lamp(input_model) or (exp_type.lower() == "nrs_ifu")
-    if is_nirspec_ifu:
-        slit_wcs.set_transform(
-            "slit_frame", "slicer", wcsobj.pipeline[3].transform.get_model(slit_name) & Identity(1)
-        )
-    else:
-        slit_wcs.set_transform(
-            "slit_frame",
-            "msa_frame",
-            wcsobj.pipeline[3].transform.get_model(slit_name) & Identity(1),
-        )
-    return slit_wcs
-
-
-def nrs_wcs_set_input_legacy(
-    input_model, slit_name, wavelength_range=None, slit_y_low=None, slit_y_high=None
-):
-    """
-    Return a WCS object for a specific slit, slice or shutter.
-
-    This function is intended to work with old-style NIRSpec WCS implementations,
-    to support reading in WCS data from existing datamodels.  For new datamodels,
-    produced after v1.18.0, use `nrs_wcs_set_input`.
-
-    Parameters
-    ----------
-    input_model : JwstDataModel
-        A WCS object for the all open slitlets in an observation.
-    slit_name : int or str
-        Slit.name of an open slit.
-    wavelength_range : list
-        Wavelength range for the combination of filter and grating.
-    slit_y_low, slit_y_high : float
-        The lower and upper bounds of the slit. Optional.
-
-    Returns
-    -------
-    wcsobj : `~gwcs.wcs.WCS`
-        WCS object for this slit.
-    """
-    warnings.warn(
-        "The nrs_wcs_set_input_legacy function is intended for use with an "
-        "old-style NIRSpec WCS pipeline. "
-        "It will be removed in a future build.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-
-    def _get_y_range(input_model):
-        # get the open slits from the model
-        # Need them to get the slit ymin,ymax
-        g2s = input_model.meta.wcs.get_transform("gwa", "slit_frame")
-        open_slits = g2s.slits
-        slit = [s for s in open_slits if s.name == slit_name][0]
-        return slit.ymin, slit.ymax
-
-    if wavelength_range is None:
-        _, wavelength_range = spectral_order_wrange_from_model(input_model)
-
-    slit_wcs = _nrs_wcs_set_slit_input_legacy(input_model, slit_name)
-    transform = slit_wcs.get_transform("detector", "slit_frame")
-    is_nirspec_ifu = (
-        is_nrs_ifu_lamp(input_model) or input_model.meta.exposure.type.lower() == "nrs_ifu"
-    )
-    if is_nirspec_ifu:
-        bb = compute_bounding_box(transform, None, wavelength_range)
-    else:
-        if slit_y_low is None or slit_y_high is None:
-            slit_y_low, slit_y_high = _get_y_range(input_model)
-        bb = compute_bounding_box(
-            transform, None, wavelength_range, slit_ymin=slit_y_low, slit_ymax=slit_y_high
-        )
-
-    slit_wcs.bounding_box = bb
-    return slit_wcs
-
-
 def _fix_slit_name(transform, slit_name):
     """
     Create a new WCS transform by fixing the slit input to a specific value.
@@ -2563,13 +2458,6 @@ def nrs_wcs_set_input(input_model, slit_name):
     # Get the full WCS object
     full_wcs = input_model.meta.wcs
 
-    # Check for an old-style WCS that needs different handling
-    for step in full_wcs.pipeline:
-        if isinstance(step.transform, Slit2MsaLegacy):
-            # There is a legacy slit2msa transform somewhere in the pipeline.
-            # Use the old deepcopy-and-replace method.
-            return nrs_wcs_set_input_legacy(input_model, slit_name)
-
     # Convert FS slit names to numbers
     if str(slit_name).upper() in FIXED_SLIT_NUMS.keys():
         slit_id = nrs_fs_slit_id(str(slit_name).upper())
diff --git a/jwst/clean_flicker_noise/clean_flicker_noise.py b/jwst/clean_flicker_noise/clean_flicker_noise.py
@@ -291,15 +291,15 @@ def mask_slits(input_model, mask):
     log.info("Finding slit/slitlet pixels")
 
     # Get the slits from the WCS object
-    slits = input_model.meta.wcs.get_transform("gwa", "slit_frame").slits
+    slits = input_model.meta.wcs.get_transform("gwa", "slit_frame").slit_ids
 
     # Loop over the slits, marking all the pixels within each bounding
     # box as False (do not use) in the mask.
     # Note that for 3D masks (TSO mode), all planes will be set to the same value.
     for slit in slits:
-        slit_wcs = nirspec.nrs_wcs_set_input(input_model, slit.name)
-        xlo, xhi = _toindex(slit_wcs.bounding_box[0])
-        ylo, yhi = _toindex(slit_wcs.bounding_box[1])
+        bbox = input_model.meta.wcs.bounding_box[slit]
+        xlo, xhi = _toindex(bbox[0])
+        ylo, yhi = _toindex(bbox[1])
         mask[..., ylo:yhi, xlo:xhi] = False
 
     return mask
diff --git a/jwst/group_scale/group_scale.py b/jwst/group_scale/group_scale.py
@@ -23,7 +23,7 @@ def do_correction(model):
 
     Parameters
     ----------
-    model : data model object
+    model : `~stdatamodels.jwst.datamodels.RampModel`
         Science data to be corrected. Model is modified in place.
     """
     # Get the meta data values that we need
diff --git a/jwst/group_scale/group_scale_step.py b/jwst/group_scale/group_scale_step.py
@@ -1,5 +1,7 @@
 import logging
+import warnings
 
+from stdatamodels.exceptions import ValidationWarning
 from stdatamodels.jwst import datamodels
 
 from jwst.group_scale import group_scale
@@ -28,53 +30,66 @@ def process(self, step_input):
 
         Parameters
         ----------
-        step_input : datamodel
-            Input data model on which to perform group scale step.
+        step_input : str or `~stdatamodels.jwst.datamodels.RampModel`
+            Input file name or data model on which to perform group scale step.
 
         Returns
         -------
-        result : datamodel
+        result : `~stdatamodels.jwst.datamodels.RampModel`
             Output data model on which the group scale step has been performed.
         """
-        # Open the input data model
-        with datamodels.RampModel(step_input) as input_model:
-            # Work on a copy
-            result = input_model.copy()
-
-            # Try to get values of NFRAMES and FRMDIVSR to see
-            # if we need to do any rescaling
-            nframes = result.meta.exposure.nframes
-            frame_divisor = result.meta.exposure.frame_divisor
-
-            # If we didn't find NFRAMES, we don't have enough info
-            # to continue. Skip the step.
-            if nframes is None:
-                log.warning("NFRAMES value not found")
-                log.warning("Step will be skipped")
-                result.meta.cal_step.group_scale = "SKIPPED"
-                return result
-
-            # If we didn't find FRMDIVSR, then check to see if NFRAMES
-            # is a power of 2. If it is, rescaling isn't needed.
-            if frame_divisor is None:
-                if nframes & (nframes - 1) == 0:
-                    log.info(f"NFRAMES={nframes} is a power of 2; correction not needed")
-                    log.info("Step will be skipped")
-                    result.meta.cal_step.group_scale = "SKIPPED"
-                    return result
-
-            # Compare NFRAMES and FRMDIVSR. If they're equal,
-            # rescaling isn't needed.
-            elif nframes == frame_divisor:
-                log.info("NFRAMES and FRMDIVSR are equal; correction not needed")
+        # Open the input data model as a RampModel, catching a specific
+        # expected warning for uncal files
+        try:
+            with warnings.catch_warnings():
+                warnings.filterwarnings(
+                    "error",
+                    message=r"(?s:.*)Array datatype .* not compatible",
+                    category=ValidationWarning,
+                )
+                result = self.prepare_output(step_input, open_as_type=datamodels.RampModel)
+        except ValidationWarning as err:
+            log.error(err)
+
+            # Inform the user and raise a clearer error message
+            msg = (
+                "Input data model does not have float-type data. "
+                "The file should be opened as a RampModel before calling the step."
+            )
+            log.error(msg)
+            raise TypeError(msg) from None
+
+        # Try to get values of NFRAMES and FRMDIVSR to see
+        # if we need to do any rescaling
+        nframes = result.meta.exposure.nframes
+        frame_divisor = result.meta.exposure.frame_divisor
+
+        # If we didn't find NFRAMES, we don't have enough info
+        # to continue. Skip the step.
+        if nframes is None:
+            log.warning("NFRAMES value not found")
+            log.warning("Step will be skipped")
+            result.meta.cal_step.group_scale = "SKIPPED"
+            return result
+
+        # If we didn't find FRMDIVSR, then check to see if NFRAMES
+        # is a power of 2. If it is, rescaling isn't needed.
+        if frame_divisor is None:
+            if nframes & (nframes - 1) == 0:
+                log.info(f"NFRAMES={nframes} is a power of 2; correction not needed")
                 log.info("Step will be skipped")
                 result.meta.cal_step.group_scale = "SKIPPED"
                 return result
 
-            # Do the scaling
-            group_scale.do_correction(result)
+        # Compare NFRAMES and FRMDIVSR. If they're equal,
+        # rescaling isn't needed.
+        elif nframes == frame_divisor:
+            log.info("NFRAMES and FRMDIVSR are equal; correction not needed")
+            log.info("Step will be skipped")
+            result.meta.cal_step.group_scale = "SKIPPED"
+            return result
 
-            # Cleanup
-            del input_model
+        # Do the scaling
+        group_scale.do_correction(result)
 
         return result
diff --git a/jwst/group_scale/tests/test_group_scale.py b/jwst/group_scale/tests/test_group_scale.py
@@ -4,7 +4,7 @@
 
 import numpy as np
 import pytest
-from stdatamodels.jwst.datamodels import RampModel
+from stdatamodels.jwst.datamodels import JwstDataModel, Level1bModel, RampModel
 
 from jwst.group_scale import GroupScaleStep
 from jwst.group_scale.group_scale import do_correction
@@ -114,6 +114,30 @@ def test_scale_value(make_rampmodel):
     assert scale == scale_from_data[0]
 
 
+def test_level1b(make_rampmodel):
+    model = make_rampmodel(2, 2, 4, 200, 200)
+    l1b_model = Level1bModel()
+    l1b_model.data = model.data.astype(np.uint16)
+    l1b_model.update(model)
+
+    with pytest.raises(
+        TypeError, match="The file should be opened as a RampModel before calling the step"
+    ):
+        GroupScaleStep.call(l1b_model)
+
+
+def test_non_ramp_model(make_rampmodel):
+    model = make_rampmodel(2, 2, 4, 200, 200)
+    generic_model = JwstDataModel(model)
+    np.testing.assert_allclose(generic_model.data, model.data)
+
+    output = GroupScaleStep.call(generic_model)
+    assert isinstance(output, RampModel)
+
+    scale = model.meta.exposure.frame_divisor / model.meta.exposure.nframes
+    np.testing.assert_allclose(output.data / model.data, scale)
+
+
 @pytest.fixture(scope="function")
 def make_rampmodel():
     """Make NIRSPEC IRS2 model for testing"""
diff --git a/jwst/msaflagopen/msaflag_open.py b/jwst/msaflagopen/msaflag_open.py
diff --git a/jwst/msaflagopen/tests/test_msa_open.py b/jwst/msaflagopen/tests/test_msa_open.py
diff --git a/jwst/stpipe/core.py b/jwst/stpipe/core.py
diff --git a/jwst/stpipe/tests/steps/__init__.py b/jwst/stpipe/tests/steps/__init__.py
diff --git a/jwst/stpipe/tests/test_prepare_output.py b/jwst/stpipe/tests/test_prepare_output.py

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	+Remove ``kwargs`` from the ``JwstStep.run`` signature to match the parent method (``Step.run``).
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+Remove legacy support for the old-style NIRSpec WCS. All processed data should now have a full slit-based WCS implementation.`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	+Simplify WCS access for NIRSpec FS and MOS data processed with the ``mask_science_regions`` option.
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+Simplify WCS access for flagging open MSA shutters and remove unnecessary data copies.`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	+Use ``Step.prepare_output`` in pipeline steps to open input models and make copies only when necessary.
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	+Add an option to ``Step.prepare_output`` to open the input with a specific datamodel class.