Merge branch 'master' into pin_numpy_build_requirement

CHANGES.rst

@@ -22,7 +22,7 @@ assign_wcs
 
 - Updated the routines that load NIRSpec MOS slit and source data from the MSA meta
   data file to properly handle background and virtual slits, and assign appropriate
-  meta data to them for use downstream. [#8442]
+  meta data to them for use downstream. [#8442, #8533]
 
 associations
 ------------
@@ -36,6 +36,16 @@ associations
 - Updated Level3 rules for new handling of NIRSpec MOS source_id formatting when
   constructing output file names. [#8442]
 
+- Added default values for new non-header keywords (``MOSTILNO`` and ``DITHPTIN``)
+  to the default values in the ``asn_make_pool`` script. [#8508]
+
+- Create WFSS Pure-Parallel associations [#8528]
+
+combine_1d
+----------
+
+- Fix weights for combining errors from 1D spectra. [#8520]
+
 dark_current
 ------------
 
@@ -79,6 +89,11 @@ extract_1d
 - Add propagation of uncertainty when annular backgrounds are subtracted
   from source spectra during IFU spectral extraction. [#8515]
 
+- Add propagation of background uncertainty when background is subtracted from 
+  source spectra during non-IFU spectral extraction. [#8532]
+
+- Fix error in application of aperture correction to variance arrays. [#8530]
+
 extract_2d
 ----------
 
@@ -103,6 +118,13 @@ general
 
 - build with Numpy 2.0 release candidate to address ABI changes [#8527]
 
+master_background_mos
+---------------------
+
+- Updated check for NIRSpec MOS background slits to use new naming convention:
+  ``slit.source_name`` now contains the string "BKG" instead of
+  "background". [#8533]
+
 outlier_detection
 -----------------
 
@@ -217,6 +239,11 @@ tweakreg
 - Change code default to use IRAF StarFinder instead of
   DAO StarFinder [#8487]
 
+- Added a check for ``(abs_)separation`` and ``(abs_)tolerance`` parameters
+  that ``separation`` > ``sqrt(2) * tolerance`` that will now log an error
+  message and skip ``tweakreg`` step when this condition is not satisfied and
+  source confusion is possible during catalog matching. [#8476]
+
 wfss_contam
 -----------
 
@@ -521,10 +548,14 @@ resample
 
 - Removed any reference to the "tophat" kernel for resample step. [#8364]
 
+- Removing unnecessary warning. Errors are propagated identically for
+  the 'exptime' and 'ivm' weight options. [#8258]
+
 - Increased specificity of several warning filters. [#8320]
 
 - Changed deprecated ``stpipe.extern.configobj`` to ``astropy.extern.configobj``. [#8320]
 
+
 residual_fringe
 ---------------
 

docs/jwst/tweakreg/README.rst

@@ -307,7 +307,8 @@ The ``tweakreg`` step has the following optional arguments:
 * ``use2dhist``: A boolean indicating whether to use 2D histogram to find
   initial offset. (Default=True)
 
-* ``separation``: Minimum object separation in arcsec. (Default=1.0)
+* ``separation``: Minimum object separation in arcsec. It **must be** at least
+  ``sqrt(2)`` times larger than ``tolerance``. (Default=1.0)
 
 * ``tolerance``: Matching tolerance for ``xyxymatch`` in arcsec. (Default=0.7)
 
@@ -374,7 +375,8 @@ Parameters used for absolute astrometry to a reference catalog.
   Otherwise the initial guess for the offsets will be set to zero
   (Default=True)
 
-* ``abs_separation``: Minimum object separation in arcsec. (Default=1.0)
+* ``abs_separation``: Minimum object separation in arcsec. It **must be** at
+  least ``sqrt(2)`` times larger than ``abs_tolerance``. (Default=1.0)
 
 * ``abs_tolerance``: Matching tolerance for ``xyxymatch`` in arcsec.
   (Default=0.7)

jwst/assign_wcs/nirspec.py

@@ -674,7 +674,13 @@ def get_open_msa_slits(prog_id, msa_file, msa_metadata_id, dither_position,
                     (s['source_name'], s['alias'], s['stellarity'], s['ra'], s['dec'])
                     for s in msa_source if s['source_id'] == source_id][0]
             except IndexError:
-                log.warning("Could not retrieve source info from MSA file")
+                source_name = f"{prog_id}_VRT{slitlet_id}"
+                source_alias = "VRT{}".format(slitlet_id)
+                stellarity = 0.0
+                source_ra = 0.0
+                source_dec = 0.0
+                log.warning(f"Could not retrieve source info from MSA file; "
+                            f"assigning virtual source_name={source_name}")
 
             if source_id < 0:
                 log.info(f'Slitlet {slitlet_id} contains virtual source, with source_id={source_id}')

jwst/assign_wcs/tests/test_nirspec.py

@@ -4,6 +4,7 @@
 import functools
 from math import cos, sin
 import os.path
+import shutil
 
 import pytest
 import numpy as np
@@ -355,6 +356,35 @@ def test_msa_configuration_multiple_returns():
     _compare_slits(slitlet_info[1], ref_slit2)
 
 
+def test_msa_missing_source(tmp_path):
+    """
+    Test the get_open_msa_slits function with missing source information.
+    """
+    # modify an existing MSA file to remove source info
+    msaconfl = get_file_path('msa_configuration.fits')
+    bad_confl = str(tmp_path / 'bad_msa_configuration.fits')
+    shutil.copy(msaconfl, bad_confl)
+
+    with fits.open(bad_confl) as msa_hdu_list:
+        source_table = table.Table(msa_hdu_list['SOURCE_INFO'].data)
+        source_table.remove_rows(slice(0, -1))
+        msa_hdu_list['SOURCE_INFO'] = fits.table_to_hdu(source_table)
+        msa_hdu_list[3].name = 'SOURCE_INFO'
+        msa_hdu_list.writeto(bad_confl, overwrite=True)
+
+    prog_id = '1234'
+    msa_meta_id = 12
+    dither_position = 1
+
+    slitlet_info = nirspec.get_open_msa_slits(
+        prog_id, bad_confl, msa_meta_id, dither_position, slit_y_range=[-.5, .5])
+
+    # MSA slit: virtual source name assigned
+    ref_slit = trmodels.Slit(55, 9376, 1, 251, 26, -5.6, 1.0, 4, 1, '1111x',
+                             '1234_VRT55', 'VRT55', 0.0,
+                             -0.31716078999999997, -0.18092266, 0.0, 0.0)
+    _compare_slits(slitlet_info[0], ref_slit)
+
 open_shutters = [[24], [23, 24], [22, 23, 25, 27], [22, 23, 25, 27, 28]]
 main_shutter = [24, 23, 25, 28]
 result = ["x", "x1", "110x01", "110101x"]

jwst/associations/lib/constraint.py

@@ -108,6 +108,7 @@ def check_and_set(self, item):
                 - List of `~jwst.associations.ProcessList`.
         """
         self.matched = True
+        self.found_values.add(self.value)
         return self.matched, []
 
     @property
@@ -140,26 +141,33 @@ def copy(self):
         """Copy ourselves"""
         return deepcopy(self)
 
-    def get_all_attr(self, attribute: str): # -> list[tuple[SimpleConstraint, typing.Any]]:
+    def get_all_attr(self, attribute, name=None):
         """Return the specified attribute
 
-        This method is meant to be overridden by classes
-        that need to traverse a list of constraints.
+        This method exists solely to support `Constraint.get_all_attr`.
+        This obviates the need for class/method checking.
 
         Parameters
         ----------
         attribute : str
             The attribute to retrieve
 
+        name : str or None
+            Only return attribute if the name of the current constraint
+            matches the requested named constraints. If None, always
+            return value.
+
         Returns
         -------
         [(self, value)] : [(SimpleConstraint, object)]
             The value of the attribute in a tuple. If there is no attribute,
             an empty tuple is returned.
         """
-        value = getattr(self, attribute)
-        if value is not None:
-            return [(self, value)]
+        if name is None or name == self.name:
+            value = getattr(self, attribute, None)
+            if value is not None:
+                if not isinstance(value, (list, set)) or len(value):
+                    return [(self, value)]
         return []
 
     def restore(self):
@@ -352,6 +360,7 @@ def check_and_set(self, item):
         if self.matched:
             if self.force_unique:
                 self.value = source_value
+            self.found_values.add(self.value)
 
         # Determine reprocessing
         reprocess = []
@@ -769,17 +778,19 @@ def copy(self):
         """Copy ourselves"""
         return deepcopy(self)
 
-    def get_all_attr(self, attribute: str): # -> list[tuple[typing.Union[SimpleConstraint, Constraint], typing.Any]]:
-        """Return the specified attribute
-
-        This method is meant to be overridden by classes
-        that need to traverse a list of constraints.
+    def get_all_attr(self, attribute, name=None):
+        """Return the specified attribute for specified constraints
 
         Parameters
         ----------
         attribute : str
             The attribute to retrieve
 
+        name : str or None
+            Only return attribute if the name of the current constraint
+            matches the requested named constraints. If None, always
+            return value.
+
         Returns
         -------
         result : [(SimpleConstraint or Constraint, object)[,...]]
@@ -792,11 +803,12 @@ def get_all_attr(self, attribute: str): # -> list[tuple[typing.Union[SimpleConst
             If the attribute is not found.
         """
         result = []
-        value = getattr(self, attribute)
-        if value is not None:
-            result = [(self, value)]
+        if name is None or name == self.name:
+            value = getattr(self, attribute, None)
+            if value is not None:
+                result = [(self, value)]
         for constraint in self.constraints:
-            result.extend(constraint.get_all_attr(attribute))
+            result.extend(constraint.get_all_attr(attribute, name=name))
 
         return result
 

jwst/associations/lib/dms_base.py

@@ -802,7 +802,12 @@ def _get_target(self):
             The Level3 Product name representation
             of the target or source ID.
         """
-        target_id = format_list(self.constraints['target'].found_values)
+        attrs = self.constraints.get_all_attr('found_values', name='target')
+        if attrs:
+            value = attrs[0][1]
+        else:
+            value = []
+        target_id = format_list(value)
         target = 't{0:0>3s}'.format(str(target_id))
         return target
 

jwst/associations/lib/rules_level2_base.py

@@ -1021,14 +1021,27 @@ def __init__(self, exclude_exp_types=None):
         )
 
 
-class Constraint_Target(DMSAttrConstraint):
+class Constraint_Target(Constraint):
     """Select on target id"""
 
     def __init__(self):
-        super(Constraint_Target, self).__init__(
-            name='target',
-            sources=['targetid'],
-        )
+        constraints = [
+            Constraint([
+                DMSAttrConstraint(
+                    name='acdirect',
+                    sources=['asn_candidate'],
+                    value=r"\[\('c\d{4}', 'direct_image'\)\]"
+                ),
+                SimpleConstraint(
+                    name='target',
+                    sources=lambda item: '000'
+                )]),
+            DMSAttrConstraint(
+                name='target',
+                sources=['targetid'],
+            )
+        ]
+        super(Constraint_Target, self).__init__(constraints, reduce=Constraint.any)
 
 
 # ---------------------------------------------
@@ -1148,32 +1161,6 @@ def add_catalog_members(self):
             )
         science = sciences[0]
 
-        # Get the exposure sequence for the science. Then, find
-        # the direct image greater than but closest to this value.
-        closest = directs[0]  # If the search fails, just use the first.
-        try:
-            expspcin = int(getattr_from_list(science.item, ['expspcin'], _EMPTY)[1])
-        except KeyError:
-            # If exposure sequence cannot be determined, just fall through.
-            logger.debug('Science exposure %s has no EXPSPCIN defined.', science)
-        else:
-            min_diff = 9999         # Initialize to an invalid value.
-            for direct in directs:
-                try:
-                    direct_expspcin = int(getattr_from_list(
-                        direct.item, ['expspcin'], _EMPTY
-                    )[1])
-                except KeyError:
-                    # Try the next one.
-                    logger.debug('Direct image %s has no EXPSPCIN defined.', direct)
-                    continue
-                diff = direct_expspcin - expspcin
-                if diff < min_diff and diff > 0:
-                    min_diff = diff
-                    closest = direct
-
-        # Note the selected direct image. Used in `Asn_Lv2WFSS._get_opt_element`
-        self.direct_image = closest
 
         # Remove all direct images from the association.
         members = self.current_product['members']
@@ -1188,6 +1175,7 @@ def add_catalog_members(self):
         ))
 
         # Add the Level3 catalog, direct image, and segmentation map members
+        self.direct_image = self.find_closest_direct(science, directs)
         lv3_direct_image_root = DMS_Level3_Base._dms_product_name(self)
         members.append(
             Member({
@@ -1239,6 +1227,49 @@ def get_exposure_type(self, item, default='science'):
 
         return exp_type
 
+    @staticmethod
+    def find_closest_direct(science, directs):
+        """Find the direct image that is closest to the science
+
+        Closeness is defined as number difference in the exposure sequence number,
+        as defined in the column EXPSPCIN.
+
+        Parameters
+        ----------
+        science : dict
+            The science member to compare against
+
+        directs : [dict[,...]]
+            The available direct members
+
+        Returns
+        -------
+        closest : dict
+            The direct image that is the "closest"
+        """
+        closest = directs[0]  # If the search fails, just use the first.
+        try:
+            expspcin = int(getattr_from_list(science.item, ['expspcin'], _EMPTY)[1])
+        except KeyError:
+            # If exposure sequence cannot be determined, just fall through.
+            logger.debug('Science exposure %s has no EXPSPCIN defined.', science)
+        else:
+            min_diff = 9999         # Initialize to an invalid value.
+            for direct in directs:
+                try:
+                    direct_expspcin = int(getattr_from_list(
+                        direct.item, ['expspcin'], _EMPTY
+                    )[1])
+                except KeyError:
+                    # Try the next one.
+                    logger.debug('Direct image %s has no EXPSPCIN defined.', direct)
+                    continue
+                diff = direct_expspcin - expspcin
+                if diff < min_diff and diff > 0:
+                    min_diff = diff
+                    closest = direct
+        return closest
+
     def _get_opt_element(self):
         """Get string representation of the optical elements