lsst-ts · jbkalmbach · Dec 16, 2025 · Dec 16, 2025
diff --git a/conftest.py b/conftest.py
@@ -19,10 +19,16 @@ def pytest_addoption(parser: Parser) -> None:
         default=False,
         help="Run WEP pipeline before all tests.",
     )
+    parser.addoption(
+        "--skip-pretest",
+        action="store_true",
+        default=False,
+        help="Skip pre-test WEP pipeline run.",
+    )
 
 
 def pytest_configure(config: Config) -> None:
-    if config.getoption("--run-pretest"):
+    if config.getoption("--run-pretest") and not config.getoption("--skip-pretest"):
         print("Running pre-test command...")
 
         # Set up the butler repository config
@@ -80,7 +86,7 @@ def pytest_configure(config: Config) -> None:
 
 
 def pytest_unconfigure(config: Config) -> None:
-    if config.getoption("--run-pretest"):
+    if config.getoption("--run-pretest") and not config.getoption("--skip-pretest"):
         print("Running cleanup...")
         for runName in [
             config.testInfo["runNameCwfs"],

diff --git a/doc/version_history.rst b/doc/version_history.rst
@@ -17,6 +17,21 @@ Version History
 
 .. towncrier release notes start
 
+v16.5.0 (2025-12-16)
+====================
+
+New Features
+------------
+
+- Correctly handling FAM by shifting entire camera in batoid model. (`DM-53134 <https://rubinobs.atlassian.net//browse/DM-53134>`_)
+
+
+Bug Fixes
+---------
+
+- Fixed bug with intrinsics in unpaired Zernike calculation task. (`DM-53632 <https://rubinobs.atlassian.net//browse/DM-53632>`_)
+
+
 16.4.0 (2025-12-09)
 ===================
 

diff --git a/policy/instruments/LsstCam.yaml b/policy/instruments/LsstCam.yaml
@@ -20,6 +20,7 @@ wavelength:
   z: 866.8e-9
   y: 973.9e-9
 batoidModelName: LSST_{band} # name used to load the Batoid model
+batoidOffsetOptic: Detector
 
 maskParams: # center and radius are in meters, theta in degrees
   M1:

diff --git a/python/lsst/ts/wep/estimation/wfAlgorithm.py b/python/lsst/ts/wep/estimation/wfAlgorithm.py
@@ -283,16 +283,16 @@ def estimateZk(
         if startWithIntrinsic or returnWfDev:
             zkIntrinsicI1 = instrument.getIntrinsicZernikes(
                 *I1.fieldAngle,
-                I1.bandLabel,
-                nollIndices,
+                band=I1.bandLabel,
+                nollIndices=nollIndices,
             )
             zkIntrinsicI2 = (
                 None
                 if I2 is None
                 else instrument.getIntrinsicZernikes(
                     *I2.fieldAngle,
-                    I2.bandLabel,
-                    nollIndices,
+                    band=I2.bandLabel,
+                    nollIndices=nollIndices,
                 )
             )
 

diff --git a/python/lsst/ts/wep/imageMapper.py b/python/lsst/ts/wep/imageMapper.py
@@ -1267,7 +1267,7 @@ def createImageMasks(
             # Get the intrinsic Zernikes
             zkCoeff = self.instrument.getIntrinsicZernikes(
                 *image.fieldAngle,
-                image.bandLabel,
+                band=image.bandLabel,
             )
 
         # Get the image grid inside the pupil
@@ -1376,7 +1376,7 @@ def getProjectionSize(
             # Get the intrinsic Zernikes
             zkCoeff = self.instrument.getIntrinsicZernikes(
                 *dummyImage.fieldAngle,
-                dummyImage.bandLabel,
+                band=dummyImage.bandLabel,
             )
 
         # Project the pupil onto the image plane
@@ -1445,7 +1445,7 @@ def centerOnProjection(
             # Get the intrinsic Zernikes
             zkCoeff = self.instrument.getIntrinsicZernikes(
                 *image.fieldAngle,
-                image.bandLabel,
+                band=image.bandLabel,
             )
 
         # Create the image template
@@ -1513,7 +1513,7 @@ def mapPupilToImage(
             # Get the intrinsic Zernikes
             zkCoeff = self.instrument.getIntrinsicZernikes(
                 *image.fieldAngle,
-                image.bandLabel,
+                band=image.bandLabel,
             )
 
         # Get the image grid inside the pupil
@@ -1606,7 +1606,7 @@ def mapImageToPupil(
             # Get the intrinsic Zernikes
             zkCoeff = self.instrument.getIntrinsicZernikes(
                 *image.fieldAngle,
-                image.bandLabel,
+                band=image.bandLabel,
             )
 
         # Construct the forward mapping

diff --git a/python/lsst/ts/wep/instrument.py b/python/lsst/ts/wep/instrument.py
@@ -633,7 +633,11 @@ def batoidModelName(self, value: str | None) -> None:
     @property
     def batoidOffsetOptic(self) -> str | None:
         """The optic that is offset in the Batoid model."""
-        return self._batoidOffsetOptic
+        # Default to the detector if value not explicitly set
+        if self._batoidOffsetOptic is None and self.batoidModelName is not None:
+            return "Detector"
+        else:
+            return self._batoidOffsetOptic
 
     @batoidOffsetOptic.setter
     def batoidOffsetOptic(self, value: str | None) -> None:
@@ -734,6 +738,7 @@ def _getIntrinsicZernikesCached(
         self,
         xAngle: float,
         yAngle: float,
+        defocalType: DefocalType | None,
         band: BandLabel | str,
         jmax: int,
     ) -> np.ndarray:
@@ -747,6 +752,9 @@ def _getIntrinsicZernikesCached(
             The x-component of the field angle in degrees.
         yAngle : float
             The y-component of the field angle in degrees.
+        defocalType : DefocalType or str or None
+            The DefocalType Enum or corresponding string, specifying which side
+            of focus to model. If None, the model is not defocused.
         band : BandLabel or str, optional
             The BandLabel Enum or corresponding string, specifying which batoid
             model to load. Only relevant if self.batoidModelName contains
@@ -769,6 +777,13 @@ def _getIntrinsicZernikesCached(
         if batoidModel is None:
             return np.zeros(jmax + 1)
 
+        # Offset the focal plane
+        if defocalType is not None:
+            defocalType = DefocalType(defocalType)
+            defocalSign = +1 if defocalType == DefocalType.Extra else -1
+            offset = [0, 0, defocalSign * self.defocalOffset]
+            batoidModel = batoidModel.withLocallyShiftedOptic(self.batoidOffsetOptic, offset)
+
         # Get the wavelength
         if len(self.wavelength) > 1:
             wavelength = self.wavelength[band]
@@ -794,6 +809,7 @@ def getIntrinsicZernikes(
         self,
         xAngle: float,
         yAngle: float,
+        defocalType: DefocalType | None = None,
         band: BandLabel | str = BandLabel.REF,
         nollIndices: Sequence[int] = tuple(np.arange(4, 79)),
     ) -> np.ndarray:
@@ -805,6 +821,9 @@ def getIntrinsicZernikes(
             The x-component of the field angle in degrees.
         yAngle : float
             The y-component of the field angle in degrees.
+        defocalType : DefocalType or str or None
+            The DefocalType Enum or corresponding string, specifying which side
+            of focus to model. If None, the model is not defocused.
         band : BandLabel or str, optional
             The BandLabel Enum or corresponding string, specifying which batoid
             model to load. Only relevant if self.batoidModelName contains
@@ -822,7 +841,13 @@ def getIntrinsicZernikes(
         nollIndices = np.array(nollIndices)
 
         # Retrieve cached Zernikes
-        zk = self._getIntrinsicZernikesCached(xAngle, yAngle, band, max(nollIndices))
+        zk = self._getIntrinsicZernikesCached(
+            xAngle=xAngle,
+            yAngle=yAngle,
+            defocalType=defocalType,
+            band=band,
+            jmax=max(nollIndices),
+        )
 
         return zk[nollIndices]
 
@@ -831,7 +856,7 @@ def _getIntrinsicZernikesTACached(
         self,
         xAngle: float,
         yAngle: float,
-        defocalType: DefocalType,
+        defocalType: DefocalType | None,
         band: BandLabel | str,
         jmax: int,
     ) -> np.ndarray:
@@ -843,9 +868,9 @@ def _getIntrinsicZernikesTACached(
             The x-component of the field angle in degrees.
         yAngle : float
             The y-component of the field angle in degrees.
-        defocalType : DefocalType or str
+        defocalType : DefocalType or str or None
             The DefocalType Enum or corresponding string, specifying which side
-            of focus to model.
+            of focus to model. If None, the model is not defocused.
         band : BandLabel or str
             The BandLabel Enum or corresponding string, specifying which
             batoid model to load. Only relevant if self.batoidModelName
@@ -877,10 +902,11 @@ def _getIntrinsicZernikesTACached(
             return np.zeros(jmax + 1)
 
         # Offset the focal plane
-        defocalType = DefocalType(defocalType)
-        defocalSign = +1 if defocalType == DefocalType.Extra else -1
-        offset = [0, 0, defocalSign * self.defocalOffset]
-        batoidModel = batoidModel.withLocallyShiftedOptic("Detector", offset)
+        if defocalType is not None:
+            defocalType = DefocalType(defocalType)
+            defocalSign = +1 if defocalType == DefocalType.Extra else -1
+            offset = [0, 0, defocalSign * self.defocalOffset]
+            batoidModel = batoidModel.withLocallyShiftedOptic(self.batoidOffsetOptic, offset)
 
         # Get the wavelength
         if len(self.wavelength) > 1:
@@ -909,7 +935,7 @@ def getOffAxisCoeff(
         self,
         xAngle: float,
         yAngle: float,
-        defocalType: DefocalType,
+        defocalType: DefocalType | None,
         band: BandLabel | str = BandLabel.REF,
         nollIndicesModel: Sequence = tuple(np.arange(4, 79)),
         nollIndicesIntr: Sequence = tuple(np.arange(4, 79)),
@@ -922,9 +948,9 @@ def getOffAxisCoeff(
             The x-component of the field angle in degrees.
         yAngle : float
             The y-component of the field angle in degrees.
-        defocalType : DefocalType or str
+        defocalType : DefocalType or str or None
             The DefocalType Enum or corresponding string, specifying which side
-            of focus to model.
+            of focus to model. If None, the model is not defocused.
         band : BandLabel or str, optional
             The BandLabel Enum or corresponding string, specifying which
             batoid model to load. Only relevant if self.batoidModelName
@@ -952,19 +978,20 @@ def getOffAxisCoeff(
 
         # Get zernikeTA
         zkTA = self._getIntrinsicZernikesTACached(
-            xAngle,
-            yAngle,
-            defocalType,
-            band,
-            max(nollIndicesModel),
+            xAngle=xAngle,
+            yAngle=yAngle,
+            defocalType=defocalType,
+            band=band,
+            jmax=max(nollIndicesModel),
         )
 
         # Get regular intrinsic zernikes
         zk = self._getIntrinsicZernikesCached(
-            xAngle,
-            yAngle,
-            band,
-            max(nollIndicesIntr),
+            xAngle=xAngle,
+            yAngle=yAngle,
+            defocalType=None,
+            band=band,
+            jmax=max(nollIndicesIntr),
         )
 
         # Subtract intrinsics from zernikeTA

diff --git a/python/lsst/ts/wep/task/calcZernikesTask.py b/python/lsst/ts/wep/task/calcZernikesTask.py
@@ -250,7 +250,7 @@ def _unpackStampData(self, stamp: DonutStamp) -> tuple[u.Quantity, u.Quantity, u
         if stamp is None:
             fieldAngle = np.array(np.nan, dtype=pos2f_dtype) * u.deg
             centroid = np.array((np.nan, np.nan), dtype=pos2f_dtype) * u.pixel
-            intrinsics = np.full_like(self.nollIndices, np.nan) * u.micron
+            intrinsics = np.full(len(self.nollIndices), np.nan) * u.micron
         else:
             fieldAngle = np.array(stamp.calcFieldXY(), dtype=pos2f_dtype) * u.deg
             centroid = (

diff --git a/python/lsst/ts/wep/utils/plotUtils.py b/python/lsst/ts/wep/utils/plotUtils.py
@@ -429,7 +429,7 @@ def plotMapperResiduals(
     uImage, vImage, *_ = mapper._constructForwardMap(
         uPupil,
         vPupil,
-        mapper.instrument.getIntrinsicZernikes(*angle, band, jmax=22),
+        mapper.instrument.getIntrinsicZernikes(*angle, band=band, nollIndices=np.arange(4, 23)),
         Image(np.zeros((1, 1)), angle, defocalType, band),
     )
 

diff --git a/tests/task/test_calcZernikesUnpairedTask.py b/tests/task/test_calcZernikesUnpairedTask.py
@@ -130,6 +130,9 @@ def testWithAndWithoutPairs(self) -> None:
             collections=["LSSTCam/aos/intrinsic"],
         )
 
+        # Modify the intrinsic table to allow explicit value testing below
+        intrinsicTable["Z4"] = 50e-9  # nm
+
         # Loop over EstimateZernikes subtasks
         for subtask in [EstimateZernikesTieTask, EstimateZernikesDanishTask]:
             # Calculate Zernikes with stamps paired
@@ -145,14 +148,22 @@ def testWithAndWithoutPairs(self) -> None:
             config.estimateZernikes.retarget(subtask)
             unpairedTask = CalcZernikesUnpairedTask(config=config)
 
-            extraZk = unpairedTask.run(donutStampsExtra, intrinsicTable).outputZernikesAvg
-            intraZk = unpairedTask.run(donutStampsIntra, intrinsicTable).outputZernikesAvg
+            outputExtra = unpairedTask.run(donutStampsExtra, intrinsicTable)
+            outputIntra = unpairedTask.run(donutStampsIntra, intrinsicTable)
+            extraZk = outputExtra.outputZernikesAvg
+            intraZk = outputIntra.outputZernikesAvg
             meanZk = np.mean([extraZk, intraZk], axis=0)
 
             # Check that results are similar
             diff = np.sqrt(np.sum((meanZk - pairedZk) ** 2))
             self.assertLess(diff, 0.17)
 
+            # Check the stored intrinsic Z4 is close to modified value
+            for struct in [outputExtra, outputIntra]:
+                table = struct.zernikes
+                intrinsicZ4 = table[table["label"] == "average"]["Z4_intrinsic"][0]
+                self.assertTrue(np.isclose(intrinsicZ4.to_value("nm"), 50.0))
+
     def testTable(self) -> None:
         # Load data from butler
         donutStampsExtra = self.butler.get(

diff --git a/tests/task/test_cutOutDonutsBase.py b/tests/task/test_cutOutDonutsBase.py
@@ -460,9 +460,9 @@ def testCutOutStampsTaskRunNormal(self) -> None:
         self.assertTrue(allowed_values.issuperset(unique_values))
 
         # test the calculation of SN
-        sn_values = [2149.093503846915, 2160.668317852145, 2041.9917562475855]
+        sn_values = [2152.969905, 2574.566976, 2981.683746]
         sn_calculated = donutStamps.metadata.getArray("SN")
-        np.testing.assert_allclose(np.sort(np.array(sn_values)), np.sort(np.array(sn_calculated)), rtol=1e-3)
+        np.testing.assert_allclose(np.sort(np.array(sn_calculated)), np.sort(np.array(sn_values)), rtol=1e-3)
 
     def testFilterBadRecentering(self) -> None:
         maxRecenter = 25

diff --git a/tests/task/test_donutStampSelectorTask.py b/tests/task/test_donutStampSelectorTask.py
@@ -142,7 +142,6 @@ def testSelectStamps(self) -> None:
         # test defaults
         selection = self.task.selectStamps(donutStampsIntra)
         donutsQuality = selection.donutsQuality
-        print(donutsQuality)
 
         # by default, config.selectWithEntropy is False,
         # so we select all donuts
@@ -196,7 +195,7 @@ def testSelectStamps(self) -> None:
         task = DonutStampSelectorTask(config=self.config, name="SN Task")
         selection = task.selectStamps(donutStampsIntra)
         donutsQuality = selection.donutsQuality
-        self.assertEqual(np.sum(donutsQuality["SN_SELECT"]), 2)
+        self.assertEqual(np.sum(donutsQuality["SN_SELECT"]), 3)
 
         # test that the SN of selected donuts is indeed above the threshold
         for v in donutsQuality["SN"][donutsQuality["SN_SELECT"]]: