Handle exceptions in CalibrateImage

Use the new Task exceptions and a pre-defined results struct to manage partial
outputs for failures of CalibrateImage subtasks.
Add tests of runQuantum exception handling.
The input is now a multiple `exposures`, so we can use that to simplify
the code by renaming output_exposure->exposure.

python/lsst/pipe/tasks/calibrateImage.py

@@ -76,9 +76,9 @@ class CalibrateImageConnections(pipeBase.PipelineTaskConnections,
         storageClass="SourceCatalog",
     )
 
-    # TODO: We want some kind of flag on Exposures/Catalogs to make it obvious
-    # which components had failed to be computed/persisted
-    output_exposure = connectionTypes.Output(
+    # TODO DM-38732: We want some kind of flag on Exposures/Catalogs to make
+    # it obvious which components had failed to be computed/persisted.
+    exposure = connectionTypes.Output(
         doc="Photometrically calibrated exposure with fitted calibrations and summary statistics.",
         name="initial_pvi",
         storageClass="ExposureF",
@@ -408,6 +408,8 @@ def __init__(self, initial_stars_schema=None, **kwargs):
 
     def runQuantum(self, butlerQC, inputRefs, outputRefs):
         inputs = butlerQC.get(inputRefs)
+        exposures = inputs.pop("exposures")
+
         id_generator = self.config.id_generator.apply(butlerQC.quantum.dataId)
 
         astrometry_loader = lsst.meas.algorithms.ReferenceObjectLoader(
@@ -424,12 +426,33 @@ def runQuantum(self, butlerQC, inputRefs, outputRefs):
             config=self.config.photometry_ref_loader, log=self.log)
         self.photometry.match.setRefObjLoader(photometry_loader)
 
-        outputs = self.run(id_generator=id_generator, **inputs)
-
-        butlerQC.put(outputs, outputRefs)
+        # This should not happen with a properly configured execution context.
+        assert not inputs, "runQuantum got more inputs than expected"
+
+        # Specify the fields that `annotate` needs below, to ensure they
+        # exist, even as None.
+        result = pipeBase.Struct(exposure=None,
+                                 stars_footprints=None,
+                                 psf_stars_footprints=None,
+                                 )
+        try:
+            self.run(exposures=exposures, result=result, id_generator=id_generator)
+        except pipeBase.AlgorithmError as e:
+            error = pipeBase.AnnotatedPartialOutputsError.annotate(
+                e,
+                self,
+                result.exposure,
+                result.psf_stars_footprints,
+                result.stars_footprints,
+                log=self.log
+            )
+            butlerQC.put(result, outputRefs)
+            raise error from e
+
+        butlerQC.put(result, outputRefs)
 
     @timeMethod
-    def run(self, *, exposures, id_generator=None):
+    def run(self, *, exposures, id_generator=None, result=None):
         """Find stars and perform psf measurement, then do a deeper detection
         and measurement and calibrate astrometry and photometry from that.
 
@@ -442,13 +465,17 @@ def run(self, *, exposures, id_generator=None):
             before doing further processing.
         id_generator : `lsst.meas.base.IdGenerator`, optional
             Object that generates source IDs and provides random seeds.
+        result : `lsst.pipe.base.Struct`, optional
+            Result struct that is modified to allow saving of partial outputs
+            for some failure conditions. If the task completes successfully,
+            this is also returned.
 
         Returns
         -------
         result : `lsst.pipe.base.Struct`
             Results as a struct with attributes:
 
-            ``output_exposure``
+            ``exposure``
                 Calibrated exposure, with pixels in nJy units.
                 (`lsst.afw.image.Exposure`)
             ``stars``
@@ -477,40 +504,44 @@ def run(self, *, exposures, id_generator=None):
                 Reference catalog stars matches used in the photometric fit.
                 (`list` [`lsst.afw.table.ReferenceMatch`] or `lsst.afw.table.BaseCatalog`)
         """
+        if result is None:
+            result = pipeBase.Struct()
         if id_generator is None:
             id_generator = lsst.meas.base.IdGenerator()
 
-        exposure = self._handle_snaps(exposures)
+        result.exposure = self._handle_snaps(exposures)
 
         # TODO remove on DM-43083: work around the fact that we don't want
         # to run streak detection in this task in production.
-        exposure.mask.addMaskPlane("STREAK")
+        result.exposure.mask.addMaskPlane("STREAK")
 
-        psf_stars, background, candidates = self._compute_psf(exposure, id_generator)
+        result.psf_stars_footprints, result.background, candidates = self._compute_psf(result.exposure,
+                                                                                       id_generator)
+        result.psf_stars = result.psf_stars_footprints.asAstropy()
 
-        self._measure_aperture_correction(exposure, psf_stars)
+        self._measure_aperture_correction(result.exposure, result.psf_stars)
 
-        stars = self._find_stars(exposure, background, id_generator)
-        self._match_psf_stars(psf_stars, stars)
+        result.stars_footprints = self._find_stars(result.exposure, result.background, id_generator)
+        self._match_psf_stars(result.psf_stars_footprints, result.stars_footprints)
+        result.stars = result.stars_footprints.asAstropy()
 
-        astrometry_matches, astrometry_meta = self._fit_astrometry(exposure, stars)
-        stars, photometry_matches, photometry_meta, photo_calib = self._fit_photometry(exposure, stars)
+        astrometry_matches, astrometry_meta = self._fit_astrometry(result.exposure, result.stars_footprints)
+        if self.config.optional_outputs:
+            result.astrometry_matches = lsst.meas.astrom.denormalizeMatches(astrometry_matches,
+                                                                            astrometry_meta)
+
+        result.stars_footprints, photometry_matches, \
+            photometry_meta, result.applied_photo_calib = self._fit_photometry(result.exposure,
+                                                                               result.stars_footprints)
+        # fit_photometry returns a new catalog, so we need a new astropy table view.
+        result.stars = result.stars_footprints.asAstropy()
+        if self.config.optional_outputs:
+            result.photometry_matches = lsst.meas.astrom.denormalizeMatches(photometry_matches,
+                                                                            photometry_meta)
 
-        self._summarize(exposure, stars, background)
+        self._summarize(result.exposure, result.stars_footprints, result.background)
 
-        if self.config.optional_outputs:
-            astrometry_matches = lsst.meas.astrom.denormalizeMatches(astrometry_matches, astrometry_meta)
-            photometry_matches = lsst.meas.astrom.denormalizeMatches(photometry_matches, photometry_meta)
-
-        return pipeBase.Struct(output_exposure=exposure,
-                               stars_footprints=stars,
-                               stars=stars.asAstropy(),
-                               psf_stars_footprints=psf_stars,
-                               psf_stars=psf_stars.asAstropy(),
-                               background=background,
-                               applied_photo_calib=photo_calib,
-                               astrometry_matches=astrometry_matches,
-                               photometry_matches=photometry_matches)
+        return result
 
     def _handle_snaps(self, exposure):
         """Combine two snaps into one exposure, or return a single exposure.

tests/test_calibrateImage.py

@@ -20,13 +20,15 @@
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 import unittest
+from unittest import mock
 import tempfile
 
 import astropy.units as u
 from astropy.coordinates import SkyCoord
 import numpy as np
 
 import lsst.afw.image as afwImage
+import lsst.afw.math as afwMath
 import lsst.afw.table as afwTable
 import lsst.daf.base
 import lsst.daf.butler
@@ -150,16 +152,24 @@ def _check_run(self, calibrate, result):
         # re-estimation during source detection.
         self.assertEqual(len(result.background), 4)
 
+        # Both afw and astropy psf_stars catalogs should be populated.
+        self.assertEqual(result.psf_stars["calib_psf_used"].sum(), 3)
+        self.assertEqual(result.psf_stars_footprints["calib_psf_used"].sum(), 3)
+
         # Check that the summary statistics are reasonable.
-        summary = result.output_exposure.info.getSummaryStats()
+        summary = result.exposure.info.getSummaryStats()
         self.assertFloatsAlmostEqual(summary.psfSigma, 2.0, rtol=1e-2)
         self.assertFloatsAlmostEqual(summary.ra, self.sky_center.getRa().asDegrees(), rtol=1e-7)
         self.assertFloatsAlmostEqual(summary.dec, self.sky_center.getDec().asDegrees(), rtol=1e-7)
 
+        # Should have finite sky coordinates in the afw and astropy catalogs.
+        self.assertTrue(np.isfinite(result.stars_footprints["coord_ra"]).all())
+        self.assertTrue(np.isfinite(result.stars["coord_ra"]).all())
+
         # Returned photoCalib should be the applied value, not the ==1 one on the exposure.
         self.assertFloatsAlmostEqual(result.applied_photo_calib.getCalibrationMean(),
                                      self.photo_calib, rtol=2e-3)
-        # Should have flux/magnitudes in the afw and astropy catalogs
+        # Should have calibrated flux/magnitudes in the afw and astropy catalogs
         self.assertIn("slot_PsfFlux_flux", result.stars_footprints.schema)
         self.assertIn("slot_PsfFlux_mag", result.stars_footprints.schema)
         self.assertEqual(result.stars["slot_PsfFlux_flux"].unit, u.nJy)
@@ -481,7 +491,7 @@ def test_runQuantum(self):
              "astrometry_ref_cat": [self.htm_id],
              "photometry_ref_cat": [self.htm_id],
              # outputs
-             "output_exposure": self.visit_id,
+             "exposure": self.visit_id,
              "stars": self.visit_id,
              "stars_footprints": self.visit_id,
              "background": self.visit_id,
@@ -498,7 +508,7 @@ def test_runQuantum(self):
         self.assertEqual(task.astrometry.refObjLoader.name, "gaia_dr3_20230707")
         self.assertEqual(task.photometry.match.refObjLoader.name, "ps1_pv3_3pi_20170110")
         # Check that the proper kwargs are passed to run().
-        self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposures", "id_generator"})
+        self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposures", "result", "id_generator"})
 
     def test_runQuantum_2_snaps(self):
         task = CalibrateImageTask()
@@ -510,7 +520,7 @@ def test_runQuantum_2_snaps(self):
              "astrometry_ref_cat": [self.htm_id],
              "photometry_ref_cat": [self.htm_id],
              # outputs
-             "output_exposure": self.visit_id,
+             "exposure": self.visit_id,
              "stars": self.visit_id,
              "stars_footprints": self.visit_id,
              "background": self.visit_id,
@@ -527,7 +537,7 @@ def test_runQuantum_2_snaps(self):
         self.assertEqual(task.astrometry.refObjLoader.name, "gaia_dr3_20230707")
         self.assertEqual(task.photometry.match.refObjLoader.name, "ps1_pv3_3pi_20170110")
         # Check that the proper kwargs are passed to run().
-        self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposures", "id_generator"})
+        self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposures", "result", "id_generator"})
 
     def test_runQuantum_no_optional_outputs(self):
         config = CalibrateImageTask.ConfigClass()
@@ -541,7 +551,7 @@ def test_runQuantum_no_optional_outputs(self):
              "astrometry_ref_cat": [self.htm_id],
              "photometry_ref_cat": [self.htm_id],
              # outputs
-             "output_exposure": self.visit_id,
+             "exposure": self.visit_id,
              "stars": self.visit_id,
              "stars_footprints": self.visit_id,
              "applied_photo_calib": self.visit_id,
@@ -553,14 +563,88 @@ def test_runQuantum_no_optional_outputs(self):
         self.assertEqual(task.astrometry.refObjLoader.name, "gaia_dr3_20230707")
         self.assertEqual(task.photometry.match.refObjLoader.name, "ps1_pv3_3pi_20170110")
         # Check that the proper kwargs are passed to run().
-        self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposures", "id_generator"})
+        self.assertEqual(mock_run.call_args.kwargs.keys(), {"exposures", "result", "id_generator"})
 
     def test_lintConnections(self):
         """Check that the connections are self-consistent.
         """
         Connections = CalibrateImageTask.ConfigClass.ConnectionsClass
         lsst.pipe.base.testUtils.lintConnections(Connections)
 
+    def test_runQuantum_exception(self):
+        """Test exception handling in runQuantum.
+        """
+        task = CalibrateImageTask()
+        lsst.pipe.base.testUtils.assertValidInitOutput(task)
+
+        quantum = lsst.pipe.base.testUtils.makeQuantum(
+            task, self.butler, self.visit_id,
+            {"exposures": [self.exposure0_id],
+             "astrometry_ref_cat": [self.htm_id],
+             "photometry_ref_cat": [self.htm_id],
+             # outputs
+             "exposure": self.visit_id,
+             "stars": self.visit_id,
+             "stars_footprints": self.visit_id,
+             "background": self.visit_id,
+             "psf_stars": self.visit_id,
+             "psf_stars_footprints": self.visit_id,
+             "applied_photo_calib": self.visit_id,
+             "initial_pvi_background": self.visit_id,
+             "astrometry_matches": self.visit_id,
+             "photometry_matches": self.visit_id,
+             })
+
+        # A generic exception should raise directly.
+        msg = "mocked run exception"
+        with (
+            mock.patch.object(task, "run", side_effect=ValueError(msg)),
+            self.assertRaisesRegex(ValueError, "mocked run exception")
+        ):
+            lsst.pipe.base.testUtils.runTestQuantum(task, self.butler, quantum, mockRun=False)
+
+        # A AlgorimthError should write annotated partial outputs.
+        error = lsst.meas.algorithms.MeasureApCorrError(name="test", nSources=100, ndof=101)
+
+        def mock_run(exposures, result=None, id_generator=None):
+            """Mock success through compute_psf, but failure after.
+            """
+            result.exposure = afwImage.ExposureF(10, 10)
+            result.psf_stars_footprints = afwTable.SourceCatalog()
+            result.psf_stars = afwTable.SourceCatalog().asAstropy()
+            result.background = afwMath.BackgroundList()
+            raise error
+
+        with (
+            mock.patch.object(task, "run", side_effect=mock_run),
+            self.assertRaises(lsst.pipe.base.AnnotatedPartialOutputsError),
+            lsst.log.UsePythonLogging(),  # so that assertLogs works with lsst.log
+        ):
+            with self.assertLogs("lsst.calibrateImage", level="ERROR") as cm:
+                lsst.pipe.base.testUtils.runTestQuantum(task,
+                                                        self.butler,
+                                                        quantum,
+                                                        mockRun=False)
+
+        logged = "\n".join(cm.output)
+        self.assertIn("Task failed with only partial outputs", logged)
+        self.assertIn("MeasureApCorrError", logged)
+
+        # NOTE: This is an integration test of afw Exposure & SourceCatalog
+        # metadata with the error annotation system in pipe_base.
+        # Check that we did get the annotated partial outputs...
+        pvi = self.butler.get("initial_pvi", self.visit_id)
+        self.assertIn("Unable to measure aperture correction", pvi.metadata["failure.message"])
+        self.assertIn("MeasureApCorrError", pvi.metadata["failure.type"])
+        self.assertEqual(pvi.metadata["failure.metadata.ndof"], 101)
+        stars = self.butler.get("initial_psf_stars_footprints_detector", self.visit_id)
+        self.assertIn("Unable to measure aperture correction", stars.metadata["failure.message"])
+        self.assertIn("MeasureApCorrError", stars.metadata["failure.type"])
+        self.assertEqual(stars.metadata["failure.metadata.ndof"], 101)
+        # ... but not the un-produced outputs.
+        with self.assertRaises(FileNotFoundError):
+            self.butler.get("initial_stars_footprints_detector", self.visit_id)
+
 
 def setup_module(module):
     lsst.utils.tests.init()