Fix overscan mean/median typo

python/lsst/ip/isr/deferredCharge.py

@@ -953,11 +953,11 @@ def fromTable(cls, tableList):
 
         # Version check
         if calibVersion < 1.1:
-            #This version might be in the wrong units (not electron), and does not
-            # contain the gain information to convert into a a new calibration
-            # version.
+            # This version might be in the wrong units (not electron),
+            # and does not contain the gain information to convert
+            # into a new calibration version.
             raise RuntimeError(f"Using old version of CTI calibration (ver. {calibVersion} < 1.1), "
-                                "which is no longer supported.")
+                               "which is no longer supported.")
 
         return cls.fromDict(inDict)
 
@@ -1054,7 +1054,8 @@ class DeferredChargeConfig(Config):
         dtype=bool,
         doc="If true, scale by the gain.",
         default=False,
-        deprecated="This field is no longer used. Will be removed after v28.",
+        deprecated="This field is no longer used. Will be removed after v28"
+                   "(TODO: DM-46721).",
     )
     zeroUnusedPixels = Field(
         dtype=bool,
@@ -1086,7 +1087,7 @@ def run(self, exposure, ctiCalib, gains=None):
         gains : `dict` [`str`, `float`]
             A dictionary, keyed by amplifier name, of the gains to
             use.  If gains is None, the nominal gains in the amplifier
-            object are used if necessary.
+            object are used.
 
         Returns
         -------
@@ -1100,8 +1101,8 @@ def run(self, exposure, ctiCalib, gains=None):
         units of electrons. If bootstrapping, the gains used
         will just be 1.0. and the input/output units will stay in
         adu. If the input image is in adu, the output image will be
-        in units of electron. If the input image is in electron, the
-        output image will be in electron.
+        in units of electrons. If the input image is in electron,
+        the output image will be in electron.
         """
         image = exposure.getMaskedImage().image
         detector = exposure.getDetector()
@@ -1116,19 +1117,18 @@ def run(self, exposure, ctiCalib, gains=None):
             applyGains = True
 
         # If we need to convert the image to electrons, check that gains
-        # were supplied, they should be used. If no external gains were
-        # supplied, use the nominal gains listed in the detector.
+        # were supplied. CTI should not be solved or corrected without
+        # supplied gains.
         if applyGains:
             if gains is None:
-                self.log.warning("No gains supplied for deferred charge correction. Using nominal gains.")
-                gains = {amp.getName(): amp.getGain() for amp in detector.getAmplifiers()}
+                raise RuntimeError("No gains supplied for deferred charge correction.")
 
         with gainContext(exposure, image, apply=applyGains, gains=gains, isTrimmed=False):
             # Both the image and the overscan are in electron units.
             for amp in detector.getAmplifiers():
                 ampName = amp.getName()
 
-                ampImage = image[amp.getRawDataBBox()]
+                ampImage = image[amp.getRawBBox()]
                 if self.config.zeroUnusedPixels:
                     # We don't apply overscan subtraction, so zero these
                     # out for now.

python/lsst/ip/isr/isrFunctions.py

@@ -1323,4 +1323,4 @@ def isTrimmedImage(image, detector):
     result : `bool`
         True if the image is trimmed, else False.
     """
-    return detector.getBBox() == image.getBBox()
+    return detector.getBBox() == image.getBBox()

python/lsst/ip/isr/isrMockLSST.py

@@ -926,7 +926,7 @@ def amplifierAddDeferredCharge(self, exposure, amp):
         # Create a fake amplifier object that contains some deferred charge
         # paramters.
         floatingOutputAmplifier = FloatingOutputAmplifier(
-            gain=1.0,  # Everyhting is already in electrons.
+            gain=1.0,  # Everything is already in electrons.
             scale=driftScale,
             decay_time=decayTime,
             noise=0.0,

python/lsst/ip/isr/isrStatistics.py

@@ -48,7 +48,8 @@ class IsrStatisticsTaskConfig(pexConfig.Config):
         dtype=bool,
         doc="Apply gain to the overscan region when measuring CTI statistics?",
         default=True,
-        deprecated="This field is no longer used. Will be removed after v28.",
+        deprecated="This field is no longer used. Will be removed after v28 "
+                   "(TODO: DM-46721).",
     )
 
     doBandingStatistics = pexConfig.Field(
@@ -365,7 +366,7 @@ def measureCti(self, inputExp, overscans, gains):
         # Ensure we have the same number of overscans as amplifiers.
         assert len(overscans) == len(detector.getAmplifiers())
 
-        with gainContext(inputExp, image, applyGain, gains, isTrimmed=isTrimmed:
+        with gainContext(inputExp, image, applyGain, gains, isTrimmed=isTrimmed):
             for ampIter, amp in enumerate(detector.getAmplifiers()):
                 ampStats = {}
                 readoutCorner = amp.getReadoutCorner()

python/lsst/ip/isr/isrTask.py

@@ -1437,23 +1437,29 @@ def run(self, ccdExposure, *, camera=None, bias=None, linearizer=None,
                         if isinstance(overscanResults.overscanMean, float):
                             # Only serial overscan was run
                             mean = overscanResults.overscanMean
+                            median = overscanResults.overscanMedian
                             sigma = overscanResults.overscanSigma
                             residMean = overscanResults.residualMean
+                            residMedian = overscanResults.residualMedian
                             residSigma = overscanResults.residualSigma
                         else:
                             # Both serial and parallel overscan were
                             # run.  Only report serial here.
                             mean = overscanResults.overscanMean[0]
+                            median = overscanResults.overscanMedian[0]
                             sigma = overscanResults.overscanSigma[0]
                             residMean = overscanResults.residualMean[0]
+                            residMedian = overscanResults.residualMedian[0]
                             residSigma = overscanResults.residualSigma[0]
 
-                        self.metadata[f"FIT MEDIAN {amp.getName()}"] = mean
+                        self.metadata[f"FIT MEDIAN {amp.getName()}"] = median
+                        self.metadata[f"FIT MEAN {amp.getName()}"] = mean
                         self.metadata[f"FIT STDEV {amp.getName()}"] = sigma
                         self.log.debug("  Overscan stats for amplifer %s: %f +/- %f",
                                        amp.getName(), mean, sigma)
 
-                        self.metadata[f"RESIDUAL MEDIAN {amp.getName()}"] = residMean
+                        self.metadata[f"RESIDUAL MEDIAN {amp.getName()}"] = residMedian
+                        self.metadata[f"RESIDUAL MEAN {amp.getName()}"] = residMean
                         self.metadata[f"RESIDUAL STDEV {amp.getName()}"] = residSigma
                         self.log.debug("  Overscan stats for amplifer %s after correction: %f +/- %f",
                                        amp.getName(), residMean, residSigma)

python/lsst/ip/isr/isrTaskLSST.py

@@ -774,6 +774,7 @@ def overscanCorrection(self, mode, detectorConfig, detector, badAmpDict, ccdExpo
         Returns
         -------
         overscans : `list` [`lsst.pipe.base.Struct` or None]
+            Overscan measurements (always in adu).
             Each result struct has components:
 
             ``imageFit``
@@ -1770,7 +1771,6 @@ def run(self, ccdExposure, *, dnlLUT=None, bias=None, deferredChargeCalib=None,
                 brighterFatterApplyGain = False
             else:
                 brighterFatterApplyGain = True
-                exposureMetadata["LSST ISR UNITS"] = "electron"
 
             if brighterFatterApplyGain and (ptc is not None) and (bfGains != gains):
                 # The supplied ptc should be the same as the ptc used to

python/lsst/ip/isr/linearize.py

@@ -498,7 +498,9 @@ def applyLinearity(self, image, detector=None, log=None, gains=None):
         self.validate(detector)
 
         # Check if the image is trimmed.
-        isTrimmed = isTrimmedImage(image, detector)
+        isTrimmed = None
+        if detector:
+            isTrimmed = isTrimmedImage(image, detector)
 
         numAmps = 0
         numLinearized = 0

python/lsst/ip/isr/ptcDataset.py

@@ -232,8 +232,8 @@ class PhotonTransferCurveDataset(IsrCalib):
     Version 1.7 adds the `noiseList` attribute.
     Version 1.8 adds the `ptcTurnoffSamplingError` attribute.
     Version 1.9 standardizes PTC noise units to electron.
-    Version 2.0 adds the `ampOffsets`, `gainUnadjusted`, and
-        `gainList` attributes.
+    Version 2.0 deprecates the `covariancesModelNoB`, `aMatrixNoB`,
+        and `noiseMatrixNoB` attributes.
     """
 
     _OBSTYPE = 'PTC'