Fix incorrect BF kernel transposes.

python/lsst/ip/isr/brighterFatterKernel.py

@@ -552,17 +552,24 @@ def repackCorrelations(self, amp, correlationShape):
     # Implementation methods
     def makeDetectorKernelFromAmpwiseKernels(self, detectorName, ampsToExclude=[]):
         """Average the amplifier level kernels to create a detector level
-        kernel.
+        kernel.  There is no change in index ordering/orientation from
+        this averaging.
+
+        Parameters
+        ----------
+        detectorName : `str`
+            Detector for which the averaged kernel will be used.
+        ampsToExclude : `list` [`str`], optional
+            Amps that should not be included in the average.
         """
         inKernels = np.array([self.ampKernels[amp] for amp in
                               self.ampKernels if amp not in ampsToExclude])
-        averagingList = np.transpose(inKernels)
         avgKernel = np.zeros_like(inKernels[0])
         sctrl = afwMath.StatisticsControl()
         sctrl.setNumSigmaClip(5.0)
         for i in range(np.shape(avgKernel)[0]):
             for j in range(np.shape(avgKernel)[1]):
-                avgKernel[i, j] = afwMath.makeStatistics(averagingList[i, j],
+                avgKernel[i, j] = afwMath.makeStatistics(inKernels[:, i, j],
                                                          afwMath.MEANCLIP, sctrl).getValue()
 
         self.detKernels[detectorName] = avgKernel

python/lsst/ip/isr/isrTask.py

@@ -1037,26 +1037,41 @@ def runQuantum(self, butlerQC, inputRefs, outputRefs):
         if self.config.doBrighterFatter:
             brighterFatterKernel = inputs.pop('newBFKernel', None)
             if brighterFatterKernel is None:
+                # This type of kernel must be in (y, x) index
+                # ordering, as it used directly as the .array
+                # component of the afwImage kernel.
                 brighterFatterKernel = inputs.get('bfKernel', None)
 
             if brighterFatterKernel is not None and not isinstance(brighterFatterKernel, numpy.ndarray):
-                # This is a ISR calib kernel
+                # This is a ISR calib kernel.  These kernels are
+                # generated in (x, y) index ordering, and need to be
+                # transposed to be used directly as the .array
+                # component of the afwImage kernel.  This is done
+                # explicitly below when setting the ``bfKernel``
+                # input.
                 detName = detector.getName()
                 level = brighterFatterKernel.level
 
                 # This is expected to be a dictionary of amp-wise gains.
                 inputs['bfGains'] = brighterFatterKernel.gain
                 if self.config.brighterFatterLevel == 'DETECTOR':
+                    kernel = None
                     if level == 'DETECTOR':
                         if detName in brighterFatterKernel.detKernels:
-                            inputs['bfKernel'] = brighterFatterKernel.detKernels[detName]
+                            kernel = brighterFatterKernel.detKernels[detName]
                         else:
                             raise RuntimeError("Failed to extract kernel from new-style BF kernel.")
                     elif level == 'AMP':
                         self.log.warning("Making DETECTOR level kernel from AMP based brighter "
                                          "fatter kernels.")
                         brighterFatterKernel.makeDetectorKernelFromAmpwiseKernels(detName)
-                        inputs['bfKernel'] = brighterFatterKernel.detKernels[detName]
+                        kernel = brighterFatterKernel.detKernels[detName]
+                    if kernel is None:
+                        raise RuntimeError("Could not identify brighter-fatter kernel!")
+                    # Do the one single transpose here so the kernel
+                    # can be directly loaded into the afwImage .array
+                    # component.
+                    inputs['bfKernel'] = numpy.transpose(kernel)
                 elif self.config.brighterFatterLevel == 'AMP':
                     raise NotImplementedError("Per-amplifier brighter-fatter correction not implemented")