add cosmicRayPostDiff.py

review comments

fix typos

python/lsst/pipe/tasks/cosmicRayPostDiff.py

@@ -0,0 +1,143 @@
+# This file is part of pipe_tasks.
+#
+# Developed for the LSST Data Management System.
+# This product includes software developed by the LSST Project
+# (https://www.lsst.org).
+# See the COPYRIGHT file at the top-level directory of this distribution
+# for details of code ownership.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+import lsst.pex.config as pexConfig
+import lsst.pipe.base as pipeBase
+import lsst.pipe.base.connectionTypes as cT
+from lsst.utils.timer import timeMethod
+from .repair import RepairTask
+
+
+__all__ = ["CosmicRayPostDiffConfig", "CosmicRayPostDiffTask"]
+
+
+class CosmicRayPostDiffConnections(pipeBase.PipelineTaskConnections,
+                                   dimensions=("instrument", "visit", "detector"),
+                                   defaultTemplates={"coaddName": "deep",
+                                                     "fakesType": ""}):
+    exposure = cT.Input(
+        doc="Input difference image",
+        name="{fakesType}{coaddName}Diff_differenceExp",
+        storageClass="ExposureF",
+        dimensions=("instrument", "visit", "detector"),
+    )
+    repaired = cT.Output(
+        doc="Output subtracted image after CR run.",
+        name="{fakesType}{coaddName}Diff_repairedExp",
+        storageClass="ExposureF",
+        dimensions=("instrument", "visit", "detector"),
+    )
+
+    def adjustQuantum(self, inputs, outputs, label, dataId):
+        # Docstring inherited from PipelineTaskConnections
+        try:
+            return super().adjustQuantum(inputs, outputs, label, dataId)
+        except pipeBase.ScalarError as err:
+            raise pipeBase.ScalarError(
+                "CosmicRayPostDiffTask can at present only be run on visits that are associated with "
+                "exactly one exposure.  Either this is not a valid exposure for this pipeline, or the "
+                "snap-combination step you probably want hasn't been configured to run between ISR and "
+                "this task (as of this writing, that would be because it hasn't been implemented yet)."
+            ) from err
+
+
+class CosmicRayPostDiffConfig(pipeBase.PipelineTaskConfig,
+                              pipelineConnections=CosmicRayPostDiffConnections):
+
+    """Config for CosmicRayPostDiffTask"""
+    repair = pexConfig.ConfigurableField(
+        target=RepairTask,
+        doc="Remove cosmic rays",
+    )
+
+    def setDefaults(self):
+        super().setDefaults()
+
+
+class CosmicRayPostDiffTask(pipeBase.PipelineTask, pipeBase.CmdLineTask):
+    r"""Measure bright sources and use this to estimate background and PSF of an exposure
+
+    @anchor CosmicRayPostDiffTask_
+
+    @section pipe_tasks_cosmicRayPostDiff_Contents  Contents
+
+     - @ref pipe_tasks_cosmicRayPostDiff_Purpose
+     - @ref pipe_tasks_cosmicRayPostDiff_Initialize
+     - @ref pipe_tasks_cosmicRayPostDiff_IO
+     - @ref pipe_tasks_cosmicRayPostDiff_Config
+
+
+    @section pipe_tasks_cosmicRayPostDiff_Purpose  Description
+
+    Given an output image from image differencing:
+    - detect and repair cosmic rays
+    - At the moment this task does NOT recompute the PSF or re-do source detection.
+
+    @section pipe_tasks_cosmicRayPostDiff_Initialize  Task initialisation
+
+    @copydoc \_\_init\_\_
+
+    @section pipe_tasks_cosmicRayPostDiff_IO  Invoking the Task
+
+    Call the `run` method.
+
+    @section pipe_tasks_cosmicRayPostDiff_Config  Configuration parameters
+
+    See @ref CosmicRayPostDiffConfig
+    """
+
+    ConfigClass = CosmicRayPostDiffConfig
+    _DefaultName = "cosmicRayPostDiff"
+    RunnerClass = pipeBase.ButlerInitializedTaskRunner
+
+    def runQuantum(self, butlerQC, inputRefs, outputRefs):
+        inputs = butlerQC.get(inputRefs)
+        outputs = self.run(**inputs)
+        butlerQC.put(outputs, outputRefs)
+
+    def __init__(self, **kwargs):
+        """Construct a CosmicRayPostDiffTask"""
+        super().__init__(**kwargs)
+        self.makeSubtask("repair")
+
+    @timeMethod
+    def run(self, exposure):
+        """Run cosmic ray detection and repair on imageDifference outputs
+
+        Parameters
+        ----------
+        exposure `lsst.afw.image.ExposureF`:
+            The following changes are made to the exposure,
+            - Blank cosmic ray mask planes, run CR detection and repair, update CR mask plane
+
+        Returns
+        -------
+        `lsst.pipe.base.Struct`:
+             Struct containing the input image with the CR mask plane first blanked,
+             and then cosmic rays detected, and the mask is updated accordingly.
+             The PSF model is NOT changed.
+        """
+        # perform final repair
+        self.repair.run(exposure=exposure)
+
+        return pipeBase.Struct(
+            repaired=exposure
+        )