Merge pull request #588 from lsst/tickets/DM-32226

DM-32226: Replace `pipe.base.timeMethod` with `utils.timer`

bin.src/dumpTaskMetadata.py

@@ -25,6 +25,7 @@
 import lsst.daf.base as dafBase
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
+from lsst.utils.timer import timeMethod
 
 __all__ = ["DumpTaskMetadataTask", ]
 
@@ -42,7 +43,7 @@ class DumpTaskMetadataTask(pipeBase.CmdLineTask):
     ConfigClass = DumpTaskMetadataConfig
     _DefaultName = "DumpTaskMetadata"
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRef):
         """Report task metadata
         """

bin.src/reportImagesInPatch.py

@@ -28,6 +28,7 @@
 import lsst.afw.geom as afwGeom
 import lsst.pipe.base as pipeBase
 from lsst.pipe.tasks.selectImages import WcsSelectImagesTask
+from lsst.utils.timer import timeMethod
 
 __all__ = ["ReportImagesInPatchTask", ]
 
@@ -56,7 +57,7 @@ def __init__(self, *args, **kwargs):
         pipeBase.CmdLineTask.__init__(self, *args, **kwargs)
         self.makeSubtask("select")
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, patchRef):
         """Select images for a region and report how many are in each tract and patch
 

bin.src/reportImagesToCoadd.py

@@ -28,6 +28,7 @@
 import lsst.afw.geom as afwGeom
 import lsst.pipe.base as pipeBase
 from lsst.pipe.tasks.selectImages import WcsSelectImagesTask
+from lsst.utils.timer import timeMethod
 
 __all__ = ["ReportImagesToCoaddTask", ]
 
@@ -67,7 +68,7 @@ def __init__(self, *args, **kwargs):
         pipeBase.CmdLineTask.__init__(self, *args, **kwargs)
         self.makeSubtask("select")
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRef):
         """Select images across the sky and report how many are in each tract and patch
 

bin.src/reportPatches.py

@@ -30,6 +30,7 @@
 import lsst.pex.config as pexConfig
 import lsst.afw.geom as afwGeom
 import lsst.pipe.base as pipeBase
+from lsst.utils.timer import timeMethod
 
 __all__ = ["ReportPatchesTask", ]
 
@@ -58,7 +59,7 @@ class ReportPatchesTask(pipeBase.CmdLineTask):
     def __init__(self, *args, **kwargs):
         pipeBase.CmdLineTask.__init__(self, *args, **kwargs)
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRef):
         """Report tracts and patches that are within a given region of a skymap
 

bin.src/reportTaskTiming.py

@@ -30,6 +30,7 @@
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
 from lsst.pipe.tasks.getRepositoryData import DataRefListRunner
+from lsst.utils.timer import timeMethod
 
 
 class ReportTaskTimingConfig(pexConfig.Config):
@@ -144,7 +145,7 @@ class ReportTaskTimingTask(pipeBase.CmdLineTask):
     def __init__(self, *args, **kwargs):
         pipeBase.CmdLineTask.__init__(self, *args, **kwargs)
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRefList):
         """Report timing statistics for a collection of task metadata
 

python/lsst/pipe/tasks/assembleCoadd.py

@@ -47,6 +47,7 @@
 from .healSparseMapping import HealSparseInputMapTask
 from lsst.meas.algorithms import SourceDetectionTask, AccumulatorMeanStack
 from lsst.daf.butler import DeferredDatasetHandle
+from lsst.utils.timer import timeMethod
 
 __all__ = ["AssembleCoaddTask", "AssembleCoaddConnections", "AssembleCoaddConfig",
            "SafeClipAssembleCoaddTask", "SafeClipAssembleCoaddConfig",
@@ -488,7 +489,7 @@ def runQuantum(self, butlerQC, inputRefs, outputRefs):
             butlerQC.put(retStruct, outputRefs)
         return retStruct
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRef, selectDataList=None, warpRefList=None):
         """Assemble a coadd from a set of Warps.
 
@@ -759,7 +760,7 @@ def prepareStats(self, mask=None):
         statsFlags = afwMath.stringToStatisticsProperty(self.config.statistic)
         return pipeBase.Struct(ctrl=statsCtrl, flags=statsFlags)
 
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, skyInfo, tempExpRefList, imageScalerList, weightList,
             altMaskList=None, mask=None, supplementaryData=None):
         """Assemble a coadd from input warps
@@ -1586,7 +1587,7 @@ def __init__(self, *args, **kwargs):
         self.makeSubtask("clipDetection", schema=schema)
 
     @utils.inheritDoc(AssembleCoaddTask)
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, skyInfo, tempExpRefList, imageScalerList, weightList, *args, **kwargs):
         """Assemble the coadd for a region.
 
@@ -2274,7 +2275,7 @@ def _noTemplateMessage(self, warpType):
         return message
 
     @utils.inheritDoc(AssembleCoaddTask)
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, skyInfo, tempExpRefList, imageScalerList, weightList,
             supplementaryData, *args, **kwargs):
         """Assemble the coadd.

python/lsst/pipe/tasks/calibrate.py

@@ -37,6 +37,7 @@
                             ApplyApCorrTask,
                             CatalogCalculationTask)
 from lsst.meas.deblender import SourceDeblendTask
+from lsst.utils.timer import timeMethod
 from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask
 from .fakes import BaseFakeSourcesTask
 from .photoCal import PhotoCalTask
@@ -549,7 +550,7 @@ def __init__(self, butler=None, astromRefObjLoader=None,
         sourceCatSchema.getTable().setMetadata(self.algMetadata)
         self.outputSchema = sourceCatSchema
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRef, exposure=None, background=None, icSourceCat=None,
                    doUnpersist=True):
         """!Calibrate an exposure, optionally unpersisting inputs and
@@ -643,7 +644,7 @@ def runQuantum(self, butlerQC, inputRefs, outputRefs):
             outputs.matches = normalizedMatches
         butlerQC.put(outputs, outputRefs)
 
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, exposure, exposureIdInfo=None, background=None,
             icSourceCat=None):
         """!Calibrate an exposure (science image or coadd)

python/lsst/pipe/tasks/characterizeImage.py

@@ -40,6 +40,7 @@
 from .repair import RepairTask
 from .computeExposureSummaryStats import ComputeExposureSummaryStatsTask
 from lsst.pex.exceptions import LengthError
+from lsst.utils.timer import timeMethod
 
 __all__ = ["CharacterizeImageConfig", "CharacterizeImageTask"]
 
@@ -389,7 +390,7 @@ def getInitOutputDatasets(self):
         outputCatSchema.getTable().setMetadata(self.algMetadata)
         return {'outputSchema': outputCatSchema}
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRef, exposure=None, background=None, doUnpersist=True):
         """!Characterize a science image and, if wanted, persist the results
 
@@ -441,7 +442,7 @@ def runDataRef(self, dataRef, exposure=None, background=None, doUnpersist=True):
 
         return charRes
 
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, exposure, exposureIdInfo=None, background=None):
         """!Characterize a science image
 
@@ -526,7 +527,7 @@ def run(self, exposure, exposureIdInfo=None, background=None):
             backgroundModel=dmeRes.background
         )
 
-    @pipeBase.timeMethod
+    @timeMethod
     def detectMeasureAndEstimatePsf(self, exposure, exposureIdInfo, background):
         """!Perform one iteration of detect, measure and estimate PSF
 

python/lsst/pipe/tasks/computeExposureSummaryStats.py

@@ -30,6 +30,7 @@
 import lsst.afw.math as afwMath
 import lsst.afw.image as afwImage
 import lsst.geom
+from lsst.utils.timer import timeMethod
 
 
 __all__ = ("ComputeExposureSummaryStatsTask", "ComputeExposureSummaryStatsConfig")
@@ -79,7 +80,7 @@ class ComputeExposureSummaryStatsTask(pipeBase.Task):
     ConfigClass = ComputeExposureSummaryStatsConfig
     _DefaultName = "computeExposureSummaryStats"
 
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, exposure, sources, background):
         """Measure exposure statistics from the exposure, sources, and background.
 

python/lsst/pipe/tasks/dcrAssembleCoadd.py

@@ -35,6 +35,7 @@
 import lsst.pipe.base as pipeBase
 import lsst.utils as utils
 from lsst.skymap import BaseSkyMap
+from lsst.utils.timer import timeMethod
 from .assembleCoadd import (AssembleCoaddTask,
                             CompareWarpAssembleCoaddConfig,
                             CompareWarpAssembleCoaddTask)
@@ -381,7 +382,7 @@ def runQuantum(self, butlerQC, inputRefs, outputRefs):
             butlerQC.put(retStruct, outputRefs)
         return retStruct
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRef, selectDataList=None, warpRefList=None):
         """Assemble a coadd from a set of warps.
 
@@ -578,7 +579,7 @@ def prepareDcrInputs(self, templateCoadd, warpRefList, weightList):
                                        psf=psf)
         return dcrModels
 
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, skyInfo, warpRefList, imageScalerList, weightList,
             supplementaryData=None):
         """Assemble the coadd.

python/lsst/pipe/tasks/exampleCmdLineTask.py

@@ -22,6 +22,7 @@
 import lsst.afw.display as afwDisplay
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
+from lsst.utils.timer import timeMethod
 from .exampleStatsTasks import ExampleSigmaClippedStatsTask
 
 __all__ = ["ExampleCmdLineConfig", "ExampleCmdLineTask"]
@@ -112,7 +113,7 @@ def __init__(self, *args, **kwargs):
         pipeBase.CmdLineTask.__init__(self, *args, **kwargs)
         self.makeSubtask("stats")
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRef):
         """!Compute a few statistics on the image plane of an exposure
 

python/lsst/pipe/tasks/exampleStatsTasks.py

@@ -23,6 +23,7 @@
 import lsst.afw.math as afwMath
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
+from lsst.utils.timer import timeMethod
 
 __all__ = ["ExampleSigmaClippedStatsConfig", "ExampleSigmaClippedStatsTask", "ExampleSimpleStatsTask"]
 
@@ -115,7 +116,7 @@ def __init__(self, *args, **kwargs):
         self._statsControl.setNumIter(self.config.numIter)
         self._statsControl.setAndMask(self._badPixelMask)
 
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, maskedImage):
         """!Compute and return statistics for a masked image
 
@@ -184,11 +185,11 @@ class ExampleSimpleStatsTask(pipeBase.Task):
     # be run by a parent task at the same time).
     _DefaultName = "exampleSimpleStats"
 
-    # The `lsst.pipe.timeMethod` decorator measures how long a task method takes to run,
+    # The `lsst.utils.timer.timeMethod` decorator measures how long a task method takes to run,
     # and the resources needed to run it. The information is recorded in the task's `metadata` field.
     # Most command-line tasks (not including the example below) save metadata for the task
     # and all of its subtasks whenver the task is run.
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, maskedImage):
         """!Compute and return statistics for a masked image
 

python/lsst/pipe/tasks/getRepositoryData.py

@@ -25,6 +25,7 @@
 """
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
+from lsst.utils.timer import timeMethod
 
 __all__ = ["DataRefListRunner", "GetRepositoryDataTask"]
 
@@ -74,7 +75,7 @@ class GetRepositoryDataTask(pipeBase.CmdLineTask):
     def __init__(self, *args, **kwargs):
         pipeBase.CmdLineTask.__init__(self, *args, **kwargs)
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, dataRefList):
         """Get data from a repository for a collection of data references
 

python/lsst/pipe/tasks/healSparseMapping.py

@@ -31,6 +31,7 @@
 import lsst.afw.geom as afwGeom
 from lsst.daf.butler import Formatter
 from lsst.skymap import BaseSkyMap
+from lsst.utils.timer import timeMethod
 from .healSparseMappingProperties import (BasePropertyMap, BasePropertyMapConfig,
                                           PropertyMapMap, compute_approx_psf_size_and_shape)
 
@@ -456,7 +457,7 @@ def __init__(self, **kwargs):
         for name, config, PropertyMapClass in self.config.property_maps.apply():
             self.property_maps[name] = PropertyMapClass(config, name)
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runQuantum(self, butlerQC, inputRefs, outputRefs):
         inputs = butlerQC.get(inputRefs)
 
@@ -868,7 +869,7 @@ def __init__(self, **kwargs):
         for name, config, PropertyMapClass in self.config.property_maps.apply():
             self.property_maps[name] = PropertyMapClass(config, name)
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runQuantum(self, butlerQC, inputRefs, outputRefs):
         inputs = butlerQC.get(inputRefs)
 

python/lsst/pipe/tasks/imageDifference.py

@@ -46,6 +46,7 @@
 import lsst.afw.display as afwDisplay
 from lsst.skymap import BaseSkyMap
 from lsst.obs.base import ExposureIdInfo
+from lsst.utils.timer import timeMethod
 
 __all__ = ["ImageDifferenceConfig", "ImageDifferenceTask"]
 FwhmPerSigma = 2*math.sqrt(2*math.log(2))
@@ -555,7 +556,7 @@ def runQuantum(self, butlerQC: pipeBase.ButlerQuantumContext,
             del outputs.diaSources
         butlerQC.put(outputs, outputRefs)
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, sensorRef, templateIdList=None):
         """Subtract an image from a template coadd and measure the result.
 
@@ -636,7 +637,7 @@ def runDataRef(self, sensorRef, templateIdList=None):
             sensorRef.put(results.scoreExposure, self.config.coaddName + "Diff_scoreExp")
         return results
 
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, exposure=None, selectSources=None, templateExposure=None, templateSources=None,
             idFactory=None, calexpBackgroundExposure=None, subtractedExposure=None):
         """PSF matches, subtract two images and perform detection on the difference image.

python/lsst/pipe/tasks/interpImage.py

@@ -27,6 +27,7 @@
 import lsst.ip.isr as ipIsr
 import lsst.meas.algorithms as measAlg
 import lsst.pipe.base as pipeBase
+from lsst.utils.timer import timeMethod
 
 __all__ = ["InterpImageConfig", "InterpImageTask"]
 
@@ -115,7 +116,7 @@ def _setFallbackValue(self, mi=None):
 
         return fallbackValue
 
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, image, planeName=None, fwhmPixels=None, defects=None):
         """!Interpolate in place over pixels in a maskedImage marked as bad
 

python/lsst/pipe/tasks/makeCoaddTempExp.py

@@ -32,6 +32,7 @@
 import lsst.geom
 from lsst.meas.algorithms import CoaddPsf, CoaddPsfConfig
 from lsst.skymap import BaseSkyMap
+from lsst.utils.timer import timeMethod
 from .coaddBase import CoaddBaseTask, makeSkyInfo, reorderAndPadList
 from .warpAndPsfMatch import WarpAndPsfMatchTask
 from .coaddHelpers import groupPatchExposures, getGroupDataRef
@@ -284,7 +285,7 @@ def __init__(self, reuse=False, **kwargs):
         else:
             self.calexpType = "calexp"
 
-    @pipeBase.timeMethod
+    @timeMethod
     def runDataRef(self, patchRef, selectDataList=[]):
         """!Produce <coaddName>Coadd_<warpType>Warp images by warping and optionally PSF-matching.
 
@@ -384,7 +385,7 @@ def runDataRef(self, patchRef, selectDataList=[]):
 
         return dataRefList
 
-    @pipeBase.timeMethod
+    @timeMethod
     def run(self, calExpList, ccdIdList, skyInfo, visitId=0, dataIdList=None, **kwargs):
         """Create a Warp from inputs