exampleStatsTasks.py

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#
# LSST Data Management System
# Copyright 2014 LSST Corporation.
#
# This product includes software developed by the
# LSST Project (http://www.lsst.org/).
#
# 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 LSST License Statement and
# the GNU General Public License along with this program.  If not,
# see <http://www.lsstcorp.org/LegalNotices/>.
#
import lsst.afw.image as afwImage
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"]
 
# The following block adds links to these tasks from the Task Documentation page.
# This works even for task(s) that are not in lsst.pipe.tasks.
 
 
 
class ExampleSigmaClippedStatsConfig(pexConfig.Config):
    """!Configuration for ExampleSigmaClippedStatsTask
    """
    badMaskPlanes = pexConfig.ListField(
        dtype=str,
        doc="Mask planes that, if set, indicate the associated pixel should "
        "not be included when the calculating statistics.",
        default=("EDGE",),
    )
    numSigmaClip = pexConfig.Field(
        doc="number of sigmas at which to clip data",
        dtype=float,
        default=3.0,
    )
    numIter = pexConfig.Field(
        doc="number of iterations of sigma clipping",
        dtype=int,
        default=2,
    )
 
 
class ExampleSigmaClippedStatsTask(pipeBase.Task):
    r"""!Example task to compute sigma-clipped mean and standard deviation of an image
 
    \section pipeTasks_ExampleSigmaClippedStatsTask_Contents Contents
 
     - \ref pipeTasks_ExampleSigmaClippedStatsTask_Purpose
     - \ref pipeTasks_ExampleSigmaClippedStatsTask_Config
     - \ref pipeTasks_ExampleSigmaClippedStatsTask_Debug
     - \ref pipeTasks_ExampleSigmaClippedStatsTask_Example
 
    \section pipeTasks_ExampleSigmaClippedStatsTask_Purpose Description
 
    \copybrief ExampleSigmaClippedStatsTask
 
    This is a simple example task designed to be run as a subtask by ExampleCmdLineTask.
    See also ExampleSimpleStatsTask as a variant that is even simpler.
 
    The main method is \ref ExampleSigmaClippedStatsTask.run "run".
 
    \section pipeTasks_ExampleSigmaClippedStatsTask_Config  Configuration parameters
 
    See \ref ExampleSigmaClippedStatsConfig
 
    \section pipeTasks_ExampleSigmaClippedStatsTask_Debug   Debug variables
 
    This task has no debug variables.
 
    \section pipeTasks_ExampleSigmaClippedStatsTask_Example A complete example
    of using ExampleSigmaClippedStatsTask
 
    This code is in examples/exampleStatsTask.py (this one example runs both
    ExampleSigmaClippedStatsTask and ExampleSimpleStatsTask), and can be run as:
    \code
    examples/exampleStatsTask.py [fitsFile]
    \endcode
    """
    ConfigClass = ExampleSigmaClippedStatsConfig
    _DefaultName = "exampleSigmaClippedStats"
 
    def __init__(self, *args, **kwargs):
        """!Construct an ExampleSigmaClippedStatsTask
 
        The init method may compute anything that that does not require data.
        In this case we create a statistics control object using the config
        (which cannot change once the task is created).
        """
        pipeBase.Task.__init__(self, *args, **kwargs)
 
        self._badPixelMask_badPixelMask = afwImage.Mask.getPlaneBitMask(self.config.badMaskPlanes)
 
        self._statsControl_statsControl = afwMath.StatisticsControl()
        self._statsControl_statsControl.setNumSigmaClip(self.config.numSigmaClip)
        self._statsControl_statsControl.setNumIter(self.config.numIter)
        self._statsControl_statsControl.setAndMask(self._badPixelMask_badPixelMask)
 
    @timeMethod
    def run(self, maskedImage):
        """!Compute and return statistics for a masked image
 
        @param[in] maskedImage: masked image (an lsst::afw::MaskedImage)
        @return a pipeBase Struct containing:
        - mean: mean of image plane
        - meanErr: uncertainty in mean
        - stdDev: standard deviation of image plane
        - stdDevErr: uncertainty in standard deviation
        """
        statObj = afwMath.makeStatistics(maskedImage, afwMath.MEANCLIP | afwMath.STDEVCLIP | afwMath.ERRORS,
                                         self._statsControl_statsControl)
        mean, meanErr = statObj.getResult(afwMath.MEANCLIP)
        stdDev, stdDevErr = statObj.getResult(afwMath.STDEVCLIP)
        self.log.info("clipped mean=%0.2f; meanErr=%0.2f; stdDev=%0.2f; stdDevErr=%0.2f",
                      mean, meanErr, stdDev, stdDevErr)
        return pipeBase.Struct(
            mean=mean,
            meanErr=meanErr,
            stdDev=stdDev,
            stdDevErr=stdDevErr,
        )
 
 
class ExampleSimpleStatsTask(pipeBase.Task):
    r"""!Example task to compute mean and standard deviation of an image
 
    \section pipeTasks_ExampleSimpleStatsTask_Contents Contents
 
     - \ref pipeTasks_ExampleSimpleStatsTask_Purpose
     - \ref pipeTasks_ExampleSimpleStatsTask_Config
     - \ref pipeTasks_ExampleSimpleStatsTask_Debug
     - \ref pipeTasks_ExampleSimpleStatsTask_Example
 
    \section pipeTasks_ExampleSimpleStatsTask_Purpose Description
 
    \copybrief ExampleSimpleStatsTask
 
    This was designed to be run as a subtask by ExampleCmdLineTask.
    It is about as simple as a task can be; it has no configuration parameters and requires no special
    initialization. See also ExampleSigmaClippedStatsTask as a variant that is slightly more complicated.
 
    The main method is \ref ExampleSimpleTask.run "run".
 
    \section pipeTasks_ExampleSimpleStatsTask_Config    Configuration parameters
 
    This task has no configuration parameters.
 
    \section pipeTasks_ExampleSimpleStatsTask_Debug     Debug variables
 
    This task has no debug variables.
 
    \section pipeTasks_ExampleSimpleStatsTask_Example A complete example of using ExampleSimpleStatsTask
 
    This code is in examples/exampleStatsTask.py (this one example runs both
    ExampleSigmaClippedStatsTask and ExampleSimpleStatsTask), and can be run as:
    \code
    examples/exampleStatsTask.py [fitsFile]
    \endcode
    """
    # Even a task with no configuration requires setting ConfigClass
    ConfigClass = pexConfig.Config
    # Having a default name simplifies construction of the task, since the parent task
    # need not specify a name. Note: having a default name is required for command-line tasks.
    # The name can be simple and need not be unique (except for multiple subtasks that will
    # be run by a parent task at the same time).
    _DefaultName = "exampleSimpleStats"
 
    # 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.
    @timeMethod
    def run(self, maskedImage):
        """!Compute and return statistics for a masked image
 
        @param[in] maskedImage: masked image (an lsst::afw::MaskedImage)
        @return a pipeBase Struct containing:
        - mean: mean of image plane
        - meanErr: uncertainty in mean
        - stdDev: standard deviation of image plane
        - stdDevErr: uncertainty in standard deviation
        """
        self._statsControl_statsControl = afwMath.StatisticsControl()
        statObj = afwMath.makeStatistics(maskedImage, afwMath.MEAN | afwMath.STDEV | afwMath.ERRORS,
                                         self._statsControl_statsControl)
        mean, meanErr = statObj.getResult(afwMath.MEAN)
        stdDev, stdDevErr = statObj.getResult(afwMath.STDEV)
        self.log.info("simple mean=%0.2f; meanErr=%0.2f; stdDev=%0.2f; stdDevErr=%0.2f",
                      mean, meanErr, stdDev, stdDevErr)
 
        return pipeBase.Struct(
            mean=mean,
            meanErr=meanErr,
            stdDev=stdDev,
            stdDevErr=stdDevErr,
        )