task.py

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#
# LSST Data Management System
# Copyright 2008-2016 AURA/LSST.
#
# This product includes software developed by the
# LSST Project (http://www.lsst.org/).
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# This program is free software: you can redistribute it and/or modify
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# 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.
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# the GNU General Public License along with this program.  If not,
# see <http://www.lsstcorp.org/LegalNotices/>.
#
__all__ = ["Task", "TaskError"]

import contextlib

import lsstDebug
from lsst.pex.config import ConfigurableField
from lsst.log import Log
import lsst.daf.base as dafBase
from .timer import logInfo


class TaskError(Exception):
    """Use to report errors for which a traceback is not useful.

    Notes
    -----
    Examples of such errors:

    - processCcd is asked to run detection, but not calibration, and no calexp is found.
    - coadd finds no valid images in the specified patch.
    """
    pass


class Task:
    r"""Base class for data processing tasks.

    See :ref:`task-framework-overview` to learn what tasks are, and :ref:`creating-a-task` for more
    information about writing tasks.

    Parameters
    ----------
    config : `Task.ConfigClass` instance, optional
        Configuration for this task (an instance of Task.ConfigClass, which is a task-specific subclass of
        `lsst.pex.config.Config`, or `None`. If `None`:

        - If parentTask specified then defaults to parentTask.config.<name>
        - If parentTask is None then defaults to self.ConfigClass()

    name : `str`, optional
        Brief name of task, or `None`; if `None` then defaults to `Task._DefaultName`
    parentTask : `Task`-type, optional
        The parent task of this subtask, if any.

        - If `None` (a top-level task) then you must specify config and name is ignored.
        - If not `None` (a subtask) then you must specify name.
    log : `lsst.log.Log`, optional
        Log whose name is used as a log name prefix, or `None` for no prefix. Ignored if is parentTask
        specified, in which case ``parentTask.log``\ 's name is used as a prefix. The task's log name is
        ``prefix + "." + name`` if a prefix exists, else ``name``. The task's log is then a child logger of
        ``parentTask.log`` (if ``parentTask`` specified), or a child logger of the log from the argument
        (if ``log`` is not `None`).

    Raises
    ------
    RuntimeError
        Raised under these circumstances:

        - If ``parentTask`` is `None` and ``config`` is `None`.
        - If ``parentTask`` is not `None` and ``name`` is `None`.
        - If ``name`` is `None` and ``_DefaultName`` does not exist.

    Notes
    -----
    Useful attributes include:

    - ``log``: an lsst.log.Log
    - ``config``: task-specific configuration; an instance of ``ConfigClass`` (see below).
    - ``metadata``: an `lsst.daf.base.PropertyList` for collecting task-specific metadata,
        e.g. data quality and performance metrics. This is data that is only meant to be
        persisted, never to be used by the task.

    Subclasses typically have a method named ``runDataRef`` to perform the main data processing. Details:

    - ``runDataRef`` should process the minimum reasonable amount of data, typically a single CCD.
      Iteration, if desired, is performed by a caller of the method. This is good design and allows
      multiprocessing without the run method having to support it directly.
    - If ``runDataRef`` can persist or unpersist data:

      - ``runDataRef`` should accept a butler data reference (or a collection of data references,
        if appropriate, e.g. coaddition).
      - There should be a way to run the task without persisting data. Typically the run method returns all
        data, even if it is persisted, and the task's config method offers a flag to disable persistence.

    **Deprecated:** Tasks other than cmdLineTask.CmdLineTask%s should *not* accept a blob such as a butler
    data reference.  How we will handle data references is still TBD, so don't make changes yet!
    RHL 2014-06-27

    Subclasses must also have an attribute ``ConfigClass`` that is a subclass of `lsst.pex.config.Config`
    which configures the task. Subclasses should also have an attribute ``_DefaultName``:
    the default name if there is no parent task. ``_DefaultName`` is required for subclasses of
    `~lsst.pipe.base.CmdLineTask` and recommended for subclasses of Task because it simplifies construction
    (e.g. for unit tests).

    Tasks intended to be run from the command line should be subclasses of `~lsst.pipe.base.CmdLineTask`
    not Task.
    """

    def __init__(self, config=None, name=None, parentTask=None, log=None):
        self.metadata = dafBase.PropertyList()
        self._parentTask = parentTask

        if parentTask is not None:
            if name is None:
                raise RuntimeError("name is required for a subtask")
            self._name = name
            self._fullName = parentTask._computeFullName(name)
            if config is None:
                config = getattr(parentTask.config, name)
            self._taskDict = parentTask._taskDict
            loggerName = parentTask.log.getName() + '.' + name
        else:
            if name is None:
                name = getattr(self, "_DefaultName", None)
                if name is None:
                    raise RuntimeError("name is required for a task unless it has attribute _DefaultName")
                name = self._DefaultName
            self._name = name
            self._fullName = self._name
            if config is None:
                config = self.ConfigClass()
            self._taskDict = dict()
            loggerName = self._fullName
            if log is not None and log.getName():
                loggerName = log.getName() + '.' + loggerName

        self.log = Log.getLogger(loggerName)
        self.config = config
        self._display = lsstDebug.Info(self.__module__).display
        self._taskDict[self._fullName] = self

    def emptyMetadata(self):
        """Empty (clear) the metadata for this Task and all sub-Tasks.
        """
        for subtask in self._taskDict.values():
            subtask.metadata = dafBase.PropertyList()

    def getSchemaCatalogs(self):
        """Get the schemas generated by this task.

        Returns
        -------
        schemaCatalogs : `dict`
            Keys are butler dataset type, values are an empty catalog (an instance of the appropriate
            `lsst.afw.table` Catalog type) for this task.

        Notes
        -----

        .. warning::

           Subclasses that use schemas must override this method. The default implemenation returns
           an empty dict.

        This method may be called at any time after the Task is constructed, which means that all task
        schemas should be computed at construction time, *not* when data is actually processed. This
        reflects the philosophy that the schema should not depend on the data.

        Returning catalogs rather than just schemas allows us to save e.g. slots for SourceCatalog as well.

        See also
        --------
        Task.getAllSchemaCatalogs
        """
        return {}

    def getAllSchemaCatalogs(self):
        """Get schema catalogs for all tasks in the hierarchy, combining the results into a single dict.

        Returns
        -------
        schemacatalogs : `dict`
            Keys are butler dataset type, values are a empty catalog (an instance of the appropriate
            lsst.afw.table Catalog type) for all tasks in the hierarchy, from the top-level task down
            through all subtasks.

        Notes
        -----
        This method may be called on any task in the hierarchy; it will return the same answer, regardless.

        The default implementation should always suffice. If your subtask uses schemas the override
        `Task.getSchemaCatalogs`, not this method.
        """
        schemaDict = self.getSchemaCatalogs()
        for subtask in self._taskDict.values():
            schemaDict.update(subtask.getSchemaCatalogs())
        return schemaDict

    def getFullMetadata(self):
        """Get metadata for all tasks.

        Returns
        -------
        metadata : `lsst.daf.base.PropertySet`
            The `~lsst.daf.base.PropertySet` keys are the full task name. Values are metadata
            for the top-level task and all subtasks, sub-subtasks, etc..

        Notes
        -----
        The returned metadata includes timing information (if ``@timer.timeMethod`` is used)
        and any metadata set by the task. The name of each item consists of the full task name
        with ``.`` replaced by ``:``, followed by ``.`` and the name of the item, e.g.::

            topLevelTaskName:subtaskName:subsubtaskName.itemName

        using ``:`` in the full task name disambiguates the rare situation that a task has a subtask
        and a metadata item with the same name.
        """
        fullMetadata = dafBase.PropertySet()
        for fullName, task in self.getTaskDict().items():
            fullMetadata.set(fullName.replace(".", ":"), task.metadata)
        return fullMetadata

    def getFullName(self):
        """Get the task name as a hierarchical name including parent task names.

        Returns
        -------
        fullName : `str`
            The full name consists of the name of the parent task and each subtask separated by periods.
            For example:

            - The full name of top-level task "top" is simply "top".
            - The full name of subtask "sub" of top-level task "top" is "top.sub".
            - The full name of subtask "sub2" of subtask "sub" of top-level task "top" is "top.sub.sub2".
        """
        return self._fullName

    def getName(self):
        """Get the name of the task.

        Returns
        -------
        taskName : `str`
            Name of the task.

        See also
        --------
        getFullName
        """
        return self._name

    def getTaskDict(self):
        """Get a dictionary of all tasks as a shallow copy.

        Returns
        -------
        taskDict : `dict`
            Dictionary containing full task name: task object for the top-level task and all subtasks,
            sub-subtasks, etc..
        """
        return self._taskDict.copy()

    def makeSubtask(self, name, **keyArgs):
        """Create a subtask as a new instance as the ``name`` attribute of this task.

        Parameters
        ----------
        name : `str`
            Brief name of the subtask.
        keyArgs
            Extra keyword arguments used to construct the task. The following arguments are automatically
            provided and cannot be overridden:

            - "config".
            - "parentTask".

        Notes
        -----
        The subtask must be defined by ``Task.config.name``, an instance of pex_config ConfigurableField
        or RegistryField.
        """
        taskField = getattr(self.config, name, None)
        if taskField is None:
            raise KeyError("%s's config does not have field %r" % (self.getFullName(), name))
        subtask = taskField.apply(name=name, parentTask=self, **keyArgs)
        setattr(self, name, subtask)

    @contextlib.contextmanager
    def timer(self, name, logLevel=Log.DEBUG):
        """Context manager to log performance data for an arbitrary block of code.

        Parameters
        ----------
        name : `str`
            Name of code being timed; data will be logged using item name: ``Start`` and ``End``.
        logLevel
            A `lsst.log` level constant.

        Examples
        --------
        Creating a timer context::

            with self.timer("someCodeToTime"):
                pass  # code to time

        See also
        --------
        timer.logInfo
        """
        logInfo(obj=self, prefix=name + "Start", logLevel=logLevel)
        try:
            yield
        finally:
            logInfo(obj=self, prefix=name + "End", logLevel=logLevel)

    @classmethod
    def makeField(cls, doc):
        """Make a `lsst.pex.config.ConfigurableField` for this task.

        Parameters
        ----------
        doc : `str`
            Help text for the field.

        Returns
        -------
        configurableField : `lsst.pex.config.ConfigurableField`
            A `~ConfigurableField` for this task.

        Examples
        --------
        Provides a convenient way to specify this task is a subtask of another task.

        Here is an example of use::

            class OtherTaskConfig(lsst.pex.config.Config)
                aSubtask = ATaskClass.makeField("a brief description of what this task does")
        """
        return ConfigurableField(doc=doc, target=cls)

    def _computeFullName(self, name):
        """Compute the full name of a subtask or metadata item, given its brief name.

        Parameters
        ----------
        name : `str`
            Brief name of subtask or metadata item.

        Returns
        -------
        fullName : `str`
            The full name: the ``name`` argument prefixed by the full task name and a period.

        Notes
        -----
        For example: if the full name of this task is "top.sub.sub2"
        then ``_computeFullName("subname")`` returns ``"top.sub.sub2.subname"``.
        """
        return "%s.%s" % (self._fullName, name)

    def __reduce__(self):
        """Pickler.
        """
        return self.__class__, (self.config, self._name, self._parentTask, None)