anetAstrometry.py

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import numpy
from contextlib import contextmanager

import lsst.pex.exceptions
import lsst.afw.geom as afwGeom
from lsst.afw.cameraGeom import TAN_PIXELS
from lsst.afw.table import Point2DKey, CovarianceMatrix2fKey
import lsst.pex.config as pexConfig
import lsst.pipe.base as pipeBase
from .anetBasicAstrometry import ANetBasicAstrometryTask
from .sip import makeCreateWcsWithSip

class ANetAstrometryConfig(pexConfig.Config):
    solver = pexConfig.ConfigField(
        dtype = ANetBasicAstrometryTask.ConfigClass,
        doc = "Configuration for the astrometry solver",
    )
    forceKnownWcs = pexConfig.Field(dtype=bool, doc=(
        "Assume that the input image's WCS is correct, without comparing it to any external reality." +
        " (In contrast to using Astrometry.net).  NOTE, if you set this, you probably also want to" +
        " un-set 'solver.calculateSip'; otherwise we'll still try to find a TAN-SIP WCS starting " +
        " from the existing WCS"), default=False)
    rejectThresh = pexConfig.RangeField(dtype=float, default=3.0, doc="Rejection threshold for Wcs fitting",
                                        min=0.0, inclusiveMin=False)
    rejectIter = pexConfig.RangeField(dtype=int, default=3, doc="Rejection iterations for Wcs fitting",
                                      min=0)


    ## \addtogroup LSST_task_documentation
    ## \{
    ## \page ANetAstrometryTask
    ## \ref ANetAstrometryTask_ "ANetAstrometryTask"
    ## Use astrometry.net to match input sources with a reference catalog and solve for the Wcs
    ## \}

class ANetAstrometryTask(pipeBase.Task):
    """!Use astrometry.net to match input sources with a reference catalog and solve for the Wcs

    The actual matching and solving is done by the 'solver'; this Task
    serves as a wrapper for taking into account the known optical distortion.

    \section pipe_tasks_astrometry_Contents Contents

     - \ref pipe_tasks_astrometry_Purpose
     - \ref pipe_tasks_astrometry_Initialize
     - \ref pipe_tasks_astrometry_IO
     - \ref pipe_tasks_astrometry_Config
     - \ref pipe_tasks_astrometry_Debug
     - \ref pipe_tasks_astrometry_Example

    \section pipe_tasks_astrometry_Purpose      Description

    \copybrief ANetAstrometryTask

    \section pipe_tasks_astrometry_Initialize   Task initialisation

    \copydoc \_\_init\_\_

    \section pipe_tasks_astrometry_IO           Invoking the Task

    \copydoc run

    \section pipe_tasks_astrometry_Config       Configuration parameters

    See \ref ANetAstrometryConfig

    \section pipe_tasks_astrometry_Debug                Debug variables

    The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a
    flag \c -d to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py files.

    The available variables in ANetAstrometryTask are:
    <DL>
      <DT> \c display
      <DD> If True call astrometry.showAstrometry while iterating ANetAstrometryConfig.rejectIter times,
      and also after converging.
      <DT> \c frame
      <DD> ds9 frame to use in astrometry.showAstrometry
      <DT> \c pause
      <DD> Pause within astrometry.showAstrometry
    </DL>

    \section pipe_tasks_astrometry_Example      A complete example of using ANetAstrometryTask

    See \ref meas_photocal_photocal_Example.

    To investigate the \ref pipe_tasks_astrometry_Debug, put something like
    \code{.py}
        import lsstDebug
        def DebugInfo(name):
            di = lsstDebug.getInfo(name)        # N.b. lsstDebug.Info(name) would call us recursively
            if name == "lsst.pipe.tasks.astrometry":
                di.display = 1

            return di

        lsstDebug.Info = DebugInfo
    \endcode
    into your debug.py file and run photoCalTask.py with the \c --debug flag.
    """
    ConfigClass = ANetAstrometryConfig

    def __init__(self, schema, **kwds):
        """!Create the astrometric calibration task.  Most arguments are simply passed onto pipe.base.Task.

        \param schema An lsst::afw::table::Schema used to create the output lsst.afw.table.SourceCatalog
        \param **kwds keyword arguments to be passed to the lsst.pipe.base.task.Task constructor

        A centroid field "centroid.distorted" (used internally during the Task's operation)
        will be added to the schema.
        """
        pipeBase.Task.__init__(self, **kwds)

        if schema.getVersion() == 0:
            self.distortedName = "centroid.distorted"
            self.centroidKey = schema.addField(self.distortedName, type="PointD",
                                           doc="centroid distorted for astrometry solver")
            self.centroidErrKey = schema.addField(self.distortedName + ".err", type="CovPointF",
                                           doc="centroid distorted err for astrometry solver")
            self.centroidFlagKey = schema.addField(self.distortedName + ".flag", type="Flag",
                                           doc="centroid distorted flag astrometry solver")
        else:
            self.distortedName = "astrom_distorted"
            self.centroidXKey = schema.addField(self.distortedName + "_x", type="D",
                                           doc="centroid distorted for astrometry solver")
            self.centroidYKey = schema.addField(self.distortedName + "_y", type="D",
                                           doc="centroid distorted for astrometry solver")
            self.centroidXErrKey = schema.addField(self.distortedName + "_xSigma", type="F",
                                           doc="centroid distorted err for astrometry solver")
            self.centroidYErrKey = schema.addField(self.distortedName + "_ySigma", type="F",
                                           doc="centroid distorted err for astrometry solver")
            self.centroidFlagKey = schema.addField(self.distortedName + "_flag", type="Flag",
                                           doc="centroid distorted flag astrometry solver")
            self.centroidKey = Point2DKey(self.centroidXKey, self.centroidYKey)
            self.centroidErrKey = CovarianceMatrix2fKey((self.centroidXErrKey, self.centroidYErrKey))
 
        self.astrometer = None

    @pipeBase.timeMethod
    def run(self, exposure, sourceCat):
        """!Match with reference sources and calculate an astrometric solution

        \param[in,out] exposure Exposure to calibrate
        \param[in] sourceCat catalog of measured sources (an lsst.afw.table.SourceCatalog)
        \return a pipeBase.Struct with fields:
        - matches: Astrometric matches, as an lsst.afw.table.ReferenceMatchVector
        - matchMeta: Metadata for astrometric matches

        The reference catalog actually used is up to the implementation
        of the solver; it will be manifested in the returned matches as
        a list of lsst.afw.table.ReferenceMatch objects (\em i.e. of lsst.afw.table.Match with
        \c first being of type lsst.afw.table.SimpleRecord and \c second type lsst.afw.table.SourceRecord ---
        the reference object and matched object respectively).

        \note
        The input sources have the centroid slot moved to a new column "centroid.distorted"
        which has the positions corrected for any known optical distortion;
        the 'solver' (which is instantiated in the 'astrometry' member)
        should therefore simply use the centroids provided by calling
        afw.table.Source.getCentroid() on the individual source records.  This column \em must
        be present in the sources table.
        """
        with self.distortionContext(sourceCat=sourceCat, exposure=exposure) as bbox:
            results = self.astrometry(sourceCat=sourceCat, exposure=exposure, bbox=bbox)

        if results.matches:
            self.refitWcs(sourceCat=sourceCat, exposure=exposure, matches=results.matches)

        return results

    @pipeBase.timeMethod
    def distort(self, sourceCat, exposure):
        """!Calculate distorted source positions

        CCD images are often affected by optical distortion that makes
        the astrometric solution higher order than linear.  Unfortunately,
        most (all?) matching algorithms require that the distortion be
        small or zero, and so it must be removed.  We do this by calculating
        (un-)distorted positions, based on a known optical distortion model
        in the Ccd.

        The distortion correction moves sources, so we return the distorted bounding box.

        \param[in]     exposure Exposure to process
        \param[in,out] sourceCat  SourceCatalog; getX() and getY() will be used as inputs,
                                with distorted points in "centroid.distorted" field.
        \return bounding box of distorted exposure
        """
        detector = exposure.getDetector()
        pixToTanXYTransform = None
        if detector is None:
            self.log.warn("No detector associated with exposure; assuming null distortion")
        else:
            tanSys = detector.makeCameraSys(TAN_PIXELS)
            pixToTanXYTransform = detector.getTransformMap().get(tanSys)

        if pixToTanXYTransform is None:
            self.log.info("Null distortion correction")
            for s in sourceCat:
                s.set(self.centroidKey, s.getCentroid())
                s.set(self.centroidErrKey, s.getCentroidErr())
                s.set(self.centroidFlagKey, s.getCentroidFlag())
            return exposure.getBBox()

        # Distort source positions
        self.log.info("Applying distortion correction")
        for s in sourceCat:
            centroid = pixToTanXYTransform.forwardTransform(s.getCentroid())
            s.set(self.centroidKey, centroid)
            s.set(self.centroidErrKey, s.getCentroidErr())
            s.set(self.centroidFlagKey, s.getCentroidFlag())


        # Get distorted image size so that astrometry_net does not clip.
        bboxD = afwGeom.Box2D()
        for corner in detector.getCorners(TAN_PIXELS):
            bboxD.include(corner)
        return afwGeom.Box2I(bboxD)

    @contextmanager
    def distortionContext(self, sourceCat, exposure):
        """!Context manager that applies and removes distortion

        We move the "centroid" definition in the catalog table to
        point to the distorted positions.  This is undone on exit
        from the context.

        The input Wcs is taken to refer to the coordinate system
        with the distortion correction applied, and hence no shift
        is required when the sources are distorted.  However, after
        Wcs fitting, the Wcs is in the distorted frame so when the
        distortion correction is removed, the Wcs needs to be
        shifted to compensate.

        \param sourceCat Sources on exposure, an lsst.afw.table.SourceCatalog
        \param exposure Exposure holding Wcs, an lsst.afw.image.ExposureF or D
        \return bounding box of distorted exposure
        """
        # Apply distortion
        bbox = self.distort(sourceCat=sourceCat, exposure=exposure)
        oldCentroidName = sourceCat.table.getCentroidDefinition()
        sourceCat.table.defineCentroid(self.distortedName)
        try:
            yield bbox # Execute 'with' block, providing bbox to 'as' variable
        finally:
            # Un-apply distortion
            sourceCat.table.defineCentroid(oldCentroidName)
            x0, y0 = exposure.getXY0()
            wcs = exposure.getWcs()
            if wcs:
                wcs.shiftReferencePixel(-bbox.getMinX() + x0, -bbox.getMinY() + y0)

    @pipeBase.timeMethod
    def astrometry(self, sourceCat, exposure, bbox=None):
        """!Solve astrometry to produce WCS

        \param sourceCat Sources on exposure, an lsst.afw.table.SourceCatalog
        \param exposure Exposure to process, an lsst.afw.image.ExposureF or D
        \param bbox Bounding box, or None to use exposure
        \return a pipe.base.Struct with fields:
         - matches: star matches
         - matchMeta: match metadata
        """
        if not self.config.forceKnownWcs:
            self.log.info("Solving astrometry")
        if bbox is None:
            bbox = exposure.getBBox()

        if not self.astrometer:
            self.astrometer = ANetBasicAstrometryTask(self.config.solver, log=self.log)

        if self.config.forceKnownWcs:
            self.log.info("Forcing the input exposure's WCS")
            if self.config.solver.calculateSip:
                self.log.warn("'forceKnownWcs' and 'solver.calculateSip' options are both set." +
                              " Will try to compute a TAN-SIP WCS starting from the input WCS.")
            astrom = self.astrometer.useKnownWcs(sourceCat=sourceCat, exposure=exposure, bbox=bbox)
        else:
            astrom = self.astrometer.determineWcs(sourceCat=sourceCat, exposure=exposure, bbox=bbox)

        if astrom is None or astrom.getWcs() is None:
            raise RuntimeError("Unable to solve astrometry")

        matches = astrom.getMatches()
        matchMeta = astrom.getMatchMetadata()
        if matches is None or len(matches) == 0:
            raise RuntimeError("No astrometric matches")
        self.log.info("%d astrometric matches" %  (len(matches)))

        if not self.config.forceKnownWcs:
            # Note that this is the Wcs for the provided positions, which may be distorted
            exposure.setWcs(astrom.getWcs())

        self.display('astrometry', exposure=exposure, sources=sourceCat, matches=matches)

        return pipeBase.Struct(matches=matches, matchMeta=matchMeta)

    @pipeBase.timeMethod
    def refitWcs(self, sourceCat, exposure, matches):
        """!A final Wcs solution after matching and removing distortion

        Specifically, fitting the non-linear part, since the linear
        part has been provided by the matching engine.

        \param sourceCat Sources on exposure, an lsst.afw.table.SourceCatalog
        \param exposure Exposure of interest, an lsst.afw.image.ExposureF or D
        \param matches Astrometric matches, as an lsst.afw.table.ReferenceMatchVector

        \return the resolved-Wcs object, or None if config.solver.calculateSip is False.
        """
        sip = None
        if self.config.solver.calculateSip:
            self.log.info("Refitting WCS")
            origMatches = matches
            wcs = exposure.getWcs()

            import lsstDebug
            display = lsstDebug.Info(__name__).display
            frame = lsstDebug.Info(__name__).frame
            pause = lsstDebug.Info(__name__).pause

            def fitWcs(initialWcs, title=None):
                """!Do the WCS fitting and display of the results"""
                sip = makeCreateWcsWithSip(matches, initialWcs, self.config.solver.sipOrder)
                resultWcs = sip.getNewWcs()
                if display:
                    showAstrometry(exposure, resultWcs, origMatches, matches, frame=frame,
                                   title=title, pause=pause)
                return resultWcs, sip.getScatterOnSky()

            numRejected = 0
            try:
                for i in range(self.config.rejectIter):
                    wcs, scatter = fitWcs(wcs, title="Iteration %d" % i)

                    ref = numpy.array([wcs.skyToPixel(m.first.getCoord()) for m in matches])
                    src = numpy.array([m.second.getCentroid() for m in matches])
                    diff = ref - src
                    rms = diff.std()
                    trimmed = []
                    for d, m in zip(diff, matches):
                        if numpy.all(numpy.abs(d) < self.config.rejectThresh*rms):
                            trimmed.append(m)
                        else:
                            numRejected += 1
                    if len(matches) == len(trimmed):
                        break
                    matches = trimmed

                # Final fit after rejection iterations
                wcs, scatter = fitWcs(wcs, title="Final astrometry")

            except lsst.pex.exceptions.LengthError as e:
                self.log.warn("Unable to fit SIP: %s" % e)

            self.log.info("Astrometric scatter: %f arcsec (%s non-linear terms, %d matches, %d rejected)" %
                          (scatter.asArcseconds(), "with" if wcs.hasDistortion() else "without",
                           len(matches), numRejected))
            exposure.setWcs(wcs)

            # Apply WCS to sources
            for index, source in enumerate(sourceCat):
                sky = wcs.pixelToSky(source.getX(), source.getY())
                source.setCoord(sky)
        else:
            self.log.warn("Not calculating a SIP solution; matches may be suspect")

        self.display('astrometry', exposure=exposure, sources=sourceCat, matches=matches)

        return sip


def showAstrometry(exposure, wcs, allMatches, useMatches, frame=0, title=None, pause=False):
    """!Show results of astrometry fitting

    \param exposure Image to display
    \param wcs Astrometric solution
    \param allMatches List of all astrometric matches (including rejects)
    \param useMatches List of used astrometric matches
    \param frame Frame number for display
    \param title Title for display
    \param pause Pause to allow viewing of the display and optional debugging?

    - Matches are shown in yellow if used in the Wcs solution, otherwise red
     - +: Detected objects
     - x: Catalogue objects
    """
    import lsst.afw.display.ds9 as ds9
    ds9.mtv(exposure, frame=frame, title=title)

    useIndices = set(m.second.getId() for m in useMatches)

    radii = []
    with ds9.Buffering():
        for i, m in enumerate(allMatches):
            x, y = m.second.getX(), m.second.getY()
            pix = wcs.skyToPixel(m.first.getCoord())

            isUsed = m.second.getId() in useIndices
            if isUsed:
                radii.append(numpy.hypot(pix[0] - x, pix[1] - y))

            color = ds9.YELLOW if isUsed else ds9.RED

            ds9.dot("+", x, y, size=10, frame=frame, ctype=color)
            ds9.dot("x", pix[0], pix[1], size=10, frame=frame, ctype=color)

    radii = numpy.array(radii)
    print "<dr> = %.4g +- %.4g pixels [%d/%d matches]" % (radii.mean(), radii.std(),
                                                          len(useMatches), len(allMatches))

    if pause:
        import sys
        while True:
            try:
                reply = raw_input("Debugging? [p]db [q]uit; any other key to continue... ").strip()
            except EOFError:
                reply = ""

            reply = reply.split()
            if len(reply) > 1:
                reply = reply[0]
            if reply == "p":
                import pdb;pdb.set_trace()
            elif reply == "q":
                sys.exit(1)
            else:
                break