diaSourceAnalysis.py

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#!/usr/bin/env python

#
# LSST Data Management System
# Copyright 2008-2016 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/>.
#
from __future__ import division
from builtins import input
from builtins import range
from builtins import object

from optparse import OptionParser
import lsst.afw.image as afwImage
import lsst.afw.geom as afwGeom
import lsst.afw.detection as afwDet
from lsst.log import Log
import lsst.pex.policy as pexPolicy
import lsst.daf.persistence as dafPersist
import lsst.daf.base as dafBase
import numpy as num
import lsst.afw.display.ds9 as ds9
import lsst.pex.config as pexConfig

scaling = 5


def parseOptions():
    """Parse the command line options."""
    parser = OptionParser(
        usage="""%prog cdDiffSources crDiffExposure

Read in sources and test for junk""")
    options, args = parser.parse_args()
    if len(args) != 2:
        parser.error("incorrect number of arguments")
    return options, args


def readSourceSet(boostFile):
    loc = dafPersist.LogicalLocation(boostFile)
    storageList = dafPersist.StorageList()
    additionalData = dafBase.PropertySet()
    persistence = dafPersist.Persistence.getPersistence(pexPolicy.Policy())
    storageList.append(persistence.getRetrieveStorage("BoostStorage", loc))
    psvptr = persistence.unsafeRetrieve("PersistableSourceVector", storageList, additionalData)
    psv = afwDet.PersistableSourceVector.swigConvert(psvptr)
    return psv.getSources()


class DiaSourceAnalystConfig(pexConfig.Config):
    srcBadMaskPlanes = pexConfig.ListField(
        dtype=str,
        doc="""Mask planes that lead to an invalid detection.
                 Options: NO_DATA EDGE SAT BAD CR INTRP
                 E.g. : NO_DATA SAT BAD allows CR-masked and interpolated pixels""",
        default=("NO_DATA", "EDGE", "SAT", "BAD")
    )
    fBadPixels = pexConfig.Field(
        dtype=float,
        doc="Fraction of bad pixels allowed in footprint",
        default=0.1
    )
    fluxPolarityRatio = pexConfig.Field(
        dtype=float,
        doc="Minimum fraction of flux in correct-polarity pixels",
        default=0.75
    )
    nPolarityRatio = pexConfig.Field(
        dtype=float,
        doc="Minimum fraction of correct-polarity pixels in unmasked subset",
        default=0.7
    )
    nMaskedRatio = pexConfig.Field(
        dtype=float,
        doc="Minimum fraction of correct-polarity unmasked to masked pixels",
        default=0.6,
    )
    nGoodRatio = pexConfig.Field(
        dtype=float,
        doc="Minimum fraction of correct-polarity unmasked to all pixels",
        default=0.5
    )


class DiaSourceAnalyst(object):

    def __init__(self, config):
        self.config = config
        self.log = Log.getLogger("ip.diffim.DiaSourceAnalysis")

        self.bitMask = 0
        srcBadMaskPlanes = self.config.srcBadMaskPlanes
        for maskPlane in srcBadMaskPlanes:
            self.bitMask |= afwImage.MaskU_getPlaneBitMask(maskPlane)

    def countDetected(self, mask):
        idxP = num.where(mask & afwImage.MaskU_getPlaneBitMask("DETECTED"))
        idxN = num.where(mask & afwImage.MaskU_getPlaneBitMask("DETECTED_NEGATIVE"))
        return len(idxP[0]), len(idxN[0])

    def countMasked(self, mask):
        idxM = num.where(mask & self.bitMask)
        return len(idxM[0])

    def countPolarity(self, mask, pixels):
        unmasked = ((mask & self.bitMask) == 0)
        idxP = num.where((pixels >= 0) & unmasked)
        idxN = num.where((pixels < 0) & unmasked)
        fluxP = num.sum(pixels[idxP])
        fluxN = num.sum(pixels[idxN])
        #import pdb; pdb.set_trace()
        return len(idxP[0]), len(idxN[0]), fluxP, fluxN

    def testSource(self, source, subMi):
        imArr, maArr, varArr = subMi.getArrays()
        flux = source.getApFlux()

        nPixels = subMi.getWidth() * subMi.getHeight()
        nPos, nNeg, fPos, fNeg = self.countPolarity(maArr, imArr)
        nDetPos, nDetNeg = self.countDetected(maArr)
        nMasked = self.countMasked(maArr)
        assert(nPixels == (nMasked + nPos + nNeg))

        # 1) Too many pixels in the detection are masked
        fMasked = (nMasked / nPixels)
        fMaskedTol = self.config.fBadPixels
        if fMasked > fMaskedTol:
            self.log.debug("Candidate %d : BAD fBadPixels %.2f > %.2f", source.getId(), fMasked, fMaskedTol)
            return False

        if flux > 0:
            # positive-going source
            fluxRatio = fPos / (fPos + abs(fNeg))
            ngoodRatio = nPos / nPixels
            maskRatio = nPos / (nPos + nMasked)
            npolRatio = nPos / (nPos + nNeg)
        else:
            # negative-going source
            fluxRatio = abs(fNeg) / (fPos + abs(fNeg))
            ngoodRatio = nNeg / nPixels
            maskRatio = nNeg / (nNeg + nMasked)
            npolRatio = nNeg / (nNeg + nPos)

        # 2) Not enough flux in unmasked correct-polarity pixels
        fluxRatioTolerance = self.config.fluxPolarityRatio
        if fluxRatio < fluxRatioTolerance:
            self.log.debug("Candidate %d : BAD flux polarity %.2f < %.2f (pos=%.2f neg=%.2f)",
                           source.getId(), fluxRatio, fluxRatioTolerance, fPos, fNeg)
            return False

        # 3) Not enough unmasked pixels of correct polarity
        polarityTolerance = self.config.nPolarityRatio
        if npolRatio < polarityTolerance:
            self.log.debug("Candidate %d : BAD polarity count %.2f < %.2f (pos=%d neg=%d)",
                           source.getId(), npolRatio, polarityTolerance, nPos, nNeg)
            return False

        # 4) Too many masked vs. correct polarity pixels
        maskedTolerance = self.config.nMaskedRatio
        if maskRatio < maskedTolerance:
            self.log.debug("Candidate %d : BAD unmasked count %.2f < %.2f (pos=%d neg=%d mask=%d)",
                           source.getId(), maskRatio, maskedTolerance, nPos, nNeg, nMasked)
            return False

        # 5) Too few unmasked, correct polarity pixels
        ngoodTolerance = self.config.nGoodRatio
        if ngoodRatio < ngoodTolerance:
            self.log.debug("Candidate %d : BAD good pixel count %.2f < %.2f (pos=%d neg=%d tot=%d)",
                           source.getId(), ngoodRatio, ngoodTolerance, nPos, nNeg, nPixels)
            return False

        self.log.debug("Candidate %d : OK flux=%.2f nPos=%d nNeg=%d nTot=%d nDetPos=%d nDetNeg=%d fPos=%.2f fNeg=%2f",
                       source.getId(), flux, nPos, nNeg, nPixels, nDetPos, nDetNeg, fPos, fNeg)
        return True


def main():
    """Main program"""
    options, args = parseOptions()
    (crDiffSourceFile, crDiffExposureFile) = args

    crDiffSources = readSourceSet(crDiffSourceFile)
    crDiffExposure = afwImage.ExposureF(crDiffExposureFile)
    #import pdb; pdb.set_trace()

    analyst = DiaSourceAnalyst()

    expX0 = crDiffExposure.getX0()
    expY0 = crDiffExposure.getY0()
    expX1 = expX0 + crDiffExposure.getWidth() - 1
    expY1 = expY0 + crDiffExposure.getHeight() - 1

    for i in range(crDiffSources.size()):
        crDiffSource = crDiffSources[i]

        # This segfaults; revisit once the stack stabilizes
        #footprint    = crDiffSource.getFootprint()
        #bbox         = footprint.getBBox()

        xAstrom = crDiffSource.getXAstrom()
        yAstrom = crDiffSource.getYAstrom()
        Ixx = max(1.0, crDiffSource.getIxx())
        Iyy = max(1.0, crDiffSource.getIyy())
        x0 = max(expX0, int(xAstrom - scaling * Ixx))
        x1 = min(expX1, int(xAstrom + scaling * Ixx))
        y0 = max(expY0, int(yAstrom - scaling * Iyy))
        y1 = min(expY1, int(yAstrom + scaling * Iyy))
        bbox = afwGeom.Box2I(afwGeom.Point2I(x0, y0),
                             afwGeom.Point2I(x1, y1))
        subExp = afwImage.ExposureF(crDiffExposure, bbox)
        subMi = subExp.getMaskedImage()
        imArr, maArr, varArr = subMi.getArrays()

        if analyst.testSource(crDiffSource, subMi):
            ds9.mtv(subExp, frame=1)
            input('Next: ')
if __name__ == "__main__":
    main()