def main(rootDir, visit, ccd, filter=None,
frame=1, title="", scale="zscale", zoom="to fit", trans=60,
useEllipse=False, maskOnly=False):
if ccd.find(",") < 0:
ccd = int(ccd)
pipeVersion = dafPersist.eupsVersions.EupsVersions().versions['hscPipe']
if StrictVersion(pipeVersion) >= StrictVersion('3.9.0'):
coaddData = "deepCoadd_calexp"
coaddCat = "meas"
else:
coaddData = "deepCoadd"
coaddCat = "src"
print "Read in %s image"%coaddData
# make a butler and specify your dataId
butler = dafPersist.Butler(rootDir)
if filter:
dataId = {'tract': visit, 'patch':ccd, 'filter': filter}
exposure = butler.get(coaddData, dataId, immediate=True)
butlerTarget='deepCoadd_'
sources = butler.get(butlerTarget + coaddCat, dataId)
else:
dataId = {'visit': visit, 'ccd':ccd}
exposure = butler.get("calexp", dataId, immediate=True)
butlerTarget=""
sources = butler.get(butlerTarget + 'src', dataId)
# put the settings in a dict object and call ds9.mtv()
settings = {'scale':scale, 'zoom': zoom, 'mask' : 'transparency %d' %(trans)}
ds9.setMaskPlaneColor('FAKE', color=ds9.CYAN)
if not maskOnly:
ds9.mtv(exposure, frame=frame, title=title, settings=settings)
else:
msk = exposure.getMaskedImage().getMask()
msk &= msk.getPlaneBitMask('FAKE')
ds9.mtv(msk, frame=frame, title=title, settings=settings)
with ds9.Buffering():
print len(sources)
x0, y0 = exposure.getXY0()
print x0, y0
for i,source in enumerate(sources):
color = ds9.RED
size = 5.0
if useEllipse:
# show an ellipse symbol
symbol = "@:{ixx},{ixy},{iyy}".format(ixx=source.getIxx(),
ixy=source.getIxy(),
iyy=source.getIyy())
else:
# just a simple point (symbols +, x, *, o are all accepted)
symbol = "o"
ds9.dot(symbol, source.getX()-x0, source.getY()-y0, ctype=color,
size=size, frame=frame, silent=True)
def subtractCrosstalkYagi(mi, coeffs1List, coeffs2List, gainsPreampSig, minPixelToMask=45000,
crosstalkStr="CROSSTALK"):
"""Subtract the crosstalk from MaskedImage mi given a set of coefficients
based on procedure presented in Yagi et al. 2012, PASP in publication; arXiv:1210.8212
The pixels affected by signal over minPixelToMask have the crosstalkStr bit set
"""
####sctrl = afwMath.StatisticsControl()
####sctrl.setAndMask(mi.getMask().getPlaneBitMask("DETECTED"))
####bkgd = afwMath.makeStatistics(mi, afwMath.MEDIAN, sctrl).getValue()
#
# These are the pixels that are bright enough to cause crosstalk (more precisely,
# the ones that we label as causing crosstalk; in reality all pixels cause crosstalk)
#
if True:
tempStr = "TEMP" # mask plane used to record the bright pixels that we need to mask
mi.getMask().addMaskPlane(tempStr)
fs = afwDetect.FootprintSet(mi, afwDetect.Threshold(minPixelToMask), tempStr)
mi.getMask().addMaskPlane(crosstalkStr)
ds9.setMaskPlaneColor(crosstalkStr, ds9.MAGENTA)
fs.setMask(mi.getMask(), crosstalkStr) # the crosstalkStr bit will now be set
# whenever we subtract crosstalk
crosstalk = mi.getMask().getPlaneBitMask(crosstalkStr)
if True:
# This python implementation is fairly fast
image = mi.getImage()
xtalk = afwImage.ImageF(image.getDimensions())
xtalk.set(0)
for i in range(4):
xAmp, xOff = getAmplifier(xtalk, i, i)
for j in range(4):
if i == j:
continue
gainRatio = gainsPreampSig[j] / gainsPreampSig[i]
jAmp, jOff = getAmplifier(image, j, i)
xAmp.scaledPlus(gainRatio*coeffs1List[i][j], jAmp)
xOff.scaledPlus(gainRatio*coeffs2List[i][j], jOff)
image -= xtalk
else:
nAmp = 4
subtractCrosstalk(mi, nAmp, coeffs1List, coeffs2List, gainsPreampSig)
#
# Clear the crosstalkStr bit in the original bright pixels, where tempStr is set
#
msk = mi.getMask()
temp = msk.getPlaneBitMask(tempStr)
xtalk_temp = crosstalk | temp
np_msk = msk.getArray()
np_msk[np.where(np.bitwise_and(np_msk, xtalk_temp) == xtalk_temp)] &= ~crosstalk
try:
msk.removeAndClearMaskPlane(tempStr, True) # added in afw #1853
except AttributeError:
ds9.setMaskPlaneVisibility(tempStr, False)
def subtractCrosstalkYagi(mi, coeffs1List, coeffs2List, gainsPreampSig, minPixelToMask=45000, crosstalkStr="CROSSTALK"):
"""Subtract the crosstalk from MaskedImage mi given a set of coefficients
based on procedure presented in Yagi et al. 2012, PASP in publication; arXiv:1210.8212
The pixels affected by signal over minPixelToMask have the crosstalkStr bit set
"""
####sctrl = afwMath.StatisticsControl()
####sctrl.setAndMask(mi.getMask().getPlaneBitMask("DETECTED"))
####bkgd = afwMath.makeStatistics(mi, afwMath.MEDIAN, sctrl).getValue()
#
# These are the pixels that are bright enough to cause crosstalk (more precisely,
# the ones that we label as causing crosstalk; in reality all pixels cause crosstalk)
#
if True:
tempStr = "TEMP" # mask plane used to record the bright pixels that we need to mask
mi.getMask().addMaskPlane(tempStr)
fs = afwDetect.FootprintSet(mi, afwDetect.Threshold(minPixelToMask), tempStr)
mi.getMask().addMaskPlane(crosstalkStr)
ds9.setMaskPlaneColor(crosstalkStr, ds9.MAGENTA)
fs.setMask(mi.getMask(), crosstalkStr) # the crosstalkStr bit will now be set whenever we subtract crosstalk
crosstalk = mi.getMask().getPlaneBitMask(crosstalkStr)
if True:
# This python implementation is fairly fast
image = mi.getImage()
xtalk = afwImage.ImageF(image.getDimensions())
xtalk.set(0)
for i in range(4):
xAmp, xOff = getAmplifier(xtalk, i, i)
for j in range(4):
if i == j:
continue
gainRatio = gainsPreampSig[j] / gainsPreampSig[i]
jAmp, jOff = getAmplifier(image, j, i)
xAmp.scaledPlus(gainRatio*coeffs1List[i][j], jAmp)
xOff.scaledPlus(gainRatio*coeffs2List[i][j], jOff)
image -= xtalk
else:
nAmp = 4
subaruLib.subtractCrosstalk(mi, nAmp, coeffs1List, coeffs2List, gainsPreampSig)
#
# Clear the crosstalkStr bit in the original bright pixels, where tempStr is set
#
msk = mi.getMask()
temp = msk.getPlaneBitMask(tempStr)
xtalk_temp = crosstalk | temp
np_msk = msk.getArray()
np_msk[np.where(np.bitwise_and(np_msk, xtalk_temp) == xtalk_temp)] &= ~crosstalk
try:
msk.removeAndClearMaskPlane(tempStr, True) # added in afw #1853
except AttributeError:
ds9.setMaskPlaneVisibility(tempStr, False)
def testTwoDisplays(self):
"""Test that we can do things with two frames"""
exp = afwImage.ExposureF(300, 350)
for frame in (0, 1):
ds9.setMaskTransparency(50, frame=frame)
if frame == 1:
ds9.setMaskPlaneColor("CROSSTALK", "ignore", frame=frame)
ds9.mtv(exp, title="parent", frame=frame)
ds9.erase(frame=frame)
ds9.dot('o', 205, 180, size=6, ctype=ds9.RED, frame=frame)
def testTwoDisplays(self):
"""Test that we can do things with two frames"""
exp = afwImage.ExposureF(300, 350)
for frame in (0, 1):
ds9.setMaskTransparency(50, frame=frame)
if frame == 1:
ds9.setMaskPlaneColor("CROSSTALK", "ignore", frame=frame)
ds9.mtv(exp, title="parent", frame=frame)
ds9.erase(frame=frame)
ds9.dot('o', 205, 180, size=6, ctype=ds9.RED, frame=frame)
def testMaskPlanes(self):
"""Test basic image display"""
ds9.setMaskTransparency(50)
ds9.setMaskPlaneColor("CROSSTALK", "orange")
def disp_turnOffAllMasks(exceptFor=None):
mpDict = afwImage.Mask().getMaskPlaneDict()
for plane in mpDict.keys():
if plane in exceptFor:
continue
ds9.setMaskPlaneColor(plane, afwDisplay.IGNORE)
def detectFootprints(exposure,
positiveThreshold,
psf=None,
negativeThreshold=None,
npixMin=1):
"""Detect sources above positiveThreshold in the provided exposure returning the
detectionSet. Only sources with at least npixMin are considered
If negativeThreshold, return a pair of detectionSets, dsPositive, dsNegative
"""
assert positiveThreshold or negativeThreshold # or both
if positiveThreshold:
positiveThreshold = afwDetection.Threshold(positiveThreshold)
if negativeThreshold:
negativeThreshold = afwDetection.Threshold(negativeThreshold)
#
# Unpack variables
#
maskedImage = exposure.getMaskedImage()
if not psf: # no need to convolve if we don't know the PSF
convolvedImage = maskedImage
goodBBox = maskedImage.getBBox()
else:
convolvedImage = maskedImage.Factory(maskedImage.getBBox())
if display:
ds9.mtv(maskedImage)
#
# Smooth the Image
#
psf.convolve(convolvedImage, maskedImage,
convolvedImage.getMask().getMaskPlane("EDGE"))
#
# Only search psf-smooth part of frame
#
goodBBox = psf.getKernel().shrinkBBox(maskedImage.getBBox())
middle = convolvedImage.Factory(convolvedImage, goodBBox)
dsNegative = None
if negativeThreshold != None:
# detect negative sources
dsNegative = afwDetection.makeDetectionSet(middle, negativeThreshold,
"DETECTED_NEGATIVE",
npixMin)
if not ds9.getMaskPlaneColor("DETECTED_NEGATIVE"):
ds9.setMaskPlaneColor("DETECTED_NEGATIVE", ds9.CYAN)
dsPositive = None
if positiveThreshold != None:
dsPositive = afwDetection.makeFootprintSet(middle, positiveThreshold,
"DETECTED", npixMin)
#
# ds only searched the middle but it belongs to the entire MaskedImage
#
dsPositive.setRegion(maskedImage.getBBox())
if dsNegative:
dsNegative.setRegion(maskedImage.getBBox())
#
# We want to grow the detections into the edge by at least one pixel so that it sees the EDGE bit
#
grow, isotropic = 1, False
dsPositive = afwDetection.FootprintSetF(dsPositive, grow, isotropic)
dsPositive.setMask(maskedImage.getMask(), "DETECTED")
if dsNegative:
dsNegative = afwDetection.FootprintSetF(dsNegative, grow, isotropic)
dsNegative.setMask(maskedImage.getMask(), "DETECTED_NEGATIVE")
#
# clean up
#
del middle
if negativeThreshold:
if positiveThreshold:
return dsPositive, dsNegative
return dsPositive, dsNegative
else:
return dsPositive
def testMaskPlanes(self):
"""Test basic image display"""
ds9.setMaskTransparency(50)
ds9.setMaskPlaneColor("CROSSTALK", "orange")
def detectFootprints(exposure, positiveThreshold, psf=None, negativeThreshold=None, npixMin=1):
"""Detect sources above positiveThreshold in the provided exposure returning the
detectionSet. Only sources with at least npixMin are considered
If negativeThreshold, return a pair of detectionSets, dsPositive, dsNegative
"""
assert positiveThreshold or negativeThreshold # or both
if positiveThreshold:
positiveThreshold = afwDetection.Threshold(positiveThreshold)
if negativeThreshold:
negativeThreshold = afwDetection.Threshold(negativeThreshold)
#
# Unpack variables
#
maskedImage = exposure.getMaskedImage()
if not psf: # no need to convolve if we don't know the PSF
convolvedImage = maskedImage
goodBBox = maskedImage.getBBox()
else:
convolvedImage = maskedImage.Factory(maskedImage.getBBox())
if display:
ds9.mtv(maskedImage)
#
# Smooth the Image
#
psf.convolve(convolvedImage,
maskedImage,
convolvedImage.getMask().getMaskPlane("EDGE"))
#
# Only search psf-smooth part of frame
#
goodBBox = psf.getKernel().shrinkBBox(maskedImage.getBBox())
middle = convolvedImage.Factory(convolvedImage, goodBBox)
dsNegative = None
if negativeThreshold != None:
#detect negative sources
dsNegative = afwDetection.makeDetectionSet(middle, negativeThreshold, "DETECTED_NEGATIVE", npixMin)
if not ds9.getMaskPlaneColor("DETECTED_NEGATIVE"):
ds9.setMaskPlaneColor("DETECTED_NEGATIVE", ds9.CYAN)
dsPositive = None
if positiveThreshold != None:
dsPositive = afwDetection.makeFootprintSet(middle, positiveThreshold, "DETECTED", npixMin)
#
# ds only searched the middle but it belongs to the entire MaskedImage
#
dsPositive.setRegion(maskedImage.getBBox())
if dsNegative:
dsNegative.setRegion(maskedImage.getBBox())
#
# We want to grow the detections into the edge by at least one pixel so that it sees the EDGE bit
#
grow, isotropic = 1, False
dsPositive = afwDetection.FootprintSetF(dsPositive, grow, isotropic)
dsPositive.setMask(maskedImage.getMask(), "DETECTED")
if dsNegative:
dsNegative = afwDetection.FootprintSetF(dsNegative, grow, isotropic)
dsNegative.setMask(maskedImage.getMask(), "DETECTED_NEGATIVE")
#
# clean up
#
del middle
if negativeThreshold:
if positiveThreshold:
return dsPositive, dsNegative
return dsPositive, dsNegative
else:
return dsPositive
