def PMaskCube(inImage, Mask, outImage, err):
"""
Blank inImage where Mask is blanked or 0.0
* inImage = input Image cube
* Mask = 1 plane mask Image
* outImage = Output Image, must be defined.
* err = Python Obit Error/message stack
"""
################################################################
# Checks
if not Image.PIsA(outImage):
print "Actually ",outImage.__class__
raise TypeError,"outImage MUST be a Python Obit Image"
if not Image.PIsA(inImage):
print "Actually ",inImage.__class__
raise TypeError,"inImage MUST be a Python Obit Image"
if not Image.PIsA(Mask):
print "Actually ",Mask.__class__
raise TypeError,"Mask MUST be a Python Obit Image"
if not OErr.OErrIsA(err):
raise TypeError,"err MUST be an OErr"
# Clone output
inImage.Clone(outImage, err)
# Open files
Image.POpen(outImage,Image.WRITEONLY, err)
Image.POpen(inImage, Image.READONLY, err)
Image.POpen(Mask, Image.READONLY, err)
OErr.printErrMsg(err, "Error opening images")
# how many planes?
ndim = inImage.Desc.Dict["naxis"]
inNaxis = inImage.Desc.Dict["inaxes"]
# list of planes to loop over (0-rel)
if (ndim>2) and (inNaxis[2]>0):
planes = range(inNaxis[2])
else:
planes = [0]
# Read Mask plane
Image.PGetPlane (Mask, None, [1,1,1,1,1], err)
OErr.printErrMsg(err, "Error reading mask image")
# Mask where exactly 0.0
FArray.PInClip(Mask.FArray, -1.0e-25, 1.0e-25, FArray.fblank)
# Loop over planes
for iPlane in planes:
doPlane = [iPlane+1,1,1,1,1]
# Get image plane
Image.PGetPlane (inImage, None, doPlane, err)
OErr.printErrMsg(err, "Error reading input image")
# Make sure compatable
if not FArray.PIsCompatable(inImage.FArray, Mask.FArray):
raise RuntimeError,"inImage and Mask incompatable"
# Mask where blanked
FArray.PBlank (inImage.FArray, Mask.FArray, outImage.FArray)
# Write
Image.PPutPlane(outImage, None, doPlane, err)
OErr.printErrMsg(err, "Error Writing blanked image ")
# end loop over planes
# close files
Image.PClose(outImage, err)
Image.PClose(inImage, err)
Image.PClose(Mask, err)
# Write history
inHistory = History.History("history", inImage.List, err)
outHistory = History.History("history", outImage.List, err)
# Copy History
History.PCopy(inHistory, outHistory, err)
outHistory.Open(History.READWRITE, err)
outHistory.TimeStamp(" Start Obit PMaskCube",err)
outHistory.Close(err)
def PWeightImageEq(inImage, factor, SumWtImage, SumWt2, err, minGain=0.1,
iblc=[1,1,1], itrc=[0,0,1], restart=0, hwidth=2, doGPU=False,
planeWt=False, OTFRA=None, OTFDec=None, inWtImage=None,
maxRMS=None, minAccWt=0.15):
"""
Sum an image onto Weighting accumulators using PB corrections
Version for equatorial in/output and no relative rotation
Calculate the weights for an image from the primary beam pattern
And accumulate into the correct locations in the accumulation images.
* inImage = Image to be accumulated
* factor = Additional multiplication factor, normally 1.0
>0 => use the factor/RMS of each image plane
* SumWtImage = First output image, must be defined (i.e. files named)
but not fully created.
* SumWt2 = Second output image, like SumWtImage
* err = Python Obit Error/message stack
* minGain = minimum allowed gain (lower values blanked).
* iblc = BLC in plane to start selection
* itrc = TRC in plane to end selection
* restart = restart channel no. 0-rel
* hwidth = half width of interpolation kernal [1-4] default 2
* doGPU = If true and GPU enables, use a GPU for the interpolation.
* NB: routine will fail if GPU is not enabled.
* planeWt = if True generate weight image per input plane
* OTFoffsets = if >1 then make beam using multiple pointing offsets
"Aussie mode" OTF. must also go=ive OTFRA, OTFDec
* OTFRA = Array of RA offsets in deg not corrected for Declination
* OTFDec = Array of Declinations offsets in deg, same size as OTFRA
* inWtImage = Beam (weight) image to use if not None
MUST have the same size as inImage
* maxRMS = if given, the maximum RMS allowed
* minAccWt = min. acceptable max. weight, otherwise ignore
"""
################################################################
# Checks
if not Image.PIsA(inImage):
print "Actually ",inImage.__class__
raise TypeError,"inImage MUST be a Python Obit Image"
if not Image.PIsA(SumWtImage):
print "Actually ",SumWtImage.__class__
raise TypeError,"SumWtImage MUST be a Python Obit Image"
if not Image.PIsA(SumWt2):
print "Actually ",SumWt2.__class__
raise TypeError,"SumWt2 MUST be a Python Obit Image"
if not OErr.OErrIsA(err):
raise TypeError,"err MUST be an OErr"
#
t0 = os.times()[4] # Initial time
haveWtImage = inWtImage != None # Weight image given
# Set BLC,TRC
inImage.List.set("BLC",[iblc[0], iblc[1],1,1,1,1,1])
inImage.List.set("TRC",[itrc[0], itrc[1],0,0,0,0,0])
# Open accumulation files
Image.POpen(inImage, Image.READONLY, err) # pythpn gets confused
Image.POpen(SumWtImage, Image.READWRITE, err)
Image.POpen(SumWt2, Image.READWRITE, err)
# Get output descriptor to see how many planes
outDesc = Image.PGetDesc(SumWtImage)
outDescDict = ImageDesc.PGetDict(outDesc)
outNaxis = outDescDict["inaxes"]
print "Accumulation naxis",outNaxis
# Get input descriptor to see how many planes
inDesc = Image.PGetDesc(inImage)
inDescDict = ImageDesc.PGetDict(inDesc)
ndim = inDescDict["naxis"]
inNaxis = inDescDict["inaxes"]
finterp = None # GPU not yet enabled
# Range of planes
bpln = max (1,iblc[2]);
epln = min (inNaxis[2], itrc[2])
if epln<bpln:
epln = inNaxis[2]
npln = epln-bpln+1
# Test if compatible
if npln < outNaxis[2]:
print "input has",npln,"planes selected and output has",outNaxis[2]
raise RuntimeError,"input image has too few planes "
if (ndim>0) and (inNaxis[2]>1): # list of 0-rel planes to loop over
planes = range(bpln+restart-1,bpln+npln-1)
else:
planes = [0]
#
if inWtImage:
inWtImage.List.set("BLC",[iblc[0], iblc[1],1,1,1,1,1])
inWtImage.List.set("TRC",[itrc[0], itrc[1],0,0,0,0,0])
inWtImage.Open(Image.READONLY,err) # Open/close to update
inWtImage.Close(err)
XPixelImage = None; YPixelImage = None; InterpWtImage = None;InterpWt = None
InterpWtWt = None; WtImage = None
# Loop over planes
for iPlane in planes:
doPlane = [iPlane+1,1,1,1,1] # Input plane
outPlane = [iPlane+2-bpln,1,1,1,1] # output plane
if not (iPlane%20):
print "At plane", iPlane+1,'t=%6.1f sec'%(os.times()[4]-t0)
# Get image
inImage.List.set("BLC",[iblc[0], iblc[1],1,1,1,1,1])
inImage.List.set("TRC",[itrc[0], itrc[1],0,0,0,0,0])
Image.PGetPlane (inImage, None, doPlane, err)
OErr.printErrMsg(err, "Error reading image "+str(iPlane)+" for "+Image.PGetName(inImage))
#
# Make weight image if needed, first pass or planeWt
if WtImage == None:
WtImage = Image.Image("WeightImage")
Image.PCloneMem(inImage, WtImage, err)
# The interpolated versions
if not InterpWtImage:
InterpWtImage = Image.Image("InterpWtImage")
Image.PClone2(inImage, SumWtImage, InterpWtImage, err)
# input x, y pixels for output
if (not XPixelImage) or (not YPixelImage):
XPixelImage = Image.Image("XPixelImage")
YPixelImage = Image.Image("YPixelImage")
Image.PClone2(inImage, SumWtImage, XPixelImage, err)
Image.PClone2(inImage, SumWtImage, YPixelImage, err)
ImageUtil.PGetXYPixels(WtImage, InterpWtImage, XPixelImage, YPixelImage, err)
# Special weighting?
if factor<0.0:
RMS = inImage.FArray.RMS
fact = abs(factor)/RMS
else:
fact = factor
if planeWt:
pln = [iPlane+1,1,1,1,1]
else:
pln = [max(1,inNaxis[2]/2),1,1,1,1]
if haveWtImage:
# Beam provided, extract relevant plane to a memory resident WtImage
OErr.printErrMsg(err, "Error reading wt image "+str(iPlane)+" for "+
Image.PGetName(inWtImage))
# Interpolate to WtImage
ImageUtil.PInterpolateImage(inWtImage, WtImage, err, \
inPlane=doPlane, hwidth=hwidth, finterp=finterp)
OErr.printErrMsg(err, "Error interpolating wt plane "+str(doPlane))
elif planeWt or (iPlane==0):
# Normal or OTF Beam?
if (OTFRA==None):
ImageUtil.PPBImage(inImage, WtImage, err, minGain, outPlane=pln)
pass
else:
ImageUtil.POTFBeam (inImage, WtImage, OTFRA, OTFDec, err, minGain, outPlane=pln)
OErr.printErrMsg(err, "Error making weight image for "+Image.PGetName(inImage))
# Check maximum weight for first plane
if iPlane==0:
pos = [0,0]
maxWt = FArray.PMax(WtImage.FArray,pos)
print "Maximum weight",maxWt
if maxWt<minAccWt:
print "Less than minAccWt",minAccWt,"skipping"
break
# Interpolated weight image
if not InterpWt:
InterpWt = Image.Image("InterpWt")
Image.PClone2(inImage, SumWtImage, InterpWt, err)
# Is GPU interpolation requested?
if doGPU:
finterp = GPUFInterpolate.PCreate("GPUinterp", WtImage.FArray,
XPixelImage.FArray, YPixelImage.FArray,
hwidth, err)
OErr.printErrMsg(err, "Creating GPU FInterpolator")
InterpWt.Desc.Dict['inaxes'], WtImage.Desc.Dict['inaxes']
ImageUtil.PInterpolateImage(WtImage, InterpWt, err, \
XPix=XPixelImage, YPix=YPixelImage,
hwidth=hwidth, finterp=finterp)
OErr.printErrMsg(err, "Error interpolating wt*wt "+Image.PGetName(inImage))
# Interpolated weight image Squared
if not InterpWtWt:
InterpWtWt = Image.Image("InterpWtWt")
Image.PClone2(inImage, SumWtImage, InterpWtWt, err)
# Determine alignment
inDesc = Image.PGetDesc(InterpWtImage) # get descriptors
inDescDict = ImageDesc.PGetDict(inDesc)
outDesc = Image.PGetDesc(SumWtImage)
outDescDict = ImageDesc.PGetDict(outDesc)
naxis = inDescDict["inaxes"] # find input center pixel in output
pos1 = [int(naxis[0]*0.5+0.5), int(naxis[1]*0.5+0.5)]
xpos1 = [float(pos1[0]),float(pos1[1])]
xpos2 = ImageDesc.PCvtPixel (inDesc, xpos1, outDesc, err)
pos2 = [int(xpos2[0]+0.5), int(xpos2[1]+0.5)]
# Is GPU interpolation requested?
if doGPU:
del finterp
finterp = GPUFInterpolate.PCreate("GPUinterp", inImage.FArray,
XPixelImage.FArray, YPixelImage.FArray,
hwidth, err)
OErr.printErrMsg(err, "Creating GPU FInterpolator")
# End init wt image
# Special weighting or editing?
if (factor<0.0) or maxRMS:
# Get image
Image.PGetPlane (inImage, None, doPlane, err)
OErr.printErrMsg(err, "Error reading image "+str(iPlane)+" for "+Image.PGetName(inImage))
RMS = inImage.FArray.RMS
# This plane acceptable?
if maxRMS and ((RMS>maxRMS) or (RMS<=0.0)):
#print 'drop plane',doPlane[0],'RMS',RMS
continue
if (factor<0.0):
fact = abs(factor)/RMS
else:
fact = factor
if not (iPlane%20):
print "Factor",fact, "plane",iPlane,"RMS",RMS
else:
fact = factor
# Interpolate image plane
ImageUtil.PInterpolateImage(inImage, InterpWtImage, err, \
inPlane=doPlane, XPix=XPixelImage, YPix=YPixelImage,
hwidth=hwidth, finterp=finterp)
OErr.printErrMsg(err, "Error interpolating plane "+str(doPlane))
# Interpolated image times beam
FArray.PMul(InterpWtImage.FArray, InterpWt.FArray, InterpWtImage.FArray)
#
# Read accumulation image planes
Image.PGetPlane(SumWtImage, None, outPlane, err)
OErr.printErrMsg(err, "Error reading accumulation image ")
#
# Accumulate
FArray.PShiftAdd (SumWtImage.FArray, pos2, InterpWtImage.FArray, pos1, fact, SumWtImage.FArray)
Image.PPutPlane(SumWtImage, None, outPlane, err)
OErr.printErrMsg(err, "Error writing accumulation image ")
# Square weight image
Image.PGetPlane(SumWt2, None, outPlane, err)
FArray.PMul(InterpWt.FArray, InterpWt.FArray, InterpWtWt.FArray)
# Blank weight whereever image is blank or zero
FArray.PInClip(InterpWt.FArray, -1.0e-20, 1.0e-20, FArray.PGetBlank())
# Blank weight squared where image * Wt is blanked
FArray.PBlank (InterpWtWt.FArray, InterpWt.FArray, InterpWtWt.FArray);
# Accumulate Wt*Wt
FArray.PShiftAdd (SumWt2.FArray, pos2, InterpWtWt.FArray,pos1, fact, SumWt2.FArray)
#
# Write output
Image.PPutPlane(SumWt2, None, outPlane, err)
OErr.printErrMsg(err, "Error writing accumulation image ")
# Cleanup if doing a weight image per plane (continuum)
if planeWt:
del WtImage, XPixelImage, YPixelImage;
WtImage = None;XPixelImage=None; YPixelImage=None;
# end loop over planes
# close output
Image.PClose(inImage, err)
Image.PClose(SumWtImage, err)
Image.PClose(SumWt2, err)
del XPixelImage, YPixelImage, InterpWtImage, InterpWtWt,
if WtImage:
del WtImage; WtImage = None
if finterp!=None:
del finterp
def PAccumIxWt(im, wt, factor, accum, accumwt, err):
"""
Accumulate im * wt into accum
Used to accumulate images which don't need PB corrections
and have a weight image.
* im = image to accumulate
* wt = weight image corresponding to accum
* factor = Additional multiplication factor, normally 1.0
* accum = image into which to accumulate im*wt
* accumwt = image into which to accumulate wt
* err = Python Obit Error/message stack
"""
################################################################
# Checks
if not Image.PIsA(im):
print "Actually ",im.__class__
raise TypeError,"im MUST be a Python Obit Image"
if not Image.PIsA(wt):
print "Actually ",wt.__class__
raise TypeError,"wt MUST be a Python Obit Image"
if not Image.PIsA(accum):
print "Actually ",accum.__class__
raise TypeError,"accum MUST be a Python Obit Image"
#
# Open files
#Image.POpen(im, 1, err)
Image.POpen(accum, Image.READWRITE, err)
Image.POpen(accumwt, Image.READWRITE, err)
# Get output descriptor to see how many planes
outDesc = accum.Desc
outDescDict = outDesc.Dict
outNaxis = outDescDict["inaxes"]
print "Accumulation naxis",outNaxis
# Get input descriptor to see how many planes
inDesc = im.Desc
inDescDict = inDesc.Dict
ndim = inDescDict["naxis"]
inNaxis = inDescDict["inaxes"]
#print "debug input naxis is ",inNaxis
# Test if compatible
if inNaxis[2] < outNaxis[2]:
print "input has",inNaxis[2],"planes and output",outNaxis[2]
raise RuntimeError,"input image has too few planes "
if (ndim>0) and (inNaxis[2]>0): # list of planes to loop over (0-rel)
planes = range(inNaxis[2])
else:
planes = [0]
#
# Loop over planes
for iPlane in planes:
doPlane = [iPlane+1,1,1,1,1]
# Get image
Image.PGetPlane (im, None, doPlane, err)
#OErr.printErrMsg(err, "Error reading image for "+Image.PGetName(im))
imArray = im.FArray
# Get Weight
Image.PGetPlane (wt, None, doPlane, err)
#OErr.printErrMsg(err, "Error reading image for "+Image.PGetName(wt))
WtArray = wt.FArray
#
# Make image*Wt memory resident image
ImageWt = Image.Image("ImageXwt")
Image.PCloneMem(im, ImageWt, err)
ImageWtArray = ImageWt.FArray
FArray.PMul(imArray, WtArray, ImageWtArray);
#
# Now the interpolated versions to be summed to the accumulation arrays
InterpWtImage = Image.Image("InterpWtImage")
Image.PClone2(im, accum, InterpWtImage, err)
ImageUtil.PInterpolateImage(ImageWt, InterpWtImage, err)
#OErr.printErrMsg(err, "Error interpolating image "+Image.PGetName(im))
InterpWt = Image.Image("InterpWt")
Image.PClone2(im, accum, InterpWt, err)
ImageUtil.PInterpolateImage(wt, InterpWt, err)
#OErr.printErrMsg(err, "Error interpolating wt "+Image.PGetName(im))
#
# Read accumulation image plane
Image.PGetPlane(accum, None, doPlane, err)
Image.PGetPlane(accumwt, None, doPlane, err)
#OErr.printErrMsg(err, "Error reading accumulation image ")
#
# Determine alignment
inDesc = InterpWtImage.Desc
inDescDict = inDesc.Dict
outDesc = accum.Desc
outDescDict = outDesc.Dict
naxis = inDescDict["inaxes"] # find input center pixel in output
pos1 = [int(naxis[0]*0.5+0.5), int(naxis[1]*0.5+0.5)]
xpos1 = [float(pos1[0]),float(pos1[1])]
xpos2 = ImageDesc.PCvtPixel (inDesc, xpos1, outDesc, err)
#OErr.printErrMsg(err, "Error converting pixel locations for "+Image.PGetName(im))
pos2 = [int(xpos2[0]+0.5), int(xpos2[1]+0.5)]
#
# Accumulate
accumArray = accum.FArray
InterpWtArray = InterpWtImage.FArray
FArray.PShiftAdd (accumArray, pos2, InterpWtArray, pos1, factor, accumArray)
accumwtArray = accumwt.FArray
InterpWtWtArray = InterpWt.FArray
# Blank weight whereever image is blank or zero
FArray.PInClip(InterpWtArray, -1.0e-20, 1.0e-20, FArray.PGetBlank())
FArray.PBlank (InterpWtWtArray, InterpWtArray, InterpWtWtArray);
FArray.PShiftAdd (accumwtArray, pos2, InterpWtWtArray,pos1, factor, accumwtArray)
#
# Write output
Image.PPutPlane(accum, None, doPlane, err)
Image.PPutPlane(accumwt, None, doPlane, err)
#OErr.printErrMsg(err, "Error writing accumulation image ")
# Cleanup,
del accumArray, accumwtArray, InterpWtArray, InterpWtWtArray, ImageWtArray, WtArray, imArray
# end loop over planes
# close output
#Image.PClose(im, err)
Image.PClose(accum, err)
Image.PClose(accumwt, err)
xpix = XPixIm.FArray
ypix = YPixIm.FArray
# Set interpolator to input image
FInterpolate.PSetDesc(fi, x.Desc)
FInterpolate.PReplace(fi, inArr)
# Interpolate
for ix in range(0, ncell):
for iy in range(0, ncell):
pos = [space * (ix - half), space * (iy - half)]
pix = ImageDesc.PGetPixel(x.Desc, pos, err)
val = FInterpolate.PPixel(fi, pix, err)
work.set(val, ix, iy)
# end interpolation loops
# Accumulate weight image, zero where image blanked
FArray.PFill(work2, weight[ires])
FArray.PBlank(work2, work, work2)
FArray.PDeblank(work2, 0.0) # Replace any blanking with 0.0
FArray.PAdd(accW, work2, accW)
# Image * wt
FArray.PDeblank(work, 0.0) # Replace any blanking with 0.0
FArray.PSMul(work, weight[ires])
# Accumulate image*wt
FArray.PAdd(accWI, work, accWI)
ires += 1
# Next resolution
# end resolution loop
FArray.PDiv(accWI, accW, accWI) # Normalize to accWI
# Write output
outIm.PutPlane(accWI, oplane, err)
iplane[0] += 1 # Next input plane