def MFPBCor(inIm, err, antSize=24.5, minGain=0.05):
"""
Apply primary beam corrections to an ImageMF
WARNING: This routine modifies the input image;
ONLY RUN IT ONCE.
* inIm = Image to be modified
* err = Python Obit Error/message stack
* antSize = Antenna diameter in m.
* minGain = Minimum antenna gain
"""
# Check
if not inIm.ImageIsA():
raise TypeError("input MUST be a Python Obit Image")
# Image info
nterm = inIm.Desc.List.Dict['NTERM'][2][0]
nspec = inIm.Desc.List.Dict['NSPEC'][2][0]
freqs = []
for i in range(1, nspec + 1):
key = 'FREQ%4.4d' % i
freqs.append(inIm.Desc.List.Dict[key][2][0])
# end loop
# Make scratch image for beam
beam = Image.Image("PBeam")
Image.PCloneMem(inIm, beam, err)
OErr.printErrMsg(err, "Error with scratch beam image")
# Loop over planes
for i in range(1, nspec + 1):
# Read plane
plane = [i + nterm, 1, 1, 1, 1]
Image.PGetPlane(inIm, None, plane, err)
OErr.printErrMsg(err, "Error reading image")
# Set frequency for PBCor
d = inIm.Desc.Dict
d['crval'][2] = freqs[i - 1]
inIm.Desc.Dict = d
# Make PB Image
ImageUtil.PPBImage(beam,
beam,
err,
minGain=minGain,
antSize=antSize,
outPlane=plane)
OErr.printErrMsg(err, "Error making PB image")
# Divide
FArray.PDivClip(inIm.FArray, beam.FArray, minGain, inIm.FArray)
# Rewrite plane
Image.PPutPlane(inIm, None, plane, err)
OErr.printErrMsg(err, "Error writing image")
# end loop
# Add history
outHistory = History.History("history", inIm.List, err)
outHistory.Open(History.READWRITE, err)
outHistory.TimeStamp(" Start Obit MFPBCor", err)
outHistory.WriteRec(-1, "MFPBCor" + " antSize = " + str(antSize), err)
outHistory.WriteRec(-1, "MFPBCor" + " minGain = " + str(minGain), err)
outHistory.Close(err)
def crop_pb(image, outimage, err, minlevel=0.15, scratch_dir='/tmp/'):
#Crop the image at the 15% level of the primary beam
wtim = Image.newPFImage("weight", scratch_dir + '/crop_pb.fits', 0, False,
err)
im = Image.newPFImage("orig", image, 0, False, err)
im.Clone(wtim, err)
ImageUtil.PPBImage(im, wtim, err, minGain=minlevel)
#Crop using pyfits
output = pyfits.open(image)
wtim = pyfits.open(scratch_dir + '/crop_pb.fits')
output[0].data[
0, 0] = output[0].data[0, 0] * wtim[0].data[0, 0] / wtim[0].data[0, 0]
output.writeto(outimage, clobber=True)
#cleanup
os.remove(scratch_dir + '/crop_pb.fits')
def pbcorr_obit(image_filename,
output_image,
err,
mingain=0.05,
scratch_dir='/tmp'):
#Load the original image into Obit
im = Image.newPFImage("in", image_filename, 0, True, err)
#Construct an output Obit Image
im_pbcorr = Image.newPFImage("wt", scratch_dir + '/crop_pb.fits', 0, False,
err)
im.Clone(im_pbcorr, err)
#PBCOrrect
#ImageUtil.PPBCorr(im, im, im_pbcorr, err, antSize=12.0, PBmin=0.1)
ImageUtil.PPBImage(im, im_pbcorr, err, minGain=mingain, antSize=13.5)
inimage = pyfits.open(image_filename)
beam = pyfits.open(scratch_dir + '/crop_pb.fits')
pbcorrdata = inimage[0].data / beam[0].data
new_hdu = pyfits.PrimaryHDU(data=pbcorrdata, header=inimage[0].header)
pyfits.HDUList([new_hdu]).writeto(output_image, clobber=True)
im_pbcorr = Image.newPFImage("wt", output_image, 0, False, err)
#cleanup
os.remove(scratch_dir + '/crop_pb.fits')
return im_pbcorr
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
inFile = sys.argv[1]
pntFile = sys.argv[2]
outFile = sys.argv[3]
inDisk = 1
outDisk = 1
# Set data
inImage = Image.newPFImage("Input image", inFile, inDisk, 1, err)
pntImage = Image.newPFImage("Pointing image", pntFile, inDisk, 1, err)
outImage = Image.newPFImage("Output image", outFile, outDisk, 0, err)
Image.PClone(inImage, outImage, err) # Same structure etc.
OErr.printErrMsg(err, "Error initializing")
# Make scratchfile for beam
beam = inImage.Scratch(err)
ImageUtil.PPBImage(pntImage, beam, err,antSize=25.,minGain=0.05)
plane = [1,1,1,1,1]
beam.GetPlane(None,plane,err)
# Multiply
nplane = inImage.Desc.Dict['inaxes'][2]
for iplane in range(0,nplane):
plane = [iplane+1,1,1,1,1]
inImage.GetPlane(None, plane, err)
FArray.PMul(inImage.FArray, beam.FArray, inImage.FArray)
outImage.PutPlane(inImage.FArray, plane, err)
beam.Zap(err)
OErr.printErrMsg(err, "Error correcting image")
# Copy History
