def PCVel (inUV, outUV, RestFreq, err, scratch=False, \
VLSR=0.0, refDate="0000-00-00", refChan=-9999.):
""" Doppler correct a UV data set
inUV = Input UV data, any calibration/editing/selection parameters
should be entered on the List member.
outUV = Output UV data, should be defined but not instantiated
if not scratch
RestFreq = Rest Frequency (GHz)
err = Obit error/message object
scratch = True if output a scratch file (destroyed on object deletion)
VLSR = desired center LSR velocity (km/s)
refDate = reference date for reference channel as 'yyyy-mm-dd'
defaults to observation date.
refChan = reference channel (-9999=> compute)
"""
################################################################
# Checks
if not UV.PIsA(inUV):
raise TypeError, "inUV MUST be a Python ObitUV"
if not UV.PIsA(outUV):
raise TypeError, "outUV MUST be a Python ObitUV"
#
if scratch:
lscratch = 1
else:
lscratch = 0
# set parameters
info = inUV.List
info.set("RestFreq", RestFreq * 1.0e9, ttype="double")
info.set("VelLSR", VLSR * 1000)
info.set("JDref", UVDesc.PDate2JD(refDate), ttype="double")
info.set("refChan", refChan)
# Correct data
Obit.DopplerCVel(inUV.me, lscratch, outUV.me, err.me)
def UVAddSource(inUV, outUV, err):
"""
Add a Source table to a UV data
Source information is derived from the UV descriptor and a Source
random parameter added if needed.
* inUV = input Obit UV object
* outUV = output Obit UV object, defined but not instantiated
Onlyt really works for AIPS
* err = Obit error/message stack
"""
################################################################
# Checks
if not UV.PIsA(inUV):
raise TypeError, "inUV MUST be a Python Obit UV"
if not UV.PIsA(outUV):
raise TypeError, "outUV MUST be a defined Python Obit UV"
# Patch UV Descriptor
DescAddSource(inUV, outUV, err)
OErr.printErrMsg(err, "Error updating Descriptor")
CreateSU(inUV, outUV, err)
OErr.printErrMsg(err, "Error creating SU Table")
# Copy data
CopyData(inUV, outUV, err)
# Update
# outUV.UpdateDesc(err)
outUV.Header(err) # show results
OErr.printErrMsg(err, "Error copying")
def PCreate(name, inUV, residUV, outUV, input=RFIXizeInput):
""" Create the parameters and underlying structures of a UVRFIXize.
Returns UVRFIXize created.
name = Name to be given to object
Most control parameters are in InfoList member
inUV = Input Python uv data to be corrected
residUV = Input Python residual uv data
outUV = Output Python uv data to be written
err = Python Obit Error/message stack
input = control parameters:
solInt = Counter rotated SN table interval [def 1 min]
doInvert = If True invert solution [def False]
timeInt = Data integration time in sec [def 10 sec]
timeAvg = Time interval (min) over which to average residual.
minRot = Min. fringe rotation (turns) in an integration,
data with smaller values flagged if > minRFI
Only reduce this if a very good model has been
subtracted to make the residual data.
maxRot = Max. fringe rotation (turns) in an integration
to estimate RFI
minRFI = Minimum RFI amplitude to subtract
"""
################################################################
# Checks
if not UV.PIsA(inUV):
raise TypeError("inUV MUST be a Python Obit UV")
if not UV.PIsA(residUV):
raise TypeError("residUV MUST be a Python Obit UV")
if not UV.PIsA(outUV):
raise TypeError("outUV MUST be a Python Obit UV")
#
# Create
out = UVRFIXize(name)
out.me = Obit.UVRFIXizeCreate(name, inUV.me, residUV.me, outUV.me)
# Set RFIXize control values on out
inInfo = PGetList(out) #
dim = [1, 1, 1, 1, 1]
# Set control values on RFIXize
InfoList.PAlwaysPutFloat(inInfo, "solInt", dim, [input["solInt"]])
InfoList.PAlwaysPutBoolean(inInfo, "doInvert", dim, [input["doInvert"]])
InfoList.PAlwaysPutFloat(inInfo, "timeInt", dim, [input["timeInt"]])
InfoList.PAlwaysPutFloat(inInfo, "timeAvg", dim, [input["timeAvg"]])
InfoList.PAlwaysPutFloat(inInfo, "minRFI", dim, [input["minRFI"]])
InfoList.PAlwaysPutFloat(inInfo, "minRot", dim, [input["minRot"]])
InfoList.PAlwaysPutFloat(inInfo, "maxRot", dim, [input["maxRot"]])
#
return out
def PInvertSN (SNTab, outUV, outVer, doRepl, err):
""" Invert the calibration in an SN table
Routine to reverse the effects of the calibration in the
input SN table and create a new SN table on outUV
Returns new SN table
SNTab = Input Python AIPS SN Table to invert
outUV = output UV data to which to attach the new SN table
outVer = Output SN table version number, 0=> create new
doRepl = If True, replace failed solutions with (1,0)
err = Python Obit Error/message stack
"""
################################################################
# Checks
if not Table.PIsA(SNTab):
raise TypeError("SNTab MUST be a Python Obit Table")
if not UV.PIsA(outUV):
raise TypeError('outUV Must be UV data ')
if not OErr.OErrIsA(err):
raise TypeError("err MUST be an OErr")
#
# Create output
outSN = Table.Table("None")
# invert table
outSN.me = Obit.SNInvert (SNTab.me, outUV.me, outVer, doRepl, err.me)
if err.isErr:
printErrMsg(err, "Error inverting solutions")
return outSN
def PReimage (inCleanVis, uvdata, err):
"""
See if an image needs to be remade
See if an image needs to be remade because a source which exceeds
the flux threshold is not centered (as determined by moments)
on the reference pixel (within toler pixel).
A new (96x96) field is added centered on the offending source and a negative
clean window added to the position of the source in its original window.
Avoid duplicates of the same source and ensure that all occurances of this
source in any exant field has a negative clean window added.
Multiple centering sources per facet are allowed
A boolean entry "autoCenField" with value True is added to the info member of any
image members added to the mosaic member.
* inCleanVis = Python CleanVis object
* uvdata = Python uv data from which image is made
* err = Python Obit Error/message stack
"""
################################################################
# Checks
if not PIsA(inCleanVis):
raise TypeError,"inCleanVis MUST be a Python ObitCleanVis"
if not UV.PIsA(uvdata):
raise TypeError,"uvData MUST be a Python Obit UV"
#
out = Obit.CleanVisReimage(inCleanVis.me, uvdata.me, err.me)
if err.isErr:
OErr.printErrMsg(err, "Error in Reimage")
return out
def GetFreqArr(inUV, err, inc = 1):
"""
Get Array of channel frequencies in data
Return list of channel Frequencies (Hz)
* inUV = Obit UV data with tables
* err = Python Obit Error/message stack
* inc = increment in channel
"""
################################################################
# Checks
if not UV.PIsA(inUV):
print("Actually ",inUV.__class__)
raise TypeError("inUV MUST be a Python Obit UV")
d = inUV.Desc.Dict # UV data descriptor dictionary
refFreq = d["crval"][ d["jlocf"]] # reference frequency
nchan = d["inaxes"][ d["jlocf"]] # Number of channels per IF
nif = d["inaxes"][ d["jlocif"]] # Number of IFs
chwid = abs(d["cdelt"][ d["jlocf"]]) # channel width from header
fqtab = inUV.NewTable(Table.READONLY,"AIPS FQ",1,err)
fqtab.Open(Table.READONLY,err)
fqrow = fqtab.ReadRow(1, err) # Only bother with first
OErr.printErrMsg(err) # catch table errors
IFfreq = fqrow['IF FREQ'] # IF offset
ChWidth = fqrow['CH WIDTH'] # IF channel width
sideband = fqrow['SIDEBAND'] # IF sizeband, 1=USB, -1=LSB
freqs = []
for iif in range(0,nif):
for ifq in range(0,nchan,inc):
frq = refFreq + IFfreq[iif] + sideband[iif] * ifq * min (chwid, ChWidth[iif])
freqs.append(frq)
# End loops
return freqs
def PMakeImage(inUV, outImage, channel, doBeam, doWeight, err):
"""
Grids UV, FFTs and makes corrections for the gridding convolution.
* inUV = Input Python uv data. Should be in form of Stokes to be imaged
will all calibration and selection applied.
* outImage = Python Image to be written. Must be previously instantiated.
Beam normalization factor is written to output Beam infoList as SUMWTS
* channel = Which frequency channel to image, 0->all.
* doBeam = if TRUE also make beam. Will make the myBeam member of outImage.
If FALSE, and myGrid->BeamNorm 0.0 then reads SUMWTS value from beam infolist
* doWeigh = if TRUE Apply uniform weighting corrections to uvdata before imaging
* err = Python Obit Error/message stack
"""
################################################################
# Checks
if not UV.PIsA(inUV):
raise TypeError("inUV MUST be a Python Obit UV")
if not Image.PIsA(outImage):
print("Actually ", outImage.__class__)
raise TypeError("outImage MUST be a Python Obit Image")
if not err.IsA():
raise TypeError("err MUST be an OErr")
#
Obit.ImageUtilMakeImage(inUV.me, outImage.me, channel, doBeam, doWeight,
err.me)
if err.isErr:
OErr.printErrMsg(err, "Error creating Image from UV data")
def PIoN2SolNTableConvert(inUV, outSNVer, NITable, pos, err):
"""
Evaluate Ionospheric model table at pos and convert to SN table
Returns resultant SN table
* inUV = UV data for output SN table.
Control parameters on inUV info member:
========== ================ ================================
"doAntOff" OBIT_bool scalar True if correctionss for antenna
offset from array center wanted [def False]
========== ================ ================================
* outSNVer = Desired output SN table version, 0=> new
* NITable = Ionospheric model table to evaluate
* pos = [RA, Dec] shift (deg) in which NITable to be evaluated.
* err = Obit Error stack, returns if not empty.
"""
################################################################
# Checks
if not UV.PIsA(inUV):
raise TypeError('PIoN2SolNTableConvert: Bad input UV data')
if not Table.PIsA(NITable):
raise TypeError('PIoN2SolNTableConvert: Bad NI input table')
# Create output SN table object
outSNTable = Table.Table("None")
# Evaluate
outSNTable.me = Obit.IoN2SolNTableConvert (inUV.me, outSNVer, \
NITable.me, pos, err.me)
if err.isErr:
OErr.printErrMsg(err, "Error Converting NI to SN table")
return outSNTable
def UVAddIF(inUV, outUV, nIF, err):
"""
Create outUV like inUV but divided into nIF IFs
* inUV = input Obit UV object
* outUV = output Obit UV object, defined but not instantiated
Onlyt really works for AIPS
* nIF = number of desired output IFs
MUST be the same number of channels per IF
* err = Obit error/message stack
"""
################################################################
# Checks
if not UV.PIsA(inUV):
raise TypeError("inUV MUST be a Python Obit UV")
if not UV.PIsA(outUV):
raise TypeError("outUV MUST be a defined Python Obit UV")
# Input can have 1 or no IFs defined
jlocif = inUV.Desc.Dict["jlocif"]
if jlocif >= 0 and inUV.Desc.Dict["inaxes"][jlocif] > 1:
raise RuntimeError("Input UV has excessive IFs already:" \
+str(inUV.Desc.Dict["inaxes"][jlocif]))
# Check number of requested IFs
if nIF < 2:
raise RuntimeError("Too few output IFs requested: " + str(nIF))
# Must be an even number of channels per output IF
jlocf = inUV.Desc.Dict["jlocf"]
nchan = inUV.Desc.Dict["inaxes"][jlocf]
if (nchan % nIF) != 0:
raise RuntimeError("Unequal numbers of channels per " + str(nIF) +
" IFs")
# Patch UV Descriptor
DescAddIF(inUV, outUV, nIF, err)
# Convert FG Table
UpdateFQ(inUV, outUV, nIF, err)
# Convert AN Table
UpdateAN(inUV, outUV, nIF, err)
# Convert SU Table
UpdateSU(inUV, outUV, nIF, err)
# Copy data
CopyData(inUV, outUV, err)
# Update
outUV.UpdateDesc(err)
OErr.printErrMsg(err, "Error updating output")
print("Any CL tables need to be regenerated")
def VLAUVFITS(inUV, filename, outDisk, err, compress=False, \
exclude=["AIPS HI", "AIPS AN", "AIPS FQ", "AIPS SL", "AIPS PL"], \
include=[], headHi=False):
""" Write UV data as FITS file
Write a UV data set as a FITAB format file
History written to header
inUV = UV data to copy
filename = name of FITS file
inDisk = FITS directory number
err = Python Obit Error/message stack
exclude = List of table types NOT to copy
NB: "AIPS HI" isn't really a table and gets copied anyway
include = List of table types to copy (FQ, AN always done )
Exclude has presidence over include
headHi = if True move history to header, else leave in History table
returns FITS UV data object
"""
################################################################
# Checks
if not UV.PIsA(inUV):
raise TypeError, "inUV MUST be a Python Obit UV"
if not OErr.OErrIsA(err):
raise TypeError, "err MUST be an OErr"
#
# Set output
outUV = UV.newPFUV("FITS UV DATA", filename, outDisk, False, err)
if err.isErr:
OErr.printErrMsg(err, "Error creating FITS data")
#Compressed?
if compress:
inInfo = UV.PGetList(outUV) #
dim = [1, 1, 1, 1, 1]
InfoList.PAlwaysPutBoolean(inInfo, "Compress", dim, [True])
# Copy
UV.PCopy(inUV, outUV, err)
if err.isErr:
OErr.printErrMsg(err, "Error copying UV data to FITS")
# History
inHistory = History.History("inhistory", outUV.List, err)
outHistory = History.History("outhistory", outUV.List, err)
# Add history
outHistory.Open(History.READWRITE, err)
outHistory.TimeStamp(" Start Obit uvtab", err)
outHistory.WriteRec(
-1, "uvtab / FITS file " + filename + " disk " + str(outDisk), err)
outHistory.Close(err)
# History in header?
if headHi:
History.PCopy2Header(inHistory, outHistory, err)
OErr.printErrMsg(err, "Error with history")
# zap table
outHistory.Zap(err)
# Copy Tables
UV.PCopyTables(inUV, outUV, exclude, include, err)
return outUV # return new object
def UVMakeIF(outUV, nIF, err, solInt=10.):
"""
Change number of IFs from 1 to nIF
Operation done in place
* outUV = output Obit UV object
Only really works for AIPS
* nIF = number of desired output IFs
MUST be the same number of channels per IF
* err = Obit error/message stack
* solInt = Solution interval for remade CL table.
"""
################################################################
# Checks
if not UV.PIsA(outUV):
raise TypeError("outUV MUST be a defined Python Obit UV")
# Input can have 1 or no IFs defined
jlocif = outUV.Desc.Dict["jlocif"]
if jlocif >= 0 and outUV.Desc.Dict["inaxes"][jlocif] > 1:
raise RuntimeError("Input UV has excessive IFs already:" \
+str(outUV.Desc.Dict["inaxes"][jlocif]))
# Check number of requested IFs
if nIF < 2:
raise RuntimeError("Too few output IFs requested: " + str(nIF))
# Must be an even number of channels per output IF
jlocf = outUV.Desc.Dict["jlocf"]
nchan = outUV.Desc.Dict["inaxes"][jlocf]
if (nchan % nIF) != 0:
raise RuntimeError("Unequal numbers of channels per " + str(nIF) +
" IFs")
# Patch UV Descriptor
DescMakeIF(outUV, nIF, err)
# Convert FQ Table
UpdateFQ2(outUV, nIF, err)
# Convert AN Table
maxant = UpdateAN2(outUV, nIF, err)
# Convert SU Table
UpdateSU2(outUV, nIF, err)
# Regenerate CL table 1 - delete any old
outUV.ZapTable("AIPS CL", -1, err)
print('(Re) generate CL table')
UV.PTableCLfromNX(outUV, maxant, err, calInt=solInt)
# dummy FG 1
print('Dummy entry in Flag table 1')
UV.PFlag(outUV,
err,
timeRange=[-10., -9.],
Ants=[200, 200],
Stokes='0000',
Reason='Dummy')
# Update
outUV.UpdateDesc(err)
OErr.printErrMsg(err, "Error updating output")
def PGenPrint(printer, data, err, VLVer=1, first=True, last=True):
"""
Print selected contents of a generic VL format catalog
Returns logical quit to indicate user wants to quit
* printer = Printer for output
* data = OData to to which VL table is attached
will cast from Image or UV types
with control parameters on the info:
Object string Name of object
equinCode long Epoch code for output,
1=>B1950, 2=>J2000, 3=>Galactic [def 2]
Fitted bool If True give fitted values [def F]
doraw bool If True give raw values from table, else
corrected/deconvolved.[def F]
RA double RA center of search, degrees in equinCode [def 0]
Dec double Dec center of search, degrees in equinCode [def 0]
Search double Search radius in arcsec, <= 0 => all selected. [def 15]
Box double[2] RA and Dec halfwidth of search
rectangle in hr,deg [0,0]
Silent double Half width asec of silent search box. [def 720]
minFlux float Minimum peak flux density. [def 0]
maxFlux float Maximum peak flux density. [def LARGE]
minGlat float Minimum abs galactic latitude [def any]
maxGlat float Minimum abs galactic latitude [def any]
Calibration Parameters
fluxScale float Flux density scaling factor, def 1.0
biasRA float RA position bias in deg, def 0.0
biasDec float Dec position bias in deg, def 0.0
calRAEr float Cal component of RA position error (squared), def 0.0
calDecEr float Cal component of Dec position error (squared), def 0.0
ClnBiasAv float Mean CLEAN bias in Jy, def 0.0
ClnBiasEr float Uncertainty in CLEAN bias in Jy, def 0.0
calAmpEr float Cal component of amplitude error as fraction, def 0.03
calSizeEr float Cal component of amplitude error as fraction, def 0.02
calPolEr float Cal component of polarization error, def 0.003
* err = Python Obit Error/message stack
* VLVer = VL table version
* first = True if this first write to printer
* last = True if this is the last write to printer
"""
################################################################
# Checks
if not OPrinter.PIsA(printer):
raise TypeError("printer MUST be a Python Obit printer")
# cast data if necessary
if Image.PIsA(data) or UV.PIsA(data):
ldata = data.cast("ObitData")
else:
ldata = data
ret = Obit.OSurveyGenPrint(printer.me, ldata.me, VLVer, first, last,
err.me)
return ret != 0
def PICreateImage(inUV, fieldNo, doBeam, err):
"""
Create an image from information on an ObitUV
returns Python Image
* inUV = Python UV object, following read from InfoList member
======== ================== =============================================
"nChAvg" OBIT_int (1,1,1) number of channels to average.
This is for spectral line observations and
is ignored if the IF axis on the uv data has
more than one IF. Default is continuum =
average all freq/IFs. 0=> all.
"rotate" OBIT_float (?,1,1) Desired rotation on sky (from N thru E) in
deg. [0]
"nx" OBIT_int (?,1,1) Dimension of image in RA [no default].
This and the following are arrays with one
entry per field.
"nxBeam" OBIT_int (?,1,1) Dimension of beam in RA, [def. nx]
"ny" OBIT_int (?,1,1) Dimension of image in declination[no default]
"nyBeam" OBIT_int (?,1,1) Dimension of beam in declination, [def. ny]
"xCells" OBIT_float (?,1,1) X (=RA) cell spacing in degrees [no default]
"yCells" OBIT_float (?,1,1) Y (=dec) cell spacing in degrees [no default]
"xShift" OBIT_float (?,1,1) Desired shift in X (=RA) in degrees. [0]
"yShift" OBIT_float (?,1,1) Desired shift in Y (=dec) in degrees. [0]
"nuGrid" OBIT_int (1,1,1) Size in pixels of weighting grid for uniform
weighting
======== ================== =============================================
* fieldNo = Which field (1-rel) in imaging parameter arrays.
* doBeam = if TRUE also create beam as the myBeam member of returned image.
* err = Python Obit Error/message stack
"""
################################################################
# Checks
if not UV.PIsA(inUV):
raise TypeError("inUV MUST be a Python Obit UV")
if not err.IsA():
raise TypeError("err MUST be an OErr")
#
out = Image("None")
out.me = Obit.ImageUtilCreateImage(inUV.me, fieldNo, doBeam, err.me)
if err.isErr:
OErr.printErrMsg(err, "Error Creating Image")
return out
def PNVSSPrint(printer, data, err, VLVer=1, first=True, last=True):
"""
Print selected contents of an NVSS (VLA 1.4 GHz D config) catalog
Returns logical quit to indicate user wants to quit
* printer = Printer for output
* data = OData to to which VL table is attached
will cast from Image or UV types
with control parameters on the info:
Object string Name of object
equinCode long Epoch code for output,
1=>B1950, 2=>J2000, 3=>Galactic [def 2]
Fitted bool If True give fitted values [def F]
doraw bool If True give raw values from table, else
corrected/deconvolved.[def F]
RA double RA center of search, degrees in equinCode [def 0]
Dec double Dec center of search, degrees in equinCode [def 0]
Search double Search radius in arcsec, <= 0 => all selected. [def 15]
Box double[2] RA and Dec halfwidth of search
rectangle in hr,deg [0,0]
Silent double Half width asec of silent search box. [def 720]
minFlux float Minimum peak flux density. [def 0]
maxFlux float Maximum peak flux density. [def LARGE]
minPol float Minimum percent integrated polarization [def 0]
minGlat float Minimum abs galactic latitude [def any]
maxGlat float Minimum abs galactic latitude [def any]
* err = Python Obit Error/message stack
* VLVer = VL table version
* first = True if this first write to printer
* last = True if this is the last write to printer
"""
################################################################
# Checks
if not OPrinter.PIsA(printer):
raise TypeError("printer MUST be a Python Obit printer")
# cast data if necessary
if Image.PIsA(data) or UV.PIsA(data):
ldata = data.cast("ObitData")
else:
ldata = data
ret = Obit.OSurveyNVSSPrint(printer.me, ldata.me, VLVer, first, last,
err.me)
return ret != 0
def PDefine(inImageM, uvData, doBeam, err):
"""
Define the parameters and underlying structures of a set of images.
* inImageM = Python ImageMosaic object
* uvData = Python uv data from which the image mosaic will be derived
* doBeam = if True then make dirty beams
* err = Python Obit err stack.
"""
################################################################
# Checks
if not PIsA(inImageM):
raise TypeError("inImageM MUST be a Python Obit ImageMosaic")
if not UV.PIsA(uvData):
raise TypeError("uvData MUST be a Python Obit UV")
if err.isErr: # existing error?
return
#
Obit.ImageMosaicDefine(inImageM.me, uvData.me, doBeam, err.me)
def PCreate(name, uvData, err):
"""
Create the parameters and underlying structures of a set of images.
* name = Name to be given to object
* uvData = Python uv data from which the image mosaic will be derived
Most control parameters are in InfoList member
* err = Python Obit err stack.
"""
################################################################
# Checks
if not UV.PIsA(uvData):
raise TypeError("uvData MUST be a Python Obit UV")
#
out = ImageMosaic("None", 1)
if err.isErr: # existing error?
return out
out.me = Obit.ImageMosaicCreate(name, uvData.me, err.me)
return out
def PInvertSN(SNTab, outUV, outVer, doRepl, err):
""" Invert the calibration in an SN table
Routine to reverse the effects of the calibration in the
input SN table and create a new SN table on outUV
Returns new SN table
SNTab = Input Python AIPS SN Table to invert
outUV = output UV data to which to attach the new SN table
outVer = Output SN table version number, 0=> create new
doRepl = If True, replace failed solutions with (1,0)
err = Python Obit Error/message stack
"""
################################################################
# Checks
if not Table.PIsA(SNTab):
raise TypeError("SNTab MUST be a Python Obit Table")
if not UV.PIsA(outUV):
raise TypeError('outUV Must be UV data ')
if not OErr.OErrIsA(err):
raise TypeError("err MUST be an OErr")
#
# Create output
outSN = Table.Table("None")
# invert table
outSN.me = Obit.SNInvert(SNTab.me, outUV.me, outVer, doRepl, err.me)
if err.isErr:
printErrMsg(err, "Error inverting solutions")
# Write history
inHistory = History.History("history", outUV.List, err)
# Add this programs history
inHistory.Open(History.READWRITE, err)
inHistory.TimeStamp(" Start Obit InvertSN", err)
inHistory.WriteRec(-1, "InvertSN / inTab = " + Table.PGetName(SNTab), err)
inHistory.WriteRec(-1, "InvertSN / outVer = " + str(outVer), err)
if doRepl:
inHistory.WriteRec(-1, "InvertSN / doRepl = True", err)
else:
inHistory.WriteRec(-1, "InvertSN / doRepl = False", err)
inHistory.Close(err)
return outSN
def PSNSmo (inSC, err, input=UVSelfSNSmoInput):
""" Smooth SN table possibly replacing blanked soln.
inSC = Selfcal object
err = Python Obit Error/message stack
input = input parameter dictionary
Input dictionary entries:
InData = Input Python UV data
InTable = Input SN table
isuba = Desired subarray, 0=> 1
smoType = Smoothing type MWF, GAUS or BOX, def BOX
smoAmp = Amplitude smoothing time in min
smpPhase = Phase smoothing time in min. (0 => fix failed only')
"""
################################################################
# Get input parameters
InData = input["InData"]
InTable = input["InTable"]
isuba = input["isuba"]
#
# Checks
if not UV.PIsA(InData):
raise TypeError('PCal: Bad input UV data')
if not Table.PIsA(InTable):
raise TypeError('PCal: Bad input table')
# Set control values on UV
dim[0] = 1;
inInfo = UV.PGetList(InData) # Add control to UV data
dim[0] = len(input["smoType"]);
InfoList.PAlwaysPutString (inInfo, "smoType", dim, [input["smoType"]])
dim[0] = 1;
InfoList.PPutFloat (inInfo, "smoAmp", dim, [input["smoAmp"]], err)
InfoList.PPutFloat (inInfo, "smoPhase",dim, [input["smoPhase"]],err)
# Smooth
Obit.UVSolnSNSmo(InTable.me, isuba, err.me)
if err.isErr:
printErrMsg(err, "Error smoothing SN table")
def PDivUV(err, input=UVDivInput):
""" Fourier transform Sky model and divide into uv data
A SkyModel is Fourier transformed and divided into
InData and written to outData.
If doCalSelect, selection by channel/IF will specify the output
err = Python Obit Error/message stack
input = input parameter dictionary
Input dictionary entries:
InData = Input UV data,
SkyModel = Input SkyModel,
OutData = Output uv data,
doCalSelect = Select/calibrate/edit data?),
REPLACE = Replace data with model?
Stokes = Stokes parameter, blank-> unchanged from input),
CCVer = CC table versions to use [def all 0 => highest]
BComp = Start CC to use per table, 1-rel [def 1 ]
EComp = Highest CC to use per table, 1-rel [def to end]
BChan = First spectral channel selected. [def all]),
EChan = Highest spectral channel selected. [def all]),
BIF = First IF selected. [def all]),
EIF = Highest IF selected. [def all]),
doPol = >0 -> calibrate polarization.),
doCalib = >0 -> calibrate, 2=> also calibrate Weights),
gainUse = SN/CL table version number, 0-> use highest),
flagVer = Flag table version, 0-> use highest, <0-> none),
BLVer = BL table version, 0> use highest, <0-> none),
BPVer = Band pass (BP) table version, 0-> use highest),
Subarray = Selected subarray, <=0->all [default all]),
freqID = Selected Frequency ID, <=0->all [default all]),
timeRange = Selected timerange in days. [8 floats] 0s -> all),
UVRange = Selected UV range in wavelengths. 0s -> all),
Sources = Source names selected unless any starts with),
Antennas = A list of selected antenna numbers, if any is negative),
corrType = Correlation type, 0=cross corr only, 1=both, 2=auto only.),
doBand = Band pass application type <0-> none),
Smooth = Specifies the type of spectral smoothing [three floats]
do3D = If 3D imaging wanted. [def false]
Factor = Model multiplication factor (-1=>add) [def 1]
PBCor = If TRUE make relative primary beam corrections. [def false]
antSize = Diameter of antennas for PBCor,.[def 25.0]
minFlux = Minimum flux density model or pixel [def -1.0e20]
Type = Model type (ObitSkyModelType) [def OBIT_SkyModel_Comps]
0=CC Comps, 1=Image, 2=Model
Mode = Model mode (ObitSkyModelMode) [def OBIT_SkyModel_Fastest]
0=fastest, 1=DFT, 2=Grid
MODPTFLX = Point model flux in Jy, [def 0.0]')
MODPTXOF = Point model x offset in deg [def 0.0]
MODPTYOF = Point model y offset in deg [def 0.0]
MODPTYPM = Point other parameters [def all 0.0]
Parm[3] = 0; Point - no other parameters
Parm[3] = 1; Gaussian on sky:
[0:2] = major_axis (asec), minor_axis (asec),
Rotation of major axis (deg) from east towards north
Parm[3] = 3; Uniform sphere:
[0] = radius (asec)
"""
################################################################
# Get input parameters
inData = input["InData"]
inSkyModel = input["SkyModel"]
outData = input["OutData"]
# Checks
if not PIsA(inSkyModel):
raise TypeError, "inSkyModel MUST be a Python Obit SkyModel"
if not UV.PIsA(inData):
raise TypeError, "inData MUST be a Python Obit UV"
if not UV.PIsA(outData):
raise TypeError, "outData MUST be a Python Obit UV"
#
#
dim = [1, 1, 1, 1, 1]
#
# Set control values on SkyModel/inData
dim[0] = 1
inInfo = PGetList(inSkyModel) #
uvInfo = inData.List #
InfoList.PPutBoolean(uvInfo, "doCalSelect", dim, [input["doCalSelect"]],
err)
InfoList.PPutBoolean(inInfo, "REPLACE", dim, [input["REPLACE"]], err)
# Put channel selection on uvdata or skymodel depending on doCalSelect
if input["doCalSelect"]:
InfoList.PPutInt(uvInfo, "BChan", dim, [input["BChan"]], err)
InfoList.PPutInt(uvInfo, "EChan", dim, [input["EChan"]], err)
InfoList.PPutInt(uvInfo, "BIF", dim, [input["BIF"]], err)
InfoList.PPutInt(uvInfo, "EIF", dim, [input["EIF"]], err)
else:
InfoList.PPutInt(inInfo, "BChan", dim, [input["BChan"]], err)
InfoList.PPutInt(inInfo, "EChan", dim, [input["EChan"]], err)
InfoList.PPutInt(inInfo, "BIF", dim, [input["BIF"]], err)
InfoList.PPutInt(inInfo, "EIF", dim, [input["EIF"]], err)
itemp = int(input["doPol"])
InfoList.PPutInt(uvInfo, "doPol", dim, [itemp], err)
InfoList.PPutInt(uvInfo, "doCalib", dim, [input["doCalib"]], err)
InfoList.PPutInt(uvInfo, "doBand", dim, [input["doBand"]], err)
InfoList.PPutInt(uvInfo, "gainUse", dim, [input["gainUse"]], err)
InfoList.PPutInt(uvInfo, "flagVer", dim, [input["flagVer"]], err)
InfoList.PPutInt(uvInfo, "BLVer", dim, [input["BLVer"]], err)
InfoList.PPutInt(uvInfo, "BPVer", dim, [input["BPVer"]], err)
InfoList.PPutInt(uvInfo, "Subarray", dim, [input["Subarray"]], err)
InfoList.PPutInt(uvInfo, "freqID", dim, [input["freqID"]], err)
InfoList.PPutInt(uvInfo, "corrType", dim, [input["corrType"]], err)
dim[0] = 4
InfoList.PAlwaysPutString(uvInfo, "Stokes", dim, [input["Stokes"]])
dim[0] = 16
dim[1] = len(input["Sources"])
InfoList.PAlwaysPutString(uvInfo, "Sources", dim, input["Sources"])
dim[0] = 2
InfoList.PPutFloat(uvInfo, "UVRange", dim, input["UVRange"], err)
dim[0] = 3
InfoList.PPutFloat(uvInfo, "Smooth", dim, input["Smooth"], err)
dim[0] = 2
InfoList.PPutFloat(uvInfo, "timeRange", dim, input["timeRange"], err)
dim[0] = len(input["Antennas"])
InfoList.PAlwaysPutInt(uvInfo, "Antennas", dim, input["Antennas"])
dim[0] = 16
dim[1] = len(input["Sources"])
InfoList.PAlwaysPutString(uvInfo, "Sources", dim, input["Sources"])
dim[0] = 1
dim[1] = 1
InfoList.PPutBoolean(inInfo, "do3D", dim, [input["do3D"]], err)
InfoList.PPutInt(inInfo, "ModelType", dim, [input["Type"]], err)
InfoList.PPutInt(inInfo, "Mode", dim, [input["Mode"]], err)
InfoList.PPutFloat(inInfo, "Factor", dim, [input["Factor"]], err)
InfoList.PPutBoolean(inInfo, "PBCor", dim, [input["PBCor"]], err)
InfoList.PPutFloat(inInfo, "antSize", dim, [input["antSize"]], err)
InfoList.PPutFloat(inInfo, "minFlux", dim, [input["minFlux"]], err)
InfoList.PPutFloat(inInfo, "MODPTFLX", dim, [input["MODPTFLX"]], err)
InfoList.PPutFloat(inInfo, "MODPTXOF", dim, [input["MODPTXOF"]], err)
InfoList.PPutFloat(inInfo, "MODPTYOF", dim, [input["MODPTYOF"]], err)
dim[0] = len(input["MODPTYPM"])
InfoList.PAlwaysPutFloat(inInfo, "MODPTYPM", dim, input["MODPTYPM"])
if input["CCVer"] != None:
dim[0] = len(input["CCVer"])
InfoList.PAlwaysPutInt(inInfo, "CCVer", dim, input["CCVer"])
if input["BComp"] != None:
dim[0] = len(input["BComp"])
InfoList.PAlwaysPutInt(inInfo, "BComp", dim, input["BComp"])
if input["EComp"] != None:
dim[0] = len(input["EComp"])
InfoList.PAlwaysPutInt(inInfo, "EComp", dim, input["EComp"])
#
# show any errors
#OErr.printErrMsg(err, "UVDiv: Error setting parameters")
#
# Do operation
sm = inSkyModel.cast(myClass) # cast pointer
Obit.SkyModelDivUV(sm, inData.me, outData.me, err.me)
if err.isErr:
OErr.printErrMsg(err, "Error dividing SkyModel into UV data")
def PCreate (name, uvdata, err, input=CleanInput):
"""
Create the parameters and underlying structures of a CleanVis.
Returns CleanVis created.
* name = Name to be given to object. Most control parameters are in
InfoList member
* uvdata = Python uv data from which image is to be made
* err = Python Obit Error/message stack
* input = control parameters:
=========== ============================================================
Niter Maximum number of CLEAN iterations
minPatch Minimum beam patch in pixels [def 100]
maxPixel Maximum number of residuals [def 20000]
BMAJ Restoring beam major axis (deg)
BMIN Restoring beam minor axis (deg)
BPA Restoring beam position angle (deg)
Gain CLEAN loop gain
minFlux Minimun flux density (Jy)
Factor CLEAN depth factor
Plane Plane being processed, 1-rel indices of axes 3-?
autoWindow True if autoWindow feature wanted.
CCVer CC table version number
Mode Model mode, 0=fastest, 1=DFT, 2=Grid
doCalSelect Select/calibrate/edit data?),
Stokes Stokes parameter, blank-> unchanged from input),
BChan First spectral channel selected. [def all]),
EChan Highest spectral channel selected. [def all]),
BIF First IF selected. [def all]),
EIF Highest IF selected. [def all]),
doPol >0 -> calibrate polarization.),
doCalib >0 -> calibrate, 2=> also calibrate Weights),
gainUse SN/CL table version number, 0-> use highest),
flagVer Flag table version, 0-> use highest, <0-> none),
BLVer BL table version, 0> use highest, <0-> none),
BPVer Band pass (BP) table version, 0-> use highest),
Subarray Selected subarray, <=0->all [default all]),
freqID Selected Frequency ID, <=0->all [default all]),
timeRange Selected timerange in days. [2 floats] 0s -> all),
UVRange Selected UV range in wavelengths. 0s -> all),
Sources Source names selected unless any starts with),
Antennas A list of selected antenna numbers, if any is negative),
corrType Correlation type, 0=cross corr only, 1=both, 2=auto only.),
doBand Band pass application type <0-> none),
Smooth Specifies the type of spectral smoothing [three floats]
DoWeight True if Weighting to be applied
PBCor If True make freq. dependent rel. pri. beam corr.
Robust Briggs robust parameter. (AIPS definition)
UVTaper UV plane taper, sigma in klambda,deg as [maj, min, pa]
WtSize Size of weighting grid in cells [same as image nx]
WtBox Size of weighting box in cells [def 1]
WtFunc Weighting convolution function [def. 1]
1=Pill box, 2=linear, 3=exponential, 4=Gaussian
if positive, function is of radius, negative in u and v.
WtPower Power to raise weights to. [def = 1.0]
Note: a power of 0.0 sets all the output weights to 1 as modified
by uniform/Tapering weighting.
Applied in determinng weights as well as after.
DoBeam True if beams are to be made
Type Underlying file type, 0=FITS, 1=AIPS
Name Name of image, used as AIPS name or to derive FITS filename
Class Root of class, used as AIPS class or to derive FITS filename
Seq Sequence number
Disk Disk number for underlying files
FOV Field of view (deg) for Mosaic
doFull If True, create full field (FOV) image
NField Number of fields defined in input,
if unspecified derive from data and FOV
xCells Cell spacing in X (asec) for all images,
if unspecified derive from data
yCells Cell spacing in Y (asec) for all images,
if unspecified derive from data
nx Minimum number of cells in X for NField images
if unspecified derive from data
ny Minimum number of cells in Y for NField images
if unspecified derive from data
RAShift Right ascension shift (AIPS convention) for each field
if unspecified derive from FOV and data
DecShift Declination for each field
if unspecified derive from FOV and data
Catalog AIPSVZ format catalog for defining outliers, None=do not use
OutlierFlux Minimum estimated outlyer flux density (Jy)
OutlierDist Maximum distance to add outlyers (deg)
OutlierSI Spectral index to estimate flux density
OutlierSize Size of outlyer field (pixels)
dispURL URL of display server
doRestore Restore image when done? [def True]
doFlatten Flatten image when done? [def True]
=========== ============================================================
"""
################################################################
# Checks
if not UV.PIsA(uvdata):
raise TypeError,"uvData MUST be a Python Obit UV"
if not OErr.OErrIsA(err):
raise TypeError,"err MUST be an OErr"
#
dim = [1,1,1,1,1]
# Set imaging control values on uvdata
dim[0] = 1;
inInfo = UV.PGetList(uvdata) #
InfoList.PPutBoolean (inInfo, "doCalSelect", dim, [input["doCalSelect"]], err)
dim[0] = 4
InfoList.PAlwaysPutString (inInfo, "Stokes", dim, [input["Stokes"]])
dim[0] = 1;
InfoList.PPutInt (inInfo, "BChan", dim, [input["BChan"]], err)
InfoList.PPutInt (inInfo, "EChan", dim, [input["EChan"]], err)
InfoList.PPutInt (inInfo, "BIF", dim, [input["BIF"]], err)
InfoList.PPutInt (inInfo, "EIF", dim, [input["EIF"]], err)
itemp = int(input["doPol"])
InfoList.PPutInt (inInfo, "doPol", dim, [itemp], err)
InfoList.PPutInt (inInfo, "doCalib", dim, [input["doCalib"]], err)
InfoList.PPutInt (inInfo, "doBand", dim, [input["doBand"]], err)
InfoList.PPutInt (inInfo, "gainUse", dim, [input["gainUse"]], err)
InfoList.PPutInt (inInfo, "flagVer", dim, [input["flagVer"]], err)
InfoList.PPutInt (inInfo, "BLVer", dim, [input["BLVer"]], err)
InfoList.PPutInt (inInfo, "BPVer", dim, [input["BPVer"]], err)
InfoList.PPutInt (inInfo, "Subarray", dim, [input["Subarray"]], err)
InfoList.PPutInt (inInfo, "freqID", dim, [input["freqID"]], err)
InfoList.PPutInt (inInfo, "corrType", dim, [input["corrType"]], err)
dim[0] = 2
InfoList.PPutFloat (inInfo, "UVRange", dim, input["UVRange"], err)
dim[0] = 3
InfoList.PPutFloat (inInfo, "Smooth", dim, input["Smooth"], err)
dim[0] = 2
InfoList.PPutFloat (inInfo, "timeRange", dim, input["timeRange"], err)
dim[0] = len(input["Antennas"])
InfoList.PPutInt (inInfo, "Antennas", dim, input["Antennas"], err)
dim[0] = 16; dim[1] = len(input["Sources"])
InfoList.PAlwaysPutString (inInfo, "Sources", dim, input["Sources"])
# Weighting parameters
dim[0] = 1; dim[1] = 1;
InfoList.PPutBoolean (inInfo,"DoWeight",dim,[input["DoWeight"]],err)
InfoList.PPutBoolean (inInfo,"PBCor", dim, [input["PBCor"]], err)
InfoList.PPutFloat (inInfo, "Robust", dim, [input["Robust"]], err)
InfoList.PPutInt (inInfo, "WtBox", dim, [input["WtBox"]], err)
InfoList.PPutInt (inInfo, "WtFunc", dim, [input["WtFunc"]], err)
InfoList.PPutFloat (inInfo, "WtPower",dim, [input["WtPower"]], err)
dim[1] = len(input["UVTaper"])
InfoList.PPutFloat (inInfo, "Taper", dim, input["UVTaper"], err)
WtSize = input["WtSize"]
if (WtSize>0):
print "WtSize", WtSize
# Change name for C routine.
dim[0] = 1;
InfoList.PPutInt (inInfo, "nuGrid", dim, [WtSize], err)
InfoList.PPutInt (inInfo, "nvGrid", dim, [WtSize], err)
# Define image
dim[0] = 1; dim[1] = 1;
InfoList.PPutInt (inInfo, "imFileType", dim, [input["Type"]], err)
InfoList.PPutInt (inInfo, "imSeq", dim, [input["Seq"]], err)
InfoList.PPutInt (inInfo, "imDisk", dim, [input["Disk"]], err)
InfoList.PPutFloat (inInfo, "FOV", dim, [input["FOV"]], err)
InfoList.PPutBoolean (inInfo, "doFull", dim, [input["doFull"]], err)
InfoList.PPutInt (inInfo, "NField", dim, [input["NField"]], err)
InfoList.PPutFloat (inInfo, "xCells", dim, [input["xCells"]], err)
InfoList.PPutFloat (inInfo, "yCells", dim, [input["yCells"]], err)
InfoList.PPutFloat (inInfo, "OutlierFlux", dim, [input["OutlierFlux"]], err)
InfoList.PPutFloat (inInfo, "OutlierDist", dim, [input["OutlierDist"]], err)
InfoList.PPutFloat (inInfo, "OutlierSI", dim, [input["OutlierSI"]], err)
InfoList.PPutInt (inInfo, "OutlierSize", dim, [input["OutlierSize"]], err)
InfoList.PPutFloat (inInfo, "BMAJ", dim, [input["BMAJ"]], err)
InfoList.PPutFloat (inInfo, "BMIN", dim, [input["BMIN"]], err)
InfoList.PPutFloat (inInfo, "BPA", dim, [input["BPA"]], err)
dim[0] = len(input["Name"])
InfoList.PAlwaysPutString (inInfo, "imName", dim, [input["Name"]])
dim[0] = len(input["Class"])
InfoList.PAlwaysPutString (inInfo, "imClass", dim, [input["Class"]])
dim[0] = len(input["Catalog"])
InfoList.PAlwaysPutString (inInfo, "Catalog", dim, [input["Catalog"]])
dim[0] = len(input["nx"])
InfoList.PAlwaysPutInt (inInfo, "nx", dim, input["nx"])
dim[0] = len(input["ny"])
InfoList.PAlwaysPutInt (inInfo, "ny", dim, input["ny"])
dim[0] = len(input["RAShift"])
InfoList.PAlwaysPutFloat (inInfo, "RAShift", dim, input["RAShift"])
dim[0] = len(input["DecShift"])
InfoList.PAlwaysPutFloat (inInfo, "DecShift", dim, input["DecShift"])
#OErr.printErrMsg(err, "CleanVisCreate: Error setting parameters")
#
# Create
out = CleanVis(name);
out.me = Obit.CleanVisCreate(name, uvdata.me, err.me)
if err.isErr:
OErr.printErrMsg(err, "Error creating CleanVis")
# Set Clean control values on out
dim[0] = 1;
inInfo = PGetList(out) #
InfoList.PPutInt (inInfo, "Niter", dim, [input["Niter"]], err)
InfoList.PPutInt (inInfo, "minPatch", dim, [input["minPatch"]], err)
InfoList.PPutInt (inInfo, "maxPixel", dim, [input["maxPixel"]], err)
InfoList.PPutInt (inInfo, "CCVer", dim, [input["CCVer"]], err)
InfoList.PPutInt (inInfo, "Mode", dim, [input["Mode"]], err)
InfoList.PPutFloat (inInfo, "BMAJ", dim, [input["BMAJ"]], err)
InfoList.PPutFloat (inInfo, "BMIN", dim, [input["BMIN"]], err)
InfoList.PPutFloat (inInfo, "BPA", dim, [input["BPA"]], err)
InfoList.PPutFloat (inInfo, "Gain", dim, [input["Gain"]], err)
InfoList.PPutFloat (inInfo, "minFlux", dim, [input["minFlux"]], err)
InfoList.PPutFloat (inInfo, "Factor", dim, [input["Factor"]], err)
InfoList.PPutBoolean (inInfo, "doRestore", dim, [input["doRestore"]], err)
InfoList.PPutBoolean (inInfo, "doFlatten", dim, [input["doFlatten"]], err)
InfoList.PPutBoolean (inInfo, "autoWindow", dim, [input["autoWindow"]],err)
dim[0] = len(input["Plane"])
InfoList.PAlwaysPutInt (inInfo, "Plane", dim, input["Plane"])
dim[0] = len(input["dispURL"])
InfoList.PAlwaysPutString (inInfo, "dispURL", dim, [input["dispURL"]])
# show any errors
#OErr.printErrMsg(err, "CleanVisCreate: Error setting parameters")
#
return out;
def PDivUV(err, input=UVSubInput):
""" Fourier transform Sky model and divide into uv data
A SkyModelVMIon is Fourier transformed and divided into
InData and written to outData.
err = Python Obit Error/message stack
input = input parameter dictionary
Input dictionary entries:
InData = Input UV data,
SkyModelVMIon = Input SkyModelVMIon,
OutData = Output uv data,
doCalSelect = Select/calibrate/edit data?),
REPLACE = Replace data with model?
Stokes = Stokes parameter, blank-> unchanged from input),
CCVer = CC table versions to use [def all 0 => highest]
BComp = Start CC to use per table, 1-rel [def 1 ]
EComp = Highest CC to use per table, 1-rel [def to end]
BChan = First spectral channel selected. [def all]),
EChan = Highest spectral channel selected. [def all]),
BIF = First IF selected. [def all]),
EIF = Highest IF selected. [def all]),
doPol = >0 -> calibrate polarization.),
doCalib = >0 -> calibrate, 2=> also calibrate Weights),
ionVer = NI table version number, 0-> use highest, def=1
flagVer = Flag table version, 0-> use highest, <0-> none),
BLVer = BL table version, 0> use highest, <0-> none),
BPVer = Band pass (BP) table version, 0-> use highest),
Subarray = Selected subarray, <=0->all [default all]),
freqID = Selected Frequency ID, <=0->all [default all]),
timeRange = Selected timerange in days. [8 floats] 0s -> all),
UVRange = Selected UV range in wavelengths. 0s -> all),
Sources = Source names selected unless any starts with),
Antennas = A list of selected antenna numbers, if any is negative),
corrType = Correlation type, 0=cross corr only, 1=both, 2=auto only.),
doBand = Band pass application type <0-> none),
Smooth = Specifies the type of spectral smoothing [three floats]
do3D = If 3D imaging wanted. [def false]
Factor = Model multiplication factor (-1=>add) [def 1]
PBCor = If TRUE make relative primary beam corrections. [def false]
antSize = Diameter of antennas for PBCor,.[def 25.0]
minFlux = Minimum flux density model or pixel [def -1.0e20]
Type = Model type (ObitSkyModelVMIonType) [def OBIT_SkyModelVMIon_Comps]
0=CC Comps, 1=Image, 2=Model
Mode = Model mode (ObitSkyModelVMIonMode) [def OBIT_SkyModelVMIon_Fastest]
0=fastest, 1=DFT, 2=Grid
MODPTFLX = Point model flux in Jy, [def 0.0]')
MODPTXOF = Point model x offset in deg [def 0.0]
MODPTYOF = Point model y offset in deg [def 0.0]
MODPTYP = Point other parameters [def all 0.0]
"""
################################################################
# Get input parameters
inData = input["InData"]
inSkyModelVMIon = input["SkyModelVMIon"]
outData = input["OutData"]
# Checks
if not PIsA(inSkyModelVMIon):
raise TypeError("inSkyModelVMIon MUST be a Python Obit SkyModelVMIon")
if not UV.PIsA(inData):
raise TypeError("inData MUST be a Python Obit UV")
if not UV.PIsA(outData):
raise TypeError("outData MUST be a Python Obit UV")
#
#
dim = [1, 1, 1, 1, 1]
#
# Set Ion control values on SkyModelVMIon/inData
dim[0] = 1
inInfo = inSkyModelVMIon.List
uvInfo = inData.List #
InfoList.PPutInt(uvInfo, "ionVer", dim, [input["ionVer"]], err)
input["SkyModel"] = inSkyModelVMIon
#
# Do operation
SkyModel.PDivUV(err, input=input)
if err.isErr:
OErr.printErrMsg(err, "Error dividing SkyModelVMIon into UV data")
def PSoln2Cal(inUV, outUV, err, input=Soln2CalInput):
""" Apply a gain solution to a calibration table
inUV = UV data with solution and input calibration
outUV = UV data for output calibration table
err = Python Obit Error/message stack
input = input parameter dictionary
Input dictionary entries:
solnVer = Input Solution (SN) table version
calIn = Input Cal (CL) table version, 0=high, -1=none
calOut = Output Calibration table version, 0=>create new
subA = Selected subarray (default 1)
interMode = Interpolation mode 2PT, SELF POLY SIMP AMBG CUBE MWF '),
"2PT " = linear vector interpolation with no SN smoothing.
"SELF" = Use only SN solution from same source which is closest in time.
"POLY" = Fit a polynomial to the SN rates and delays.
Use the integral of the rate polynomial for the phases. (NYI)
"SIMP" = Simple linear phase connection between SN phase
entries, assumes phase difference less than 180 degrees.
"AMBG" = Linear phase connection using rates to resolve phase ambiguities.
"CUBE" = As AMBG but fit third order polynomial to phases and rates.
"MWF " = Median window filter of SN table before 2PT interpolation
"GAUS" = Gaussian smoothing of SN table before 2PT interpolation,
"BOX " = Boxcar smoothing of SN table before 2PT interpolation,
interParm = interpolation parameters, smoothing time (hr)
amplitude, phase, delay/rate
interNPoly = number of terms in polynomial'),
allPass = If true copy unmodified entries as well (default False)
refAnt = Ref ant to use. (default 1)
"""
################################################################
# Get input parameters
InData = input["InData"]
InTable = input["InTable"]
isuba = input["isuba"]
#
# Checks
if not UV.PIsA(inUV):
raise TypeError, 'PSoln2Cal: Bad input UV data'
if not UV.PIsA(outUV):
raise TypeError, 'PSoln2Cal: Bad output UV data'
# Set control values on UV
dim[0] = 1
inInfo = UV.PGetList(InData) # Add control to UV data
dim[0] = 4
InfoList.PAlwaysPutString(inInfo, "interMode", dim, [input["interMode"]])
dim[0] = 1
InfoList.PAlwaysPutInt(inInfo, "solnVer", dim, [input["solnVer"]])
InfoList.PAlwaysPutInt(inInfo, "calIn", dim, [input["calIn"]])
InfoList.PAlwaysPutInt(inInfo, "calOut", dim, [input["calOut"]])
InfoList.PAlwaysPutInt(inInfo, "subA", dim, [input["subA"]])
InfoList.PAlwaysPutInt(inInfo, "interNPoly", dim, [input["interNPoly"]])
InfoList.PAlwaysPutInt(inInfo, "refAnt", dim, [input["refAnt"]])
InfoList.PAlwaysPutBool(inInfo, "allPass", dim, [input["allPass"]])
dim[0] = len(input["interParm"])
InfoList.PAlwaysPutFloat(inInfo, "allPass", dim, input["interParm"])
# Calibrate
Obit.UVSoln2Cal(inUV, outUV, err)
if err.isErr:
printErrMsg(err, "Error applying SN table to CL table")
def pipeline(aipsSetup, parmFile):
"""
VLBA Continuum pipeline.
* *aipsSetup* = AIPS setup file
* *parmFile* = pipeline input parameters file
"""
############################# Initialize OBIT ##########################################
noScrat = []
exec(open(aipsSetup).read())
VLBAAddOutFile(aipsSetup, 'project', "Obit's AIPS setup file")
############################# Default parameters ##########################################
# Define data
project = "Unspecified" # Project name (12 char or less, used as AIPS Name)
session = "?" # Project session code
band = "?" # Observing band
logFile = project + "_" + session + "_" + band + ".log" # Processing log file
seq = 1 # AIPS sequence number
gain = 0.10 # CLEAN loop gain
doLoadIDI = True # Load data from IDI FITS?
doLoadUVF = False # Load the "AIPS Friendly" (uvfits) FITS version
dataInUVF = None # Input uvfits data file name
dataInIDI = None # Input FITS-IDI file or list
dataClass = "Raw" # AIPS class of raw uv data
Compress = False # Use compressed UV data?
calInt = 0.15 # Calibration table interval in min.
wtThresh = 0.8 # Data weight threshold
check = False # Only check script, don't execute tasks
debug = False # run tasks debug
prtLv = 2 # Print level
# Initialize parameters
parms = VLBAInitContParms()
############################# Set Project Processing parameters ##################
exec(open(parmFile).read())
VLBAAddOutFile(parmFile, 'project', 'Pipeline input parameters')
################################## Process #####################################
# Init cal pickle jars
goodCalPicklefile = project + "_" + session + "_" + band + "_GoodCal.pickle" # Where results saved
# Default "best" calibration
goodCal = {
"Source": " ",
"souID": 0,
"timeRange": (0.0, 100.0),
"Fract": 0.0,
"SNR": 0.0,
"bestRef": 0
}
# Save initial default if it doesn't already exist
SaveObject(goodCal, goodCalPicklefile, False)
VLBAAddOutFile(goodCalPicklefile, 'project', 'Best calibrator information')
OKCalPicklefile = project + "_" + session + "_" + band + "_OKCal.pickle" # Where results saved
SaveObject(parms["contCals"], OKCalPicklefile, False)
VLBAAddOutFile(OKCalPicklefile, 'project', 'List of calibrators')
targetsPicklefile = project + "_" + session + "_" + band + "_targets.pickle" # Where results saved
if (not parms["targets"]) and os.path.exists(targetsPicklefile):
parms["targets"] = FetchObject(targetsPicklefile)
else:
SaveObject(parms["targets"], targetsPicklefile, False)
VLBAAddOutFile(targetsPicklefile, 'project', 'List of targets')
# Load the outputs pickle jar
VLBAFetchOutFiles()
# Logging directly to logFile
OErr.PInit(err, prtLv, logFile)
retCode = 0
VLBAAddOutFile(logFile, 'project', 'Pipeline log file')
mess = "Start project " + project + " session " + session + " " + band + " Band" + " AIPS user no. " + str(
AIPS.userno)
printMess(mess, logFile)
logger.info(mess)
if debug:
pydoc.ttypager = pydoc.plainpager # don't page task input displays
mess = "Using Debug mode "
printMess(mess, logFile)
if check:
mess = "Only checking script"
printMess(mess, logFile)
# Load Data from FITS
uv = None # Raw data
uvc = None # Cal/averaged data
if doLoadIDI:
logger.info("--> Load IDI data file (doLoadIDI)")
if type(dataInIDI) == list:
logger.info(
"--> Loading a list of IDI files (dataInIDI is a list)\n" +
" This data appears to be from the old correlator.\n" +
" IDI corrections will be applied when loading is\n" +
" complete.")
# Read list
for dataIn in dataInIDI:
uv = VLBAIDILoad(dataIn, project, session, band, dataClass, disk, seq, err, logfile=logFile, \
wtThresh=wtThresh, calInt=calInt, Compress=Compress, \
check=check, debug=debug)
if not UV.PIsA(uv):
raise RuntimeError("Cannot load " + dataIn)
# Fix IDI files:
uv = IDIFix.IDIFix(uv, err)
seq = uv.Aseq
else:
logger.info(
"--> Loading a single IDI file (dataInIDI is not a list)\n" +
" This data appears to be from the DiFX correlator.\n" +
" No IDI corrections will be applied.")
# Single IDI file
uv = VLBAIDILoad(dataInIDI, project, session, band, dataClass, disk, seq, err, logfile=logFile, \
wtThresh=wtThresh, calInt=calInt, Compress=Compress, \
check=check, debug=debug)
if not UV.PIsA(uv):
raise RuntimeError("Cannot load " + dataInIDI)
if doLoadUVF:
logger.info("--> Load UVFITS data file (doLoadUVF)")
uv = VLBAIDILoad(dataInUVF, project, session, band, dataClass, disk, seq, err, logfile=logFile, \
wtThresh=wtThresh, calInt=calInt, Compress=Compress, \
check=check, debug=debug)
# Adding check condition to avoid error when checking
if not UV.PIsA(uv) and not check:
raise RuntimeError("Cannot load " + dataInUVF)
# Otherwise set uv
if uv == None and not check:
Aname = VLBAAIPSName(project, session)
uvname = project + "_" + session + "_" + band
uv = UV.newPAUV(uvname, Aname, dataClass, disk, seq, True, err)
if err.isErr:
OErr.printErrMsg(err, "Error creating AIPS data")
# frequency dependent default parameters
VLBAInitContFQParms(uv, parms, err, \
logfile=logFile, check=check, debug=debug)
# Setup target source list
if os.path.exists(targetsPicklefile):
parms["targets"] = \
setupSourceList( parms["targets"], uv, err, logFile, check, debug )
logger.debug("parms['targets'] = " + str(parms["targets"]))
# Clear any old calibration/editing
if parms["doClearTab"]:
logger.info("--> Clear old calibration/editing (doClearTab)")
VLBAClearCal(uv, err, doGain=parms["doGain"], doFlag=parms["doFlag"], doBP=parms["doBP"], \
check=check, logfile=logFile)
OErr.printErrMsg(err, "Error resetting calibration")
# Copy FG 1 to FG 2
if parms["doCopyFG"]:
logger.info("--> Copy flag (FG) table 1 to flag table 2 (doCopyFG)")
retCode = VLBACopyFG(uv,
err,
logfile=logFile,
check=check,
debug=debug)
if retCode != 0:
raise RuntimeError("Error Copying FG table")
# Special editing
if parms["doEditList"] and not check:
logger.info("--> Special editing (doEditList)")
for edt in parms["editList"]:
UV.PFlag(uv,err,timeRange=[dhms2day(edt["timer"][0]),dhms2day(edt["timer"][1])], \
flagVer=editFG, Ants=edt["Ant"], Chans=edt["Chans"], IFs=edt["IFs"], \
Stokes=edt["Stokes"], Reason=edt["Reason"])
OErr.printErrMsg(err, "Error Flagging")
# Quack to remove data from start and end of each scan
if parms["doQuack"]:
logger.info("--> Remove data from start and end of scans (doQuack)")
retCode = VLBAQuack (uv, err, \
begDrop=parms["quackBegDrop"], endDrop=parms["quackEndDrop"], \
Reason=parms["quackReason"], \
logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error Quacking data")
# Median window time editing, for RFI impulsive in time or dropouts
if parms["doMedn"]:
logger.info("--> Median window time editing (doMedn)")
retCode = VLBAMedianFlag (uv, " ", err, noScrat=noScrat, nThreads=nThreads, \
avgTime=parms["mednAvgTime"], avgFreq=parms["mednAvgFreq"], \
chAvg=parms["mednChAvg"], timeWind=parms["mednTimeWind"], \
flagSig=parms["mednSigma"], flagVer=2, \
logfile=logFile, check=check, debug=False)
if retCode != 0:
raise RuntimeError("Error in MednFlag")
# Quantization correction?
if parms["doQuantCor"]:
logger.info("--> Quantization correction (doQuantCor)")
plotFile = project + "_" + session + "_" + band + ".Quant.ps"
retCode = VLBAQuantCor(uv, parms["QuantSmo"], parms["QuantFlag"], err, \
doSNPlot=parms["doSNPlot"], plotFile=plotFile, \
logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in quantization correcting/flagging")
# Parallactic angle correction?
if parms["doPACor"]:
logger.info("--> Parallactic angle correction (doPACor)")
retCode = VLBAPACor(uv, err, noScrat=noScrat, \
logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in quantization correcting/flagging")
# Opacity/Tsys/gain correction
if parms["doOpacCor"]:
logger.info("--> Opacity/Tsys/Gain correction (doOpacCor)")
plotFile = project + "_" + session + "_" + band + ".Opacity.ps"
retCode = VLBAOpacCor(uv, parms["OpacSmoo"], err, \
doSNPlot=parms["doSNPlot"], plotFile=plotFile, \
logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in opacity/gain.Tsys correction")
VLBASaveOutFiles() # Save plot file in Outfiles
# Need to determine a list of calibrators?
if (parms["contCals"] == None) or (len(parms["contCals"]) <= 0):
logger.info("--> Get list of calibrators (contCals = None or [])")
if parms["doFindOK"]:
slist = VLBAAllSource(uv,
err,
logfile=logFile,
check=check,
debug=debug)
parms["contCals"] = VLBAOKCal(uv, parms["minOKFract"], err, \
solInt=parms["findSolInt"], \
calSou=slist, minSNR=parms["minOKSNR"], \
doCalib=-1, flagVer=2, refAnts=parms["refAnts"], \
noScrat=noScrat, nThreads=nThreads, \
logfile=logFile, check=check, debug=debug)
if not parms["contCals"] and not check:
raise RuntimeError("Error in finding acceptable calibrators")
logger.info("Calibrators = " + str(parms["contCals"]))
else:
# Snatch from pickle jar
parms["contCals"] = FetchObject(OKCalPicklefile)
# Save contCals to a pickle jar
SaveObject(parms["contCals"], OKCalPicklefile, True)
# Find best calibration source
if parms["doFindCal"]:
logger.info("--> Find best calibration source (doFindCal)")
goodCal = VLBAGoodCal(uv, err, \
solInt=parms["findSolInt"], timeInt=parms["findTimeInt"], \
calSou=parms["contCals"], \
#CalModel=parms["contCalModel"], \
doCalib=-1, flagVer=2, refAnts=parms["refAnts"], \
noScrat=noScrat, nThreads=nThreads, \
logfile=logFile, check=check, debug=debug)
if not goodCal and not check:
raise RuntimeError("Error in finding best calibration data")
# Save it to a pickle jar
SaveObject(goodCal, goodCalPicklefile, True)
else:
# Fetch from pickle
goodCal = FetchObject(goodCalPicklefile)
# Apply Phase cals from PC table?
if parms["doPCcor"] and not check:
logger.info("--> Apply phase cals (doPCcor)")
plotFile = project + "_" + session + "_" + band + ".PC.ps"
retCode = VLBAPCcor(uv, err, calSou=goodCal["Source"], \
timeRange=goodCal["timeRange"], \
doCalib=-1, flagVer=2, solInt=parms["manPCsolInt"], \
PCin=1, SNout=0, refAnt=goodCal["bestRef"], \
doPCPlot=parms["doPCPlot"], plotFile=plotFile, \
noScrat=noScrat, logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in PC calibration")
VLBASaveOutFiles() # Save plot file in Outfiles
# manual phase cal
if parms["doManPCal"] and not check:
logger.info("--> Manual phase cal (doManPCal)")
plotFile = project + session + band + ".ManPCal.ps"
retCode = VLBAManPCal(uv, err, calSou=goodCal["Source"], \
#CalModel=parms["contCalModel"], \
timeRange=goodCal["timeRange"], \
solInt=parms["manPCsolInt"], smoTime=parms["manPCSmoo"], \
refAnts=[goodCal["bestRef"]], doCalib=2, flagVer=2, \
doManPCalPlot=parms["doManPCalPlot"], \
plotFile=plotFile, noScrat=noScrat, \
nThreads=nThreads, logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in manual phase calibration")
# image cals
if parms["doImgCal"] and not check:
logger.info("--> Image calibrators (doImgCal)")
VLBAImageCals(uv,
err,
Sources=parms["contCals"],
seq=seq,
sclass=parms["outCclass"],
doCalib=2,
flagVer=2,
doBand=0,
FOV=parms["FOV"],
Robust=parms["Robust"],
maxPSCLoop=parms["maxPSCLoop"],
minFluxPSC=parms["minFluxPSC"],
solPInt=parms["solPInt"],
solMode=parms["solMode"],
maxASCLoop=parms["maxASCLoop"],
minFluxASC=parms["minFluxASC"],
solAInt=parms["solAInt"],
avgPol=parms["avgPol"],
avgIF=parms["avgIF"],
minSNR=parms["minSNR"],
refAnt=goodCal["bestRef"],
nThreads=nThreads,
noScrat=noScrat,
logfile=logFile,
check=check,
debug=debug)
# Rewrite OKCal pickle file because calibrators may have been updated
SaveObject(parms["contCals"], OKCalPicklefile, True)
if len(parms["contCals"]) <= 0:
logger.error(
"No calibration sources have been detected! Stopping pipeline."
)
raise RuntimeError("No calibration sources have been detected!")
# Check if calibrator models now available
parms["contCalModel"] = VLBAImageModel(parms["contCals"],
parms["outCclass"], disk, seq, err)
# delay calibration
if parms["doDelayCal"] and not check:
logger.info("--> Delay calibration (doDelayCal)")
plotFile = project + "_" + session + "_" + band + ".DelayCal.ps"
retCode = VLBADelayCal(uv, err, calSou=parms["contCals"], CalModel=parms["contCalModel"], \
doCalib=2, flagVer=2, doBand=0, \
solInt=parms["manPCsolInt"], smoTime=parms["delaySmoo"], \
refAnts=[goodCal["bestRef"]], \
doSNPlot=parms["doSNPlot"], plotFile=plotFile, \
nThreads=nThreads, noScrat=noScrat, logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in delay calibration")
VLBASaveOutFiles() # Save plot file in Outfiles
# Bandpass calibration if needed
if parms["doBPCal"] and not check:
logger.info("--> Bandpass calibration (doBPCal)")
retCode = VLBABPass(uv, goodCal["Source"], err, CalModel=parms["contCalModel"], \
timeRange=goodCal["timeRange"], doCalib=2, flagVer=2, \
noScrat=noScrat, solInt1=parms["bpsolint1"], \
solInt2=parms["bpsolint2"], solMode=parms["bpsolMode"], \
BChan1=parms["bpBChan1"], EChan1=parms["bpEChan1"], BChan2=parms["bpBChan2"], \
EChan2=parms["bpEChan2"], ChWid2=parms["bpChWid2"], \
doCenter1=parms["bpDoCenter1"], refAnt=goodCal["bestRef"], specIndex=parms["specIndex"], \
doAuto = parms["bpdoAuto"], \
nThreads=nThreads, logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in Bandpass calibration")
# Plot amplitude and phase vs. frequency
if parms["doSpecPlot"]:
logger.info("--> Spectral plotting (doSpecPlot)")
plotFile = project + '_' + session + '_' + band + ".spec.ps"
VLBASpecPlot(uv,
goodCal,
err,
doband=1,
check=check,
plotFile=plotFile,
logfile=logFile,
debug=debug)
VLBASaveOutFiles() # Save plot file in Outfiles
# Phase calibration using calibrator models
if parms["doPhaseCal"]:
logger.info(
"--> Phase calibration using calibrator models (doPhaseCal)")
plotFile = project + "_" + session + "_" + band + ".PhaseCal0.ps"
retCode = VLBAPhaseCal(uv, err, calSou=parms["contCals"], CalModel=parms["contCalModel"], \
doCalib=-1, flagVer=0, doBand=-1, \
refAnt=goodCal["bestRef"], solInt=parms["solPInt"], \
doSNPlot=parms["doSNPlot"], plotFile=plotFile, \
nThreads=nThreads, noScrat=noScrat, logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in phase calibration")
VLBASaveOutFiles() # Save plot file in Outfiles
# Rewrite contCals pickle file because contCals may have been updated
SaveObject(parms["contCals"], OKCalPicklefile, True)
if len(parms["contCals"]) <= 0:
logger.error(
"No calibrator sources have been detected! Stopping pipeline.")
raise RuntimeError("No calibrator sources have been detected!")
# Amplitude calibration
if parms["doAmpCal"] and not check:
logger.info("--> Amplitude calibration (doAmpCal)")
plotFile = project + "_" + session + "_" + band + ".AmpCal.ps"
retCode = VLBAAmpCal(uv,
err,
calSou=parms["contCals"],
CalModel=parms["contCalModel"],
doCalib=2,
flagVer=2,
doBand=1,
minSumCC=parms["minFluxASC"],
refAnt=goodCal["bestRef"],
solInt=parms["solAInt"],
smoTimeA=2.0,
smoTimeP=1. / 60.,
doSNPlot=parms["doSNPlot"],
plotFile=plotFile,
nThreads=nThreads,
noScrat=noScrat,
logfile=logFile,
check=check,
debug=debug)
if retCode != 0:
raise RuntimeError("Error in amplitude calibration")
VLBASaveOutFiles() # Save plot file in Outfiles
# Rewrite contCals pickle file because contCals may have been updated
SaveObject(parms["contCals"], OKCalPicklefile, True)
if len(parms["contCals"]) <= 0:
logger.error(
"No calibrator sources have been detected! Stopping pipeline.")
raise RuntimeError("No calibrator sources have been detected!")
# Calibrate and average data
if parms["doCalAvg"]:
logger.info("--> Calibration and average data (doCalAvg)")
retCode = VLBACalAvg (uv, parms["avgClass"], seq, parms["CalAvgTime"], err, \
flagVer=2, doCalib=2, gainUse=0, doBand=1, BPVer=1, \
BIF=parms["CABIF"], EIF=parms["CAEIF"], \
BChan=parms["CABChan"], EChan=parms["CAEChan"], \
chAvg=parms["chAvg"], avgFreq=parms["avgFreq"], Compress=Compress, \
logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in CalAvg")
# image targets phase only self-cal - NOTE: actually A&P
if parms["doImgTarget"] and not check:
logger.info("--> Image targets (doImgTargets)")
if not uvc:
# Get calibrated/averaged data
Aname = VLBAAIPSName(project, session)
uvname = project + "_" + session + "_" + band + "_Cal"
uvc = UV.newPAUV(uvname, Aname, parms["avgClass"], disk, seq, True,
err)
if err.isErr:
OErr.printErrMsg(err, "Error creating cal/avg AIPS data")
logger.debug("parms['targets'] = " + str(parms["targets"]))
VLBAImageCals(uv,
err,
Sources=parms["targets"],
seq=seq,
sclass=parms["outTclass"],
doCalib=2,
flagVer=2,
doBand=1,
FOV=parms["FOV"],
Robust=parms["Robust"],
maxPSCLoop=parms["maxPSCLoop"],
minFluxPSC=parms["minFluxPSC"],
solPInt=parms["solPInt"],
solMode=parms["solMode"],
maxASCLoop=parms["maxASCLoop"],
minFluxASC=parms["minFluxASC"],
solAInt=parms["solAInt"],
avgPol=parms["avgPol"],
avgIF=parms["avgIF"],
minSNR=parms["minSNR"],
refAnt=goodCal["bestRef"],
nThreads=nThreads,
noScrat=noScrat,
logfile=logFile,
check=check,
debug=debug)
# Rewrite targets pickle file because targets may have been updated
SaveObject(parms["targets"], targetsPicklefile, True)
if len(parms["targets"]) <= 0:
logger.error(
"No target sources have been detected! Stopping pipeline.")
raise RuntimeError("No target sources have been detected!")
# Phase calibration using target models
if parms["doPhaseCal"]:
logger.info("--> Phase calibration using target models (doPhaseCal)")
if not uvc:
# Get calibrated/averaged data
Aname = VLBAAIPSName(project, session)
uvname = project + "_" + session + "_" + band + "_Cal"
uvc = UV.newPAUV(uvname, Aname, parms["avgClass"], disk, seq, True,
err)
if err.isErr:
OErr.printErrMsg(err, "Error creating cal/avg AIPS data")
parms["targetModel"] = VLBAImageModel(parms["targets"],
parms["outTclass"], disk, seq,
err)
plotFile = project + "_" + session + "_" + band + ".PhaseCal.ps"
retCode = VLBAPhaseCal(uvc, err, calSou=parms["targets"], CalModel=parms["targetModel"], \
doCalib=-1, flagVer=0, doBand=-1, \
refAnt=goodCal["bestRef"], solInt=parms["manPCsolInt"], \
doSNPlot=parms["doSNPlot"], plotFile=plotFile, \
nThreads=nThreads, noScrat=noScrat, logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in phase calibration")
VLBASaveOutFiles() # Save plot file in Outfiles
# Rewrite targets pickle file because targets may have been updated
SaveObject(parms["targets"], targetsPicklefile, True)
if len(parms["targets"]) <= 0:
logger.error(
"No target sources have been detected! Stopping pipeline.")
raise RuntimeError("No target sources have been detected!")
# Instrumental polarization calibration
if parms["doInstPol"]:
logger.info("--> Instrumental polarization calibration (doInstPol)")
# calibrators defaults to strong calibrator list
if not parms["instPolCal"]:
instPolCal = contCals
else:
instPolCal = parms["instPolCal"]
if not uvc:
# Get calibrated/averaged data
Aname = VLBAAIPSName(project, session)
uvname = project + "_" + session + "_" + band + "_Cal"
uvc = UV.newPAUV(uvname, Aname, parms["avgClass"], disk, seq, True,
err)
if err.isErr:
OErr.printErrMsg(err, "Error creating cal/avg AIPS data")
retCode = VLBAPolCal(uvc, instPolCal, err, \
doCalib=2, flagVer=0, doBand=-1, doSetJy=True, \
refAnt=goodCal["bestRef"], solInt=2.0, \
noScrat=noScrat, logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in instrumental poln calibration")
# RL Phase (EVPA) calibration as BP table
if parms["doRLCal"] and parms["RLCal"]:
logger.info("--> RL phase calibration (doRLCal)")
if not uvc:
# Get calibrated/averaged data
Aname = VLBAAIPSName(project, session)
uvname = project + "_" + session + "_" + band + "_Cal"
uvc = UV.newPAUV(uvname, Aname, parms["avgClass"], disk, seq, True,
err)
if err.isErr:
OErr.printErrMsg(err, "Error creating cal/avg AIPS data")
retCode = VLBARLCal2(uvc, err, RLPCal=parms["RLCal"], \
doCalib=2, gainUse=2, flagVer=0, doBand=-1, doPol=True, \
refAnt=goodCal["bestRef"], niter=300, FOV=0.02/3600.0, \
nThreads=nThreads, noScrat=noScrat, logfile=logFile, check=check, debug=debug)
if retCode != 0:
raise RuntimeError("Error in RL phase calibration")
# image targets possible with Stokes I(QU)
if parms["doImgFullTarget"]:
logger.info("--> Image targets (doImgFullTargets)")
if not uvc:
# Get calibrated/averaged data
Aname = VLBAAIPSName(project, session)
uvname = project + "_" + session + "_" + band + "_Cal"
uvc = UV.newPAUV(uvname, Aname, parms["avgClass"], disk, seq, True,
err)
if err.isErr:
OErr.printErrMsg(err, "Error creating cal/avg AIPS data")
VLBAImageTargets(uvc,
err,
Sources=parms["targets"],
seq=seq,
sclass=parms["outIclass"],
doCalib=2,
flagVer=0,
doBand=-1,
Stokes=parms["Stokes"],
FOV=parms["FOV"],
Robust=parms["Robust"],
maxPSCLoop=2,
minFluxPSC=parms["minFluxPSC"],
solPInt=parms["solPInt"],
solMode="P",
maxASCLoop=parms["maxASCLoop"],
minFluxASC=parms["minFluxASC"],
solAInt=parms["solAInt"],
avgPol=parms["avgPol"],
avgIF=parms["avgIF"],
minSNR=parms["minSNR"],
refAnt=goodCal["bestRef"],
nTaper=parms["nTaper"],
Tapers=parms["Tapers"],
do3D=parms["do3D"],
nThreads=nThreads,
noScrat=noScrat,
logfile=logFile,
check=check,
debug=debug)
# Save UV data?
if parms["doSaveUV"] and (not check):
logger.info("--> Save UV data (doSaveUV)")
mess = "Write calibrated and averaged UV data to disk"
printMess(mess, logFile)
# Get calibrated/averaged data
if not uvc:
Aname = VLBAAIPSName(project, session)
uvname = project + "_" + session + "_" + band + "_Cal"
uvc = UV.newPAUV(uvname, Aname, parms["avgClass"], disk, seq, True,
err)
if err.isErr:
OErr.printErrMsg(err, "Error creating cal/avg AIPS data")
# Write
filename = project + session + band + "CalAvg.uvtab"
fuv = VLBAUVFITS(uvc, filename, 0, err, compress=Compress)
VLBAAddOutFile(filename, 'project', "Calibrated Averaged UV data")
# Save list of output files
VLBASaveOutFiles()
# Save UV data tables?
if parms["doSaveTab"] and (not check):
logger.info("--> Save UV data tables (doSaveTab)")
mess = "Write UV data tables to disk."
printMess(mess, logFile)
filename = project + session + band + "CalTab.uvtab"
fuv = VLBAUVFITSTab(uv, filename, 0, err)
VLBAAddOutFile(filename, 'project', "Calibrated AIPS tables")
# Save list of output files
VLBASaveOutFiles()
# Imaging results
outDisk = 0
if parms["doSaveImg"]:
logger.info("--> Save images (doSaveImg)")
mess = "Write images to disk."
printMess(mess, logFile)
# How many Stokes images
nstok = len(parms["Stokes"])
# Targets
logger.debug("parms['targets'] = " + str(parms['targets']))
for target in parms["targets"]:
if not check:
# intermediate images
oclass = parms["outTclass"]
x = Image.newPAImage("out", target, oclass, disk, seq, True,
err)
if (not x.exist):
print(target, "image not found. Skipping.")
continue
outfile = project + session + band + target + "." + oclass + ".fits"
mess = "Write Intermediate target " + outfile + " on disk " + str(
outDisk)
VLBAAddOutFile(outfile, target, 'Intermediate target image')
printMess(mess, logFile)
xf = VLBAImFITS(x, outfile, outDisk, err, fract=0.1)
# Save list of output files
VLBASaveOutFiles()
# Statistics
zz = imstat(x, err, logfile=logFile)
del x, xf
# Final images
for istok in range(0, nstok):
oclass = parms["Stokes"][istok:istok +
1] + parms["outIclass"][1:]
x = Image.newPAImage("out", target, oclass, disk, seq,
True, err)
outfile = project + session + band + target + "." + oclass + ".fits"
logger.info("Write " + outfile + " on disk " +
str(outDisk))
xf = VLBAImFITS(x, outfile, outDisk, err, fract=0.1)
VLBAAddOutFile(outfile, target, 'Image')
logger.info("Writing file " + outfile)
# Statistics
zz = imstat(x, err, logfile=logFile)
del x, xf
# Save list of output files
VLBASaveOutFiles()
# Calibrators
for target in parms["contCals"]:
if not check:
oclass = parms["outCclass"]
x = Image.newPAImage("out", target, oclass, disk, seq, True,
err)
if (not x.exist):
print(target, "image not found. Skipping.")
continue
outfile = project + session + band + target + "." + oclass + ".fits"
mess = "Write Calibrator " + outfile + " on disk " + str(
outDisk)
printMess(mess, logFile)
xf = VLBAImFITS(x, outfile, outDisk, err, fract=0.1)
VLBAAddOutFile(outfile, target, 'Calibrator Image')
# Statistics
zz = imstat(x, err, logfile=logFile)
del x, xf
# Save list of output files
VLBASaveOutFiles()
# end writing images loop
# Contour plots
if parms["doKntrPlots"]:
logger.info("--> Contour plots (doKntrPlots)")
VLBAKntrPlots(err,
imName=parms["targets"],
project=project,
session=session,
band=band,
disk=disk,
debug=debug)
# Save list of output files
VLBASaveOutFiles()
elif debug:
print("Not creating contour plots ( doKntrPlots = ",
parms["doKntrPlots"], " )")
# Source uv plane diagnostic plots
if parms["doDiagPlots"]:
logger.info("--> Diagnostic plots (doDiagPlots)")
# Get the highest number avgClass catalog file
Aname = VLBAAIPSName(project, session)
uvc = None
if not check:
uvname = project + "_" + session + "_" + band + "_Cal"
uvc = UV.newPAUV(uvname, Aname, parms["avgClass"], disk, seq, True,
err)
VLBADiagPlots( uvc, err, cleanUp=parms["doCleanup"], \
project=project, session=session, band=band, \
logfile=logFile, check=check, debug=debug )
# Save list of output files
VLBASaveOutFiles()
elif debug:
print("Not creating diagnostic plots ( doDiagPlots = ",
parms["doDiagPlots"], " )")
# Save metadata
srcMetadata = None
projMetadata = None
if parms["doMetadata"]:
logger.info("--> Save metadata (doMetadata)")
if not uvc:
# Get calibrated/averaged data
Aname = VLBAAIPSName(project, session)
uvname = project + "_" + session + "_" + band + "_Cal"
uvc = UV.newPAUV(uvname, Aname, parms["avgClass"], disk, seq, True,
err)
if err.isErr:
OErr.printErrMsg(err, "Error creating cal/avg AIPS data")
# Get source metadata; save to pickle file
srcMetadata = VLBASrcMetadata(uvc,
err,
Sources=parms["targets"],
seq=seq,
sclass=parms["outIclass"],
Stokes=parms["Stokes"],
logfile=logFile,
check=check,
debug=debug)
picklefile = project + "_" + session + "_" + band + "SrcReport.pickle"
SaveObject(srcMetadata, picklefile, True)
VLBAAddOutFile(picklefile, 'project', 'All source metadata')
# Get project metadata; save to pickle file
projMetadata = VLBAProjMetadata(uvc,
AIPS_VERSION,
err,
contCals=parms["contCals"],
goodCal=goodCal,
project=project,
session=session,
band=band,
dataInUVF=dataInUVF,
archFileID=archFileID)
picklefile = project + "_" + session + "_" + band + "ProjReport.pickle"
SaveObject(projMetadata, picklefile, True)
VLBAAddOutFile(picklefile, 'project', 'Project metadata')
# Write report
if parms["doHTML"]:
logger.info("--> Write HTML report (doHTML)")
VLBAHTMLReport( projMetadata, srcMetadata, \
outfile=project+"_"+session+"_"+band+"report.html", \
logFile=logFile )
# Write VOTable
if parms["doVOTable"]:
logger.info("--> Write VOTable (doVOTable)")
VLBAAddOutFile('VOTable.xml', 'project', 'VOTable report')
VLBAWriteVOTable(projMetadata, srcMetadata, filename='VOTable.xml')
# Save list of output files
VLBASaveOutFiles()
# Cleanup - delete AIPS files
if parms["doCleanup"] and (not check):
logger.info("--> Clean up (doCleanup)")
# Delete target images
# How many Stokes images
nstok = len(parms["Stokes"])
for istok in range(0, nstok):
oclass = parms["Stokes"][istok:istok + 1] + parms["outIclass"][1:]
AllDest(err, disk=disk, Aseq=seq, Aclass=oclass)
# delete Calibrator images
AllDest(err, disk=disk, Aseq=seq, Aclass=parms["outCclass"])
# Delete intermediate target images
AllDest(err, disk=disk, Aseq=seq, Aclass=parms["outTclass"])
OErr.printErrMsg(err, "Deleting AIPS images")
# Delete UV data
uv.Zap(err)
# Zap calibrated/averaged data
if not uvc:
Aname = VLBAAIPSName(project, session)
uvc = UV.newPAUV("AIPS UV DATA", Aname, parms["avgClass"], disk,
seq, True, err)
if err.isErr:
OErr.printErrMsg(err, "Error creating cal/avg AIPS data")
uvc.Zap(err)
OErr.printErrMsg(err, "Writing output/cleanup")
# Shutdown
mess = "Finished project " + project
printMess(mess, logFile)
OErr.printErr(err)
OSystem.Shutdown(ObitSys)
def PUVCreateImager(err, name='myUVImager', input=UVCreateImagerInput):
""" Create an imager to generate a set of images needed to cover a region.
Create and return a Python Obit UVImager based on input parameters and
uv data to be imaged. Images should be fully defined when returned.
err = Python Obit Error/message stack
name = Name for output object
input = input parameter dictionary
Input dictionary entries:
InData = Input Python UV data to image
doCalSelect = Select/calibrate/edit data?),
Stokes = Stokes parameter, blank-> unchanged from input),
BChan = First spectral channel selected. [def all]),
EChan = Highest spectral channel selected. [def all]),
BIF = First IF selected. [def all]),
EIF = Highest IF selected. [def all]),
doPol = >0 -> calibrate polarization.),
doCalib = >0 -> calibrate, 2=> also calibrate Weights),
gainUse = SN/CL table version number, 0-> use highest),
flagVer = Flag table version, 0-> use highest, <0-> none),
BLVer = BL table version, 0> use highest, <0-> none),
BPVer = Band pass (BP) table version, 0-> use highest),
Subarray = Selected subarray, <=0->all [default all]),
freqID = Selected Frequency ID, <=0->all [default all]),
timeRange= Selected timerange in days. [2 floats] 0s -> all),
UVRange = Selected UV range in wavelengths. 0s -> all),
Sources = Source names selected unless any starts with),
Antennas = A list of selected antenna numbers, if any is negative),
corrType = Correlation type, 0=cross corr only, 1=both, 2=auto only.),
doBand = Band pass application type <0-> none),
Smooth = Specifies the type of spectral smoothing [three floats]
DoWeight = True if Weighting to be applied
Robust = Briggs robust parameter. (AIPS definition)
UVTaper = UV plane taper, sigma in klambda,deg as [maj, min, pa]
WtSize = Size of weighting grid in cells [same as image nx]
WtBox = Size of weighting box in cells [def 1]
WtFunc = Weighting convolution function [def. 1]
1=Pill box, 2=linear, 3=exponential, 4=Gaussian
if positive, function is of radius, negative in u and v.
WtPower = Power to raise weights to. [def = 1.0]
Note: a power of 0.0 sets all the output weights to 1 as modified
by uniform/Tapering weighting.
Applied in determinng weights as well as after.
DoBeam = True if beams are to be made
Type = Underlying file type, 0=FITS, 1=AIPS
Name = Name of image, used as AIPS name or to derive FITS filename
Class = Root of class, used as AIPS class or to derive FITS filename
Seq = Sequence number
Disk = Disk number for underlying files
FOV = Field of view (deg) for Mosaic
doFull = If True, create full field (FOV) image
NField = Number of fields defined in input,
if unspecified derive from data and FOV
xCells = Cell spacing in X (asec) for all images,
if unspecified derive from data
yCells = Cell spacing in Y (asec) for all images,
if unspecified derive from data
nx = Minimum number of cells in X for NField images
if unspecified derive from data
ny = Minimum number of cells in Y for NField images
if unspecified derive from data
RAShift = Right ascension shift (AIPS convention) for each field
if unspecified derive from FOV and data
DecShift = Declination for each field
if unspecified derive from FOV and data
Catalog = AIPSVZ format catalog for defining outliers, None=do not use
OutlierFlux = Minimum estimated outlyer flux density (Jy)
OutlierDist = Maximum distance to add outlyers (deg)
OutlierSI = Spectral index to estimate flux density
OutlierSize = Size of outlyer field (pixels)
returns = Output UVImager with defined ImageMosaic
"""
################################################################
# Get input parameters
InData = input["InData"]
#
# Checks
if not UV.PIsA(InData):
raise TypeError, 'UVCreateImage: Bad input UV data'
# Set control values on UV
dim[0] = 1
dim[1] = 1
dim[2] = 1
dim[3] = 1
dim[4] = 1
inInfo = UV.PGetList(InData) # Add control to UV data
# Calibration/editing/selection
InfoList.PAlwaysPutBoolean(inInfo, "doCalSelect", dim,
[input["doCalSelect"]])
dim[0] = 4
InfoList.PAlwaysPutString(inInfo, "Stokes", dim, [input["Stokes"]])
dim[0] = 1
InfoList.PAlwaysPutInt(inInfo, "BChan", dim, [input["BChan"]])
InfoList.PAlwaysPutInt(inInfo, "EChan", dim, [input["EChan"]])
InfoList.PAlwaysPutInt(inInfo, "BIF", dim, [input["BIF"]])
InfoList.PAlwaysPutInt(inInfo, "EIF", dim, [input["EIF"]])
itemp = int(input["doPol"])
InfoList.PAlwaysPutInt(inInfo, "doPol", dim, [itemp])
InfoList.PAlwaysPutInt(inInfo, "doCalib", dim, [input["doCalib"]])
InfoList.PAlwaysPutInt(inInfo, "doBand", dim, [input["doBand"]])
InfoList.PAlwaysPutInt(inInfo, "gainUse", dim, [input["gainUse"]])
InfoList.PAlwaysPutInt(inInfo, "flagVer", dim, [input["flagVer"]])
InfoList.PAlwaysPutInt(inInfo, "BLVer", dim, [input["BLVer"]])
InfoList.PAlwaysPutInt(inInfo, "BPVer", dim, [input["BPVer"]])
InfoList.PAlwaysPutInt(inInfo, "Subarray", dim, [input["Subarray"]])
InfoList.PAlwaysPutInt(inInfo, "freqID", dim, [input["freqID"]])
InfoList.PAlwaysPutInt(inInfo, "corrType", dim, [input["corrType"]])
dim[0] = 2
InfoList.PAlwaysPutFloat(inInfo, "UVRange", dim, input["UVRange"])
dim[0] = 3
InfoList.PAlwaysPutFloat(inInfo, "Smooth", dim, input["Smooth"])
dim[0] = 2
InfoList.PAlwaysPutFloat(inInfo, "timeRange", dim, input["timeRange"])
dim[0] = len(input["Antennas"])
InfoList.PAlwaysPutInt(inInfo, "Antennas", dim, input["Antennas"])
dim[0] = 16
dim[1] = len(input["Sources"])
InfoList.PAlwaysPutString(inInfo, "Sources", dim, input["Sources"])
# Weighting parameters
dim[0] = 1
dim[1] = 1
InfoList.PAlwaysPutFloat(inInfo, "Robust", dim, [input["Robust"]])
InfoList.PAlwaysPutInt(inInfo, "WtBox", dim, [input["WtBox"]])
InfoList.PAlwaysPutInt(inInfo, "WtFunc", dim, [input["WtFunc"]])
InfoList.PAlwaysPutFloat(inInfo, "WtPower", dim, [input["WtPower"]])
dim[0] = len(input["UVTaper"])
InfoList.PAlwaysPutFloat(inInfo, "UVTaper", dim, input["UVTaper"])
WtSize = input["WtSize"]
if (WtSize > 0):
print "WtSize", WtSize
# Change name for C routine.
dim[0] = 1
InfoList.PAlwaysPutInt(inInfo, "nuGrid", dim, [WtSize])
InfoList.PAlwaysPutInt(inInfo, "nvGrid", dim, [WtSize])
# Define image
dim[0] = 1
dim[1] = 1
InfoList.PAlwaysPutInt(inInfo, "imFileType", dim, [input["Type"]])
InfoList.PAlwaysPutInt(inInfo, "imSeq", dim, [input["Seq"]])
InfoList.PAlwaysPutInt(inInfo, "imDisk", dim, [input["Disk"]])
InfoList.PAlwaysPutFloat(inInfo, "FOV", dim, [input["FOV"]])
InfoList.PAlwaysPutBoolean(inInfo, "doFull", dim, [input["doFull"]])
InfoList.PAlwaysPutInt(inInfo, "NField", dim, [input["NField"]])
InfoList.PAlwaysPutFloat(inInfo, "xCells", dim, [input["xCells"]])
InfoList.PAlwaysPutFloat(inInfo, "yCells", dim, [input["yCells"]])
InfoList.PAlwaysPutFloat(inInfo, "OutlierFlux", dim,
[input["OutlierFlux"]])
InfoList.PAlwaysPutFloat(inInfo, "OutlierDist", dim,
[input["OutlierDist"]])
InfoList.PAlwaysPutFloat(inInfo, "OutlierSI", dim, [input["OutlierSI"]])
InfoList.PAlwaysPutInt(inInfo, "OutlierSize", dim, [input["OutlierSize"]])
dim[0] = len(input["Name"])
InfoList.PAlwaysPutString(inInfo, "imName", dim, [input["Name"]])
dim[0] = len(input["Class"])
InfoList.PAlwaysPutString(inInfo, "imClass", dim, [input["Class"]])
dim[0] = len(input["Catalog"])
InfoList.PAlwaysPutString(inInfo, "Catalog", dim, [input["Catalog"]])
dim[0] = len(input["nx"])
InfoList.PAlwaysPutInt(inInfo, "nx", dim, input["nx"])
dim[0] = len(input["ny"])
InfoList.PAlwaysPutInt(inInfo, "ny", dim, input["ny"])
dim[0] = len(input["RAShift"])
InfoList.PAlwaysPutFloat(inInfo, "RAShift", dim, input["RAShift"])
dim[0] = len(input["DecShift"])
InfoList.PAlwaysPutFloat(inInfo, "DecShift", dim, input["DecShift"])
#
# Create
out = UVImager(name, InData.me, err.me)
# show any errors
#OErr.printErrMsg(err, "UVImage: Error creating UVImager object")
#
return out
mess = "Start project " + project + " session " + session + " " + band + " Band"
printMess(mess, logFile)
if debug:
mess = "Using Debug mode "
printMess(mess, logFile)
if check:
mess = "Only checking script"
printMess(mess, logFile)
# Load Data from FITS
uv = None
if doLoadIDI:
uv = VLBAIDILoad(dataIn, project, session, band, dataClass, disk, seq, err, logfile=logFile, \
wtThresh=wtThresh, calInt=calInt, Compress=Compress, \
check=check, debug=debug)
if not UV.PIsA(uv):
raise RuntimeError, "Cannot load " + dataIn
# Otherwise set uv
if uv == None and not check:
Aname = VLBAAIPSName(project, session)
uv = UV.newPAUV("AIPS UV DATA", Aname, dataClass, disk, seq, True, err)
if err.isErr:
OErr.printErrMsg(err, "Error creating AIPS data")
# Clear any old calibration/editing
if doClearTab:
VLBAClearCal(uv,
err,
doGain=doGain,
doFlag=doFlag,
doBP=doBP,
def ExtractPD (inUV, ant, err, PDVer=1, inc=1):
""" Extract data from PD table
return dict:
'Elip1' array of elipticities poln 1 in deg
'Ori1' array of orientations poln 1 in deg
'Elip2' array of elipticities poln 2 in deg
'Ori2' array of orientations poln 2 in deg
'Freqs' array of frequencies corresponding to data
'refant' reference antenna
'ant' antenna
* inUV = Obit UV data with tables
* ant = antenna number
* err = Obit error/message stack
* PDVer = PD table version
* inc = increment in spectrum
"""
################################################################
# Checks
if not UV.PIsA(inUV):
print("Actually ",inUV.__class__)
raise TypeError("inUV MUST be a Python Obit UV")
e1 = []; e2 = []; o1 = []; o2 = []
# Get table
PDTab = inUV.NewTable(Table.READONLY,"AIPS PD",PDVer,err)
# Open table, find antenna
PDTab.Open(Table.READONLY, err)
nrow = PDTab.Desc.Dict['nrow']
for irow in range (1,nrow+1):
row = PDTab.ReadRow(irow, err)
if row['ANTENNA'][0]==ant:
break
for i in range(0,len(row['REAL 1']),inc):
e = row['REAL 1'][i]
# Bad soln?
if e==fblank:
e1.append(fblank); e2.append(fblank);
o1.append(fblank); o2.append(fblank);
else:
# Fold elipticities to range [-45, 45]
e = math.degrees(e)
o = math.degrees(row['IMAG 1'][i])
if e>45.0:
e = 90.0 - e
o = -o
if o>180.0:
o -= 360.
if o<-180.0:
o += 360
# Default values probably bad
if e>=44.999 and o==0.0:
e = fblank; o = fblank
e1.append(e)
o1.append(o)
e = math.degrees(row['REAL 2'][i])
o = math.degrees(row['IMAG 2'][i])
if e<-45.0:
e = -(90.0 + e)
o = -o
if o>180.0:
o -= 360.
if o<-180.0:
o += 360
if e<=-44.999 and o==0.0:
e = fblank; o = fblank
e2.append(e)
o2.append(o)
refant = row['REFANT'][0]
ant = row['ANTENNA'][0]
del row
PDTab.Close(err)
# Get frequencies
f = GetFreqArr(inUV, err)
# select by inc in GHz
frqs = []
for i in range(0,len(f),inc):
frqs.append(f[i]*1.0e-9)
return {'Elip1':e1, 'Ori1':o1, 'Elip2':e2, 'Ori2':o2, 'refant':refant, 'ant':ant, 'Freqs':frqs}
def FitSource(inUV, souID, err, CPVer=1, inc=1):
"""
Fit the RM of a source in a CP table
Return a dict with:
"RM" = fitted RM (rad/m**2)
"RMErr" = fitted RM error
"EVPA0" = EVPA at "RefLamb2 (rad)
"EVPAErr" = error in EVPA
"RefLamb2" = reference Lambda^2
"Lamb2" = array of lamb2 (m**2)
"FPol" = array of fractional poln
"EVPA = array of EVPA (rad) of poln
* inUV = Obit UV data with tables
* souID = source ID
* err = Python Obit Error/message stack
* CPVer = CP table version
* inc = incremant between channels to use
"""
################################################################
# Checks
if not UV.PIsA(inUV):
print("Actually ",inUV.__class__)
raise TypeError("inUV MUST be a Python Obit UV")
# Get table
cptab = inUV.NewTable(Table.READONLY,"AIPS CP",CPVer,err)
cptab.Open(Table.READONLY,err)
nrow = cptab.Desc.Dict["nrow"]
# Find souID
IPol = None
for irow in range (1,nrow+1):
cprow=cptab.ReadRow(irow,err)
if souID == cprow["SOURCE ID"][0]:
IPol = cprow["I"]
QPol = cprow["Q"]
UPol = cprow["U"]
break
# end loop looking for souID
# Find it?
if IPol==None:
raise RuntimeError("No CP entry for source ID "+str(souID))
# Get lambda^2 array
lamb2 = GetLamb2(inUV, err)
# Check consistency
if len(IPol)!=len(lamb2):
raise RuntimeError("Size of CP entries ("+str(len(IPol))+") NOT number of channels ("+str(len(lamb2))+")")
# Get fitting parameters with descimation by inc
l2 = []; QObs = []; Qsig = []; UObs = []; Usig = [];
FPol = []; EVPA = []
for i in range (0, len(lamb2), inc):
if IPol[i]>0.0:
l2.append(lamb2[i])
QObs.append(QPol[i]); Qsig.append(0.001)
UObs.append(UPol[i]); Usig.append(0.001)
EVPA.append(0.5*math.atan2(UPol[i], QPol[i]))
FPol.append(((QPol[i]**2+UPol[i]**2)**0.5)/IPol[i])
# end loop getting data arrays
# Fit RM
refLamb2 = l2[len(l2)/2]
RMParms = RMFit.PSingle(refLamb2, l2, QObs, Qsig, UObs, Usig, err)
print("debug RMParms",RMParms)
print("Fitted RM=%f (%f), EVPA=%f(%f)"\
%(RMParms[0],RMParms[2],math.degrees(RMParms[1]),math.degrees(RMParms[3])))
return{"RM":RMParms[0], "RMErr":RMParms[2], "EVPA0":RMParms[1], "EVPAErr":RMParms[3], \
"RefLamb2":refLamb2 ,"Lamb2":l2, "FPol":FPol, "EVPA":EVPA}
def UVSub4Peel(uv, source, im, inCC, err, \
nfield=1, doGPU=False, gainUse=1, flagVer=-1, \
nThreads=1, noScrat=[0,0,0], taskLog='', debug=False):
"""
Sets up for subtraction of non peel sources from data
UV data should be have calibration tables from self calibration
Output data will be on the same disk as the input, seq=1, class='4Peel' and
with the name of the source (up to 12 char)
Returns UVSub task object
* uv Dataset to be subtracted from
* source source name
* im Python Image with CC Tables
* inCC input CC version, should have had the peel source CCs removed
using SelectCC
* err Python Obit Error/message stack
* doGPU Use GPU if available?
* nfield Number of facet images
* gainUse CL (SN) table to apply, -1=> no cal
* flagVer FG table to apply, -1=> no flag
* noThreads number of threads to use
* noScrat AIPS disks not to use for scratch
* taskLog Log file
* debug If True leave debug Input file in /tmp
"""
################################################################
# Checks
if not UV.PIsA(uv):
raise TypeError("uv MUST be a Python Obit UV data")
if not Image.PIsA(im):
raise TypeError("im MUST be a Python Obit Image")
if not OErr.OErrIsA(err):
raise TypeError("err MUST be an OErr")
uvsub = ObitTask('UVSub')
setname(uv, uvsub)
set2name(im, uvsub)
uvsub.CCVer = inCC
uvsub.nfield = nfield
if uv.FileType == 'AIPS':
uvsub.DataType = 'AIPS'
else:
uvsub.DataType = 'FITS'
if im.FileType == 'AIPS':
uvsub.DataType2 = 'AIPS'
else:
uvsub.DataType2 = 'FITS'
uvsub.outDisk = uvsub.inDisk
uvsub.outSeq = 1
uvsub.outClass = '4Peel'
uvsub.outName = source[0:12]
uvsub.nThreads = nThreads
uvsub.noScrat = noScrat
uvsub.Cmethod = 'DFT'
uvsub.noNeg = False
uvsub.doGPU = doGPU
uvsub.PBCor = False
uvsub.taskLog = taskLog
uvsub.debug = debug
uvsub.flagVer = flagVer
uvsub.Sources[0] = source
if gainUse >= 0:
uvsub.doCalib = 2
uvsub.gainUse = gainUse
return uvsub
def SubPeel(uv, source, imp, uvp, err, addBack=False, seq=999, \
flagVer=0, nThreads=1, doGPU=False, noScrat=[0,0,0], taskLog='', debug=False):
"""
Subtract Peel model w/ solutions, then optionally add back w/o corruptions
UV data should have calibration tables from self calibration
Output data will be on the same disk as the input, seq=seq, class='PelSub' and
with name = source (up to 12 char).
Returns Peel source subtracted/replaced data
* uv Dataset with cal tables
Needs at least the self cal gain table
* source source name
* imp Peel source model (CC table from ImagePeel)
* uvp UV data the result of peel (ImagePeel)
* err Python Obit Error/message stack
* seq Sequence number for output
* addBack Add model back to data w/o corruptions? Not recommended.
* flagVer FG table to apply, -1=> no flag
* nThreads number of threads to use
* doGPU Use GPU if available?
* noScrat AIPS disks not to use for scratch
* taskLog Log file
* debug If True leave debug Input file in /tmp
"""
################################################################
# Checks
if not UV.PIsA(uv):
raise TypeError("uv MUST be a Python Obit UV data")
if not Image.PIsA(imp):
raise TypeError("imp MUST be a Python Obit Image")
if not OErr.OErrIsA(err):
raise TypeError("err MUST be an OErr")
# Split main data set
OErr.PLog(err, OErr.Info, "Copy data")
OErr.printErr(err)
split = ObitTask('Split')
setname(uv, split)
split.outDisk = split.inDisk
split.outSeq = seq
split.outClass = 'UPeel'
split.Sources[0] = source
split.flagVer = flagVer
if uv.GetHighVer('AIPS SN') > 0:
split.doCalib = 2
split.gainUse = 0
split.doCalWt = True
else:
split.doCalib = -1
split.taskLog = taskLog
split.debug = debug
split.g
outClass = split.outClass
outDisk = split.outDisk
outSeq = split.outSeq
# Get data
OErr.PLog(err, OErr.Info, "Make Peel model with corruptions")
OErr.printErr(err)
if UV.AExist(source[0:12], outClass, outDisk, outSeq, err):
datauv = UV.newPAUV('data', source[0:12], outClass, outDisk, outSeq,
True, err)
else:
datauv = UV.newPAUV('data', source[0:8], outClass, outDisk, outSeq,
True, err)
# Make data set with the model peel source with peel cal applied
uvsub = ObitTask('UVSub')
setname(uv, uvsub)
uvsub.outName = source[0:12]
uvsub.outDisk = uvsub.inDisk
uvsub.outSeq = 1
uvsub.outClass = 'Model'
uvsub.Sources[0] = source
uvsub.flagVer = flagVer
uvsub.doCalib = -1
uvsub.gainUse = 0
set2name(imp, uvsub)
uvsub.CCVer = 1
uvsub.nfield = 1
uvsub.Cmethod = 'DFT'
uvsub.Opcode = 'MODL'
uvsub.PBCor = False
uvsub.noScrat = noScrat
uvsub.noNeg = False
uvsub.taskLog = taskLog
uvsub.nThreads = nThreads
uvsub.doGPU = doGPU
uvsub.debug = debug
uvsub.g
# Get model data
modeluv = UV.newPAUV('model', uvsub.outName, uvsub.outClass, uvsub.outDisk,
uvsub.outSeq, True, err)
# Copy/invert/unblank SN table from peeluv
hiPeelSN = uvp.GetHighVer('AIPS SN')
inTab = max(1, hiPeelSN)
sntab = uvp.NewTable(Table.READONLY, 'AIPS SN', inTab, err)
z = UVSelfCal.PInvertSN(sntab, modeluv, 1, True, err)
# Apply calibration table in subtract
modeluv.List.set('doCalSelect', True)
modeluv.List.set('doCalib', 2)
modeluv.List.set('gainUse', 1)
modeluv.List.set('passAll', True)
# Subtract model from main data
OErr.PLog(err, OErr.Info, "Subtract Corrupted Peel model from uv data")
UV.PUtilVisSub(datauv, modeluv, datauv, err)
OErr.printErr(err)
# Add model without corrupting calibration
if addBack:
OErr.PLog(err, OErr.Info, "Add Peel model without corruptions")
uvsub = ObitTask('UVSub')
setname(datauv, uvsub)
setoname(datauv, uvsub)
uvsub.outSeq = uvsub.inSeq + 1
uvsub.Sources[0] = source
uvsub.flagVer = flagVer
uvsub.doCalib = -1
uvsub.gainUse = 0
set2name(imp, uvsub)
uvsub.CCVer = 1
uvsub.nfield = 1
uvsub.Cmethod = 'DFT'
uvsub.Factor = -1.
uvsub.PBCor = False
uvsub.noScrat = noScrat
uvsub.noNeg = False
uvsub.taskLog = taskLog
uvsub.nThreads = nThreads
uvsub.doGPU = doGPU
uvsub.debug = debug
uvsub.g
outClass = uvsub.outClass
outDisk = uvsub.outDisk
outSeq = uvsub.outSeq
# end add back
OErr.printErr(err)
# Delete model dataset
if not debug:
modeluv.Zap(err)
# final data
if UV.AExist(source[0:12], outClass, outDisk, outSeq, err):
datauv2 = UV.newPAUV('data', source[0:12], outClass, outDisk, outSeq,
True, err)
else:
datauv2 = UV.newPAUV('data', source[0:8], outClass, outDisk, outSeq,
True, err)
return datauv2
def PCal (inSC, err, input=UVSelfCalCalInput):
""" Self calibrate data
Determine a gain table from a set of data assumed divided by model.
Solution table attached to OutData
inSC = Selfcal object
err = Python Obit Error/message stack
input = input parameter dictionary
Input dictionary entries:
InData = Input Python UV data from which to determine calibration
Should have been divided by model if not a point source.
OutData = UV data to which output SN table will be attached.
subA = Selected subarray (default 1)
solInt = Solution interval (min). (default 1 sec)
refAnt = Ref ant to use. (default 1)
avgPol = True if RR and LL to be averaged (false)
avgIF = True if all IFs to be averaged (false)
minSNR = Minimum acceptable SNR (5)
doMGM = True then find the mean gain modulus (true)
solType = Solution type ' ', 'L1', (' ')
solMode = Solution mode: 'A&P', 'P', 'P!A', 'GCON' ('P')
minNo = Min. no. antennas. (default 4)
WtUV = Weight outside of UV_Full. (default 1.0)
antWt = Weight per antenna, def all 1
prtLv = Print level (default no print)
returns = Output SN Table with solution
"""
################################################################
# Get input parameters
InData = input["InData"]
OutData = input["OutData"]
#
# Checks
if not PIsA(inSC):
raise TypeError('Bad input selfcalibrator')
if not UV.PIsA(InData):
raise TypeError('Bad input UV data')
if not UV.PIsA(OutData):
raise TypeError('Bad output UV data')
dim = [1,1,1,1,1]
# Create solver
solver = UVGSolve.newObit("Selfcal Solver", err)
# Set control values on solver
dim[0] = 1;
inInfo = PGetList(solver) #
InfoList.PPutInt (inInfo, "subA", dim, [input["subA"]], err)
InfoList.PPutInt (inInfo, "refAnt", dim, [input["refAnt"]],err)
InfoList.PPutInt (inInfo, "minNo", dim, [input["minNo"]], err)
InfoList.PPutInt (inInfo, "prtLv", dim, [input["prtLv"]], err)
InfoList.PPutBoolean (inInfo, "avgPol", dim, [input["avgPol"]],err)
InfoList.PPutBoolean (inInfo, "avgIF", dim, [input["avgIF"]], err)
InfoList.PPutBoolean (inInfo, "doMGM", dim, [input["doMGM"]], err)
InfoList.PPutFloat (inInfo, "solInt", dim, [input["solInt"]], err)
InfoList.PPutFloat (inInfo, "minSNR", dim, [input["minSNR"]], err)
InfoList.PPutFloat (inInfo, "WtUV", dim, [input["WtUV"]], err)
dim[0] = len(input["solType"])
InfoList.PAlwaysPutString (inInfo, "solType",dim, [input["solType"]])
dim[0] = len(input["solMode"])
InfoList.PAlwaysPutString (inInfo, "solMode",dim, [input["solMode"]])
# antWt if given
if input["antWt"].__class__!=None.__class__:
dim[0] = len(input["antWt"])
InfoList.PAlwaysPutFloat (inInfo, "antWt", dim, input["antWt"])
# show any errors
OErr.printErrMsg(err, "UVSelfCalCreate: Error setting parameters")
#
# Create output
outTable = Table.Table("None")
# Solve
outTable.me = UVGSolveCal(solver.me, InData.me, OutData.me, err)
#outTable.me = UVSelfCalCal(inSC.me, InData.me, OutData.me, err)
# show any errors
OErr.printErrMsg(err, "UVSelfCalCal: Error Self-calibrating")
#
return outTable