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polconvert_standalone.py
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# Copyright (c) Ivan Marti-Vidal 2012-2021
# EU ALMA Regional Center. Nordic node.
# Universitat de Valencia (Spain)
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>,
# or write to the Free Software Foundation, Inc.,
# 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# a. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# b. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the
# distribution.
# c. Neither the name of the author nor the names of contributors may
# be used to endorse or promote products derived from this software
# without specific prior written permission.
#
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
#
#
from __future__ import absolute_import
from __future__ import print_function
__version__ = "2.0.4 " # 7 characters
date = "Dec 5, 2022"
################
# Import all necessary modules.
########
# Execute twice, to avoid the silly (and harmless)
# error regarding the different API versions of
# numpy between the local system and CASA:
import os, sys
try:
mypath = os.path.dirname(__file__)
sys.path.append(mypath)
import _PolConvert as PC
goodclib = True
print("\nC++ shared library loaded successfully (first try)\n")
except:
goodclib = False
print("\n There has been an error related to the numpy")
print(" API version used by CASA. This is related to PolConvert")
print(" (which uses the API version of your system) and should")
print(" be *harmless*.\n")
if not goodclib:
try:
import _PolConvert as PC
goodclib = True
print("\nC++ shared library loaded successfully (2nd try)\n")
except:
goodclib = False
print("\nNo, the shared library did not load successfully\n")
#############
if not goodclib:
try:
import _PolConvert as PC
goodclib = True
print("\nC++ shared library loaded successfully (3rd try)\n")
except:
goodclib = False
print("\nNo, the shared library still did not load successfully\n")
#############
### ... and we could keep on trying! (with an infinite loop! XD ).
import os, sys, shutil, re
import gc
import time
import struct as stk
import scipy.optimize as spopt
import scipy.interpolate as spint
import numpy as np
import pylab as pl
import datetime as dt
import sys
import pickle as pk
def polconvert(
IDI="",
OUTPUTIDI="",
DiFXinput="",
DiFXcalc="",
doIF=[],
linAntIdx=[],
Range=[],
XYadd={},
XYdel={},
XYratio={},
usePcal={},
swapXY=[],
swapRL=False,
feedRotation=[],
correctParangle=False,
IDI_conjugated=False,
plotIF=[],
plotRange=[],
plotAnt="",
excludeAnts=[],
excludeBaselines=[],
doSolve=-1,
solint=[1, 1],
doTest=True,
npix=-1,
solveAmp=True,
solveMethod="COBYLA",
calstokes=[1.0, 0.0, 0.0, 0.0],
calfield=-1,
plotSuffix="",
pcalSuffix="",
ALMAstuff=[],
saveArgs=False,
amp_norm=0.0,
IFoffset=0,
AC_MedianWindow=0,
XYpcalMode="bandpass",
UVTaper=1.e9,
useRates = False,
mounts = {}
):
"""POLCONVERT - STANDALONE VERSION 2.0.1b.
Similar parameters as the method defined in polconvert_CASA. The parameters specific
of this task (i.e., polconvert_standalone::polconvert) may be useful to parallelize polconvert:
plotSuffix: Suffix to add to the names of the plot files.
pcalSuffix: Suffix to add to the names of the original pcal files in the difx directories.
ALMAstuff: List of ALMA-specific parameters passed by polconvert_CASA::polconvert.
Other new parameters are:
IFoffset: treats the IF with index "i" as the same IF with index "i+IFoffset". This is
useful to process correctly the autocorrelations with multi-file has been
used in the observations.
AC_MedianWindow: Size (in channels) of a median window filter to be applied to the
autocorrelations. This is useful if we want to filter out phasecal peaks
(for a better fringe normalization).
XYpcalModel: Controls how the X-Y pcal differences are interpolated in frequency.
It can be either "bandpass" (default) or "multitone" (similar to fourfit's).
UVTaper: Apply a UVtaper (in meters) to the X-pol gain estimator (to avoid too high
cross-polarization fringes).
useRates: If True, the pol-wise weighted rate average will be use to increase
(hopefully) the coherence time of the data when the x-pol gains are
being estimated.
mounts: Antenna mounts (for SWIN case), given as a dictionary. The keywords are
the antenna codes and the elements are the mount types. The default antenna
mount is alt-azimuth. Recognized mounts are:
AZ (alt-az), EQ (equatorial), OB (orbit), XY (X-Y), NR (Nasmyth right), NL (Nasmyth left)
Example: if antenna Yebes-40m (code YB) has Nasmyth left, and all the other antennas
have alt-az mounts, then: mounts = {'YB':'NL'}
"""
if saveArgs:
ARGS = {
"IDI": IDI,
"OUTPUTIDI": OUTPUTIDI,
"DiFXinput": DiFXinput,
"DiFXcalc": DiFXcalc,
"doIF": doIF,
"linAntIdx": linAntIdx,
"Range": Range,
"XYadd": XYadd,
"XYdel": XYdel,
"XYratio": XYratio,
"usePcal": usePcal,
"swapXY": swapXY,
"swapRL": swapRL,
"feedRotation": feedRotation,
"correctParangle": correctParangle,
"IDI_conjugated": IDI_conjugated,
"plotIF": plotIF,
"plotRange": plotRange,
"plotAnt": plotAnt,
"excludeAnts": excludeAnts,
"excludeBaselines": excludeBaselines,
"doSolve": doSolve,
"solint": solint,
"doTest": doTest,
"npix": npix,
"solveAmp": solveAmp,
"solveMethod": solveMethod,
"calstokes": calstokes,
"calfield": calfield,
"ALMAstuff": ALMAstuff,
"IFoffset": IFoffset,
"AC_MedianWindow": AC_MedianWindow,
"XYpcalMode": XYpcalMode,
"UVTaper": UVTaper,
"useRates":useRates,
"mounts":mounts
}
OFF = open("PolConvert_standalone.last", "wb")
pk.dump(ARGS, OFF)
OFF.close()
## Set to non-ALMA:
if len(ALMAstuff) == 0:
PC.setPCMode(0)
# amp_norm=0.0
logName = "PolConvert%s.log" % plotSuffix
## Codes for antenna mounts:
MntCodes = {'AZ':0, 'EQ':1, 'OB':2, 'XY':3, 'NR':4, 'NL':5}
############################################
# this turns into the verbosity argument of _PolConvert.so
print("Entered polconvert_standalone::polconvert()")
DEBUG = False
if "POLCONVERTDEBUG" in os.environ:
if os.environ["POLCONVERTDEBUG"] == "True":
DEBUG = True
else:
DEBUG = False
print("DEBUG setting is " + str(DEBUG))
print("__name__ is " + __name__)
# Auxiliary function: print error and raise exception:
def printError(msg):
print(msg, "\n")
lfile = open(logName, "a")
print("\n" + msg + "\n", file=lfile)
lfile.close()
sys.stdout.flush()
raise Exception(msg)
# Auxiliary function: print message (terminal and log):
def printMsg(msg, doterm=True, dolog=True):
if doterm:
print(msg)
if dolog:
lfile = open(logName, "a")
print(msg, file=lfile)
lfile.close()
# Auxiliary function: derive job label from DiFXinput
def jobLabel(inputname):
label = inputname
try:
label = re.sub(".input", "", os.path.basename(label))
except:
pass
return label
tic = time.time()
greet = """
##########################################################################'
# POLCONVERT -- version. #'
# Please, add the POLCONVERT reference to your publications: #'
# #'
# Marti-Vidal, Roy, Conway & Zensus 2016, A&A, 587, 143 #'
# #'
##########################################################################'
"""
greetings = re.sub("version", __version__, greet)
printMsg(greetings, dolog=False)
printMsg("\n\nPOLCONVERT - VERSION %s" % __version__, doterm=False)
#########################################
# DO SOME SANITY CHECKS OF PARAMETERS
try:
doSolve = float(doSolve)
except:
printError("ERROR! doSolve should be a float!")
scipyMethods = ["COBYLA", "Nelder-Mead", "Powell", "BFGS", "Newton-CG", "SLSQP"]
allMethods = scipyMethods + ["gradient", "Levenberg-Marquardt"]
if solveMethod not in allMethods:
printError("ERROR! 'solveMethod' must be any of: %s" % (", ".join(allMethods)))
if type(calstokes) is not list:
printError("ERROR! Wrong calstokes!")
elif len(calstokes) != 4 and doSolve > 0.0:
printError(
"ERROR! calstokes should have 4 elements, not %d (%s)!"
% (len(calstokes), str(calstokes))
)
for ii, item in enumerate(calstokes):
try:
calstokes[ii] = float(item)
except:
printError(
"ERROR! calstokes should only have float elements; got %s!"
% str(type(item))
)
Stokes = list(calstokes)
if doSolve >= 0.0 and (
Stokes[0] <= 0.0
or Stokes[0] < np.sqrt(Stokes[1] ** 2.0 + Stokes[2] ** 2.0 + Stokes[3] ** 2.0)
):
printError("ERROR! Inconsistent Stokes parameters!")
# Will implement solveQU soon!
solveQU = False
# calfield = -1
if type(solveQU) is not bool:
printError("ERROR! Wrong solveQU!")
if type(calfield) is not int:
printError("ERROR! Wrong calfield!")
doConj = True
if type(IDI_conjugated) is not bool:
printError("ERROR! IDI_cojugated should be a boolean!")
else:
doConj = IDI_conjugated
if type(swapRL) is not bool:
printError("ERROR! swapRL should be a boolean!")
if type(doIF) is not list:
printError("ERROR! doIF should be a list of integers!")
else:
for elem in doIF:
if type(elem) is not int:
printError("ERROR! doIF should be a list of integers!")
if elem == 0:
printError(
"ERROR! IF numbers are given in AIPS (and FITS-IDI) convention\n(i.e., starting from 1; not from 0).\n"
)
if type(doTest) is not bool:
printError("ERROR! doTest should be a boolean!")
if doTest:
printMsg("Will only compute, but not update the output file(s)", doterm=False)
if type(linAntIdx) is not list:
printError("ERROR! linAntIdx should be a list of antenna indices or names!")
for elem in linAntIdx:
if type(elem) not in [int, str]:
printError("ERROR! linAntIdx should be a list of antenna indices or names!")
if type(solint) is not list or (len(solint) not in [2, 3]):
printError(
"ERROR! solint (%s) must be a list of two/three numbers!" % str(solint)
)
else:
try:
solint[0] = int(solint[0])
solint[1] = int(solint[1])
except:
printError(
"ERROR! solint (%s) must be a list of two/three numbers!" % str(solint)
)
if len(solint) == 3:
solint[2] = float(solint[2])
else: # Default dt
solint.append(100.0)
nALMA = len(linAntIdx)
if not os.path.exists(IDI):
printError("ERROR! IDI file (or SWIN folder) does not exist!")
if type(OUTPUTIDI) is not str:
printError("ERROR! OUTPUTIDI should be a string!")
if type(plotIF) is int:
if plotIF > 0:
plotIF = [plotIF]
else:
plotIF = []
for pli in plotIF:
if type(pli) is not int:
printError("ERROR! plotIF should be an integer or a list of integers!")
for pli in plotIF:
if pli not in doIF:
printError("ERROR! Only converted IFs can be plotted!")
if type(usePcal) is not dict:
printError("Invalid format for usePcal! Should be a dictionary!\n")
pcant = 0
for k in usePcal.keys():
if type(usePcal[k]) is not bool:
printError("The elements of usePcal must be booleans!\n")
elif usePcal[k]:
pcant += 1
isPcalUsed = pcant > 0
if len(swapXY) == 0:
swapXY = [False for swp in range(nALMA)]
if len(swapXY) != nALMA:
printError(
"Invalid format for swapXY!\n Should be a list of booleans, as large as the number of linear-polarization VLBI stations!"
)
for sxy in swapXY:
if type(sxy) is not bool:
printError(
"Invalid format for swapXY!\n Should be a list of booleans, as large as the number of linear-polarization VLBI stations!"
)
if len(Range) not in [0, 8]:
printError(
"Invalid format for Range! Should be either an empty list or a list of 8 integers!"
)
for rr in Range:
if type(rr) is not int:
printError(
"Invalid format for Range! Should be either an empty list or a list of 8 integers!"
)
if len(plotRange) not in [0, 8]:
printError(
"Invalid format for Range! Should be either an empty list or a list of 8 integers!"
)
for rr in plotRange:
if type(rr) is not int:
printError(
"Invalid format for Range! Should be either an empty list or a list of 8 integers!"
)
#########################################
#######
# CHECK IF THIS IS A FITS-IDI FILE OR A SWIN DIR.:
if os.path.isdir(IDI):
isSWIN = True
printMsg("\n\nYou have asked to convert a set of SWIN files.")
if len(DiFXinput) == 0:
DiFXinput = IDI[:-4] + "input"
if len(DiFXcalc) == 0:
DiFXcalc = IDI[:-4] + "calc"
if not os.path.exists(DiFXinput) or not os.path.isfile(DiFXinput):
printError("Invalid DiFX input file! %s" % DiFXinput)
printMsg("Opening calc file... %s" % DiFXcalc)
try:
printMsg('Opening "%s"' % (DiFXcalc))
antcoords = []
calcsoucoords = [[], []]
antmounts = []
antcodes = []
calc = open(DiFXcalc)
lines = calc.readlines()
calc.close()
printMsg("Read %d lines from %s" % (len(lines), DiFXcalc))
for ii, line in enumerate(lines):
if "TELESCOPE" in line and "NAME" in line:
antcodes.append(line.split()[-1])
if "TELESCOPE" in line and "X (m):" in line:
antcoords.append(list(map(float, [ll.split()[-1] for ll in lines[ii : ii + 3]])))
printMsg(
"TELESCOPE %s AT X: %.3f ; Y: %.3f ; Z: %.3f"
% tuple([antcodes[-1]] + antcoords[-1])
)
# DEFAULT MOUNTS ARE ALT-AZ:
antmounts.append(0)
if "SOURCE" in line and " NAME: " in line:
SNAM = line.split()[-1]
calcsoucoords[0].append(float(lines[ii + 1].split()[-1]))
calcsoucoords[1].append(float(lines[ii + 2].split()[-1]))
printMsg(
"SOURCE %s AT RA: %.8f rad, DEC: %.8f rad"
% (SNAM, calcsoucoords[0][-1], calcsoucoords[1][-1])
)
antcoords = np.array(antcoords, dtype=np.float, order="C")
antmounts = np.array(antmounts, order="C")
calcsoucoords[0] = np.array(calcsoucoords[0], dtype=np.float, order="C")
calcsoucoords[1] = np.array(calcsoucoords[1], dtype=np.float, order="C")
printMsg("done parsing calc")
except Exception as ex:
printMsg(str(ex))
printMsg(
(
"WARNING! Invalid DiFX calc file '%s'!\n"
+ "PolConvert may not calibrate properly."
)
% DiFXcalc
)
if len(antmounts) == 0:
printError("ERROR! NO ANTENNAS FOUND IN CALC FILE!")
else:
printMsg("There are %i antennas." % len(antmounts))
## Read antenna mounts from dictionary:
for antName in mounts.keys():
if antName in antcodes:
if mounts[antName] not in MntCodes.keys():
printError("ERROR! Mount %s not recognized!"%mounts[antName])
else:
code = mounts[antName]
mnt = MntCodes[code]
antmounts[antcodes.index(antName)] = int(mnt)
printMsg("Setting mount %s (%i) to antenna %s"%(code,mnt,antName))
elif os.path.isfile(IDI):
isSWIN = False
# Currently, PCALs are not supported for FITS-IDI:
isPcalUsed = False
printMsg("\n\nYou have asked to convert a FITS-IDI file.")
printMsg("Reading array geometry...")
try:
from astropy.io import fits as pf
ffile = pf.open(IDI)
for ii, group in enumerate(ffile):
if group.name == "ARRAY_GEOMETRY":
grarr = ii
elif group.name == "SOURCE":
grsou = ii
raappUnit = (
ffile[grsou]
.data.columns[
[coln.name for coln in ffile[grsou].data.columns].index("RAAPP")
]
.unit
)
decappUnit = (
ffile[grsou]
.data.columns[
[coln.name for coln in ffile[grsou].data.columns].index("DECAPP")
]
.unit
)
soucoords = [
np.array(ffile[grsou].data["RAAPP"], dtype=np.float, order="C"),
np.array(ffile[grsou].data["DECAPP"], dtype=np.float, order="C"),
]
if raappUnit == "DEGREES":
soucoords[0] *= np.pi / 180.0
if decappUnit == "DEGREES":
soucoords[1] *= np.pi / 180.0
antcodes = [ff[:2] for ff in ffile["ANTENNA"].data["ANNAME"]]
print("ANTENNA NAMES: ")
print(",".join(antcodes))
ffile.close()
# THESE LINES FAIL IF ORBPARM IS PRESENT IN ARRAY GEOMETRY!
import _getAntInfo as gA
success = gA.getAntInfo(IDI)
if success != 0:
printError("ERROR GETTING FITS-IDI METADATA! ERR: %i" % success)
else:
antcoords = gA.getCoords()
antmounts = gA.getMounts()
# FIXME: need a way to find antenna codes if above fails:
# antcodes = ['%02i'%i for i in range(1,len(antmounts)+1)]
except:
printMsg(
"WARNING! This FITS-IDI file has missing information!\nPolConvert may not calibrate properly."
)
else:
printError("Invalid input data!")
######
######
# IF THIS IS A SWIN DATASET, READ THE INPUT FILE INTO
# A METADATA LIST:
if isSWIN:
printMsg("Reading the DiFX input file\n")
ifile = open(DiFXinput)
inputlines = ifile.readlines()
ifile.close()
FreqL = [inputlines.index(l) for l in inputlines if "FREQ TABLE" in l]
# ONLY ONE FREQ TABLE IS ALLOWED:
try:
fr = FreqL[0]
Nfreq = int(
list(filter(lambda x: "FREQ ENTRIES" in x, inputlines[fr + 1 :]))[
0
].split()[-1]
)
Nr = list(range(Nfreq))
except Exception as ex:
printMsg(str(ex))
printError("BAD input file!")
FrInfo = {
"FREQ (MHZ)": [0.0 for i in Nr],
"BW (MHZ)": [0.0 for i in Nr],
"SIDEBAND": ["U" for i in Nr],
"NUM CHANNELS": [1 for i in Nr],
"CHANS TO AVG": [1 for i in Nr],
"OVERSAMPLE FAC.": [1 for i in Nr],
"DECIMATION FAC.": [1 for i in Nr],
"SIGN": [1.0 for i in Nr],
}
# READ METADATA FOR ALL FREQUENCIES:
for entry in FrInfo.keys():
for line in inputlines[fr + 1 :]:
if entry in line:
index = int((line.split(":")[0]).split()[-1])
FrInfo[entry][index] = type(FrInfo[entry][0])(line.split(":")[-1])
# SORT OUT THE CHANNEL FREQUENCIES:
if len(doIF) == 0:
doIF = list(range(1, len(Nr) + 1))
metadata = []
IFchan = 0
for nu in Nr:
nu0 = FrInfo["FREQ (MHZ)"][nu]
bw = FrInfo["BW (MHZ)"][nu]
nchan = FrInfo["NUM CHANNELS"][nu]
# MAX. NUMBER OF CHANNELS:
chav = FrInfo["CHANS TO AVG"][nu]
if nu in doIF:
IFchan = max([IFchan, int(nchan / chav)])
sb = {True: 1.0, False: -1.0}[FrInfo["SIDEBAND"][nu] == "U"]
FrInfo["SIGN"][nu] = float(sb)
freqs = (
nu0 + np.linspace((sb-1.0)/2.0, (sb+1.0)/2.0, nchan//chav, endpoint=False)*bw)*1.0e6
if float(nchan // chav) != float(nchan / chav):
printMsg("linspace check chan: %d / %d = %f"%(nchan, chav, float(nchan / chav)))
freqs = (
nu0 + np.linspace((sb-1.0)/2.0, (sb+1.0)/2.0, nchan//chav, endpoint=False)*bw)*1.0e6
metadata.append(freqs)
#####
######
# IF THIS IS A FITS-IDI FILE, READ THE METADATA LIST:
else:
# READ FREQUENCY INFO:
from astropy.io import fits as pf
fitsf = pf.open(IDI)
nu0 = fitsf["FREQUENCY"].header["REF_FREQ"]
bw = fitsf["FREQUENCY"].header["CHAN_BW"]
nch = fitsf["FREQUENCY"].header[
"NO_CHAN"
] # *fitsf['FREQUENCY'].header['NO_BAND']
IFchan = nch
Nr = fitsf["FREQUENCY"].header["NO_BAND"]
sgn = {True: 1.0, False: -1.0}[bw > 0.0]
FrInfo = {"FREQ (MHZ)": [], "BW (MHZ)": [], "SIGN": [], "NUM CHANNELS": []}
if sgn:
FrInfo["SIDEBAND"] = ["U" for i in range(Nr)]
else:
FrInfo["SIDEBAND"] = ["L" for i in range(Nr)]
metadata = []
for i in range(Nr):
FrInfo["FREQ (MHZ)"] += [(nu0 + i * bw * nch) / 1.0e6]
FrInfo["BW (MHZ)"] += [bw * nch / 1.0e6]
FrInfo["SIGN"] += [sgn]
FrInfo["NUM CHANNELS"] += [int(nch)]
freqs = (
nu0 + np.linspace((sgn - 1.0) / 2.0, (sgn + 1.0) / 2.0, nch, endpoint=False)*bw)
metadata.append(freqs)
FrInfo["CHANS TO AVG"] = [1 for i in range(Nr)]
FrInfo["OVERSAMPLE FAC."] = [1 for i in range(Nr)]
FrInfo["DECIMATION FAC."] = [1 for i in range(Nr)]
if len(doIF) == 0:
doIF = list(range(1, 1 + fitsf["FREQUENCY"].header["NO_BAND"]))
fitsf.close()
# ANTENNAS TO PARTICIPATE IN THE GAIN ESTIMATES:
nTotAnt = len(antcoords)
calAnts = []
for exA in antcodes:
if exA not in excludeAnts:
calAnts.append(antcodes.index(exA) + 1)
else:
printMsg("Excluding antenna %s from the solution." % str(exA))
##z following section
if type(plotAnt) is str and len(plotAnt) == 0:
plotAnt = 1
try:
plotAnt = int(plotAnt)
except:
if plotAnt not in antcodes:
printError("Reference antenna %s is not found in metadata among %s!" % (str(plotAnt), antcodes))
else:
plotAnt = antcodes.index(plotAnt) + 1
if plotAnt in linAntIdx or antcodes[plotAnt - 1] in linAntIdx:
printMsg(
"WARNING: Plotting will involve autocorrelations. \nThis has not been fully tested!"
)
FlagBas1 = []
FlagBas2 = []
for fbi in excludeBaselines:
printMsg("Excluding baseline %s from solution." % str(fbi))
if fbi[0] in antcodes and fbi[1] in antcodes:
FlagBas1.append(
antcodes.index(fbi[0]) + 1
) ### = np.array([int(i[0]+1) for i in excludeBaselines])
FlagBas2.append(
antcodes.index(fbi[1]) + 1
) ### = np.array([int(i[1]+1) for i in excludeBaselines])
else:
printError(
"Unknown antenna(s) %s and/or %s in excludeBaselines!\n"
% (fbi[0], fbi[1])
)
FlagBas1 = np.array(FlagBas1, order="C", dtype=np.int32)
FlagBas2 = np.array(FlagBas2, order="C", dtype=np.int32)
if plotAnt not in calAnts:
if doSolve >= 0:
printError(
"ERROR! plotAnt/Reference antenna is NOT in list of calibratable antennas!"
)
else:
printMsg(
"plotAnt (%d) is not in antenna list, so plots will be missing"
% plotAnt
)
if type(feedRotation) is not list:
printError("feedRotation must be a list of numbers")
elif len(feedRotation) == 0:
feedRot = np.zeros(nTotAnt, order="C", dtype=np.float)
elif len(feedRotation) != nTotAnt:
printError("feedRotation must have %i entries!" % nTotAnt)
else:
feedRot = np.pi / 180.0 * np.array(feedRotation, dtype=np.float, order="C")
# Get the REAL number (and names) of linear-pol antennas in this dataset:
nALMATrue = 0
linAntIdxTrue = []
linAntNamTrue = []
OrigLinIdx = []
for i, idd in enumerate(linAntIdx):
if type(idd) is int and idd <= len(antcodes):
nALMATrue += 1
linAntIdxTrue.append(idd)
linAntNamTrue.append(antcodes[idd - 1])
OrigLinIdx.append(i)
elif idd in antcodes:
nALMATrue += 1
linAntNamTrue.append(idd)
linAntIdxTrue.append(antcodes.index(idd) + 1)
OrigLinIdx.append(i)
# Setting isLinear list of booleans:
isLinear = []
for antc in antcodes:
isLinear.append(antc in linAntNamTrue)
# Check that pcals are (or not) set for this antenna:
for idd in linAntNamTrue:
if idd not in usePcal.keys():
printMsg(
"WARNING: Antenna %s not in usePcal dictionary. Will NOT use Pcals for this antenna"
% idd
)
usePcal[idd] = False
printMsg("There are %i linear-polarization antennas in THIS dataset" % nALMATrue)
# COMPUTE TIME RANGES:
if len(plotRange) == 0:
plRan = np.array([0.0, 0.0])
plotFringe = False
else:
try:
plRan = np.array(
[
plotRange[0]
+ plotRange[1]/24.0
+ plotRange[2]/1440.0
+ plotRange[3]/86400.0,
plotRange[4]
+ plotRange[5]/24.0
+ plotRange[6]/1440.0
+ plotRange[7]/86400.0,
]
)
plotFringe = True
if len(plotIF) == 0:
plotIF = list(doIF)
except:
printError("Bad time range format for plotRange!")
if len(Range) == 0:
Ran = np.array([0.0, 1.0e20])
else:
try:
Ran = np.array(
[
Range[0] + Range[1] / 24.0 + Range[2] / 1440.0 + Range[3] / 86400.0,
Range[4] + Range[5] / 24.0 + Range[6] / 1440.0 + Range[7] / 86400.0,
]
)
except:
printError("Bad time range format for Range!")
#######
# WARNING! UNCOMMENT THIS IF NOT DEBUGGING!
if os.path.exists(OUTPUTIDI) and IDI != OUTPUTIDI:
printMsg("Will REMOVE the existing OUTPUT file (or directory)!\n")
printMsg("Copying IDI to OUTPUTIDI!\n")
os.system("rm -rf %s" % OUTPUTIDI)
os.system("cp -r %s %s" % (IDI, OUTPUTIDI))
elif not os.path.exists(OUTPUTIDI):
printMsg("Copying IDI to OUTPUTIDI!\n")
os.system("cp -r %s %s" % (IDI, OUTPUTIDI))
#
#######
if isSWIN:
OUTPUT_UNSORT = []
PHASECALS_UNSORT = []
walk = [f for f in os.walk(OUTPUTIDI)]
for subd in walk:
ADD2OUTPUT = [
os.path.join(subd[0], fi)
for fi in filter(lambda x: x.startswith("DIFX_"), subd[2])
]
OUTPUT_UNSORT += ADD2OUTPUT
for difxfile in ADD2OUTPUT:
prefix = (os.path.basename(difxfile).split(".")[0])[5:]
PHASECALS_UNSORT.append(
[
os.path.join(subd[0], fi)
for fi in filter(
lambda x: x.startswith("PCAL_%s" % prefix), subd[2]
)
]
)
if len(OUTPUT_UNSORT) == 0:
printError("No *.difx files found in directory!")
OUTPUT = []
PHASECALS = []
TOOUT = np.argsort(
[
float(os.path.basename(fi).split(".")[0].split("_")[-1])
for fi in OUTPUT_UNSORT
]
)
for i in range(len(OUTPUT_UNSORT)):
OUTPUT.append(OUTPUT_UNSORT[TOOUT[i]])
PHASECALS.append(PHASECALS_UNSORT[TOOUT[i]])
# Derive the days of observation of each difx file:
mjd = np.zeros(len(OUTPUT))
mjs = np.zeros(len(OUTPUT))
for i, fi in enumerate(OUTPUT):
mjd[i], mjs[i] = list(
map(float, ((os.path.basename(fi)).split(".")[0]).split("_")[1:3])
)
mjd0 = np.min(mjd)
mjp = Ran + mjd0
metadata.append(mjd0)
# Filter out files outside the computing time window:
t0 = mjd + mjs / 86400.0
i0 = np.logical_and(t0 <= mjp[1], t0 >= mjp[0])
OUTPUT = [OUTPUT[i] for i in range(len(i0)) if i0[i]]
# Get source coordinate for each file (if possible):
#CALCS = ["%s.calc" % os.path.dirname(ci)[:-5] for ci in OUTPUT] # NB the [:-5] fails when user suffix used like '.pcdifx' or '.difx_PC' like by EUVGOS_PY3/POLCONVERTER.py
CALCS = ["%s.calc" % os.path.dirname(ci)[:os.path.dirname(ci).rfind('.')] for ci in OUTPUT]
##OBSOLETE! NOW, WE ARE CONCATENATING SWIN METADATA TO ENSURE CONSISTENCY!
# There will be one source per SWIN file:
# soucoords = [np.ones(len(OUTPUT))*calcsoucoords[0][0], np.ones(len(OUTPUT))*calcsoucoords[0][0]]
# for sui,Fcalc in enumerate(CALCS):
# # print(sui,Fcalc)
# if os.path.exists(Fcalc):
# FCin = open(Fcalc)
# lines = FCin.readlines()
# FCin.close()
# for ii,line in enumerate(lines):
# if 'SOURCE' in line and ' NAME: ' in line:
# SNAM = line.split()[-1]
# soucoords[0][sui] = float(lines[ii+1].split()[-1])
# soucoords[1][sui] = float(lines[ii+2].split()[-1])
# printMsg('FOUND SOURCE %s AT RA: %.8f rad, DEC: %.8f rad'%(SNAM,soucoords[0][sui],soucoords[1][sui]))
FCin = open(CALCS[0])
lines = FCin.readlines()
FCin.close()
for line in lines:
if line.startswith("NUM SOURCES: "):
NSOU = int(line.split()[-1].replace("\n", ""))
soucoords = [np.ones(NSOU), np.ones(NSOU)]
break
for ii, line in enumerate(lines):
if "SOURCE" in line and " NAME: " in line:
tempLine = line.split()
SID = int(tempLine[1])
soucoords[0][SID] = float(lines[ii + 1].split()[-1])
soucoords[1][SID] = float(lines[ii + 2].split()[-1])
else:
metadata = []
OUTPUT = [OUTPUTIDI]
##########################################
#########
# COMPUTE XY delays:
XYdelF = [[0.0, 0.0] for i in range(nALMATrue)]
if type(XYdel) is not dict: # or len(XYdel) != nALMA:
printError(
"Invalid format for XYdel!\n"
) # Should be a LIST of numbers, as large as the number of linear-polarization VLBI stations!")
for i, doant in enumerate(linAntNamTrue):
if doant in XYdel.keys():
if type(XYdel[doant]) is list:
try:
XYdelF[i] = list(
map(float, XYdel[doant])
) # float(XYdel[i]*np.pi/180.)
except:
printError(