def WriteFitsThisDir(self,iDir,Weight=False):
""" Store the dynamic spectrum in a FITS file
"""
ra,dec=self.DynSpecMS.PosArray.ra[iDir],self.DynSpecMS.PosArray.dec[iDir]
strRA=rad2hmsdms(ra,Type="ra").replace(" ",":")
strDEC=rad2hmsdms(dec,Type="dec").replace(" ",":")
fitsname = "%s/%s/%s_%s_%s.fits"%(self.DIRNAME,self.GiveSubDir(self.DynSpecMS.PosArray.Type[iDir]),self.DynSpecMS.OutName, strRA, strDEC)
if Weight:
fitsname = "%s/%s.fits"%(self.DIRNAME,"Weights")
print(iDir,self.DynSpecMS.PosArray.Type[iDir],fitsname)
# Create the fits file
prihdr = fits.Header()
prihdr.set('CTYPE1', 'Time', 'Time')
prihdr.set('CRPIX1', 1., 'Reference')
prihdr.set('CRVAL1', 0., 'Time at the reference pixel (sec since OBS-STAR)')
deltaT = (Time(self.DynSpecMS.times[1]/(24*3600.), format='mjd', scale='utc') - Time(self.DynSpecMS.times[0]/(24*3600.), format='mjd', scale='utc')).sec
prihdr.set('CDELT1', deltaT, 'Delta time (sec)')
prihdr.set('CUNIT1', 'Time', 'unit')
prihdr.set('CTYPE2', 'Frequency', 'Frequency')
prihdr.set('CRPIX2', 1., 'Reference')
prihdr.set('CRVAL2', self.DynSpecMS.fMin*1e-6, 'Frequency at the reference pixel (MHz)')
prihdr.set('CDELT2', self.DynSpecMS.ChanWidth*1e-6, 'Delta freq (MHz)')
prihdr.set('CUNIT2', 'MHz', 'unit')
prihdr.set('CTYPE3', 'Stokes parameter', '1=I, 2=Q, 3=U, 4=V')
prihdr.set('CRPIX3', 1., 'Reference')
prihdr.set('CRVAL3', 1., 'frequence at the reference pixel')
prihdr.set('CDELT3', 1., 'Delta stokes')
prihdr.set('CUNIT3', '', 'unit')
prihdr.set('DATE-CRE', Time.now().iso.split()[0], 'Date of file generation')
prihdr.set('OBSID', self.DynSpecMS.OutName, 'LOFAR Observation ID')
prihdr.set('CHAN-WID', self.DynSpecMS.ChanWidth, 'Frequency channel width')
prihdr.set('FRQ-MIN', self.DynSpecMS.fMin, 'Minimal frequency')
prihdr.set('FRQ-MAX', self.DynSpecMS.fMax, 'Maximal frequency')
prihdr.set('OBS-STAR', self.DynSpecMS.tStart, 'Observation start date')
prihdr.set('OBS-STOP', self.DynSpecMS.tStop, 'Observation end date')
prihdr.set('RA_RAD', ra, 'Pixel right ascension')
prihdr.set('DEC_RAD', dec, 'Pixel declination')
name=self.DynSpecMS.PosArray.Name[iDir]
if not isinstance(name,str):
# it must be a byte string, this must be Python 3, act accordingly
name=name.decode('utf-8')
prihdr.set('NAME', name, 'Name of the source in the source list')
prihdr.set('ORIGIN', 'DynSpecMS '+version(),'Created by')
if Weight:
Gn = self.DynSpecMS.DicoGrids["GridWeight"][iDir,:, :, :].real # dir, time, freq, pol
else:
Gn = self.DynSpecMS.GOut[iDir,:, :, :].real
hdu = fits.PrimaryHDU(np.rollaxis(Gn, 2), header=prihdr)
hdu.writeto(fitsname, overwrite=True)
def __init__(self,
ListMSName=None,
ColName="DATA",
ModelName="PREDICT_KMS",
UVRange=[1., 1000.],
ColWeights=None,
SolsName=None,
FileCoords="Transient_LOTTS.csv",
Radius=3.,
NOff=-1,
ImageI=None,
ImageV=None,
SolsDir=None,
NCPU=1,
BaseDirSpecs=None,
BeamModel=None,
BeamNBand=1):
self.ColName = ColName
self.ModelName = ModelName
self.ColWeights = ColWeights
self.BeamNBand = BeamNBand
self.UVRange = UVRange
self.Mode = "Spec"
self.BaseDirSpecs = BaseDirSpecs
self.NOff = NOff
self.SolsName = SolsName
self.NCPU = NCPU
self.BeamModel = BeamModel
if ListMSName is None:
print(ModColor.Str("WORKING IN REPLOT MODE"), file=log)
self.Mode = "Plot"
self.Radius = Radius
self.ImageI = ImageI
self.ImageV = ImageV
self.SolsDir = SolsDir
#self.PosArray=np.genfromtxt(FileCoords,dtype=[('Name','S200'),("ra",np.float64),("dec",np.float64),('Type','S200')],delimiter="\t")
# identify version in logs
print("DynSpecMS version %s starting up" % version(), file=log)
self.FileCoords = FileCoords
if self.Mode == "Spec":
self.ListMSName = sorted(ListMSName) #[0:2]
self.nMS = len(self.ListMSName)
self.OutName = self.ListMSName[0].split("/")[-1].split("_")[0]
self.ReadMSInfos()
self.InitFromCatalog()
elif self.Mode == "Plot":
self.OutName = self.BaseDirSpecs.split("_")[-1]
self.InitFromSpecs()
#!/usr/bin/env python
__author__ = "Cyril Tasse, and Alan Loh"
#__copyright__ = "Copyright 2007, The Cogent Project"
__credits__ = ["Cyril Tasse", "Alan Loh"]
#__license__ = "GPL"
from dynspecms_version import version
__version__ = version()
#__maintainer__ = "Rob Knight"
#__email__ = "*****@*****.**"
#__status__ = "Production"
SaveFile = "last_dynspec.obj"
"""
=========================================================================
DESCRIPTION
Blablabla
Modif
Example:
python ms2dynspec.py --msfile /usr/data/ --data CORRECTED --model PREDICT --sols killms.npz --srclist SRCPOS.txt --rad 10
-------------------------------------------------------------------------
TO DO
- convertSrclist: only keep (RA, Dec) wich are within the field -- DONE
- convertSrclist: add some other ~random positions on wich to compute dynamic spectra for comparison
- stokes computation: CHECK correct I Q U V computation! -- DONE
=========================================================================
"""
import sys
import os
def __init__(self,
ListMSName,
ColName="DATA",
ModelName="PREDICT_KMS",
UVRange=[1., 1000.],
SolsName=None,
FileCoords=None,
Radius=3.,
NOff=-1,
Image=None,
SolsDir=None,
NCPU=1):
self.ListMSName = sorted(ListMSName) #[0:2]
self.nMS = len(self.ListMSName)
self.ColName = ColName
self.ModelName = ModelName
self.OutName = self.ListMSName[0].split("/")[-1].split("_")[0]
self.UVRange = UVRange
self.ReadMSInfos()
self.Radius = Radius
self.Image = Image
self.SolsDir = SolsDir
#self.PosArray=np.genfromtxt(FileCoords,dtype=[('Name','S200'),("ra",np.float64),("dec",np.float64),('Type','S200')],delimiter="\t")
# identify version in logs
print >> log, "DynSpecMS version %s starting up" % version()
# should we use the surveys DB?
if 'DDF_PIPELINE_DATABASE' in os.environ:
print >> log, "Using the surveys database"
from surveys_db import SurveysDB
with SurveysDB() as sdb:
sdb.cur.execute('select * from transients')
result = sdb.cur.fetchall()
# convert to a list, then to ndarray, then to recarray
l = []
for r in result:
l.append((r['id'], r['ra'], r['decl'], r['type']))
self.PosArray = np.asarray(l,
dtype=[('Name', 'S200'),
("ra", np.float64),
("dec", np.float64),
('Type', 'S200')])
print >> log, "Created an array with %i records" % len(result)
else:
if FileCoords is None:
FileCoords = "Transient_LOTTS.csv"
if not os.path.isfile(FileCoords):
ssExec = "wget -q --user=anonymous ftp://ftp.strw.leidenuniv.nl/pub/tasse/%s -O %s" % (
FileCoords, FileCoords)
print >> log, "Downloading %s" % FileCoords
print >> log, " Executing: %s" % ssExec
os.system(ssExec)
self.PosArray = np.genfromtxt(FileCoords,
dtype=[('Name', 'S200'),
("ra", np.float64),
("dec", np.float64),
('Type', 'S200')],
delimiter=",")[()]
self.PosArray = self.PosArray.view(np.recarray)
self.PosArray.ra *= np.pi / 180.
self.PosArray.dec *= np.pi / 180.
NOrig = self.PosArray.shape[0]
Dist = AngDist(self.ra0, self.PosArray.ra, self.dec0,
self.PosArray.dec)
ind = np.where(Dist < Radius * np.pi / 180)[0]
self.PosArray = self.PosArray[ind]
self.NDirSelected = self.PosArray.shape[0]
print >> log, "Selected %i target [out of the %i in the original list]" % (
self.NDirSelected, NOrig)
if self.NDirSelected == 0:
print >> log, ModColor.Str(" Have found no sources - returning")
self.killWorkers()
return
if NOff == -1:
NOff = self.PosArray.shape[0] * 2
if NOff is not None:
print >> log, "Including %i off targets" % (NOff)
self.PosArray = np.concatenate(
[self.PosArray, self.GiveOffPosArray(NOff)])
self.PosArray = self.PosArray.view(np.recarray)
self.NDir = self.PosArray.shape[0]
print >> log, "For a total of %i targets" % (self.NDir)
self.DicoDATA = shared_dict.create("DATA")
self.DicoGrids = shared_dict.create("Grids")
self.DicoGrids["GridLinPol"] = np.zeros(
(self.NDir, self.NChan, self.NTimes, 4), np.complex128)
self.DicoGrids["GridWeight"] = np.zeros(
(self.NDir, self.NChan, self.NTimes, 4), np.complex128)
self.SolsName = SolsName
self.DoJonesCorr = False
if self.SolsName:
self.DoJonesCorr = True
self.DicoJones = shared_dict.create("DicoJones")
APP.registerJobHandlers(self)
AsyncProcessPool.init(ncpu=NCPU, affinity=0)
APP.startWorkers()