def savedat(self, fname, withnoise=True):
"""
Save a presto-readable .dat file (with a corresponding .inf file)
containing the time series.
fname: filename without suffix, to be used for .inf and .dat files
"""
inf = infodata()
inf.name = fname
inf.telescope = 'NA'
inf.instrument = 'NA'
inf.object = self.profile.pars['PSR']
inf.observer = 'NA'
inf.mjd_i = self.start.day_int
inf.mjd_f = self.start.day_frac
inf.bary = int(self.bary)
inf.N = self.nbins
inf.dt = self.tres
inf.band = 'Radio'
inf.filt = 'NA'
inf.analyzer = 'NA'
inf.notes = 'Completely fake data set.'
print "Writing %s.dat and %s.inf..." % (fname, fname)
# round since .dat files use integers
if withnoise:
write_dat(np.round(self.ts_pulses+self.ts_noise), fname)
else:
write_dat(np.round(self.ts_pulses), fname)
writeinf(inf)
print "Done."
def multi_psr_ts_add(psr_list, amp_list, in_fname, out_fname, in_fpath='.',\
out_fpath='.'):
"""
edit of multi_psr_ts to allow adding to existing datfile...
in_fname and out_fname: no extension
amp_list: amps as fraction of time series 1-sigma noise level
NOTE: Should be edited so that it doesn't read and also write the whole
time series in one big chunk, more like how multi_psr_ts now works.
"""
in_inffile = read_inffile('%s/%s' % (in_fpath, in_fname))
nbins = in_inffile.N
tres = in_inffile.dt
length = nbins*tres
start = MJD(in_inffile.mjd_i, in_inffile.mjd_f)
full_ts = load_dat('%s/%s' % (in_fpath, in_fname))
amp_list = np.array(amp_list)
noise = np.std(full_ts)
amp_list *= noise
for ii in range(len(psr_list)):
ts = TimeSeries(psr_list[ii], amp_list[ii], start, tres, 0, length)
full_ts += ts.ts_pulses
print "Writing %s.dat and %s.inf..." % (out_fname, out_fname)
write_dat(np.round(full_ts), '%s/%s' % (out_fpath, out_fname))
inf = in_inffile
inf.name = out_fname
inf.observer = 'Nobody (edited data)'
inf.analyzer = 'Nobody (edited data)'
inf.notes = 'Edited file %s.dat' % in_fname
writeinf(inf)
print "Done."
outfile = optlist['o']+'0.dat'
for filenum in range(1, len(files)):
infile = optlist['o']+repr(filenum)+'.dat'
command = 'cat '+infile+' >> '+outfile
print("")
print(command)
print("")
os.system(command)
os.remove(infile)
os.remove(optlist['o']+repr(filenum)+'.inf')
# Adjust infofile for the pasted data set
inf = presto.read_inffile(optlist['o']+'0')
inf.N = os.stat(outfile)[6] / 4
presto.writeinf(inf)
# Run prepdata on the big file to barycenter it
print("\n\n**** Barycentering...\n\n")
if (numout):
command = ('prepdata -numout '+repr(numout)+' -o '+
optlist['o']+' '+outfile)
else:
command = ('prepdata -o '+optlist['o']+' '+outfile)
print("")
print(command)
print("")
os.system(command)
os.remove(outfile)
def main():
usage = "usage: %prog [options]"
parser = OptionParser(usage)
parser.add_option("-n",
"--number",
type="int",
dest="nM",
default=40,
help="Number of points in each chunk (millions)")
parser.add_option("-o",
"--outdir",
type="string",
dest="outdir",
default=".",
help="Output directory to store results")
parser.add_option("-d",
"--workdir",
type="string",
dest="workdir",
default=".",
help="Working directory for search")
parser.add_option("-l",
"--flo",
type="float",
dest="flo",
default=10.0,
help="Low frequency (Hz) to search")
parser.add_option("-f",
"--frac",
type="float",
dest="frac",
default=0.5,
help="Fraction to overlap")
parser.add_option("-x",
"--fhi",
type="float",
dest="fhi",
default=10000.0,
help="High frequency (Hz) to search")
parser.add_option("-z",
"--zmax",
type="int",
dest="zmax",
default=160,
help="Maximum fourier drift (bins) to search")
parser.add_option("-w",
"--wmax",
type="int",
dest="wmax",
default=400,
help="Maximum fourier drift deriv (bins) to search")
parser.add_option("-a",
"--numharm",
type="int",
dest="numharm",
default=4,
help="Number of harmonics to sum when searching")
parser.add_option("-s",
"--sigma",
type="float",
dest="sigma",
default=2.0,
help="Cutoff sigma to consider a candidate")
(options, args) = parser.parse_args()
if (options.outdir[-1] != "/"):
options.outdir = options.outdir + "/"
if (options.workdir != '.'):
chdir(options.workdir)
if (options.nM >= 1000000):
if (options.nM % 1000000):
print "If you specify --num nM to be > 1000000, it must be divisible by 1000000."
exit(1)
else:
options.nM *= 1000000
short_nM = options.nM / 1000000
# The basename of the data files
if argv[1].endswith(".dat"):
basename = "../" + argv[1][:-4]
else:
basename = "../" + argv[1]
# Get the bird file (the first birdie file in the directory!)
birdname = glob("../*.birds")
if birdname:
birdname = birdname[0]
outnamebase = options.outdir + basename[3:]
inf = read_inffile(basename)
idata = infodata.infodata(basename + ".inf")
N = inf.N
t0i = inf.mjd_i
t0f = inf.mjd_f
num = 0
point = 0
T = options.nM * inf.dt / 86400.0
baryv = get_baryv(idata.RA, idata.DEC, idata.epoch, T, obs='GB')
print "Baryv = ", baryv
inf.N = options.nM
inf.numonoff = 0
nM = options.nM / 1000000
while (point + options.nM < N):
pM = point / 1000000
outname = basename[3:] + '_%03dM' % nM + '_%02d' % num
stdout.write('\n' + outname + '\n\n')
inf.name = outname
tstartf = inf.mjd_f + num * T * options.frac
if (tstartf > 1.0):
tstartf = tstartf - 1.0
inf.mjd_i = inf.mjd_i + 1
inf.mjd_f = tstartf
writeinf(inf)
myexecute('dd if=' + basename + '.dat of=' + outname +
'.dat bs=4000000 skip=' + ` pM ` + ' count=' + ` nM `)
myexecute('realfft ' + outname + '.dat')
myexecute('rm -f ' + outname + '.dat')
myexecute('cp ' + birdname + ' ' + outname + '.birds')
myexecute('makezaplist.py ' + outname + '.birds')
myexecute('rm -f ' + outname + '.birds')
myexecute('zapbirds -zap -zapfile ' + outname +
'.zaplist -baryv %g ' % baryv + outname + '.fft')
myexecute('rm -f ' + outname + '.zaplist')
myexecute(
'accelsearch -sigma %.2f -zmax %d -wmax %d -numharm %d -flo %f -fhi %f '
% (options.sigma, options.zmax, options.wmax, options.numharm,
options.flo, options.fhi) + outname + '.fft')
myexecute('rm ' + outname + '.fft ' + outname +
'_ACCEL_%d.txtcand' % options.zmax)
myexecute('cp ' + outname + '.inf ' + options.outdir)
num = num + 1
point = point + int(options.nM * options.frac)
outfile = optlist['o'] + '0.dat'
for filenum in xrange(1, len(files)):
infile = optlist['o'] + ` filenum ` + '.dat'
command = 'cat ' + infile + ' >> ' + outfile
print ""
print command
print ""
os.system(command)
os.remove(infile)
os.remove(optlist['o'] + ` filenum ` + '.inf')
# Adjust infofile for the pasted data set
inf = presto.read_inffile(optlist['o'] + '0')
inf.N = os.stat(outfile)[6] / 4
presto.writeinf(inf)
# Run prepdata on the big file to barycenter it
print "\n\n**** Barycentering...\n\n"
if (numout):
command = ('prepdata -numout ' + ` numout ` + ' -o ' + optlist['o'] + ' ' +
outfile)
else:
command = ('prepdata -o ' + optlist['o'] + ' ' + outfile)
print ""
print command
print ""
os.system(command)
os.remove(outfile)
def multi_psr_ts(psr_list, amp_list, start, tres, noise, length, fname,\
fpath='.', obs=-1, zero=0.):
"""
fname: no extension
fpath: directory to place dat and inf files into
psr_list: iterable set of psrProfile objects
amp_list: corresponding list of pulse heights as fraction of noise sigma
(if no noise is present, values are simply used as heights)
start: start time as MJD object
noise: sigma of white noise in time series
"""
amp_list = np.array(amp_list)
if noise: amp_list *= noise
nbins = int(np.ceil(length/tres))
if nbins % 2: nbins -= 1
chunk_nbins = 2**22
chunk_length = chunk_nbins * tres
n_full_chunks = nbins / chunk_nbins
extra_nbins = nbins % chunk_nbins
# So we can correctly print which chunk we're on:
if extra_nbins: n_chunks = n_full_chunks + 1
else: n_chunks = n_full_chunks
outfile = open("%s/%s.dat" % (fpath, fname), 'w')
for chunk_ii in range(n_full_chunks):
chunk_start = start + chunk_ii*(chunk_length/86400.)
print "Writing time series chunk %d of %d to %s.dat..." % (chunk_ii+1,\
n_chunks, fname)
write_to_dat(outfile, psr_list, amp_list, chunk_start, tres, noise,\
chunk_nbins, obs, zero)
print "Time series chunk complete."
if extra_nbins:
chunk_start = start + n_full_chunks*(chunk_length/86400.)
print "Writing time series chunk %d of %d to %s.dat..." % (n_chunks,\
n_chunks, fname)
write_to_dat(outfile, psr_list, amp_list, chunk_start, tres, noise,\
extra_nbins, obs, zero)
print "Time series chunk complete."
outfile.close()
print "Writing %s.inf..." % fname
inf = infodata()
inf.name = fname
inf.telescope = 'NA'
inf.instrument = 'NA'
inf.object = 'NA'
inf.observer = 'NA'
inf.mjd_i = start.day_int
inf.mjd_f = start.day_frac
inf.bary = 1
inf.N = nbins
inf.dt = tres
inf.band = 'Radio'
inf.filt = 'NA'
inf.analyzer = 'NA'
inf.notes = 'Completely fake data set.'
writeinf(inf)
print "Done."
