def pkmb_prepdata(optlist, file, filenum):
# Runs prepdata and returns a tuple containg number of points
# written, time per point, and starting time (MJD)
outfile = optlist['o'] + ` filenum `
command = 'prepdata -pkmb -nobary -dm '+optlist['dm']+' -o '+\
outfile+' '+file
print ""
print command
print ""
os.system(command)
inf = presto.read_inffile(outfile)
return (int(inf.N), inf.dt, inf.mjd_i + inf.mjd_f)
def pkmb_prepdata(optlist, file, filenum):
# Runs prepdata and returns a tuple containg number of points
# written, time per point, and starting time (MJD)
outfile = optlist['o']+repr(filenum)
command = 'prepdata -pkmb -nobary -dm '+optlist['dm']+' -o '+\
outfile+' '+file
print("")
print(command)
print("")
os.system(command)
inf = presto.read_inffile(outfile)
return (int(inf.N), inf.dt, inf.mjd_i+inf.mjd_f)
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."
hdr += prep_double("src_raj", inf.ra_h*10000.0 + inf.ra_m*100.0 + inf.ra_s)
if inf.dec_d > 0.0:
hdr += prep_double("src_dej", inf.dec_d*10000.0 + inf.dec_m*100.0 + inf.dec_s)
else:
hdr += prep_double("src_dej", inf.dec_d*10000.0 - inf.dec_m*100.0 - inf.dec_s)
hdr += prep_int("nbits", 32)
hdr += prep_int("nifs", 1)
hdr += prep_int("nchans", 1)
hdr += prep_double("fch1", inf.freq)
hdr += prep_double("foff", 1)
hdr += prep_double("tstart", inf.mjd_i + inf.mjd_f)
hdr += prep_double("tsamp", inf.dt)
hdr += prep_double("refdm", inf.dm)
hdr += prep_string("HEADER_END")
return hdr
if __name__ == "__main__":
if len(sys.argv)==1:
print "\nusage: dat2tim.py file.dat\n"
sys.exit()
if sys.argv[1].endswith(".dat"):
basefilenm = sys.argv[1][:sys.argv[1].rfind(".dat")]
else:
basefilenm = sys.argv[1]
inf = presto.read_inffile(basefilenm)
outfile = open(basefilenm+".tim", "wb")
outfile.write(infodata_to_sigproc_header(inf))
outfile.close()
# Do this the simple (but kludgey) way
os.system("cat %s >> %s"%(sys.argv[1], basefilenm+".tim"))
print("\n\n**** Joining files...\n\n")
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("")
ncx = np.array(cx, copy=1)
presto.fftwcall(cx, -1)
presto.fftwcall(cx, 1)
assert(np.allclose(cx/N, ncx, atol=1e-6))
print "success"
print "Testing tablesixstepfft call...",
cx = np.random.standard_normal(N).astype(np.complex64)
ncx = np.array(cx, copy=1)
presto.tablesixstepfft(cx, -1)
presto.tablesixstepfft(cx, 1)
assert(np.allclose(cx/N, ncx, atol=1e-6))
print "success"
print "Testing reading infiles...",
x = presto.read_inffile("1937_DM71.02_zerodm.inf", verbose=False)
assert(x.telescope=="GBT")
assert(x.mjd_i==55267)
assert(x.dt==8.192e-05)
assert(x.numonoff==1)
assert(x.analyzer=="sransom")
print "success"
print "Testing writing infiles...",
x.analyzer="test"
x.name="xxx"
x.dt=0.125
presto.write_inffile(x, verbose=False)
y = presto.read_inffile("xxx", verbose=False)
assert(y.analyzer=="test")
assert(y.bary==0)
ncx = np.array(cx, copy=1)
presto.fftwcall(cx, -1)
presto.fftwcall(cx, 1)
assert (np.allclose(cx / N, ncx, atol=1e-6))
print "success"
print "Testing tablesixstepfft call...",
cx = np.random.standard_normal(N).astype(np.complex64)
ncx = np.array(cx, copy=1)
presto.tablesixstepfft(cx, -1)
presto.tablesixstepfft(cx, 1)
assert (np.allclose(cx / N, ncx, atol=1e-6))
print "success"
print "Testing reading infiles...",
x = presto.read_inffile("1937_DM71.02_zerodm.inf", verbose=False)
assert (x.telescope == "GBT")
assert (x.mjd_i == 55267)
assert (x.dt == 8.192e-05)
assert (x.numonoff == 1)
assert (x.analyzer == "sransom")
print "success"
print "Testing writing infiles...",
x.analyzer = "test"
x.name = "xxx"
x.dt = 0.125
presto.write_inffile(x, verbose=False)
y = presto.read_inffile("xxx", verbose=False)
assert (y.analyzer == "test")
assert (y.bary == 0)
inf.dec_d * 10000.0 + inf.dec_m * 100.0 + inf.dec_s)
else:
hdr += prep_double("src_dej",
inf.dec_d * 10000.0 - inf.dec_m * 100.0 - inf.dec_s)
hdr += prep_int("nbits", 32)
hdr += prep_int("nifs", 1)
hdr += prep_int("nchans", 1)
hdr += prep_double("fch1", inf.freq)
hdr += prep_double("foff", 1)
hdr += prep_double("tstart", inf.mjd_i + inf.mjd_f)
hdr += prep_double("tsamp", inf.dt)
hdr += prep_double("refdm", inf.dm)
hdr += prep_string("HEADER_END")
return hdr
if __name__ == "__main__":
if len(sys.argv) == 1:
print "\nusage: dat2tim.py file.dat\n"
sys.exit()
if sys.argv[1].endswith(".dat"):
basefilenm = sys.argv[1][:sys.argv[1].rfind(".dat")]
else:
basefilenm = sys.argv[1]
inf = presto.read_inffile(basefilenm)
outfile = open(basefilenm + ".tim", "wb")
outfile.write(infodata_to_sigproc_header(inf))
outfile.close()
# Do this the simple (but kludgey) way
os.system("cat %s >> %s" % (sys.argv[1], basefilenm + ".tim"))
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)
print "\n\n**** Joining files...\n\n"
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 ""
