def get_tempo_result(parfile, timfile):
"""This function is to get the results from tempo and write them to a file.
Parameter
---------
parfile : str
The file to read parameters.
timfile : str
The file to read toas.
Return
----------
A file named as parfile name ends with '.tempo_test' stored residuals in the
first column
"""
t1_toas = t1u.read_toa_file(timfile)
t1u.run_tempo(t1_toas, parfile)
t1_resids = t1_toas.get_resids(units="phase")
outfile = parfile + ".tempo_test"
f = open(outfile, "w")
outstr = "residuals_phase "
outstr += "\n"
f.write(outstr)
for res in t1_resids:
outstr = longdouble2str(res) + "\n"
f.write(outstr)
f.close()
def get_tempo2_result(parfile, timfile, general2=None):
"""This function is to get the results from tempo and write them to a file.
Parameter
---------
parfile : str
The file to read parameters.
timfile : str
The file to read toas.
general2 : list/ None
The values required from tempo2 general2 plugin.
Return
----------
A file named as parfile name ends with '.tempo2_test' stored residuals in the
first column, binary delay in the second column and general2 results if
general2 are provided.
"""
if not has_tempo2_utils:
raise ImportError(
"To get tempo2 general2 results, tempo2_utils are"
" required. See page"
" https://github.com/demorest/tempo_utils"
)
residuals = t2u.general2(parfile, timfile, ["pre"])["pre"]
outfile = parfile + ".tempo2_test"
f = open(outfile, "w")
outstr = "residuals "
if general2 is not None and general2 != []:
tempo2_vals = t2u.general2(parfile, timfile, general2)
for keys in general2:
outstr += keys + " "
outstr += "\n"
f.write(outstr)
for ii in range(len(residuals)):
outstr = longdouble2str(residuals[ii]) + " "
if general2 is not None:
for keys in general2:
outstr += longdouble2str(tempo2_vals[keys][ii]) + " "
outstr += "\n"
f.write(outstr)
f.close()
def test_longdouble_str_roundtrip_is_exact(i, f):
ld = np.longdouble(i) + np.longdouble(f)
assert ld == str2longdouble(longdouble2str(ld))
def test_longdouble2str_same_as_str_and_repr(i, f):
ld = np.longdouble(i) + np.longdouble(f)
assert longdouble2str(ld) == str(ld)
assert longdouble2str(ld) == repr(ld)
def tempo_polyco_table_writer(polycoTable, filename='polyco.dat'):
"""
Write tempo style polyco file from an astropy table
Tempo style polyco file:
The polynomial ephemerides are written to file 'polyco.dat'. Entries
are listed sequentially within the file. The file format is::
Line Columns Item
---- ------- -----------------------------------
1 1-10 Pulsar Name
11-19 Date (dd-mmm-yy)
20-31 UTC (hhmmss.ss)
32-51 TMID (MJD)
52-72 DM
74-79 Doppler shift due to earth motion (10^-4)
80-86 Log_10 of fit rms residual in periods
2 1-20 Reference Phase (RPHASE)
21-38 Reference rotation frequency (F0)
39-43 Observatory number
44-49 Data span (minutes)
50-54 Number of coefficients
55-75 Observing frequency (MHz)
76-80 Binary phase
3* 1-25 Coefficient 1 (COEFF(1))
26-50 Coefficient 2 (COEFF(2))
51-75 Coefficient 3 (COEFF(3))
* Subsequent lines have three coefficients each, up to NCOEFF
One polyco file could include more then one entrie
The pulse phase and frequency at time T are then calculated as::
DT = (T-TMID)*1440
PHASE = RPHASE + DT*60*F0 + COEFF(1) + DT*COEFF(2) + DT^2*COEFF(3) + ....
FREQ(Hz) = F0 + (1/60)*(COEFF(2) + 2*DT*COEFF(3) + 3*DT^2*COEFF(4) + ....)
Parameters
---------
polycoTable: astropy table
Polycos style table
filename : str
Name of the output poloco file.
References
----------
http://tempo.sourceforge.net/ref_man_sections/tz-polyco.txt
"""
f = open(filename, 'w')
lenTable = len(polycoTable)
if lenTable == 0:
errorMssg = ("Insufficent polyco data." +
" Please make sure polycoTable has data.")
raise AttributeError(errorMssg)
for i in range(lenTable):
entry = polycoTable['entry'][i]
psrname = polycoTable['psr'][i].ljust(10)
dateDMY = polycoTable['date'][i].ljust(10)
utcHMS = polycoTable['utc'][i][0:9].ljust(10)
tmid_mjd = utils.longdouble2str(entry.tmid.value) + ' '
dm = str(polycoTable['dm'][i]).ljust(72 - 52 + 1)
dshift = str(polycoTable['doppler'][i]).ljust(79 - 74 + 1)
logrms = str(polycoTable['logrms'][i]).ljust(80 - 86 + 1)
line1 = psrname + dateDMY + utcHMS + tmid_mjd + dm + dshift + logrms + '\n'
# Get the reference phase
rph = (entry.rphase.int + entry.rphase.frac).value[0]
# FIXME: sometimes raises error, sometimes loses precision!
rphase = utils.longdouble2str(rph)[0:19].ljust(20)
f0 = ('%.12lf' % entry.f0).ljust(38 - 21 + 1)
obs = entry.obs.ljust(43 - 39 + 1)
tspan = str(round(entry.mjdspan.to('min').value,
4))[0].ljust(49 - 44 + 1)
if len(tspan) >= (49 - 44 + 1): # Hack to fix read errors in python
tspan = tspan + ' '
ncoeff = str(entry.ncoeff).ljust(54 - 50 + 1)
obsfreq = str(polycoTable['obsfreq'][i]).ljust(75 - 55 + 1)
binPhase = str(polycoTable['binary_phase'][i]).ljust(80 - 76 + 1)
line2 = rphase + f0 + obs + tspan + ncoeff + obsfreq + binPhase + '\n'
coeffBlock = ""
for j, coeff in enumerate(entry.coeffs):
coeffBlock += ('%.17e' % coeff).ljust(25)
if (j + 1) % 3 == 0:
coeffBlock += '\n'
f.write(line1 + line2 + coeffBlock)
f.close()