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 = longdouble2string(res) + '\n'
f.write(outstr)
f.close()
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 = longdouble2string(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.
"""
psr = lt.tempopulsar(parfile, timfile)
residuals = psr.residuals()
binary_delay = psr.binarydelay()
outfile = parfile + '.tempo2_test'
f = open(outfile, 'w')
outstr = 'residuals BinaryDelay '
if general2 is not None and general2 != []:
if not has_tempo2_utils:
raise ImportError("To get tempo2 general2 results, tempo2_utils are"
" required. See page"
" https://github.com/demorest/tempo_utils")
else:
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 = longdouble2string(residuals[ii]) + ' ' +longdouble2string(binary_delay[ii]) +' '
if general2 is not None:
for keys in general2:
outstr += longdouble2string(tempo2_vals[keys][ii])+' '
outstr += '\n'
f.write(outstr)
f.close()
def change_parfile(filename, param, value):
"""A function to change parfile parameter value and fit flag
"""
strv = ut.longdouble2string(value)
fh, abs_path = mkstemp()
with open(abs_path, 'w') as new_file:
with open(filename) as old_file:
for line in old_file:
if line.startswith(param + ' '):
l = line.split()
line = line.replace(l[1], strv)
line = line.replace(' 0 ', ' 1 ')
new_file.write(line)
close(fh)
#Remove original file
remove(filename)
#Move new file
move(abs_path, filename)
def change_parfile(filename, param, value):
"""A function to change parfile parameter value and fit flag
"""
strv = ut.longdouble2string(value)
fh, abs_path = mkstemp()
with open(abs_path,'w') as new_file:
with open(filename) as old_file:
for line in old_file:
if line.startswith(param+' '):
l = line.split()
line = line.replace(l[1], strv)
line = line.replace(' 0 ', ' 1 ')
new_file.write(line)
close(fh)
#Remove original file
remove(filename)
#Move new file
move(abs_path, filename)
def tempo_polyco_table_writer(polycoTable, filename = 'polyco.dat'):
"""
Write tempo style polyco file from an astropy table
Parameters
---------
polycoTalbe: astropy table
Polycos style table
filename : str
Name of the output poloco file.
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) + ....)
Reference:
http://tempo.sourceforge.net/ref_man_sections/tz-polyco.txt
"""
f = open(filename,'w')
try:
lenTable = len(polycoTable)
if lenTable == 0:
errorMssg = ("No sufficent polyco data."+
" Plese make sure polycoTable has data.")
raise AttributeError(errorMssg)
except:
errorMssg = "No sufficent polycoTable. "
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)
tmidMjd = utils.longdouble2string(entry.tmid.value)+' '
dm = str(polycoTable['dm'][i]).ljust(72-52+1)
dshift = str(polycoTable['dopper'][i]).ljust(79-74+1)
logrms = str(polycoTable['logrms'][i]).ljust(80-86+1)
line1 = psrname+dateDMY+utcHMS+tmidMjd+dm+dshift+logrms+'\n'
# Get the reference phase
rph = (entry.rphase.int+entry.rphase.frac).data[0]
rphase = utils.longdouble2string(rph)[0:19].ljust(20)
f0 = ('%.12lf' % entry.f0).ljust(38-21+1)
obs = entry.obs.ljust(43-39+1)
tspan = (str(entry.mjdspan.to('min')).split())[0].ljust(49-44+1)
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()
def tempo_polyco_table_writer(polycoTable, filename='polyco.dat'):
"""
Write tempo style polyco file from an astropy table
Parameters
---------
polycoTalbe: astropy table
Polycos style table
filename : str
Name of the output poloco file.
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) + ....)
Reference:
http://tempo.sourceforge.net/ref_man_sections/tz-polyco.txt
"""
f = open(filename, 'w')
try:
lenTable = len(polycoTable)
if lenTable == 0:
errorMssg = ("No sufficent polyco data." +
" Plese make sure polycoTable has data.")
raise AttributeError(errorMssg)
except:
errorMssg = "No sufficent polycoTable. "
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)
tmidMjd = utils.longdouble2string(entry.tmid.value) + ' '
dm = str(polycoTable['dm'][i]).ljust(72 - 52 + 1)
dshift = str(polycoTable['dopper'][i]).ljust(79 - 74 + 1)
logrms = str(polycoTable['logrms'][i]).ljust(80 - 86 + 1)
line1 = psrname + dateDMY + utcHMS + tmidMjd + dm + dshift + logrms + '\n'
# Get the reference phase
rph = (entry.rphase.int + entry.rphase.frac).data[0]
rphase = utils.longdouble2string(rph)[0:19].ljust(20)
f0 = ('%.12lf' % entry.f0).ljust(38 - 21 + 1)
obs = entry.obs.ljust(43 - 39 + 1)
tspan = (str(entry.mjdspan.to('min')).split())[0].ljust(49 - 44 + 1)
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()
print "param1 num unit is ", param1.num_unit
# Change num_value
print "Change num_values"
param1.num_value = 10.0
print "param1 num value is ", param1.num_value
print "param1 value is ", param1.value, "With type ", type(param1.value)
print "param1 unit is ", param1.units
print "param1 num unit is ", param1.num_unit
# Test MJDparameter Class
paramMJD = p.MJDParameter(
name="TZRMJD",
description="Reference epoch for phase = 0.0",
parse_value=lambda x: time_from_mjd_string(x, scale="tdb"),
)
print "Before assigning paramMJD value."
print "paramMJD num value is ", longdouble2string(paramMJD.num_value)
print "paramMJD value is ", paramMJD.value, "With type ", type(paramMJD.value)
print "paramMJD unit is ", paramMJD.units
print "paramMJD num unit is ", paramMJD.num_unit
paramMJD.set("54001.012345678901234")
print "After assigning paramMJD value."
print "paramMJD num value is ", longdouble2string(paramMJD.num_value)
print "paramMJD value is ", paramMJD.value, "With type ", type(paramMJD.value)
print "paramMJD unit is ", paramMJD.units
print "paramMJD num unit is ", paramMJD.num_unit
# change num_value
paramMJD.num_value = data2longdouble("54001.012345678901234")
print "After assigning paramMJD num_value."
print "paramMJD num value is ", longdouble2string(paramMJD.num_value)
print "paramMJD value is ", paramMJD.value, "With type ", type(paramMJD.value)
print "paramMJD unit is ", paramMJD.units
