def fold_event_prof(ph_mjd, par_file, nbins=16):
params = read_par(par_file, file_format='tempo2')
# Fold data with psr_utils by first calculating phases for each MJD based on par file's F0, F1, ... only good for isolated puslar
ph_phase = pu.calc_phs(ph_mjd, params['pepoch'], params['f'][0], params['f'][1], params['f'][2], params['f'][3])
# Cast all negative phases to be between 0 and 1
while (len(np.where(ph_phase <= 0.)[0]) > 0 ): # Need the [0] because output is a tuple...
below_zero_ind = np.where(ph_phase <= 0.)
ph_phase[below_zero_ind] += 1.0
# Now do the same to ensure anything greater than 1.0 is between (0., 1.0)
while (len(np.where(ph_phase > 1.0)[0]) > 0 ): # Need the [0] because output is a tuple...
above_zero_ind = np.where(ph_phase > 1.0)
ph_phase[below_zero_ind] -= 1.0
# Now histogram phases to create profile for a given number of bins (and thus bin size), and give user option to split data into N equal parts
prof, bin_edges = np.histogram(ph_phase, bins=nbins, range=(0.,1.))
bin_size = (bin_edges[1] - bin_edges[0])
bin_val = bin_edges[0: len(bin_edges)-1] + bin_size/2.
prof_err = np.sqrt(prof)
# Calculate central MJD and MJD span for profile from min/max event MJDs
if(len(ph_mjd) > 0):
mjd_mean = 0.5*(np.min(ph_mjd) + np.max(ph_mjd))
mjd_span = np.max(ph_mjd) - np.min(ph_mjd)
# spin phase at representative MJD of profile
ref_phase = pu.calc_phs(mjd_mean, params['pepoch'], params['f'][0], params['f'][1], params['f'][2], params['f'][3])
# Cast to be between 0 and 1
while(ref_phase <= 0.):
ref_phase += 1.0
while(ref_phase > 1.0):
ref_phase -= 1.0
ref_freq = pu.calc_freq(mjd_mean, params['pepoch'], params['f'][0], params['f'][1], params['f'][2], params['f'][3])
else:
mjd_mean = 0.
ref_phase = 0.
ref_freq = 0.
profile = {'i':prof, 'i_err':prof_err, 'phase':bin_val, 'mjd':mjd_mean, 'mjd_span': mjd_span, 'psrname':params['psr'], 'ref_phase':ref_phase, 'ref_freq':ref_freq}
return profile
def main():
progname = 'show_resid_info.py'
args = get_opt(progname)
# First, read in residuals data file, and assign each column to a separate
# numpy array
resid_data = read_resid(args.resfile,
tempo2=args.tempo2, info_file=args.infofile,
info_flag=args.infoflag)
# For now worry about ntoa in calculating chi2's but will implement
# par file reader to determine the number of DOF
# ( = n_toa + n_free_param + 1 for fit for phase)
if(args.parfile==None):
n_param = 0
else:
if(args.tempo2):
ffmt='tempo2'
else:
ffmt='tempo1'
param_name, para_val, param_fit = read_par(args.parfile, file_format=ffmt, return_tuple=True)
n_param = param_fit.count(True)
# param_data = read_par(args.parfile, file_format=ffmt)
# Now get information from residuals
rinfo = get_resid_info(resid_data, nparam=n_param)
# Now print out results, to stdout for now:
print ''
print 'Residual file: ', args.resfile
print 'Par file: ', args.parfile
print 'Number of TOAs: ', rinfo['ntoa']
print 'Number of parameters: ', rinfo['nparam']
print 'Number of DOF: ', rinfo['ndof']
print '\n'
print 'Info Total Avg weight Number Chi^2 Adjusted chi^2 rms rms MJD range Years Centre'
print ' weight per TOA of TOAs per TOA (per DOF) unweighted weighted freq '
print ''
for i_info in range(len(resid_data['info_val'])):
print '{0:8} {1:7.5f} {2:7.5f} {3:7d} {4:10.4f} {5:10.4f} {6:10.4f} {7:10.4f} {8:5d} - {9:5d} {10:5.2f} {11:6.1f}'.format(
resid_data['info_val'][i_info], rinfo['normwgt'][i_info],
rinfo['avgwgt'][i_info], rinfo['npts'][i_info],
rinfo['rchi2'][i_info], rinfo['rchi2x'][i_info],
rinfo['resrms'][i_info], rinfo['resrmsw'][i_info],
int(rinfo['mjdstart'][i_info]), int(rinfo['mjdend'][i_info]),
(rinfo['mjdend'][i_info]-rinfo['mjdstart'][i_info])/365.25,
rinfo['cfreq'][i_info] )
print ''
print '{0:8} {1:7.5f} {2:7.5f} {3:7d} {4:10.4f} {5:10.4f} {6:10.4f} {7:10.4f} {8:5d} - {9:5d} {10:5.2f} {11:6.1f}'.format(
'Total', rinfo['sum_normwgt'],
rinfo['sum_avgwgt'], rinfo['sum_npts'],
rinfo['sum_rchi2'], rinfo['sum_rchi2x'],
rinfo['sum_resrms'], rinfo['sum_resrmsw'],
int(rinfo['sum_mjdstart']), int(rinfo['sum_mjdend']),
(rinfo['sum_mjdend']-rinfo['sum_mjdstart'])/365.25,
rinfo['sum_cfreq'] )
def main():
progname = 'm2mtot_grid.py'
args = get_opt(progname)
if(args.psrname == None):
outfile_base = ''
else:
outfile_base = args.psrname
# Set par and tim files
# par_base = '/Users/ferdman/Work/pulsar/1756-2251/timing/tempo/1756.dd.par.BASE'
# tim_file = '/Users/ferdman/Work/pulsar/1756-2251/timing/tempo/1756.tempo.tim'
# Prepare par file for grid fitting
# First, read in par file:
par_base_contents = []
f_par = open(args.parfile, 'r')
for par_line in f_par.readlines():
if ((par_line.split()[0] != 'SINI') & (par_line.split()[0]!='M2')):
par_base_contents.append(par_line.split())
#par_base_contents = [par_line.split() for par_line in f_par.readlines()]
f_par.close()
parfile_base = 'par_base.par'
f_par_base = open(parfile_base, 'w')
for par_line in par_base_contents:
f_par_base.write(' '.join(par_line)+'\n')
f_par_base.close()
# read in pb and asini from par file, adn calculation mass function:
if(args.tempo2):
tempo_ver = 'tempo2'
else:
tempo_ver = 'tempo1'
params=read_par(args.parfile, file_format=tempo_ver)
# asini is in (light) seconds. Convert pb to secs as well.
# tsun is in us to give f_mass in solar units.
tsun = 4.925490947
tsun_secs = tsun*10**(-6)
pb_secs = float(params['pb'])*86400.0
f_mass = 4*np.pi*np.pi*(float(params['a1'])**3.)/(tsun_secs*(pb_secs**2.))
# f_mass = 4*np.pi*np.pi*(float(params['a1'])**3.)/(tsun*(float(params['pb'])**2.))
print 'pb = ', float(params['pb']), ' = ', pb_secs, ' sec'
print 'a1 = ', float(params['a1'])
print 'fmass = ', f_mass
if(args.loadfile==None):
p_out = grid_fit_shapiro_tempo(parfile_base, args.timfile,
m2_range=args.m2lim,
cosi_range=args.cosilim,
n_m2=args.nm2, n_cosi=args.ncosi,
fmass=f_mass,
tempo2=args.tempo2)
if(args.savefile):
save_file = 'm2cosi_grid_{0}_{1}'.format(args.nm2, args.ncosi)
save_array = np.array([p_out['m2'], p_out['cosi'], p_out['sini'],
p_out['m1'], p_out['m1_prob']])
np.save(save_file+'_params', save_array)
np.save(save_file+'_prob', p_out['norm_like'])
else:
load_array = np.load(args.loadfile+'_params.npy')
# for the purposes of this routine, only need the following
# things in p_out
p_out = {'m2':load_array[0],
'cosi':load_array[1],
'sini':load_array[2],
'm1':load_array[3],
'm1_prob':load_array[4]}
p_out['norm_like'] = np.load(args.loadfile+'_prob.npy')
# Now make contour plots
plot_contour_pdf(p_out['cosi'], p_out['m2'], p_out['norm_like'],
xlabel='|cos $i$|',
ylabel='Companion mass ($M_\\odot$)')
# Add in m1 curves
if(args.m1curve != None):
for i_m1 in np.arange(len(args.m1curve)):
sini_plot = ( (f_mass*(args.m1curve[i_m1]+p_out['m2'])**2.)**(1./3.) )/p_out['m2']
cosi_plot = np.sqrt(1.0 - sini_plot**2.)
plt.plot(cosi_plot, p_out['m2'], linestyle='dashed', color='black')
plt.savefig('1756_m2cosi_contours.'+args.plotformat)
# Now plot 1D pdfs for m2 and cosi
m2_pdf = np.sum(p_out['norm_like'], axis=1)
m2_med, m2_prob_min, m2_prob_max = \
get_pdf_prob(p_out['m2'], m2_pdf, prob_intervals)
plot_pdf(p_out['m2'], m2_pdf,
xlabel='Companion mass ($M_\\odot$)', ylabel='Probability density',
prob_lines=np.append(m2_prob_min, m2_prob_max),
prob_linestyle=['dashed','dashdot','dotted',
'dashed','dashdot','dotted'])
plt.savefig('1756_m2_m2sini_pdf.'+args.plotformat)
print 'M2 = ', m2_med
print ' 68%: ', m2_prob_min[0], m2_prob_max[0]
print ' 95%: ', m2_prob_min[1], m2_prob_max[1]
print ' 99%: ', m2_prob_min[2], m2_prob_max[2]
print ' '
sini_pdf = np.sum(p_out['norm_like'], axis=0)
sini_med, sini_prob_min, sini_prob_max = \
get_pdf_prob(p_out['sini'], sini_pdf, prob_intervals)
plot_pdf(p_out['sini'], sini_pdf,
xlabel='Sine of inclination angle', ylabel='Probability density',
prob_lines=np.append(sini_prob_min, sini_prob_max),
prob_linestyle=['dashed','dashdot','dotted',
'dashed','dashdot','dotted'])
plt.savefig('1756_sini_m2sini_pdf.'+args.plotformat)
print 'SINI = ', sini_med
print ' 68%: ', sini_prob_min[0], sini_prob_max[0]
print ' 95%: ', sini_prob_min[1], sini_prob_max[1]
print ' 99%: ', sini_prob_min[2], sini_prob_max[2]
print ' '
cosi_pdf = np.sum(p_out['norm_like'], axis=0)
cosi_med, cosi_prob_min, cosi_prob_max = \
get_pdf_prob(p_out['cosi'], cosi_pdf, prob_intervals)
plot_pdf(p_out['cosi'], cosi_pdf,
xlabel='Total system mass ($M_\\odot$)', ylabel='Probability density',
prob_lines=np.append(cosi_prob_min, cosi_prob_max),
prob_linestyle=['dashed','dashdot','dotted',
'dashed','dashdot','dotted'])
plt.savefig('1756_cosi_m2sini_pdf.'+args.plotformat)
print 'COSI = ', cosi_med
print ' 68%: ', cosi_prob_min[0], cosi_prob_max[0]
print ' 95%: ', cosi_prob_min[1], cosi_prob_max[1]
print ' 99%: ', cosi_prob_min[2], cosi_prob_max[2]
print ' '
# Now deal with m1's: create histogram weighted by likelihood
m1_pdf, bin_edges = np.histogram(p_out['m1'], args.m1bins,
density=True, weights=p_out['m1_prob'])
# We can define the bin centres as follows since our call to np/histogram gives
# back evenly spaced bins
bin_size = bin_edges[1] - bin_edges[0]
m1_val = bin_edges[0:len(bin_edges)-1] + 0.5*bin_size
# Get PDF intervals and values:
# pdf_rho = rho_hist/np.sum(rho_hist)
m1_med, m1_prob_min, m1_prob_max = \
get_pdf_prob(m1_val, m1_pdf,prob_intervals, norm=True)
plot_pdf(m1_val, m1_pdf,
xlabel='Pulsar mass ($M_\\odot$)', ylabel='Probability density',
prob_lines=np.append(m1_prob_min, m1_prob_max),
prob_linestyle=['dashed','dashdot','dotted',
'dashed','dashdot','dotted'])
plt.savefig('1756_m1_m2sini_pdf.'+args.plotformat)
print ' '
print 'M1 = ', m1_med
print ' 68%: ', m1_prob_min[0], ' ', m1_prob_max[0]
print ' 95%: ', m1_prob_min[1], ' ', m1_prob_max[1]
print ' 99%: ', m1_prob_min[2], ' ', m1_prob_max[2]
print ' '