def plotmdp():
spin00_pol_degree_spline = buildspline(0.5)
spin00_mcube = xBinnedModulationCube(fetch_mcubepath(0.5))
spin998_pol_degree_spline = buildspline(0.998)
spin998_mcube = xBinnedModulationCube(fetch_mcubepath(0.998))
spin00_mcube.fit()
spin998_mcube.fit()
spin00_fit_results = spin00_mcube.fit_results[0]
spin998_fit_results = spin998_mcube.fit_results[0]
plt.figure('MDP')
spin00_mdp = spin00_mcube.mdp99[:-1]
spin998_mdp = spin998_mcube.mdp99[:-1]
emean = spin00_mcube.emean[:-1]
emin = spin00_mcube.emin[:-1]
emax = spin00_mcube.emax[:-1]
width = (emax-emin)/2.
plt.errorbar(emean,spin00_mdp,xerr=width, label='Spin 0.5',marker='o',linestyle='--')
plt.errorbar(emean,spin998_mdp,xerr=width, label='Spin 0.998',marker='o',linestyle='--')
plt.figtext(0.2, 0.85,'XIPE %s ks'%((SIM_DURATION*NUM_RUNS)/1000.),size=18)
plt.xlim([1,10])
plt.ylabel('MPD 99\%')
plt.xlabel('Energy (keV)')
plt.legend()
plt.show()
def analyze():
"""
"""
if os.path.exists(ANALYSIS_FILE_PATH):
logger.info('%s exists, delete it if you want to recreate it.' %\
ANALYSIS_FILE_PATH)
return
logger.info('Opening output file %s...' % ANALYSIS_FILE_PATH)
analysis_file = open(ANALYSIS_FILE_PATH, 'w')
for i, (_min, _max) in enumerate(PHASE_BINNING):
_mcube = xBinnedModulationCube(_mcube_file_path(i))
_mcube.fit()
_fit_results = _mcube.fit_results[-1]
print _fit_results
_phase = 0.5*(_min + _max)
_phase_err = 0.5*(_max - _min)
_pol_deg = _fit_results.polarization_degree
_pol_deg_err = _fit_results.polarization_degree_error
_pol_angle = _fit_results.phase
_pol_angle_err = _fit_results.phase_error
_data = (_phase, _phase_err, _pol_deg, _pol_deg_err, _pol_angle,
_pol_angle_err)
_fmt = ('%.4e ' * len(_data)).strip()
_fmt = '%s\n' % _fmt
_line = _fmt % _data
analysis_file.write(_line)
analysis_file.close()
def analyze():
"""Analyze the data.
"""
logger.info('Opening output file %s...' % ANALYSIS_FILE_PATH)
analysis_file = open(ANALYSIS_FILE_PATH, 'w')
for i, (_min, _max) in enumerate(zip(TIME_BINNING[:-1], TIME_BINNING[1:])):
_mcube = xBinnedModulationCube(_mcube_file_path(i))
_mcube.fit()
_fit_results = _mcube.fit_results[0]
_sel_file = xEventFile(_sel_file_path(i))
_time = numpy.average(_sel_file.event_data['TIME'])
_sel_file.close()
_time_errp = _max - _time
_time_errm = _time - _min
_pol_deg = _fit_results.polarization_degree
_pol_deg_err = _fit_results.polarization_degree_error
_pol_angle = _fit_results.phase
_pol_angle_err = _fit_results.phase_error
_spec_fitter = PIPELINE.xpxspec(_pha1_file_path(i), plot=False)
(_index, _index_err), (_norm,
_norm_err) = _spec_fitter.fit_parameters()
# The division by the phase interval is a workaround and we should
# keep track of that in xpselect.
_norm /= (_max - _min)
_norm_err /= (_max - _min)
_data = (_time, _time_errp, _time_errm, _pol_deg, _pol_deg_err,
_pol_angle, _pol_angle_err, _index, _index_err, _norm,
_norm_err)
_fmt = ('%.4e ' * len(_data)).strip()
_fmt = '%s\n' % _fmt
_line = _fmt % _data
analysis_file.write(_line)
analysis_file.close()
def view():
_mcube = xBinnedModulationCube(MCUBE_FILE_PATH)
_mcube.fit()
_fit_results = _mcube.fit_results[0]
plt.figure('Polarization degree')
_mcube.plot_polarization_degree(show=False, color='blue')
pol_degree_spline.plot(color='lightgray',label='Spin %s'%spindegree, show=False)
plt.figtext(0.2, 0.85,'XIPE %s ks'%(SIM_DURATION/1000.),size=18)
#plt.errorbar(_energy_mean, _pol_deg, yerr=_pol_deg_err, color='blue',marker='o')
plt.legend()
plt.figure('Polarization angle')
_mcube.plot_polarization_angle(show=False, color='blue', degree=False)
pol_angle_spline.plot(color='lightgray',label='Spin %s'%spindegree, show=False)
plt.figtext(0.2, 0.85,'XIPE %s ks'%(SIM_DURATION/1000.),size=18)
#plt.errorbar(_energy_mean,_pol_angle, yerr= _pol_angle_err,color='blue',marker='o')
plt.xlim([1,10])
plt.legend()
plt.figure('MDP %s'%base_name)
mdp = _mcube.mdp99[:-1]
emean = _mcube.emean[:-1]
emin = _mcube.emin[:-1]
emax = _mcube.emax[:-1]
width = (emax-emin)/2.
plt.errorbar(emean,mdp,xerr=width, label='MDP99',marker='o',linestyle='--')
plt.figtext(0.2, 0.85,'XIPE %s ks'%(SIM_DURATION/1000.),size=18)
plt.xlim([1,10])
plt.ylabel('MPD 99\%')
plt.xlabel('Energy (keV)')
#plt.legend()
plt.show()
def analyze():
"""Analyze the data.
"""
logger.info('Opening output file %s...' % ANALYSIS_FILE_PATH)
analysis_file = open(ANALYSIS_FILE_PATH, 'w')
for i, (_min, _max) in enumerate(zip(TIME_BINNING[:-1],
TIME_BINNING[1:])):
_mcube = xBinnedModulationCube(_mcube_file_path(i))
_mcube.fit()
_fit_results = _mcube.fit_results[0]
_sel_file = xEventFile(_sel_file_path(i))
_time = numpy.average(_sel_file.event_data['TIME'])
_sel_file.close()
_time_errp = _max - _time
_time_errm = _time - _min
_pol_deg = _fit_results.polarization_degree
_pol_deg_err = _fit_results.polarization_degree_error
_pol_angle = _fit_results.phase
_pol_angle_err = _fit_results.phase_error
_spec_fitter = PIPELINE.xpxspec(_pha1_file_path(i), plot=False)
(_index, _index_err), (_norm, _norm_err) = _spec_fitter.fit_parameters()
# The division by the phase interval is a workaround and we should
# keep track of that in xpselect.
_norm /= (_max - _min)
_norm_err /= (_max - _min)
_data = (_time, _time_errp, _time_errm, _pol_deg, _pol_deg_err,
_pol_angle, _pol_angle_err, _index, _index_err, _norm,
_norm_err)
_fmt = ('%.4e ' * len(_data)).strip()
_fmt = '%s\n' % _fmt
_line = _fmt % _data
analysis_file.write(_line)
analysis_file.close()
def plot():
spherical_mcube = xBinnedModulationCube(SPHERICAL_MCUBE_PATH)
wedge_mcube = xBinnedModulationCube(WEDGE_MCUBE_PATH)
spherical_mcube.fit()
wedge_mcube.fit()
spherical_fit_results = spherical_mcube.fit_results[0]
wedge_fit_results = wedge_mcube.fit_results[0]
plt.figure('Polarization degree')
spherical_mcube.plot_polarization_degree(show=False, color='blue')
pol_degree_spline_spherical.plot(color='lightblue',label='Spherical corona model (40 degree inclination)', show=False)
wedge_mcube.plot_polarization_degree(show=False, color='red')
pol_degree_spline_wedge.plot(color='lightsalmon',label='Wedge corona model (40 degree inclination)', show=False)
plt.figtext(0.2, 0.85,'XIPE %s ks'%((SIM_DURATION*NUM_RUNS)/1000.),size=18)
plt.xlim([1,10])
plt.legend()
plt.show()
def view():
#_energy_mean,_emin, _emax, _pol_deg, _pol_deg_err, _pol_angle, \
# _pol_angle_err = \
# numpy.loadtxt(ANALYSIS_FILE_PATH, unpack=True)
_mcube = xBinnedModulationCube(MCUBE_FILE_PATH)
_mcube.fit()
_fit_results = _mcube.fit_results[0]
plt.figure('Polarization degree')
_mcube.plot_polarization_degree(show=False, color='blue')
pol_degree_spline.plot(color='lightgray', label='Model', show=False)
#plt.errorbar(_energy_mean, _pol_deg, yerr=_pol_deg_err, color='blue',marker='o')
plt.figure('Polarization angle')
_mcube.plot_polarization_angle(show=False, color='blue', degree=False)
pol_angle_spline.plot(color='lightgray', label='Model', show=False)
#plt.errorbar(_energy_mean,_pol_angle, yerr= _pol_angle_err,color='blue',marker='o')
plt.legend()
plt.show()
def analyze():
"""Analyze the data.Testing this method, but I must be missing something, it does not work yet.
"""
logger.info('Opening output file %s...' % ANALYSIS_FILE_PATH)
analysis_file = open(ANALYSIS_FILE_PATH, 'w')
_mcube = xBinnedModulationCube(MCUBE_FILE_PATH)
_mcube.fit()
_fit_results = _mcube.fit_results[0]
_pol_deg = _fit_results.polarization_degree
_pol_deg_err = _fit_results.polarization_degree_error
_pol_angle = _fit_results.phase
_pol_angle_err = _fit_results.phase_error
#_energy_mean = _mcube.emean[0]
#_emin = _mcube.emean[1]
#_emax = _mcube.emean[2]
#_data = (_energy_mean,_emin, _emax,_pol_deg, _pol_deg_err, _pol_angle, _pol_angle_err)
print _data
_fmt = ('%.4e ' * len(_data)).strip()
_fmt = '%s\n' % _fmt
_line = _fmt % _data
analysis_file.write(_line)
analysis_file.close()
def analyze():
"""Analyze the data.
"""
for j in range(len(E_BINNING)):
if (j==len(E_BINNING)-1):
logger.info('Opening output file %s...' % ANALYSIS_FILE_PATH)
analysis_file = open(ANALYSIS_FILE_PATH, 'w')
else:
logger.info('Opening output file %s_%d ...' % (ANALYSIS_FILE_PATH,j))
analysis_file = open('%s_%d' % (ANALYSIS_FILE_PATH,j), 'w')
for i, (_min, _max) in enumerate(zip(PHASE_BINNING[:-1],
PHASE_BINNING[1:])):
_mcube = xBinnedModulationCube(_mcube_file_path(i))
_mcube.fit()
_fit_results = _mcube.fit_results[j]
_emean = _mcube.emean[j]
_emin = _mcube.emin[j]
_emax = _mcube.emax[j]
print("%g - %g - %g\n" % (_emin,_emean,_emax))
_phase = 0.5*(_min + _max)
_phase_err = 0.5*(_max - _min)
_pol_deg = _fit_results.polarization_degree
_pol_deg_err = _fit_results.polarization_degree_error
_pol_angle = _fit_results.phase
_pol_angle_err = _fit_results.phase_error
_spec_fitter = PIPELINE.xpxspec(_pha1_file_path(i), plot=False,model='powerlaw')
(_index, _index_err), (_norm, _norm_err) = _spec_fitter.fit_parameters()
# The division by the phase interval is a workaround and we should
# keep track of that in xpselect.
_norm /= (_max - _min)
_norm_err /= (_max - _min)
_data = (_phase, _phase_err, _pol_deg, _pol_deg_err, _pol_angle,
_pol_angle_err, _index, _index_err, _norm, _norm_err)
_fmt = ('%.4e ' * len(_data)).strip()
_fmt = '%s\n' % _fmt
_line = _fmt % _data
analysis_file.write(_line)
analysis_file.close()
def fit_pol_map():
output_file = file('%s/%s'%(XIMPOL_DATA,OUTPUT_FILE),'w')
_ra = numpy.linspace(ra_min, ra_max, num_points)
_dec = numpy.linspace(dec_min, dec_max, num_points)
for i,ra in enumerate(_ra):
for j,dec in enumerate(_dec):
mcube_file_path = get_mcube_file_path(i,j)
mcube = xBinnedModulationCube(mcube_file_path)
mcube.fit()
for j,fit in enumerate(mcube.fit_results):
degree = fit.polarization_degree
degree_error = fit.polarization_degree_error
angle = fit.phase
angle_error = fit.phase_error
counts = mcube.counts[j]
emin = mcube.emin[j]
emax = mcube.emax[j]
#These conditions are needed to make sure that we do not get unphysical values for the polarization degree due to low statistics in the fitting stage.
if degree_error > degree or counts < 10000:
degree = 0.0
# degree_error = 0.0
else:
degree = degree*100
degree_error = degree_error*100
if degree > 50:
mcube.plot_bin(0)
#write the fit values to a txt file the first time you run the code and then simply read the txt file for fast plotting after.
line = '%s,%s,%s,%s,%s,%s,%s\n'%(emin,emax,degree, degree_error, angle, angle_error, counts)
print "Info",line
output_file.write(line)
output_file.close()
def analyze():
"""
"""
if os.path.exists(ANALYSIS_FILE_PATH):
logger.info('%s exists, delete it if you want to recreate it.' %\
ANALYSIS_FILE_PATH)
return
modf = load_mrf('xipe_goal')
logger.info('Opening output file %s...' % ANALYSIS_FILE_PATH)
analysis_file = open(ANALYSIS_FILE_PATH, 'w')
for i, (_min, _max) in enumerate(PHASE_BINNING):
_evt_file = xEventFile(_sel_file_path(i))
_energy = _evt_file.event_data['ENERGY']
_phase = _evt_file.event_data['PHASE']
exp = (polarization_degree(_energy, _phase, 0, 0)*modf(_energy)).sum()/\
modf(_energy).sum()
_mcube = xBinnedModulationCube(_mcube_file_path(i))
_mcube.fit()
_fit_results = _mcube.fit_results[-1]
print _fit_results
print exp
print polarization_degree(_mcube.emean[-1], _phase, 0, 0)
raw_input()
_phase = 0.5*(_min + _max)
_phase_err = 0.5*(_max - _min)
_pol_deg = _fit_results.polarization_degree
_pol_deg_err = _fit_results.polarization_degree_error
_pol_angle = _fit_results.phase
_pol_angle_err = _fit_results.phase_error
_data = (_phase, _phase_err, _pol_deg, _pol_deg_err, _pol_angle,
_pol_angle_err)
_fmt = ('%.4e ' * len(_data)).strip()
_fmt = '%s\n' % _fmt
_line = _fmt % _data
analysis_file.write(_line)
analysis_file.close()
def analyze():
"""Analyze the data.Testing this method, but I must be missing something, it does not work yet.
"""
logger.info('Opening output file %s...' % ANALYSIS_FILE_PATH)
analysis_file = open(ANALYSIS_FILE_PATH, 'w')
_mcube = xBinnedModulationCube(MCUBE_FILE_PATH)
_mcube.fit()
for j, fit in enumerate(_mcube.fit_results):
#_fit_results = _mcube.fit_results[0]
_pol_deg = fit.polarization_degree
_pol_deg_err = fit.polarization_degree_error
_pol_angle = fit.phase
_pol_angle_err = fit.phase_error
_energy_mean = _mcube.emean[j]
_emin = _mcube.emin[j]
_emax = _mcube.emax[j]
_data = (_energy_mean,_emin, _emax,_pol_deg, _pol_deg_err, _pol_angle, _pol_angle_err)
print _data
_fmt = ('%.4e ' * len(_data)).strip()
_fmt = '%s\n' % _fmt
_line = _fmt % _data
analysis_file.write(_line)
analysis_file.close()
def view():
#_energy_mean,_emin, _emax, _pol_deg, _pol_deg_err, _pol_angle, \
# _pol_angle_err = \
# # numpy.loadtxt(ANALYSIS_FILE_PATH, unpack=True)
_mcube = xBinnedModulationCube(MCUBE_FILE_PATH)
_mcube.fit()
_fit_results = _mcube.fit_results[0]
plt.figure('Polarization degree')
_mcube.plot_polarization_degree(show=False, color='blue')
pol_degree_spline.plot(color='lightgray',label='Model %s corona'%model_type, show=False)
plt.figtext(0.2, 0.85,'XIPE %s ks'%(SIM_DURATION/1000.),size=18)
#plt.errorbar(_energy_mean, _pol_deg, yerr=_pol_deg_err, color='blue',marker='o')
plt.legend()
plt.figure('Polarization angle')
_mcube.plot_polarization_angle(show=False, color='blue', degree=False)
pol_angle_spline.plot(color='lightgray',label='Model %s corona'%model_type, show=False)
plt.figtext(0.2, 0.85,'XIPE %s ks'%(SIM_DURATION/1000.),size=18)
#plt.errorbar(_energy_mean,_pol_angle, yerr= _pol_angle_err,color='blue',marker='o')
plt.legend()
plt.figure('MDP %s'%base_name)
mdp = _mcube.mdp99
emean = _mcube.emean
emin = _mcube.emin
emax = _mcube.emax
width = (emax-emin)/2.
plt.errorbar(emean,mdp,xerr=width, label='MDP99',marker='o',linestyle='--')
plt.figtext(0.2, 0.85,'XIPE %s ks'%(SIM_DURATION/1000.),size=18)
plt.xlim([1,10])
plt.ylabel('MPD 99 %')
plt.xlabel('Energy (keV)')
#plt.legend()
plt.show()
elif '-o' in a: outfile = sys.argv[i+1]
pass
fig=xBinnedMap(file_map).plot(show=False,subplot=(1,2,1))#,figure=fig)
fig.show_circles(ra,dec,rad,lw=1)
rad*=60
evtSelect=xEventSelect(evt_file_path, ra=ra, dec=dec, rad=rad, outfile=file_selected_path,
emax=None, emin=None, mc=False, mcsrcid=[], phasemax=None, phasemin=None, phimax=None, phimin=None, tmax=None, tmin=None)
evtSelect.select()
evtBin=xEventBinningMCUBE(file_selected_path, ebins=1, outfile=file_selected_cube_path, evfile=file_selected_path,
emax=10.0,nypix=256, ebinfile=None, phasebins=50,ebinalg='LIN',
xref=None,phibins=75,nxpix=256,tbins=100,proj='TAN',tstart=None,tbinalg='LIN',algorithm='MCUBE',mc=False,binsz=2.5,yref=None,tbinfile=None,emin=1.0,tstop=None)
evtBin.bin_()
binModulation = xBinnedModulationCube(file_selected_cube_path)
binModulation.plot(show=False,xsubplot=1)
for fit in binModulation.fit_results:
print fit
angle = fit.phase
angle_err = fit.phase_error
visibility = fit.visibility
scale=10.
dx1=visibility/scale*numpy.cos(angle+10*angle_err)
dy1=visibility/scale*numpy.sin(angle+10*angle_err)
dx2=visibility/scale*numpy.cos(angle-10*angle_err)
dy2=visibility/scale*numpy.sin(angle-10*angle_err)
def plot(save=False):
logger.info('Plotting stuff...')
pipeline.xpbin(evt_file_path, algorithm='CMAP', outfile=map_file_path)
regions = pyregion.open(reg_file_path)
full_map = xBinnedMap(map_file_path)
fig_all = full_map.plot(show=False)
for i, region in enumerate(regions):
ra, dec, rad = region.coord_list
#fig_all.show_circles(ra, dec, rad, lw=1)
fig = full_map.plot(show=False, subplot=(1, 2, 1))
plt.subplots_adjust(hspace=0.001)
fig.show_circles(ra, dec, rad, lw=1)
mcube_file_path = get_mcube_file_path(i)
mcube = xBinnedModulationCube(mcube_file_path)
mcube.plot(show=False, analyze=False, xsubplot=1)
scale_x = rad/numpy.cos(numpy.deg2rad(dec)) # This is to take into account the effect of the projection.
scale_y = rad
for j,fit in enumerate(mcube.fit_results):
angle = fit.phase
angle_error = fit.phase_error
degree = fit.polarization_degree
#nangles=20
#for t in range(nangles):
# dx = scale_x*numpy.cos(numpy.pi*2.0*t/float(nangles))#angle)
# dy = scale_y*numpy.sin(numpy.pi*2.0*t/float(nangles))#angle)
# fig.show_arrows(ra, dec, dx, dy, color='w', alpha=1, width=1,head_width=0, head_length=0)
# pass
dx = scale_x*numpy.cos(angle)
dy = scale_y*numpy.sin(angle)
dx1 = scale_x*degree*numpy.cos(angle+angle_error)
dy1 = scale_y*degree*numpy.sin(angle+angle_error)
dx2 = scale_x*degree*numpy.cos(angle-angle_error)
dy2 = scale_y*degree*numpy.sin(angle-angle_error)
fig.show_arrows(ra, dec, dx, dy, color=xpColor(j), alpha=1, linestyle='dashed', width=0.2,head_width=0, head_length=0)
fig.show_arrows(ra, dec, -dx, -dy, color=xpColor(j), alpha=1, linestyle='dashed', width=0.2,head_width=0, head_length=0)
fig.show_arrows(ra, dec, dx1, dy1, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig.show_arrows(ra, dec, -dx1, -dy1, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig.show_arrows(ra, dec, dx2, dy2, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig.show_arrows(ra, dec, -dx2, -dy2, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, dx, dy, color=xpColor(j), alpha=1, linestyle='dashed', width=0.2,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, -dx, -dy, color=xpColor(j), alpha=1, linestyle='dashed', width=0.2,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, dx1, dy1, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, -dx1, -dy1, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, dx2, dy2, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, -dx2, -dy2, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
if save:
fig.save(mcube_file_path.replace('.fits', '.png'))
plt.clf()
else:
plt.show()
pass
fig_all.save(os.path.join(XIMPOL_DATA, 'tycho_reg_all.png'))
def run():
outfile = PIPELINE.chandra2ximpol(
INPUT_FILE_PATH, acis=ACIS, seed=SEED, duration=TIME, regfile=REG_FILE_PATH, configfile=CONFIG_FILE_PATH
)
cmap_file = PIPELINE.xpbin(outfile, algorithm=ALGORITHM[1], nxpix=512, nypix=512, binsz=1.25)
# outfile = PIPELINE.xpselect(outfile, ra=RA, dec=DEC, rad=RAD)
# outfile = PIPELINE.xpselect(outfile, ra=RA_CORE, dec=DEC_CORE, rad=RAD_PSF)
outfile = PIPELINE.xpselect(outfile, ra=RA_JET, dec=DEC_JET, rad=RAD_PSF)
mod_file = PIPELINE.xpbin(outfile, algorithm=ALGORITHM[0], emin=EMIN, emax=EMAX, ebins=EBINS)
mod_cube = xBinnedModulationCube(mod_file)
mod_cube.fit()
event = xEventFile(outfile)
energy = event.event_data["ENERGY"]
src_id = event.event_data["MC_SRC_ID"]
jet_tot = 0
core_tot = 0
bkg_tot = 0
mu_tot = 0.0
for i in range(0, len(mod_cube.emax)):
mask_jet = (energy > mod_cube.emin[i]) * (energy < mod_cube.emax[i]) * (src_id == 1)
mask_bkg = (energy > mod_cube.emin[i]) * (energy < mod_cube.emax[i]) * (src_id == 0)
mask_core = (energy > mod_cube.emin[i]) * (energy < mod_cube.emax[i]) * (src_id == 2)
cnts_jet = len(energy[mask_jet])
cnts_bkg = len(energy[mask_bkg])
cnts_core = len(energy[mask_core])
jet_tot += cnts_jet
bkg_tot += cnts_bkg
core_tot += cnts_core
cnts_tot = cnts_jet + cnts_bkg + cnts_core
mu_tot += mod_cube.effective_mu[i] * cnts_tot
mdp = mdp99(mod_cube.effective_mu[i], cnts_jet, cnts_bkg + cnts_core)
logger.info(
"%.2f--%.2f keV: %d jet counts (%.1f%%) in %d s, mu %.3f, MDP %.2f%%"
% (
mod_cube.emin[i],
mod_cube.emax[i],
cnts_jet,
100 * cnts_jet / float(cnts_tot),
TIME,
mod_cube.effective_mu[i],
100 * mdp,
)
)
# print cnts_jet, cnts_bkg, cnts_core
if EBINS > 1:
cnts_tot = jet_tot + bkg_tot + core_tot
mu_tot /= cnts_tot
mdp_tot = mdp99(mu_tot, jet_tot, bkg_tot + core_tot)
logger.info(
"%.2f--%.2f keV: %d jet counts (%.1f%%) in %d s, mu %.3f, MDP %.2f%%"
% (
mod_cube.emin[0],
mod_cube.emax[len(mod_cube.emax) - 1],
jet_tot,
100 * jet_tot / float(cnts_tot),
TIME,
mu_tot,
100 * mdp_tot,
)
)
# print jet_tot, bkg_tot, core_tot
if PLOT is True:
plot(cmap_file)
plt.show()
logger.info("Done.")
def calcMDP(plot=False):
mdp_file = open(MDP_OUTPUT_FILE,'w')
mdp_file.write('#Simulation time %s sec \n'%SIM_DURATION)
mdp_file.write('#Phase Ave delta phase Mean energy delta energy mdp99\n')
nebula_mcube_file = xBinnedModulationCube(NEBULA_MCUBE_FILE_PATH)
nebula_counts = nebula_mcube_file.counts
nebula_mdp = nebula_mcube_file.mdp99
txt = "Pulsar phase\t Emin - Emax\t Pulsar counts\t Nebula counts\t MDP\n"
MDP99_PULSAR = []
phase = []
phase_err = []
for i, (_min, _max) in enumerate(PHASE_BINS):
#zip(PHASE_BINS[:-1],PHASE_BINS[1:])):
pulse_diff = numpy.fabs(_max -_min)
_phase_ave = 0.5*(_min + _max)
phase.append(_phase_ave)
_phase_err = 0.5*(_max - _min)
phase_err.append(_phase_err)
pulsar_phase_mcube_file = xBinnedModulationCube(_mcube_file_path(i))
pulsar_emean = pulsar_phase_mcube_file.emean
for j, _energy_mean in enumerate(pulsar_emean):
pulsar_emin = pulsar_phase_mcube_file.emin[j]
pulsar_emax = pulsar_phase_mcube_file.emax[j]
pulsar_e_err = 0.5*(pulsar_emax-pulsar_emin)
pulsar_phase_counts = pulsar_phase_mcube_file.counts[j]
pulsar_mdp = pulsar_phase_mcube_file.mdp99[j]
#scale the nebula counts for the time used for the pulsar phase
scaled_nebula_counts = pulse_diff*nebula_counts[j]
count_sqrt = numpy.sqrt(pulsar_phase_counts + scaled_nebula_counts)
eff_mu_pulsar = pulsar_phase_mcube_file.effective_mu[j]
mdp = 4.292/eff_mu_pulsar*count_sqrt/pulsar_phase_counts
MDP99_PULSAR.append(100*mdp)
_data = (_phase_ave, _phase_err, _energy_mean, pulsar_e_err, pulsar_e_err, mdp)
_fmt = ('%.4e ' * len(_data)).strip()
_fmt = '%s\n' % _fmt
_line = _fmt % _data
mdp_file.write(_line)
#txt += "%s\t %s - %s\t %s\t %s\t %.3f\n"%(PHASE_BINS[i], pulsar_emin[0], pulsar_emax[0], pulsar_phase_counts[0], scaled_nebula_counts[0], 100*mdp)
MDP99_PULSAR = numpy.array(MDP99_PULSAR)
PHASE = numpy.array(phase)
mdp_file.close()
if plot:
scale_factor = 10
sim_label = 'XIPE %s ks' % (SIM_DURATION*scale_factor/1000.)
lc_label = 'Light curve'
plt.errorbar(PHASE, MDP99_PULSAR*(1/numpy.sqrt(10)),xerr=phase_err, label=sim_label,fmt='o')
pl_normalization_spline.plot(scale=10., show=False,
color='lightgray',label=lc_label)
plt.ylabel('MDP 99\%')
plt.legend()
plt.savefig('crab_complex_mdp_nonimaging_%i.png'%(SIM_DURATION*scale_factor/1000.))
#plt.show()
print txt
def plot(angle=False):
spin05_pol_degree_spline, spin05_pol_angle_spline = buildspline(0.5)
spin05_mcube = xBinnedModulationCube(fetch_mcubepath(0.5))
spin09_pol_degree_spline, spin09_pol_angle_spline = buildspline(0.9)
spin09_mcube = xBinnedModulationCube(fetch_mcubepath(0.9))
spin998_pol_degree_spline, spin998_pol_angle_spline = buildspline(0.998)
spin998_mcube = xBinnedModulationCube(fetch_mcubepath(0.998))
spin05_mcube.fit()
spin09_mcube.fit()
spin998_mcube.fit()
spin05_fit_results = spin05_mcube.fit_results[0]
spin09_fit_results = spin09_mcube.fit_results[0]
spin998_fit_results = spin998_mcube.fit_results[0]
plt.figure('Polarization degree')
spin05_mcube.plot_polarization_degree(show=False, color='blue')
spin05_pol_degree_spline.plot(color='lightblue',label='Spin 0.5', show=False)
spin998_mcube.plot_polarization_degree(show=False, color='red')
spin998_pol_degree_spline.plot(color='lightsalmon',label='Spin 0.998', show=False)
plt.figtext(0.2, 0.85,'XIPE %s ks'%((SIM_DURATION*NUM_RUNS)/1000.),size=18)
plt.ylim([0.00,0.045])
plt.xlim([1,10])
plt.legend()
plt.show()
if angle:
plt.figure('Polarization angle')
spin05_mcube.plot_polarization_angle(show=False, degree=True, color='blue')
#Converting to degrees
spin05_y = numpy.degrees(spin05_pol_angle_spline.y)
energy = spin05_pol_angle_spline.x
plt.plot(energy, spin05_y, color='lightblue',label='Spin 0.5')
spin09_mcube.plot_polarization_angle(show=False, degree=True, color='gray')
#Converting to degrees
spin09_y = numpy.degrees(spin09_pol_angle_spline.y)
energy = spin09_pol_angle_spline.x
plt.plot(energy, spin09_y, color='lightgray',label='Spin 0.9')
spin998_mcube.plot_polarization_angle(show=False, degree=True, color='red')
spin998_y = numpy.degrees(spin998_pol_angle_spline.y)
energy = spin998_pol_angle_spline.x
plt.plot(energy, spin998_y, color='lightsalmon',label='Spin 0.998')
#spin998_pol_angle_spline.plot(color='lightsalmon',label='Spin 0.998', show=False)
plt.figtext(0.2, 0.85,'XIPE %s ks'%((SIM_DURATION*NUM_RUNS)/1000.),size=18)
plt.xlim([1,10])
plt.ylim([40,200])
plt.legend()
plt.show()
from ximpol.evt.binning import xBinnedModulationCube
from ximpol.utils.matplotlib_ import pyplot as plt
from ximpol.config.lamp_post_accreting_bh_XTE import pol_degree, pol_angle
CFG_FILE = os.path.join(XIMPOL_CONFIG, 'lamp_post_accreting_bh_XTE.py')
DURATION = 100000.
E_BINNING = [1., 2., 3., 4., 5., 7., 10.]
SEED = 0
pipeline = xPipeline(clobber=False)
evt_file_path = pipeline.xpobssim(configfile=CFG_FILE, duration=DURATION, seed=SEED)
pipeline.xpbin(evt_file_path, algorithm='CMAP')
mcube_file_path = pipeline.xpbin(evt_file_path, algorithm='MCUBE',
ebinalg='LIST', ebinning=E_BINNING)
mcube = xBinnedModulationCube(mcube_file_path)
mcube.fit()
fig = plt.figure('Polarization degree')
mcube.plot_polarization_degree(show=False, label='Data')
pol_degree.plot(show=False, label='Model', linestyle='dashed')
plt.legend(bbox_to_anchor=(0.30, 0.95))
plt.axis([1, 10, None, None])
fig = plt.figure('Polarization angle')
mcube.plot_polarization_angle(show=False, label='Data')
pol_angle.plot(show=False, label='Model', linestyle='dashed')
plt.legend(bbox_to_anchor=(0.95, 0.95))
plt.axis([1, 10, None, None])
plt.show()
def analyze():
"""Analyze the data.
"""
logger.info('Opening output file %s...' % ANALYSIS_FILE_PATH)
analysis_file = open(ANALYSIS_FILE_PATH, 'w')
_nevents=[]
for i, (_min, _max) in enumerate(zip(PHASE_BINNING[:-1],
PHASE_BINNING[1:])):
_nevents.append(fits.open(_sel_file_path(i))['EVENTS'].header['NAXIS2'])
logger.info("PHASE BIN %d [%.1f-%.1f] - EVENTS = %d" %(i,_min,_max,_nevents[i]))
pass
out_phase=numpy.min(_nevents)
for i, (_min, _max) in enumerate(zip(PHASE_BINNING[:-1],
PHASE_BINNING[1:])):
_mcube = xBinnedModulationCube(_mcube_file_path(i))
_mcube.fit()
_fit_results = _mcube.fit_results[0]
_phase = 0.5*(_min + _max)
_phase_err = 0.5*(_max - _min)
_pol_deg = _fit_results.polarization_degree
_pol_deg_err = _fit_results.polarization_degree_error
_pol_angle = _fit_results.phase
_pol_angle_err = _fit_results.phase_error
if (_nevents[i]-out_phase)>0:
_factor=(_nevents[i])/(_nevents[i]-out_phase)
print '------->',_nevents[i],out_phase,_nevents[i]-out_phase,_factor
_pol_deg*=_factor
_pol_deg_err*=_factor
else:
_pol_deg=1e-6
_pol_deg_err=1e-6
pass
if _pol_deg>1.0: _pol_deg=1.0
#_total_px=_pol_deg*numpy.cos(_pol_angle)
#_total_py=_pol_deg*numpy.sin(_pol_angle)
#_nebula_px=0.157*numpy.cos(numpy.radians(161.1))
#_nebula_py=0.157*numpy.sin(numpy.radians(161.1))
#_pulsar_px=_total_px-_nebula_px
#_pulsar_py=_total_py-_nebula_py
#_pol_angle=numpy.arctan2(_pulsar_py,_pulsar_px)
#_pol_deg=numpy.sqrt(_pulsar_px*_pulsar_px+_pulsar_py*_pulsar_py)
if False:
_spec_fitter = PIPELINE.xpxspec(_pha1_file_path(i), plot=False)
(_index, _index_err), (_norm, _norm_err) = _spec_fitter.fit_parameters()
# The division by the phase interval is a workaround and we should
# keep track of that in xpselect.
_norm /= (_max - _min)
_norm_err /= (_max - _min)
else:
_norm=0.0
_norm_err=0.0
_index=0.0
_index_err=0.0
pass
_data = (_phase, _phase_err, _pol_deg, _pol_deg_err, _pol_angle,
_pol_angle_err, _index, _index_err, _norm, _norm_err)
_fmt = ('%.4e ' * len(_data)).strip()
_fmt = '%s\n' % _fmt
_line = _fmt % _data
analysis_file.write(_line)
### Plot the cmap with the arrow...
full_map = xBinnedMap(_cmap_file_path(i))
full_map.image.vmin=0
full_map.image.vmax=10000
fig_map = full_map.plot(show=False)
fig_map.show_circles(RA, DEC, RAD_ANA/60.0, lw=1)
_plot_arrows(ra=RA,dec=DEC,rad=RAD_ANA/60.,
angle=_phase,angle_error=_phase_err,
degree=_pol_deg,fig=fig_map,color='b')
fig_map_file=_cmap_file_path(i).replace('.fits','.png')
print 'saving map in...',fig_map_file
fig_map.save(fig_map_file)
###
analysis_file.close()
E_BINNING = [2.,3.,5.,8.]
SIM_NUM = 10
pol_degree_array = numpy.empty([SIM_NUM, len(E_BINNING)])
pol_degree_error_array = numpy.empty([SIM_NUM, len(E_BINNING)])
pol_angle_array = numpy.empty([SIM_NUM, len(E_BINNING)])
pol_angle_error_array = numpy.empty([SIM_NUM, len(E_BINNING)])
pipeline = xPipeline(clobber=True)
for j in range(0, SIM_NUM):
SEED = j
evt_file_path = pipeline.xpobssim(configfile=CFG_FILE, duration=TIME, seed=SEED)
#pipeline.xpbin(evt_file_path, algorithm='CMAP')
mod_cube_file_path = pipeline.xpbin(evt_file_path, algorithm='MCUBE',
ebinalg='LIST', ebinning=E_BINNING)
mod_cube = xBinnedModulationCube(mod_cube_file_path)
mod_cube.fit()
pol_degree_array[j,:] = numpy.array([r.polarization_degree for
r in mod_cube.fit_results])
pol_degree_error_array[j,:] = numpy.array([r.polarization_degree_error for
r in mod_cube.fit_results])
pol_angle_array[j,:] = numpy.array([numpy.degrees(r.phase) for
r in mod_cube.fit_results])
pol_angle_error_array[j,:] = numpy.array([numpy.degrees(r.phase_error) for
r in mod_cube.fit_results])
for i in range(0, len(mod_cube.emax)):
cnts = mod_cube.counts[i]
logger.info('%.2f--%.2f keV: %d counts in %d s, mu %.3f, MDP %.2f%%' %\
(mod_cube.emin[i], mod_cube.emax[i], mod_cube.counts[i], TIME,
mod_cube.effective_mu[i], 100*mod_cube.mdp99[i]))
def plot(save=False):
logger.info('Plotting stuff...')
pipeline.xpbin(evt_file_path, algorithm='CMAP', outfile=map_file_path)
regions = pyregion.open(reg_file_path)
full_map = xBinnedMap(map_file_path)
fig_all = full_map.plot(show=False)
for i, region in enumerate(regions):
ra, dec, rad = region.coord_list
#fig_all.show_circles(ra, dec, rad, lw=1)
fig = full_map.plot(show=False, subplot=(1, 2, 1))
plt.subplots_adjust(hspace=0.001)
fig.show_circles(ra, dec, rad, lw=1)
mcube_file_path = get_mcube_file_path(i)
mcube = xBinnedModulationCube(mcube_file_path)
mcube.plot(show=False, analyze=False, xsubplot=1)
scale_x = rad/numpy.cos(numpy.deg2rad(dec)) # This is to take into account the effect of the projection.
scale_y = rad
for j,fit in enumerate(mcube.fit_results):
angle = fit.phase
angle_error = fit.phase_error
degree = fit.polarization_degree
#nangles=20
#for t in range(nangles):
# dx = scale_x*numpy.cos(numpy.pi*2.0*t/float(nangles))#angle)
# dy = scale_y*numpy.sin(numpy.pi*2.0*t/float(nangles))#angle)
# fig.show_arrows(ra, dec, dx, dy, color='w', alpha=1, width=1,head_width=0, head_length=0)
# pass
dx = scale_x*numpy.cos(angle)
dy = scale_y*numpy.sin(angle)
dx1 = scale_x*degree*numpy.cos(angle+angle_error)
dy1 = scale_y*degree*numpy.sin(angle+angle_error)
dx2 = scale_x*degree*numpy.cos(angle-angle_error)
dy2 = scale_y*degree*numpy.sin(angle-angle_error)
fig.show_arrows(ra, dec, dx, dy, color=xpColor(j), alpha=1, linestyle='dashed', width=0.2,head_width=0, head_length=0)
fig.show_arrows(ra, dec, -dx, -dy, color=xpColor(j), alpha=1, linestyle='dashed', width=0.2,head_width=0, head_length=0)
fig.show_arrows(ra, dec, dx1, dy1, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig.show_arrows(ra, dec, -dx1, -dy1, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig.show_arrows(ra, dec, dx2, dy2, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig.show_arrows(ra, dec, -dx2, -dy2, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, dx, dy, color=xpColor(j), alpha=1, linestyle='dashed', width=0.2,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, -dx, -dy, color=xpColor(j), alpha=1, linestyle='dashed', width=0.2,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, dx1, dy1, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, -dx1, -dy1, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, dx2, dy2, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
fig_all.show_arrows(ra, dec, -dx2, -dy2, color=xpColor(j), alpha=1, width=1,head_width=0, head_length=0)
if save:
fig.save(mcube_file_path.replace('.fits', '.png'))
plt.clf()
else:
plt.show()
pass
fig_all.save(os.path.join(XIMPOL_DATA, 'tycho_reg_all.png'))
phibins=75,
nxpix=256,
tbins=100,
proj='TAN',
tstart=None,
tbinalg='LIN',
algorithm='MCUBE',
mc=False,
binsz=2.5,
yref=None,
tbinfile=None,
emin=1.0,
tstop=None)
evtBin.bin_()
binModulation = xBinnedModulationCube(file_selected_cube_path)
binModulation.plot(show=False, xsubplot=1)
for fit in binModulation.fit_results:
print fit
angle = fit.phase
angle_err = fit.phase_error
visibility = fit.visibility
scale = 10.
dx1 = visibility / scale * numpy.cos(angle + 10 * angle_err)
dy1 = visibility / scale * numpy.sin(angle + 10 * angle_err)
dx2 = visibility / scale * numpy.cos(angle - 10 * angle_err)
dy2 = visibility / scale * numpy.sin(angle - 10 * angle_err)