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bkg_rate_estimation.py
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bkg_rate_estimation.py
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import numpy as np
from astropy.io import fits
from scipy import stats
import os
from scipy import optimize
from counting_and_quad_funcs import get_quad_cnts_tbins, get_cnts_per_tbins,\
get_quad_cnts_tbins_fast
from dbread_funcs import get_rate_fits_tab
def lin_func(x, m, b):
return m*x + b
def cubic_func(x, a0, a1, a2, a3):
return a0 + a1*x + a2*x**2 + a3*x**3
def cov2err(cov_mat, t_ax):
sigs2 = np.diag(cov_mat)
cov = cov_mat[1,0]
err = np.sqrt((t_ax**2)*sigs2[0] + sigs2[1] + 2.*t_ax*cov)
return err
def cubic_err(cov_mat, t_ax):
sigs2 = np.sqrt(np.diag(cov_mat))
err = np.sqrt(sigs2[0]**2 + (sigs2[1]*t_ax)**2 + (sigs2[2]*(t_ax**2))**2 +\
(sigs2[3]*(t_ax**3))**2)
# ignoring correlated errors
return err
def get_cub_rate_quad_objs(quad_dicts, ev_data, trig_time, ebins0, ebins1,\
bin_size=.512, tstep=.512, quad_cnts_mat=None,\
post=True, trng=60, poly_trng=15):
t_bins0 = np.arange(-trng*1.024, trng*1.024, tstep) + trig_time
t_bins1 = t_bins0 + bin_size
if quad_cnts_mat is None:
quad_cnts_mat = get_quad_cnts_tbins(t_bins0, t_bins1, ebins0, ebins1, ev_data)
rate_quad_dict = {}
for direc, quad_dict in quad_dicts.iteritems():
cnts_per_tbin = np.sum( [quad_cnts_mat[:,:,q] for\
q in quad_dict['quads']], axis=0)
rate_quad_dict[direc] = Cubic_Rates(cnts_per_tbin, t_bins0, t_bins1,\
trig_time, bkg_post=post,\
poly_trng=poly_trng)
rate_quad_dict[direc].do_fits()
return rate_quad_dict
def get_lin_rate_quad_objs(quad_dicts, ev_data, trig_time, ebins0, ebins1,\
bin_size=.512, tstep=.512, quad_cnts_mat=None,\
post=True, trng=45, poly_trng=15):
t_bins0 = np.arange(-trng*1.024, trng*1.024, tstep) + trig_time
t_bins1 = t_bins0 + bin_size
if quad_cnts_mat is None:
quad_cnts_mat = get_quad_cnts_tbins(t_bins0, t_bins1, ebins0, ebins1, ev_data)
lin_rate_quad_dict = {}
for direc, quad_dict in quad_dicts.iteritems():
cnts_per_tbin = np.sum( [quad_cnts_mat[:,:,q] for\
q in quad_dict['quads']], axis=0)
lin_rate_quad_dict[direc] = Linear_Rates(cnts_per_tbin, t_bins0, t_bins1,\
trig_time, bkg_post=post,\
poly_trng=poly_trng)
lin_rate_quad_dict[direc].do_fits()
return lin_rate_quad_dict
def get_avg_rate_quad_objs(quad_dicts, ev_data, trig_time, ebins0, ebins1,\
bin_size=.512, tstep=.512, quad_cnts_mat=None,\
post=True, trng=45, poly_trng=15):
t_bins0 = np.arange(-trng*1.024, trng*1.024, tstep) + trig_time
t_bins1 = t_bins0 + bin_size
if quad_cnts_mat is None:
quad_cnts_mat = get_quad_cnts_tbins(t_bins0, t_bins1, ebins0, ebins1, ev_data)
avg_rate_quad_dict = {}
for direc, quad_dict in quad_dicts.iteritems():
cnts_per_tbin = np.sum( [quad_cnts_mat[:,:,q] for\
q in quad_dict['quads']], axis=0)
avg_rate_quad_dict[direc] = Average_Rates(cnts_per_tbin, t_bins0, t_bins1,\
trig_time, bkg_post=post,\
poly_trng=poly_trng)
avg_rate_quad_dict[direc].do_fits()
return avg_rate_quad_dict
def get_avg_lin_cub_rate_quad_obs(quad_dicts, ev_data, trig_time,\
ebins0, ebins1, bin_size=.512,\
tstep=.512, trng=60, post=True,\
poly_trng=15):
t_bins0 = np.arange(-trng*1.024, trng*1.024, tstep) + trig_time
t_bins1 = t_bins0 + bin_size
quad_cnts_mat = get_quad_cnts_tbins_fast(t_bins0, t_bins1, ebins0, ebins1, ev_data)
avg_rate_quad_dict = get_avg_rate_quad_objs(quad_dicts, ev_data, trig_time,\
ebins0, ebins1, bin_size=bin_size,\
tstep=tstep, quad_cnts_mat=quad_cnts_mat,
poly_trng=poly_trng, trng=trng)
lin_rate_quad_dict = get_lin_rate_quad_objs(quad_dicts, ev_data, trig_time,\
ebins0, ebins1, bin_size=bin_size,\
tstep=tstep, quad_cnts_mat=quad_cnts_mat,\
poly_trng=poly_trng, trng=trng)
cub_rate_quad_dict = get_cub_rate_quad_objs(quad_dicts, ev_data, trig_time,\
ebins0, ebins1, bin_size=bin_size,\
tstep=tstep, quad_cnts_mat=quad_cnts_mat,\
poly_trng=poly_trng, trng=trng)
return avg_rate_quad_dict, lin_rate_quad_dict, cub_rate_quad_dict
def get_lin_rate_obj(ev_data, trig_time, ebins0, ebins1,\
bin_size=.512, tstep=.512,\
trng=45, sig_clip=None):
t_bins0 = np.arange(-trng*1.024, trng*1.024, tstep) + trig_time
t_bins1 = t_bins0 + bin_size
cnts_per_tbin = get_cnts_per_tbins(t_bins0, t_bins1,\
ebins0, ebins1,\
ev_data, None)
lin_rate_obj = Linear_Rates(cnts_per_tbin, t_bins0,\
t_bins1, trig_time, sig_clip=sig_clip)
lin_rate_obj.do_fits()
return lin_rate_obj
def get_chi2(cnts, predics):
chi2 = np.sum( np.square(cnts - predics) / cnts )
return chi2
class Cubic_Rates(object):
def __init__(self, cnts_per_tbin, t_bins0, t_bins1,\
trig_time, t_poly_step=1.024, bkg_post=True,\
bkg_rng=45, poly_trng=15):
self.cnts_per_tbin = cnts_per_tbin
self.t_bins0 = t_bins0
self.t_bins1 = t_bins1
self.tstep = t_bins0[1] - t_bins0[0]
self.bin_size = t_bins1[0] - t_bins0[0]
self.sig_window = (-5.*1.024, 10.*1.024)
self.sig_exp = self.sig_window[1] - self.sig_window[0]
self.post = bkg_post
self.deg = 3
if bkg_post:
self.bkg_window = (-bkg_rng*1.024, bkg_rng*1.024)
self.bkg_exp = self.bkg_window[1] - self.bkg_window[0] - self.sig_exp
else:
self.bkg_window = (-bkg_rng*1.024, self.sig_window[0])
self.bkg_exp = self.bkg_window[1] - self.bkg_window[0]
self.trig_time = trig_time
self.nebins = cnts_per_tbin.shape[1]
self.t_poly_step = t_poly_step
self.t0 = trig_time - poly_trng*self.t_poly_step
self.t1 = trig_time + poly_trng*self.t_poly_step
self.t_poly_ax = np.arange(self.t0, self.t1, self.t_poly_step)
self.n_lin_pnts = len(self.t_poly_ax)
self.A0s = np.zeros((self.n_lin_pnts, self.nebins))
self.A1s = np.zeros((self.n_lin_pnts, self.nebins))
self.A2s = np.zeros((self.n_lin_pnts, self.nebins))
self.A3s = np.zeros((self.n_lin_pnts, self.nebins))
self.errs = np.zeros((self.n_lin_pnts, self.nebins))
self.chi2s = np.zeros_like(self.errs)
self.dof = np.zeros((self.n_lin_pnts, self.nebins), dtype=np.int)
self.npars = self.deg + 1
# self.dof = int(self.bkg_exp/self.bin_size) - self.npars
def do_fits(self):
for i in xrange(self.n_lin_pnts):
t_mid = self.t_poly_ax[i]
t_0 = t_mid + self.bkg_window[0]
t_1 = t_mid + self.bkg_window[1]
t_sig0 = t_mid + self.sig_window[0]
t_sig1 = t_mid + self.sig_window[1]
ind0 = np.argmin(np.abs(self.t_bins0 - t_0))
ind1 = np.argmin(np.abs(self.t_bins1 - t_1))
ind0_sig = np.argmin(np.abs(self.t_bins1 - t_sig0))
ind1_sig = np.argmin(np.abs(self.t_bins0 - t_sig1))
_t_ax0 = ((self.t_bins0 + self.t_bins1)/2.)[ind0:ind0_sig]
_t_ax1 = ((self.t_bins0 + self.t_bins1)/2.)[ind1_sig:ind1]
_t_ax = np.append(_t_ax0, _t_ax1) - self.trig_time
_cnts = np.append(self.cnts_per_tbin[ind0:ind0_sig],\
self.cnts_per_tbin[ind1_sig:ind1], axis=0)
for j in xrange(self.nebins):
res_ = optimize.curve_fit(cubic_func, _t_ax,\
_cnts[:,j],\
sigma=np.sqrt(_cnts[:,j]),\
absolute_sigma=False)
tot_cnts = np.sum(_cnts[:,j])
cnt_err = np.sqrt(tot_cnts)/(len(_cnts[:,j]))
fit_err = cubic_err(np.array(res_[1]), t_mid-self.trig_time)
err = np.hypot(cnt_err, fit_err)
self.A0s[i,j] = res_[0][0]
self.A1s[i,j] = res_[0][1]
self.A2s[i,j] = res_[0][2]
self.A3s[i,j] = res_[0][3]
self.errs[i,j] = err
preds = cubic_func(_t_ax, self.A0s[i,j], self.A1s[i,j],\
self.A2s[i,j], self.A3s[i,j])
self.chi2s[i,j] = get_chi2(_cnts[:,j],preds)
self.dof[i,j] = len(_cnts[:,j]) - self.npars
def get_rate(self, t, chi2=False):
ind = np.argmin(np.abs(t - self.t_poly_ax))
rate = cubic_func(t - self.trig_time, self.A0s[ind],\
self.A1s[ind], self.A2s[ind], self.A3s[ind])/self.bin_size
error = self.errs[ind]/self.bin_size
if chi2:
chi2 = self.chi2s[ind]
dof = self.dof[ind]
return rate, error, chi2/dof
return rate, error
class Linear_Rates(object):
def __init__(self, cnts_per_tbin, t_bins0, t_bins1,\
trig_time, t_poly_step=1.024,\
bkg_post=True, poly_trng=15,\
sig_clip=None):
self.cnts_per_tbin = cnts_per_tbin
self.t_bins0 = t_bins0
self.t_bins1 = t_bins1
self.tstep = t_bins0[1] - t_bins0[0]
self.bin_size = t_bins1[0] - t_bins0[0]
self.sig_window = (-5.*1.024, 10.*1.024)
self.sig_exp = self.sig_window[1] - self.sig_window[0]
self.post = bkg_post
self.deg = 1
if bkg_post:
self.bkg_window = (-30.*1.024, 30.*1.024)
self.bkg_exp = self.bkg_window[1] - self.bkg_window[0] - self.sig_exp
else:
self.bkg_window = (-30.*1.024, self.sig_window[0])
self.bkg_exp = self.bkg_window[1] - self.bkg_window[0]
self.trig_time = trig_time
self.nebins = cnts_per_tbin.shape[1]
self.t_poly_step = t_poly_step
self.t0 = trig_time - poly_trng*self.t_poly_step
self.t1 = trig_time + poly_trng*self.t_poly_step
self.t_poly_ax = np.arange(self.t0, self.t1, self.t_poly_step)
self.n_lin_pnts = len(self.t_poly_ax)
self.slopes = np.zeros((self.n_lin_pnts, self.nebins))
self.ints = np.zeros_like(self.slopes)
self.errs = np.zeros_like(self.slopes)
self.chi2s = np.zeros_like(self.errs)
self.dof = np.zeros((self.n_lin_pnts, self.nebins), dtype=np.int)
self.sig_clip = sig_clip
self.npars = self.deg + 1
# self.dof = int(self.bkg_exp/self.bin_size) - self.npars
def do_fits(self):
for i in xrange(self.n_lin_pnts):
t_mid = self.t_poly_ax[i]
t_0 = t_mid + self.bkg_window[0]
t_1 = t_mid + self.bkg_window[1]
t_sig0 = t_mid + self.sig_window[0]
t_sig1 = t_mid + self.sig_window[1]
ind0 = np.argmin(np.abs(self.t_bins0 - t_0))
ind1 = np.argmin(np.abs(self.t_bins1 - t_1))
ind0_sig = np.argmin(np.abs(self.t_bins1 - t_sig0))
ind1_sig = np.argmin(np.abs(self.t_bins0 - t_sig1))
_t_ax0 = ((self.t_bins0 + self.t_bins1)/2.)[ind0:ind0_sig]
_t_ax1 = ((self.t_bins0 + self.t_bins1)/2.)[ind1_sig:ind1]
_t_ax = np.append(_t_ax0, _t_ax1) - self.trig_time
_cnts = np.append(self.cnts_per_tbin[ind0:ind0_sig],\
self.cnts_per_tbin[ind1_sig:ind1], axis=0)
for j in xrange(self.nebins):
try:
bl = np.ones(len(_cnts[:,j]), dtype=np.bool)
if self.sig_clip is not None:
avg = np.mean(_cnts[:,j])
std = np.std(_cnts[:,j])
std_res = np.abs(_cnts[:,j] - avg)/std
while np.any(std_res[bl] > self.sig_clip):
bl[np.argmax(std_res)] = False
avg = np.mean(_cnts[:,j][bl])
std = np.std(_cnts[:,j][bl])
std_res = np.zeros_like(_cnts[:,j])
std_res[bl] = np.abs(_cnts[:,j][bl] - avg)/std
if (np.sum(bl)/float(len(bl)) < .7) or (np.sum(bl) < 10):
break
res_lin = optimize.curve_fit(lin_func, _t_ax[bl],\
_cnts[:,j][bl],\
sigma=np.sqrt(_cnts[:,j][bl]),\
absolute_sigma=False)
except Exception as E:
print E
print "_cnts[:,j].shape: ", _cnts[:,j].shape
print "_t_ax.shape: ", _t_ax.shape
raise E
tot_cnts = np.sum(_cnts[:,j][bl])
cnt_err = np.sqrt(tot_cnts)/(len(_cnts[:,j][bl]))
fit_err = cov2err(np.array(res_lin[1]), t_mid-self.trig_time)
err = np.hypot(cnt_err, fit_err)
self.slopes[i,j] = res_lin[0][0]
self.ints[i,j] = res_lin[0][1]
self.errs[i,j] = err
preds = lin_func(_t_ax[bl], self.slopes[i,j], self.ints[i,j])
self.chi2s[i,j] = get_chi2(_cnts[:,j][bl],preds)
self.dof[i,j] = len(_cnts[:,j][bl]) - self.npars
def get_rate(self, t, chi2=False):
ind = np.argmin(np.abs(t - self.t_poly_ax))
rate = lin_func(t - self.trig_time, self.slopes[ind], self.ints[ind])/self.bin_size
error = self.errs[ind]/self.bin_size
if chi2:
chi2 = self.chi2s[ind]
dof = self.dof[ind]
return rate, error, chi2/dof
return rate, error
class Average_Rates(object):
def __init__(self, cnts_per_tbin, t_bins0, t_bins1,\
trig_time, t_poly_step=1.024,\
bkg_post=True, poly_trng=15):
self.cnts_per_tbin = cnts_per_tbin
self.t_bins0 = t_bins0
self.t_bins1 = t_bins1
self.tstep = t_bins0[1] - t_bins0[0]
self.bin_size = t_bins1[0] - t_bins0[0]
self.sig_window = (-5.*1.024, 10.*1.024)
self.sig_exp = self.sig_window[1] - self.sig_window[0]
self.post = bkg_post
self.deg = 0
if bkg_post:
self.bkg_window = (-30.*1.024, 30.*1.024)
self.bkg_exp = self.bkg_window[1] - self.bkg_window[0] - self.sig_exp
else:
self.bkg_window = (-30.*1.024, self.sig_window[0])
self.bkg_exp = self.bkg_window[1] - self.bkg_window[0]
self.trig_time = trig_time
self.nebins = cnts_per_tbin.shape[1]
self.t_poly_step = t_poly_step
self.t0 = trig_time - poly_trng*self.t_poly_step
self.t1 = trig_time + poly_trng*self.t_poly_step
self.t_poly_ax = np.arange(self.t0, self.t1, self.t_poly_step)
self.n_lin_pnts = len(self.t_poly_ax)
self.means = np.zeros((self.n_lin_pnts, self.nebins))
self.errs = np.zeros_like(self.means)
self.chi2s = np.zeros_like(self.errs)
self.dof = np.zeros((self.n_lin_pnts, self.nebins), dtype=np.int)
self.npars = self.deg + 1
# self.dof = int(self.bkg_exp/self.bin_size) - self.npars
def do_fits(self):
for i in xrange(self.n_lin_pnts):
t_mid = self.t_poly_ax[i]
t_0 = t_mid + self.bkg_window[0]
t_1 = t_mid + self.bkg_window[1]
t_sig0 = t_mid + self.sig_window[0]
t_sig1 = t_mid + self.sig_window[1]
ind0 = np.argmin(np.abs(self.t_bins0 - t_0))
ind1 = np.argmin(np.abs(self.t_bins1 - t_1))
ind0_sig = np.argmin(np.abs(self.t_bins1 - t_sig0))
ind1_sig = np.argmin(np.abs(self.t_bins0 - t_sig1))
_t_ax0 = ((self.t_bins0 + self.t_bins1)/2.)[ind0:ind0_sig]
_t_ax1 = ((self.t_bins0 + self.t_bins1)/2.)[ind1_sig:ind1]
_t_ax = np.append(_t_ax0, _t_ax1) - self.trig_time
_cnts = np.append(self.cnts_per_tbin[ind0:ind0_sig],\
self.cnts_per_tbin[ind1_sig:ind1], axis=0)
for j in xrange(self.nebins):
mean = np.mean(_cnts[:,j])
tot_cnts = np.sum(_cnts[:,j])
cnt_err = np.sqrt(tot_cnts)/(len(_cnts[:,j]))
fit_err = np.std(_cnts[:,j])
err = np.hypot(cnt_err, fit_err)
self.means[i,j] = mean
self.errs[i,j] = err
self.chi2s[i,j] = get_chi2(_cnts[:,j], mean)
self.dof[i,j] = len(_cnts[:,j]) - self.npars
def get_rate(self, t, chi2=False):
ind = np.argmin(np.abs(t - self.t_poly_ax))
rate = self.means[ind]/self.bin_size
error = self.errs[ind]/self.bin_size
if chi2:
chi2 = self.chi2s[ind]
dof = self.dof[ind]
return rate, error, chi2/dof
return rate, error
def get_linear_bkg_rates(quad_cnts_mat, t_bins0, t_bins1, trig_time, quad_dicts):
tstep = .512
bin_size = .512
tstep = t_bins0[1] - t_bins0[0]
bin_size = t_bins1[0] - t_bins0[0]
#t_bins0 = np.arange(-15.008, 15.008, tstep) + trig_time
# t_bins0 = np.arange(-150.*1.024, 300.*1.024, tstep) + trig_time
# t_bins1 = t_bins0 + bin_size
ntbins = len(t_bins0)
print ntbins
nebins = quad_cnts_mat.shape[1]
sig_window = (-5.*1.024, 10.24)
bkg_window = (-30.*1.024, 30.*1.024)
# fit for signal windows at 1.024 intervals
t_poly_step = 1.024
t0 = trig_time - 15.*t_poly_step
t1 = trig_time + 15.*t_poly_step
t_poly_ax = np.arange(t0, t1, t_poly_step)
nptbins = len(t_poly_ax)
print nptbins
lin_params = np.zeros((nptbins, nebins, 3))
#lin_cov = np.zeros((nptbins, nebins, 2, 2))
quads_lin_resdict = {}
#quads_lin_covdict = {}
for k in quad_dicts.keys():
quads_lin_resdict[k] = np.copy(lin_params)
#quads_lin_covdict[k] = np.copy(lin_cov)
for i in xrange(len(t_poly_ax)):
t_mid = t_poly_ax[i]
t_0 = t_mid + bkg_window[0]
t_1 = t_mid + bkg_window[1]
t_sig0 = t_mid + sig_window[0]
t_sig1 = t_mid + sig_window[1]
ind0 = np.argmin(np.abs(t_bins0 - t_0))
ind1 = np.argmin(np.abs(t_bins1 - t_1))
ind0_sig = np.argmin(np.abs(t_bins1 - t_sig0))
ind1_sig = np.argmin(np.abs(t_bins0 - t_sig1))
_t_ax0 = ((t_bins0 + t_bins1)/2.)[ind0:ind0_sig]
_t_ax1 = ((t_bins0 + t_bins1)/2.)[ind1_sig:ind1]
_t_ax = np.append(_t_ax0, _t_ax1) - trig_time
quad_cnts = np.append(quad_cnts_mat[ind0:ind0_sig],\
quad_cnts_mat[ind1_sig:ind1], axis=0)
for direc, quad_dict in quad_dicts.iteritems():
cnts_per_tbin = np.sum( [quad_cnts[:,:,q] for\
q in quad_dict['quads']], axis=0 )
for ii in xrange(nebins):
res_lin = optimize.curve_fit(lin_func, _t_ax,\
cnts_per_tbin[:,ii],\
sigma=np.sqrt(cnts_per_tbin[:,ii]),\
)
quads_lin_covdict[direc][i,ii] =\
np.array(res_lin[1])
tot_cnts = np.sum(cnts_per_tbin[:,ii])
cnt_err = np.sqrt(tot_cnts)/(len(cnts_per_tbin[:,ii]))
fit_err = cov2err(np.array(res_lin[1]), t_mid-trig_time)
err = np.hypot(cnt_err, fit_err)
quads_lin_resdict[direc][i,ii] = np.array(np.append(res_lin[0], [err]))
return quads_lin_resdict, t_poly_ax
class rate_obj_from_sqltab(object):
def __init__(self, rate_fits_df, quadID, deg):
self.deg = deg
self.quadID = quadID
bl = (rate_fits_df.quadID == quadID)&(rate_fits_df.deg==deg)
self.df = rate_fits_df[bl]
self.groups = self.df.groupby('ebin')
self.nebins = len(self.groups)
self.bkg_exp = 1.0
self.t0 = np.min(self.df['time'])
self.t1 = np.max(self.df['time'])
def get_rate(self, t, chi2=False):
rates = np.zeros(self.nebins)
errors = np.zeros(self.nebins)
chi2s = np.zeros(self.nebins)
for i, ebin_grp in enumerate(self.groups):
ind = np.argmin(np.abs(t - ebin_grp[1]['time']))
rates[i] = ebin_grp[1]['rate'][ind]
errors[i] = ebin_grp[1]['error'][ind]
chi2s[i] = ebin_grp[1]['chi2'][ind]
if chi2:
return rates, errors, chi2s
return rates, errors
def get_quad_rate_objs_from_db(conn, quad_dicts):
rate_fits_tab = get_rate_fits_tab(conn)
lin_rate_quad_obj = {}
avg_rate_quad_obj = {}
for direc, quad_dict in quad_dicts.iteritems():
avg_rate_quad_obj[direc] = rate_obj_from_sqltab(rate_fits_tab, quad_dict['id'], 0)
lin_rate_quad_obj[direc] = rate_obj_from_sqltab(rate_fits_tab, quad_dict['id'], 1)
return avg_rate_quad_obj, lin_rate_quad_obj