def test_fitness_function_results():
"""Test results for several fitness functions"""
rng = np.random.RandomState(42)
# Event Data
t = rng.randn(100)
edges = bayesian_blocks(t, fitness='events')
assert_allclose(edges, [-2.6197451, -0.71094865, 0.36866702, 1.85227818])
# Event data with repeats
t[80:] = t[:20]
edges = bayesian_blocks(t, fitness='events', p0=0.01)
assert_allclose(edges, [-2.6197451, -0.47432431, -0.46202823, 1.85227818])
# Regular event data
dt = 0.01
t = dt * np.arange(1000)
x = np.zeros(len(t))
N = len(t) // 10
x[rng.randint(0, len(t), N)] = 1
x[rng.randint(0, len(t) // 2, N)] = 1
edges = bayesian_blocks(t, x, fitness='regular_events', dt=dt)
assert_allclose(edges, [0, 5.105, 9.99])
# Measured point data with errors
t = 100 * rng.rand(20)
x = np.exp(-0.5 * (t - 50) ** 2)
sigma = 0.1
x_obs = x + sigma * rng.randn(len(x))
edges = bayesian_blocks(t, x_obs, sigma, fitness='measures')
assert_allclose(edges, [4.360377, 48.456895, 52.597917, 99.455051])
def bin_edges_f(bin_method, mags_cols_cl):
'''
Obtain bin edges for each photometric dimension using the cluster region
diagram. The 'bin_edges' list will contain all magnitudes first, and then
all colors (in the same order in which they are read).
'''
bin_edges = []
if bin_method in (
'auto', 'fd', 'doane', 'scott', 'rice', 'sturges', 'sqrt'):
for mag in mags_cols_cl[0]:
bin_edges.append(np.histogram(mag, bins=bin_method)[1])
for col in mags_cols_cl[1]:
bin_edges.append(np.histogram(col, bins=bin_method)[1])
elif bin_method == 'fixed':
# Based on Bonatto & Bica (2007) 377, 3, 1301-1323 but using larger
# the values used by them (0.25 for colors and 0.5 for magnitudes)
for mag in mags_cols_cl[0]:
b_num = max(2, (max(mag) - min(mag)) / 1.)
bin_edges.append(np.histogram(mag, bins=int(b_num))[1])
for col in mags_cols_cl[1]:
b_num = max(2, (max(col) - min(col)) / .5)
bin_edges.append(np.histogram(col, bins=int(b_num))[1])
elif bin_method == 'knuth':
for mag in mags_cols_cl[0]:
bin_edges.append(knuth_bin_width(
mag, return_bins=True, quiet=True)[1])
for col in mags_cols_cl[1]:
bin_edges.append(knuth_bin_width(
col, return_bins=True, quiet=True)[1])
elif bin_method == 'blocks':
for mag in mags_cols_cl[0]:
bin_edges.append(bayesian_blocks(mag))
for col in mags_cols_cl[1]:
bin_edges.append(bayesian_blocks(col))
# TODO this method is currently hidden from the params file.
# To be used when #325 is implemented. Currently used to test
# multi-dimensional likelihoods.
#
# For 4 to 6 dimensions the rule below appears to be a somewhat reasonable
# rule of thumb for the number of bins for each dimension.
# There is a trade-off between a large number of smaller bins which
# better match features of the observed cluster but benefits larger
# mass values, and fewer larger bins which better match masses but losing
# finer details of the cluster.
elif bin_method == 'man':
d = len(mags_cols_cl[0]) + len(mags_cols_cl[1])
b_num = [15, 10, 7][d - 4]
for mag in mags_cols_cl[0]:
bin_edges.append(np.histogram(mag, bins=int(b_num))[1])
for col in mags_cols_cl[1]:
bin_edges.append(np.histogram(col, bins=int(b_num))[1])
return bin_edges
def test_duplicate_events(rseed=0):
rng = np.random.RandomState(rseed)
t = rng.rand(100)
t[80:] = t[:20]
x = np.ones_like(t)
x[:20] += 1
bins1 = bayesian_blocks(t)
bins2 = bayesian_blocks(t[:80], x[:80])
assert_allclose(bins1, bins2)
def test_duplicate_events(rseed=0):
rng = np.random.RandomState(rseed)
t = rng.rand(100)
t[80:] = t[:20]
x = np.ones_like(t)
x[:20] += 1
bins1 = bayesian_blocks(t)
bins2 = bayesian_blocks(t[:80], x[:80])
assert_allclose(bins1, bins2)
def test_duplicate_events(rseed=0):
rng = np.random.default_rng(rseed)
t = rng.random(100)
t[80:] = t[:20]
# Using int array as a regression test for gh-6877
x = np.ones(t.shape, dtype=int)
x[:20] += 1
bins1 = bayesian_blocks(t)
bins2 = bayesian_blocks(t[:80], x[:80])
assert_allclose(bins1, bins2)
def test_duplicate_events(rseed=0):
rng = np.random.RandomState(rseed)
t = rng.rand(100)
t[80:] = t[:20]
x = np.ones_like(t)
x[:20] += 1
with pytest.warns(AstropyUserWarning,
match=r'p0 does not seem to accurate'):
bins1 = bayesian_blocks(t)
bins2 = bayesian_blocks(t[:80], x[:80])
assert_allclose(bins1, bins2)
def test_duplicate_events(rseed=0):
rng = np.random.RandomState(rseed)
t = rng.rand(100)
t[80:] = t[:20]
# Using int array as a regression test for gh-6877
x = np.ones(t.shape, dtype=int)
x[:20] += 1
with pytest.warns(AstropyUserWarning,
match=r'p0 does not seem to accurate'):
bins1 = bayesian_blocks(t)
bins2 = bayesian_blocks(t[:80], x[:80])
assert_allclose(bins1, bins2)
def Bayesian(self, x):
I = bayesian_blocks(x[:, 0], p0=0.01) #Interval partition
I = np.ceil(I).astype(int)
self.I = zip(I[:-1], I[1:])
if self.I[-1][0] == self.I[-1][1]:
del self.I[-1]
self.I_number = len(self.I)
def timeslice(self, lcbinwidth=0.05, gamma=1e-300):
det = ['n3', 'n4']
for i in range(1):
file = glob(self.datadir + 'glg_tte_' + det2[i] + '_' +
self.bnname + '_v*.fit')
print(file)
fitfile = file
hdu = fits.open(fitfile)
data = hdu['events'].data['time']
trigtime = hdu[0].header['trigtime']
time = data - trigtime
tte = time[(time > -10) & (time < 50)]
fig = plt.figure()
edges = np.arange(tte[0], tte[-1] + lcbinwidth, lcbinwidth)
histvalue, histbin = np.histogram(tte, bins=edges)
plottime = histbin
plotrate = histvalue / lcbinwidth
plotrate = np.concatenate(([plotrate[0]], plotrate))
edges = bayesian_blocks(plottime,
plotrate,
fitness='events',
p0=1e-1,
gamma=1e-300)
histvalue, histbin = np.histogram(tte, bins=edges)
plottime = histbin
plotrate = histvalue / (histbin[1:] - histbin[:-1])
plotrate = np.concatenate(([plotrate[0]], plotrate))
l = len(edges)
for i in range(1, l - 1):
time_slice.append(edges[i])
print(time_slice)
def histogram(a, bins=10, range=None, **kwargs):
"""Enhanced histogram
This is a histogram function that enables the use of more sophisticated
algorithms for determining bins. Aside from the `bins` argument allowing
a string specified how bins are computed, the parameters are the same
as numpy.histogram().
Parameters
----------
a : array_like
array of data to be histogrammed
bins : int or list or str (optional)
If bins is a string, then it must be one of:
'blocks' : use bayesian blocks for dynamic bin widths
'knuth' : use Knuth's rule to determine bins
'scotts' : use Scott's rule to determine bins
'freedman' : use the Freedman-diaconis rule to determine bins
range : tuple or None (optional)
the minimum and maximum range for the histogram. If not specified,
it will be (x.min(), x.max())
other keyword arguments are described in numpy.hist().
Returns
-------
hist : array
The values of the histogram. See `normed` and `weights` for a
description of the possible semantics.
bin_edges : array of dtype float
Return the bin edges ``(length(hist)+1)``.
See Also
--------
numpy.histogram
astroML.plotting.hist
"""
a = np.asarray(a)
# if range is specified, we need to truncate the data for
# the bin-finding routines
if (range is not None and (bins in ['blocks', 'knuth',
'scotts', 'freedman'])):
a = a[(a >= range[0]) & (a <= range[1])]
if isinstance(bins, str):
if bins == 'blocks':
bins = astropy_stats.bayesian_blocks(a)
elif bins == 'knuth':
da, bins = astropy_stats.knuth_bin_width(a, True)
elif bins == 'scotts':
da, bins = astropy_stats.scott_bin_width(a, True)
elif bins == 'freedman':
da, bins = astropy_stats.freedman_bin_width(a, True)
else:
raise ValueError("unrecognized bin code: '{}'".format(bins))
return np.histogram(a, bins, range, **kwargs)
def estimate_bayesian_blocks(self, x, y, yerr):
'''
:param x: x-data points (typically JD dates)
:param y: y-data points (typically mag/fluxes)
:param yerr: y-data errors (in the same units
:return: bayesianblocks dict with the x values,
the xerr (extension of the block) and
y/yerr (weighted average and errors).
'''
# make sure we have have numpy arrays
x = np.asarray(x)
y = np.asarray(y)
yerr = np.asarray(yerr)
# false alarm probability
p0 = self.run_config['bblocks_p0']
edges = astats.bayesian_blocks(x, y, yerr, fitness='measures', p0=p0)
bayesianblocks = {'x': [], 'xerr': [], 'y': [], 'yerr': []}
for xmin, xmax in zip(edges[:-1], edges[1:]):
filt = (x >= xmin) * (x < xmax)
if np.sum(filt) == 0: continue
xave = (xmin + xmax) / 2.
xerr = (xmax - xmin) / 2.
yave = np.average(y[filt], weights=1. / yerr[filt]**2)
ystd = (np.sum(1. / yerr[filt]**2))**(-1. / 2)
bayesianblocks['x'].append(xave)
bayesianblocks['xerr'].append(xerr)
bayesianblocks['y'].append(yave)
bayesianblocks['yerr'].append(ystd)
return (bayesianblocks)
def test_zero_change_points(rseed=0):
''' Ensure that edges contains both endpoints when there are no change points '''
np.random.seed(rseed)
# Using the failed edge case from https://github.com/astropy/astropy/issues/8558
values = np.array([1, 1, 1, 1, 1, 1, 1, 1, 2])
bins = bayesian_blocks(values)
assert values.min() == bins[0]
assert values.max() == bins[-1]
def test_single_change_point(rseed=0):
rng = np.random.default_rng(rseed)
x = np.concatenate([rng.random(100), 1 + rng.random(200)])
bins = bayesian_blocks(x)
assert (len(bins) == 3)
assert_allclose(bins[1], 0.927289, rtol=0.02)
def test_single_change_point(rseed=0):
rng = np.random.RandomState(rseed)
x = np.concatenate([rng.rand(100), 1 + rng.rand(200)])
bins = bayesian_blocks(x)
assert (len(bins) == 3)
assert_allclose(bins[1], 1, rtol=0.02)
def bbduration(self, lcbinwidth=0.05, gamma=1e-300):
os.chdir(self.resultdir)
det = ['n9', 'n4']
file = glob(self.datadir + 'glg_tte_' + det[0] + '_' + self.bnname +
'_v*.fit')
print(file)
fitfile = file[0]
hdu = fits.open(fitfile)
data = hdu['events'].data['time']
trigtime = hdu[0].header['trigtime']
time = data - trigtime
tte = time[(time > -10) & (time < 50)]
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax2 = ax1.twinx()
edges = np.arange(tte[0], tte[-1] + lcbinwidth, lcbinwidth)
histvalue, histbin = np.histogram(tte, bins=edges)
plottime = histbin
plotrate = histvalue / lcbinwidth
plotrate = np.concatenate(([plotrate[0]], plotrate))
ax1.plot(plottime, plotrate, linestyle='steps', color='lightgreen')
edges = bayesian_blocks(plottime,
plotrate,
fitness='events',
p0=1e-1,
gamma=1e-300)
histvalue, histbin = np.histogram(tte, bins=edges)
plottime = histbin
plotrate = histvalue / (histbin[1:] - histbin[:-1])
plotrate = np.concatenate(([plotrate[0]], plotrate))
#ax1.plot(plottime,plotrate,linestyle='steps',color='b')
ax1.set_xlabel('time')
ax1.set_ylabel('Count')
l = len(edges)
x = []
dx = []
for i in range(l - 3):
s = (edges[i + 1] + edges[i + 2]) / 2
z = (edges[i + 2] - edges[i + 1]) / 2
x.append(s)
dx.append(z)
dy = [epeak_error_p, epeak_error_n]
ax2.scatter(x, epeak, color='black', zorder=2, marker='.', s=50.)
ax2.errorbar(x,
epeak,
xerr=dx,
yerr=dy,
zorder=1,
fmt='o',
color='0.15',
markersize=1e-50)
ax2.set_ylim(0, 600)
ax2.set_ylabel('Epeak')
plt.savefig('bbdurations.png')
def test_single_change_point(rseed=0):
rng = np.random.RandomState(rseed)
x = np.concatenate([rng.rand(100),
1 + rng.rand(200)])
bins = bayesian_blocks(x)
assert (len(bins) == 3)
assert_allclose(bins[1], 1, rtol=0.02)
def test_fitness_function_results():
"""Test results for several fitness functions"""
rng = np.random.RandomState(42)
# Event Data
t = rng.randn(100)
with pytest.warns(AstropyUserWarning,
match=r'p0 does not seem to accurate'):
edges = bayesian_blocks(t, fitness='events')
assert_allclose(edges, [-2.6197451, -0.71094865, 0.36866702, 1.85227818])
# Event data with repeats
t[80:] = t[:20]
with pytest.warns(AstropyUserWarning,
match=r'p0 does not seem to accurate'):
edges = bayesian_blocks(t, fitness='events', p0=0.01)
assert_allclose(edges, [-2.6197451, -0.47432431, -0.46202823, 1.85227818])
# Regular event data
dt = 0.01
t = dt * np.arange(1000)
x = np.zeros(len(t))
N = len(t) // 10
x[rng.randint(0, len(t), N)] = 1
x[rng.randint(0, len(t) // 2, N)] = 1
edges = bayesian_blocks(t, x, fitness='regular_events', dt=dt)
assert_allclose(edges, [0, 5.105, 9.99])
# Measured point data with errors
t = 100 * rng.rand(20)
x = np.exp(-0.5 * (t - 50)**2)
sigma = 0.1
x_obs = x + sigma * rng.randn(len(x))
edges = bayesian_blocks(t, x_obs, sigma, fitness='measures')
expected = [4.360377, 48.456895, 52.597917, 99.455051]
assert_allclose(edges, expected)
# Optional arguments are passed (p0)
p0_sel = 0.05
edges = bayesian_blocks(t, x_obs, sigma, fitness='measures', p0=p0_sel)
assert_allclose(edges, expected)
# Optional arguments are passed (ncp_prior)
ncp_prior_sel = 4 - np.log(73.53 * p0_sel * (len(t)**-0.478))
edges = bayesian_blocks(t,
x_obs,
sigma,
fitness='measures',
ncp_prior=ncp_prior_sel)
assert_allclose(edges, expected)
# Optional arguments are passed (gamma)
gamma_sel = np.exp(-ncp_prior_sel)
edges = bayesian_blocks(t,
x_obs,
sigma,
fitness='measures',
gamma=gamma_sel)
assert_allclose(edges, expected)
def test_single_change_point(rseed=0):
rng = np.random.RandomState(rseed)
x = np.concatenate([rng.rand(100), 1 + rng.rand(200)])
with pytest.warns(AstropyUserWarning,
match=r'p0 does not seem to accurate'):
bins = bayesian_blocks(x)
assert (len(bins) == 3)
assert_allclose(bins[1], 1, rtol=0.02)
def test_regular_events():
rng = np.random.RandomState(0)
dt = 0.01
steps = np.concatenate([np.unique(rng.randint(0, 500, 100)),
np.unique(rng.randint(500, 1000, 200))])
t = dt * steps
# string fitness
bins1 = bayesian_blocks(t, fitness='regular_events', dt=dt)
assert (len(bins1) == 3)
assert_allclose(bins1[1], 5, rtol=0.05)
# class name fitness
bins2 = bayesian_blocks(t, fitness=RegularEvents, dt=dt)
assert_allclose(bins1, bins2)
# class instance fitness
bins3 = bayesian_blocks(t, fitness=RegularEvents(dt=dt))
assert_allclose(bins1, bins3)
def test_measures_fitness_heteroscedastic():
rng = np.random.RandomState(1)
t = np.linspace(0, 1, 11)
x = np.exp(-0.5 * (t - 0.5)**2 / 0.01**2)
sigma = 0.02 + 0.02 * rng.rand(len(x))
x = x + sigma * rng.randn(len(x))
bins = bayesian_blocks(t, x, sigma, fitness='measures')
assert_allclose(bins, [0, 0.45, 0.55, 1])
def test_regular_events():
rng = np.random.RandomState(0)
dt = 0.01
steps = np.concatenate([np.unique(rng.randint(0, 500, 100)),
np.unique(rng.randint(500, 1000, 200))])
t = dt * steps
# string fitness
bins1 = bayesian_blocks(t, fitness='regular_events', dt=dt)
assert (len(bins1) == 3)
assert_allclose(bins1[1], 5, rtol=0.05)
# class name fitness
bins2 = bayesian_blocks(t, fitness=RegularEvents, dt=dt)
assert_allclose(bins1, bins2)
# class instance fitness
bins3 = bayesian_blocks(t, fitness=RegularEvents(dt=dt))
assert_allclose(bins1, bins3)
def test_measures_fitness_homoscedastic(rseed=0):
rng = np.random.default_rng(rseed)
t = np.linspace(0, 1, 11)
x = np.exp(-0.5 * (t - 0.5)**2 / 0.01**2)
sigma = 0.05
x = x + sigma * rng.standard_normal(len(x))
bins = bayesian_blocks(t, x, sigma, fitness='measures')
assert_allclose(bins, [0, 0.45, 0.55, 1])
def test_measures_fitness_heteroscedastic():
rng = np.random.RandomState(1)
t = np.linspace(0, 1, 11)
x = np.exp(-0.5 * (t - 0.5) ** 2 / 0.01 ** 2)
sigma = 0.02 + 0.02 * rng.rand(len(x))
x = x + sigma * rng.randn(len(x))
bins = bayesian_blocks(t, x, sigma, fitness='measures')
assert_allclose(bins, [0, 0.45, 0.55, 1])
def prepObsMass(obs_mass, bin_edges):
"""
"""
# Obtain histogram for observed cluster.
if bin_edges == 'knuth':
bin_edges = knuth_bin_width(obs_mass, return_bins=True, quiet=True)[1]
elif bin_edges == 'block':
bin_edges = bayesian_blocks(obs_mass)
cl_histo, bin_edges = np.histogram(obs_mass, bins=bin_edges)
return [bin_edges, cl_histo]
def test_fitness_function_results():
"""Test results for several fitness functions"""
rng = np.random.default_rng(42)
# Event Data
t = rng.standard_normal(100)
edges = bayesian_blocks(t, fitness='events')
assert_allclose(edges, [-1.95103519, -1.01861547, 0.95442154, 2.1416476])
# Event data with repeats
t[80:] = t[:20]
edges = bayesian_blocks(t, fitness='events', p0=0.01)
assert_allclose(edges, [-1.95103519, -1.08663566, 1.17575682, 2.1416476])
# Regular event data
dt = 0.01
t = dt * np.arange(1000)
x = np.zeros(len(t))
N = len(t) // 10
x[rng.integers(0, len(t), N)] = 1
x[rng.integers(0, len(t) // 2, N)] = 1
edges = bayesian_blocks(t, x, fitness='regular_events', dt=dt)
assert_allclose(edges, [0, 4.365, 4.995, 9.99])
# Measured point data with errors
t = 100 * rng.random(20)
x = np.exp(-0.5 * (t - 50)**2)
sigma = 0.1
x_obs = x + sigma * rng.standard_normal(len(x))
edges = bayesian_blocks(t, x_obs, sigma, fitness='measures')
expected = [1.39362877, 44.30811196, 49.46626158, 54.37232704, 92.7562551]
assert_allclose(edges, expected)
# Optional arguments are passed (p0)
p0_sel = 0.05
edges = bayesian_blocks(t, x_obs, sigma, fitness='measures', p0=p0_sel)
assert_allclose(edges, expected)
# Optional arguments are passed (ncp_prior)
ncp_prior_sel = 4 - np.log(73.53 * p0_sel * (len(t)**-0.478))
edges = bayesian_blocks(t,
x_obs,
sigma,
fitness='measures',
ncp_prior=ncp_prior_sel)
assert_allclose(edges, expected)
# Optional arguments are passed (gamma)
gamma_sel = np.exp(-ncp_prior_sel)
edges = bayesian_blocks(t,
x_obs,
sigma,
fitness='measures',
gamma=gamma_sel)
assert_allclose(edges, expected)
def fit(self, X, sample_weight=None, **kwargs):
# Checks
X = check_array(X)
if sample_weight is not None and len(sample_weight) != len(X):
raise ValueError
# Compute histogram and edges
if self.bins == "blocks":
bins = bayesian_blocks(X.ravel(), fitness="events", p0=0.0001)
range_ = self.range[0] if self.range else None
h, e = np.histogram(X.ravel(), bins=bins, range=range_,
weights=sample_weight, normed=False)
e = [e]
elif self.variable_width:
ticks = [np.percentile(X.ravel(), 100. * k / self.bins) for k
in range(self.bins + 1)]
ticks[-1] += 1e-5
range_ = self.range[0] if self.range else None
h, e = np.histogram(X.ravel(), bins=ticks, range=range_,
normed=False, weights=sample_weight)
h, e = h.astype(float), e.astype(float)
widths = e[1:] - e[:-1]
h = h / widths / h.sum()
e = [e]
else:
bins = self.bins
h, e = np.histogramdd(X, bins=bins, range=self.range,
weights=sample_weight, normed=True)
# Add empty bins for out of bound samples
for j in range(X.shape[1]):
h = np.insert(h, 0, 0., axis=j)
h = np.insert(h, h.shape[j], 0., axis=j)
e[j] = np.insert(e[j], 0, -np.inf)
e[j] = np.insert(e[j], len(e[j]), np.inf)
if X.shape[1] == 1 and self.interpolation:
inputs = e[0][2:-1] - (e[0][2] - e[0][1]) / 2.
inputs[0] = e[0][1]
inputs[-1] = e[0][-2]
outputs = h[1:-1]
self.interpolation_ = interp1d(inputs, outputs,
kind=self.interpolation,
bounds_error=False,
fill_value=0.)
self.histogram_ = h
self.edges_ = e
self.ndim_ = X.shape[1]
return self
def test_zero_change_points(rseed=0):
"""
Ensure that edges contains both endpoints when there are no change points
"""
np.random.seed(rseed)
# Using the failed edge case from
# https://github.com/astropy/astropy/issues/8558
values = np.array([1, 1, 1, 1, 1, 1, 1, 1, 2])
with pytest.warns(AstropyUserWarning,
match=r'p0 does not seem to accurate'):
bins = bayesian_blocks(values)
assert values.min() == bins[0]
assert values.max() == bins[-1]
def get_bin_sizes_x(x, algo='scott'):
""" Smartly get bin size to have a loer bias due to binning"""
from astropy.stats import freedman_bin_width, scott_bin_width, knuth_bin_width, bayesian_blocks
logger.info(" > Get smart bin sizes in 1D")
if algo == 'scott':
logger.info("use scott rule of thumb")
width_x, bins_x = scott_bin_width(x, return_bins=True)
elif algo == 'knuth':
logger.info("use knuth rule of thumb")
width_x, bins_x = knuth_bin_width(x, return_bins=True)
elif algo == 'freedman':
logger.info("use freedman rule of thumb")
width_x, bins_x = freedman_bin_width(x, return_bins=True)
elif algo == 'blocks':
logger.info("use bayesian blocks rule of thumb")
width_x, bins_x = bayesian_blocks(x, return_bins=True)
else:
raise NotImplementedError("use scott, knuth, freedman or blocks")
return bins_x, width_x
def timeslice(self, lcbinwidth=0.05, gamma=1e-300):
os.chdir(self.resultdir)
det = ['n9', 'n4']
file = glob(self.datadir + 'glg_tte_' + det[0] + '_' + self.bnname +
'_v*.fit')
print(file)
fitfile = file[0]
hdu = fits.open(fitfile)
data = hdu['events'].data['time']
trigtime = hdu[0].header['trigtime']
time = data - trigtime
tte = time[(time > -10) & (time < 50)]
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax2 = ax1.twinx()
edges = np.arange(tte[0], tte[-1] + lcbinwidth, lcbinwidth)
histvalue, histbin = np.histogram(tte, bins=edges)
plottime = histbin
plotrate = histvalue / lcbinwidth
plotrate = np.concatenate(([plotrate[0]], plotrate))
ax1.plot(plottime, plotrate, linestyle='steps', color='lightgreen')
edges = bayesian_blocks(plottime,
plotrate,
fitness='events',
p0=1e-1,
gamma=1e-300)
histvalue, histbin = np.histogram(tte, bins=edges)
plottime = histbin
plotrate = histvalue / (histbin[1:] - histbin[:-1])
plotrate = np.concatenate(([plotrate[0]], plotrate))
ax1.plot(plottime, plotrate, linestyle='steps', color='b')
l = len(edges)
for i in range(1, l - 1):
time_slice.append(edges[i])
print('time_slice', time_slice)
plt.savefig('bb.png')
def mf(haloes, edges):
"""Bins FoF haloes
"""
if edges == "bayes":
edges = bayesian_blocks(haloes["M200Crit"])
try:
counts, edges = np.histogram(haloes["M200Crit"], edges)
except ValueError:
logging.exception("Error binning haloes")
sys.exit(1)
centres = 0.5 * (edges[1:] + edges[:-1])
haloes = np.lib.recfunctions.append_fields(
haloes,
"bin",
np.digitize(haloes["M200Crit"], edges, right=True),
dtypes=[int],
usemask=False,
)
return haloes, centres, counts
def test_errors():
rng = np.random.RandomState(0)
t = rng.rand(100)
# x must be integer or None for events
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='events', x=t)
# x must be binary for regular events
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='regular_events', x=10 * t, dt=1)
# x must be specified for measures
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='measures')
# sigma cannot be specified without x
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='events', sigma=0.5)
# length of x must match length of t
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='measures', x=t[:-1])
# repeated values in t fail when x is specified
t2 = t.copy()
t2[1] = t2[0]
with pytest.raises(ValueError):
bayesian_blocks(t2, fitness='measures', x=t)
# sigma must be broadcastable with x
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='measures', x=t, sigma=t[:-1])
def hist(x, bins=10, range=None, *args, **kwargs):
"""Enhanced histogram
This is a histogram function that enables the use of more sophisticated
algorithms for determining bins. Aside from the `bins` argument allowing
a string specified how bins are computed, the parameters are the same
as pylab.hist().
Parameters
----------
x : array_like
array of data to be histogrammed
bins : int or list or str (optional)
If bins is a string, then it must be one of:
'blocks' : use bayesian blocks for dynamic bin widths
'knuth' : use Knuth's rule to determine bins
'scott' : use Scott's rule to determine bins
'freedman' : use the Freedman-diaconis rule to determine bins
range : tuple or None (optional)
the minimum and maximum range for the histogram. If not specified,
it will be (x.min(), x.max())
ax : Axes instance (optional)
specify the Axes on which to draw the histogram. If not specified,
then the current active axes will be used.
**kwargs :
other keyword arguments are described in pylab.hist().
"""
if isinstance(bins, str) and "weights" in kwargs:
warnings.warn("weights argument is not supported: it will be ignored.")
kwargs.pop('weights')
x = np.asarray(x)
if 'ax' in kwargs:
ax = kwargs['ax']
del kwargs['ax']
else:
# import here so that testing with Agg will work
from matplotlib import pyplot as plt
ax = plt.gca()
# if range is specified, we need to truncate the data for
# the bin-finding routines
if (range is not None and (bins in ['blocks',
'knuth', 'knuths',
'scott', 'scotts',
'freedman', 'freedmans'])):
x = x[(x >= range[0]) & (x <= range[1])]
if bins in ['blocks']:
bins = bayesian_blocks(x)
elif bins in ['knuth', 'knuths']:
dx, bins = knuth_bin_width(x, True)
elif bins in ['scott', 'scotts']:
dx, bins = scott_bin_width(x, True)
elif bins in ['freedman', 'freedmans']:
dx, bins = freedman_bin_width(x, True)
elif isinstance(bins, str):
raise ValueError("unrecognized bin code: '{}'".format(bins))
return ax.hist(x, bins, range, **kwargs)
def describe_numeric_1d(series: pd.Series, series_description: dict) -> dict:
"""Describe a numeric series.
Args:
series: The Series to describe.
series_description: The dict containing the series description so far.
Returns:
A dict containing calculated series description values.
Notes:
When 'bins_type' is set to 'bayesian_blocks', astropy.stats.bayesian_blocks is used to determine the number of
bins. Read the docs:
https://docs.astropy.org/en/stable/visualization/histogram.html
https://docs.astropy.org/en/stable/api/astropy.stats.bayesian_blocks.html
This method might print warnings, which we suppress.
https://github.com/astropy/astropy/issues/4927
"""
quantiles = config["vars"]["num"]["quantiles"].get(list)
stats = {
"mean": series.mean(),
"std": series.std(),
"variance": series.var(),
"min": series.min(),
"max": series.max(),
"kurtosis": series.kurt(),
"skewness": series.skew(),
"sum": series.sum(),
"mad": series.mad(),
"n_zeros": (len(series) - np.count_nonzero(series)),
"histogramdata": series,
}
stats["range"] = stats["max"] - stats["min"]
stats.update(
{
"{:.0%}".format(percentile): value
for percentile, value in series.quantile(quantiles).to_dict().items()
}
)
stats["iqr"] = stats["75%"] - stats["25%"]
stats["cv"] = stats["std"] / stats["mean"] if stats["mean"] else np.NaN
stats["p_zeros"] = float(stats["n_zeros"]) / len(series)
bins = config["plot"]["histogram"]["bins"].get(int)
# Bins should never be larger than the number of distinct values
bins = min(series_description["distinct_count_with_nan"], bins)
stats["histogram_bins"] = bins
bayesian_blocks_bins = config["plot"]["histogram"]["bayesian_blocks_bins"].get(bool)
if bayesian_blocks_bins:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
ret = bayesian_blocks(stats["histogramdata"])
# Sanity check
if not np.isnan(ret).any() and ret.size > 1:
stats["histogram_bins_bayesian_blocks"] = ret
return stats
def _MakeTimeBins(self):
from astropy.stats import bayesian_blocks
from astropy.table import Table
evtfile = str("%s/AppertureLightCurve/%s_%s_MkTime.fits" %
(self.folder, self.srcname, self.Tag))
evtlist = Table.read(evtfile, hdu='EVENTS')['TIME'].data
expfile = str("%s/AppertureLightCurve/%s_%s_applc.fits" %
(self.folder, self.srcname, self.Tag))
expbins = Table.read(expfile, hdu='RATE')
meanRate = float(len(evtlist)) / float(self.tmax - self.tmin)
print("Mean photon rate %s s^-1" % meanRate)
print("Mean photon rate %s day^-1" % (meanRate * 3600. * 24))
#Sort table in function of time just to be sure
evtlist.sort()
evtlistExpCorrected = np.empty_like(evtlist)
expbins[expbins.argsort('TIME')]
# Calculate relative exposure time and time correction associated for each exposure bins
j = 0
surfaceFermi = 10000 # in cm^2
timeCorrection = np.zeros((len(expbins) + 1, 2))
exposure = np.zeros(len(expbins))
timeCorrection[j, 0] = expbins['TIME'][j] - 0.5 * expbins['TIMEDEL'][j]
timeCorrection[j, 1] = 0.
exposure[j] = expbins['EXPOSURE'][j] / (expbins['TIMEDEL'][j] *
surfaceFermi)
for j in range(1, len(expbins)):
exposure[j] = expbins['EXPOSURE'][j] / (expbins['TIMEDEL'][j] *
surfaceFermi)
timeCorrection[
j, 0] = expbins['TIME'][j] - 0.5 * expbins['TIMEDEL'][j]
timeCorrection[j, 1] = timeCorrection[
j - 1, 1] + exposure[j - 1] * expbins['TIMEDEL'][j - 1]
timeCorrection[j + 1,
0] = expbins['TIME'][j] + 0.5 * expbins['TIMEDEL'][j]
timeCorrection[
j + 1,
1] = timeCorrection[j, 1] + exposure[j] * expbins['TIMEDEL'][j]
#Apply exposure time correction
evtlistcorrected = np.interp(evtlist, timeCorrection[:, 0],
timeCorrection[:, 1])
meanRateCorrected = float(
len(evtlistcorrected)) / float(timeCorrection[-1, 1] -
timeCorrection[0, 1])
print("Mean photon rate exposure corrected %s s^-1" %
meanRateCorrected)
print("Mean photon rate exposure corrected %s day^-1" %
(meanRateCorrected * 3600. * 24))
#Calculate bayesian block
edgesCorrected = bayesian_blocks(evtlistcorrected,
fitness='events',
p0=self.p0)
edgesCorrected[0] = timeCorrection[0, 1]
edgesCorrected[-1] = timeCorrection[-1, 1]
#Calculate bin event for apperture photometry
count, tmp = np.histogram(evtlistcorrected, bins=edgesCorrected)
errcount = np.sqrt(count)
#Correct edges from exposure
edges = np.interp(edgesCorrected, timeCorrection[:, 1],
timeCorrection[:, 0])
edges[0] = self.tmin
edges[-1] = self.tmax
#Calculate apperture phtometry flux
flux = np.array(count / (edgesCorrected[1:] - edgesCorrected[:-1]))
errflux = np.array(errcount /
(edgesCorrected[1:] - edgesCorrected[:-1]))
self.Nbin = len(edges) - 1
self.time_array = np.zeros(self.Nbin * 2)
self.gtifile = []
for i in xrange(self.Nbin):
self.time_array[2 * i] = edges[i]
self.time_array[2 * i + 1] = edges[i + 1]
self.info("Running LC with " + str(self.Nbin) + " bins")
for i in xrange(self.Nbin):
print "Bin ", i, " Start=", self.time_array[
2 * i], " Stop=", self.time_array[
2 * i + 1], 'Apperture Photometry=', flux[
i], '+/-', errflux[i], 'ph.s^-1'
#Dump into ascii
bbfile = str("%s/BayesianBlocks/%s_bb.dat" %
(self.folder, self.srcname))
np.savetxt(bbfile,
np.transpose(
np.array([
np.array(edges[:-1]),
np.array(edges[1:]),
np.array(edgesCorrected[1:] - edgesCorrected[:-1]),
np.array(count)
])),
header='tstart tend dt_exposure_corrected count')
#Load apperture flux point
time_pt, dTime_pt, flux_pt, errflux_pt = self.readApperturePhotometryPoint(
)
plt.figure()
plt.xlabel(r"Time (s)")
plt.ylabel(r"${\rm Flux\ (photon\ cm^{-2}\ s^{-1})}$")
plot_bayesianblocks(np.array(edges[:-1]), np.array(edges[1:]),
flux / surfaceFermi, errflux / surfaceFermi,
errflux / surfaceFermi,
np.zeros(flux.shape).astype(np.bool))
plt.errorbar(time_pt,
flux_pt / surfaceFermi,
yerr=errflux_pt / surfaceFermi,
xerr=dTime_pt / 2.,
color='k',
ls='None')
plt.ylim(ymin=max(plt.ylim()[0],
np.percentile(flux / surfaceFermi, 1) * 0.1),
ymax=min(plt.ylim()[1],
np.percentile(flux / surfaceFermi, 99) * 2.0))
plt.xlim(xmin=max(
plt.xlim()[0], 1.02 * min(np.array(edges[:-1])) -
0.02 * max(np.array(edges[1:]))),
xmax=min(
plt.xlim()[1], 1.02 * max(np.array(edges[1:])) -
0.02 * min(np.array(edges[:-1]))))
# Move the offset to the axis label
ax = plt.gca()
ax.get_yaxis().get_major_formatter().set_useOffset(False)
offset_factor = int(np.mean(np.log10(np.abs(ax.get_ylim()))))
if (offset_factor != 0):
ax.set_yticklabels([float(round(k,5)) \
for k in ax.get_yticks()*10**(-offset_factor)])
ax.yaxis.set_label_text(ax.yaxis.get_label_text() +\
r" [${\times 10^{%d}}$]" %offset_factor)
# Secondary axis with MJD
mjdaxis = ax.twiny()
mjdaxis.set_xlim([utils.met_to_MJD(k) for k in ax.get_xlim()])
mjdaxis.set_xlabel(r"Time (MJD)")
mjdaxis.xaxis.set_major_formatter(
matplotlib.ticker.ScalarFormatter(useOffset=False))
plt.setp(mjdaxis.xaxis.get_majorticklabels(), rotation=15)
plt.tight_layout()
LcOutPath = self.LCfolder + self.config['target']['name']
plt.savefig(LcOutPath + "_AP.png",
dpi=150,
facecolor='w',
edgecolor='w',
orientation='portrait',
papertype=None,
format=None,
transparent=False,
bbox_inches=None,
pad_inches=0.1,
frameon=None)
def light_curve_analysis(file, NaI, BGO, good_ni, good_bi, txtdir, plotsave,
plotsave1):
dt = 0.064
maxx = 0
new_c = {}
if os.path.exists(txtdir) == False:
os.makedirs(txtdir)
myfile.printdatatofile(txtdir + 'N_good_ni.txt', data=[good_ni])
myfile.printdatatofile(txtdir + 'N_good_bi.txt', data=[good_bi])
for ni in NaI:
if file[ni] is not None:
hl = file[ni]
trigtime = hl[0].header['TRIGTIME']
time = hl[2].data.field(0)
ch = hl[2].data.field(1)
ch_n = hl[1].data.field(0)
e1 = hl[1].data.field(1)
e2 = hl[1].data.field(2)
t = time - trigtime
ch_index = np.where((ch >= 3) & (ch < 123))[0]
ch_n1 = np.arange(3, 123, 1, dtype=int)
t = t[ch_index]
ch = ch[ch_index]
bins = np.arange(t[0], t[-1], dt)
bin_n, bin_edges = np.histogram(t, bins=bins)
t_c = (bin_edges[1:] + bin_edges[:-1]) * 0.5
rate = bin_n / dt
t_c, cs_rate, bs_rate = TD_baseline(t_c, rate)
new_c[ni] = [t_c, rate, bs_rate]
if ni in good_ni:
if rate.max() > maxx:
maxx = rate.max()
rate_sm = cs_rate + bs_rate.mean()
bin_n_sm = np.round(rate_sm * dt)
edges = bayesian_blocks(t_c,
bin_n_sm,
fitness='events',
p0=0.05)
result = background_correction(t_c, rate_sm, edges, degree=7)
startedges, stopedges = get_bayesian_duration(result, sigma=3)
new_c[ni + 'bb'] = [startedges, stopedges]
if len(startedges) > 0:
if os.path.exists(txtdir) == False:
os.makedirs(txtdir)
myfile.printdatatofile(txtdir + 'Z_' + ni +
'_bayesian_duration.txt',
data=[startedges, stopedges],
format=['.5f', '.5f'])
flash_start, flash_stop = get_bayesian_flash(
result, startedges, stopedges)
myfile.printdatatofile(txtdir + 'Y_' + ni +
'_bayesian_flash.txt',
data=[flash_start, flash_stop],
format=['.5f', '.5f'])
'''
txx_result = get_bayesian_txx(result,startedges,stopedges,txx = 0.9,it = 400,lamd = 200.)
myplt = Plot(txx_result)
plt.title(ni)
myplt.plot_light_curve(sigma = 5)
plt.xlim(t[0],t[-1])
plt.savefig(txtdir + 'X_'+ni+'_bayesian_txx.png')
plt.close()
print('***********',len(txx_result['txx']),len(txx_result['txx_list']))
for ij in range(len(txx_result['txx'])):
plt.title(ni)
myplt.plot_distribution('90',num = ij)
plt.savefig(txtdir + 'W_'+ni+'_distribution_'+str(ij)+'.png')
plt.close()
plt.figure(figsize = (10,10))
plt.subplot(2,1,1)
plt.title(ni)
myplt.plot_Txx1('90')
plt.xlim(t[0],t[-1])
plt.subplot(2,1,2)
myplt.plot_Txx2('90')
plt.xlim(t[0],t[-1])
plt.savefig(txtdir + 'U_'+ni+'_txx.png')
plt.close()
save_result(txx_result,txtdir+'V_'+ni+'_distribution_T90.csv')
'''
if (ni == good_ni[0]):
ni_event = Separate_source(t, ch, ch_n1, WT=False)
s_t, s_ch = ni_event.get_S_t_and_ch()
new_t, new_energy = ch_to_energy(s_t, s_ch, ch_n, e1, e2)
fig = plt.figure(figsize=(20, 20))
ax1 = fig.add_subplot(2, 2, 1)
ax1.set_title('light curve', size=20)
ax1.step(t_c, rate, color='k', label=ni)
ax1.set_xlabel('time (s)', size=20)
ax1.set_ylabel('counts rate /s', size=20)
ax1.set_xlim(t[0], t[-1])
ax1.legend()
ax2 = fig.add_subplot(2, 2, 2)
ax2.set_title('point map', size=20)
ax2.plot(new_t, new_energy, ',', color='k')
ax2.set_xlabel('time (s)', size=20)
ax2.set_ylabel('energy (kev)', size=20)
ax2.set_yscale('log')
ax2.set_xlim(t[0], t[-1])
ax2.set_ylim(8, 9.1e2)
ax3 = fig.add_subplot(2, 2, 3)
ax3.step(t_c, rate, color='k', label=ni)
if len(startedges) > 0:
for i in range(len(startedges)):
ax3.axvline(x=startedges[i], color='r')
ax3.axvline(x=stopedges[i], color='g')
ax3.set_xlabel('time (s)', size=20)
ax3.set_ylabel('counts rate /s', size=20)
ax3.set_xlim(t[0], t[-1])
ax3.legend()
ax4 = fig.add_subplot(2, 2, 4)
ax4.plot(new_t, new_energy, ',', color='k')
if len(startedges) > 0:
for i in range(len(startedges)):
ax4.axvline(x=startedges[i], color='r')
ax4.axvline(x=stopedges[i], color='g')
ax4.set_xlabel('time (s)', size=20)
ax4.set_ylabel('energy (kev)', size=20)
ax4.set_yscale('log')
ax4.set_xlim(t[0], t[-1])
ax4.set_ylim(8, 9.1e2)
for k in plotsave:
dir_, file_ = os.path.split(k)
if os.path.exists(dir_) == False:
os.makedirs(dir_)
fig.savefig(k)
plt.close(fig)
else:
new_c[ni + 'bb'] = None
else:
new_c[ni] = None
new_c[ni + 'bb'] = None
for bi in BGO:
if file[bi] is not None:
hl = file[bi]
trigtime = hl[0].header['TRIGTIME']
time = hl[2].data.field(0)
t = time - trigtime
bins = np.arange(t[0], t[-1], dt)
bin_n, bin_edges = np.histogram(t, bins=bins)
t_c = (bin_edges[1:] + bin_edges[:-1]) * 0.5
rate = bin_n / dt
t_c, cs_rate, bs_rate = TD_baseline(t_c, rate)
new_c[bi] = [t_c, rate, bs_rate]
if bi in good_bi:
rate_sm = cs_rate + bs_rate.mean()
bin_n_sm = np.round(rate_sm * dt)
edges = bayesian_blocks(t_c,
bin_n_sm,
fitness='events',
gamma=np.exp(-5))
result = background_correction(t_c, rate_sm, edges, degree=7)
startedges, stopedges = get_bayesian_duration(result, sigma=5)
if len(startedges) > 0:
if os.path.exists(txtdir) == False:
os.makedirs(txtdir)
myfile.printdatatofile(txtdir + 'Z_' + bi +
'_bayesian_duration.txt',
data=[startedges, stopedges],
format=['.5f', '.5f'])
else:
new_c[bi] = None
plt.figure(figsize=(30, 60))
plt.subplots_adjust(left=0.1, right=0.9, top=0.95, bottom=0.05)
for index, value in enumerate(NaI):
plt.subplot(14, 1, index + 1)
if new_c[value] is not None:
tm, rate, bs = new_c[value]
plt.plot(tm, rate, color='k', label=value)
plt.plot(tm, bs, color='r', label='back')
if new_c[value + 'bb'] is not None:
started, stoped = new_c[value + 'bb']
for kk in range(len(started)):
plt.axvline(x=started[kk], color='r')
plt.axvline(x=stoped[kk], color='g')
plt.ylabel('the count rate (N/s)')
plt.xlim(tm[0], tm[-1])
plt.ylim(0, maxx * 0.5 + maxx)
plt.legend(loc='upper left')
for index, value in enumerate(BGO):
plt.subplot(14, 1, index + 13)
if new_c[value] is not None:
tm, rate, bs = new_c[value]
plt.plot(tm, rate, color='k', label=value)
plt.plot(tm, bs, color='r', label='back')
plt.ylabel('the count rate (N/s)')
plt.xlim(tm[0], tm[-1])
plt.ylim(0, maxx * 0.5 + maxx)
plt.legend(loc='upper left')
for vv in plotsave1:
dir_, file_ = os.path.split(vv)
if os.path.exists(dir_) == False:
os.makedirs(dir_)
plt.savefig(vv)
plt.close()
def read_times(dir_list):
"""Reads xrt data from given directory list and appends all the times"""
time = []
with open(dir_list, 'r') as reader:
for dire in reader.readlines():
fits_name = "sw" + dire[:-2] + "xpcw3po_cl.evt.gz"
path = "./" + dire[:-1] + "xrt/event/" + fits_name
with fits.open(path) as hdul:
time.append(hdul['EVENTS'].data["Time"])
return np.concatenate(time)
time = read_times(dir_list)
edges = bayesian_blocks(time, fitness='events', p0=0.01)
edges1 = bayesian_blocks(time, fitness='event')
# edges = bayesian_blocks(t, fitness='events')
# edges = bayesian_blocks(t, x,fitness='measures')
# edges1 = bayesian_blocks(t, x,sigma=s,fitness='measures')
# edges2 = bayesian_blocks(t, x,sigma=s,fitness='measures',p0=0.01)
# plt.scatter(range(len(edges)),edges)
# Out[19]: <matplotlib.collections.PathCollection at 0x7f303bb3c250>
# plt.scatter(range(len(edges1)),edges1)
# Out[20]: <matplotlib.collections.PathCollection at 0x7f30380653d0>
# plt.scatter(range(len(edges2)),edges2)
# Out[21]: <matplotlib.collections.PathCollection at 0x7f303806c760>
def test_errors():
rng = np.random.RandomState(0)
t = rng.rand(100)
# x must be integer or None for events
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='events', x=t)
# x must be binary for regular events
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='regular_events', x=10 * t, dt=1)
# x must be specified for measures
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='measures')
# sigma cannot be specified without x
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='events', sigma=0.5)
# length of x must match length of t
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='measures', x=t[:-1])
# repeated values in t fail when x is specified
t2 = t.copy()
t2[1] = t2[0]
with pytest.raises(ValueError):
bayesian_blocks(t2, fitness='measures', x=t)
# sigma must be broadcastable with x
with pytest.raises(ValueError):
bayesian_blocks(t, fitness='measures', x=t, sigma=t[:-1])
line = "spec" + str(i) + " " + str(tstart) + "-" + str(tstop)
f.write(line + "\n")
f.close()
lc_filename = "curve_mod.qdp"
bin_textfile = "tbin_bb.txt"
modes, data = Read_lc_qdp(lc_filename)
PC_data = np.array(data[-1], dtype=np.float32)
t = PC_data[:, 0]
x = PC_data[:, 3]
del_t = np.diff(t)
s = (PC_data[:, 4] - PC_data[:, 5]) / 2
# edges = bayesian_blocks(t, fitness='events')
# edges = bayesian_blocks(t, x,fitness='measures')
# edges1 = bayesian_blocks(t, x,sigma=s,fitness='measures')
edges = bayesian_blocks(t, x, sigma=s, fitness='measures', p0=0.01)
CreateBinFile(edges, bin_textfile)
# plt.scatter(range(len(edges)),edges)
# Out[19]: <matplotlib.collections.PathCollection at 0x7f303bb3c250>
# plt.scatter(range(len(edges1)),edges1)
# Out[20]: <matplotlib.collections.PathCollection at 0x7f30380653d0>
# plt.scatter(range(len(edges2)),edges2)
# Out[21]: <matplotlib.collections.PathCollection at 0x7f303806c760>
# plt.yscale("log")
time = data[2].data.field(0)
ch = data[2].data.field(1)
t = time - trigtime
ch_n = data[1].data.field(0)
e1 = data[1].data.field(1)
e2 = data[1].data.field(2)
#t = t[np.where((ch>=3) & (ch <=109))]
#ch = ch[np.where((ch>=3) & (ch <=109))]
start_edges, stop_edges = get_pulse_duration(t)
dt = 1
edges0 = np.arange(start_edges - 2, stop_edges + 2 + dt, dt)
bin_n, edges0 = np.histogram(t, bins=edges0)
bin_c = (edges0[1:] + edges0[:-1]) * 0.5
edges = bayesian_blocks(bin_c, np.rint(bin_n), fitness='events',
p0=0.001)[1:-1] #从第二到倒数第二个。
slic_start = edges[:-1]
slic_top = edges[1:]
block_time = []
block_time_err = []
Ep = []
Ep_err1 = []
Ep_err2 = []
for dete_n in dete:
make_phaI(name,
dete_n,
sampledir,
save_dir,
slic_start,