def test_Nstates_py_vs_cy():
burstsph, _ = load_burstsph()
ns = 1.0
nm = 1.0
R0 = 6 * nm
R_mean = np.array([5.5 * nm, 8 * nm])
R_sigma = np.array([0.8 * nm, 1 * nm])
τ_relax = np.array([0.1 * ns, 0.1 * ns])
k_s01, k_s10 = np.array([1 / (1e6 * ns), 1 / (1e6 * ns)])
K_s = np.array([[-k_s01, k_s01], [k_s10, -k_s10]])
δt = 1e-2 * ns
τ_D = 3.8 * ns
k_D = 1 / τ_D
D_fract = np.atleast_1d(1.)
ts = burstsph.timestamp.values[:5000]
rg = RandomGenerator(Xoroshiro128(1))
A_em, R_ph, T_ph, S_ph = depi_ref.sim_DA_from_timestamps2_p2_Nstates(
ts, δt, k_D, R0, R_mean, R_sigma, τ_relax, K_s, rg=rg)
rg = RandomGenerator(Xoroshiro128(1))
R_php, T_php, S_php = depi_cy.sim_DA_from_timestamps2_p2_Nstates_cy(
ts,
δt,
np.atleast_1d(k_D),
D_fract,
R0,
R_mean,
R_sigma,
τ_relax,
K_s,
rg=rg,
ndt=0)
assert np.allclose(R_php, R_ph)
assert np.allclose(T_php, T_ph)
assert np.allclose(S_php, S_ph)
def test_dt_tollerance():
"""
Using small enough dt approximated and correct expression should be similar
"""
burstsph, _ = load_burstsph()
ns = 1.0
nm = 1.0
δt = 5e-4 * ns
R0 = 6 * nm
R_mean = 6.5 * nm
R_sigma = 1 * nm
τ_relax = 0.5 * ns
τ_D = 4 * ns
k_D = 1 / τ_D
ts = burstsph.timestamp.values[:10000]
rg = RandomGenerator(Xoroshiro128(1))
A_em, R_ph, T_ph = depi_ref.sim_DA_from_timestamps(ts, δt, k_D, R0, R_mean,
R_sigma, τ_relax, rg)
rg = RandomGenerator(Xoroshiro128(1))
A_emp, R_php, T_php = depi_ref.sim_DA_from_timestamps_p(
ts, δt, k_D, R0, R_mean, R_sigma, τ_relax, rg)
rg = RandomGenerator(Xoroshiro128(1))
A_emp2, R_php2, T_php2 = depi_ref.sim_DA_from_timestamps_p2(
ts, δt, k_D, R0, R_mean, R_sigma, τ_relax, rg)
assert not all([
not np.allclose(A_em, A_emp), not np.allclose(R_ph, R_php),
not np.allclose(T_ph, T_php)
])
assert not all([
not np.allclose(A_em, A_emp2), not np.allclose(R_ph, R_php2),
not np.allclose(T_ph, T_php2)
])
# Test R from nanotime vs R_mean
R_a = fret.dist_from_E(1 - T_ph.mean() / τ_D, R0)
R_c = fret.dist_from_E(1 - T_php.mean() / τ_D, R0)
assert abs(R_c - R_a) < 0.12 * nm
# Test E from nanotime vs ratiometric vs from P(R)
E_PoR = fret.mean_E_from_gauss_PoR(R_mean, R_sigma, R0)
E_ratio_a = A_em.sum() / A_em.size
E_lifetime_a = 1 - T_ph.mean() / τ_D
E_ratio_c = A_emp.sum() / A_emp.size
E_lifetime_c = 1 - T_php.mean() / τ_D
E_ratio_c2 = A_emp2.sum() / A_emp2.size
E_lifetime_c2 = 1 - T_php2.mean() / τ_D
assert abs(E_PoR - E_ratio_a) < 0.03
assert abs(E_PoR - E_lifetime_a) < 0.03
assert abs(E_ratio_c - E_ratio_a) < 0.03
assert abs(E_ratio_c2 - E_ratio_a) < 0.03
assert abs(E_lifetime_c - E_ratio_a) < 0.03
assert abs(E_lifetime_c2 - E_ratio_a) < 0.03
def test_approx_vs_correct():
"""
With α=np.inf, ndt=0 the adaptive functions should give the same
results as the approximeated function.
"""
burstsph, _ = load_burstsph()
ns = 1.0
nm = 1.0
δt = 1e-1 * ns
R0 = 6 * nm
R_mean = 6.5 * nm
R_sigma = 0.01 * nm
τ_relax = 0.08 * ns
τ_D = 4 * ns
k_D = 1 / τ_D
ts = burstsph.timestamp.values[:1000]
for R_sigma in (0.01, 0.1, 1, 10):
for R_mean in (4, 5, 6, 7, 8):
R_sigma *= nm
R_mean *= nm
rg = RandomGenerator(Xoroshiro128(1))
A_em, R_ph, T_ph = depi_ref.sim_DA_from_timestamps(
ts, δt, k_D, R0, R_mean, R_sigma, τ_relax, rg)
rg = RandomGenerator(Xoroshiro128(1))
A_emp, R_php, T_php = depi_ref.sim_DA_from_timestamps_p(ts,
δt,
k_D,
R0,
R_mean,
R_sigma,
τ_relax,
rg,
α=np.inf,
ndt=0)
rg = RandomGenerator(Xoroshiro128(1))
A_emp2, R_php2, T_php2 = depi_ref.sim_DA_from_timestamps_p2(
ts, δt, k_D, R0, R_mean, R_sigma, τ_relax, rg, α=np.inf, ndt=0)
assert all([
np.allclose(A_em, A_emp),
np.allclose(R_ph, R_php),
np.allclose(T_ph, T_php)
])
assert all([
np.allclose(A_em, A_emp2),
np.allclose(R_ph, R_php2),
np.allclose(T_ph, T_php2)
])
def _recolor_burstsph(ts, params, cache=False, seed=1):
if cache:
bph = depi.recolor_burstsph_cache(ts, **params)
else:
rg = RandomGenerator(Xoroshiro128(seed))
bph = depi.recolor_burstsph(ts, rg=rg, **params)
return bph
def test_py_vs_cy():
ns = 1.0
nm = 1.0
δt = 1e-1 * ns
R0 = 6 * nm
R_mean = 5.5 * nm
R_sigma = 0.01 * nm
τ_relax = 0.08 * ns
τ_D = 4 * ns
k_D = 1 / τ_D
burstsph, _ = load_burstsph()
ts = burstsph.timestamp.values[:1000]
rg = RandomGenerator(Xoroshiro128(1))
A_em, R_ph, T_ph = depi_ref.sim_DA_from_timestamps(ts, δt, k_D, R0, R_mean,
R_sigma, τ_relax, rg)
rg = RandomGenerator(Xoroshiro128(1))
R_phc, T_phc = depi_cy.sim_DA_from_timestamps_cy(ts, δt, k_D, R0, R_mean,
R_sigma, τ_relax, rg)
assert all([np.allclose(R_ph, R_phc), np.allclose(T_ph, T_phc)])
# Test R from nanotime vs R_mean
R_est = fret.dist_from_E(1 - T_ph.mean() / τ_D, R0)
assert abs(R_est - R_mean) < 0.12 * nm
# Test E from nanotime vs ratiometric vs from P(R)
E_PoR = fret.mean_E_from_gauss_PoR(R_mean, R_sigma, R0)
E_ratio = A_em.sum() / A_em.size
E_lifetime = 1 - T_ph.mean() / τ_D
assert abs(E_PoR - E_ratio) < 0.03
assert abs(E_PoR - E_lifetime) < 0.03
rg = RandomGenerator(Xoroshiro128(1))
A_em, R_ph, T_ph = depi_ref.sim_DA_from_timestamps2_p(
ts, δt, k_D, R0, R_mean, R_sigma, τ_relax, rg)
rg = RandomGenerator(Xoroshiro128(1))
R_phc, T_phc = depi_cy.sim_DA_from_timestamps2_p_cy(
ts, δt, k_D, R0, R_mean, R_sigma, τ_relax, rg)
assert all([np.allclose(R_ph, R_phc), np.allclose(T_ph, T_phc)])
# Test R from nanotime vs R_mean
R_est = fret.dist_from_E(1 - T_ph.mean() / τ_D, R0)
assert abs(R_est - R_mean) < 0.12 * nm
# Test E from nanotime vs ratiometric vs from P(R)
E_PoR = fret.mean_E_from_gauss_PoR(R_mean, R_sigma, R0)
E_ratio = A_em.sum() / A_em.size
E_lifetime = 1 - T_ph.mean() / τ_D
assert abs(E_PoR - E_ratio) < 0.03
assert abs(E_PoR - E_lifetime) < 0.03
def test_cdf_vs_dt_cy():
"""
Test CDF vs small-dt correction in cython code
"""
burstsph, _ = load_burstsph()
ns = 1.0
nm = 1.0
δt = 1e-2 * ns
R0 = 6 * nm
R_mean = 6.5 * nm
R_sigma = 1 * nm
τ_relax = 0.2 * ns
τ_D = 4. * ns
k_D = 1. / τ_D
D_fract = np.atleast_1d(1.)
ts = burstsph.timestamp.values[:100000]
rg = RandomGenerator(Xoroshiro128(1))
R_ph, T_ph = depi_cy.sim_DA_from_timestamps2_p_cy(ts,
δt,
k_D,
R0,
R_mean,
R_sigma,
τ_relax,
rg,
ndt=0,
alpha=np.inf)
rg = RandomGenerator(Xoroshiro128(1))
R_php, T_php = depi_cy.sim_DA_from_timestamps2_p2_cy(ts,
δt,
np.atleast_1d(k_D),
D_fract,
R0,
R_mean,
R_sigma,
τ_relax,
rg=rg,
ndt=0,
alpha=np.inf)
assert not all(
[not np.allclose(R_ph, R_php), not np.allclose(T_ph, T_php)])
def test_cdf_vs_dt_python():
"""
Test CDF vs small-dt correction in python code
"""
burstsph, _ = load_burstsph()
ns = 1.0
nm = 1.0
δt = 1e-2 * ns
R0 = 6 * nm
R_mean = 6.5 * nm
R_sigma = 1 * nm
τ_relax = 0.2 * ns
τ_D = 4 * ns
k_D = 1 / τ_D
ts = burstsph.timestamp.values[:2000]
rg = RandomGenerator(Xoroshiro128(1))
A_em, R_ph, T_ph = depi_ref.sim_DA_from_timestamps2_p(ts,
δt,
k_D,
R0,
R_mean,
R_sigma,
τ_relax,
rg,
ndt=0,
alpha=np.inf)
rg = RandomGenerator(Xoroshiro128(1))
A_emp, R_php, T_php = depi_ref.sim_DA_from_timestamps2_p2(ts,
δt,
k_D,
R0,
R_mean,
R_sigma,
τ_relax,
rg,
ndt=0,
alpha=np.inf)
assert not all([
not np.allclose(A_em, A_emp), not np.allclose(R_ph, R_php),
not np.allclose(T_ph, T_php)
])
def test_calc_intrisic_nanotime():
rg = RandomGenerator(Xoroshiro128(1))
n = int(1e6)
τ = 2
fract = None
nanot = depi._calc_intrisic_nanotime(n, τ, fract, rg)
assert np.allclose(nanot.mean(), τ, rtol=5e-3)
n = int(1e6)
τ = np.array([1, 7])
fract = np.array([0.3, 0.7])
nanot = depi._calc_intrisic_nanotime(n, τ, fract, rg)
assert np.allclose(sum(fract * τ), nanot.mean(), rtol=1e-2)
def generate_image(size, prng):
allowed_prngs = [
"java",
"python",
"numpy",
"Xoroshiro128",
"MT19937",
"Philox",
"SFC64",
"Xorshift1024",
"ThreeFry",
]
if prng not in allowed_prngs:
raise ValueError(f"prng={prng} is not in {allowed_prngs}")
arr = np.zeros((size, size))
for i in range(size):
if prng == "python":
random.seed(i)
elif prng == "numpy":
np.random.seed(i)
elif prng == "java":
rnd = javarandom.Random(i)
elif prng == "Xoroshiro128":
rnd = RandomGenerator(Xoroshiro128())
elif prng == "Xorshift1024":
rnd = RandomGenerator(Xorshift1024())
elif prng == "ThreeFry":
rnd = RandomGenerator(ThreeFry())
elif prng == "MT19937":
rnd = Generator(MT19937())
elif prng == "Philox":
rnd = Generator(Philox())
elif prng == "SFC64":
rnd = Generator(SFC64())
for j in range(size):
if prng == "python":
random_number = random.random()
elif prng == "numpy":
random_number = np.random.random()
elif prng == "java":
random_number = rnd.nextDouble()
elif prng in ["Xoroshiro128", "Xorshift1024", "ThreeFry"]:
random_number = rnd.random_sample()
elif prng in ["MT19937", "Philox", "SFC64"]:
random_number = rnd.random()
arr[j, i] = random_number
print("{}\t{}\t{}".format(i, arr[0, i], arr[1, i]))
imageio.imwrite(f"1000-random-numbers-{prng}.png", arr)
def _get_randomgens(num_threads):
"""Cached generation of random number generators, enables
``random_seed_fn`` functionality and greater efficiency.
"""
global _RANDOM_GENS
num_gens = len(_RANDOM_GENS)
if num_gens < num_threads:
from randomgen import Xoroshiro128
# add more generators if not enough
for _ in range(num_threads - num_gens):
_RANDOM_GENS.append(Xoroshiro128())
return _RANDOM_GENS[:num_threads]
def test_background():
N = 100000
burstsph, meta = load_burstsph()
burstsph = burstsph.iloc[:N]
ns = nm = 1.
params = dict(
name='gaussian',
# physical parameters
R_mean=6.5 * nm,
R_sigma=0.01 * nm,
R0=6 * nm,
τ_relax=200 * ns,
τ_D=[3.8 * ns, 1 * ns],
D_fract=[0.5, 0.5],
τ_A=[4 * ns, 1 * ns],
A_fract=[0.3, 0.7],
bg_rate_d=1000,
bg_rate_a=1500,
ts_unit=meta['timestamp_unit'],
tcspc_unit=30 * ns,
# simulation parameters
δt=1e-2 * ns,
ndt=10,
α=0.1,
gamma=0.6,
lk=0.4,
dir_ex_t=0.3,
)
rg = RandomGenerator(Xoroshiro128(1))
burstsph_sim = depi.recolor_burstsph(burstsph.timestamp, rg=rg, **params)
def func(burst):
bg_counts = burst.bg_ph.sum()
bg_counts_d = burst.bg_ph.loc[burst.stream == 'DexDem'].sum()
bg_counts_a = burst.bg_ph.loc[burst.stream == 'DexAem'].sum()
burst_width = (burst.timestamp.iloc[-1] -
burst.timestamp.iloc[0]) * 1e-9
bg_rate = bg_counts / burst_width
bg_rate_d = bg_counts_d / burst_width
bg_rate_a = bg_counts_a / burst_width
return pd.Series([bg_rate, bg_rate_d, bg_rate_a],
index=['bg', 'bg_d', 'bg_a'])
bg = burstsph_sim.groupby('burst').apply(func)
assert np.allclose(bg.bg.mean(), 2500, atol=0, rtol=3e-2)
assert np.allclose(bg.bg_d.mean(), 1000, atol=0, rtol=6e-2)
assert np.allclose(bg.bg_a.mean(), 1500, atol=0, rtol=6e-2)
def test_corrections():
N = 50000
burstsph, _ = load_burstsph()
burstsph = burstsph.iloc[:N]
ns = nm = 1.
params = dict(
name='gaussian',
# physical parameters
R_mean=[6.37 * nm, 4 * ns],
R_sigma=[0.01 * nm] * 2,
R0=6. * nm,
τ_relax=[200 * ns] * 2,
τ_D=[3.8 * ns, 1 * ns],
D_fract=[0.5, 0.5],
τ_A=4 * ns,
k_s=[1, 1],
# simulation parameters
δt=1e-2 * ns,
ndt=10,
α=0.1,
gamma=2,
lk=0.3,
dir_ex_t=0.4,
)
# 2-states Gaussian
rg = RandomGenerator(Xoroshiro128(1))
burstsph_sim = depi.recolor_burstsph(burstsph.timestamp, rg=rg, **params)
E_corr = fret.E_from_dist(np.array(params['R_mean']), R0=params['R0'])
state0 = burstsph_sim.state == 0
state1 = burstsph_sim.state == 1
FA = burstsph_sim.stream == 'DexAem'
Eraw0 = (FA & state0).sum() / state0.sum()
Eraw1 = (FA & state1).sum() / state1.sum()
Eraw = np.array([Eraw0, Eraw1])
Eraw2 = fret.uncorrect_E_gamma_leak_dir(E_corr,
params['gamma'],
params['lk'],
dir_ex_t=params['dir_ex_t'])
assert np.allclose(Eraw, Eraw2, atol=5e-3, rtol=0)
# 1-state Gaussian
params.update(R_mean=params['R_mean'][0],
R_sigma=params['R_sigma'][0],
τ_relax=params['τ_relax'][0])
burstsph_sim = depi.recolor_burstsph(burstsph.timestamp, rg=rg, **params)
E_corr = fret.E_from_dist(np.array(params['R_mean']), R0=params['R0'])
FA = (burstsph_sim.stream == 'DexAem').sum()
Eraw = FA / burstsph_sim.shape[0]
Eraw2 = fret.uncorrect_E_gamma_leak_dir(E_corr,
params['gamma'],
params['lk'],
dir_ex_t=params['dir_ex_t'])
assert np.allclose(Eraw, Eraw2, atol=5e-3, rtol=0)
# 1-state Radial Gaussian
params.update(name='radial_gaussian',
mu=4 * nm,
sigma=0.01 * nm,
offset=1,
du=0.01,
u_max=6.,
dr=0.001)
del params['R_mean'], params['R_sigma']
d = dd.distribution(params)
E_corr = d.mean_E(params['R0'])
rg = RandomGenerator(Xoroshiro128(1))
burstsph_sim = depi.recolor_burstsph(burstsph.timestamp, rg=rg, **params)
FA = (burstsph_sim.stream == 'DexAem').sum()
Eraw = FA / burstsph_sim.shape[0]
Eraw2 = fret.uncorrect_E_gamma_leak_dir(E_corr,
params['gamma'],
params['lk'],
dir_ex_t=params['dir_ex_t'])
assert np.allclose(Eraw, Eraw2, atol=5e-3, rtol=0)
from cffi import FFI
from randomgen import Xoroshiro128
ffi = FFI()
if os.path.exists('./distributions.dll'):
lib = ffi.dlopen('./distributions.dll')
elif os.path.exists('./libdistributions.so'):
lib = ffi.dlopen('./libdistributions.so')
else:
raise RuntimeError('Required DLL/so file was not found.')
ffi.cdef("""
double random_gauss_zig(void *brng_state);
""")
x = Xoroshiro128()
xffi = x.cffi
brng = xffi.brng
random_gauss_zig = lib.random_gauss_zig
def normals(n, brng):
out = np.empty(n)
for i in range(n):
out[i] = random_gauss_zig(brng)
return out
normalsj = nb.jit(normals, nopython=True)
def recolor_burstsph_cache(timestamp, seed=1, **params):
"""Cached version of :func:`recolor_burstsph`."""
from randomgen import RandomGenerator, Xoroshiro128
rg = RandomGenerator(Xoroshiro128(seed))
burstsph = recolor_burstsph(timestamp, rg=rg, **params)
return burstsph