Commit f54038f7 authored by Martin Reinecke's avatar Martin Reinecke
Browse files

cleanup

parent d7b80547
...@@ -25,51 +25,47 @@ def get_random_LOS(n_los): ...@@ -25,51 +25,47 @@ def get_random_LOS(n_los):
ends = list(np.random.uniform(0, 1, (n_los, 2)).T) ends = list(np.random.uniform(0, 1, (n_los, 2)).T)
return starts, ends return starts, ends
if __name__ == '__main__': if __name__ == '__main__':
# FIXME description of the tutorial # FIXME description of the tutorial
np.random.seed(42) np.random.seed(42)
position_space = ift.RGSpace([128, 128]) position_space = ift.RGSpace([128, 128])
# Setting up an amplitude model # Setting up an amplitude model
A, amplitude_internals = ift.make_amplitude_model( A = ift.AmplitudeModel(position_space, 16, 1, 10, -4., 1, 0., 1.)
position_space, 16, 1, 10, -4., 1, 0., 1.) dummy = ift.from_random('normal', A.domain)
# Building the model for a correlated signal # Building the model for a correlated signal
harmonic_space = position_space.get_default_codomain() harmonic_space = position_space.get_default_codomain()
ht = ift.HarmonicTransformOperator(harmonic_space, position_space) ht = ift.HarmonicTransformOperator(harmonic_space, position_space)
power_space = A.value.domain[0] power_space = A.target[0]
power_distributor = ift.PowerDistributor(harmonic_space, power_space) power_distributor = ift.PowerDistributor(harmonic_space, power_space)
position = ift.MultiField.from_dict( dummy = ift.Field.from_random('normal', harmonic_space)
{'xi': ift.Field.from_random('normal', harmonic_space)})
xi = ift.Variable(position)['xi'] correlated_field = lambda inp: ht(power_distributor(A(inp))*inp["xi"])
Amp = power_distributor(A)
correlated_field_h = Amp * xi
correlated_field = ht(correlated_field_h)
# alternatively to the block above one can do: # alternatively to the block above one can do:
# correlated_field,_ = ift.make_correlated_field(position_space, A) # correlated_field,_ = ift.make_correlated_field(position_space, A)
# apply some nonlinearity # apply some nonlinearity
signal = ift.PointwisePositiveTanh(correlated_field) signal = lambda inp: correlated_field(inp).positive_tanh()
# Building the Line of Sight response # Building the Line of Sight response
LOS_starts, LOS_ends = get_random_LOS(100) LOS_starts, LOS_ends = get_random_LOS(100)
R = ift.LOSResponse(position_space, starts=LOS_starts, R = ift.LOSResponse(position_space, starts=LOS_starts,
ends=LOS_ends) ends=LOS_ends)
# build signal response model and model likelihood # build signal response model and model likelihood
signal_response = R(signal) signal_response = lambda inp: R(signal(inp))
# specify noise # specify noise
data_space = R.target data_space = R.target
noise = .001 noise = .001
N = ift.ScalingOperator(noise, data_space) N = ift.ScalingOperator(noise, data_space)
# generate mock data # generate mock data
MOCK_POSITION = ift.from_random('normal', signal.position.domain) domain = ift.MultiDomain.union((A.domain, ift.MultiDomain.make({'xi': harmonic_space})))
data = signal_response.at(MOCK_POSITION).value + N.draw_sample() MOCK_POSITION = ift.from_random('normal', domain)
data = signal_response(MOCK_POSITION) + N.draw_sample()
# set up model likelihood # set up model likelihood
likelihood = ift.GaussianEnergy(signal_response, mean=data, covariance=N) likelihood = lambda inp: ift.GaussianEnergy(mean=data, covariance=N)(signal_response(inp))
# set up minimization and inversion schemes # set up minimization and inversion schemes
ic_cg = ift.GradientNormController(iteration_limit=10) ic_cg = ift.GradientNormController(iteration_limit=10)
...@@ -80,40 +76,38 @@ if __name__ == '__main__': ...@@ -80,40 +76,38 @@ if __name__ == '__main__':
# build model Hamiltonian # build model Hamiltonian
H = ift.Hamiltonian(likelihood, ic_sampling) H = ift.Hamiltonian(likelihood, ic_sampling)
INITIAL_POSITION = ift.from_random('normal', H.position.domain) INITIAL_POSITION = ift.from_random('normal', domain)
position = INITIAL_POSITION position = INITIAL_POSITION
ift.plot(signal.at(MOCK_POSITION).value, title='ground truth') ift.plot(signal(MOCK_POSITION), title='ground truth')
ift.plot(R.adjoint_times(data), title='data') ift.plot(R.adjoint_times(data), title='data')
ift.plot([A.at(MOCK_POSITION).value], title='power') ift.plot([A(MOCK_POSITION)], title='power')
ift.plot_finish(nx=3, xsize=16, ysize=5, title="setup", name="setup.png") ift.plot_finish(nx=3, xsize=16, ysize=5, title="setup", name="setup.png")
# number of samples used to estimate the KL # number of samples used to estimate the KL
N_samples = 20 N_samples = 20
for i in range(2): for i in range(2):
H = H.at(position) metric = H(ift.Linearization.make_var(position)).metric
samples = [H.metric.draw_sample(from_inverse=True) samples = [metric.draw_sample(from_inverse=True)
for _ in range(N_samples)] for _ in range(N_samples)]
KL = ift.SampledKullbachLeiblerDivergence(H, samples) KL = ift.SampledKullbachLeiblerDivergence(H, samples)
KL = ift.EnergyAdapter(position, KL)
KL = KL.make_invertible(ic_cg) KL = KL.make_invertible(ic_cg)
KL, convergence = minimizer(KL) KL, convergence = minimizer(KL)
position = KL.position position = KL.position
ift.plot(signal.at(position).value, title="reconstruction") ift.plot(signal(position), title="reconstruction")
ift.plot([A(position), A(MOCK_POSITION)], title="power")
ift.plot([A.at(position).value, A.at(MOCK_POSITION).value],
title="power")
ift.plot_finish(nx=2, xsize=12, ysize=6, title="loop", name="loop.png") ift.plot_finish(nx=2, xsize=12, ysize=6, title="loop", name="loop.png")
sc = ift.StatCalculator() sc = ift.StatCalculator()
for sample in samples: for sample in samples:
sc.add(signal.at(sample+position).value) sc.add(signal(sample+position))
ift.plot(sc.mean, title="mean") ift.plot(sc.mean, title="mean")
ift.plot(ift.sqrt(sc.var), title="std deviation") ift.plot(ift.sqrt(sc.var), title="std deviation")
powers = [A.at(s+position).value for s in samples] powers = [A(s+position) for s in samples]
ift.plot([A.at(position).value, A.at(MOCK_POSITION).value]+powers, ift.plot([A(position), A(MOCK_POSITION)]+powers, title="power")
title="power")
ift.plot_finish(nx=3, xsize=16, ysize=5, title="results", ift.plot_finish(nx=3, xsize=16, ysize=5, title="results",
name="results.png") name="results.png")
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Copyright(C) 2013-2018 Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
import nifty5 as ift
import numpy as np
def get_random_LOS(n_los):
starts = list(np.random.uniform(0, 1, (n_los, 2)).T)
ends = list(np.random.uniform(0, 1, (n_los, 2)).T)
return starts, ends
if __name__ == '__main__':
# FIXME description of the tutorial
np.random.seed(42)
position_space = ift.RGSpace([128, 128])
# Setting up an amplitude model
A = ift.AmplitudeModel(position_space, 16, 1, 10, -4., 1, 0., 1.)
dummy = ift.from_random('normal', A.domain)
# Building the model for a correlated signal
harmonic_space = position_space.get_default_codomain()
ht = ift.HarmonicTransformOperator(harmonic_space, position_space)
power_space = A.target[0]
power_distributor = ift.PowerDistributor(harmonic_space, power_space)
dummy = ift.Field.from_random('normal', harmonic_space)
correlated_field = lambda inp: ht(power_distributor(A(inp))*inp["xi"])
# alternatively to the block above one can do:
# correlated_field,_ = ift.make_correlated_field(position_space, A)
# apply some nonlinearity
signal = lambda inp: correlated_field(inp).positive_tanh()
# Building the Line of Sight response
LOS_starts, LOS_ends = get_random_LOS(100)
R = ift.LOSResponse(position_space, starts=LOS_starts,
ends=LOS_ends)
# build signal response model and model likelihood
signal_response = lambda inp: R(signal(inp))
# specify noise
data_space = R.target
noise = .001
N = ift.ScalingOperator(noise, data_space)
# generate mock data
domain = ift.MultiDomain.union((A.domain, ift.MultiDomain.make({'xi': harmonic_space})))
MOCK_POSITION = ift.from_random('normal', domain)
data = signal_response(MOCK_POSITION) + N.draw_sample()
# set up model likelihood
likelihood = lambda inp: ift.GaussianEnergy(mean=data, covariance=N)(signal_response(inp))
# set up minimization and inversion schemes
ic_cg = ift.GradientNormController(iteration_limit=10)
ic_sampling = ift.GradientNormController(iteration_limit=100)
ic_newton = ift.GradientNormController(name='Newton', iteration_limit=100)
minimizer = ift.RelaxedNewton(ic_newton)
# build model Hamiltonian
H = ift.Hamiltonian(likelihood, ic_sampling)
INITIAL_POSITION = ift.from_random('normal', domain)
position = INITIAL_POSITION
ift.plot(signal(MOCK_POSITION), title='ground truth')
ift.plot(R.adjoint_times(data), title='data')
ift.plot([A(MOCK_POSITION)], title='power')
ift.plot_finish(nx=3, xsize=16, ysize=5, title="setup", name="setup.png")
# number of samples used to estimate the KL
N_samples = 20
for i in range(2):
metric = H(ift.Linearization.make_var(position)).metric
samples = [metric.draw_sample(from_inverse=True)
for _ in range(N_samples)]
KL = ift.SampledKullbachLeiblerDivergence(H, samples)
KL = ift.EnergyAdapter(position, KL)
KL = KL.make_invertible(ic_cg)
KL, convergence = minimizer(KL)
position = KL.position
ift.plot(signal(position), title="reconstruction")
ift.plot([A(position), A(MOCK_POSITION)], title="power")
ift.plot_finish(nx=2, xsize=12, ysize=6, title="loop", name="loop.png")
sc = ift.StatCalculator()
for sample in samples:
sc.add(signal(sample+position))
ift.plot(sc.mean, title="mean")
ift.plot(ift.sqrt(sc.var), title="std deviation")
powers = [A(s+position) for s in samples]
ift.plot([A(position), A(MOCK_POSITION)]+powers, title="power")
ift.plot_finish(nx=3, xsize=16, ysize=5, title="results",
name="results.png")
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