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Commit 0a688d2b authored by Martin Reinecke's avatar Martin Reinecke
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extensive cleanups

parent d0c9a8ab
Pipeline #21555 passed with stage
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Showing with 173 additions and 153 deletions
demos/critical_filtering.py
View file @ 0a688d2b
......@@ -106,7 +106,9 @@ if __name__ == "__main__":
def ps0(k):
return (1./(1.+k)**2)
t0 = ift.Field(p_space, val=np.log(1./(1+p_space.k_lengths)**2))
t0 = ift.Field(p_space,
val=ift.dobj.from_global_data(np.log(1./(1+p_space.k_lengths)**2)))
for i in range(500):
S0 = ift.create_power_operator(h_space, power_spectrum=ps0)
......@@ -138,6 +140,6 @@ if __name__ == "__main__":
t0 = power_energy.position.real
# Plot current estimate
print(i)
ift.dobj.mprint(i)
if i % 5 == 0:
plot_parameters(m0, t0, ift.log(sp), data_power)
demos/log_normal_wiener_filter.py
View file @ 0a688d2b
......@@ -3,35 +3,38 @@ import numpy as np
if __name__ == "__main__":
np.random.seed(42)
# Setting up parameters |\label{code:wf_parameters}|
# Setting up parameters
correlation_length = 1. # Typical distance over which the field is correlated
field_variance = 2. # Variance of field in position space
response_sigma = 0.02 # Smoothing length of response (in same unit as L)
signal_to_noise = 100 # The signal to noise ratio
np.random.seed(43) # Fixing the random seed
def power_spectrum(k): # Defining the power spectrum
a = 4 * correlation_length * field_variance**2
return a / (1 + k * correlation_length) ** 4
# Setting up the geometry |\label{code:wf_geometry}|
L = 2. # Total side-length of the domain
N_pixels = 128 # Grid resolution (pixels per axis)
#signal_space = ift.RGSpace([N_pixels, N_pixels], distances=L/N_pixels)
# Setting up the geometry
L = 2. # Total side-length of the domain
N_pixels = 128 # Grid resolution (pixels per axis)
# signal_space = ift.RGSpace([N_pixels, N_pixels], distances=L/N_pixels)
signal_space = ift.HPSpace(16)
harmonic_space = signal_space.get_default_codomain()
fft = ift.FFTOperator(harmonic_space, target=signal_space)
power_space = ift.PowerSpace(harmonic_space)
# Creating the mock signal |\label{code:wf_mock_signal}|
S = ift.create_power_operator(harmonic_space, power_spectrum=power_spectrum)
# Creating the mock signal
S = ift.create_power_operator(harmonic_space,
power_spectrum=power_spectrum)
mock_power = ift.PS_field(power_space, power_spectrum)
mock_signal = fft(ift.power_synthesize(mock_power, real_signal=True))
# Setting up an exemplary response
mask = ift.Field.ones(signal_space)
N10 = int(N_pixels/10)
#mask.val[N10*5:N10*9, N10*5:N10*9] = 0.
R = ift.ResponseOperator(signal_space, sigma=(response_sigma,), exposure=(mask,)) #|\label{code:wf_response}|
# mask.val[N10*5:N10*9, N10*5:N10*9] = 0.
R = ift.ResponseOperator(signal_space, sigma=(response_sigma,),
exposure=(mask,))
data_domain = R.target[0]
R_harmonic = ift.ComposedOperator([fft, R])
......@@ -39,40 +42,52 @@ if __name__ == "__main__":
ndiag = ift.Field.full(data_domain, mock_signal.var()/signal_to_noise)
N = ift.DiagonalOperator(ndiag.weight(1))
noise = ift.Field.from_random(domain=data_domain, random_type='normal',
std=mock_signal.std()/np.sqrt(signal_to_noise), mean=0)
data = R(ift.exp(mock_signal)) + noise #|\label{code:wf_mock_data}|
std=mock_signal.std()/np.sqrt(signal_to_noise), mean=0)
data = R(ift.exp(mock_signal)) + noise
# Wiener filter
m0 = ift.Field.zeros(harmonic_space)
ctrl = ift.GradientNormController(verbose=False,tol_abs_gradnorm=1)
ctrl2 = ift.GradientNormController(verbose=True,tol_abs_gradnorm=0.1, name="outer")
ctrl = ift.GradientNormController(verbose=False, tol_abs_gradnorm=1)
ctrl2 = ift.GradientNormController(verbose=True, tol_abs_gradnorm=0.1,
name="outer")
inverter = ift.ConjugateGradient(controller=ctrl)
energy = ift.library.LogNormalWienerFilterEnergy(m0, data, R_harmonic, N, S, inverter=inverter)
minimizer1 = ift.VL_BFGS(controller=ctrl2,max_history_length=20)
energy = ift.library.LogNormalWienerFilterEnergy(m0, data, R_harmonic,
N, S, inverter=inverter)
# minimizer1 = ift.VL_BFGS(controller=ctrl2, max_history_length=20)
minimizer2 = ift.RelaxedNewton(controller=ctrl2)
minimizer3 = ift.SteepestDescent(controller=ctrl2)
# minimizer3 = ift.SteepestDescent(controller=ctrl2)
#me1 = minimizer1(energy)
# me1 = minimizer1(energy)
me2 = minimizer2(energy)
#me3 = minimizer3(energy)
# me3 = minimizer3(energy)
#m1 = fft(me1[0].position)
# m1 = fft(me1[0].position)
m2 = fft(me2[0].position)
#m3 = fft(me3[0].position)
# m3 = fft(me3[0].position)
#Plotting #|\label{code:wf_plotting}|
ift.plotting.plot(mock_signal.real,name='mock_signal.pdf', colormap="plasma",xlabel="Pixel Index",ylabel="Pixel Index")
ift.plotting.plot(ift.Field(signal_space, val=np.log(data.val.real).reshape(signal_space.shape)),name="log_of_data.pdf", colormap="plasma",xlabel="Pixel Index",ylabel="Pixel Index")
#ift.plotting.plot(m1.real,name='m_LBFGS.pdf', colormap="plasma",xlabel="Pixel Index",ylabel="Pixel Index")
ift.plotting.plot(m2.real,name='m_Newton.pdf', colormap="plasma",xlabel="Pixel Index",ylabel="Pixel Index")
#ift.plotting.plot(m3.real,name='m_SteepestDescent.pdf', colormap="plasma",xlabel="Pixel Index",ylabel="Pixel Index")
# Plotting
ift.plotting.plot(mock_signal.real, name='mock_signal.pdf',
colormap="plasma", xlabel="Pixel Index",
ylabel="Pixel Index")
logdata = np.log(ift.dobj.to_global_data(data.val.real)).reshape(signal_space.shape)
ift.plotting.plot(ift.Field(signal_space,
val=ift.dobj.from_global_data(logdata)),
name="log_of_data.pdf", colormap="plasma",
xlabel="Pixel Index", ylabel="Pixel Index")
# ift.plotting.plot(m1.real,name='m_LBFGS.pdf', colormap="plasma",
# xlabel="Pixel Index", ylabel="Pixel Index")
ift.plotting.plot(m2.real, name='m_Newton.pdf', colormap="plasma",
xlabel="Pixel Index", ylabel="Pixel Index")
# ift.plotting.plot(m3.real, name='m_SteepestDescent.pdf',
# colormap="plasma", xlabel="Pixel Index",
# ylabel="Pixel Index")
# Probing the variance
class Proby(ift.DiagonalProberMixin, ift.Prober): pass
class Proby(ift.DiagonalProberMixin, ift.Prober):
pass
proby = Proby(signal_space, probe_count=1)
proby(lambda z: fft(me2[0].curvature.inverse_times(fft.adjoint_times(z))))
sm = ift.FFTSmoothingOperator(signal_space, sigma=0.02)
variance = sm(proby.diagonal.weight(-1))
ift.plotting.plot(variance, name = 'variance.pdf')
ift.plotting.plot(variance, name='variance.pdf')
demos/paper_demos/cartesian_wiener_filter.py
View file @ 0a688d2b
......@@ -2,82 +2,82 @@ import numpy as np
import nifty2go as ift
if __name__ == "__main__":
signal_to_noise = 1.5 # The signal to noise ratio
signal_to_noise = 1.5 # The signal to noise ratio
# Setting up parameters |\label{code:wf_parameters}|
correlation_length_1 = 1. # Typical distance over which the field is correlated
field_variance_1 = 2. # Variance of field in position space
# Setting up parameters
correlation_length_1 = 1. # Typical distance over which the field is correlated
field_variance_1 = 2. # Variance of field in position space
response_sigma_1 = 0.05 # Smoothing length of response (in same unit as L)
response_sigma_1 = 0.05 # Smoothing length of response (in same unit as L)
def power_spectrum_1(k): # note: field_variance**2 = a*k_0/4.
def power_spectrum_1(k): # note: field_variance**2 = a*k_0/4.
a = 4 * correlation_length_1 * field_variance_1**2
return a / (1 + k * correlation_length_1) ** 4.
# Setting up the geometry |\label{code:wf_geometry}|
L_1 = 2. # Total side-length of the domain
N_pixels_1 = 512 # Grid resolution (pixels per axis)
# Setting up the geometry
L_1 = 2. # Total side-length of the domain
N_pixels_1 = 512 # Grid resolution (pixels per axis)
signal_space_1 = ift.RGSpace([N_pixels_1], distances=L_1/N_pixels_1)
harmonic_space_1 = signal_space_1.get_default_codomain()
# Setting up the geometry |\label{code:wf_geometry}|
L_2 = 2. # Total side-length of the domain
N_pixels_2 = 512 # Grid resolution (pixels per axis)
# Setting up the geometry
L_2 = 2. # Total side-length of the domain
N_pixels_2 = 512 # Grid resolution (pixels per axis)
signal_space_2 = ift.RGSpace([N_pixels_2], distances=L_2/N_pixels_2)
harmonic_space_2 = signal_space_2.get_default_codomain()
signal_domain = ift.DomainTuple.make((signal_space_1, signal_space_2))
mid_domain = ift.DomainTuple.make((signal_space_1, harmonic_space_2))
harmonic_domain = ift.DomainTuple.make((harmonic_space_1, harmonic_space_2))
harmonic_domain = ift.DomainTuple.make((harmonic_space_1,
harmonic_space_2))
fft_1 = ift.FFTOperator(harmonic_domain, space=0)
power_space_1 = ift.PowerSpace(harmonic_space_1)
mock_power_1 = ift.Field(power_space_1, val=power_spectrum_1(power_space_1.k_lengths))
mock_power_1 = ift.PS_field(power_space_1, power_spectrum_1)
# Setting up parameters
correlation_length_2 = 1. # Typical distance over which the field is correlated
field_variance_2 = 2. # Variance of field in position space
response_sigma_2 = 0.01 # Smoothing length of response (in same unit as L)
# Setting up parameters |\label{code:wf_parameters}|
correlation_length_2 = 1. # Typical distance over which the field is correlated
field_variance_2 = 2. # Variance of field in position space
response_sigma_2 = 0.01 # Smoothing length of response (in same unit as L)
def power_spectrum_2(k): # note: field_variance**2 = a*k_0/4.
def power_spectrum_2(k): # note: field_variance**2 = a*k_0/4.
a = 4 * correlation_length_2 * field_variance_2**2
return a / (1 + k * correlation_length_2) ** 2.5
fft_2 = ift.FFTOperator(mid_domain, space=1)
power_space_2 = ift.PowerSpace(harmonic_space_2)
mock_power_2 = ift.Field(power_space_2, val=power_spectrum_2(power_space_2.k_lengths))
mock_power_2 = ift.PS_field(power_space_2, power_spectrum_2)
fft = ift.ComposedOperator((fft_1, fft_2))
mock_power = ift.Field(domain=(power_space_1, power_space_2),
val=np.outer(mock_power_1.val, mock_power_2.val))
val=ift.dobj.from_global_data(np.outer(ift.dobj.to_global_data(mock_power_1.val), ift.dobj.to_global_data(mock_power_2.val))))
diagonal = ift.power_synthesize_special(mock_power, spaces=(0, 1))**2
diagonal = diagonal.real
S = ift.DiagonalOperator(diagonal)
np.random.seed(10)
mock_signal = fft(ift.power_synthesize(mock_power, real_signal=True))
# Setting up a exemplary response
N1_10 = int(N_pixels_1/10)
mask_1 = ift.Field.ones(signal_space_1)
mask_1.val[N1_10*7:N1_10*9] = 0.
mask_1 = np.ones(signal_space_1.shape)
mask_1[N1_10*7:N1_10*9] = 0.
mask_1 = ift.Field(signal_space_1, ift.dobj.from_global_data(mask_1))
N2_10 = int(N_pixels_2/10)
mask_2 = ift.Field.ones(signal_space_2)
mask_2.val[N2_10*7:N2_10*9] = 0.
mask_2 = np.ones(signal_space_2.shape)
mask_2[N2_10*7:N2_10*9] = 0.
mask_2 = ift.Field(signal_space_2, ift.dobj.from_global_data(mask_2))
R = ift.ResponseOperator(signal_domain,spaces=(0,1),
R = ift.ResponseOperator(signal_domain, spaces=(0, 1),
sigma=(response_sigma_1, response_sigma_2),
exposure=(mask_1, mask_2)) #|\label{code:wf_response}|
exposure=(mask_1, mask_2))
data_domain = R.target
R_harmonic = ift.ComposedOperator([fft, R])
......@@ -87,21 +87,23 @@ if __name__ == "__main__":
noise = ift.Field.from_random(domain=data_domain, random_type='normal',
std=mock_signal.std()/np.sqrt(signal_to_noise),
mean=0)
data = R(mock_signal) + noise #|\label{code:wf_mock_data}|
data = R(mock_signal) + noise
# Wiener filter
j = R_harmonic.adjoint_times(N.inverse_times(data))
ctrl = ift.GradientNormController(verbose=True, tol_abs_gradnorm=0.1)
inverter = ift.ConjugateGradient(controller=ctrl)
wiener_curvature = ift.library.WienerFilterCurvature(S=S, N=N, R=R_harmonic)
wiener_curvature = ift.library.WienerFilterCurvature(S=S, N=N,
R=R_harmonic)
wiener_curvature = ift.InversionEnabler(wiener_curvature, inverter)
m_k = wiener_curvature.inverse_times(j) #|\label{code:wf_wiener_filter}|
m_k = wiener_curvature.inverse_times(j)
m = fft(m_k)
# Probing the variance
class Proby(ift.DiagonalProberMixin, ift.Prober): pass
proby = Proby((signal_space_1, signal_space_2), probe_count=1,ncpu=1)
class Proby(ift.DiagonalProberMixin, ift.Prober):
pass
proby = Proby((signal_space_1, signal_space_2), probe_count=1, ncpu=1)
proby(lambda z: fft(wiener_curvature.inverse_times(fft.inverse_times(z))))
# sm = SmoothingOperator(signal_space, sigma=0.02)
# variance = sm(proby.diagonal.weight(-1))
......
demos/paper_demos/wiener_filter.py
View file @ 0a688d2b
......@@ -3,34 +3,38 @@ import numpy as np
if __name__ == "__main__":
# Setting up parameters |\label{code:wf_parameters}|
# Setting up parameters
correlation_length_scale = 1. # Typical distance over which the field is correlated
fluctuation_scale = 2. # Variance of field in position space
response_sigma = 0.05 # Smoothing length of response (in same unit as L)
signal_to_noise = 1.5 # The signal to noise ratio
np.random.seed(43) # Fixing the random seed
def power_spectrum(k): # Defining the power spectrum
a = 4 * correlation_length_scale * fluctuation_scale**2
return a / (1 + (k * correlation_length_scale)**2) ** 2
# Setting up the geometry |\label{code:wf_geometry}|
# Setting up the geometry
L = 2. # Total side-length of the domain
N_pixels = 512 # Grid resolution (pixels per axis)
signal_space = ift.RGSpace([N_pixels, N_pixels], distances=L/N_pixels)
harmonic_space = signal_space.get_default_codomain()
fft = ift.FFTOperator(harmonic_space, target=signal_space)
power_space = ift.PowerSpace(harmonic_space,binbounds=ift.PowerSpace.useful_binbounds(harmonic_space,logarithmic=True))
power_space = ift.PowerSpace(harmonic_space, binbounds=ift.PowerSpace.useful_binbounds(harmonic_space,logarithmic=True))
# Creating the mock signal |\label{code:wf_mock_signal}|
S = ift.create_power_operator(harmonic_space, power_spectrum=power_spectrum)
# Creating the mock signal
S = ift.create_power_operator(harmonic_space,
power_spectrum=power_spectrum)
mock_power = ift.PS_field(power_space, power_spectrum)
mock_signal = fft(ift.power_synthesize(mock_power, real_signal=True))
# Setting up an exemplary response
mask = ift.Field.ones(signal_space)
mask = np.ones(signal_space.shape)
N10 = int(N_pixels/10)
mask.val[N10*5:N10*9, N10*5:N10*9] = 0.
R = ift.ResponseOperator(signal_space, sigma=(response_sigma,), exposure=(mask,)) #|\label{code:wf_response}|
mask[N10*5:N10*9, N10*5:N10*9] = 0.
mask = ift.Field(signal_space, ift.dobj.from_global_data(mask))
R = ift.ResponseOperator(signal_space, sigma=(response_sigma,),
exposure=(mask,))
data_domain = R.target[0]
R_harmonic = ift.ComposedOperator([fft, R])
......@@ -39,28 +43,29 @@ if __name__ == "__main__":
N = ift.DiagonalOperator(ndiag.weight(1))
noise = ift.Field.from_random(domain=data_domain, random_type='normal',
std=mock_signal.std()/np.sqrt(signal_to_noise), mean=0)
data = R(mock_signal) + noise #|\label{code:wf_mock_data}|
data = R(mock_signal) + noise
# Wiener filter
j = R_harmonic.adjoint_times(N.inverse_times(data))
ctrl = ift.GradientNormController(verbose=True,tol_abs_gradnorm=0.1)
ctrl = ift.GradientNormController(verbose=True, tol_abs_gradnorm=0.1)
inverter = ift.ConjugateGradient(controller=ctrl)
wiener_curvature = ift.library.WienerFilterCurvature(S=S, N=N, R=R_harmonic)
wiener_curvature =ift.InversionEnabler(wiener_curvature, inverter)
m_k = wiener_curvature.inverse_times(j) #|\label{code:wf_wiener_filter}|
wiener_curvature = ift.library.WienerFilterCurvature(S=S, N=N,
R=R_harmonic)
wiener_curvature = ift.InversionEnabler(wiener_curvature, inverter)
m_k = wiener_curvature.inverse_times(j)
m = fft(m_k)
# Probing the uncertainty |\label{code:wf_uncertainty_probing}|
class Proby(ift.DiagonalProberMixin, ift.Prober): pass
proby = Proby(signal_space, probe_count=1,ncpu=1)
proby(lambda z: fft(wiener_curvature.inverse_times(fft.inverse_times(z)))) #|\label{code:wf_variance_fft_wrap}|
# Probing the uncertainty
class Proby(ift.DiagonalProberMixin, ift.Prober):
pass
proby = Proby(signal_space, probe_count=1, ncpu=1)
proby(lambda z: fft(wiener_curvature.inverse_times(fft.inverse_times(z))))
sm = ift.FFTSmoothingOperator(signal_space, sigma=0.03)
variance = ift.sqrt(sm(proby.diagonal.weight(-1))) #|\label{code:wf_variance_weighting}|
variance = ift.sqrt(sm(proby.diagonal.weight(-1)))
# Plotting #|\label{code:wf_plotting}|
# Plotting
ift.plotting.plot(variance,name="uncertainty.pdf",xlabel='Pixel index', ylabel='Pixel index')
ift.plotting.plot(mock_signal,name="mock_signal.pdf",xlabel='Pixel index', ylabel='Pixel index')
ift.plotting.plot(ift.Field(signal_space, val=data.val),name="data.pdf",xlabel='Pixel index', ylabel='Pixel index')
ift.plotting.plot(m,name="map.pdf",xlabel='Pixel index', ylabel='Pixel index')
demos/probing.py
View file @ 0a688d2b
from __future__ import print_function
import nifty2go as ift
import numpy as np
......@@ -20,9 +19,9 @@ diagOp = ift.DiagonalOperator(f)
diagProber = DiagonalProber(domain=x)
diagProber(diagOp)
print((f - diagProber.diagonal).norm())
ift.dobj.mprint((f - diagProber.diagonal).norm())
multiProber = MultiProber(domain=x)
multiProber(diagOp)
print((f - multiProber.diagonal).norm())
print(f.sum() - multiProber.trace)
ift.dobj.mprint((f - multiProber.diagonal).norm())
ift.dobj.mprint(f.sum() - multiProber.trace)
demos/wiener_filter_via_curvature.py
View file @ 0a688d2b
......@@ -3,7 +3,8 @@ import nifty2go as ift
import numericalunits as nu
if __name__ == "__main__":
nu.reset_units("SI")
# In MPI mode, the random seed for numericalunits must be set by hand
nu.reset_units(43)
dimensionality = 2
np.random.seed(43)
......@@ -44,8 +45,7 @@ if __name__ == "__main__":
power_spectrum=power_spectrum)
np.random.seed(43)
mock_power = ift.Field(power_space,
val=ift.dobj.from_global_data(power_spectrum(power_space.k_lengths)))
mock_power = ift.PS_field(power_space, power_spectrum)
mock_harmonic = ift.power_synthesize(mock_power, real_signal=True)
mock_harmonic = mock_harmonic.real
mock_signal = fft(mock_harmonic)
......@@ -81,7 +81,7 @@ if __name__ == "__main__":
ift.plotting.plot(ift.Field(sspace2, mock_signal.real.val)/nu.K,
name="mock_signal.pdf")
ift.plotting.plot(ift.Field(
sspace2, val=ift.dobj.from_global_data(ift.dobj.to_global_data(data.val.real).reshape(signal_space.shape)))/nu.K,
name="data.pdf")
data = ift.dobj.to_global_data(data.val.real).reshape(sspace2.shape)/nu.K
data = ift.Field(sspace2, val=ift.dobj.from_global_data(data))/nu.K
ift.plotting.plot(ift.Field(sspace2, val=data), name="data.pdf")
ift.plotting.plot(ift.Field(sspace2, m_s.real.val)/nu.K, name="map.pdf")
demos/wiener_filter_via_hamiltonian.py
View file @ 0a688d2b
......@@ -50,7 +50,7 @@ if __name__ == "__main__":
S = ift.create_power_operator(h_space, power_spectrum=p_spec)
# Drawing a sample sh from the prior distribution in harmonic space
sp = ift.Field(p_space, ift.dobj.from_global_data(p_spec(p_space.k_lengths)))
sp = ift.PS_field(p_space, p_spec)
sh = ift.power_synthesize(sp, real_signal=True)
ss = fft.adjoint_times(sh)
......@@ -58,7 +58,7 @@ if __name__ == "__main__":
# Instrument = ift.FFTSmoothingOperator(s_space, sigma=0.05)
diag = np.ones(s_space.shape)
diag[20:80, 20:80] = 0
diag = ift.Field(s_space,ift.dobj.from_global_data(diag))
diag = ift.Field(s_space, ift.dobj.from_global_data(diag))
Instrument = ift.DiagonalOperator(diag)
# Adding a harmonic transformation to the instrument
......
nifty/basic_arithmetics.py
View file @ 0a688d2b
......@@ -17,7 +17,6 @@
# and financially supported by the Studienstiftung des deutschen Volkes.
from __future__ import division
import numpy as np
from .field import Field
from . import dobj
......@@ -29,7 +28,7 @@ def _math_helper(x, function, out):
if not isinstance(x, Field):
raise TypeError("This function only accepts Field objects.")
if out is not None:
if not isinstance(out, Field) or x.domain!=out.domain:
if not isinstance(out, Field) or x.domain != out.domain:
raise ValueError("Bad 'out' argument")
function(x.val, out=out.val)
return out
......
nifty/data_objects/distributed_do.py
View file @ 0a688d2b
from __future__ import print_function
import numpy as np
from .random import Random
from mpi4py import MPI
__all__ = ["ntask", "rank", "master", "local_shape", "data_object", "full",
"empty", "zeros", "ones", "empty_like", "vdot", "abs", "exp",
"log", "sqrt", "from_object", "from_random",
"local_data", "ibegin", "np_allreduce_sum", "distaxis",
"from_local_data", "from_global_data", "to_global_data",
"redistribute", "default_distaxis"]
_comm = MPI.COMM_WORLD
ntask = _comm.Get_size()
rank = _comm.Get_rank()
master = (rank == 0)
def mprint(*args):
if master:
print(*args)
def _shareSize(nwork, nshares, myshare):
return (nwork//nshares) + int(myshare < nwork % nshares)
......
nifty/data_objects/numpy_do.py
View file @ 0a688d2b
# Data object module for NIFTy that uses simple numpy ndarrays.
from __future__ import print_function
import numpy as np
from numpy import ndarray as data_object
from numpy import full, empty, empty_like, sqrt, ones, zeros, vdot, abs, \
exp, log
from .random import Random
__all__ = ["ntask", "rank", "master", "local_shape", "data_object", "full",
"empty", "zeros", "ones", "empty_like", "vdot", "abs", "exp",
"log", "sqrt", "from_object", "from_random",
"local_data", "ibegin", "np_allreduce_sum", "distaxis",
"from_local_data", "from_global_data", "to_global_data",
"redistribute", "default_distaxis"]
ntask = 1
rank = 0
master = True
def mprint(*args):
print(*args)
def from_object(object, dtype=None, copy=True):
return np.array(object, dtype=dtype, copy=copy)
......
nifty/dobj.py
View file @ 0a688d2b
#from __future__ import print_function
try:
from mpi4py import MPI
if MPI.COMM_WORLD.Get_size()==1:
#print ("MPI found, but only with one task, using numpy_do...")
if MPI.COMM_WORLD.Get_size() == 1:
from .data_objects.numpy_do import *
# mprint("MPI found, but only with one task, using numpy_do...")
else:
#if MPI.COMM_WORLD.Get_rank() == 0:
# print ("MPI with multiple tasks found, using distributed_do...")
from .data_objects.distributed_do import *
# mprint("MPI with multiple tasks found, using distributed_do...")
except ImportError:
#print ("MPI not found, using numpy_do...")
from .data_objects.numpy_do import *
# mprint("MPI not found, using numpy_do...")
__all__ = ["ntask", "rank", "master", "local_shape", "data_object", "full",
"empty", "zeros", "ones", "empty_like", "vdot", "abs", "exp",
"log", "sqrt", "from_object", "from_random",
"local_data", "ibegin", "np_allreduce_sum", "distaxis",
"from_local_data", "from_global_data", "to_global_data",
"redistribute", "default_distaxis", "mprint"]
nifty/domain_tuple.py
View file @ 0a688d2b
......@@ -19,6 +19,7 @@
from functools import reduce
from .domain_object import DomainObject
class DomainTuple(object):
_tupleCache = {}
......@@ -122,7 +123,6 @@ class DomainTuple(object):
of pixels in the requested space in res[1], and the remaining pixels in
res[2].
"""
dims = (dom.dim for dom in self._dom)
return (self._accdims[ispace],
self._accdims[ispace+1]//self._accdims[ispace],
self._accdims[-1]//self._accdims[ispace+1])
nifty/energies/line_energy.py
View file @ 0a688d2b
......@@ -16,8 +16,6 @@
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from __future__ import print_function
class LineEnergy(object):
""" Evaluates an underlying Energy along a certain line direction.
......@@ -114,6 +112,7 @@ class LineEnergy(object):
def directional_derivative(self):
res = self.energy.gradient.vdot(self.line_direction)
if abs(res.imag) / max(abs(res.real), 1.) > 1e-12:
print("directional derivative has non-negligible "
"imaginary part:", res)
from ..dobj import mprint
mprint("directional derivative has non-negligible "
"imaginary part:", res)
return res.real
nifty/field.py
View file @ 0a688d2b
......@@ -16,7 +16,7 @@
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from __future__ import division, print_function
from __future__ import division
from builtins import range
import numpy as np
from .