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Commit 5ba0b66d authored by Martin Reinecke's avatar Martin Reinecke
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Merge branch 'NIFTy_5' into docs_lp

parents 86945e26 3755c48d
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README.md
View file @ 5ba0b66d
NIFTy - Numerical Information Field Theory
==========================================
[![build status](https://gitlab.mpcdf.mpg.de/ift/nifty-dev/badges/NIFTy_5/build.svg)](https://gitlab.mpcdf.mpg.de/ift/nifty-dev/commits/NIFTy_5)
[![coverage report](https://gitlab.mpcdf.mpg.de/ift/nifty-dev/badges/NIFTy_5/coverage.svg)](https://gitlab.mpcdf.mpg.de/ift/nifty-dev/commits/NIFTy_5)
[![build status](https://gitlab.mpcdf.mpg.de/ift/NIFTy/badges/NIFTy_5/build.svg)](https://gitlab.mpcdf.mpg.de/ift/NIFTy/commits/NIFTy_5)
[![coverage report](https://gitlab.mpcdf.mpg.de/ift/NIFTy/badges/NIFTy_5/coverage.svg)](https://gitlab.mpcdf.mpg.de/ift/NIFTy/commits/NIFTy_5)
**NIFTy** project homepage:
[http://ift.pages.mpcdf.de/NIFTy](http://ift.pages.mpcdf.de/NIFTy)
......@@ -66,14 +66,15 @@ NIFTy5 and its mandatory dependencies can be installed via:
Plotting support is added via:
pip3 install --user matplotlib
sudo apt-get install python3-matplotlib
FFTW support is added via:
NIFTy uses Numpy's FFT implementation by default. For large problems FFTW may be
used because of its higher performance. It can be installed via:
sudo apt-get install libfftw3-dev
pip3 install --user pyfftw
To actually use FFTW in your Nifty calculations, you need to call
To enable FFTW usage in NIFTy, call
nifty5.fft.enable_fftw()
......@@ -90,14 +91,13 @@ Support for spherical harmonic transforms is added via:
MPI support is added via:
sudo apt-get install openmpi-bin libopenmpi-dev
pip3 install --user mpi4py
sudo apt-get install python3-mpi4py
### Running the tests
To run the tests, additional packages are required:
sudo apt-get install python3-coverage python3-pytest python3-pytest-cov
sudo apt-get install python3-pytest-cov
Afterwards the tests (including a coverage report) can be run using the
following command in the repository root:
......
docs/source/installation.rst
View file @ 5ba0b66d
......@@ -12,7 +12,7 @@ NIFTy5 and its mandatory dependencies can be installed via::
Plotting support is added via::
pip3 install --user matplotlib
sudo apt-get install python3-matplotlib
NIFTy uses Numpy's FFT implementation by default. For large problems FFTW may be
used because of its higher performance. It can be installed via::
......@@ -37,5 +37,4 @@ Support for spherical harmonic transforms is added via::
MPI support is added via::
sudo apt-get install openmpi-bin libopenmpi-dev
pip3 install --user mpi4py
sudo apt-get install python3-mpi4py
docs/source/volume.rst
View file @ 5ba0b66d
This diff is collapsed.
nifty5/minimization/iteration_controllers.py
View file @ 5ba0b66d
......@@ -133,7 +133,7 @@ class GradientNormController(IterationController):
if self._iteration_limit is not None:
if self._itcount >= self._iteration_limit:
logger.warning(
"{} Iteration limit reached. Assuming convergence"
"{}Iteration limit reached. Assuming convergence"
.format("" if self._name is None else self._name+": "))
return self.CONVERGED
if self._ccount >= self._convergence_level:
......
nifty5/minimization/metric_gaussian_kl.py
View file @ 5ba0b66d
......@@ -15,62 +15,79 @@
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
from .energy import Energy
from ..linearization import Linearization
from .. import utilities
from ..linearization import Linearization
from ..operators.energy_operators import StandardHamiltonian
from .energy import Energy
class MetricGaussianKL(Energy):
"""Provides the sampled Kullback-Leibler divergence between a distribution
and a Metric Gaussian.
A Metric Gaussian is used to approximate some other distribution.
It is a Gaussian distribution that uses the Fisher Information Metric
of the other distribution at the location of its mean to approximate the
variance. In order to infer the mean, the a stochastic estimate of the
A Metric Gaussian is used to approximate another probability distribution.
It is a Gaussian distribution that uses the Fisher information metric of
the other distribution at the location of its mean to approximate the
variance. In order to infer the mean, a stochastic estimate of the
Kullback-Leibler divergence is minimized. This estimate is obtained by
drawing samples from the Metric Gaussian at the current mean.
During minimization these samples are kept constant, updating only the
mean. Due to the typically nonlinear structure of the true distribution
these samples have to be updated by re-initializing this class at some
point. Here standard parametrization of the true distribution is assumed.
sampling the Metric Gaussian at the current mean. During minimization
these samples are kept constant; only the mean is updated. Due to the
typically nonlinear structure of the true distribution these samples have
to be updated eventually by intantiating `MetricGaussianKL` again. For the
true probability distribution the standard parametrization is assumed.
Parameters
----------
mean : Field
The current mean of the Gaussian.
Mean of the Gaussian probability distribution.
hamiltonian : StandardHamiltonian
The StandardHamiltonian of the approximated probability distribution.
Hamiltonian of the approximated probability distribution.
n_samples : integer
The number of samples used to stochastically estimate the KL.
Number of samples used to stochastically estimate the KL.
constants : list
A list of parameter keys that are kept constant during optimization.
List of parameter keys that are kept constant during optimization.
Default is no constants.
point_estimates : list
A list of parameter keys for which no samples are drawn, but that are
optimized for, corresponding to point estimates of these.
List of parameter keys for which no samples are drawn, but that are
(possibly) optimized for, corresponding to point estimates of these.
Default is to draw samples for the complete domain.
mirror_samples : boolean
Whether the negative of the drawn samples are also used,
as they are equaly legitimate samples. If true, the number of used
as they are equally legitimate samples. If true, the number of used
samples doubles. Mirroring samples stabilizes the KL estimate as
extreme sample variation is counterbalanced. (default : False)
Notes
-----
For further details see: Metric Gaussian Variational Inference
(FIXME in preparation)
extreme sample variation is counterbalanced. Default is False.
_samples : None
Only a parameter for internal uses. Typically not to be set by users.
Note
----
The two lists `constants` and `point_estimates` are independent from each
other. It is possible to sample along domains which are kept constant
during minimization and vice versa.
See also
--------
Metric Gaussian Variational Inference (FIXME in preparation)
"""
def __init__(self, mean, hamiltonian, n_samples, constants=[],
point_estimates=None, mirror_samples=False,
point_estimates=[], mirror_samples=False,
_samples=None):
super(MetricGaussianKL, self).__init__(mean)
if not isinstance(hamiltonian, StandardHamiltonian):
raise TypeError
if hamiltonian.domain is not mean.domain:
raise ValueError
if not isinstance(n_samples, int):
raise TypeError
self._constants = list(constants)
self._point_estimates = list(point_estimates)
if not isinstance(mirror_samples, bool):
raise TypeError
self._hamiltonian = hamiltonian
self._constants = constants
if point_estimates is None:
point_estimates = constants
self._constants_samples = point_estimates
if _samples is None:
met = hamiltonian(Linearization.make_partial_var(
mean, point_estimates, True)).metric
......@@ -96,7 +113,7 @@ class MetricGaussianKL(Energy):
def at(self, position):
return MetricGaussianKL(position, self._hamiltonian, 0,
self._constants, self._constants_samples,
self._constants, self._point_estimates,
_samples=self._samples)
@property
......
nifty5/operators/energy_operators.py
View file @ 5ba0b66d
......@@ -261,7 +261,6 @@ class BernoulliEnergy(EnergyOperator):
"""
def __init__(self, d):
print(d.dtype)
if not isinstance(d, Field) or not np.issubdtype(d.dtype, np.integer):
raise TypeError
if not np.all(np.logical_or(d.local_data == 0, d.local_data == 1)):
......
nifty5/operators/regridding_operator.py
View file @ 5ba0b66d
......@@ -26,7 +26,7 @@ from .linear_operator import LinearOperator
class RegriddingOperator(LinearOperator):
"""Linearly interpolates a RGSpace to an RGSpace with coarser resolution.
"""Linearly interpolates an RGSpace to an RGSpace with coarser resolution.
Parameters
----------
......@@ -47,7 +47,6 @@ class RegriddingOperator(LinearOperator):
if not isinstance(dom, RGSpace):
raise TypeError("RGSpace required")
if len(new_shape) != len(dom.shape):
print(new_shape, dom.shape)
raise ValueError("Shape mismatch")
if any([a > b for a, b in zip(new_shape, dom.shape)]):
raise ValueError("New shape must not be larger than old shape")
......
nifty5/plot.py
View file @ 5ba0b66d
......@@ -55,6 +55,115 @@ def _mollweide_helper(xsize):
return res, mask, theta, phi
def _rgb_data(spectral_cube):
_xyz = np.array(
[[0.000160, 0.000662, 0.002362, 0.007242, 0.019110,
0.043400, 0.084736, 0.140638, 0.204492, 0.264737,
0.314679, 0.357719, 0.383734, 0.386726, 0.370702,
0.342957, 0.302273, 0.254085, 0.195618, 0.132349,
0.080507, 0.041072, 0.016172, 0.005132, 0.003816,
0.015444, 0.037465, 0.071358, 0.117749, 0.172953,
0.236491, 0.304213, 0.376772, 0.451584, 0.529826,
0.616053, 0.705224, 0.793832, 0.878655, 0.951162,
1.014160, 1.074300, 1.118520, 1.134300, 1.123990,
1.089100, 1.030480, 0.950740, 0.856297, 0.754930,
0.647467, 0.535110, 0.431567, 0.343690, 0.268329,
0.204300, 0.152568, 0.112210, 0.081261, 0.057930,
0.040851, 0.028623, 0.019941, 0.013842, 0.009577,
0.006605, 0.004553, 0.003145, 0.002175, 0.001506,
0.001045, 0.000727, 0.000508, 0.000356, 0.000251,
0.000178, 0.000126, 0.000090, 0.000065, 0.000046,
0.000033],
[0.000017, 0.000072, 0.000253, 0.000769, 0.002004,
0.004509, 0.008756, 0.014456, 0.021391, 0.029497,
0.038676, 0.049602, 0.062077, 0.074704, 0.089456,
0.106256, 0.128201, 0.152761, 0.185190, 0.219940,
0.253589, 0.297665, 0.339133, 0.395379, 0.460777,
0.531360, 0.606741, 0.685660, 0.761757, 0.823330,
0.875211, 0.923810, 0.961988, 0.982200, 0.991761,
0.999110, 0.997340, 0.982380, 0.955552, 0.915175,
0.868934, 0.825623, 0.777405, 0.720353, 0.658341,
0.593878, 0.527963, 0.461834, 0.398057, 0.339554,
0.283493, 0.228254, 0.179828, 0.140211, 0.107633,
0.081187, 0.060281, 0.044096, 0.031800, 0.022602,
0.015905, 0.011130, 0.007749, 0.005375, 0.003718,
0.002565, 0.001768, 0.001222, 0.000846, 0.000586,
0.000407, 0.000284, 0.000199, 0.000140, 0.000098,
0.000070, 0.000050, 0.000036, 0.000025, 0.000018,
0.000013],
[0.000705, 0.002928, 0.010482, 0.032344, 0.086011,
0.197120, 0.389366, 0.656760, 0.972542, 1.282500,
1.553480, 1.798500, 1.967280, 2.027300, 1.994800,
1.900700, 1.745370, 1.554900, 1.317560, 1.030200,
0.772125, 0.570060, 0.415254, 0.302356, 0.218502,
0.159249, 0.112044, 0.082248, 0.060709, 0.043050,
0.030451, 0.020584, 0.013676, 0.007918, 0.003988,
0.001091, 0.000000, 0.000000, 0.000000, 0.000000,
0.000000, 0.000000, 0.000000, 0.000000, 0.000000,
0.000000, 0.000000, 0.000000, 0.000000, 0.000000,
0.000000, 0.000000, 0.000000, 0.000000, 0.000000,
0.000000, 0.000000, 0.000000, 0.000000, 0.000000,
0.000000, 0.000000, 0.000000, 0.000000, 0.000000,
0.000000, 0.000000, 0.000000, 0.000000, 0.000000,
0.000000, 0.000000, 0.000000, 0.000000, 0.000000,
0.000000, 0.000000, 0.000000, 0.000000, 0.000000,
0.000000]])
MATRIX_SRGB_D65 = np.array(
[[3.2404542, -1.5371385, -0.4985314],
[-0.9692660, 1.8760108, 0.0415560],
[0.0556434, -0.2040259, 1.0572252]])
def _gammacorr(inp):
mask = np.zeros(inp.shape, dtype=np.float64)
mask[inp <= 0.0031308] = 1.
r1 = 12.92*inp
a = 0.055
r2 = (1 + a) * (np.maximum(inp, 0.0031308) ** (1/2.4)) - a
return r1*mask + r2*(1.-mask)
def lambda2xyz(lam):
lammin = 380.
lammax = 780.
lam = np.asarray(lam, dtype=np.float64)
lam = np.clip(lam, lammin, lammax)
idx = (lam-lammin)/(lammax-lammin)*(_xyz.shape[1]-1)
ii = np.maximum(0, np.minimum(79, int(idx)))
w1 = 1.-(idx-ii)
w2 = 1.-w1
c = w1*_xyz[:, ii] + w2*_xyz[:, ii+1]
return c
def getxyz(n):
E0, E1 = 1./700., 1./400.
E = E0 + np.arange(n)*(E1-E0)/(n-1)
res = np.zeros((3, n), dtype=np.float64)
for i in range(n):
res[:, i] = lambda2xyz(1./E[i])
return res
def to_logscale(arr, lo, hi):
res = arr.clip(lo, hi)
res = np.log(res/hi)
tmp = np.log(hi/lo)
res += tmp
res /= tmp
return res
spectral_cube = spectral_cube.reshape((-1, spectral_cube.shape[-1]))
xyz = getxyz(spectral_cube.shape[-1])
xyz_data = np.tensordot(spectral_cube, xyz, axes=[-1, -1])
xyz_data /= xyz_data.max()
xyz_data = to_logscale(xyz_data, max(1e-3, xyz_data.min()), 1.)
rgb_data = xyz_data.copy()
it = np.nditer(xyz_data[:, 0], flags=['multi_index'])
for x in range(xyz_data.shape[0]):
rgb_data[x] = _gammacorr(np.matmul(MATRIX_SRGB_D65, xyz_data[x]))
rgb_data = rgb_data.clip(0., 1.)
return rgb_data.reshape(spectral_cube.shape[:-1]+(-1,))
def _find_closest(A, target):
# A must be sorted
idx = np.clip(A.searchsorted(target), 1, len(A)-1)
......@@ -229,8 +338,16 @@ def _plot2D(f, ax, **kwargs):
dom = f.domain
if len(dom) > 1:
raise ValueError("DomainTuple must have exactly one entry.")
if len(dom) > 2:
raise ValueError("DomainTuple can have at most two entries.")
# check for multifrequency plotting
have_rgb = False
if len(dom) == 2:
if (not isinstance(dom[1], RGSpace)) or len(dom[1].shape) != 1:
raise TypeError("need 1D RGSpace as second domain")
rgb = _rgb_data(f.to_global_data())
have_rgb = True
label = kwargs.pop("label", None)
......@@ -243,39 +360,58 @@ def _plot2D(f, ax, **kwargs):
ax.set_xlabel(kwargs.pop("xlabel", ""))
ax.set_ylabel(kwargs.pop("ylabel", ""))
dom = dom[0]
cmap = kwargs.pop("colormap", plt.rcParams['image.cmap'])
if not have_rgb:
cmap = kwargs.pop("colormap", plt.rcParams['image.cmap'])
if isinstance(dom, RGSpace):
nx, ny = dom.shape
dx, dy = dom.distances
im = ax.imshow(
f.to_global_data().T, extent=[0, nx*dx, 0, ny*dy],
vmin=kwargs.get("zmin"), vmax=kwargs.get("zmax"),
cmap=cmap, origin="lower", **norm, **aspect)
plt.colorbar(im)
if have_rgb:
im = ax.imshow(
rgb, extent=[0, nx*dx, 0, ny*dy], origin="lower", **norm,
**aspect)
else:
im = ax.imshow(
f.to_global_data().T, extent=[0, nx*dx, 0, ny*dy],
vmin=kwargs.get("zmin"), vmax=kwargs.get("zmax"),
cmap=cmap, origin="lower", **norm, **aspect)
plt.colorbar(im)
_limit_xy(**kwargs)
return
elif isinstance(dom, (HPSpace, GLSpace)):
import pyHealpix
xsize = 800
res, mask, theta, phi = _mollweide_helper(xsize)
if have_rgb:
res = np.full(shape=res.shape+(3,), fill_value=1.,
dtype=np.float64)
if isinstance(dom, HPSpace):
ptg = np.empty((phi.size, 2), dtype=np.float64)
ptg[:, 0] = theta
ptg[:, 1] = phi
base = pyHealpix.Healpix_Base(int(np.sqrt(dom.size//12)), "RING")
res[mask] = f.to_global_data()[base.ang2pix(ptg)]
if have_rgb:
res[mask] = rgb[base.ang2pix(ptg)]
else:
res[mask] = f.to_global_data()[base.ang2pix(ptg)]
else:
ra = np.linspace(0, 2*np.pi, dom.nlon+1)
dec = pyHealpix.GL_thetas(dom.nlat)
ilat = _find_closest(dec, theta)
ilon = _find_closest(ra, phi)
ilon = np.where(ilon == dom.nlon, 0, ilon)
res[mask] = f.to_global_data()[ilat*dom.nlon + ilon]
if have_rgb:
res[mask] = rgb[ilat*dom[0].nlon + ilon]
else:
res[mask] = f.to_global_data()[ilat*dom.nlon + ilon]
plt.axis('off')
plt.imshow(res, vmin=kwargs.get("zmin"), vmax=kwargs.get("zmax"),
cmap=cmap, origin="lower")
plt.colorbar(orientation="horizontal")
if have_rgb:
plt.imshow(res, origin="lower")
else:
plt.imshow(res, vmin=kwargs.get("zmin"), vmax=kwargs.get("zmax"),
cmap=cmap, origin="lower")
plt.colorbar(orientation="horizontal")
return
raise ValueError("Field type not(yet) supported")
......
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