Merge branch 'NIFTy_5' into more_tests

Dockerfile

 FROM debian:testing-slim
 
 RUN apt-get update && apt-get install -y \
-    # Needed for gitlab tests
-    git \
+    # Needed for setup
+    git python3-pip \
     # Packages needed for NIFTy
-    libfftw3-dev \
-    python3 python3-pip python3-dev python3-scipy \
+    python3-scipy \
     # Documentation build dependencies
-    python3-sphinx python3-sphinx-rtd-theme \
+    python3-sphinx-rtd-theme \
     # Testing dependencies
-    python3-coverage python3-pytest python3-pytest-cov \
+    python3-pytest-cov jupyter \
     # Optional NIFTy dependencies
-    openmpi-bin libopenmpi-dev python3-mpi4py \
-    # Packages needed for NIFTy
+    libfftw3-dev python3-mpi4py python3-matplotlib \
+  # more optional NIFTy dependencies
   && pip3 install pyfftw \
-  # Optional NIFTy dependencies
   && pip3 install git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git \
-  # Testing dependencies
-  && rm -rf /var/lib/apt/lists/*
-
-# Needed for demos to be running
-RUN apt-get update && apt-get install -y python3-matplotlib \
-  && python3 -m pip install --upgrade pip && python3 -m pip install jupyter \
+  && pip3 install jupyter \
   && rm -rf /var/lib/apt/lists/*
 
 # Set matplotlib backend

docs/source/conf.py

@@ -29,4 +29,4 @@ add_module_names = False
 html_theme = "sphinx_rtd_theme"
 html_logo = 'nifty_logo_black.png'
 
-exclude_patterns = ['mod/modules.rst']
+exclude_patterns = ['mod/modules.rst', 'mod/*version.rst']

docs/source/ift.rst

@@ -219,14 +219,14 @@ Here, the uncertainty of the field and the power spectrum of its generating proc
 | **Output of tomography demo getting_started_3.py** |
 +----------------------------------------------------+
 | .. image:: images/getting_started_3_setup.png      |
-|     :width:  50 %                                  |
+|                                                    |
 +----------------------------------------------------+
 | Non-Gaussian signal field,                         |
 | data backprojected into the image domain, power    |
 | spectrum of underlying Gausssian process.          |
 +----------------------------------------------------+
 | .. image:: images/getting_started_3_results.png    |
-|     :width:  50 %                                  |
+|                                                    |
 +----------------------------------------------------+
 | Posterior mean field signal                        |
 | reconstruction, its uncertainty, and the power     |
@@ -235,10 +235,10 @@ Here, the uncertainty of the field and the power spectrum of its generating proc
 | orange line).                                      |
 +----------------------------------------------------+
 
-Maximim a Posteriori
+Maximum a Posteriori
 --------------------
 
-One popular field estimation method is Maximim a Posteriori (MAP).
+One popular field estimation method is Maximum a Posteriori (MAP).
 
 It only requires to minimize the information Hamiltonian, e.g by a gradient descent method that stops when
 
@@ -246,7 +246,7 @@ It only requires to minimize the information Hamiltonian, e.g by a gradient desc
 
     \frac{\partial \mathcal{H}(d,\xi)}{\partial \xi} = 0.
 
-NIFTy5 automatically calculates the necessary gradient from a generative model of the signal and the data and to minimize the Hamiltonian.
+NIFTy5 automatically calculates the necessary gradient from a generative model of the signal and the data and uses this to minimize the Hamiltonian.
 
 However, MAP often provides unsatisfactory results in cases of deep hirachical Bayesian networks.
 The reason for this is that MAP ignores the volume factors in parameter space, which are not to be neglected in deciding whether a solution is reasonable or not.
@@ -270,7 +270,7 @@ As a compromise between being optimal and being computationally affordable, the
     \int \mathcal{D}\xi \,\mathcal{Q}(\xi) \log \left( \frac{\mathcal{Q}(\xi)}{\mathcal{P}(\xi)} \right)
 
 Minimizing this with respect to all entries of the covariance :math:`D` is unfeasible for fields.
-Therefore, Metric Gaussian Variational Inference (MGVI) approximates the precision matrix at the location of the current mean :math:`M=D^{-1}` by the Bayesian Fisher information metric,
+Therefore, Metric Gaussian Variational Inference (MGVI) approximates the posterior precision matrix :math:`D^{-1}` at the location of the current mean :math:`m` by the Bayesian Fisher information metric,
 
 .. math::
 

nifty5/__init__.py

@@ -64,7 +64,7 @@ from .minimization.nonlinear_cg import NonlinearCG
 from .minimization.descent_minimizers import (
     DescentMinimizer, SteepestDescent, VL_BFGS, L_BFGS, RelaxedNewton,
     NewtonCG)
-from .minimization.scipy_minimizer import (ScipyMinimizer, L_BFGS_B, ScipyCG)
+from .minimization.scipy_minimizer import L_BFGS_B
 from .minimization.energy import Energy
 from .minimization.quadratic_energy import QuadraticEnergy
 from .minimization.energy_adapter import EnergyAdapter
@@ -73,7 +73,7 @@ from .minimization.metric_gaussian_kl import MetricGaussianKL
 from .sugar import *
 from .plot import Plot
 
-from .library.smooth_linear_amplitude import (SLAmplitude, CepstrumOperator)
+from .library.smooth_linear_amplitude import SLAmplitude, CepstrumOperator
 from .library.inverse_gamma_operator import InverseGammaOperator
 from .library.los_response import LOSResponse
 from .library.dynamic_operator import (dynamic_operator,

nifty5/extra.py

@@ -19,6 +19,7 @@ import numpy as np
 
 from .field import Field
 from .linearization import Linearization
+from .operators.linear_operator import LinearOperator
 from .sugar import from_random
 
 __all__ = ["consistency_check", "check_value_gradient_consistency",
@@ -62,8 +63,40 @@ def _full_implementation(op, domain_dtype, target_dtype, atol, rtol):
     _inverse_implementation(op, domain_dtype, target_dtype, atol, rtol)
 
 
+def _check_linearity(op, domain_dtype, atol, rtol):
+    fld1 = from_random("normal", op.domain, dtype=domain_dtype)
+    fld2 = from_random("normal", op.domain, dtype=domain_dtype)
+    alpha = np.random.random()
+    val1 = op(alpha*fld1+fld2)
+    val2 = alpha*op(fld1)+op(fld2)
+    _assert_allclose(val1, val2, atol=atol, rtol=rtol)
+
+
 def consistency_check(op, domain_dtype=np.float64, target_dtype=np.float64,
                       atol=0, rtol=1e-7):
+    """Checks whether times(), adjoint_times(), inverse_times() and
+    adjoint_inverse_times() (if in capability list) is implemented
+    consistently. Additionally, it checks whether the operator is linear
+    actually.
+
+    Parameters
+    ----------
+    op : LinearOperator
+        Operator which shall be checked.
+    domain_dtype : FIXME
+        The data type of the random vectors in the operator's domain. Default
+        is `np.float64`.
+    target_dtype : FIXME
+        The data type of the random vectors in the operator's target. Default
+        is `np.float64`.
+    atol : float
+        FIXME. Default is 0.
+    rtol : float
+        FIXME. Default is 0.
+    """
+    if not isinstance(op, LinearOperator):
+        raise TypeError('This test tests only linear operators.')
+    _check_linearity(op, domain_dtype, atol, rtol)
     _full_implementation(op, domain_dtype, target_dtype, atol, rtol)
     _full_implementation(op.adjoint, target_dtype, domain_dtype, atol, rtol)
     _full_implementation(op.inverse, target_dtype, domain_dtype, atol, rtol)
@@ -124,8 +157,10 @@ def _check_consistency(op, loc, tol, ntries, do_metric):
 
 
 def check_value_gradient_consistency(op, loc, tol=1e-8, ntries=100):
+    """FIXME"""
     _check_consistency(op, loc, tol, ntries, False)
 
 
 def check_value_gradient_metric_consistency(op, loc, tol=1e-8, ntries=100):
+    """FIXME"""
     _check_consistency(op, loc, tol, ntries, True)

nifty5/field.py

@@ -31,13 +31,13 @@ class Field(object):
     Parameters
     ----------
     domain : DomainTuple
-        the domain of the new Field
+        The domain of the new Field.
     val : data_object
         This object's global shape must match the domain shape
         After construction, the object will no longer be writeable!
 
-    Notes
-    -----
+    Note
+    ----
     If possible, do not invoke the constructor directly, but use one of the
     many convenience functions for instantiation!
     """
@@ -76,14 +76,14 @@ class Field(object):
         Parameters
         ----------
         domain : Domain, tuple of Domain, or DomainTuple
-            domain of the new Field
+            Domain of the new Field.
         val : float/complex/int scalar
-            fill value. Data type of the field is inferred from val.
+            Fill value. Data type of the field is inferred from val.
 
         Returns
         -------
         Field
-            the newly created field
+            The newly created Field.
         """
         if not np.isscalar(val):
             raise TypeError("val must be a scalar")
@@ -99,7 +99,7 @@ class Field(object):
         Parameters
         ----------
         domain : DomainTuple, tuple of Domain, or Domain
-            the domain of the new Field
+            The domain of the new Field.
         arr : numpy.ndarray
             The data content to be used for the new Field.
             Its shape must match the shape of `domain`.
@@ -132,8 +132,9 @@ class Field(object):
 
         Returns
         -------
-        numpy.ndarray : array containing all field entries, which can be
-            modified. Its shape is identical to `self.shape`.
+        numpy.ndarray
+            Array containing all field entries, which can be modified. Its
+            shape is identical to `self.shape`.
         """
         return dobj.to_global_data_rw(self._val)
 
@@ -171,9 +172,9 @@ class Field(object):
         random_type : 'pm1', 'normal', or 'uniform'
             The random distribution to use.
         domain : DomainTuple
-            The domain of the output random field
+            The domain of the output random Field.
         dtype : type
-            The datatype of the output random field
+            The datatype of the output random Field.
 
         Returns
         -------
@@ -187,10 +188,10 @@ class Field(object):
 
     @property
     def val(self):
-        """dobj.data_object : the data object storing the field's entries
+        """dobj.data_object : the data object storing the field's entries.
 
-        Notes
-        -----
+        Note
+        ----
         This property is intended for low-level, internal use only. Do not use
         from outside of NIFTy's core; there should be better alternatives.
         """
@@ -236,13 +237,13 @@ class Field(object):
         Parameters
         ----------
         spaces : int, tuple of int or None
-            indices of the sub-domains of the field's domain to be considered.
+            Indices of the sub-domains of the field's domain to be considered.
             If `None`, the entire domain is used.
 
         Returns
         -------
         float or None
-            if the requested sub-domain has a uniform volume element, it is
+            If the requested sub-domain has a uniform volume element, it is
             returned. Otherwise, `None` is returned.
         """
         if np.isscalar(spaces):
@@ -264,7 +265,7 @@ class Field(object):
         Parameters
         ----------
         spaces : int, tuple of int or None
-            indices of the sub-domains of the field's domain to be considered.
+            Indices of the sub-domains of the field's domain to be considered.
             If `None`, the entire domain is used.
 
         Returns
@@ -331,8 +332,9 @@ class Field(object):
         x : Field
 
         Returns
-        ----------
-        Field, defined on the product space of self.domain and x.domain
+        -------
+        Field
+            Defined on the product space of self.domain and x.domain.
         """
         if not isinstance(x, Field):
             raise TypeError("The multiplier must be an instance of " +

nifty5/library/adjust_variances.py

@@ -18,7 +18,8 @@
 from ..minimization.energy_adapter import EnergyAdapter
 from ..multi_field import MultiField
 from ..operators.distributors import PowerDistributor
-from ..operators.energy_operators import StandardHamiltonian, InverseGammaLikelihood
+from ..operators.energy_operators import (StandardHamiltonian,
+                                          InverseGammaLikelihood)
 from ..operators.scaling_operator import ScalingOperator
 from ..operators.simple_linear_operators import ducktape
 
@@ -72,7 +73,8 @@ def make_adjust_variances(a,
     if scaling is not None:
         x = ScalingOperator(scaling, x.target)(x)
 
-    return StandardHamiltonian(InverseGammaLikelihood(d_eval)(x), ic_samp=ic_samp)
+    return StandardHamiltonian(InverseGammaLikelihood(d_eval/2.)(x),
+                               ic_samp=ic_samp)
 
 
 def do_adjust_variances(position,

nifty5/library/correlated_fields.py

@@ -16,6 +16,7 @@
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
 
 from functools import reduce
+from operator import mul
 
 from ..domain_tuple import DomainTuple
 from ..operators.contraction_operator import ContractionOperator
@@ -61,6 +62,10 @@ def CorrelatedField(target, amplitude_operator, name='xi', codomain=None):
     power_distributor = PowerDistributor(h_space, p_space)
     A = power_distributor(amplitude_operator)
     vol = h_space.scalar_dvol**-0.5
+    # When doubling the resolution of `tgt` the value of the highest k-mode
+    # will scale with a square root. `vol` cancels this effect such that the
+    # same power spectrum can be used for the spaces with the same volume,
+    # different resolutions and the same object in them.
     return ht(vol*A*ducktape(h_space, None, name))
 
 
@@ -107,7 +112,8 @@ def MfCorrelatedField(target, amplitudes, name='xi'):
     d = [dd0, dd1]
 
     a = [dd @ amplitudes[ii] for ii, dd in enumerate(d)]
-    a = reduce(lambda x, y: x*y, a)
+    a = reduce(mul, a)
     A = pd @ a
-    vol = reduce(lambda x, y: x*y, [sp.scalar_dvol**-0.5 for sp in hsp])
+    # For `vol` see comment in `CorrelatedField`
+    vol = reduce(mul, [sp.scalar_dvol**-0.5 for sp in hsp])
     return ht(vol*A*ducktape(hsp, None, name))

nifty5/library/inverse_gamma_operator.py

@@ -26,12 +26,13 @@ from ..sugar import makeOp
 
 
 class InverseGammaOperator(Operator):
-    """Operator which transforms a Gaussian into an inverse gamma distribution.
+    """Transforms a Gaussian into an inverse gamma distribution.
 
     The pdf of the inverse gamma distribution is defined as follows:
 
-    .. math ::
-        \\frac{q^\\alpha}{\\Gamma(\\alpha)}x^{-\\alpha -1}\\exp \\left(-\\frac{q}{x}\\right)
+    .. math::
+        \\frac{q^\\alpha}{\\Gamma(\\alpha)}x^{-\\alpha -1}
+        \\exp \\left(-\\frac{q}{x}\\right)
 
     That means that for large x the pdf falls off like :math:`x^(-\\alpha -1)`.
     The mean of the pdf is at :math:`q / (\\alpha - 1)` if :math:`\\alpha > 1`.
@@ -54,7 +55,8 @@ class InverseGammaOperator(Operator):
     """
     def __init__(self, domain, alpha, q, delta=0.001):
         self._domain = self._target = DomainTuple.make(domain)
-        self._alpha, self._q, self._delta = float(alpha), float(q), float(delta)
+        self._alpha, self._q, self._delta = \
+            float(alpha), float(q), float(delta)
         self._xmin, self._xmax = -8.2, 8.2
         # Precompute
         xs = np.arange(self._xmin, self._xmax+2*delta, delta)

nifty5/library/smooth_linear_amplitude.py

@@ -138,7 +138,8 @@ def SLAmplitude(*, target, n_pix, a, k0, sm, sv, im, iv, keys=['tau', 'phi']):
     of the linear function.
 
     The prior on the smooth component is parametrized by two real numbers: the
-    strength and the cutoff of the smoothness prior (see :class:`CepstrumOperator`).
+    strength and the cutoff of the smoothness prior
+    (see :class:`CepstrumOperator`).
 
     Parameters
     ----------

nifty5/minimization/metric_gaussian_kl.py

@@ -130,4 +130,4 @@ class MetricGaussianKL(Energy):
 
     def __repr__(self):
         return 'KL ({} samples):\n'.format(len(
-            self._samples)) + utilities.indent(self._ham.__repr__())
+            self._samples)) + utilities.indent(self._hamiltonian.__repr__())

nifty5/minimization/scipy_minimizer.py

@@ -93,7 +93,7 @@ class _MinHelper(object):
         return _toArray_rw(res)
 
 
-class ScipyMinimizer(Minimizer):
+class _ScipyMinimizer(Minimizer):
     """Scipy-based minimizer
 
     Parameters
@@ -136,19 +136,19 @@ class ScipyMinimizer(Minimizer):
 
 
 def L_BFGS_B(ftol, gtol, maxiter, maxcor=10, disp=False, bounds=None):
-    """Returns a ScipyMinimizer object carrying out the L-BFGS-B algorithm.
+    """Returns a _ScipyMinimizer object carrying out the L-BFGS-B algorithm.
 
     See Also
     --------
-    ScipyMinimizer
+    _ScipyMinimizer
     """
     options = {"ftol": ftol, "gtol": gtol, "maxiter": maxiter,
                "maxcor": maxcor, "disp": disp}
-    return ScipyMinimizer("L-BFGS-B", options, False, bounds)
+    return _ScipyMinimizer("L-BFGS-B", options, False, bounds)
 
 
-class ScipyCG(Minimizer):
-    """Returns a ScipyMinimizer object carrying out the conjugate gradient
+class _ScipyCG(Minimizer):
+    """Returns a _ScipyMinimizer object carrying out the conjugate gradient
     algorithm as implemented by SciPy.
 
     This class is only intended for double-checking NIFTy's own conjugate

nifty5/operators/contraction_operator.py

@@ -24,7 +24,8 @@ from .linear_operator import LinearOperator
 
 
 class ContractionOperator(LinearOperator):
-    """A  :class:`LinearOperator` which sums up fields into the direction of subspaces.
+    """A  :class:`LinearOperator` which sums up fields into the direction of
+    subspaces.
 
     This Operator sums up a field with is defined on a :class:`DomainTuple`
     to a :class:`DomainTuple` which contains the former as a subset.

nifty5/operators/domain_tuple_field_inserter.py

@@ -23,31 +23,38 @@ from .linear_operator import LinearOperator
 
 
 class DomainTupleFieldInserter(LinearOperator):
-    """Writes the content of a :class:`Field` into one slice of a :class:`DomainTuple`.
+    """Writes the content of a :class:`Field` into one slice of a
+    :class:`DomainTuple`.
 
     Parameters
     ----------
-    domain : Domain, tuple of Domain or DomainTuple
-    new_space : Domain, tuple of Domain or DomainTuple
-    index : Integer
-        Index at which new_space shall be added to domain.
-    position : tuple
-        Slice in new_space in which the input field shall be written into.
+    target : Domain, tuple of Domain or DomainTuple
+    space : int
+       The index of the sub-domain which is inserted.
+    index : tuple
+        Slice in new sub-domain in which the input field shall be written into.