Merge branch 'NIFTy_4' into fix_nonlinear_cg

.gitignore

-# custom 
+# never store the git version file
+git_version.py
+
+# custom
 setup.cfg
 .idea
 .DS_Store

docs/source/conf.py

@@ -82,9 +82,9 @@ author = u'Theo Steininger / Martin Reinecke'
 # built documents.
 #
 # The short X.Y version.
-version = u'3.9'
+version = u'4.0'
 # The full version, including alpha/beta/rc tags.
-release = u'3.9.0'
+release = u'4.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

nifty4/library/noise_energy.py

@@ -16,52 +16,27 @@
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
-from .. import Field, exp
-from ..operators.diagonal_operator import DiagonalOperator
+from ..field import Field, exp
 from ..minimization.energy import Energy
-
-# TODO Take only residual_sample_list as argument
+from ..operators.diagonal_operator import DiagonalOperator
 
 
 class NoiseEnergy(Energy):
-    def __init__(self, position, d, xi, D, t, ht, Instrument,
-                 nonlinearity, alpha, q, Distributor, samples=3,
-                 xi_sample_list=None, inverter=None):
-        super(NoiseEnergy, self).__init__(position=position)
-        self.xi = xi
-        self.D = D
-        self.d = d
-        self.N = DiagonalOperator(diagonal=exp(self.position))
-        self.t = t
-        self.samples = samples
-        self.ht = ht
-        self.Instrument = Instrument
-        self.nonlinearity = nonlinearity
+    def __init__(self, position, alpha, q, res_sample_list):
+        super(NoiseEnergy, self).__init__(position)
 
+        self.N = DiagonalOperator(diagonal=exp(self.position))
         self.alpha = alpha
         self.q = q
-        self.Distributor = Distributor
-        self.power = self.Distributor(exp(0.5 * self.t))
-        if xi_sample_list is None:
-            if samples is None or samples == 0:
-                xi_sample_list = [xi]
-            else:
-                xi_sample_list = [D.draw_sample() + xi
-                                  for _ in range(samples)]
-        self.xi_sample_list = xi_sample_list
-        self.inverter = inverter
-
-        A = Distributor(exp(.5*self.t))
+        alpha_field = Field(self.position.domain, val=alpha)
+        q_field = Field(self.position.domain, val=q)
+        self.res_sample_list = res_sample_list
 
         self._gradient = None
-        for sample in self.xi_sample_list:
-            map_s = self.ht(A * sample)
-
-            residual = self.d - \
-                self.Instrument(self.nonlinearity(map_s))
-            lh = .5 * residual.vdot(self.N.inverse_times(residual))
-            grad = -.5 * self.N.inverse_times(residual.conjugate()*residual)
 
+        for s in self.res_sample_list:
+            lh = .5 * s.vdot(self.N.inverse_times(s))
+            grad = -.5 * self.N.inverse_times(s.conjugate()*s)
             if self._gradient is None:
                 self._value = lh
                 self._gradient = grad.copy()
@@ -69,20 +44,19 @@ class NoiseEnergy(Energy):
                 self._value += lh
                 self._gradient += grad
 
-        self._value *= 1. / len(self.xi_sample_list)
+        expmpos = exp(-position)
+        self._value *= 1./len(self.res_sample_list)
         self._value += .5 * self.position.sum()
-        self._value += (self.alpha - 1.).vdot(self.position) + \
-            self.q.vdot(exp(-self.position))
+        self._value += (alpha_field-1.).vdot(self.position) + \
+            q_field.vdot(expmpos)
 
-        self._gradient *= 1. / len(self.xi_sample_list)
-        self._gradient += (self.alpha-0.5) - self.q*(exp(-self.position))
+        self._gradient *= 1./len(self.res_sample_list)
+        self._gradient += (alpha_field-0.5) - q_field*expmpos
+        self._gradient.lock()
 
     def at(self, position):
-        return self.__class__(
-            position, self.d, self.xi, self.D, self.t, self.ht,
-            self.Instrument, self.nonlinearity, self.alpha, self.q,
-            self.Distributor, xi_sample_list=self.xi_sample_list,
-            samples=self.samples, inverter=self.inverter)
+        return self.__class__(position, self.alpha, self.q,
+                              self.res_sample_list)
 
     @property
     def value(self):

nifty4/minimization/descent_minimizer.py

@@ -81,11 +81,13 @@ class DescentMinimizer(Minimizer):
 
             # compute a step length that reduces energy.value sufficiently
             try:
-                new_energy = self.line_searcher.perform_line_search(
+                new_energy, success = self.line_searcher.perform_line_search(
                     energy=energy, pk=self.get_descent_direction(energy),
                     f_k_minus_1=f_k_minus_1)
             except ValueError:
                 return energy, controller.ERROR
+            if not success:
+                self.reset()
 
             f_k_minus_1 = energy.value
 
@@ -103,6 +105,9 @@ class DescentMinimizer(Minimizer):
             if status != controller.CONTINUE:
                 return energy, status
 
+    def reset(self):
+        pass
+
     @abc.abstractmethod
     def get_descent_direction(self, energy):
         """ Calculates the next descent direction.

nifty4/minimization/energy.py

@@ -109,3 +109,19 @@ class Energy(NiftyMetaBase()):
             curvature of the potential at the given `position`.
         """
         raise NotImplementedError
+
+    def longest_step(self, dir):
+        """Returns the longest allowed step size along `dir`
+
+        Parameters
+        ----------
+        dir : Field
+            the search direction
+
+        Returns
+        -------
+        float or None
+            the longest allowed step when starting from `self.position` along
+            `dir`. If None, the step size is not limited.
+        """
+        return None

nifty4/minimization/line_search.py

@@ -54,5 +54,7 @@ class LineSearch(NiftyMetaBase()):
         -------
         Energy
             The new Energy object on the new position.
+        bool
+            whether the line search was considered successful or not
         """
         raise NotImplementedError

nifty4/minimization/line_search_strong_wolfe.py

@@ -41,7 +41,7 @@ class LineSearchStrongWolfe(LineSearch):
         Parameter for curvature condition rule. (Default: 0.9)
     max_step_size : float
         Maximum step allowed in to be made in the descent direction.
-        (Default: 1000000000)
+        (Default: 1e30)
     max_iterations : int, optional
         Maximum number of iterations performed by the line search algorithm.
         (Default: 100)
@@ -51,7 +51,7 @@ class LineSearchStrongWolfe(LineSearch):
     """
 
     def __init__(self, preferred_initial_step_size=None, c1=1e-4, c2=0.9,
-                 max_step_size=1000000000, max_iterations=100,
+                 max_step_size=1e30, max_iterations=100,
                  max_zoom_iterations=100):
 
         super(LineSearchStrongWolfe, self).__init__(
@@ -85,19 +85,26 @@ class LineSearchStrongWolfe(LineSearch):
         -------
         Energy
             The new Energy object on the new position.
+        bool
+            whether the line search was considered successful or not
         """
         le_0 = LineEnergy(0., energy, pk, 0.)
 
+        maxstepsize = energy.longest_step(pk)
+        if maxstepsize is None:
+            maxstepsize = self.max_step_size
+        maxstepsize = min(maxstepsize, self.max_step_size)
+
         # initialize the zero phis
         old_phi_0 = f_k_minus_1
         phi_0 = le_0.value
         phiprime_0 = le_0.directional_derivative
         if phiprime_0 == 0:
             dobj.mprint("Directional derivative is zero; assuming convergence")
-            return energy
+            return energy, False
         if phiprime_0 > 0:
             dobj.mprint("Error: search direction is not a descent direction")
-            raise ValueError("search direction must be a descent direction")
+            return energy, False
 
         # set alphas
         alpha0 = 0.
@@ -112,49 +119,44 @@ class LineSearchStrongWolfe(LineSearch):
                 alpha1 = 1.0
         else:
             alpha1 = 1.0/pk.norm()
+        alpha1 = min(alpha1, 0.99*maxstepsize)
 
         # start the minimization loop
         iteration_number = 0
         while iteration_number < self.max_iterations:
             iteration_number += 1
             if alpha1 == 0:
-                result_energy = le_0.energy
-                break
+                return le_0.energy, False
 
             le_alpha1 = le_0.at(alpha1)
             phi_alpha1 = le_alpha1.value
 
             if (phi_alpha1 > phi_0 + self.c1*alpha1*phiprime_0) or \
                ((phi_alpha1 >= phi_alpha0) and (iteration_number > 1)):
-                le_star = self._zoom(alpha0, alpha1, phi_0, phiprime_0,
-                                     phi_alpha0, phiprime_alpha0, phi_alpha1,
-                                     le_0)
-                result_energy = le_star.energy
-                break
+                return self._zoom(alpha0, alpha1, phi_0, phiprime_0,
+                                  phi_alpha0, phiprime_alpha0, phi_alpha1,
+                                  le_0)
 
             phiprime_alpha1 = le_alpha1.directional_derivative
             if abs(phiprime_alpha1) <= -self.c2*phiprime_0:
-                result_energy = le_alpha1.energy
-                break
+                return le_alpha1.energy, True
 
             if phiprime_alpha1 >= 0:
-                le_star = self._zoom(alpha1, alpha0, phi_0, phiprime_0,
-                                     phi_alpha1, phiprime_alpha1, phi_alpha0,
-                                     le_0)
-                result_energy = le_star.energy
-                break
+                return self._zoom(alpha1, alpha0, phi_0, phiprime_0,
+                                  phi_alpha1, phiprime_alpha1, phi_alpha0,
+                                  le_0)
 
             # update alphas
-            alpha0, alpha1 = alpha1, min(2*alpha1, self.max_step_size)
-            if alpha1 == self.max_step_size:
-                return le_alpha1.energy
+            alpha0, alpha1 = alpha1, min(2*alpha1, maxstepsize)
+            if alpha1 == maxstepsize:
+                dobj.mprint("max step size reached")
+                return le_alpha1.energy, False
 
             phi_alpha0 = phi_alpha1
             phiprime_alpha0 = phiprime_alpha1
-        else:
-            dobj.mprint("max iterations reached")
-            return le_alpha1.energy
-        return result_energy
+
+        dobj.mprint("max iterations reached")
+        return le_alpha1.energy, False
 
     def _zoom(self, alpha_lo, alpha_hi, phi_0, phiprime_0,
               phi_lo, phiprime_lo, phi_hi, le_0):
@@ -238,7 +240,7 @@ class LineSearchStrongWolfe(LineSearch):
                 phiprime_alphaj = le_alphaj.directional_derivative
                 # If the second Wolfe condition is met, return the result
                 if abs(phiprime_alphaj) <= -self.c2*phiprime_0:
-                    return le_alphaj
+                    return le_alphaj.energy, True
                 # If not, check the sign of the slope
                 if phiprime_alphaj*delta_alpha >= 0:
                     alpha_recent, phi_recent = alpha_hi, phi_hi
@@ -251,7 +253,7 @@ class LineSearchStrongWolfe(LineSearch):
 
         else:
             dobj.mprint("The line search algorithm (zoom) did not converge.")
-            return le_alphaj
+            return le_alphaj.energy, False
 
     def _cubicmin(self, a, fa, fpa, b, fb, c, fc):
         """Estimating the minimum with cubic interpolation.

nifty4/minimization/nonlinear_cg.py

@@ -63,8 +63,10 @@ class NonlinearCG(Minimizer):
         while True:
             grad_old = energy.gradient
             f_k = energy.value
-            energy = self._line_searcher.perform_line_search(energy, p,
-                                                             f_k_minus_1)
+            energy, success = self._line_searcher.perform_line_search(
+                energy, p, f_k_minus_1)
+            if not success:
+                return energy, controller.ERROR
             f_k_minus_1 = f_k
             status = self._controller.check(energy)
             if status != controller.CONTINUE:

nifty4/minimization/scipy_minimizer.py

@@ -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 .minimizer import Minimizer
 from ..field import Field
 from .. import dobj
@@ -97,9 +97,9 @@ class ScipyMinimizer(Minimizer):
             status = self._controller.check(hlp._energy)
             return hlp._energy, self._controller.check(hlp._energy)
         if not r.success:
-            print("Problem in Scipy minimization:", r.message)
+            dobj.mprint("Problem in Scipy minimization:", r.message)
         else:
-            print("Problem in Scipy minimization")
+            dobj.mprint("Problem in Scipy minimization")
         return hlp._energy, self._controller.ERROR
 
 

nifty4/minimization/vl_bfgs.py

@@ -49,6 +49,9 @@ class VL_BFGS(DescentMinimizer):
         self._information_store = None
         return super(VL_BFGS, self).__call__(energy)
 
+    def reset(self):
+        self._information_store = None
+
     def get_descent_direction(self, energy):
         x = energy.position
         gradient = energy.gradient

nifty4/operators/linear_operator.py

@@ -138,11 +138,10 @@ class LinearOperator(NiftyMetaBase()):
         other = self._toOperator(other, self.domain)
         return SumOperator.make([self, other], [False, True])
 
-    # MR FIXME: this might be more complicated ...
     def __rsub__(self, other):
         from .sum_operator import SumOperator
         other = self._toOperator(other, self.domain)
-        return SumOperator.make(other, self, [False, True])
+        return SumOperator.make([other, self], [False, True])
 
     @abc.abstractproperty
     def capability(self):

nifty4/plotting/plot.py

@@ -198,6 +198,18 @@ def plot(f, **kwargs):
     if not isinstance(label, list):
         label = [label]
 
+    linewidth = _get_kw("linewidth", None, **kwargs)
+    if linewidth is None:
+        linewidth = [1.] * len(f)
+    if not isinstance(linewidth, list):
+        linewidth = [linewidth]
+
+    alpha = _get_kw("alpha", None, **kwargs)
+    if alpha is None:
+        alpha = [None] * len(f)
+    if not isinstance(alpha, list):
+        alpha = [alpha]
+
     dom = dom[0]
     fig = plt.figure()
     ax = fig.add_subplot(1, 1, 1)
@@ -216,7 +228,8 @@ def plot(f, **kwargs):
             xcoord = np.arange(npoints, dtype=np.float64)*dist
             for i, fld in enumerate(f):
                 ycoord = fld.to_global_data()
-                plt.plot(xcoord, ycoord, label=label[i])
+                plt.plot(xcoord, ycoord, label=label[i],
+                         linewidth=linewidth[i], alpha=alpha[i])
             _limit_xy(**kwargs)
             if label != ([None]*len(f)):
                 plt.legend()
@@ -249,7 +262,8 @@ def plot(f, **kwargs):
         xcoord = dom.k_lengths
         for i, fld in enumerate(f):
             ycoord = fld.to_global_data()
-            plt.plot(xcoord, ycoord, label=label[i])
+            plt.plot(xcoord, ycoord, label=label[i],
+                     linewidth=linewidth[i], alpha=alpha[i])
         _limit_xy(**kwargs)
         if label != ([None]*len(f)):
             plt.legend()

nifty4/version.py

@@ -2,4 +2,13 @@
 # 1) we don't load dependencies by storing it in __init__.py
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module module
-__version__ = '3.9.0'
+
+__version__ = '4.0.0'
+
+
+def gitversion():
+    try:
+        from .git_version import gitversion
+    except ImportError:
+        return "unknown"
+    return gitversion

setup.py

@@ -18,6 +18,17 @@
 
 from setuptools import setup, find_packages
 
+
+def write_version():
+    import subprocess
+    p = subprocess.Popen(["git", "describe", "--dirty", "--tags"],
+                         stdout=subprocess.PIPE)
+    res = p.communicate()[0].strip().decode('utf-8')
+    with open("nifty4/git_version.py", "w") as file:
+        file.write('gitversion = "{}"\n'.format(res))
+
+
+write_version()
 exec(open('nifty4/version.py').read())
 
 setup(name="nifty4",

test/test_energies/test_noise.py

@@ -73,7 +73,7 @@ class Noise_Energy_Tests(unittest.TestCase):
         inverter = ift.ConjugateGradient(IC)
 
         S = ift.create_power_operator(hspace, power_spectrum=_flat_PS)
-        D = ift.library.NonlinearWienerFilterEnergy(
+        C = ift.library.NonlinearWienerFilterEnergy(
             position=xi,
             d=d,
             Instrument=R,
@@ -84,10 +84,10 @@ class Noise_Energy_Tests(unittest.TestCase):
             S=S,
             inverter=inverter).curvature
 
-        energy0 = ift