Some Bugfixes.

propagator_operator still not working to full extend.

demos/demo_excaliwir.py

@@ -46,7 +46,7 @@ from nifty import *
 
 class problem(object):
 
-    def __init__(self, x_space, s2n=0.5, **kwargs):
+    def __init__(self, x_space, s2n=12, **kwargs):
         """
             Sets up a Wiener filter problem.
 
@@ -67,7 +67,7 @@ class problem(object):
         #self.k.set_power_indices(**kwargs)
 
         ## set some power spectrum
-        self.power = (lambda k: 42 / (k + 1) ** 5)
+        self.power = (lambda k: 42 / (k + 1) ** 3)
 
         ## define signal covariance
         self.S = power_operator(self.k, spec=self.power, bare=True)
@@ -82,7 +82,8 @@ class problem(object):
         d_space = self.R.target
 
         ## define noise covariance
-        self.N = diagonal_operator(d_space, diag=abs(s2n) * self.s.var(), bare=True)
+        #self.N = diagonal_operator(d_space, diag=abs(s2n) * self.s.var(), bare=True)
+        self.N = diagonal_operator(d_space, diag=abs(s2n), bare=True)
         ## define (plain) projector
         self.Nj = projection_operator(d_space)
         ## generate noise
@@ -95,7 +96,9 @@ class problem(object):
         #self.j = self.R.adjoint_times(self.N.inverse_times(self.d), target=self.k)
         self.j = self.R.adjoint_times(self.N.inverse_times(self.d))
         ## define information propagator
-        self.D = propagator_operator(S=self.S, N=self.N, R=self.R)
+        self.D = propagator_operator(S=self.S,
+                                     N=self.N,
+                                     R=self.R)
 
         ## reserve map
         self.m = None
@@ -186,7 +189,7 @@ class problem(object):
             print ('power', power)
             print 'Calculated power'
 
-            power = np.clip(power, 0.00000001, np.max(power))
+            #power = np.clip(power, 0.00000001, np.max(power))
             self.store += [{'tr_B1': tr_B1,
                             'tr_B2': tr_B2,
                             'num': numerator,
@@ -253,7 +256,7 @@ class problem(object):
 ##-----------------------------------------------------------------------------
 #
 if(__name__=="__main__"):
-    x = rg_space((128,128), zerocenter=True)
+    x = rg_space((128), zerocenter=True)
     p = problem(x, log = False)
     about.warnings.off()
 ##    pl.close("all")

demos/demo_tomography.py

@@ -8,12 +8,21 @@ shape = (256, 256)
 x_space = rg_space(shape)
 k_space = x_space.get_codomain()
 
-power = lambda k: 42/((1+k*shape[0])**2)
+power = lambda k: 42/((1+k*shape[0])**3)
 
 S = power_operator(k_space, codomain=x_space, spec=power)
 s = S.get_random_field(domain=x_space)
 
 
+#n_points = 360.
+#starts = [[(np.cos(i/n_points*np.pi)+1)*shape[0]/2.,
+#           (np.sin(i/n_points*np.pi)+1)*shape[0]/2.] for i in xrange(int(n_points))]
+#starts = list(np.array(starts).T)
+#
+#ends = [[(np.cos(i/n_points*np.pi + np.pi)+1)*shape[0]/2.,
+#         (np.sin(i/n_points*np.pi + np.pi)+1)*shape[0]/2.] for i in xrange(int(n_points))]
+#ends = list(np.array(ends).T)
+
 def make_los(n=10, angle=0, d=1):
     starts_list = []
     ends_list = []
@@ -29,9 +38,9 @@ def make_los(n=10, angle=0, d=1):
     ends_list = rot_matrix.dot(ends_list.T-0.5*d).T+0.5*d
     return (starts_list, ends_list)
 
-temp_coords = (np.empty((0,2)), np.empty((0,2)))
-n = 256
-m = 256
+temp_coords = (np.empty((0, 2)), np.empty((0, 2)))
+n = 250
+m = 250
 for alpha in [np.pi/n*j for j in xrange(n)]:
     temp = make_los(n=m, angle=alpha)
     temp_coords = np.concatenate([temp_coords, temp], axis=1)
@@ -39,27 +48,19 @@ for alpha in [np.pi/n*j for j in xrange(n)]:
 starts = list(temp_coords[0].T)
 ends = list(temp_coords[1].T)
 
-#n_points = 360.
-#starts = [[(np.cos(i/n_points*np.pi)+1)*shape[0]/2.,
-#           (np.sin(i/n_points*np.pi)+1)*shape[0]/2.] for i in xrange(int(n_points))]
-#starts = list(np.array(starts).T)
-#
-#ends = [[(np.cos(i/n_points*np.pi + np.pi)+1)*shape[0]/2.,
-#         (np.sin(i/n_points*np.pi + np.pi)+1)*shape[0]/2.] for i in xrange(int(n_points))]
-#ends = list(np.array(ends).T)
-
-R = los_response(x_space, starts=starts, ends=ends, sigmas_up=0.1, sigmas_low=0.1)
+R = los_response(x_space, starts=starts, ends=ends,
+                 sigmas_up=0.1, sigmas_low=0.1)
 d_space = R.target
 
-N = diagonal_operator(d_space, diag=s.var(), bare=True)
+N = diagonal_operator(d_space, diag=s.var()/100000, bare=True)
 n = N.get_random_field(domain=d_space)
 
 d = R(s) + n
 j = R.adjoint_times(N.inverse_times(d))
 D = propagator_operator(S=S, N=N, R=R)
 
+m = D(j, W=S, tol=1E-14, limii=100, note=True)
 
-m = D(j, W=S, tol=1E-14, limii=50, note=True)
 
 s.plot(title="signal", save='1_plot_s.png')
 s.plot(save='plot_s_power.png', power=True, other=power)

demos/demo_wf1.py

@@ -44,25 +44,28 @@ from nifty import *                                              # version 0.8.0
 about.warnings.off()
 
 # some signal space; e.g., a two-dimensional regular grid
-x_space = rg_space([128, 128])                                   # define signal space
+shape = [1024,]
+x_space = rg_space(shape)
 #y_space = point_space(1280*1280)
-
 #x_space = hp_space(32)
-
 #x_space = gl_space(800)
 
 k_space = x_space.get_codomain()                                 # get conjugate space
 
 # some power spectrum
-power = (lambda k: 42 / (k + 1) ** 3)
+power = (lambda k: 42 / (k + 1) ** 4)
 
 S = power_operator(k_space, codomain=x_space, spec=power)                          # define signal covariance
 s = S.get_random_field(domain=x_space)                           # generate signal
 #my_mask = x_space.cast(1)
-#my_mask[400:900,400:900] = 0
+#stretch = 0.6
+#my_mask[shape[0]/2*stretch:shape[0]/2/stretch, shape[1]/2*stretch:shape[1]/2/stretch] = 0
 my_mask = 1
 
 R = response_operator(x_space, sigma=0.01, mask=my_mask, assign=None) # define response
+R = response_operator(x_space, assign=None) #
+#R = identity_operator(x_space)
+
 d_space = R.target                                               # get data space
 
 # some noise variance; e.g., signal-to-noise ratio of 1
@@ -79,14 +82,34 @@ D = propagator_operator(S=S, N=N, R=R)                           # define inform
 #m = D(j, tol=1E-8, limii=20, note=True, force=True)
 ident = identity(x_space)
 
-xi = field(x_space, random='gau', target=k_space)
-m = D(xi, W=ident, tol=1E-8, limii=10, note=True, force=True)
-temp_result = (D.inverse_times(m)-xi)
-print (temp_result.dot(temp_result))
-print (temp_result.val)
+#xi = field(x_space, random='gau', target=k_space)
+
+
+m = D(j, W=S, tol=1E-8, limii=100, note=True)
+
+
+#temp_result = (D.inverse_times(m)-xi)
+
 
-s.plot(title="signal", save = 'plot_s.png')                                           # plot signal
-d_ = field(x_space, val=d.val, target=k_space)
-d_.plot(title="data", vmin=s.min(), vmax=s.max(), save = 'plot_d.png')                # plot data
-m.plot(title="reconstructed map", vmin=s.min(), vmax=s.max(), save = 'plot_m.png')    # plot map
+#n_power = x_space.enforce_power(s.var()/np.prod(shape))
+#s_power = S.get_power()
+
+#s.plot(title="signal", save = 'plot_s.png')
+#s.plot(title="signal power", power=True, other=power,
+#       mono=False, save = 'power_plot_s.png', nbin=1000, log=True,
+#       vmax = 100, vmin=10e-7)
+
+#d_ = field(x_space, val=d.val, target=k_space)
+#d_.plot(title="data", vmin=s.min(), vmax=s.max(), save = 'plot_d.png')
+
+
+#n_ = field(x_space, val=n.val, target=k_space)
+#n_.plot(title="data", vmin=s.min(), vmax=s.max(), save = 'plot_n.png')
+
+
+#
+#m.plot(title="reconstructed map", vmin=s.min(), vmax=s.max(), save = 'plot_m.png')
+#m.plot(title="reconstructed power", power=True, other=(n_power, s_power),
+#       save = 'power_plot_m.png', vmin=0.001, vmax=10, mono=False)
+#
 #

nifty_core.py

@@ -1921,7 +1921,8 @@ class field(object):
 
     """
 
-    def __init__(self, domain, val=None, codomain=None, ishape=None, **kwargs):
+    def __init__(self, domain=None, val=None, codomain=None, ishape=None,
+                 **kwargs):
         """
             Sets the attributes for a field class instance.
 
@@ -1944,6 +1945,9 @@ class field(object):
         Nothing
 
         """
+        # If the given val was a field, try to cast it accordingly to the given
+        # domain and codomain, etc...
+
         # check domain
         if not isinstance(domain, space):
             raise TypeError(about._errors.cstring("ERROR: invalid input."))
@@ -2359,7 +2363,7 @@ class field(object):
 
             # whether the domain matches exactly or not:
             # extract the data from x and try to dot with this
-            return self.dot(x=x.get_val(), axis=axis)
+            return self.dot(x=x.get_val(), axis=axis, bare=bare)
 
         # Case 3: x is something else
         else:

nifty_mpi_data.py

@@ -631,6 +631,7 @@ class distributed_data_object(object):
         temp_d2o = self.copy_empty()
         temp_data = np.conj(self.get_local_data())
         temp_d2o.set_local_data(temp_data)
+        temp_d2o.hermitian = self.hermitian
         return temp_d2o
 
     def conj(self):

nifty_power_indices.py

@@ -53,7 +53,9 @@ class power_indices(object):
         # Initialize the dictonary which stores all individual index-dicts
         self.global_dict = {}
         # Set self.default_parameters
-        self.set_default(log=log, nbin=nbin, binbounds=binbounds)
+        self.set_default(config_dict={'log': log,
+                                      'nbin': nbin,
+                                      'binbounds': binbounds})
 
     # Redirect the direct calls approaching a power_index instance to the
     # default_indices dict
@@ -217,7 +219,10 @@ class power_indices(object):
         # indices, bin them, compute the pundex and then return everything.
         else:
             # Get the unbinned indices
-            temp_unbinned_indices = self.get_index_dict(store=False)
+            temp_unbinned_indices = self.get_index_dict(nbin=None,
+                                                        binbounds=None,
+                                                        log=False,
+                                                        store=False)
             # Bin them
             (temp_pindex, temp_kindex, temp_rho, temp_pundex) = \
                 self._bin_power_indices(

nifty_utilities.py

@@ -2,23 +2,24 @@
 
 import numpy as np
 
-def hermitianize(x):
-    ## make the point inversions
+
+def hermitianize_gaussian(x):
+    # make the point inversions
     flipped_x = _hermitianize_inverter(x)
     flipped_x = flipped_x.conjugate()
-    ## check if x was already hermitian
+    # check if x was already hermitian
     if (x == flipped_x).all():
         return x
-    ## average x and flipped_x.
-    ## Correct the variance by multiplying sqrt(0.5)
+    # average x and flipped_x.
+    # Correct the variance by multiplying sqrt(0.5)
     x = (x + flipped_x) * np.sqrt(0.5)
-    ## The fixed points of the point inversion must not be avaraged.
-    ## Hence one must multiply them again with sqrt(0.5)
-    ## -> Get the middle index of the array
+    # The fixed points of the point inversion must not be avaraged.
+    # Hence one must multiply them again with sqrt(0.5)
+    # -> Get the middle index of the array
     mid_index = np.array(x.shape, dtype=np.int)//2
     dimensions = mid_index.size
-    ## Use ndindex to iterate over all combinations of zeros and the
-    ## mid_index in order to correct all fixed points.
+    # Use ndindex to iterate over all combinations of zeros and the
+    # mid_index in order to correct all fixed points.
     for i in np.ndindex((2,)*dimensions):
         temp_index = tuple(i*mid_index)
         x[temp_index] *= np.sqrt(0.5)
@@ -30,18 +31,35 @@ def hermitianize(x):
     return x
 
 
+def hermitianize(x):
+    # make the point inversions
+    flipped_x = _hermitianize_inverter(x)
+    flipped_x = flipped_x.conjugate()
+    # check if x was already hermitian
+    if (x == flipped_x).all():
+        return x
+    # average x and flipped_x.
+    # Correct the variance by multiplying sqrt(0.5)
+    x = (x + flipped_x) / 2.
+    try:
+        x.hermitian = True
+    except(AttributeError):
+        pass
+
+    return x
+
 
 def _hermitianize_inverter(x):
-    ## calculate the number of dimensions the input array has
+    # calculate the number of dimensions the input array has
     dimensions = len(x.shape)
-    ## prepare the slicing object which will be used for mirroring
-    slice_primitive = [slice(None),]*dimensions
-    ## copy the input data
+    # prepare the slicing object which will be used for mirroring
+    slice_primitive = [slice(None), ]*dimensions
+    # copy the input data
     y = x.copy()
-    ## flip in every direction
+    # flip in every direction
     for i in xrange(dimensions):
         slice_picker = slice_primitive[:]
-        slice_picker[i] = slice(1, None,None)
+        slice_picker[i] = slice(1, None, None)
         slice_inverter = slice_primitive[:]
         slice_inverter[i] = slice(None, 0, -1)
 
@@ -54,7 +72,7 @@ def _hermitianize_inverter(x):
 
 
 def direct_dot(x, y):
-    ## the input could be fields. Try to extract the data
+    # the input could be fields. Try to extract the data
     try:
         x = x.get_val()
     except(AttributeError):
@@ -63,7 +81,7 @@ def direct_dot(x, y):
         y = y.get_val()
     except(AttributeError):
         pass
-    ## try to make a direct vdot
+    # try to make a direct vdot
     try:
         return x.vdot(y)
     except(AttributeError):
@@ -74,16 +92,16 @@ def direct_dot(x, y):
     except(AttributeError):
         pass
 
-    ## fallback to numpy
+    # fallback to numpy
     return np.vdot(x, y)
 
 
 def convert_nested_list_to_object_array(x):
-    ## if x is a nested_list full of ndarrays all having the same size,
-    ## np.shape returns the shape of the ndarrays, too, i.e. too many
-    ## dimensions
+    # if x is a nested_list full of ndarrays all having the same size,
+    # np.shape returns the shape of the ndarrays, too, i.e. too many
+    # dimensions
     possible_shape = np.shape(x)
-    ## Check if possible_shape goes too deep.
+    # Check if possible_shape goes too deep.
     dimension_counter = 0
     current_extract = x
     for i in xrange(len(possible_shape)):
@@ -93,11 +111,11 @@ def convert_nested_list_to_object_array(x):
         current_extract = current_extract[0]
         dimension_counter += 1
     real_shape = possible_shape[:dimension_counter]
-    ## if the numpy array was not encapsulated at all, return x directly
+    # if the numpy array was not encapsulated at all, return x directly
     if real_shape == ():
         return x
-    ## Prepare the carrier-object
-    carrier = np.empty(real_shape, dtype = np.object)
+    # Prepare the carrier-object
+    carrier = np.empty(real_shape, dtype=np.object)
     for i in xrange(np.prod(real_shape)):
         ii = np.unravel_index(i, real_shape)
         try:
@@ -121,10 +139,10 @@ def field_map(ishape, function, *args):
                 result[ii] = function()
             return result
         else:
-            ## define a helper function in order to clip the get-indices
-            ## to be suitable for the foreign arrays in args.
-            ## This allows you to do operations, like adding to fields
-            ## with ishape (3,4,3) and (3,4,1)
+            # define a helper function in order to clip the get-indices
+            # to be suitable for the foreign arrays in args.
+            # This allows you to do operations, like adding to fields
+            # with ishape (3,4,3) and (3,4,1)
             def get_clipped(w, ind):
                 w_shape = np.array(np.shape(w))
                 get_tuple = tuple(np.clip(ind, 0, w_shape-1))
@@ -135,5 +153,5 @@ def field_map(ishape, function, *args):
                 result[ii] = function(*map(
                                         lambda z: get_clipped(z, ii), args)
                                       )
-                #result[ii] = function(*map(lambda z: z[ii], args))
-            return result
\ No newline at end of file
+                # result[ii] = function(*map(lambda z: z[ii], args))
+            return result

operators/nifty_operators.py

@@ -2292,7 +2292,7 @@ class projection_operator(operator):
                 raise TypeError(about._errors.cstring("ERROR: Invalid bands."))
 
             if bands_was_scalar:
-                new_field = x * (self.assign == bands[0])
+                new_field = fx * (self.assign == bands[0])
             else:
                 # build up the projection results
                 # prepare the projector-carrier
@@ -2392,15 +2392,18 @@ class projection_operator(operator):
             vecvec = vecvec_operator(val=x)
             return self.pseudo_tr(x=vecvec, axis=axis, **kwargs)
 
-        # Case 2: x is not an operator
-        elif isinstance(x, operator) == False:
+        # Case 2: x is an operator
+        # -> take the diagonal
+        elif isinstance(x, operator):
+            working_field = x.diag(bare=False)
+            if self.domain != working_field.domain:
+                working_field = working_field.transform(codomain=self.domain)
+
+        # Case 3: x is something else
+        else:
             raise TypeError(about._errors.cstring(
                 "ERROR: x must be a field or an operator."))
 
-        # Case 3: x is an operator
-        # -> take the diagonal
-        working_field = x.diag()
-
         # Check for hidden degrees of freedom and compensate the trace
         # accordingly
         if self.domain.get_dim() != self.domain.get_dof():

operators/nifty_probing.py

-## NIFTY (Numerical Information Field Theory) has been developed at the
-## Max-Planck-Institute for Astrophysics.
-##
-## Copyright (C) 2015 Max-Planck-Society
-##
-## Author: Theo Steininger
-## Project homepage: <http://www.mpa-garching.mpg.de/ift/nifty/>
-##
-## 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/>.
+# NIFTY (Numerical Information Field Theory) has been developed at the
+# Max-Planck-Institute for Astrophysics.
+#
+# Copyright (C) 2015 Max-Planck-Society
+#
+# Author: Theo Steininger
+# Project homepage: <http://www.mpa-garching.mpg.de/ift/nifty/>
+#
+# 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/>.
 
 from __future__ import division
 
@@ -27,7 +27,7 @@ from nifty.nifty_core import space, \
 from nifty.nifty_utilities import direct_dot
 
 
-##=============================================================================
+
 
 class prober(object):
     """
@@ -177,59 +177,61 @@ class prober(object):
             zeroth entry and the variance in the first entry. (default: False)
 
         """
-        ## Case 1: no operator given. Check function and domain for general
-        ## sanity
+        # Case 1: no operator given. Check function and domain for general
+        # sanity
         if operator is None:
-            ## check whether the given function callable
-            if function is None or hasattr(function, "__call__") == False:
+            # check whether the given function callable
+            if function is None or not hasattr(function, "__call__"):
                 raise ValueError(about._errors.cstring(
-                "ERROR: invalid input: No function given or not callable."))
-            ## check given domain
-            if domain is None or isinstance(domain, space) == False:
+                  "ERROR: invalid input: No function given or not callable."))
+            # check given domain
+            if domain is None or not isinstance(domain, space):
                 raise ValueError(about._errors.cstring(
-                "ERROR: invalid input: given domain is not a nifty space"))
+                    "ERROR: invalid input: given domain is not a nifty space"))
 
-        ## Case 2: An operator is given. Take domain and function from that
-        ## if not given explicitly
+        # Case 2: An operator is given. Take domain and function from that
+        # if not given explicitly
         else:
 
-            ## Case 2.1 extract function
-            ## explicit function overrides operator function
-            if function is None or hasattr(function,"__call__") == False:
+            # Check 2.1 extract function
+            # explicit function overrides operator function
+            if function is None or not hasattr(function, "__call__"):
                 try:
                     function = operator.times
                 except(AttributeError):
                     raise ValueError(about._errors.cstring(
-   "ERROR: no explicit function given and given operator has no times method!"))
-            ## check whether the given function is correctly bound to the
-            ## operator
+                        "ERROR: no explicit function given and given " +
+                        "operator has no times method!"))
+
+            # Check 2.2 check whether the given function is correctly bound to
+            # the operator
             if operator != function.im_self:
                     raise ValueError(about._errors.cstring(
-   "ERROR: the given function is not a bound function of the operator!"))
-
-
-
-            ## Case 2.2 extract domain
-            if domain is None or isinstance(domain, space):
-                 if (function in [operator.inverse_times,
-                                  operator.adjoint_times]):
-                     try:
-                         domain = operator.target
-                     except(AttributeError):
-                         raise ValueError(about._errors.cstring(
-   "ERROR: no explicit domain given and given operator has no target!"))
-
-                 else:
-                     try:
-                         domain = operator.domain
-                     except(AttributeError):
-                         raise ValueError(about._errors.cstring(
-   "ERROR: no explicit domain given and given operator has no domain!"))
+                        "ERROR: the given function is not a bound function " +
+                        "of the operator!"))
+
+            # Check 2.3 extract domain
+            if domain is None or not isinstance(domain, space):
+                if (function in [operator.inverse_times,
+                                 operator.adjoint_times]):
+                    try:
+                        domain = operator.target
+                    except(AttributeError):
+                        raise ValueError(about._errors.cstring(
+                            "ERROR: no explicit domain given and given " +
+                            "operator has no target!"))
+                else:
+                    try:
+                        domain = operator.domain
+                    except(AttributeError):
+                        raise ValueError(about._errors.cstring(
+                            "ERROR: no explicit domain given and given " +
+                            "operator has no domain!"))
 
         self.function = function
         self.domain = domain
 
-        ## Check the given target
+        # Check the given codomain
         if codomain is None:
             codomain = self.domain.get_codomain()
         else:
@@ -237,71 +239,16 @@ class prober(object):
 
         self.codomain = codomain
 
-        if(random not in ["pm1","gau"]):
+        if random not in ["pm1", "gau"]:
             raise ValueError(about._errors.cstring(
-                "ERROR: unsupported random key '"+str(random)+"'."))
+                "ERROR: unsupported random key '" + str(random) + "'."))
         self.random = random
 
-        ## Parse the remaining arguments
+        # Parse the remaining arguments
         self.nrun = int(nrun)
         self.varQ = bool(varQ)
         self.kwargs = kwargs
 
-        """
-            from nifty_operators import operator