Merge branch 'units' into 'master'

Wiener filter example with units and a little plot routine.

See merge request !59

demos/wiener_filter.py

 
 from nifty import *
-#import plotly.offline as pl
-#import plotly.graph_objs as go
+import plotly.offline as pl
+import plotly.graph_objs as go
 
 from mpi4py import MPI
 comm = MPI.COMM_WORLD
 rank = comm.rank
 
+np.random.seed(42)
 
 if __name__ == "__main__":
 
-    distribution_strategy = 'fftw'
+    distribution_strategy = 'not'
 
     # Setting up the geometry
     s_space = RGSpace([512, 512], dtype=np.float64)
@@ -50,8 +51,8 @@ if __name__ == "__main__":
     d_data = d.val.get_full_data().real
     m_data = m.val.get_full_data().real
     ss_data = ss.val.get_full_data().real
-#    if rank == 0:
-#        pl.plot([go.Heatmap(z=d_data)], filename='data.html')
-#        pl.plot([go.Heatmap(z=m_data)], filename='map.html')
-#        pl.plot([go.Heatmap(z=ss_data)], filename='map_orig.html')
+    if rank == 0:
+       pl.plot([go.Heatmap(z=d_data)], filename='data.html')
+       pl.plot([go.Heatmap(z=m_data)], filename='map.html')
+       pl.plot([go.Heatmap(z=ss_data)], filename='map_orig.html')
 #

demos/wiener_filter_hamiltonian.py

@@ -53,7 +53,7 @@ class WienerFilterEnergy(Energy):
 
 if __name__ == "__main__":
 
-    distribution_strategy = 'fftw'
+    distribution_strategy = 'not'
 
     # Set up spaces and fft transformation
     s_space = RGSpace([512, 512], dtype=np.float)

demos/wiener_filter_unit.py

+from nifty import *
+from mpi4py import MPI
+import plotly.offline as py
+import plotly.graph_objs as go
+
+comm = MPI.COMM_WORLD
+rank = comm.rank
+
+
+
+
+def plot_maps(x, name):
+
+    trace = [None]*len(x)
+
+    keys = x.keys()
+    field = x[keys[0]]
+    domain = field.domain[0]
+    shape = len(domain.shape)
+    max_n = domain.shape[0]*domain.distances[0]
+    step = domain.distances[0]
+    x_axis = np.arange(0, max_n, step)
+
+    if shape == 1:
+        for ii in xrange(len(x)):
+            trace[ii] = go.Scatter(x= x_axis, y=x[keys[ii]].val.get_full_data(), name=keys[ii])
+        fig = go.Figure(data=trace)
+
+        py.plot(fig, filename=name)
+
+    elif shape == 2:
+        for ii in xrange(len(x)):
+            py.plot([go.Heatmap(z=x[keys[ii]].val.get_full_data())], filename=keys[ii])
+    else:
+        raise TypeError("Only 1D and 2D field plots are supported")
+
+def plot_power(x, name):
+
+    layout = go.Layout(
+        xaxis=dict(
+            type='log',
+            autorange=True
+        ),
+        yaxis=dict(
+            type='log',
+            autorange=True
+        )
+    )
+
+    trace = [None]*len(x)
+
+    keys = x.keys()
+    field = x[keys[0]]
+    domain = field.domain[0]
+    x_axis = domain.kindex
+
+    for ii in xrange(len(x)):
+        trace[ii] = go.Scatter(x= x_axis, y=x[keys[ii]].val.get_full_data(), name=keys[ii])
+
+    fig = go.Figure(data=trace, layout=layout)
+    py.plot(fig, filename=name)
+
+np.random.seed(42)
+
+if __name__ == "__main__":
+
+    distribution_strategy = 'not'
+
+    # setting spaces
+    npix = np.array([500])  # number of pixels
+    total_volume = 1.  # total length
+
+    # setting signal parameters
+    lambda_s = .05  # signal correlation length
+    sigma_s = 10.  # signal variance
+
+
+    #setting response operator parameters
+    length_convolution = .025
+    exposure = 2000.
+
+
+
+    # calculating parameters
+    k_0 = 4. / (2 * np.pi * lambda_s)
+    a_s = sigma_s ** 2. * lambda_s * total_volume
+
+    # creation of spaces
+    x1 = RGSpace(npix, dtype=np.float64, distances=total_volume / npix,
+                 zerocenter=False)
+    k1 = RGRGTransformation.get_codomain(x1)
+    p1 = PowerSpace(harmonic_domain=k1, log=False, dtype=np.float64)
+
+    # creating Power Operator with given spectrum
+    spec = (lambda k: a_s / (1 + (k / k_0) ** 2) ** 2)
+    p_field = Field(p1, val=spec)
+    S_op = create_power_operator(k1, spec)
+
+    # creating FFT-Operator and Response-Operator with Gaussian convolution
+    Fft_op = FFTOperator(domain=x1, target=k1,
+                        domain_dtype=np.float64,
+                        target_dtype=np.complex128)
+    R_op = ResponseOperator(x1, sigma=length_convolution,
+                            exposure=exposure)
+
+    # drawing a random field
+    sk = p_field.power_synthesize(real_signal=True, mean=0.)
+    s = Fft_op.inverse_times(sk)
+
+    signal_to_noise = 1
+    N_op = DiagonalOperator(R_op.target, diagonal=s.var()/signal_to_noise, bare=True)
+    n = Field.from_random(domain=R_op.target,
+                          random_type='normal',
+                          std=s.std()/np.sqrt(signal_to_noise),
+                          mean=0)
+
+    d = R_op(s) + n
+
+    # Wiener filter
+    j = R_op.adjoint_times(N_op.inverse_times(d))
+    D = PropagatorOperator(S=S_op, N=N_op, R=R_op)
+
+    m = D(j)
+
+    z={}
+    z["signal"] = s
+    z["reconstructed_map"] = m
+    z["data"] = d
+    z["lambda"] = R_op(s)
+
+    plot_maps(z, "Wiener_filter.html")
+
+

nifty/operators/__init__.py

@@ -38,3 +38,6 @@ from projection_operator import ProjectionOperator
 from propagator_operator import PropagatorOperator
 
 from composed_operator import ComposedOperator
+
+from response_operator import ResponseOperator
+

nifty/operators/response_operator/__init__.py

+from response_operator import ResponseOperator
\ No newline at end of file

nifty/operators/response_operator/response_operator.py

+from nifty import Field
+
+from nifty.field_types.field_array import FieldArray
+
+from nifty.operators.linear_operator import LinearOperator
+from nifty.operators.smoothing_operator import SmoothingOperator
+
+import numpy as np
+
+class ResponseOperator(LinearOperator):
+
+    def __init__(self, domain,
+                 sigma=1., exposure=1., implemented=True,
+                 unitary=False):
+
+        self._domain = self._parse_domain(domain)
+        self._target = self._parse_domain(FieldArray(self._domain[0].shape,
+                                      dtype=np.float64))
+        self._sigma = sigma
+        self._implemented = implemented
+        self._unitary = unitary
+
+        self._kernel = SmoothingOperator(self._domain,
+                                        sigma=self._sigma)
+
+        self._exposure = exposure
+
+    @property
+    def domain(self):
+        return self._domain
+
+    @property
+    def target(self):
+        return self._target
+
+    @property
+    def implemented(self):
+        return self._implemented
+
+    @property
+    def unitary(self):
+        return self._unitary
+
+    def _times(self, x, spaces):
+        res = self._kernel.times(x)
+        res = self._exposure * res
+        res = res.weight(power=1)
+        # removing geometric information
+        return Field(self._target, val=res.val)
+
+    def _adjoint_times(self, x, spaces):
+        # setting correct spaces
+        res = x*self._exposure
+        res = Field(self.domain, val=res.val)
+        res = self._kernel.adjoint_times(res)
+        return res

nifty/sugar.py

@@ -24,6 +24,6 @@ def create_power_operator(domain, power_spectrum, dtype=None,
 
     f = fp.power_synthesize(mean=1, std=0, real_signal=False)
 
-    power_operator = DiagonalOperator(domain, diagonal=f)
+    power_operator = DiagonalOperator(domain, diagonal=f, bare=True)
 
     return power_operator