docu adjustments; changed to pre-release version 0.3.9; TODO: nifty reference.

demos/demo_excaliwir.py

@@ -52,7 +52,7 @@ g = gl_space(48)
 z = s_space = k = k_space = p = d_space = None
 
 ## power spectrum (and more)
-power = powerindex = powerundex = kindex = rho = None
+power = kindex = rho = powerindex = powerundex = None
 
 ## operators
 S = Sk = R = N = Nj = D = None
@@ -111,7 +111,7 @@ def setup(space,s2n=3,nvar=None):
             the noise variance, `nvar` will be calculated according to
             `s2n` if not specified (default: None)
     """
-    global z,s_space,k,k_space,p,d_space,power,powerindex,powerundex,kindex,rho,S,Sk,R,N,Nj,D,s,n,d,j,m
+    global z,s_space,k,k_space,p,d_space,power,kindex,rho,powerindex,powerundex,S,Sk,R,N,Nj,D,s,n,d,j,m
 
     ## signal space
     z = s_space = space
@@ -119,17 +119,15 @@ def setup(space,s2n=3,nvar=None):
     ## conjugate space
     k = k_space = s_space.get_codomain()
     ## the power indices are calculated once and saved
-    powerindex = k_space.get_power_index()
-    powerundex = k_space.get_power_undex()
-    kindex,rho = k_space.get_power_index(irreducible=True)
+    kindex,rho,powerindex,powerundex = k_space.get_power_indices()
 
     ## power spectrum
-    power = [42/(kk+1)**3 for kk in kindex]
+    power = (lambda kk: 42/(kk+1)**3)
 
     ## prior signal covariance operator (power operator)
-    S = power_operator(k_space,spec=power,pindex=powerindex)
+    S = power_operator(k_space,spec=power)
     ## projection operator to the spectral bands
-    Sk = S.get_projection_operator(pindex=powerindex)
+    Sk = S.get_projection_operator()
     ## the Gaussian random field generated from its power operator S
     s = S.get_random_field(domain=s_space,target=k_space)
 
@@ -169,7 +167,7 @@ def run(space=r1,s2n=3,nvar=None,**kwargs):
             the noise variance, `nvar` will be calculated according to
             `s2n` if not specified (default: None)
     """
-    global z,s_space,k,k_space,p,d_space,power,powerindex,powerundex,kindex,rho,S,Sk,R,N,Nj,D,s,n,d,j,m
+    global s_space,k_space,d_space,power,S,Sk,R,N,Nj,D,s,n,d,j,m
 
     ## setting up signal, noise, data and the operators S, N and R
     setup(space,s2n=s2n,nvar=nvar)
@@ -196,7 +194,7 @@ def run(space=r1,s2n=3,nvar=None,**kwargs):
     m.plot(title="reconstructed map",vmin=np.min(s.val),vmax=np.max(s.val),**kwargs)
 
     ## power spectrum
-#    s.plot(title="power spectra",power=True,other=(m,power),mono=False,kindex=kindex)
+#    s.plot(title="power spectra",power=True,other=(m,power),mono=False)
 
     ## uncertainty
 #    uncertainty = D.hat(bare=True,nrun=D.domain.dim()//4,target=k_space)
@@ -234,7 +232,7 @@ def run_critical(space=r2,s2n=3,nvar=None,q=1E-12,alpha=1,perception=[1,0],**kwa
         infer_power
 
     """
-    global z,s_space,k,k_space,p,d_space,power,powerindex,powerundex,kindex,rho,S,Sk,R,N,Nj,D,s,n,d,j,m
+    global s_space,k_space,d_space,power,rho,S,Sk,R,N,Nj,D,s,n,d,j,m
 
     ## setting up signal, noise, data and the operators S, N and R
     setup(space,s2n=s2n,nvar=nvar)
@@ -245,7 +243,7 @@ def run_critical(space=r2,s2n=3,nvar=None,q=1E-12,alpha=1,perception=[1,0],**kwa
     j = R.adjoint_times(N.inverse_times(d))
 
     ## unknown power spectrum, the power operator is given an initial value
-    S.set_power(42,bare=True,pindex=powerindex) ## The answer is 42. I double checked.
+    S.set_power(42,bare=True) ## The answer is 42. I double checked.
     ## the power spectrum is drawn from the first guess power operator
     pk = S.get_power(bare=False) ## non-bare(!)
 
@@ -266,14 +264,14 @@ def run_critical(space=r2,s2n=3,nvar=None,q=1E-12,alpha=1,perception=[1,0],**kwa
         b1 = Sk.pseudo_tr(m) ## == Sk(m).pseudo_dot(m), but faster
         b2 = Sk.pseudo_tr(D,nrun=np.sqrt(Sk.domain.dim())//4) ## probing of the partial traces of D
         pk_new = (2*q+b1+perception[0]*b2)/(rho+2*(alpha-1+perception[1])) ## non-bare(!)
-        pk_new = smooth_power(pk_new,kindex,mode="2s",exclude=min(8,len(power))) ## smoothing
+        pk_new = smooth_power(pk_new,domain=k_space,mode="2s",exclude=min(8,len(rho))) ## smoothing
         ## the power operator is given the new spectrum
-        S.set_power(pk_new,bare=False,pindex=powerindex) ## auto-updates D
+        S.set_power(pk_new,bare=False) ## auto-updates D
 
         ## check convergence
         log_change = np.max(np.abs(log(pk_new/pk)))
         if(log_change<=0.01):
-            note.cprint("NOTE: accuracy reached in iteration %u."%(iteration))
+            note.cprint("NOTE: desired accuracy reached in iteration %u."%(iteration))
             break
         else:
             note.cprint("NOTE: log-change == %4.3f ( > 1%% ) in iteration %u."%(log_change,iteration))
@@ -290,7 +288,7 @@ def run_critical(space=r2,s2n=3,nvar=None,q=1E-12,alpha=1,perception=[1,0],**kwa
     m.plot(title="reconstructed map",vmin=np.min(s.val),vmax=np.max(s.val),**kwargs)
 
     ## power spectrum
-    s.plot(title="power spectra",power=True,other=(S.get_power(pundex=powerundex),power),mono=False,kindex=kindex)
+    s.plot(title="power spectra",power=True,other=(S.get_power(),power),mono=False)
 
     ## uncertainty
 #    uncertainty = D.hat(bare=True,nrun=D.domain.dim()//4,target=k_space)

demos/demo_faraday.py

@@ -91,8 +91,7 @@ def run(projection=False, power=False):
     m1 = m0.transform(l)
     if(projection):
         ## define projection operator
-        powerindex = l.get_power_index()
-        Sk = projection_operator(l, assign=powerindex)
+        Sk = projection_operator(l)
         ## project quadrupole
         m2 = Sk(m0, band=2)
 
@@ -116,7 +115,7 @@ def run(projection=False, power=False):
     m3.plot(title=r"$m$ on a spherical Gauss-Legendre grid", vmin=-4, vmax=4, cmap=ncmap.fm())
     m4.plot(title=r"$m$ on a regular 2D grid", vmin=-4, vmax=4, cmap=ncmap.fm())
     if(power):
-        m5.plot(title=r"(restricted) Fourier power spectrum of $m$", vmin=1E-3, vmax=1E+0, mono=False)
+        m5.plot(title=r"(restricted, binned) Fourier power spectrum of $m$", vmin=1E-3, vmax=1E+0, mono=False, log=True)
 
 ##=============================================================================
 

nifty_core.py

@@ -483,7 +483,7 @@ class _about(object): ## nifty support class for global settings
 
         """
         ## version
-        self._version = "0.3.1"
+        self._version = "0.3.9" ## FIXME: release veriosn 0.4.0 << REFERENCE + README
 
         ## switches and notifications
         self._errors = notification(default=True,ccode=notification._code)
@@ -1071,7 +1071,7 @@ class space(object):
 
     def get_power_index(self,irreducible=False): ## TODO: remove in future version
         """
-            Provides the indexing array of the power spectrum.
+            **DEPRECATED** Provides the indexing array of the power spectrum.
 
             Provides either an array giving for each component of a field the
             corresponding index of a power spectrum (if ``irreducible==False``)
@@ -1105,9 +1105,9 @@ class space(object):
         about.warnings.cprint("WARNING: 'get_power_index' is deprecated.")
         raise NotImplementedError(about._errors.cstring("ERROR: no generic instance method 'get_power_index'."))
 
-    def get_power_undex(self,pindex=None):
+    def get_power_undex(self,pindex=None): ## TODO: remove in future version
         """
-            Provides the unindexing list for an indexed power spectrum.
+            **DEPRECATED** Provides the unindexing list for an indexed power spectrum.
 
             Parameters
             ----------
@@ -1948,8 +1948,8 @@ class point_space(space):
 
     def get_power_index(self,irreducible=False): ## TODO: remove in future version
         """
-            Raises an error since the power spectrum is ill-defined for point
-            spaces.
+            **DEPRECATED** Raises an error since the power spectrum is
+            ill-defined for point spaces.
         """
         about.warnings.cprint("WARNING: 'get_power_index' is deprecated.")
         raise AttributeError(about._errors.cstring("ERROR: power spectra ill-defined for (unstructured) point spaces."))
@@ -2454,7 +2454,7 @@ class rg_space(space):
 
     def get_power_index(self,irreducible=False):  ## TODO: remove in future version
         """
-            Provides the indexing array of the power spectrum.
+            **DEPRECATED** Provides the indexing array of the power spectrum.
 
             Provides either an array giving for each component of a field the
             corresponding index of a power spectrum (if ``irreducible==False``)
@@ -3542,7 +3542,7 @@ class lm_space(space):
 
     def get_power_index(self,irreducible=False): ## TODO: remove in future version
         """
-            Provides the indexing array of the power spectrum.
+            **DEPRECATED** Provides the indexing array of the power spectrum.
 
             Provides either an array giving for each component of a field the
             corresponding index of a power spectrum (if ``irreducible==False``)
@@ -4367,7 +4367,7 @@ class gl_space(space):
 
     def get_power_index(self,irreducible=False): ## TODO: remove in future version
         """
-            Raises an error since the power spectrum for a field on the sphere
+            **DEPRECATED** Raises an error since the power spectrum for a field on the sphere
             is defined via the spherical harmonics components and not its
             position-space representation.
         """
@@ -5000,7 +5000,7 @@ class hp_space(space):
 
     def get_power_index(self,irreducible=False): ## TODO: remove in future version
         """
-            Raises an error since the power spectrum for a field on the sphere
+            **DEPRECATED** Raises an error since the power spectrum for a field on the sphere
             is defined via the spherical harmonics components and not its
             position-space representation.
         """
@@ -5528,8 +5528,8 @@ class nested_space(space):
 
     def get_power_index(self,irreducible=False): ## TODO: remove in future version
         """
-            Raises an error since there is no canonical definition for the
-            power spectrum on a generic product space.
+            **DEPRECATED** Raises an error since there is no canonical
+            definition for the power spectrum on a generic product space.
         """
         about.warnings.cprint("WARNING: 'get_power_index' is deprecated.")
         raise AttributeError(about._errors.cstring("ERROR: power spectra indexing ill-defined."))

nifty_power.py

@@ -41,9 +41,9 @@
 
 """
 from __future__ import division
-from scipy.interpolate import interp1d as ip
+from scipy.interpolate import interp1d as ip ##
 #import numpy as np
-from nifty_core import *
+from nifty.nifty_core import *
 import smoothing as gs
 
 

setup.py

@@ -23,7 +23,7 @@ from distutils.core import setup
 import os
 
 setup(name="nifty",
-      version="0.3.1",
+      version="0.4.0",
       description="Numerical Information Field Theory",
       author="Marco Selig",
       author_email="mselig@mpa-garching.mpg.de",