Updated documentation

Added more examples
Added more tests

pywafo/src/wafo/covariance/core.py

@@ -130,8 +130,8 @@ class CovData1D(WafoData):
     CovData
     """
 
-    def __init__(self,*args,**kwds):
-        super(CovData1D, self).__init__(*args,**kwds)
+    def __init__(self, *args, **kwds):
+        super(CovData1D, self).__init__(*args, **kwds)
 
         self.name = 'WAFO Covariance Object'
         self.type = 'time'
@@ -143,7 +143,7 @@ class CovData1D(WafoData):
         self.norm = 0
         somekeys = ['phi', 'name', 'h', 'tr', 'lagtype', 'v', 'type', 'norm']
 
-        self.__dict__.update(sub_dict_select(kwds,somekeys))
+        self.__dict__.update(sub_dict_select(kwds, somekeys))
 
         self.setlabels()
     def setlabels(self):
@@ -153,10 +153,10 @@ class CovData1D(WafoData):
         '''
 
         N = len(self.type)
-        if N==0:
+        if N == 0:
             raise ValueError('Object does not appear to be initialized, it is empty!')
 
-        labels = ['','ACF','']
+        labels = ['', 'ACF', '']
 
         if self.lagtype.startswith('t'):
             labels[0] = 'Lag [s]'
@@ -252,36 +252,36 @@ class CovData1D(WafoData):
         if rate is None:
             rate = 1 ##interpolation rate
         else:
-            rate = 2**nextpow2(rate) ##make sure rate is a power of 2
+            rate = 2 ** nextpow2(rate) ##make sure rate is a power of 2
 
 
         ## add a nugget effect to ensure that round off errors
         ## do not result in negative spectral estimates
-        ACF[0] = ACF[0] +nugget
+        ACF[0] = ACF[0] + nugget
         n = ACF.size
         # embedding a circulant vector and Fourier transform
         if fast:
-            nfft = 2**nextpow2(2*n-2)
+            nfft = 2 ** nextpow2(2 * n - 2)
         else:
-            nfft = 2*n-2
+            nfft = 2 * n - 2
 
-        nf   = nfft/2 ## number of frequencies
-        ACF  = r_[ACF,zeros(nfft-2*n+2),ACF[n-1:0:-1]]
+        nf = nfft / 2 ## number of frequencies
+        ACF = r_[ACF, zeros(nfft - 2 * n + 2), ACF[n - 1:0:-1]]
 
-        Rper = (fft(ACF,nfft).real).clip(0) ## periodogram
+        Rper = (fft(ACF, nfft).real).clip(0) ## periodogram
         RperMax = Rper.max()
-        Rper = where(Rper<trunc*RperMax,0,Rper)
+        Rper = where(Rper < trunc * RperMax, 0, Rper)
         pi = pi
-        S = abs(Rper[0:(nf+1)])*dT/pi
-        w = linspace(0,pi/dT,nf+1)
+        S = abs(Rper[0:(nf + 1)]) * dT / pi
+        w = linspace(0, pi / dT, nf + 1)
         So = _wafospec.SpecData1D(S, w, type=spectype, freqtype=ftype)
         So.tr = self.tr
         So.h = self.h
         So.norm = self.norm
 
         if rate > 1:
-            So.args = linspace(0, pi/dT, nf*rate)
-            if method=='stineman':
+            So.args = linspace(0, pi / dT, nf * rate)
+            if method == 'stineman':
                 So.data = stineman_interp(So.args, w, S)
             else:
                 intfun = interpolate.interp1d(w, S, kind=method)
@@ -300,11 +300,11 @@ class CovData1D(WafoData):
             [s] if lagtype=='t'
             [m] otherwise
         '''
-        dt1 = self.args[1]-self.args[0]
-        n = size(self.args)-1
-        t = self.args[-1]-self.args[0]
-        dt = t/n
-        if abs(dt-dt1) > 1e-10:
+        dt1 = self.args[1] - self.args[0]
+        n = size(self.args) - 1
+        t = self.args[-1] - self.args[0]
+        dt = t / n
+        if abs(dt - dt1) > 1e-10:
             warnings.warn('Data is not uniformly sampled!')
         return dt
 
@@ -385,7 +385,7 @@ class CovData1D(WafoData):
 
         dT = self.sampling_period()
 
-        x = zeros((ns, cases+1))
+        x = zeros((ns, cases + 1))
 
         if derivative:
             xder = x.copy()
@@ -399,22 +399,22 @@ class CovData1D(WafoData):
         ## Covariance matrix
         floatinfo = finfo(float)
         if (abs(ACF[-1]) > floatinfo.eps): ## assuming ACF(n+1)==0
-            m2 = 2*n-1
-            nfft = 2**nextpow2(max(m2, 2*ns))
-            ACF = r_[ACF, zeros((nfft-m2,1)), ACF[-1:0:-1,:]]
+            m2 = 2 * n - 1
+            nfft = 2 ** nextpow2(max(m2, 2 * ns))
+            ACF = r_[ACF, zeros((nfft - m2, 1)), ACF[-1:0:-1, :]]
             #disp('Warning: I am now assuming that ACF(k)=0 ')
             #disp('for k>MAXLAG.')
         else: # # ACF(n)==0
-            m2 = 2*n-2
-            nfft = 2**nextpow2(max(m2, 2*ns))
-            ACF = r_[ACF, zeros((nfft-m2, 1)), ACF[n-1:1:-1, :]]
+            m2 = 2 * n - 2
+            nfft = 2 ** nextpow2(max(m2, 2 * ns))
+            ACF = r_[ACF, zeros((nfft - m2, 1)), ACF[n - 1:1:-1, :]]
 
         ##m2=2*n-2
-        S = fft(ACF,nfft,axis=0).real ## periodogram
+        S = fft(ACF, nfft, axis=0).real ## periodogram
 
         I = S.argmax()
-        k = flatnonzero(S<0)
-        if k.size>0:
+        k = flatnonzero(S < 0)
+        if k.size > 0:
             #disp('Warning: Not able to construct a nonnegative circulant ')
             #disp('vector from the ACF. Apply the parzen windowfunction ')
             #disp('to the ACF in order to avoid this.')
@@ -425,57 +425,57 @@ class CovData1D(WafoData):
 
             S[k] = 0.
 
-            ix = flatnonzero(k>2*I)
-            if ix.size>0:
+            ix = flatnonzero(k > 2 * I)
+            if ix.size > 0:
 ##    # truncating all oscillating values above 2 times the peak
 ##    # frequency to zero to ensure that
 ##    # that high frequency noise is not added to
 ##    # the simulated timeseries.
                 ix0 = k[ix[0]]
-                S[ix0:-ix0] =0.0
+                S[ix0:-ix0] = 0.0
 
 
        
         trunc = 1e-5
         maxS = S[I]
-        k = flatnonzero(S[I:-I]<maxS*trunc)
-        if k.size>0:
-            S[k+I]=0.
+        k = flatnonzero(S[I:-I] < maxS * trunc)
+        if k.size > 0:
+            S[k + I] = 0.
             ## truncating small values to zero to ensure that
             ## that high frequency noise is not added to
             ## the simulated timeseries
 
-        cases1 = floor(cases/2)
-        cases2 = ceil(cases/2)
+        cases1 = floor(cases / 2)
+        cases2 = ceil(cases / 2)
 # Generate standard normal random numbers for the simulations
 
         #randn = np.random.randn
-        epsi = randn(nfft,cases2)+1j*randn(nfft,cases2)
-        Ssqr = sqrt(S/(nfft)) # #sqrt(S(wn)*dw )
-        ephat = epsi*Ssqr #[:,np.newaxis]
-        y = fft(ephat,nfft,axis=0)
-        x[:, 1:cases+1] = hstack((y[2:ns+2, 0:cases2].real, y[2:ns+2, 0:cases1].imag))
+        epsi = randn(nfft, cases2) + 1j * randn(nfft, cases2)
+        Ssqr = sqrt(S / (nfft)) # #sqrt(S(wn)*dw )
+        ephat = epsi * Ssqr #[:,np.newaxis]
+        y = fft(ephat, nfft, axis=0)
+        x[:, 1:cases + 1] = hstack((y[2:ns + 2, 0:cases2].real, y[2:ns + 2, 0:cases1].imag))
 
-        x[:, 0] = linspace(0,(ns-1)*dT,ns) ##(0:dT:(dT*(np-1)))'
+        x[:, 0] = linspace(0, (ns - 1) * dT, ns) ##(0:dT:(dT*(np-1)))'
 
         if derivative:
-            Ssqr = Ssqr*r_[0:(nfft/2+1), -(nfft/2-1):0]*2*pi/nfft/dT
-            ephat = epsi*Ssqr #[:,newaxis]
-            y = fft(ephat,nfft,axis=0)
-            xder[:, 1:(cases+1)] = hstack((y[2:ns+2, 0:cases2].imag -y[2:ns+2, 0:cases1].real))
-            xder[:, 0] = x[:,0]
+            Ssqr = Ssqr * r_[0:(nfft / 2 + 1), -(nfft / 2 - 1):0] * 2 * pi / nfft / dT
+            ephat = epsi * Ssqr #[:,newaxis]
+            y = fft(ephat, nfft, axis=0)
+            xder[:, 1:(cases + 1)] = hstack((y[2:ns + 2, 0:cases2].imag - y[2:ns + 2, 0:cases1].real))
+            xder[:, 0] = x[:, 0]
 
         if self.tr is not None:
             print('   Transforming data.')
             g = self.tr
             if derivative:
                 for ix in range(cases):
-                    tmp = g.gauss2dat(x[:,ix+1], xder[:,ix+1])
-                    x[:,ix+1] = tmp[0]
-                    xder[:,ix+1] = tmp[1]
+                    tmp = g.gauss2dat(x[:, ix + 1], xder[:, ix + 1])
+                    x[:, ix + 1] = tmp[0]
+                    xder[:, ix + 1] = tmp[1]
             else:
                 for ix in range(cases):
-                    x[:, ix+1] = g.gauss2dat(x[:, ix+1])
+                    x[:, ix + 1] = g.gauss2dat(x[:, ix + 1])
 
         if derivative:
             return x, xder
@@ -574,7 +574,7 @@ class CovData1D(WafoData):
             warnings.warn(txt)
             return self.sim(ns=N, cases=cases), zeros(Ns), zeros(Ns)
         
-        indg = where(1-isnan(x))[0] #indices to the known observations
+        indg = where(1 - isnan(x))[0] #indices to the known observations
         
         #initializing variables
         mu1o = zeros(Ns, 1)
@@ -588,121 +588,121 @@ class CovData1D(WafoData):
         if method.startswith('dec1'):
             # only correct for variables having the Markov property
             # but still seems to give a reasonable answer. Slow procedure.
-            Sigma = sptoeplitz(hstack((acf, zeros(N-n))))
+            Sigma = sptoeplitz(hstack((acf, zeros(N - n))))
          
             #Soo=Sigma(~inds,~inds); # covariance between known observations
             #S11=Sigma(inds,inds); # covariance between unknown observations
             #S1o=Sigma(inds,~inds);# covariance between known and unknown observations
             #tmp=S1o*pinv(full(Soo)); 
             #tmp=S1o/Soo; # this is time consuming if Soo large
-            tmp = 2*Sigma[inds, indg]/(Sigma[indg, indg] + Sigma[indg, indg].T )
+            tmp = 2 * Sigma[inds, indg] / (Sigma[indg, indg] + Sigma[indg, indg].T)
             
             if compute_sigma:
                 #standard deviation of the expected surface
                 #mu1o_std=sqrt(diag(S11-tmp*S1o'));
-                mu1o_std = sqrt(diag(Sigma[inds, inds]-tmp*Sigma[indg, inds]))
+                mu1o_std = sqrt(diag(Sigma[inds, inds] - tmp * Sigma[indg, inds]))
             
             
             #expected surface conditioned on the known observations from x
-            mu1o = tmp*x[indg]
+            mu1o = tmp * x[indg]
             #expected surface conditioned on the known observations from xs
-            mu1os = tmp*(xs[indg,:])
+            mu1os = tmp * (xs[indg, :])
             # sampled surface conditioned on the known observations
-            sample = mu1o + xs[inds,:] - mu1os 
+            sample = mu1o + xs[inds, :] - mu1os 
             
         elif method.startswith('dec2'):
             # only correct for variables having the Markov property
             # but still seems to give a reasonable answer
             # approximating the expected surfaces conditioned on 
             # the known observations from x and xs by only using the closest points
-            Sigma = sptoeplitz(hstack((acf,zeros(n))))
-            n2 = int(floor(n/2))
-            idx = r_[0:2*n] + max(0,inds[0]-n2) # indices to the points used
-            tmpinds = zeros(N,dtype=bool)
+            Sigma = sptoeplitz(hstack((acf, zeros(n))))
+            n2 = int(floor(n / 2))
+            idx = r_[0:2 * n] + max(0, inds[0] - n2) # indices to the points used
+            tmpinds = zeros(N, dtype=bool)
             tmpinds[inds] = True # temporary storage of indices to missing points
             tinds = where(tmpinds[idx])[0] # indices to the points used
-            tindg = where(1-tmpinds[idx])[0]
+            tindg = where(1 - tmpinds[idx])[0]
             ns = len(tinds); # number of missing data in the interval
             nprev = 0; # number of previously simulated points
-            xsinds = xs[inds,:]
-            while ns>0:
-                tmp=2*Sigma[tinds, tindg]/(Sigma[tindg, tindg]+Sigma[tindg, tindg].T)
+            xsinds = xs[inds, :]
+            while ns > 0:
+                tmp = 2 * Sigma[tinds, tindg] / (Sigma[tindg, tindg] + Sigma[tindg, tindg].T)
                 if compute_sigma:
                     #standard deviation of the expected surface
                     #mu1o_std=sqrt(diag(S11-tmp*S1o'));
-                    ix = slice(nprev+1,nprev+ns+1)
-                    mu1o_std[ix] = max(mu1o_std[ix], 
-                            sqrt(diag(Sigma[tinds, tinds]-tmp*Sigma[tindg,tinds])))
+                    ix = slice(nprev + 1, nprev + ns + 1)
+                    mu1o_std[ix] = max(mu1o_std[ix],
+                            sqrt(diag(Sigma[tinds, tinds] - tmp * Sigma[tindg, tinds])))
                 #end
               
                 #expected surface conditioned on the closest known observations
                 # from x and xs2
-                mu1o[(nprev+1):(nprev+ns+1)] = tmp*x[idx[tindg]]
-                mu1os[(nprev+1):(nprev+ns+1),:] = tmp*xs[idx[tindg],:]      
+                mu1o[(nprev + 1):(nprev + ns + 1)] = tmp * x[idx[tindg]]
+                mu1os[(nprev + 1):(nprev + ns + 1), :] = tmp * xs[idx[tindg], :]      
                
-                if idx[-1]==N-1:# 
-                    ns =0  # no more points to simulate
+                if idx[-1] == N - 1:# 
+                    ns = 0  # no more points to simulate
                 else:
                     # updating by  putting expected surface into x     
-                    x[idx[tinds]] = mu1o[(nprev+1):(nprev+ns+1)]
-                    xs[idx[tinds]] = mu1os[(nprev+1):(nprev+ns+1)]
+                    x[idx[tinds]] = mu1o[(nprev + 1):(nprev + ns + 1)]
+                    xs[idx[tinds]] = mu1os[(nprev + 1):(nprev + ns + 1)]
         
                     nw = sum(tmpinds[idx[-n2:]])# # data which we want to simulate once 
                     tmpinds[idx[:-n2]] = False # removing indices to data ..
                     # which has been simulated
-                    nprev = nprev+ns-nw # update # points simulated so far
+                    nprev = nprev + ns - nw # update # points simulated so far
                               
-                    if (nw==0) and (nprev<Ns): 
-                        idx= r_[0:2*n]+(inds[nprev+1]-n2) # move to the next missing data
+                    if (nw == 0) and (nprev < Ns): 
+                        idx = r_[0:2 * n] + (inds[nprev + 1] - n2) # move to the next missing data
                     else:
-                        idx = idx+n
+                        idx = idx + n
                     #end
-                    tmp = N-idx[-1]
-                    if tmp<0: # checking if tmp exceeds the limits
-                        idx = idx+tmp
+                    tmp = N - idx[-1]
+                    if tmp < 0: # checking if tmp exceeds the limits
+                        idx = idx + tmp
                     #end
                     # find new interval with missing data
                     tinds = where(tmpinds[idx])[0]
-                    tindg = where(1-tmpinds[idx])[0]
+                    tindg = where(1 - tmpinds[idx])[0]
                     ns = len(tinds);# # missing data
                 #end  
             #end
             # sampled surface conditioned on the known observations
-            sample = mu1o+(xsinds-mu1os) 
+            sample = mu1o + (xsinds - mu1os) 
         elif method.startswith('dec3'): 
             # this is not correct for even for variables having the 
             # Markov property but still seems to give a reasonable answer
             # a quasi approach approximating the expected surfaces conditioned on 
             # the known observations from x and xs with a spline
             
-            mu1o = interp1(indg, x[indg],inds,'spline')
-            mu1os = interp1(indg, xs[indg,:],inds,'spline')
+            mu1o = interp1(indg, x[indg], inds, 'spline')
+            mu1os = interp1(indg, xs[indg, :], inds, 'spline')
             # sampled surface conditioned on the known observations
-            sample = mu1o + (xs[inds,:]-mu1os) 
+            sample = mu1o + (xs[inds, :] - mu1os) 
         
         elif method.startswith('exac') or method.startswith('pseu'):
             # exact but slow. It also may not return any result
-            Sigma = sptoeplitz(hstack((acf,zeros(N-n))))
+            Sigma = sptoeplitz(hstack((acf, zeros(N - n))))
             #Soo=Sigma(~inds,~inds); # covariance between known observations
             #S11=Sigma(inds,inds); # covariance between unknown observations
             #S1o=Sigma(inds,~inds);# covariance between known and unknown observations
             #tmp=S1o/Soo; # this is time consuming if Soo large
-            if method[0]=='e': #exact
-                tmp = 2*Sigma[inds,indg]/(Sigma[indg,indg]+Sigma[indg,indg].T);
+            if method[0] == 'e': #exact
+                tmp = 2 * Sigma[inds, indg] / (Sigma[indg, indg] + Sigma[indg, indg].T);
             else: # approximate the inverse with pseudo inverse
-                tmp = dot(Sigma[inds, indg],pinv(Sigma[indg,indg]))
+                tmp = dot(Sigma[inds, indg], pinv(Sigma[indg, indg]))
             #end
             #expected surface conditioned on the known observations from x
-            mu1o = dot(tmp,x[indg])
+            mu1o = dot(tmp, x[indg])
             # Covariance conditioned on the known observations
-            Sigma1o = Sigma[inds,inds] - tmp*Sigma[indg,inds]
+            Sigma1o = Sigma[inds, inds] - tmp * Sigma[indg, inds]
             #sample conditioned on the known observations from x
             sample = random.multivariate_normal(mu1o, Sigma1o, cases)
             #rndnormnd(mu1o,Sigma1o,cases )
             
             if compute_sigma:
                 #standard deviation of the expected surface
-                mu1o_std=sqrt(diag(Sigma1o));
+                mu1o_std = sqrt(diag(Sigma1o));
             #end
  
         elif method.startswith('appr'):
@@ -714,58 +714,58 @@ class CovData1D(WafoData):
             # approximately the same bandstructure as the inverse of the
             # covariance matrix
             
-            Nsig = 2*n;
+            Nsig = 2 * n;
             
-            Sigma = sptoeplitz(hstack((ACF,zeros(Nsig-n))))
-            n2 = floor(Nsig/4)
-            idx = r_[0:Nsig]+max(0,inds[0]-n2) # indices to the points used
-            tmpinds = zeros(N,dtype=bool)
+            Sigma = sptoeplitz(hstack((ACF, zeros(Nsig - n))))
+            n2 = floor(Nsig / 4)
+            idx = r_[0:Nsig] + max(0, inds[0] - n2) # indices to the points used
+            tmpinds = zeros(N, dtype=bool)
             tmpinds[inds] = True # temporary storage of indices to missing points
             tinds = where(tmpinds[idx])[0] # indices to the points used
-            tindg = where(1-tmpinds[idx])[0]
+            tindg = where(1 - tmpinds[idx])[0]
             ns = len(tinds) # number of missing data in the interval
             
             nprev = 0  # number of previously simulated points
             x2 = x
             
-            while ns>0:
+            while ns > 0:
                 #make sure MATLAB uses a symmetric matrix solver
-                tmp = 2*Sigma[tinds,tindg]/(Sigma[tindg,tindg]+Sigma[tindg,tindg].T)
-                Sigma1o = Sigma[tinds,tinds] - tmp*Sigma[tindg,tinds]
+                tmp = 2 * Sigma[tinds, tindg] / (Sigma[tindg, tindg] + Sigma[tindg, tindg].T)
+                Sigma1o = Sigma[tinds, tinds] - tmp * Sigma[tindg, tinds]
                 if compute_sigma:
                     #standard deviation of the expected surface
                     #mu1o_std=sqrt(diag(S11-tmp*S1o'));
-                    mu1o_std[(nprev+1):(nprev+ns+1)] = max( mu1o_std[(nprev+1):(nprev+ns)] , 
+                    mu1o_std[(nprev + 1):(nprev + ns + 1)] = max(mu1o_std[(nprev + 1):(nprev + ns)] ,
                                                             sqrt(diag(Sigma1o)))
                 #end
         
                 #expected surface conditioned on the closest known observations from x
-                mu1o[(nprev+1):(nprev+ns+1)] = tmp*x2[idx[tindg]]
+                mu1o[(nprev + 1):(nprev + ns + 1)] = tmp * x2[idx[tindg]]
                 #sample conditioned on the known observations from x
-                sample[(nprev+1):(nprev+ns+1),:] = rndnormnd(tmp*x[idx[tindg]],Sigma1o, cases)     
-                if idx[-1] == N-1: 
+                sample[(nprev + 1):(nprev + ns + 1), :] = rndnormnd(tmp * x[idx[tindg]], Sigma1o, cases)     
+                if idx[-1] == N - 1: 
                     ns = 0 # no more points to simulate
                 else:
                     # updating
-                    x2[idx[tinds]] = mu1o[(nprev+1):(nprev+ns+1)] #expected surface
-                    x[idx[tinds]] = sample[(nprev+1):(nprev+ns+1)]#sampled surface
-                    nw = sum(tmpinds[idx[-n2::]]==True)# # data we want to simulate once more
+                    x2[idx[tinds]] = mu1o[(nprev + 1):(nprev + ns + 1)] #expected surface
+                    x[idx[tinds]] = sample[(nprev + 1):(nprev + ns + 1)]#sampled surface
+                    nw = sum(tmpinds[idx[-n2::]] == True)# # data we want to simulate once more
                     tmpinds[idx[:-n2]] = False # removing indices to data ..
                     # which has been simulated
-                    nprev = nprev+ns-nw # update # points simulated so far
+                    nprev = nprev + ns - nw # update # points simulated so far
             
-                    if (nw==0) and (nprev<Ns):
-                        idx = r_[0:Nsig]+(inds[nprev+1]-n2) # move to the next missing data
+                    if (nw == 0) and (nprev < Ns):
+                        idx = r_[0:Nsig] + (inds[nprev + 1] - n2) # move to the next missing data
                     else:
-                        idx = idx+n
+                        idx = idx + n
                     #end
-                    tmp = N-idx[-1]
-                    if tmp<0: # checking if tmp exceeds the limits
+                    tmp = N - idx[-1]
+                    if tmp < 0: # checking if tmp exceeds the limits
                         idx = idx + tmp
                     #end
                     # find new interval with missing data
                     tinds = where(tmpinds[idx])[0]
-                    tindg = where(1-tmpinds[idx])[0]
+                    tindg = where(1 - tmpinds[idx])[0]
                     ns = len(tinds);# # missing data in the interval
               #end
             #end
@@ -787,17 +787,17 @@ class CovData1D(WafoData):
 def sptoeplitz(x):
     k = where(x.ravel())[0]
     n = len(x)
-    if len(k)>0.3*n:
+    if len(k) > 0.3 * n:
         return toeplitz(x)
     else:
         spdiags = sparse.dia_matrix
-        data = x[k].reshape(-1,1).repeat(n,axis=-1)
+        data = x[k].reshape(-1, 1).repeat(n, axis= -1)
         offsets = k
-        y = spdiags((data, offsets), shape=(n,n))
-        if k[0]==0:
+        y = spdiags((data, offsets), shape=(n, n))
+        if k[0] == 0:
             offsets = k[1::]
-            data = data[1::,:]
-        return y + spdiags((data, -offsets), shape=(n,n))
+            data = data[1::, :]
+        return y + spdiags((data, -offsets), shape=(n, n))
 
 def test_covdata():
     import wafo.data
@@ -823,4 +823,4 @@ if __name__ == '__main__':
         import doctest
         doctest.testmod()
     else:
-        main()
+        main()

pywafo/src/wafo/integrate.py

@@ -6,9 +6,8 @@ from numpy import pi, sqrt, ones, zeros #@UnresolvedImport
 from scipy import integrate as intg
 import scipy.special.orthogonal as ort
 from scipy import special as sp
-import matplotlib
 import pylab as plb
-matplotlib.interactive(True)
+
 _POINTS_AND_WEIGHTS = {}
 
 def humps(x=None):
@@ -344,7 +343,7 @@ def h_roots(n, method='newton'):
     >>> import numpy as np
     >>> [x,w] = h_roots(10)
     >>> np.sum(x*w)
-    -5.2516042729766621e-019
+    -5.2516042729766621e-19
 
     See also
     --------
@@ -453,7 +452,7 @@ def j_roots(n, alpha, beta, method='newton'):
     --------
     >>> [x,w]= j_roots(10,0,0)
     >>> sum(x*w)
-    2.7755575615628914e-016
+    2.7755575615628914e-16
 
     See also
     --------
@@ -554,7 +553,7 @@ def la_roots(n, alpha=0, method='newton'):
     >>> import numpy as np
     >>> [x,w] = h_roots(10)
     >>> np.sum(x*w)
-    -5.2516042729766621e-019
+    -5.2516042729766621e-19
 
     See also
     --------
@@ -939,7 +938,7 @@ def gaussq(fun, a, b, reltol=1e-3, abstol=1e-3, alpha=0, beta=0, wfun=1,
     integration of x**2        from 0 to 2 and from 1 to 4
 
     >>> from scitools import numpyutils as npt
-    scitools.easyviz backend is gnuplot
+    scitools.easyviz backend is matplotlib
     >>> A = [0, 1]; B = [2,4]
     >>> fun = npt.wrap2callable('x**2')
     >>> [val1,err1] = gaussq(fun,A,B)
@@ -1165,22 +1164,22 @@ def quadgr(fun,a,b,abseps=1e-5):
     >>> import numpy as np
     >>> Q, err = quadgr(np.log,0,1)
     >>> quadgr(np.exp,0,9999*1j*np.pi)
-    (-2.0000000000122617, 2.1933275196062141e-009)
+    (-2.0000000000122617, 2.1933275196062141e-09)
 
     >>> quadgr(lambda x: np.sqrt(4-x**2),0,2,1e-12)
-    (3.1415926535897811, 1.5809575870662229e-013)
+    (3.1415926535897811, 1.5809575870662229e-13)
 
     >>> quadgr(lambda x: x**-0.75,0,1)
-    (4.0000000000000266, 5.6843418860808015e-014)
+    (4.0000000000000266, 5.6843418860808015e-14)
 
     >>> quadgr(lambda x: 1./np.sqrt(1-x**2),-1,1)
-    (3.141596056985029, 6.2146261559092864e-006)
+    (3.141596056985029, 6.2146261559092864e-06)
 
     >>> quadgr(lambda x: np.exp(-x**2),-np.inf,np.inf,1e-9) #% sqrt(pi)
-    (1.7724538509055152, 1.9722334876348668e-011)
+    (1.7724538509055152, 1.9722334876348668e-11)
 
     >>> quadgr(lambda x: np.cos(x)*np.exp(-x),0,np.inf,1e-9)
-    (0.50000000000000044, 7.3296813063450372e-011)
+    (0.50000000000000044, 7.3296813063450372e-11)
 
     See also
     --------
@@ -1418,7 +1417,7 @@ def qdemo(f,a,b):
         #[x, w]=qrule(n,1)
         #x = (b-a)/2*x + (a+b)/2     % Transform base points X.
         #w = (b-a)/2*w               % Adjust weigths.
-        #q = sum(feval(f,x).*w)
+        #q = sum(feval(f,x)*w)
         qg[k] = q
         eg[k] = abs(q - true_val)
 

pywafo/src/wafo/kdetools.py

@@ -15,7 +15,7 @@ from numpy import pi, atleast_2d #@UnresolvedImport
 from misc import tranproc, trangood
 def sphere_volume(d, r=1.0):
     """
-     Returns volume of  d-dimensional sphere with radius r
+    Returns volume of  d-dimensional sphere with radius r
 
     Parameters
     ----------

pywafo/src/wafo/objects.py

@@ -694,8 +694,9 @@ class TimeSeries(WafoData):
     Examples
     --------
     >>> import wafo.data
+    >>> import wafo.objects as wo
     >>> x = wafo.data.sea()
-    >>> ts = wafo.objects.mat2timeseries(x)
+    >>> ts = wo.mat2timeseries(x)
     >>> rf = ts.tocovdata(lag=150)
     >>> h = rf.plot()
 
@@ -771,8 +772,9 @@ class TimeSeries(WafoData):
          Example:
          --------
          >>> import wafo.data
+         >>> import wafo.objects as wo
          >>> x = wafo.data.sea()
-         >>> ts = mat2timeseries(x)
+         >>> ts = wo.mat2timeseries(x)
          >>> acf = ts.tocovdata(150)
          >>> h = acf.plot()
         '''
@@ -814,6 +816,7 @@ class TimeSeries(WafoData):
         acf = _wafocov.CovData1D(R[lags], t)
         acf.stdev = sqrt(r_[ 0, 1 , 1 + 2 * cumsum(R[1:] ** 2)] / Ncens)
         acf.children = [WafoData(-2. * acf.stdev[lags], t), WafoData(2. * acf.stdev[lags], t)]
+        acf.plot_args_children = ['r:']
         acf.norm = norm
         return acf
 

pywafo/src/wafo/spectrum/__init__.py

@@ -8,4 +8,3 @@ Spectrum package in WAFO Toolbox.
 from wafo.spectrum.core import SpecData1D
 import wafo.spectrum.models
 import wafo.spectrum.dispersion_relation
-#from wafo.data_structures import SpecData1D

pywafo/src/wafo/spectrum/core.py

@@ -1,9 +1,9 @@
 from __future__ import division
-from scipy.misc.ppimport import ppimport
+from wafo.misc import meshgrid
 from wafo.objects import mat2timeseries, TimeSeries
 import warnings
 import numpy as np
-from numpy import (pi, inf, meshgrid, zeros, ones, where, nonzero, #@UnresolvedImport
+from numpy import (pi, inf, zeros, ones, where, nonzero, #@UnresolvedImport
            flatnonzero, ceil, sqrt, exp, log, arctan2, #@UnresolvedImport
            tanh, cosh, sinh, random, atleast_1d, maximum, #@UnresolvedImport
            minimum, diff, isnan, any, r_, conj, mod, #@UnresolvedImport
@@ -945,7 +945,8 @@ class SpecData1D(WafoData):
         ...     res = fun(x2[:,1::],axis=0)
         ...     m = res.mean()
         ...     sa = res.std()
-        ...     assert(np.abs(m-trueval)<sa)
+        ...     trueval, m, sa
+        ...     np.abs(m-trueval)<sa
 
         waveplot(x1,'r',x2,'g',1,1)
 
@@ -1316,8 +1317,6 @@ class SpecData1D(WafoData):
         if verbose:
             print('2nd order frequency Limits = %g,%g' % (f_limit_lo, f_limit_up))
 
-
-
 ##        if nargout>3,
 ##        %compute the sum and frequency effects separately
 ##        [svec, dvec] = disufq((amp.'),w,kw,min(h,10^30),g,nmin,nmax)
@@ -1402,7 +1401,10 @@ class SpecData1D(WafoData):
 
         See also
         ---------
-        hermitetr, ochitr, lc2tr, dat2tr
+        transform.TrHermite
+        transform.TrOchi
+        objects.LevelCrossings.trdata
+        objects.TimeSeries.trdata
 
         References:
         -----------
@@ -1429,7 +1431,7 @@ class SpecData1D(WafoData):
         w = ravel(self.args)
         S = ravel(self.data)
         if self.freqtype in ['f', 'w']:
-            vari = 't'
+            #vari = 't'
             if self.freqtype == 'f':
                 w = 2. * pi * w
                 S = S / (2. * pi)
@@ -1514,7 +1516,7 @@ class SpecData1D(WafoData):
 ##            skew = sum((6*C2+8*E2).*E)/sa^3   % skewness
 ##            kurt = 3+48*sum((C2+E2).*E2)/sa^4 % kurtosis
         return output
-    def testgaussian(self, ns,test0=None, cases=100, method='nonlinear',**opt):
+    def testgaussian(self, ns,test0=None, cases=100, method='nonlinear',verbose=False,**opt):
         '''
         TESTGAUSSIAN Test if a stochastic process is Gaussian.
         
@@ -1607,7 +1609,8 @@ class SpecData1D(WafoData):
             #xs = cov2sdat(R,[ns Nstep]);
             #[g, tmp] = dat2tr(xs,method, **opt);
             #test1 = [test1; tmp(:)]
-            print('finished %d of %d ' % (ix+1,rep) )
+            if verbose:
+                print('finished %d of %d ' % (ix+1,rep) )
         
         if rep>1:
             xs = acf.sim(ns=ns, cases=np.remainder(cases,rep))
@@ -1704,6 +1707,14 @@ class SpecData1D(WafoData):
     def nyquist_freq(self):
         """
         Return Nyquist frequency
+        
+        Example
+        -------
+        >>> import wafo.spectrum.models as sm
+        >>> Sj = sm.Jonswap(Hm0=5)
+        >>> S = Sj.tospecdata() #Make spectrum ob
+        >>> S.nyquist_freq()
+        3.0
         """
         return self.args[-1]
     
@@ -1722,8 +1733,11 @@ class SpecData1D(WafoData):
 
         Example
         -------
-        S = jonswap
-        dt = spec2dt(S)
+        >>> import wafo.spectrum.models as sm
+        >>> Sj = sm.Jonswap(Hm0=5)
+        >>> S = Sj.tospecdata() #Make spectrum ob
+        >>> S.sampling_period()
+        1.0471975511965976
 
         See also
         '''
@@ -1880,9 +1894,16 @@ class SpecData1D(WafoData):
     
         Example:
         ------- 
-        S = jonswap
-        [Sn,mn4] = specnorm(S)
-        mts = spec2mom(S,2)     % Should be equal to one!
+        >>> import wafo.spectrum.models as sm
+        >>> Sj = sm.Jonswap(Hm0=5)
+        >>> S = Sj.tospecdata() #Make spectrum ob
+        >>> S.moment(2)
+        ([1.5614600345079888, 0.95567089481941048], ['m0', 'm0tt'])
+        >>> Sn = S.copy(); Sn.normalize()
+        
+        Now the moments should be one
+        >>> Sn.moment(2)
+        ([1.0000000000000004, 0.99999999999999967], ['m0', 'm0tt'])
         '''
         mom, unused_mtext = self.moment(nr=4, even=True)
         m0 = mom[0] 
@@ -2018,7 +2039,6 @@ class SpecData1D(WafoData):
 
         Examples:
         ---------
-        >>> import numpy as np
         >>> import wafo.spectrum.models as sm
         >>> Sj = sm.Jonswap(Hm0=5)
         >>> S = Sj.tospecdata() #Make spectrum ob

pywafo/src/wafo/spectrum/models.py

@@ -53,8 +53,6 @@ from numpy import (inf, atleast_1d, newaxis, any, minimum, maximum, array, #@Unr
     isfinite, mod, expm1, tanh, cosh, finfo, ones, ones_like, isnan, #@UnresolvedImport
     zeros_like, flatnonzero, sinc, hstack, vstack, real, flipud, clip) #@UnresolvedImport
 from dispersion_relation import w2k
-#ppimport.enable()
-#_wafospectrum = ppimport.ppimport('wafo.spectrum')
 from wafo.spectrum import SpecData1D
 sech = lambda x: 1.0 / cosh(x)
 
@@ -638,8 +636,6 @@ class Jonswap(ModelSpectrum):
 def phi1(wi, h, g=9.81):
     ''' Factor transforming spectra to finite water depth spectra.
 
-     CALL: tr = phi1(w,h)
-
     Input
     -----
          w : arraylike
@@ -743,7 +739,8 @@ class Tmaspec(Jonswap):
     phi1,
     Torsethaugen
 
-    References:
+    References
+    ----------
     Buows, E., Gunther, H., Rosenthal, W., and Vincent, C.L. (1985)
     'Similarity of the wind wave spectrum in finite depth water: 1 spectral form.'
     J. Geophys. Res., Vol 90, No. C1, pp 975-986
@@ -1361,8 +1358,8 @@ class Spreading(object):
     (Hasselman: spa ~= spb)  (cos-2s) [6.97 9.77  4.06 -2.3  0    1.05 3  ]
     (Banner   : spa ~= spb)  (sech2)  [2.61 2.28  1.3  -1.3  0.56 0.95 1.6]
 
-    Examples :
-
+    Examples
+    --------
     >>> import pylab as plb
     >>> D = Spreading('cos2s',s_a=10.0)
 
@@ -1385,9 +1382,12 @@ class Spreading(object):
     >>> plb.close('all')
 
 
-    See also  mkdspec, plotspec, spec2spec
+    See also
+    --------
+    mkdspec, plotspec, spec2spec
 
     References
+    ---------
     Krogstad, H.E. and Barstow, S.F. (1999)
     "Directional Distributions in Ocean Wave Spectra"
     Proceedings of the 9th ISOPE Conference, Vol III, pp. 79-86

pywafo/src/wafo/transform/core.py

@@ -159,7 +159,7 @@ class TrData(WafoData, TrCommon):
     >>> g.sigma
     5
     >>> g.dat2gauss(1,2,3)
-    
+    [array([ 0.]), array([ 0.4]), array([ 0.6])]
     
     Check that the departure from a Gaussian model is zero
     >>> g.dist2gauss() < 1e-16

pywafo/src/wafo/transform/models.py

@@ -3,6 +3,7 @@ Transform Gaussian models
 -------------------------
 TrHermite
 TrOchi
+TrLinear
 '''
 #-------------------------------------------------------------------------------
 # Name:        transform.models
@@ -84,7 +85,10 @@ class TrHermite(TrCommon):
     
     See also
     --------  
-    spec2skew, ochitr, lc2tr, dat2tr
+    SpecData1d.stats_nl
+    wafo.transform.TrOchi
+    wafo.objects.LevelCrossings.trdata
+    wafo.objects.TimeSeries.trdata
 
     References
     ----------
@@ -306,6 +310,11 @@ class TrLinear(TrCommon):
     
     See also
     --------  
+    TrOchi
+    TrHermite
+    SpecData1D.stats_nl
+    LevelCrossings.trdata
+    TimeSeries.trdata
     spec2skew, ochitr, lc2tr, dat2tr
 
     """

pywafo/src/wafo/transform/test/test_models.py

@@ -0,0 +1,47 @@
+from wafo.transform.models import TrHermite, TrOchi, TrLinear
+
+def test_trhermite():
+    '''
+    >>> std = 7./4
+    >>> g = TrHermite(sigma=std, ysigma=std)
+    >>> g.dist2gauss()
+    3.9858776379926808
+    
+    >>> g.mean
+    0.0
+    >>> g.sigma
+    1.75
+    >>> g.dat2gauss([0,1,2,3])
+    array([ 0.04654321,  1.03176393,  1.98871279,  2.91930895])
+    
+    '''
+def test_trochi():
+    '''
+    >>> std = 7./4
+    >>> g = TrOchi(sigma=std, ysigma=std)
+    >>> g.dist2gauss()
+    5.9322684525265501
+    >>> g.mean
+    0.0
+    >>> g.sigma
+    1.75
+    >>> g.dat2gauss([0,1,2,3])
+    array([  6.21927960e-04,   9.90237621e-01,   1.96075606e+00,
+             2.91254576e+00])
+    '''
+def test_trlinear():
+    '''
+    >>> std = 7./4
+    >>> g = TrLinear(sigma=std, ysigma=std)
+    >>> g.dist2gauss()
+    0.0
+    >>> g.mean
+    0.0
+    >>> g.sigma
+    1.75
+    >>> g.dat2gauss([0,1,2,3])
+    array([ 0.,  1.,  2.,  3.])
+    '''
+if __name__=='__main__':
+    import doctest
+    doctest.testmod()

pywafo/src/wafo/transform/test/test_trdata.py

@@ -0,0 +1,32 @@
+from wafo.transform import TrData
+
+def test_trdata():
+    '''
+    Construct a linear transformation model
+    >>> import numpy as np
+    >>> sigma = 5; mean = 1
+    >>> u = np.linspace(-5,5); x = sigma*u+mean; y = u
+    >>> g = TrData(y,x)
+    >>> g.mean
+    array([ 1.])
+    >>> g.sigma
+    array([ 5.])
+    
+    >>> g = TrData(y,x,mean=1,sigma=5)
+    >>> g.mean
+    1
+    >>> g.sigma
+    5
+    >>> g.dat2gauss(1,2,3)
+    [array([ 0.]), array([ 0.4]), array([ 0.6])]
+    >>> g.dat2gauss([0,1,2,3])
+    array([-0.2,  0. ,  0.2,  0.4])
+    
+    Check that the departure from a Gaussian model is zero
+    >>> g.dist2gauss() < 1e-16
+    True
+    '''
+    
+if __name__=='__main__':
+    import doctest
+    doctest.testmod()