Cosmetic fixes

pywafo/src/wafo/covariance/core.py

@@ -17,7 +17,7 @@ date : Date and time of creation or change.
 from __future__ import division
 import warnings
 #import numpy as np
-from numpy import (zeros, sqrt, dot, newaxis, inf, where, pi, nan, #@UnresolvedImport
+from numpy import (zeros, sqrt, dot, inf, where, pi, nan, #@UnresolvedImport
                    atleast_1d, hstack, vstack, r_, linspace, flatnonzero, size, #@UnresolvedImport
                    isnan, finfo, diag, ceil, floor, random, pi) #@UnresolvedImport
 from numpy.fft import fft #as fft
@@ -810,7 +810,7 @@ def sptoeplitz(x):
             data = data[1::, :]
         return y + spdiags((data, -offsets), shape=(n, n))
 
-def test_covdata():
+def _test_covdata():
     import wafo.data
     x = wafo.data.sea()
     ts = wafo.objects.mat2timeseries(x)

pywafo/src/wafo/doc/tutorial_scripts/chapter1.py

@@ -195,7 +195,7 @@ ylabel('(m)')
 
 #! Formation of 5 min maxima
 yura = xn[:85500, 1]
-yura = np.reshape(yura, (300, 285))
+yura = np.reshape(yura, (285,300)).T
 maxyura = yura.max(axis=0)
 subplot(212)
 plot(xn[299:85500:300, 0] / 3600, maxyura, '.')
@@ -207,7 +207,7 @@ show()
 #! Estimation of GEV for yuramax
 clf()
 import wafo.stats as ws
-phat = ws.genextreme.fit2(maxyura, method='mps')
+phat = ws.genextreme.fit2(maxyura, method='ml')
 phat.plotfitsummary()
 show()
 #disp('Block = 11, Last block')

pywafo/src/wafo/misc.py

@@ -1942,21 +1942,26 @@ def tranproc(x, f, x0, *xi):
     return y #y0,y1,y2,y3,y4
 
 def histgrm(data, n=None, odd=False, scale=False, lintype='b-'):
-    '''HISTGRM Plot histogram
+    '''
-     
+    Plot histogram
-     CALL:  binwidth = histgrm(x,N,odd,scale)
-            binwidth = the width of each bin
              
     Parameters
     -----------
-    x = the data
+    data : array-like
-    n = approximate number of bins wanted 
+        the data
-        (default depending on length(x))  
+    n : scalar integer
-    odd = placement of bins (0 or 1) (default 0)
+        approximate number of bins wanted  (default depending on length(data))  
-    scale = argument for scaling (default 0)
+    odd : bool
-    scale = 1 yields the area 1 under the histogram
+        placement of bins (0 or 1) (default 0)
+    scale : bool
+        argument for scaling (default 0)
+        scale = 1 yields the area 1 under the histogram
     lintype : specify color and lintype, see PLOT for possibilities.
     
+    Returns
+    -------
+    binwidth = the width of each bin
+    
      Example:
        R=rndgumb(2,2,1,100);
        histgrm(R,20,0,1)
@@ -1985,8 +1990,6 @@ def histgrm(data, n=None, odd=False, scale=False, lintype='b-'):
     mx = (np.ceil(mx / d) + 1) * d + odd * d / 2
     limits = np.arange(mn, mx, d)
     
-   
-    
     bin, limits = np.histogram(data, bins=limits, normed=scale) #, new=True)
     limits.shape = (-1, 1)
     xx = limits.repeat(3, axis=1)

pywafo/src/wafo/objects.py

@@ -25,7 +25,7 @@ import warnings
 import numpy as np
 
 from numpy import (inf, pi, zeros, ones, sqrt, where, log, exp, sin, arcsin, mod, finfo, interp, #@UnresolvedImport
-                   newaxis, linspace, arange, sort, all, abs, vstack, hstack, atleast_1d, #@UnresolvedImport
+                   linspace, arange, sort, all, abs, vstack, hstack, atleast_1d, #@UnresolvedImport
                    finfo, polyfit, r_, nonzero, cumsum, ravel, size, isnan, nan, floor, ceil, diff, array) #@UnresolvedImport
 from numpy.fft import fft
 from numpy.random import randn
@@ -34,7 +34,7 @@ from pylab import stineman_interp
 from matplotlib.mlab import psd, detrend_mean
 import scipy.signal
 
-from wafo.misc import (nextpow2, findtp, findtc, findcross, sub_dict_select,
+from wafo.misc import (nextpow2, findtp, findtc, findcross,  
                        ecross, JITImport, DotDict)
 from wafodata import WafoData
 from plotbackend import plotbackend

pywafo/src/wafo/source/mreg/build_all_.py

@@ -7,29 +7,15 @@ gfortran -W -Wall -pedantic-errors -fbounds-check -Werror -c dsvdc.f mregmodule.
 import os
 
 def compile_all():
-    files = ['mregmodule',  'dsvdc']
+    files = ['dsvdc','mregmodule']
     compile1_format = 'gfortran -fPIC -c %s.f'
     format1 = '%s.o ' * len(files)
     for file in files:
         os.system(compile1_format % file)
     file_objects = format1  % tuple(files)
-    #f2py --fcompiler=gnu95 --compiler=mingw32 -lmsvcr71 -m mymod  -c mymod.f90
     
-    os.system('f2py -m cov2mod  -c %s cov2mmpdfreg_intfc.f --fcompiler=gnu95 --compiler=mingw32 -lmsvcr71' % file_objects)
+    os.system('f2py.py -m cov2mod  -c %s cov2mmpdfreg_intfc.f' % file_objects)
-    #compile1_txt = 'gfortran -fPIC -c mvnprd.f'
-    #compile2_txt = 'f2py -m mvnprdmod  -c mvnprd.o mvnprd_interface.f --fcompiler=gnu95 --compiler=mingw32 -lmsvcr71'
-    #os.system(compile1_txt)
-    #os.system(compile2_txt)
-    # Install gfortran and run the following to build the module:
-    #compile_format = 'f2py %s %s -c --fcompiler=gnu95 --compiler=mingw32 -lmsvcr71'
      
-    # Install microsoft visual c++ .NET 2003 and run the following to build the module:
-    #compile_format = 'f2py %s %s -c'
-    #pyfs = ('c_library.pyf',)
-    #files =('c_functions.c',)
-
-    #for pyf,file in zip(pyfs,files):
-    #    os.system(compile_format % (pyf,file))
     
 if __name__=='__main__':
     compile_all()

pywafo/src/wafo/source/mreg/mregmod.mod

@@ -1,5 +1,5 @@
-GFORTRAN module version '0' created from mregmodule.f on Wed Aug 05 19:21:17 2009
+GFORTRAN module version '0' created from mregmodule.f on Tue Jan 25 20:12:17 2011
-MD5:35f9c2506fae455bf63c0bcfadd75d2e -- If you edit this, you'll get what you deserve.
+MD5:a058cc3e6c0e8bedef8f214da2f5fbdc -- If you edit this, you'll get what you deserve.
 
 (()
 () () () () () () () () () () () () () () () () () () () () () () () ()
@@ -61,8 +61,6 @@ INTEGER ()) 0 '1') (CONSTANT (INTEGER 4 0 0 INTEGER ()) 0 '40401')) 0 ()
 DUMMY) (REAL 8 0 0 REAL ()) 0 0 () (1 EXPLICIT (CONSTANT (INTEGER 4 0 0
 INTEGER ()) 0 '1') (CONSTANT (INTEGER 4 0 0 INTEGER ()) 0 '201')) 0 () ()
 () 0 0)
-18 'n' '' 'n' 7 ((VARIABLE IN UNKNOWN-PROC UNKNOWN UNKNOWN DUMMY) (
-INTEGER 4 0 0 INTEGER ()) 0 0 () () 0 () () () 0 0)
 11 'db' '' 'db' 7 ((VARIABLE INOUT UNKNOWN-PROC UNKNOWN UNKNOWN
 DIMENSION DUMMY) (REAL 8 0 0 REAL ()) 0 0 () (1 EXPLICIT (CONSTANT (
 INTEGER 4 0 0 INTEGER ()) 0 '1') (CONSTANT (INTEGER 4 0 0 INTEGER ()) 0
@@ -76,14 +74,10 @@ INTEGER 4 0 0 INTEGER ()) 0 '1') (CONSTANT (INTEGER 4 0 0 INTEGER ()) 0
 DIMENSION DUMMY) (REAL 8 0 0 REAL ()) 0 0 () (1 EXPLICIT (CONSTANT (
 INTEGER 4 0 0 INTEGER ()) 0 '1') (CONSTANT (INTEGER 4 0 0 INTEGER ()) 0
 '7')) 0 () () () 0 0)
-19 'nit' '' 'nit' 7 ((VARIABLE IN UNKNOWN-PROC UNKNOWN UNKNOWN DUMMY) (
-INTEGER 4 0 0 INTEGER ()) 0 0 () () 0 () () () 0 0)
 14 'a' '' 'a' 7 ((VARIABLE INOUT UNKNOWN-PROC UNKNOWN UNKNOWN DIMENSION
 DUMMY) (REAL 8 0 0 REAL ()) 0 0 () (1 EXPLICIT (CONSTANT (INTEGER 4 0 0
 INTEGER ()) 0 '1') (CONSTANT (INTEGER 4 0 0 INTEGER ()) 0 '1407')) 0 ()
 () () 0 0)
-20 'infr' '' 'infr' 7 ((VARIABLE IN UNKNOWN-PROC UNKNOWN UNKNOWN DUMMY)
-(INTEGER 4 0 0 INTEGER ()) 0 0 () () 0 () () () 0 0)
 15 'da' '' 'da' 7 ((VARIABLE INOUT UNKNOWN-PROC UNKNOWN UNKNOWN
 DIMENSION DUMMY) (REAL 8 0 0 REAL ()) 0 0 () (1 EXPLICIT (CONSTANT (
 INTEGER 4 0 0 INTEGER ()) 0 '1') (CONSTANT (INTEGER 4 0 0 INTEGER ()) 0
@@ -92,6 +86,12 @@ INTEGER 4 0 0 INTEGER ()) 0 '1') (CONSTANT (INTEGER 4 0 0 INTEGER ()) 0
 (REAL 8 0 0 REAL ()) 0 0 () () 0 () () () 0 0)
 17 'm' '' 'm' 7 ((VARIABLE IN UNKNOWN-PROC UNKNOWN UNKNOWN DUMMY) (
 INTEGER 4 0 0 INTEGER ()) 0 0 () () 0 () () () 0 0)
+18 'n' '' 'n' 7 ((VARIABLE IN UNKNOWN-PROC UNKNOWN UNKNOWN DUMMY) (
+INTEGER 4 0 0 INTEGER ()) 0 0 () () 0 () () () 0 0)
+19 'nit' '' 'nit' 7 ((VARIABLE IN UNKNOWN-PROC UNKNOWN UNKNOWN DUMMY) (
+INTEGER 4 0 0 INTEGER ()) 0 0 () () 0 () () () 0 0)
+20 'infr' '' 'infr' 7 ((VARIABLE IN UNKNOWN-PROC UNKNOWN UNKNOWN DUMMY)
+(INTEGER 4 0 0 INTEGER ()) 0 0 () () 0 () () () 0 0)
 )
 
 ('fi' 0 2 'mreg' 0 4 'rind' 0 3)

pywafo/src/wafo/source/rind2007/build_all.py

@@ -11,7 +11,6 @@ def compile_all():
         os.system(compile1_format % file)
     file_objects = format1  % tuple(files)
     
-    #os.system('f2py.py -m rindmod  -c %s rind_interface.f --fcompiler=gnu95 --compiler=mingw32 -lmsvcr71' % file_objects)
     os.system('f2py.py -m rindmod  -c %s rind_interface.f ' % file_objects)
     
 if __name__=='__main__':

pywafo/src/wafo/spectrum/core.py

@@ -803,6 +803,9 @@ class SpecData1D(WafoData):
         >>> S.data[100:-1] = 0.0
         >>> Nt = len(S.data)-1
         >>> acf = S.tocovdata(nr=0, nt=Nt)
+        >>> S1 = acf.tospecdata()
+        >>> h = S.plot('r')
+        >>> h1 = S1.plot('b:')
 
         R   = spec2cov(spec,0,Nt)
         win = parzen(2*Nt+1)
@@ -2345,8 +2348,8 @@ class SpecData1D(WafoData):
 
             newNfft = 2 ** nextpow2(ceil(wnNew / dwMin)) + 1
             if newNfft > nfft:
-                if (nfft <= 2 ** 15 + 1) and (newNfft > 2 ** 15 + 1):
+                #if (nfft <= 2 ** 15 + 1) and (newNfft > 2 ** 15 + 1):
-                    warnings.warn('Spectrum matrix is very large (>33k). Memory problems may occur.')
+                #    warnings.warn('Spectrum matrix is very large (>33k). Memory problems may occur.')
 
                 nfft = newNfft
             self.args = linspace(0, wnNew, nfft)
@@ -2442,18 +2445,16 @@ class SpecData1D(WafoData):
         >>> Sj = sm.Jonswap(Hm0=3, Tp=7)
         >>> w = np.linspace(0,4,256)
         >>> S = SpecData1D(Sj(w),w) #Make spectrum object from numerical values
-        >>> S.bandwidth([0,1,2,3])
+        >>> S.bandwidth([0,'eps2',2,3])
         array([ 0.73062845,  0.34476034,  0.68277527,  2.90817052])
         '''
-
-#        if self.freqtype in 'k':
-#            vari = 'k'
-#        else:
-#            vari = 'w'
-
         m, unused_mtxt = self.moment(nr=4, even=False)
         
-        fact = atleast_1d(factors)
+        fact_dict=dict(alpha=0,eps2=1,eps4=3,qp=3,Qp=3)
+        fun = lambda fact: fact_dict.get(fact,fact)
+        fact = atleast_1d(map(fun,list(factors)))
+        
+        #fact = atleast_1d(fact)
         alpha = m[2] / sqrt(m[0] * m[4])
         eps2 = sqrt(m[0] * m[2] / m[1] ** 2. - 1.)
         eps4 = sqrt(1. - m[2] ** 2. / m[0] / m[4])
@@ -2956,8 +2957,8 @@ class SpecData2D(WafoData):
         >>> SD = D.tospecdata2d(sm.Jonswap().tospecdata(),nt=101)
         >>> m,mtext = SD.moment(nr=2,vari='xyt')
         >>> np.round(m,3),mtext
-        (array([ 3.061,  0.132,  0.   ,  2.13 ,  0.011,  0.008,  1.677, -0.   ,
+        (array([ 3.061,  0.132, -0.   ,  2.13 ,  0.011,  0.008,  1.677, -0.   ,
-            0.109,  0.109]), ['m0', 'mx', 'my', 'mt', 'mxx', 'myy', 'mtt', 'mxy', 'mxt', 'myt'])
+                0.109,  0.109]), ['m0', 'mx', 'my', 'mt', 'mxx', 'myy', 'mtt', 'mxy', 'mxt', 'myt'])
 
         References
         ----------
@@ -3137,7 +3138,7 @@ class SpecData2D(WafoData):
         self.labels.ylab = labels[1]
         self.labels.zlab = labels[2]
         
-def test_specdata():
+def _test_specdata():
     import wafo.spectrum.models as sm
     Sj = sm.Jonswap()
     S = Sj.tospecdata()

pywafo/src/wafo/spectrum/models.py

@@ -1965,7 +1965,7 @@ class Spreading(object):
         #Snew.note = specdata.note + ', spreading: %s' % self.type
         return Snew
 
-def test_some_spectra():
+def _test_some_spectra():
     S = Jonswap()
 
     w = arange(3.0)
@@ -2024,7 +2024,7 @@ def test_some_spectra():
     plb.show()
     plb.close('all')
 
-def test_spreading():
+def _test_spreading():
     import pylab as plb
     pi = plb.pi
     w = plb.linspace(0, 3, 257)
@@ -2045,7 +2045,7 @@ def test_spreading():
 
 def main():
     if False: # True: #
-        test_some_spectra()
+        _test_some_spectra()
     else:
         import doctest
         doctest.testmod()