Small bugfixes

pywafo/.project

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>PYWAFO</name>
+	<name>google_pywafo</name>
 	<comment></comment>
 	<projects>
 	</projects>

pywafo/.pydevproject

@@ -3,7 +3,7 @@
 
 <pydev_project>
 <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
-<path>/PYWAFO/src</path>
+<path>/google_pywafo/src</path>
 </pydev_pathproperty>
 <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.6</pydev_property>
 <pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>

pywafo/setup.py

@@ -17,6 +17,7 @@ python setup.py sdist bdist_wininst upload --show-response
 import os, sys
 
 sys.argv.append("develop")
+#sys.argv.append("install")
 DISTUTILS_DEBUG = True
 pkg_name = 'wafo'
 root_dir = os.path.join('src',pkg_name)
@@ -44,7 +45,9 @@ testscripts = [os.path.join(subtst, f) for subtst in subtests
                        f.endswith('.old') or f.endswith('.bak'))]
 datadir = 'data'
 datafiles = [os.path.join(datadir, f)   for f in os.listdir(os.path.join(root_dir, datadir))
-				if  not (f.endswith('.py') or f.endswith('test') )]
+				if  not (f.startswith('.') or f.endswith('~') or
+                       f.endswith('.old') or f.endswith('.bak') or 
+                       f.endswith('.py') or f.endswith('test') )]
 libs = [f   for f in os.listdir(os.path.join(root_dir)) if  f.endswith('.pyd') ]
 packagedata = testscripts + datafiles + libs #['c_library.pyd'] #,'disufq1.c','diffsumfunq.pyd','diffsumfunq.pyf','findrfc.c','rfc.pyd','rfc.pyf']
 

pywafo/src/Wafo.egg-info/PKG-INFO

@@ -1,29 +1,34 @@
 Metadata-Version: 1.0
-Name: WAFO
+Name: wafo
 Version: 0.11
-Summary: 
+Summary: UNKNOWN
-WAFO
+Home-page: http://www.maths.lth.se/matstat/wafo/
-=====
+Author: WAFO-group
+Author-email: wafo@maths.lth.se
+License: GPL
+Description: 
+        WAFO
+        =====
         WAFO is a toolbox Python routines for statistical analysis and simulation of random waves and random loads.
         WAFO is freely redistributable software, see WAFO licence, cf. the GNU General Public License (GPL) and
         contain tools for:
         
-Fatigue Analysis
+        Fatigue Analysis
-----------------
+        ----------------
--Fatigue life prediction for random loads
+        -Fatigue life prediction for random loads
--Theoretical density of rainflow cycles
+        -Theoretical density of rainflow cycles
         
-Sea modelling
+        Sea modelling
--------------
+        -------------
--Simulation of linear and non-linear Gaussian waves
+        -Simulation of linear and non-linear Gaussian waves
--Estimation of seamodels (spectrums)
+        -Estimation of seamodels (spectrums)
--Joint wave height, wave steepness, wave period distributions
+        -Joint wave height, wave steepness, wave period distributions
         
-Statistics
+        Statistics
-------------
+        ------------
--Extreme value analysis
+        -Extreme value analysis
--Kernel density estimation
+        -Kernel density estimation
--Hidden markov models
+        -Hidden markov models
         
         WAFO consists of several modules with short descriptions below.
         The modules SPECTRUM, COVARIANCE, TRANSFORM, WAVEMODELS, and MULTIDIM are
@@ -84,9 +89,4 @@ Statistics
         - Reported bugs.
         - List of publications related to WAFO.
         
-Home-page: http://www.maths.lth.se/matstat/wafo/
-Author: WAFO-group
-Author-email: wafo@maths.lth.se
-License: GPL
-Description: UNKNOWN
 Platform: UNKNOWN

pywafo/src/Wafo.egg-info/top_level.txt

@@ -1,5 +1 @@
-wafo\spectrum
-wafo\covariance
 wafo
-wafo\data
-wafo\transform

pywafo/src/wafo/interpolate.py

@@ -19,7 +19,7 @@ from numpy.lib.shape_base import vstack
 from numpy.lib.function_base import linspace
 import polynomial as pl
 
-class PPform1(object):
+class PPform(object):
     """The ppform of the piecewise polynomials is given in terms of coefficients
     and breaks.  The polynomial in the ith interval is
     x_{i} <= x < x_{i+1}

pywafo/src/wafo/kdetools.py

@@ -9,7 +9,7 @@
 # Licence:     LGPL
 #-------------------------------------------------------------------------------
 #!/usr/bin/env python
-#import numpy as np
+import numpy as np
 from scipy.special import gamma
 from numpy import pi, atleast_2d #@UnresolvedImport
 from misc import tranproc, trangood
@@ -112,29 +112,29 @@ class kde(object):
         if d != self.d:
             if d == 1 and m == self.d:
                 # points was passed in as a row vector
-                points = reshape(points, (self.d, 1))
+                points = np.reshape(points, (self.d, 1))
                 m = 1
             else:
                 msg = "points have dimension %s, dataset has dimension %s" % (d,
                     self.d)
                 raise ValueError(msg)
 
-        result = zeros((m,), points.dtype)
+        result = np.zeros((m,), points.dtype)
 
         if m >= self.n:
             # there are more points than data, so loop over data
             for i in range(self.n):
-                diff = self.dataset[:,i,newaxis] - points
+                diff = self.dataset[:,i, np.newaxis] - points
-                tdiff = dot(self.inv_cov, diff)
+                tdiff = np.dot(self.inv_cov, diff)
-                energy = sum(diff*tdiff,axis=0)/2.0
+                energy = np.sum(diff*tdiff,axis=0)/2.0
-                result += exp(-energy)
+                result += np.exp(-energy)
         else:
             # loop over points
             for i in range(m):
-                diff = self.dataset - points[:,i,newaxis]
+                diff = self.dataset - points[:,i,np.newaxis]
-                tdiff = dot(self.inv_cov, diff)
+                tdiff = np.dot(self.inv_cov, diff)
                 energy = sum(diff*tdiff,axis=0)/2.0
-                result[i] = sum(exp(-energy),axis=0)
+                result[i] = np.sum(np.exp(-energy),axis=0)
 
         result /= self._norm_factor
 

pywafo/src/wafo/misc.py

@@ -1563,7 +1563,7 @@ def meshgrid(*xi, ** kwargs):
             return broadcast_arrays(*output)
 
 
-def ndgrid(*args, ** kwargs):
+def ndgrid(*args, **kwargs):
     """
     Same as calling meshgrid with indexing='ij' (see meshgrid for
     documentation).
@@ -1666,7 +1666,7 @@ def trangood(x, f, min_n=None, min_x=None, max_x=None, max_n=inf):
 
     return xo, fo
 
-def tranproc(x, f, x0, * xi):
+def tranproc(x, f, x0, *xi):
     """
     Transforms process X and up to four derivatives
           using the transformation f.
@@ -1779,7 +1779,7 @@ def tranproc(x, f, x0, * xi):
                     y.append(y4)
                     if N > 4:
                         warnings.warn('Transformation of derivatives of order>4 not supported.')
-    return y #0,y1,y2,y3,y4
+    return y #y0,y1,y2,y3,y4
 
 
 def test_common_shape():

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

@@ -5,10 +5,10 @@ import os
 
 def compile_all():
     # Install gfortran and run the following to build the module:
-    #compile_format = 'f2py %s %s -c --fcompiler=gnu95 --compiler=mingw32 -lmsvcr71'
+    compile_format = 'f2py.py %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.py %s %s -c'
+    #compile_format = 'f2py.py %s %s -c'
     pyfs = ('c_library.pyf',)
     files =('c_functions.c',)
 

pywafo/src/wafo/spectrum/core.py

@@ -16,16 +16,15 @@ from pylab import stineman_interp
 
 from dispersion_relation import w2k #, k2w
 from wafo.wafodata import WafoData, now
-from wafo.misc import sub_dict_select, nextpow2, discretize, JITImport
+from wafo.misc import sub_dict_select, nextpow2, discretize, JITImport, tranproc
 try:
     from wafo.gaussian import Rind
 except ImportError:
-    
     Rind = None
 try:
     from wafo import c_library
 except ImportError:
-    warnings.warn('Compile the c_libraray.pyd again!')
+    warnings.warn('Compile the c_library.pyd again!')
     c_library = None
     
 from wafo.transform import TrData
@@ -751,8 +750,7 @@ class SpecData1D(WafoData):
         tn = paramt[1]
         Ntime = paramt[2]
         t = linspace(0, tn / A, Ntime) #normalized times
-        Nstart = max(round(t0 / tn * (Ntime - 1)), 1)  #% index to starting point to
+        Nstart = max(round(t0 / tn * (Ntime - 1)), 1)  #% index to starting point to evaluate
-                                             #% evaluate
                                     
         dt = t[1] - t[0]
         nr = 2
@@ -1055,16 +1053,22 @@ class SpecData1D(WafoData):
         if spec.tr is not None:
             print('   Transforming data.')
             g = spec.tr
-            G = fliplr(g) #% the invers of g
             if derivative:
                 for i in range(cases):
-                    tmp = tranproc(hstack((x[:, i + 1], xder[:, i + 1])), G)
+                    x[:, i + 1], xder[:, i + 1] = g.gauss2dat(x[:, i + 1], xder[:, i + 1])
-                    x[:, i + 1] = tmp[:, 0]
-                    xder[:, i + 1] = tmp[:, 1]
-
             else:
                 for i in range(cases):
-                    x[:, i + 1] = tranproc(x[:, i + 1], G)
+                    x[:, i + 1] = g.gauss2dat(x[:, i + 1])
+#            G = fliplr(g) #% the invers of g
+#            if derivative:
+#                for i in range(cases):
+#                    tmp = tranproc(hstack((x[:, i + 1], xder[:, i + 1])), G)
+#                    x[:, i + 1] = tmp[:, 0]
+#                    xder[:, i + 1] = tmp[:, 1]
+#
+#            else:
+#                for i in range(cases):
+#                    x[:, i + 1] = tranproc(x[:, i + 1], G)
 
         if derivative:
             return x, xder

pywafo/src/wafo/transform/core.py

@@ -82,7 +82,7 @@ class TrCommon(object):
         t0 = trapz(xn,(xn-yn)**2.)
         return t0
 
-    def gauss2dat(self,y, *yi):
+    def gauss2dat(self, y, *yi):
         """
         Transforms Gaussian data, y, to non-linear scale.
 
@@ -153,12 +153,19 @@ class TrData(WafoData, TrCommon):
     >>> g.sigma
     array([ 5.])
     
+    >>> g = TrData(y,x,mean=1,sigma=5)
+    >>> g.mean
+    1
+    >>> g.sigma
+    5
+    
+    
     Check that the departure from a Gaussian model is zero
     >>> g.dist2gauss() < 1e-16
     True
     """
     def __init__(self, *args, **kwds):
-        WafoData.__init__(self, *args, **kwds)
+        super(TrData, self).__init__(*args, **kwds)
         self.labels.title = 'Transform'
         self.labels.ylab = 'g(x)'
         self.labels.xlab = 'x'