* Imported more recent function fitting facility from Cr2 project.

math/fitting/__init__.py

@@ -104,7 +104,8 @@ def fit_func(Funct, Data=None, Guess=None, Params=None,
     N is the dimensionality of the domain, while
     M is the number of data points, whose count must be equal to the
     size of y data below.
-    For a 2-D fitting, for example, x should be a column array.
+    For a 2-D curve (y = f(x)) fitting, for example,
+    x should be a column array.
 
   An input guess for the parameters can be specified via Guess argument.
   It is an ordered list of scalar values for these parameters.
@@ -120,8 +121,8 @@ def fit_func(Funct, Data=None, Guess=None, Params=None,
   If "dy" is specified, then "w" is defined to be (1.0 / dy**2), per usual
   convention.
 
-  Inspect Poly_base, Poly_order2, and other similar function classes in this
+  Inspect Poly_base, Poly_order2, and other similar function classes in the
-  module to see the example of the Funct function.
+  funcs_poly module to see the example of the Funct function.
 
   The measurement (input) datasets, against which the function is to be fitted,
   can be specified in one of two ways:
@@ -209,7 +210,9 @@ def fit_func(Funct, Data=None, Guess=None, Params=None,
     # Try to provide an initial guess
     # This is an older version with y-only argument
     Guess = Funct.Guess(y)
-  elif Guess == None: # VERY OLD, DO NOT USE ANYMORE!
+  elif Guess == None:
+    # VERY OLD, DO NOT USE ANYMORE! Will likely not work for anythingnonlinear
+    # functions.
     Guess = [ y.mean() ] + [0.0, 0.0] * len(x)
 
   if use_lmfit:
@@ -471,7 +474,8 @@ class fit_func_base(object):
   - TODO: dict-like Guess should be made possible.
   - otherwise, the guess values will be used as the initial values.
 
-
+  Refer to various function objects in wpylib.math.fitting.funcs_simple
+  for actual examples of how to use and create your own fit_func_base object.
   """
   class multi_fit_opts(dict):
     """A class for defining default control parameters for different fit methods.

math/fitting/funcs_pec.py

@@ -0,0 +1,141 @@
+#
+# wpylib.math.fitting.funcs_pec module
+# Created: 20150521
+# Wirawan Purwanto
+#
+# Imported 20150521 from Cr2_analysis_cbs.py
+# (dated 20141017, CVS rev 1.143).
+#
+
+"""
+wpylib.math.fitting.funcs_pec module
+A library of simple f(x) functions for PEC fitting
+
+For use with OO-style x-y curve fitting interface.
+"""
+
+import numpy
+
+
+class harm_fit_func(fit_func_base):
+  """Harmonic function object.
+  For use with fit_func function on a PEC.
+
+  Functional form:
+
+      E0 + 0.5 * k * (x - re)**2
+
+  Coefficients:
+  * C[0] = energy minimum
+  * C[1] = spring constant
+  * C[2] = equilibrium distance
+  """
+  dim = 1  # a function with 1-D domain
+  param_names = ('E0', 'k', 'r0')
+  def __call__(self, C, x):
+    xdisp = (x[0] - C[2])
+    y = C[0] + 0.5 * C[1] * xdisp**2
+    self.func_call_hook(C, x, y)
+    return y
+  def Guess_xy(self, x, y):
+    fit_rslt = fit_harm(x[0], y)
+    self.guess_params = tuple(fit_rslt[0])
+    return self.guess_params
+
+
+class harmcube_fit_func(fit_func_base):
+  """Harmonic + cubic term function object.
+  For use with fit_func function on a PEC.
+
+  Functional form:
+
+      E0 + 0.5 * k * (x - re)**2 + cub * (x - re)**3;
+
+  Coefficients:
+  * C[0] = energy minimum
+  * C[1] = spring constant
+  * C[2] = equilibrium distance
+  * C[3] = nonlinear (cubic) constant
+  """
+  dim = 1  # a function with 1-D domain
+  param_names = ('E0', 'k', 'r0', 'c3')
+  def __call__(self, C, x):
+    xdisp = (x[0] - C[2])
+    y = C[0] + 0.5 * C[1] * xdisp**2 + C[3] * xdisp**3
+    self.func_call_hook(C, x, y)
+    return y
+  def Guess_xy(self, x, y):
+    fit_rslt = fit_harm(x[0], y)
+    self.guess_params = tuple(fit_rslt[0]) + (0,)
+    return self.guess_params
+  def Guess_xy_old(self, x, y):
+    imin = numpy.argmin(y)
+    return (y[imin], 2, x[0][imin], 0.00001)
+
+
+class morse2_fit_func(fit_func_base):
+  """Morse2 function object.
+  For use with fit_func function.
+
+  Functional form:
+
+      E0 + 0.5 * k / a**2 * (1 - exp(-a * (x - re)))**2
+
+  Coefficients:
+  * C[0] = energy minimum
+  * C[1] = spring constant
+  * C[2] = equilibrium distance
+  * C[3] = nonlinear constant
+  """
+  dim = 1  # a function with 1-D domain
+  param_names = ('E0', 'k', 'r0', 'a')
+  def __call__(self, C, x):
+    from numpy import exp
+    E0, k, r0, a = self.get_params(C, *(self.param_names))
+    y = E0 + 0.5 * k / a**2 * (1 - exp(-a * (x[0] - r0)))**2
+    self.func_call_hook(C, x, y)
+    return y
+  def Guess_xy(self, x, y):
+    imin = numpy.argmin(y)
+    harm_params = fit_harm(x[0], y)
+    if self.debug >= 10:
+      print "Initial guess by fit_harm gives: ", harm_params
+    self.guess_params = (y[imin], harm_params[0][1], x[0][imin], 0.01 * harm_params[0][1])
+    return self.guess_params
+  def Guess_xy_old(self, x, y):
+    imin = numpy.argmin(y)
+    return (y[imin], 2, x[0][imin], 0.01)
+
+
+class ext3Bmorse2_fit_func(fit_func_base):
+  """ext3Bmorse2 function object.
+  For use with fit_func function.
+
+  Functional form:
+
+      E0 + 0.5 * k / a**2 * (1 - exp(-a * (x - re)))**2
+         + C3 * (1 - exp(-a * (x - re)))**3
+
+  Coefficients:
+  * C[0] = energy minimum
+  * C[1] = spring constant
+  * C[2] = equilibrium distance
+  * C[3] = nonlinear constant
+  * C[4] = coefficient of cubic term
+  """
+  dim = 1  # a function with 1-D domain
+  def __call__(self, C, x):
+    from numpy import exp
+    E = 1 - exp(-C[3] * (x[0] - C[2]))
+    y = C[0] + 0.5 * C[1] / C[3]**2 * E**2 + C[4] * E**3
+    self.func_call_hook(C, x, y)
+    return y
+  def Guess_xy(self, x, y):
+    imin = numpy.argmin(y)
+    harm_params = fit_harm(x[0], y)
+    if self.debug >= 10:
+      print "Initial guess by fit_harm gives: ", harm_params
+    self.guess_params = (y[imin], harm_params[0][1], x[0][imin], 0.01 * harm_params[0][1], 0)
+    return self.guess_params
+
+

math/fitting/funcs_physics.py

@@ -0,0 +1,49 @@
+#
+# wpylib.math.fitting.funcs_physics module
+# Created: 20150521
+# Wirawan Purwanto
+#
+# Imported 20150521 from Cr2_analysis_cbs.py
+# (dated 20141017, CVS rev 1.143).
+#
+
+"""
+wpylib.math.fitting.funcs_physics module
+A library of simple f(x) functions for physics-related common functional fitting
+
+For use with OO-style x-y curve fitting interface.
+"""
+
+import numpy
+
+
+class FermiDirac_fit_func(fit_func_base):
+  """Fermi-Dirac function object.
+  For use with fit_func function.
+
+  Functional form:
+
+      C[0] * (exp((x - C[1]) / C[2]) + 1)^-1
+
+  Coefficients:
+  * C[0] = amplitude
+  * C[1] = transition "temperature"
+  * C[2] = "smearing temperature"
+  """
+  dim = 1  # a function with 1-D domain
+  param_names = ('A', 'F', 'T')
+  # FIXME: Not good yet!!!
+  F_guess = 1.9
+  T_guess = 0.05
+  def __call__(self, C, x):
+    from numpy import exp
+    A, F, T = self.get_params(C, *(self.param_names))
+    y = A * (exp((x[0] - F) / T) + 1)**(-1)
+    self.func_call_hook(C, x, y)
+    return y
+  def Guess_xy(self, x, y):
+    imin = numpy.argmin(y)
+    self.guess_params = (y[imin], self.F_guess, self.T_guess)
+    return self.guess_params
+
+

math/fitting/funcs_simple.py

@@ -0,0 +1,276 @@
+#
+# wpylib.math.fitting.funcs_simple module
+# Created: 20150520
+# Wirawan Purwanto
+#
+# Imported 20150520 from Cr2_analysis_cbs.py
+# (dated 20141017, CVS rev 1.143).
+#
+
+"""
+wpylib.math.fitting.funcs_simple module
+A library of simple f(x) functions for fitting
+
+For use with OO-style x-y curve fitting interface.
+"""
+
+import numpy
+
+
+# Some simple function fitting--to aid fitting the complex ones later
+
+def fit_linear(x, y):
+  """Warning: the ansatz for fitting is
+      C[0] + C[1]*x
+  so I have to reverse the order of fit parameters.
+  """
+  rslt = numpy.polyfit(x, y, 1, full=True)
+  return (rslt[0][::-1],) + rslt
+
+
+def fit_harm(x, y):
+  """Do a quadratic fit using poly fit and return it in terms of coeffs
+  like this one:
+
+      C0 + 0.5 * C1 * (x - C2)**2
+
+  =>  0.5*C1*x**2 - C1*C2*x + (C0 + 0.5 * C1 * C2**2)
+
+  Polyfit gives:
+      a * x**2 + b * x + c
+
+  Equating the two, we get:
+
+      C1 = 2 * a
+      C2 = -b/C1
+      C0 = c - 0.5*C1*C2**2
+
+  This function returns the recast parameters plus the original
+  fit output.
+  """
+  rslt = numpy.polyfit(x, y, 2, full=True)
+
+  (a,b,c) = rslt[0]
+  C1 = 2*a
+  C2 = -b/C1
+  C0 = c - 0.5*C1*C2**2
+
+  return ((C0,C1,C2),) + rslt
+
+
+
+# fit_func-style functional ansatz
+
+class const_fit_func(fit_func_base):
+  """Constant function object.
+  For use with fit_func function on a PEC.
+
+  Functional form:
+
+      C[0]
+
+  Coefficients:
+  * C[0] = the constant sought
+  """
+  dim = 1  # a function with 1-D domain
+  param_names = ('c')
+  def __call__(self, C, x):
+    from numpy import exp
+    y = C[0]
+    self.func_call_hook(C, x, y)
+    return y
+  def Guess_xy(self, x, y):
+    self.guess_params = (numpy.average(y),)
+    return self.guess_params
+
+
+class linear_fit_func(fit_func_base):
+  """Linear function object.
+  For use with fit_func function.
+
+  Functional form:
+
+      a + b * x
+
+  Coefficients:
+  * C[0] = a
+  * C[1] = b
+  """
+  dim = 1  # a function with 1-D domain
+  param_names = ('a', 'b')
+  def __call__(self, C, x):
+    y = C[0] + C[1] * x[0]
+    self.func_call_hook(C, x, y)
+    return y
+  def Guess_xy(self, x, y):
+    fit_rslt = fit_linear(x[0], y)
+    self.guess_params = tuple(fit_rslt[0])
+    return self.guess_params
+
+
+class linear_leastsq_fit_func(linear_fit_func):
+  def fit(self, x, y, dy=None, fit_opts=None, Funct_hook=None, Guess=None):
+    from wpylib.math.fitting.linear import linregr2d_SZ
+    # Changed from:
+    #   rslt = fit_linear_weighted(x,y,dy)
+    # to:
+    rslt = (x, y, sigma=None)
+
+    self.last_fit = rslt[1]
+    # Retrofit for API compatibility: not necessarily meaningful
+    self.guess_params = rslt[0]
+    return rslt[0]
+
+
+class exp_fit_func(fit_func_base):
+  """Exponential function object.
+  For use with fit_func function.
+
+  Functional form:
+
+      C[0] * (exp(C[1] * (x - C[2]))
+
+  Coefficients:
+  * C[0] = amplitude
+  * C[1] = damping factor
+  * C[2] = offset
+  """
+  dim = 1  # a function with 1-D domain
+  param_names = ['A', 'B', 'x0']
+  A_guess =  -2.62681
+  B_guess =  -9.05046
+  x0_guess = 1.57327
+  def __call__(self, C, x):
+    from numpy import exp
+    A, B, x0 = self.get_params(C, *(self.param_names))
+    y = A * exp(B * (x[0] - x0))
+    self.func_call_hook(C, x, y)
+    return y
+  def Guess_xy(self, x, y):
+    from numpy import abs
+    #y_abs = abs(y)
+    # can do linear fit to guess the params,
+    # but how to separate A and B*x0, I don't know.
+    #imin = numpy.argmin(y)
+    self.guess_params = (self.A_guess, self.B_guess, self.x0_guess)
+    return self.guess_params
+
+
+class expm_fit_func(exp_fit_func):
+  """Similar to exp_fit_func but the exponent is always negative.
+  """
+  def __call__(self, C, x):
+    from numpy import exp,abs
+    A, B, x0 = self.get_params(C, *(self.param_names))
+    y = A * exp(-abs(B) * (x[0] - x0))
+    self.func_call_hook(C, x, y)
+    return y
+
+
+class powx_fit_func(fit_func_base):
+  """Power of x function object.
+  For use with fit_func function.
+
+  Functional form:
+
+      C[0] * ((x - C[2])**C[1])
+
+  Coefficients:
+  * C[0] = amplitude
+  * C[1] = exponent (< 0)
+  * C[2] = offset
+  """
+  dim = 1  # a function with 1-D domain
+  param_names = ['A', 'B', 'x0']
+  A_guess =  -2.62681
+  B_guess =  -9.05046
+  x0_guess = 1.57327
+  def __call__(self, C, x):
+    from numpy import exp
+    A, B, x0 = self.get_params(C, *(self.param_names))
+    y = A * (x[0] - x0)**B
+    self.func_call_hook(C, x, y)
+    return y
+  def Guess_xy(self, x, y):
+    from numpy import abs
+    #y_abs = abs(y)
+    # can do linear fit to guess the params,
+    # but how to separate A and B*x0, I don't know.
+    #imin = numpy.argmin(y)
+    self.guess_params = (self.A_guess, self.B_guess, self.x0_guess)
+    return self.guess_params
+
+
+class invx_fit_func(powx_fit_func):
+  """Inverse of x function object that leads to 0 as x->infinity.
+  For use with fit_func function.
+
+  Functional form:
+
+      C[0] * ((x - C[2])**C[1])
+
+  Specialized for CBX1 extrapolation
+  Coefficients:
+  * C[0] = amplitude (< 0)
+  * C[1] = exponent (< 0)
+  * C[2] = offset (> 0)
+  """
+  """
+  /home/wirawan/Work/GAFQMC/expt/qmc/Cr2/CBS-TZ-QZ/UHF-CBS/20140128/Exp-CBX1.d/fit-invx.plt
+
+     Iteration 154
+     WSSR        : 0.875715          delta(WSSR)/WSSR   : -9.96404e-06
+     delta(WSSR) : -8.72566e-06      limit for stopping : 1e-05
+     lambda	  : 0.00174063
+
+    resultant parameter values
+
+    A               = -29.7924
+    B               = -13.2967
+    x0              = 0.399396
+
+    After 154 iterations the fit converged.
+    final sum of squares of residuals : 0.875715
+    rel. change during last iteration : -9.96404e-06
+
+    degrees of freedom    (FIT_NDF)                        : 2
+    rms of residuals      (FIT_STDFIT) = sqrt(WSSR/ndf)    : 0.661708
+    variance of residuals (reduced chisquare) = WSSR/ndf   : 0.437858
+
+    Final set of parameters            Asymptotic Standard Error
+    =======================            ==========================
+
+    A               = -29.7924         +/- 8027         (2.694e+04%)
+    B               = -13.2967         +/- 196.1        (1474%)
+    x0              = 0.399396         +/- 21.4         (5357%)
+
+
+    correlation matrix of the fit parameters:
+
+                   A      B      x0
+    A               1.000
+    B               1.000  1.000
+    x0              1.000  1.000  1.000
+
+  For some reason the fit code in python gives:
+  A,B,x0 = (-7028.1498486021028, -16.916447508009664, 2.2572321406455487e-06)
+  but they fit almost exactly the same in the region 1.8 <= r <= 3.0.
+
+  """
+  A_guess =  -29.7924
+  B_guess =  -13.2967
+  x0_guess = 0.399396
+  def __init__(self):
+    from lmfit import Parameters
+    self.fit_method = "lmfit:leastsq"
+    p = Parameters()
+    p.add_many(
+      # (Name,  Value,  Vary,   Min,  Max,  Expr)
+        ('A',   -2.6,   True,  -1e6, -1e-9,  None),
+        ('B',   -2.0,   True,  None, -1e-9,  None),
+        ('x0',   1.9,   True,  1e-6, None,   None),
+      # The values are just a placeholder. They will be set later.
+    )
+    self.Params = p
+
+