From: W. Trevor King <wking@drexel.edu>
Date: Wed, 4 Aug 2010 14:45:28 +0000 (-0400)
Subject: Added rescaling option to hooke.util.fit.ModelFitter
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=3e7afbaeee5d9b833148641dbd509451859d2b44;p=hooke.git

Added rescaling option to hooke.util.fit.ModelFitter
---

diff --git a/hooke/util/fit.py b/hooke/util/fit.py
index 8b519e4..aaa1ee4 100644
--- a/hooke/util/fit.py
+++ b/hooke/util/fit.py
@@ -36,6 +36,9 @@ class ModelFitter (object):
     info :
         Store any extra information useful inside your overridden
         methods.
+    rescale : boolean
+        Rescale parameters so the scale of each is 1.0.  Also rescale
+        the data so data.std() == 1.0.
 
     Examples
     --------
@@ -83,9 +86,13 @@ class ModelFitter (object):
     >>> slope,offset = m.fit(outqueue=outqueue)
     >>> info = outqueue.get()
     >>> pprint(info)  # doctest: +ELLIPSIS, +REPORT_UDIFF
-    {'convergence flag': 2,
+    {'active fitted parameters': array([  6.999..., -32.889...]),
+     'active parameters': array([  6.999..., -32.889...]),
+     'active scale': [0.699..., 202.071...],
+     'convergence flag': 2,
      'covariance matrix': array([[  1.199...e-08,  -5.993...e-06],
            [ -5.993...e-06,   3.994...e-03]]),
+     'data scale factor': 1.0,
      'fitted parameters': array([  6.999..., -32.889...]),
      'info': {'fjac': array([[...]]),
               'fvec': array([...]),
@@ -94,6 +101,7 @@ class ModelFitter (object):
               'qtf': array([  2.851...e-07,   1.992...e-06])},
      'initial parameters': [6.992..., -33.0],
      'message': 'The relative error between two consecutive iterates is at most 0.000...',
+     'rescaled': False,
      'scale': [0.699..., 202.071...]}
 
     We round the outputs to protect the doctest against differences in
@@ -107,14 +115,29 @@ class ModelFitter (object):
 
     The offset is a bit off because, the range is not a multiple of
     :math:`2\pi`.
+
+    We could also use rescaled parameters:
+
+    >>> m = LinearModel(data, rescale=True)
+    >>> outqueue = Queue()
+    >>> slope,offset = m.fit(outqueue=outqueue)
+    >>> print '%.3f' % slope
+    7.000
+    >>> print '%.3f' % offset
+    -32.890
     """
-    def __init__(self, data, info=None):
-        self.set_data(data, info)
+    def __init__(self, *args, **kwargs):
+        self.set_data(*args, **kwargs)
 
-    def set_data(self, data, info=None):
+    def set_data(self, data, info=None, rescale=False):
         self._data = data
         self._model_data = ndarray(shape=data.shape, dtype=data.dtype)
         self.info = info
+        self._rescale = rescale
+        if rescale == True:
+            self._data_scale_factor = data.std()
+        else:
+            self._data_scale_factor = 1.0
 
     def model(self, params):
         p = params  # convenient alias
@@ -128,7 +151,12 @@ class ModelFitter (object):
         return None
 
     def residual(self, params):
-        return self._data - self.model(params)
+        if self._rescale == True:
+            params = [p*s for p,s in zip(params, self._param_scale_factors)]
+        residual = self._data - self.model(params)
+        if self._rescale == True or False:
+            residual /= self._data_scale_factor
+        return residual
 
     def fit(self, initial_params=None, scale=None, outqueue=None, **kwargs):
         """
@@ -153,13 +181,31 @@ class ModelFitter (object):
         if scale == None:
             scale = self.guess_scale(initial_params, outqueue)
         assert min(scale) > 0, scale
+        if self._rescale == True:
+            self._param_scale_factors = scale
+            active_scale = [1.0 for s in scale]
+            active_params = [p/s for p,s in zip(initial_params,
+                                                self._param_scale_factors)]
+        else:
+            active_scale = scale
+            active_params = initial_params
         params,cov,info,mesg,ier = leastsq(
-            func=self.residual, x0=initial_params, full_output=True,
-            diag=scale, **kwargs)
+            func=self.residual, x0=active_params, full_output=True,
+            diag=active_scale, **kwargs)
+        if self._rescale == True:
+            active_params = params
+            params = [p*s for p,s in zip(params, self._param_scale_factors)]
+        else:
+            active_params = params
         if outqueue != None:
             outqueue.put({
+                    'rescaled': self._rescale,
                     'initial parameters': initial_params,
+                    'active parameters': active_params,
                     'scale': scale,
+                    'active scale': active_scale,
+                    'data scale factor': self._data_scale_factor,
+                    'active fitted parameters': active_params,
                     'fitted parameters': params,
                     'covariance matrix': cov,
                     'info': info,