"""
Glue's fitting classes are designed to be easily subclassed for performing
custom model fitting in Glue.
See the guide on :ref:`writing custom fit plugins <fit_plugins>` for
help with using custom fitting utilities in Glue.
"""
from __future__ import absolute_import, division, print_function
import numpy as np
from glue.core.simpleforms import IntOption, Option
__all__ = ['BaseFitter1D',
'PolynomialFitter',
'AstropyFitter1D',
'SimpleAstropyGaussianFitter',
'BasicGaussianFitter']
[docs]class BaseFitter1D(object):
"""
Base class for 1D fitters.
This abstract class must be overwritten.
"""
label = "Fitter"
"""A short label for the fit, used by the GUI"""
param_names = []
"""list of parameter names that support restrictions"""
def __init__(self, **params):
self._constraints = {}
for k, v in params.items():
if k in self.param_names:
self.set_constraint(k, value=v)
else:
setattr(self, k, v)
[docs] def plot(self, fit_result, axes, x):
"""
Plot the result of a fit.
:param fit_result: The output from fit
:param axes: The Matplotlib axes to add the fit to
:param x: The values of X at which to visualize the model
:returns: A list of matplotlib artists. **This is important:**
plots will not be properly cleared if this isn't provided
"""
y = self.predict(fit_result, x)
result = axes.plot(x, y, '#4daf4a',
lw=3, alpha=0.8,
scalex=False, scaley=False)
return result
def _sigma_to_weights(self, dy):
if dy is not None:
return 1. / np.asarray(dy) ** 2
@property
def options(self):
"""
A dictionary of the current setting of each model hyperparameter.
Hyperparameters are defined in subclasses by creating class-level
:mod:`Option <glue.core.simpleforms>` attributes. This attribute
dict maps ``{hyperparameter_name: current_value}``
"""
result = []
for typ in type(self).mro():
result.extend(k for k, v in typ.__dict__.items()
if isinstance(v, Option))
return dict((o, getattr(self, o)) for o in result)
[docs] def summarize(self, fit_result, x, y, dy=None):
"""
Return a textual summary of the fit.
:param fit_result: The return value from :meth:`fit`
:param x: The x values passed to :meth:`fit`
:returns: A description of the fit result
:rtype: str
"""
return str(fit_result)
@property
def constraints(self):
"""
A dict of the constraints on each parameter in :attr:`param_names`.
Each value is itself a dict with 3 items:
:key value: The default value
:key fixed: True / False, indicating whether the parameter is fixed
:key bounds: [min, max] or None, indicating lower/upper limits
"""
result = {}
for p in self.param_names:
result[p] = dict(value=None, fixed=False, limits=None)
result[p].update(self._constraints.get(p, {}))
return result
[docs] def set_constraint(self, parameter_name, value=None,
fixed=None, limits=None):
"""
Update a constraint.
:param parameter_name: name of the parameter to update
:type parameter_name: str
:param value: Set the default value (optional)
:param limits: Set the limits to[min, max] (optional)
:param fixed: Set whether the parameter is fixed (optional)
"""
c = self._constraints.setdefault(parameter_name, {})
if value is not None:
c['value'] = value
if fixed is not None:
c['fixed'] = fixed
if limits is not None:
c['limits'] = limits
[docs] def build_and_fit(self, x, y, dy=None):
"""
Method which builds the arguments to fit, and calls that method
"""
x = np.asarray(x).ravel()
y = np.asarray(y).ravel()
if dy is not None:
dy = np.asarray(dy).ravel()
return self.fit(x, y, dy=dy,
constraints=self.constraints,
**self.options)
[docs] def fit(self, x, y, dy, constraints, **options):
"""
Fit the model to data.
*This must be overriden by a subclass.*
:param x: The x values of the data
:type x: :class:`numpy.ndarray`
:param y: The y values of the data
:type y: :class:`numpy.ndarray`
:param dy: 1 sigma uncertainties on each datum (optional)
:type dy: :class:`numpy.ndarray`
:param constraints: The current value of :attr:`constraints`
:param options: kwargs for model hyperparameters.
:returns: An object representing the fit result.
"""
raise NotImplementedError()
[docs] def predict(self, fit_result, x):
"""
Evaulate the model at a set of locations.
**This must be overridden in a subclass.**
:param fit_result: The result from the fit method
:param x: Locations to evaluate model at
:type x: :class:`numpy.ndarray`
:returns: model(x)
:rtype: :class:`numpy.ndarray`
"""
raise NotImplementedError()
[docs]class AstropyFitter1D(BaseFitter1D):
"""
A base class for wrapping :mod:`astropy.modeling`.
Subclasses must override :attr:`model_cls` :attr:`fitting_cls`
to point to the desired Astropy :mod:`model <astropy.modeling>`
and :mod:`fitter <astropy.modeling.fitting>` classes.
In addition, they should override :attr:`label` with a better label,
and :meth:`parameter_guesses` to generate initial guesses
"""
model_cls = None
"""class describing the model"""
fitting_cls = None
"""class to fit the model"""
label = "Base Astropy Fitter"
"""UI Label"""
@property
def param_names(self):
return self.model_cls.param_names
[docs] def predict(self, fit_result, x):
model, _ = fit_result
return model(x)
[docs] def summarize(self, fit_result, x, y, dy=None):
model, fitter = fit_result
result = [_report_fitter(fitter), ""]
pnames = list(sorted(model.param_names))
maxlen = max(map(len, pnames))
result.extend("%s = %e" % (p.ljust(maxlen), getattr(model, p).value)
for p in pnames)
return "\n".join(result)
[docs] def fit(self, x, y, dy, constraints):
m, f = self._get_model_fitter(x, y, dy, constraints)
dy = self._sigma_to_weights(dy)
return f(m, x, y, weights=dy), f
def _get_model_fitter(self, x, y, dy, constraints):
if self.model_cls is None or self.fitting_cls is None:
raise NotImplementedError("Model or fitting class is unspecified.")
params = dict((k, v['value']) for k, v in constraints.items())
# update unset parameters with guesses from data
for k, v in self.parameter_guesses(x, y, dy).items():
if params[k] is not None or constraints[k]['fixed']:
continue
params[k] = v
m = self.model_cls(**params)
f = self.fitting_cls()
for param_name, constraint in constraints.items():
param = getattr(m, param_name)
if constraint['fixed']:
param.fixed = True
if constraint['limits']:
param.min, param.max = constraint['limits']
return m, f
[docs] def parameter_guesses(self, x, y, dy):
"""
Provide initial guesses for each model parameter.
**The base implementation does nothing, and should be overridden**
:param x: X - values of the data
:type x: :class:`numpy.ndarray`
:param y: Y - values of the data
:type y: :class:`numpy.ndarray`
:param dy: ncertainties on Y(assumed to be 1 sigma)
:type dy: :class:`numpy.ndarray`
:returns: A dict maping ``{parameter_name: value guess}`` for each
parameter
"""
return {}
def _gaussian_parameter_estimates(x, y, dy):
amplitude = np.percentile(y, 95)
y = np.maximum(y / y.sum(), 0)
mean = (x * y).sum()
stddev = np.sqrt((y * (x - mean) ** 2).sum())
return dict(mean=mean, stddev=stddev, amplitude=amplitude)
[docs]class BasicGaussianFitter(BaseFitter1D):
"""
Fallback Gaussian fitter, for astropy < 0.3.
If :mod:`astropy.modeling` is installed, this class is replaced by
:class:`SimpleAstropyGaussianFitter`
"""
label = "Gaussian"
def _errorfunc(self, params, x, y, dy):
yp = self.eval(x, *params)
result = (yp - y)
if dy is not None:
result /= dy
return result
@staticmethod
[docs] def eval(x, amplitude, mean, stddev):
return np.exp(-(x - mean) ** 2 / (2 * stddev ** 2)) * amplitude
@staticmethod
[docs] def fit_deriv(x, amplitude, mean, stddev):
"""
Gaussian1D model function derivatives.
"""
d_amplitude = np.exp(-0.5 / stddev ** 2 * (x - mean) ** 2)
d_mean = amplitude * d_amplitude * (x - mean) / stddev ** 2
d_stddev = amplitude * d_amplitude * (x - mean) ** 2 / stddev ** 3
return [d_amplitude, d_mean, d_stddev]
[docs] def fit(self, x, y, dy, constraints):
from scipy import optimize
init_values = _gaussian_parameter_estimates(x, y, dy)
init_values = [init_values[p] for p in ['amplitude', 'mean', 'stddev']]
farg = (x, y, dy)
dfunc = None
fitparams, status, dinfo, mess, ierr = optimize.leastsq(
self._errorfunc, init_values, args=farg, Dfun=dfunc,
full_output=True)
return fitparams
[docs] def predict(self, fit_result, x):
return self.eval(x, *fit_result)
[docs] def summarize(self, fit_result, x, y, dy=None):
return ("amplitude = %e\n"
"mean = %e\n"
"stddev = %e" % tuple(fit_result))
GaussianFitter = BasicGaussianFitter
try:
from astropy.modeling import models, fitting
[docs] class SimpleAstropyGaussianFitter(AstropyFitter1D):
"""
Guassian fitter using astropy.modeling.
"""
model_cls = models.Gaussian1D
try:
fitting_cls = fitting.LevMarLSQFitter
except AttributeError: # astropy v0.3
fitting_cls = fitting.NonLinearLSQFitter
label = "Gaussian"
parameter_guesses = staticmethod(_gaussian_parameter_estimates)
GaussianFitter = SimpleAstropyGaussianFitter
except ImportError:
pass
[docs]class PolynomialFitter(BaseFitter1D):
"""
A polynomial model.
The degree of the polynomial is specified by :attr:`degree`
"""
label = "Polynomial"
degree = IntOption(min=0, max=5, default=3, label="Polynomial Degree")
[docs] def fit(self, x, y, dy, constraints, degree=2):
"""
Fit a ``degree``-th order polynomial to the data.
"""
w = self._sigma_to_weights(dy)
return np.polyfit(x, y, degree, w=w)
[docs] def predict(self, fit_result, x):
return np.polyval(fit_result, x)
[docs] def summarize(self, fit_result, x, y, dy=None):
return "Coefficients:\n" + "\n".join("%e" % coeff
for coeff in fit_result.tolist())
def _report_fitter(fitter):
if "nfev" in fitter.fit_info:
return "Converged in %i iterations" % fitter.fit_info['nfev']
return 'Converged'
__FITTERS__ = [PolynomialFitter, GaussianFitter]