"""
Wrap sasmodels for direct use by bumps.
:class:`Model` is a wrapper for the sasmodels kernel which defines a
bumps *Parameter* box for each kernel parameter. *Model* accepts keyword
arguments to set the initial value for each parameter.
:class:`Experiment` combines the *Model* function with a data file loaded by
the sasview data loader. *Experiment* takes a *cutoff* parameter controlling
how far the polydispersity integral extends.
"""
from __future__ import print_function
__all__ = ["Model", "Experiment"]
import numpy as np # type: ignore
from .data import plot_theory
from .direct_model import DataMixin
# pylint: disable=unused-import
try:
from typing import Dict, Union, Tuple, Any, Optional
from .data import Data1D, Data2D
from .kernel import KernelModel
from .modelinfo import ModelInfo
from .resolution import Resolution
Data = Union[Data1D, Data2D]
except ImportError:
pass
# pylint: enable=unused-import
try:
# Optional import. This allows the doc builder and nosetests to run even
# when bumps is not on the path.
from bumps.names import Parameter # type: ignore
from bumps.parameter import Reference # type: ignore
except ImportError:
pass
def create_parameters(model_info, **kwargs):
# type: (ModelInfo, Union[float, str, Parameter]) -> Tuple[Dict[str, Parameter], Dict[str, str]]
"""
Generate Bumps parameters from the model info.
*model_info* is returned from :func:`.generate.model_info` on the
model definition module.
Any additional *key=value* pairs are initial values for the parameters
to the models. Uninitialized parameters will use the model default
value. The value can be a float, a bumps parameter, or in the case
of the distribution type parameter, a string.
Returns a dictionary of *{name: Parameter}* containing the bumps
parameters for each model parameter, and a dictionary of
*{name: str}* containing the polydispersity distribution types.
"""
pars = {} # type: Dict[str, Parameter]
pd_types = {} # type: Dict[str, str]
for p in model_info.parameters.call_parameters:
value = kwargs.pop(p.name, p.default)
pars[p.name] = Parameter.default(value, name=p.name, limits=p.limits)
if p.polydisperse:
for part, default, limits in [
('_pd', 0., pars[p.name].limits),
('_pd_n', 35., (0, 1000)),
('_pd_nsigma', 3., (0, 10)),
]:
name = p.name + part
value = kwargs.pop(name, default)
pars[name] = Parameter.default(value, name=name, limits=limits)
name = p.name + '_pd_type'
pd_types[name] = str(kwargs.pop(name, 'gaussian'))
if kwargs: # args not corresponding to parameters
raise TypeError("unexpected parameters: %s"
% (", ".join(sorted(kwargs.keys()))))
return pars, pd_types
[docs]class Model(object):
"""
Bumps wrapper for a SAS model.
*model* is a runnable module as returned from :func:`.core.load_model`.
*cutoff* is the polydispersity weight cutoff.
Any additional *key=value* pairs are model dependent parameters.
"""
def __init__(self, model, **kwargs):
# type: (KernelModel, **Dict[str, Union[float, Parameter]]) -> None
self.sasmodel = model
pars, pd_types = create_parameters(model.info, **kwargs)
for k, v in pars.items():
setattr(self, k, v)
for k, v in pd_types.items():
setattr(self, k, v)
self._parameter_names = list(pars.keys())
self._pd_type_names = list(pd_types.keys())
[docs] def parameters(self):
# type: () -> Dict[str, Parameter]
"""
Return a dictionary of parameters objects for the parameters,
excluding polydispersity distribution type.
"""
return dict((k, getattr(self, k)) for k in self._parameter_names)
[docs] def state(self):
# type: () -> Dict[str, Union[Parameter, str]]
"""
Return a dictionary of current values for all the parameters,
including polydispersity distribution type.
"""
pars = dict((k, getattr(self, k).value) for k in self._parameter_names)
pars.update((k, getattr(self, k)) for k in self._pd_type_names)
return pars
[docs]class Experiment(DataMixin):
r"""
Bumps wrapper for a SAS experiment.
*data* is a :class:`.data.Data1D`, :class:`.data.Data2D` or
:class:`.data.SesansData` object. Use :func:`.data.empty_data1D` or
:func:`.data.empty_data2D` to define $q, \Delta q$ calculation
points for displaying the SANS curve when there is no measured data.
*model* is a :class:`Model` object.
*cutoff* is the integration cutoff, which avoids computing the
the SAS model where the polydispersity weight is low.
The resulting model can be used directly in a Bumps FitProblem call.
"""
_cache = None # type: Dict[str, np.ndarray]
def __init__(self, data, model, cutoff=1e-5, name=None, extra_pars=None):
# type: (Data, Model, float, Optional[str], Optional[Dict[str, Parameter]]) -> None
# Allow resolution function to define fittable parameters. We do this
# by creating reference parameters within the resolution object rather
# than modifying the object itself to use bumps parameters. We need
# to reset the parameters each time the object has changed. These
# additional parameters need to be returned from the fitting engine.
# To make them available to the user, they are added as top-level
# attributes to the experiment object. The only change to the
# resolution function is that it needs an optional 'fittable' attribute
# which maps the internal name to the user visible name for the
# for the parameter.
self._resolution = None
self._resolution_pars = {}
# remember inputs so we can inspect from outside
self.name = data.filename if name is None else name
self.model = model
self.cutoff = cutoff
self._interpret_data(data, model.sasmodel)
self._cache = {}
# CRUFT: no longer need extra parameters
# Multiple scattering probability is now retrieved directly from the
# multiple scattering resolution function.
self.extra_pars = extra_pars
[docs] def update(self):
# type: () -> None
"""
Call when model parameters have changed and theory needs to be
recalculated.
"""
self._cache.clear()
[docs] def numpoints(self):
# type: () -> float
"""
Return the number of data points
"""
return len(self.Iq)
@property
def resolution(self):
# type: () -> Union[None, Resolution]
"""
:class:`.resolution.Resolution` applied to the data, if any.
"""
return self._resolution
@resolution.setter
def resolution(self, value):
# type: (Resolution) -> None
"""
:class:`.resolution.Resolution` applied to the data, if any.
"""
self._resolution = value
# Remove old resolution fitting parameters from experiment
for name in self._resolution_pars:
delattr(self, name)
# Create new resolution fitting parameters
res_pars = getattr(self._resolution, 'fittable', {})
self._resolution_pars = {
name: Reference(self._resolution, refname, name=name)
for refname, name in res_pars.items()
}
# Add new resolution fitting parameters as experiment attributes
for name, ref in self._resolution_pars.items():
setattr(self, name, ref)
[docs] def parameters(self):
# type: () -> Dict[str, Parameter]
"""
Return a dictionary of parameters
"""
pars = self.model.parameters()
if self.extra_pars is not None:
pars.update(self.extra_pars)
pars.update(self._resolution_pars)
return pars
[docs] def theory(self):
# type: () -> np.ndarray
"""
Return the theory corresponding to the model parameters.
This method uses lazy evaluation, and requires model.update() to be
called when the parameters have changed.
"""
if 'theory' not in self._cache:
pars = self.model.state()
self._cache['theory'] = self._calc_theory(pars, cutoff=self.cutoff)
return self._cache['theory']
[docs] def residuals(self):
# type: () -> np.ndarray
"""
Return theory minus data normalized by uncertainty.
"""
#if np.any(self.err ==0): print("zeros in err")
return (self.theory() - self.Iq) / self.dIq
[docs] def nllf(self):
# type: () -> float
"""
Return the negative log likelihood of seeing data given the model
parameters, up to a normalizing constant which depends on the data
uncertainty.
"""
delta = self.residuals()
#if np.any(np.isnan(R)): print("NaN in residuals")
return 0.5 * np.sum(delta**2)
#def __call__(self):
# return 2 * self.nllf() / self.dof
[docs] def plot(self, view=None):
# type: (str) -> None
"""
Plot the data and residuals.
"""
data, theory, resid = self._data, self.theory(), self.residuals()
# TODO: hack to display oriented usans 2-D pattern
Iq_calc = self.Iq_calc if isinstance(self.Iq_calc, tuple) else None
plot_theory(data, theory, resid, view, Iq_calc=Iq_calc)
[docs] def simulate_data(self, noise=None):
# type: (float) -> None
"""
Generate simulated data.
"""
Iq = self.theory()
self._set_data(Iq, noise)
[docs] def save(self, basename):
# type: (str) -> None
"""
Save the model parameters and data into a file.
Not Implemented except for sesans fits.
"""
if self.data_type == "sesans":
np.savetxt(basename+".dat", np.array([self._data.x, self.theory()]).T)
def __getstate__(self):
# type: () -> Dict[str, Any]
# Can't pickle gpu functions, so instead make them lazy
state = self.__dict__.copy()
state['_kernel'] = None
return state
def __setstate__(self, state):
# type: (Dict[str, Any]) -> None
# pylint: disable=attribute-defined-outside-init
self.__dict__ = state