Source code for astropy.modeling.parameters

# Licensed under a 3-clause BSD style license - see LICENSE.rst

"""
This module defines two classes that deal with parameters.

It is unlikely users will need to work with these classes directly, unless they
define their own models.
"""


import functools
import numbers
import types
import operator

import numpy as np

from astropy import units as u
from astropy.units import Quantity, UnitsError
from astropy.utils import isiterable, OrderedDescriptor
from .utils import array_repr_oneline

from .utils import get_inputs_and_params

__all__ = ['Parameter', 'InputParameterError', 'ParameterError']


[docs]class ParameterError(Exception): """Generic exception class for all exceptions pertaining to Parameters."""
[docs]class InputParameterError(ValueError, ParameterError): """Used for incorrect input parameter values and definitions."""
class ParameterDefinitionError(ParameterError): """Exception in declaration of class-level Parameters.""" def _tofloat(value): """Convert a parameter to float or float array""" if isiterable(value): try: value = np.asanyarray(value, dtype=float) except (TypeError, ValueError): # catch arrays with strings or user errors like different # types of parameters in a parameter set raise InputParameterError( "Parameter of {0} could not be converted to " "float".format(type(value))) elif isinstance(value, Quantity): # Quantities are fine as is pass elif isinstance(value, np.ndarray): # A scalar/dimensionless array value = float(value.item()) elif isinstance(value, (numbers.Number, np.number)): value = float(value) elif isinstance(value, bool): raise InputParameterError( "Expected parameter to be of numerical type, not boolean") else: raise InputParameterError( "Don't know how to convert parameter of {0} to " "float".format(type(value))) return value # Helpers for implementing operator overloading on Parameter def _binary_arithmetic_operation(op, reflected=False): @functools.wraps(op) def wrapper(self, val): if self._model is None: return NotImplemented if self.unit is not None: self_value = Quantity(self.value, self.unit) else: self_value = self.value if reflected: return op(val, self_value) else: return op(self_value, val) return wrapper def _binary_comparison_operation(op): @functools.wraps(op) def wrapper(self, val): if self._model is None: if op is operator.lt: # Because OrderedDescriptor uses __lt__ to work, we need to # call the super method, but only when not bound to an instance # anyways return super(self.__class__, self).__lt__(val) else: return NotImplemented if self.unit is not None: self_value = Quantity(self.value, self.unit) else: self_value = self.value return op(self_value, val) return wrapper def _unary_arithmetic_operation(op): @functools.wraps(op) def wrapper(self): if self._model is None: return NotImplemented if self.unit is not None: self_value = Quantity(self.value, self.unit) else: self_value = self.value return op(self_value) return wrapper
[docs]class Parameter(OrderedDescriptor): """ Wraps individual parameters. This class represents a model's parameter (in a somewhat broad sense). It acts as both a descriptor that can be assigned to a class attribute to describe the parameters accepted by an individual model (this is called an "unbound parameter"), or it can act as a proxy for the parameter values on an individual model instance (called a "bound parameter"). Parameter instances never store the actual value of the parameter directly. Rather, each instance of a model stores its own parameters parameter values in an array. A *bound* Parameter simply wraps the value in a Parameter proxy which provides some additional information about the parameter such as its constraints. In other words, this is a high-level interface to a model's adjustable parameter values. *Unbound* Parameters are not associated with any specific model instance, and are merely used by model classes to determine the names of their parameters and other information about each parameter such as their default values and default constraints. See :ref:`modeling-parameters` for more details. Parameters ---------- name : str parameter name .. warning:: The fact that `Parameter` accepts ``name`` as an argument is an implementation detail, and should not be used directly. When defining a new `Model` class, parameter names are always automatically defined by the class attribute they're assigned to. description : str parameter description default : float or array default value to use for this parameter unit : `~astropy.units.Unit` if specified, the parameter will be in these units, and when the parameter is updated in future, it should be set to a :class:`~astropy.units.Quantity` that has equivalent units. getter : callable a function that wraps the raw (internal) value of the parameter when returning the value through the parameter proxy (eg. a parameter may be stored internally as radians but returned to the user as degrees) setter : callable a function that wraps any values assigned to this parameter; should be the inverse of getter fixed : bool if True the parameter is not varied during fitting tied : callable or False if callable is supplied it provides a way to link the value of this parameter to another parameter (or some other arbitrary function) min : float the lower bound of a parameter max : float the upper bound of a parameter bounds : tuple specify min and max as a single tuple--bounds may not be specified simultaneously with min or max model : `Model` instance binds the the `Parameter` instance to a specific model upon instantiation; this should only be used internally for creating bound Parameters, and should not be used for `Parameter` descriptors defined as class attributes """ constraints = ('fixed', 'tied', 'bounds', 'prior', 'posterior') """ Types of constraints a parameter can have. Excludes 'min' and 'max' which are just aliases for the first and second elements of the 'bounds' constraint (which is represented as a 2-tuple). 'prior' and 'posterior' are available for use by user fitters but are not used by any built-in fitters as of this writing. """ # Settings for OrderedDescriptor _class_attribute_ = '_parameters_' _name_attribute_ = '_name' def __init__(self, name='', description='', default=None, unit=None, getter=None, setter=None, fixed=False, tied=False, min=None, max=None, bounds=None, prior=None, posterior=None, model=None): super().__init__() self._name = name self.__doc__ = self._description = description.strip() # We only need to perform this check on unbound parameters if model is None and isinstance(default, Quantity): if unit is not None and not unit.is_equivalent(default.unit): raise ParameterDefinitionError( "parameter default {0} does not have units equivalent to " "the required unit {1}".format(default, unit)) unit = default.unit default = default.value self._default = default self._unit = unit # NOTE: These are *default* constraints--on model instances constraints # are taken from the model if set, otherwise the defaults set here are # used if bounds is not None: if min is not None or max is not None: raise ValueError( 'bounds may not be specified simultaneously with min or ' 'or max when instantiating Parameter {0}'.format(name)) else: bounds = (min, max) self._fixed = fixed self._tied = tied self._bounds = bounds self._posterior = posterior self._prior = prior self._order = None self._model = None # The getter/setter functions take one or two arguments: The first # argument is always the value itself (either the value returned or the # value being set). The second argument is optional, but if present # will contain a reference to the model object tied to a parameter (if # it exists) self._getter = self._create_value_wrapper(getter, None) self._setter = self._create_value_wrapper(setter, None) self._validator = None # Only Parameters declared as class-level descriptors require # and ordering ID if model is not None: self._bind(model) def __get__(self, obj, objtype): if obj is None: return self # All of the Parameter.__init__ work should already have been done for # the class-level descriptor; we can skip that stuff and just copy the # existing __dict__ and then bind to the model instance parameter = self.__class__.__new__(self.__class__) parameter.__dict__.update(self.__dict__) parameter._bind(obj) return parameter def __set__(self, obj, value): value = _tofloat(value) # Check that units are compatible with default or units already set param_unit = obj._param_metrics[self.name]['orig_unit'] if param_unit is None: if isinstance(value, Quantity): obj._param_metrics[self.name]['orig_unit'] = value.unit else: if not isinstance(value, Quantity): raise UnitsError("The '{0}' parameter should be given as a " "Quantity because it was originally initialized " "as a Quantity".format(self._name)) else: # We need to make sure we update the unit because the units are # then dropped from the value below. obj._param_metrics[self.name]['orig_unit'] = value.unit # Call the validator before the setter if self._validator is not None: self._validator(obj, value) if self._setter is not None: setter = self._create_value_wrapper(self._setter, obj) if self.unit is not None: value = setter(value * self.unit).value else: value = setter(value) self._set_model_value(obj, value) def __len__(self): if self._model is None: raise TypeError('Parameter definitions do not have a length.') return len(self._model) def __getitem__(self, key): value = self.value if len(self._model) == 1: # Wrap the value in a list so that getitem can work for sensible # indices like [0] and [-1] value = [value] return value[key] def __setitem__(self, key, value): # Get the existing value and check whether it even makes sense to # apply this index oldvalue = self.value n_models = len(self._model) # if n_models == 1: # # Convert the single-dimension value to a list to allow some slices # # that would be compatible with a length-1 array like [:] and [0:] # oldvalue = [oldvalue] if isinstance(key, slice): if len(oldvalue[key]) == 0: raise InputParameterError( "Slice assignment outside the parameter dimensions for " "'{0}'".format(self.name)) for idx, val in zip(range(*key.indices(len(self))), value): self.__setitem__(idx, val) else: try: oldvalue[key] = value except IndexError: raise InputParameterError( "Input dimension {0} invalid for {1!r} parameter with " "dimension {2}".format(key, self.name, n_models)) def __repr__(self): args = "'{0}'".format(self._name) if self._model is None: if self._default is not None: args += ', default={0}'.format(self._default) else: args += ', value={0}'.format(self.value) if self.unit is not None: args += ', unit={0}'.format(self.unit) for cons in self.constraints: val = getattr(self, cons) if val not in (None, False, (None, None)): # Maybe non-obvious, but False is the default for the fixed and # tied constraints args += ', {0}={1}'.format(cons, val) return "{0}({1})".format(self.__class__.__name__, args) @property def name(self): """Parameter name""" return self._name @property def default(self): """Parameter default value""" if (self._model is None or self._default is None or len(self._model) == 1): return self._default # Otherwise the model we are providing for has more than one parameter # sets, so ensure that the default is repeated the correct number of # times along the model_set_axis if necessary n_models = len(self._model) model_set_axis = self._model._model_set_axis default = self._default new_shape = (np.shape(default) + (1,) * (model_set_axis + 1 - np.ndim(default))) default = np.reshape(default, new_shape) # Now roll the new axis into its correct position if necessary default = np.rollaxis(default, -1, model_set_axis) # Finally repeat the last newly-added axis to match n_models default = np.repeat(default, n_models, axis=-1) # NOTE: Regardless of what order the last two steps are performed in, # the resulting array will *look* the same, but only if the repeat is # performed last will it result in a *contiguous* array return default @property def value(self): """The unadorned value proxied by this parameter.""" if self._model is None: raise AttributeError('Parameter definition does not have a value') value = self._get_model_value(self._model) if self._getter is None: return value else: raw_unit = self._model._param_metrics[self.name]['raw_unit'] orig_unit = self._model._param_metrics[self.name]['orig_unit'] if raw_unit is not None: return np.float64(self._getter(value, raw_unit, orig_unit).value) else: return self._getter(value) @value.setter def value(self, value): if self._model is None: raise AttributeError('Cannot set a value on a parameter ' 'definition') if self._setter is not None: val = self._setter(value) if isinstance(value, Quantity): raise TypeError("The .value property on parameters should be set to " "unitless values, not Quantity objects. To set a " "parameter to a quantity simply set the parameter " "directly without using .value") self._set_model_value(self._model, value) @property def unit(self): """ The unit attached to this parameter, if any. On unbound parameters (i.e. parameters accessed through the model class, rather than a model instance) this is the required/ default unit for the parameter. """ if self._model is None: return self._unit else: # orig_unit may be undefined early on in model instantiation return self._model._param_metrics[self.name].get('orig_unit', self._unit) @unit.setter def unit(self, unit): self._set_unit(unit) def _set_unit(self, unit, force=False): if self._model is None: raise AttributeError('Cannot set unit on a parameter definition') orig_unit = self._model._param_metrics[self.name]['orig_unit'] if force: self._model._param_metrics[self.name]['orig_unit'] = unit else: if orig_unit is None: raise ValueError('Cannot attach units to parameters that were ' 'not initially specified with units') else: raise ValueError('Cannot change the unit attribute directly, ' 'instead change the parameter to a new quantity') @property def quantity(self): """ This parameter, as a :class:`~astropy.units.Quantity` instance. """ if self.unit is not None: return self.value * self.unit else: return None @quantity.setter def quantity(self, quantity): if not isinstance(quantity, Quantity): raise TypeError("The .quantity attribute should be set to a Quantity object") self.value = quantity.value self._set_unit(quantity.unit, force=True) @property def shape(self): """The shape of this parameter's value array.""" if self._model is None: raise AttributeError('Parameter definition does not have a ' 'shape.') shape = self._model._param_metrics[self._name]['shape'] if len(self._model) > 1: # If we are dealing with a model *set* the shape is the shape of # the parameter within a single model in the set model_axis = self._model._model_set_axis if model_axis < 0: model_axis = len(shape) + model_axis shape = shape[:model_axis] + shape[model_axis + 1:] else: # When a model set is initialized, the dimension of the parameters # is increased by model_set_axis+1. To find the shape of a parameter # within a single model the extra dimensions need to be removed first. # The following dimension shows the number of models. # The rest of the shape tuple represents the shape of the parameter # in a single model. shape = shape[model_axis + 1:] return shape @property def size(self): """The size of this parameter's value array.""" # TODO: Rather than using self.value this could be determined from the # size of the parameter in _param_metrics return np.size(self.value) @property def prior(self): if self._model is not None: prior = self._model._constraints['prior'] return prior.get(self._name, self._prior) else: return self._prior @prior.setter def prior(self, val): if self._model is not None: self._model._constraints['prior'][self._name] = val else: raise AttributeError("can't set attribute 'prior' on Parameter " "definition") @property def posterior(self): if self._model is not None: posterior = self._model._constraints['posterior'] return posterior.get(self._name, self._posterior) else: return self._posterior @posterior.setter def posterior(self, val): if self._model is not None: self._model._constraints['posterior'][self._name] = val else: raise AttributeError("can't set attribute 'posterior' on Parameter " "definition") @property def fixed(self): """ Boolean indicating if the parameter is kept fixed during fitting. """ if self._model is not None: fixed = self._model._constraints['fixed'] return fixed.get(self._name, self._fixed) else: return self._fixed @fixed.setter def fixed(self, value): """Fix a parameter""" if self._model is not None: if not isinstance(value, bool): raise TypeError("Fixed can be True or False") self._model._constraints['fixed'][self._name] = value else: raise AttributeError("can't set attribute 'fixed' on Parameter " "definition") @property def tied(self): """ Indicates that this parameter is linked to another one. A callable which provides the relationship of the two parameters. """ if self._model is not None: tied = self._model._constraints['tied'] return tied.get(self._name, self._tied) else: return self._tied @tied.setter def tied(self, value): """Tie a parameter""" if self._model is not None: if not callable(value) and value not in (False, None): raise TypeError("Tied must be a callable") self._model._constraints['tied'][self._name] = value else: raise AttributeError("can't set attribute 'tied' on Parameter " "definition") @property def bounds(self): """The minimum and maximum values of a parameter as a tuple""" if self._model is not None: bounds = self._model._constraints['bounds'] return bounds.get(self._name, self._bounds) else: return self._bounds @bounds.setter def bounds(self, value): """Set the minimum and maximum values of a parameter from a tuple""" if self._model is not None: _min, _max = value if _min is not None: if not isinstance(_min, numbers.Number): raise TypeError("Min value must be a number") _min = float(_min) if _max is not None: if not isinstance(_max, numbers.Number): raise TypeError("Max value must be a number") _max = float(_max) bounds = self._model._constraints.setdefault('bounds', {}) self._model._constraints['bounds'][self._name] = (_min, _max) else: raise AttributeError("can't set attribute 'bounds' on Parameter " "definition") @property def min(self): """A value used as a lower bound when fitting a parameter""" return self.bounds[0] @min.setter def min(self, value): """Set a minimum value of a parameter""" if self._model is not None: self.bounds = (value, self.max) else: raise AttributeError("can't set attribute 'min' on Parameter " "definition") @property def max(self): """A value used as an upper bound when fitting a parameter""" return self.bounds[1] @max.setter def max(self, value): """Set a maximum value of a parameter.""" if self._model is not None: self.bounds = (self.min, value) else: raise AttributeError("can't set attribute 'max' on Parameter " "definition") @property def validator(self): """ Used as a decorator to set the validator method for a `Parameter`. The validator method validates any value set for that parameter. It takes two arguments--``self``, which refers to the `Model` instance (remember, this is a method defined on a `Model`), and the value being set for this parameter. The validator method's return value is ignored, but it may raise an exception if the value set on the parameter is invalid (typically an `InputParameterError` should be raised, though this is not currently a requirement). The decorator *returns* the `Parameter` instance that the validator is set on, so the underlying validator method should have the same name as the `Parameter` itself (think of this as analogous to ``property.setter``). For example:: >>> from astropy.modeling import Fittable1DModel >>> class TestModel(Fittable1DModel): ... a = Parameter() ... b = Parameter() ... ... @a.validator ... def a(self, value): ... # Remember, the value can be an array ... if np.any(value < self.b): ... raise InputParameterError( ... "parameter 'a' must be greater than or equal " ... "to parameter 'b'") ... ... @staticmethod ... def evaluate(x, a, b): ... return a * x + b ... >>> m = TestModel(a=1, b=2) # doctest: +IGNORE_EXCEPTION_DETAIL Traceback (most recent call last): ... InputParameterError: parameter 'a' must be greater than or equal to parameter 'b' >>> m = TestModel(a=2, b=2) >>> m.a = 0 # doctest: +IGNORE_EXCEPTION_DETAIL Traceback (most recent call last): ... InputParameterError: parameter 'a' must be greater than or equal to parameter 'b' On bound parameters this property returns the validator method itself, as a bound method on the `Parameter`. This is not often as useful, but it allows validating a parameter value without setting that parameter:: >>> m.a.validator(42) # Passes >>> m.a.validator(-42) # doctest: +IGNORE_EXCEPTION_DETAIL Traceback (most recent call last): ... InputParameterError: parameter 'a' must be greater than or equal to parameter 'b' """ if self._model is None: # For unbound parameters return the validator setter def validator(func, self=self): self._validator = func return self return validator else: # Return the validator method, bound to the Parameter instance with # the name "validator" def validator(self, value): if self._validator is not None: return self._validator(self._model, value) return types.MethodType(validator, self)
[docs] def copy(self, name=None, description=None, default=None, unit=None, getter=None, setter=None, fixed=False, tied=False, min=None, max=None, bounds=None, prior=None, posterior=None): """ Make a copy of this `Parameter`, overriding any of its core attributes in the process (or an exact copy). The arguments to this method are the same as those for the `Parameter` initializer. This simply returns a new `Parameter` instance with any or all of the attributes overridden, and so returns the equivalent of: .. code:: python Parameter(self.name, self.description, ...) """ kwargs = locals().copy() del kwargs['self'] for key, value in kwargs.items(): if value is None: # Annoying special cases for min/max where are just aliases for # the components of bounds if key in ('min', 'max'): continue else: if hasattr(self, key): value = getattr(self, key) elif hasattr(self, '_' + key): value = getattr(self, '_' + key) kwargs[key] = value return self.__class__(**kwargs)
@property def _raw_value(self): """ Currently for internal use only. Like Parameter.value but does not pass the result through Parameter.getter. By design this should only be used from bound parameters. This will probably be removed are retweaked at some point in the process of rethinking how parameter values are stored/updated. """ return self._get_model_value(self._model) def _bind(self, model): """ Bind the `Parameter` to a specific `Model` instance; don't use this directly on *unbound* parameters, i.e. `Parameter` descriptors that are defined in class bodies. """ self._model = model self._getter = self._create_value_wrapper(self._getter, model) self._setter = self._create_value_wrapper(self._setter, model) # TODO: These methods should probably be moved to the Model class, since it # has entirely to do with details of how the model stores parameters. # Parameter should just act as a user front-end to this. def _get_model_value(self, model): """ This method implements how to retrieve the value of this parameter from the model instance. See also `Parameter._set_model_value`. These methods take an explicit model argument rather than using self._model so that they can be used from unbound `Parameter` instances. """ if not hasattr(model, '_parameters'): # The _parameters array hasn't been initialized yet; just translate # this to an AttributeError raise AttributeError(self._name) # Use the _param_metrics to extract the parameter value from the # _parameters array param_metrics = model._param_metrics[self._name] param_slice = param_metrics['slice'] param_shape = param_metrics['shape'] value = model._parameters[param_slice] if param_shape: value = value.reshape(param_shape) else: value = value[0] return value def _set_model_value(self, model, value): """ This method implements how to store the value of a parameter on the model instance. Currently there is only one storage mechanism (via the ._parameters array) but other mechanisms may be desireable, in which case really the model class itself should dictate this and *not* `Parameter` itself. """ def _update_parameter_value(model, name, value): # TODO: Maybe handle exception on invalid input shape param_metrics = model._param_metrics[name] param_slice = param_metrics['slice'] param_shape = param_metrics['shape'] param_size = np.prod(param_shape) if np.size(value) != param_size: raise InputParameterError( "Input value for parameter {0!r} does not have {1} elements " "as the current value does".format(name, param_size)) model._parameters[param_slice] = np.array(value).ravel() _update_parameter_value(model, self._name, value) if hasattr(model, "_param_map"): submodel_ind, param_name = model._param_map[self._name] if hasattr(model._submodels[submodel_ind], "_param_metrics"): _update_parameter_value(model._submodels[submodel_ind], param_name, value) @staticmethod def _create_value_wrapper(wrapper, model): """Wraps a getter/setter function to support optionally passing in a reference to the model object as the second argument. If a model is tied to this parameter and its getter/setter supports a second argument then this creates a partial function using the model instance as the second argument. """ if isinstance(wrapper, np.ufunc): if wrapper.nin != 1: raise TypeError("A numpy.ufunc used for Parameter " "getter/setter may only take one input " "argument") elif wrapper is None: # Just allow non-wrappers to fall through silently, for convenience return None else: inputs, params = get_inputs_and_params(wrapper) nargs = len(inputs) if nargs == 1: pass elif nargs == 2: if model is not None: # Don't make a partial function unless we're tied to a # specific model instance model_arg = inputs[1].name wrapper = functools.partial(wrapper, **{model_arg: model}) else: raise TypeError("Parameter getter/setter must be a function " "of either one or two arguments") return wrapper def __array__(self, dtype=None): # Make np.asarray(self) work a little more straightforwardly arr = np.asarray(self.value, dtype=dtype) if self.unit is not None: arr = Quantity(arr, self.unit, copy=False) return arr def __bool__(self): if self._model is None: return True else: return bool(self.value) __add__ = _binary_arithmetic_operation(operator.add) __radd__ = _binary_arithmetic_operation(operator.add, reflected=True) __sub__ = _binary_arithmetic_operation(operator.sub) __rsub__ = _binary_arithmetic_operation(operator.sub, reflected=True) __mul__ = _binary_arithmetic_operation(operator.mul) __rmul__ = _binary_arithmetic_operation(operator.mul, reflected=True) __pow__ = _binary_arithmetic_operation(operator.pow) __rpow__ = _binary_arithmetic_operation(operator.pow, reflected=True) __div__ = _binary_arithmetic_operation(operator.truediv) __rdiv__ = _binary_arithmetic_operation(operator.truediv, reflected=True) __truediv__ = _binary_arithmetic_operation(operator.truediv) __rtruediv__ = _binary_arithmetic_operation(operator.truediv, reflected=True) __eq__ = _binary_comparison_operation(operator.eq) __ne__ = _binary_comparison_operation(operator.ne) __lt__ = _binary_comparison_operation(operator.lt) __gt__ = _binary_comparison_operation(operator.gt) __le__ = _binary_comparison_operation(operator.le) __ge__ = _binary_comparison_operation(operator.ge) __neg__ = _unary_arithmetic_operation(operator.neg) __abs__ = _unary_arithmetic_operation(operator.abs)
def param_repr_oneline(param): """ Like array_repr_oneline but works on `Parameter` objects and supports rendering parameters with units like quantities. """ out = array_repr_oneline(param.value) if param.unit is not None: out = '{0} {1!s}'.format(out, param.unit) return out