Source code for sasmodels.product

"""
Product model
-------------

The product model multiplies the structure factor by the form factor,
modulated by the effective radius of the form.  The resulting model
has a attributes of both the model description (with parameters, etc.)
and the module evaluator (with call, release, etc.).

To use it, first load form factor P and structure factor S, then create
*make_product_info(P, S)*.
"""
from __future__ import print_function, division

from copy import copy
import numpy as np  # type: ignore

from .modelinfo import ParameterTable, ModelInfo
from .kernel import KernelModel, Kernel
from .details import make_details, dispersion_mesh

# pylint: disable=unused-import
try:
    from typing import Tuple
except ImportError:
    pass
else:
    from .modelinfo import ParameterSet
# pylint: enable=unused-import

# TODO: make estimates available to constraints
#ESTIMATED_PARAMETERS = [
#    ["est_radius_effective", "A", 0.0, [0, np.inf], "", "Estimated effective radius"],
#    ["est_volume_ratio", "", 1.0, [0, np.inf], "", "Estimated volume ratio"],
#]

ER_ID = "radius_effective"
VF_ID = "volfraction"

# TODO: core_shell_sphere model has suppressed the volume ratio calculation
# revert it after making VR and ER available at run time as constraints.
[docs]def make_product_info(p_info, s_info): # type: (ModelInfo, ModelInfo) -> ModelInfo """ Create info block for product model. """ # Make sure effective radius is the first parameter and # make sure volume fraction is the second parameter of the # structure factor calculator. Structure factors should not # have any magnetic parameters if not len(s_info.parameters.kernel_parameters) >= 2: raise TypeError("S needs {} and {} as its first parameters".format(ER_ID, VF_ID)) if not s_info.parameters.kernel_parameters[0].id == ER_ID: raise TypeError("S needs {} as first parameter".format(ER_ID)) if not s_info.parameters.kernel_parameters[1].id == VF_ID: raise TypeError("S needs {} as second parameter".format(VF_ID)) if not s_info.parameters.magnetism_index == []: raise TypeError("S should not have SLD parameters") p_id, p_name, p_pars = p_info.id, p_info.name, p_info.parameters s_id, s_name, s_pars = s_info.id, s_info.name, s_info.parameters # Create list of parameters for the combined model. Skip the first # parameter of S, which we verified above is effective radius. If there # are any names in P that overlap with those in S, modify the name in S # to distinguish it. p_set = set(p.id for p in p_pars.kernel_parameters) s_list = [(_tag_parameter(par) if par.id in p_set else par) for par in s_pars.kernel_parameters[1:]] # Check if still a collision after renaming. This could happen if for # example S has volfrac and P has both volfrac and volfrac_S. if any(p.id in p_set for p in s_list): raise TypeError("name collision: P has P.name and P.name_S while S has S.name") translate_name = dict((old.id, new.id) for old, new in zip(s_pars.kernel_parameters[1:], s_list)) combined_pars = p_pars.kernel_parameters + s_list parameters = ParameterTable(combined_pars) parameters.max_pd = p_pars.max_pd + s_pars.max_pd def random(): combined_pars = p_info.random() s_names = set(par.id for par in s_pars.kernel_parameters[1:]) combined_pars.update((translate_name[k], v) for k, v in s_info.random().items() if k in s_names) return combined_pars model_info = ModelInfo() model_info.id = '@'.join((p_id, s_id)) model_info.name = '@'.join((p_name, s_name)) model_info.filename = None model_info.title = 'Product of %s and %s'%(p_name, s_name) model_info.description = model_info.title model_info.docs = model_info.title model_info.category = "custom" model_info.parameters = parameters model_info.random = random #model_info.single = p_info.single and s_info.single model_info.structure_factor = False model_info.variant_info = None #model_info.tests = [] #model_info.source = [] # Iq, Iqxy, form_volume, ER, VR and sesans # Remember the component info blocks so we can build the model model_info.composition = ('product', [p_info, s_info]) model_info.control = p_info.control model_info.hidden = p_info.hidden if getattr(p_info, 'profile', None) is not None: profile_pars = set(p.id for p in p_info.parameters.kernel_parameters) def profile(**kwargs): # extract the profile args kwargs = dict((k, v) for k, v in kwargs.items() if k in profile_pars) return p_info.profile(**kwargs) else: profile = None model_info.profile = profile model_info.profile_axes = p_info.profile_axes # TODO: delegate random to p_info, s_info #model_info.random = lambda: {} ## Show the parameter table #from .compare import get_pars, parlist #print("==== %s ====="%model_info.name) #values = get_pars(model_info) #print(parlist(model_info, values, is2d=True)) return model_info
def _tag_parameter(par): """ Tag the parameter name with _S to indicate that the parameter comes from the structure factor parameter set. This is only necessary if the form factor model includes a parameter of the same name as a parameter in the structure factor. """ par = copy(par) # Protect against a vector parameter in S by appending the vector length # to the renamed parameter. Note: haven't tested this since no existing # structure factor models contain vector parameters. vector_length = par.name[len(par.id):] par.id = par.id + "_S" par.name = par.id + vector_length return par
[docs]class ProductModel(KernelModel): def __init__(self, model_info, P, S): # type: (ModelInfo, KernelModel, KernelModel) -> None #: Combined info plock for the product model self.info = model_info #: Form factor modelling individual particles. self.P = P #: Structure factor modelling interaction between particles. self.S = S #: Model precision. This is not really relevant, since it is the #: individual P and S models that control the effective dtype, #: converting the q-vectors to the correct type when the kernels #: for each are created. Ideally this should be set to the more #: precise type to avoid loss of precision, but precision in q is #: not critical (single is good enough for our purposes), so it just #: uses the precision of the form factor. self.dtype = P.dtype # type: np.dtype
[docs] def make_kernel(self, q_vectors): # type: (List[np.ndarray]) -> Kernel # Note: may be sending the q_vectors to the GPU twice even though they # are only needed once. It would mess up modularity quite a bit to # handle this optimally, especially since there are many cases where # separate q vectors are needed (e.g., form in python and structure # in opencl; or both in opencl, but one in single precision and the # other in double precision). p_kernel = self.P.make_kernel(q_vectors) s_kernel = self.S.make_kernel(q_vectors) return ProductKernel(self.info, p_kernel, s_kernel)
[docs] def release(self): # type: (None) -> None """ Free resources associated with the model. """ self.P.release() self.S.release()
[docs]class ProductKernel(Kernel): def __init__(self, model_info, p_kernel, s_kernel): # type: (ModelInfo, Kernel, Kernel) -> None self.info = model_info self.p_kernel = p_kernel self.s_kernel = s_kernel self.dtype = p_kernel.dtype self.results = [] # type: List[np.ndarray] def __call__(self, call_details, values, cutoff, magnetic): # type: (CallDetails, np.ndarray, float, bool) -> np.ndarray p_info, s_info = self.info.composition[1] # if there are magnetic parameters, they will only be on the # form factor P, not the structure factor S. nmagnetic = len(self.info.parameters.magnetism_index) if nmagnetic: spin_index = self.info.parameters.npars + 2 magnetism = values[spin_index: spin_index+3+3*nmagnetic] else: magnetism = [] nvalues = self.info.parameters.nvalues nweights = call_details.num_weights weights = values[nvalues:nvalues + 2*nweights] # Construct the calling parameters for P. p_npars = p_info.parameters.npars p_length = call_details.length[:p_npars] p_offset = call_details.offset[:p_npars] p_details = make_details(p_info, p_length, p_offset, nweights) # Set p scale to the volume fraction in s, which is the first of the # 'S' parameters in the parameter list, or 2+np in 0-origin. volfrac = values[2+p_npars] p_values = [[volfrac, 0.0], values[2:2+p_npars], magnetism, weights] spacer = (32 - sum(len(v) for v in p_values)%32)%32 p_values.append([0.]*spacer) p_values = np.hstack(p_values).astype(self.p_kernel.dtype) # Call ER and VR for P since these are needed for S. p_er, p_vr = calc_er_vr(p_info, p_details, p_values) s_vr = (volfrac/p_vr if p_vr != 0. else volfrac) #print("volfrac:%g p_er:%g p_vr:%g s_vr:%g"%(volfrac,p_er,p_vr,s_vr)) # Construct the calling parameters for S. # The effective radius is not in the combined parameter list, so # the number of 'S' parameters is one less than expected. The # computed effective radius needs to be added into the weights # vector, especially since it is a polydisperse parameter in the # stand-alone structure factor models. We will added it at the # end so the remaining offsets don't need to change. s_npars = s_info.parameters.npars-1 s_length = call_details.length[p_npars:p_npars+s_npars] s_offset = call_details.offset[p_npars:p_npars+s_npars] s_length = np.hstack((1, s_length)) s_offset = np.hstack((nweights, s_offset)) s_details = make_details(s_info, s_length, s_offset, nweights+1) v, w = weights[:nweights], weights[nweights:] s_values = [ # scale=1, background=0, radius_effective=p_er, volfraction=s_vr [1., 0., p_er, s_vr], # structure factor parameters start after scale, background and # all the form factor parameters. Skip the volfraction parameter # as well, since it is computed elsewhere, and go to the end of the # parameter list. values[2+p_npars+1:2+p_npars+s_npars], # no magnetism parameters to include for S # add er into the (value, weights) pairs v, [p_er], w, [1.0] ] spacer = (32 - sum(len(v) for v in s_values)%32)%32 s_values.append([0.]*spacer) s_values = np.hstack(s_values).astype(self.s_kernel.dtype) # Call the kernels p_result = self.p_kernel(p_details, p_values, cutoff, magnetic) s_result = self.s_kernel(s_details, s_values, cutoff, False) #print("p_npars",p_npars,s_npars,p_er,s_vr,values[2+p_npars+1:2+p_npars+s_npars]) #call_details.show(values) #print("values", values) #p_details.show(p_values) #print("=>", p_result) #s_details.show(s_values) #print("=>", s_result) # remember the parts for plotting later self.results = [p_result, s_result] #import pylab as plt #plt.subplot(211); plt.loglog(self.p_kernel.q_input.q, p_result, '-') #plt.subplot(212); plt.loglog(self.s_kernel.q_input.q, s_result, '-') #plt.figure() return values[0]*(p_result*s_result) + values[1]
[docs] def release(self): # type: () -> None self.p_kernel.release() self.s_kernel.release()
[docs]def calc_er_vr(model_info, call_details, values): # type: (ModelInfo, ParameterSet) -> Tuple[float, float] if model_info.ER is None and model_info.VR is None: return 1.0, 1.0 nvalues = model_info.parameters.nvalues value = values[nvalues:nvalues + call_details.num_weights] weight = values[nvalues + call_details.num_weights: nvalues + 2*call_details.num_weights] npars = model_info.parameters.npars # Note: changed from pairs ([v], [w]) to triples (p, [v], [w]), but the # dispersion mesh code doesn't actually care about the nominal parameter # value, p, so set it to None. pairs = [(None, value[offset:offset+length], weight[offset:offset+length]) for p, offset, length in zip(model_info.parameters.call_parameters[2:2+npars], call_details.offset, call_details.length) if p.type == 'volume'] value, weight = dispersion_mesh(model_info, pairs) if model_info.ER is not None: individual_radii = model_info.ER(*value) radius_effective = np.sum(weight*individual_radii) / np.sum(weight) else: radius_effective = 1.0 if model_info.VR is not None: whole, part = model_info.VR(*value) volume_ratio = np.sum(weight*part)/np.sum(weight*whole) else: volume_ratio = 1.0 return radius_effective, volume_ratio