Source code for sasmodels.details

Kernel Call Details

When calling sas computational kernels with polydispersity there are a
number of details that need to be sent to the caller.  This includes the
list of polydisperse parameters, the number of points in the polydispersity
weight distribution, and which parameter is the "theta" parameter for
polar coordinate integration.  The :class:`CallDetails` object maintains
this data.  Use :func:`make_details` to build a *details* object which
can be passed to one of the computational kernels.

from __future__ import print_function

import numpy as np  # type: ignore
from numpy import cos, sin, radians

    meshgrid = np.meshgrid
except Exception:
    # CRUFT: np.meshgrid requires multiple vectors
    def meshgrid(*args):
        """See docs from a recent version of numpy"""
        if len(args) > 1:
            return np.meshgrid(*args)
            return [np.asarray(v) for v in args]

# pylint: disable=unused-import
    from typing import List, Tuple, Sequence
    from .modelinfo import ModelInfo, ParameterTable
    from .kernel import Kernel
except ImportError:
# pylint: enable=unused-import

[docs]class CallDetails(object): """ Manage the polydispersity information for the kernel call. Conceptually, a polydispersity calculation is an integral over a mesh in n-D space where n is the number of polydisperse parameters. In order to keep the program responsive, and not crash the GPU, only a portion of the mesh is computed at a time. Meshes with a large number of points will therefore require many calls to the polydispersity loop. Restarting a nested loop in the middle requires that the indices of the individual mesh dimensions can be computed for the current loop location. This is handled by the *pd_stride* vector, with n//stride giving the loop index and n%stride giving the position in the sub loops. One of the parameters may be the latitude. When integrating in polar coordinates, the total circumference decreases as latitude varies from pi r^2 at the equator to 0 at the pole, and the weight associated with a range of latitude values needs to be scaled by this circumference. This scale factor needs to be updated each time the theta value changes. *theta_par* indicates which of the values in the parameter vector is the latitude parameter, or -1 if there is no latitude parameter in the model. In practice, the normalization term cancels if the latitude is not a polydisperse parameter. """ parts = None # type: List["CallDetails"] def __init__(self, model_info): # type: (ModelInfo) -> None parameters = model_info.parameters max_pd = parameters.max_pd # Structure of the call details buffer: # pd_par[max_pd] pd params in order of length # pd_length[max_pd] length of each pd param # pd_offset[max_pd] offset of pd values in parameter array # pd_stride[max_pd] index of pd value in loop = n//stride[k] # num_eval total length of pd loop # num_weights total length of the weight vector # num_active number of pd params # theta_par parameter number for theta parameter self.buffer = np.empty(4*max_pd + 4, 'i4') # generate views on different parts of the array self._pd_par = self.buffer[0 * max_pd:1 * max_pd] self._pd_length = self.buffer[1 * max_pd:2 * max_pd] self._pd_offset = self.buffer[2 * max_pd:3 * max_pd] self._pd_stride = self.buffer[3 * max_pd:4 * max_pd] # theta_par is fixed self.theta_par = parameters.theta_offset # offset and length are for all parameters, not just pd parameters # They are not sent to the kernel function, though they could be. # They are used by the composite models (sum and product) to # figure out offsets into the combined value list. self.offset = None # type: np.ndarray self.length = None # type: np.ndarray # keep hold of ifno show() so we can break a values vector # into the individual components = model_info @property def pd_par(self): """List of polydisperse parameters""" return self._pd_par @property def pd_length(self): """Number of weights for each polydisperse parameter""" return self._pd_length @property def pd_offset(self): """Offsets for the individual weight vectors in the set of weights""" return self._pd_offset @property def pd_stride(self): """Stride in the pd mesh for each pd dimension""" return self._pd_stride @property def num_eval(self): """Total size of the pd mesh""" return self.buffer[-4] @num_eval.setter def num_eval(self, v): """Total size of the pd mesh""" self.buffer[-4] = v @property def num_weights(self): """Total length of all the weight vectors""" return self.buffer[-3] @num_weights.setter def num_weights(self, v): """Total length of all the weight vectors""" self.buffer[-3] = v @property def num_active(self): """Number of active polydispersity loops""" return self.buffer[-2] @num_active.setter def num_active(self, v): """Number of active polydispersity loops""" self.buffer[-2] = v @property def theta_par(self): """Location of the theta parameter in the parameter vector""" return self.buffer[-1] @theta_par.setter def theta_par(self, v): """Location of the theta parameter in the parameter vector""" self.buffer[-1] = v
[docs] def show(self, values=None): """Print the polydispersity call details to the console""" print("===== %s details ====" print("num_active:%d num_eval:%d num_weights:%d theta=%d" % (self.num_active, self.num_eval, self.num_weights, self.theta_par)) if self.pd_par.size: print("pd_par", self.pd_par) print("pd_length", self.pd_length) print("pd_offset", self.pd_offset) print("pd_stride", self.pd_stride) if values is not None: nvalues = print("scale, background", values[:2]) print("val", values[2:nvalues]) print("pd", values[nvalues:nvalues+self.num_weights]) print("wt", values[nvalues+self.num_weights:nvalues+2*self.num_weights]) print("offsets", self.offset)
[docs]def make_details(model_info, length, offset, num_weights): # type: (ModelInfo, np.ndarray, np.ndarray, int) -> CallDetails """ Return a :class:`CallDetails` object for a polydisperse calculation of the model defined by *model_info*. Polydispersity is defined by the *length* of the polydispersity distribution for each parameter and the *offset* of the distribution in the polydispersity array. Monodisperse parameters should use a polydispersity length of one with weight 1.0. *num_weights* is the total length of the polydispersity array. """ #pars = model_info.parameters.call_parameters[2:model_info.parameters.npars+2] #print(", ".join(str(i)+"-" for i,p in enumerate(pars))) #print("len:",length) #print("off:",offset) # Check that we aren't using too many polydispersity loops num_active = np.sum(length > 1) max_pd = model_info.parameters.max_pd if num_active > max_pd: raise ValueError("Too many polydisperse parameters") # Decreasing list of polydpersity lengths # Note: the reversing view, x[::-1], does not require a copy idx = np.argsort(length)[::-1][:max_pd] pd_stride = np.cumprod(np.hstack((1, length[idx]))) call_details = CallDetails(model_info) call_details.pd_par[:max_pd] = idx call_details.pd_length[:max_pd] = length[idx] call_details.pd_offset[:max_pd] = offset[idx] call_details.pd_stride[:max_pd] = pd_stride[:-1] call_details.num_eval = pd_stride[-1] call_details.num_weights = num_weights call_details.num_active = num_active call_details.length = length call_details.offset = offset return call_details
ZEROS = tuple([0.]*31)
[docs]def make_kernel_args(kernel, mesh): # type: (Kernel, Tuple[List[np.ndarray], List[np.ndarray]]) -> Tuple[CallDetails, np.ndarray, bool] """ Converts (value, dispersity, weight) for each parameter into kernel pars. Returns a CallDetails object indicating the polydispersity, a data object containing the different values, and the magnetic flag indicating whether any magnetic magnitudes are non-zero. Magnetic vectors (M0, phi, theta) are converted to rectangular coordinates (mx, my, mz). """ npars = nvalues = scalars = [value for value, dispersity, weight in mesh] # skipping scale and background when building values and weights _, dispersity, weight = zip(*mesh[2:npars+2]) if npars else ((), (), ()) #weight = correct_theta_weights(, dispersity, weight) length = np.array([len(w) for w in weight]) offset = np.cumsum(np.hstack((0, length))) call_details = make_details(, length, offset[:-1], offset[-1]) # Pad value array to a 32 value boundary data_len = nvalues + 2*sum(len(v) for v in dispersity) extra = (32 - data_len%32)%32 data = np.hstack((scalars,) + dispersity + weight + ZEROS[:extra]) data = data.astype(kernel.dtype) is_magnetic = convert_magnetism(, data) #print("data", data) return call_details, data, is_magnetic
[docs]def correct_theta_weights(parameters, dispersity, weights): # type: (ParameterTable, Sequence[np.ndarray], Sequence[np.ndarray]) -> Sequence[np.ndarray] """ **Deprecated** Theta weights will be computed in the kernel wrapper if they are needed. If there is a theta parameter, update the weights of that parameter so that the cosine weighting required for polar integration is preserved. Avoid evaluation strictly at the pole, which would otherwise send the weight to zero. This is probably not a problem in practice (if dispersity is +/- 90, then you probably should be using a 1-D model of the circular average). Note: scale and background parameters are not include in the tuples for dispersity and weights, so index is parameters.theta_offset, not parameters.theta_offset+2 Returns updated weights vectors """ # Apparently the parameters.theta_offset similarly skips scale and # and background, so the indexing works out, but they are still shipped # to the kernel, so we need to add two there. if parameters.theta_offset >= 0: index = parameters.theta_offset theta = dispersity[index] theta_weight = abs(cos(radians(theta))) weights = tuple(theta_weight*w if k == index else w for k, w in enumerate(weights)) return weights
[docs]def convert_magnetism(parameters, values): # type: (ParameterTable, Sequence[np.ndarray]) -> bool """ Convert magnetism values from polar to rectangular coordinates. Returns True if any magnetism is present. """ mag = values[parameters.nvalues-3*parameters.nmagnetic:parameters.nvalues] mag = mag.reshape(-1, 3) if np.any(mag[:, 0] != 0.0): M0 = mag[:, 0].copy() theta, phi = radians(mag[:, 1]), radians(mag[:, 2]) mag[:, 0] = +M0*cos(theta)*cos(phi) # mx mag[:, 1] = +M0*sin(theta) # my mag[:, 2] = -M0*cos(theta)*sin(phi) # mz return True else: return False
[docs]def dispersion_mesh(model_info, mesh): # type: (ModelInfo, List[Tuple[float, np.ndarray, np.ndarray]]) -> Tuple[List[np.ndarray], List[np.ndarray]] """ Create a mesh grid of dispersion parameters and weights. *mesh* is a list of (value, dispersity, weights), where the values are the individual parameter values, and (dispersity, weights) is the distribution of parameter values. Only the volume parameters should be included in this list. Orientation parameters do not affect the calculation of effective radius or volume ratio. This is convenient since it avoids the distinction between value and dispersity that is present in orientation parameters but not shape parameters. Returns [p1,p2,...],w where pj is a vector of values for parameter j and w is a vector containing the products for weights for each parameter set in the vector. """ _, dispersity, weight = zip(*mesh) #weight = [w if len(w)>0 else [1.] for w in weight] weight = np.vstack([v.flatten() for v in meshgrid(*weight)]) weight =, axis=0) dispersity = [v.flatten() for v in meshgrid(*dispersity)] lengths = [par.length for par in model_info.parameters.kernel_parameters if par.type == 'volume'] if any(n > 1 for n in lengths): pars = [] offset = 0 for n in lengths: pars.append(np.vstack(dispersity[offset:offset+n]) if n > 1 else dispersity[offset]) offset += n dispersity = pars return dispersity, weight