[803f835] | 1 | """ |
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| 2 | Class interface to the model calculator. |
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| 3 | |
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| 4 | Calling a model is somewhat non-trivial since the functions called depend |
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| 5 | on the data type. For 1D data the *Iq* kernel needs to be called, for |
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| 6 | 2D data the *Iqxy* kernel needs to be called, and for SESANS data the |
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| 7 | *Iq* kernel needs to be called followed by a Hankel transform. Before |
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| 8 | the kernel is called an appropriate *q* calculation vector needs to be |
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| 9 | constructed. This is not the simple *q* vector where you have measured |
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| 10 | the data since the resolution calculation will require values beyond the |
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| 11 | range of the measured data. After the calculation the resolution calculator |
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| 12 | must be called to return the predicted value for each measured data point. |
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| 13 | |
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| 14 | :class:`DirectModel` is a callable object that takes *parameter=value* |
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| 15 | keyword arguments and returns the appropriate theory values for the data. |
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| 16 | |
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| 17 | :class:`DataMixin` does the real work of interpreting the data and calling |
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| 18 | the model calculator. This is used by :class:`DirectModel`, which uses |
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| 19 | direct parameter values and by :class:`bumps_model.Experiment` which wraps |
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| 20 | the parameter values in boxes so that the user can set fitting ranges, etc. |
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| 21 | on the individual parameters and send the model to the Bumps optimizers. |
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| 22 | """ |
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| 23 | from __future__ import print_function |
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[ae7b97b] | 24 | |
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[7ae2b7f] | 25 | import numpy as np # type: ignore |
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[ae7b97b] | 26 | |
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[7ae2b7f] | 27 | # TODO: fix sesans module |
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| 28 | from . import sesans # type: ignore |
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[6d6508e] | 29 | from . import weights |
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[7cf2cfd] | 30 | from . import resolution |
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| 31 | from . import resolution2d |
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[bde38b5] | 32 | from .details import make_kernel_args, dispersion_mesh |
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[7b9e4dd] | 33 | from .modelinfo import DEFAULT_BACKGROUND |
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[5024a56] | 34 | from .product import RADIUS_MODE_ID |
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[6d6508e] | 35 | |
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[2d81cfe] | 36 | # pylint: disable=unused-import |
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[a5b8477] | 37 | try: |
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| 38 | from typing import Optional, Dict, Tuple |
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| 39 | except ImportError: |
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| 40 | pass |
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| 41 | else: |
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| 42 | from .data import Data |
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| 43 | from .kernel import Kernel, KernelModel |
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| 44 | from .modelinfo import Parameter, ParameterSet |
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[2d81cfe] | 45 | # pylint: enable=unused-import |
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[a5b8477] | 46 | |
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[0ff62d4] | 47 | def call_kernel(calculator, pars, cutoff=0., mono=False): |
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[a5b8477] | 48 | # type: (Kernel, ParameterSet, float, bool) -> np.ndarray |
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[6d6508e] | 49 | """ |
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| 50 | Call *kernel* returned from *model.make_kernel* with parameters *pars*. |
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| 51 | |
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| 52 | *cutoff* is the limiting value for the product of dispersion weights used |
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| 53 | to perform the multidimensional dispersion calculation more quickly at a |
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| 54 | slight cost to accuracy. The default value of *cutoff=0* integrates over |
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| 55 | the entire dispersion cube. Using *cutoff=1e-5* can be 50% faster, but |
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| 56 | with an error of about 1%, which is usually less than the measurement |
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| 57 | uncertainty. |
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| 58 | |
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| 59 | *mono* is True if polydispersity should be set to none on all parameters. |
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| 60 | """ |
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[3c24ccd] | 61 | mesh = get_mesh(calculator.info, pars, dim=calculator.dim, mono=mono) |
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[9e771a3] | 62 | #print("pars", list(zip(*mesh))[0]) |
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[8698a0d] | 63 | call_details, values, is_magnetic = make_kernel_args(calculator, mesh) |
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[32e3c9b] | 64 | #print("values:", values) |
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[9eb3632] | 65 | return calculator(call_details, values, cutoff, is_magnetic) |
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[6d6508e] | 66 | |
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[304c775] | 67 | def call_Fq(calculator, pars, cutoff=0., mono=False): |
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| 68 | # type: (Kernel, ParameterSet, float, bool) -> np.ndarray |
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[40a87fa] | 69 | """ |
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[23df833] | 70 | Like :func:`call_kernel`, but returning F, F^2, R_eff, V_shell, V_form/V_shell. |
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[40a87fa] | 71 | |
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[23df833] | 72 | For solid objects V_shell is equal to V_form and the volume ratio is 1. |
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[40a87fa] | 73 | |
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[5024a56] | 74 | Use parameter *radius_effective_mode* to select the effective radius |
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| 75 | calculation. |
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[40a87fa] | 76 | """ |
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[5024a56] | 77 | R_eff_type = int(pars.pop(RADIUS_MODE_ID, 1.0)) |
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[304c775] | 78 | mesh = get_mesh(calculator.info, pars, dim=calculator.dim, mono=mono) |
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| 79 | #print("pars", list(zip(*mesh))[0]) |
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| 80 | call_details, values, is_magnetic = make_kernel_args(calculator, mesh) |
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| 81 | #print("values:", values) |
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| 82 | return calculator.Fq(call_details, values, cutoff, is_magnetic, R_eff_type) |
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[40a87fa] | 83 | |
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[23df833] | 84 | def call_profile(model_info, pars=None): |
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| 85 | # type: (ModelInfo, ParameterSet) -> Tuple[np.ndarray, np.ndarray, Tuple[str, str]] |
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[40a87fa] | 86 | """ |
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| 87 | Returns the profile *x, y, (xlabel, ylabel)* representing the model. |
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| 88 | """ |
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[23df833] | 89 | if pars is None: |
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| 90 | pars = {} |
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[40a87fa] | 91 | args = {} |
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| 92 | for p in model_info.parameters.kernel_parameters: |
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| 93 | if p.length > 1: |
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| 94 | value = np.array([pars.get(p.id+str(j), p.default) |
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| 95 | for j in range(1, p.length+1)]) |
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| 96 | else: |
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| 97 | value = pars.get(p.id, p.default) |
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| 98 | args[p.id] = value |
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| 99 | x, y = model_info.profile(**args) |
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| 100 | return x, y, model_info.profile_axes |
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| 101 | |
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[3c24ccd] | 102 | def get_mesh(model_info, values, dim='1d', mono=False): |
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| 103 | # type: (ModelInfo, Dict[str, float], str, bool) -> List[Tuple[float, np.ndarray, np.ndarry]] |
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| 104 | """ |
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| 105 | Retrieve the dispersity mesh described by the parameter set. |
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| 106 | |
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| 107 | Returns a list of *(value, dispersity, weights)* with one tuple for each |
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| 108 | parameter in the model call parameters. Inactive parameters return the |
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| 109 | default value with a weight of 1.0. |
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| 110 | """ |
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| 111 | parameters = model_info.parameters |
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| 112 | if mono: |
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| 113 | active = lambda name: False |
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| 114 | elif dim == '1d': |
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| 115 | active = lambda name: name in parameters.pd_1d |
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| 116 | elif dim == '2d': |
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| 117 | active = lambda name: name in parameters.pd_2d |
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| 118 | else: |
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| 119 | active = lambda name: True |
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| 120 | |
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| 121 | #print("pars",[p.id for p in parameters.call_parameters]) |
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| 122 | mesh = [_get_par_weights(p, values, active(p.name)) |
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| 123 | for p in parameters.call_parameters] |
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| 124 | return mesh |
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| 125 | |
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[40a87fa] | 126 | |
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[3c24ccd] | 127 | def _get_par_weights(parameter, values, active=True): |
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| 128 | # type: (Parameter, Dict[str, float]) -> Tuple[float, np.ndarray, np.ndarray] |
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[6d6508e] | 129 | """ |
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| 130 | Generate the distribution for parameter *name* given the parameter values |
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| 131 | in *pars*. |
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| 132 | |
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| 133 | Uses "name", "name_pd", "name_pd_type", "name_pd_n", "name_pd_sigma" |
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| 134 | from the *pars* dictionary for parameter value and parameter dispersion. |
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| 135 | """ |
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| 136 | value = float(values.get(parameter.name, parameter.default)) |
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| 137 | npts = values.get(parameter.name+'_pd_n', 0) |
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| 138 | width = values.get(parameter.name+'_pd', 0.0) |
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[32f87a5] | 139 | relative = parameter.relative_pd |
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[9e771a3] | 140 | if npts == 0 or width == 0.0 or not active: |
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[8698a0d] | 141 | # Note: orientation parameters have the viewing angle as the parameter |
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| 142 | # value and the jitter in the distribution, so be sure to set the |
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| 143 | # empty pd for orientation parameters to 0. |
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[9e771a3] | 144 | pd = [value if relative or not parameter.polydisperse else 0.0], [1.0] |
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[8698a0d] | 145 | else: |
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| 146 | limits = parameter.limits |
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| 147 | disperser = values.get(parameter.name+'_pd_type', 'gaussian') |
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| 148 | nsigma = values.get(parameter.name+'_pd_nsigma', 3.0) |
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| 149 | pd = weights.get_weights(disperser, npts, width, nsigma, |
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[2d81cfe] | 150 | value, limits, relative) |
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[8698a0d] | 151 | return value, pd[0], pd[1] |
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[ae7b97b] | 152 | |
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[745b7bb] | 153 | |
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[9e771a3] | 154 | def _vol_pars(model_info, values): |
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[40a87fa] | 155 | # type: (ModelInfo, ParameterSet) -> Tuple[np.ndarray, np.ndarray] |
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[9e771a3] | 156 | vol_pars = [_get_par_weights(p, values) |
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[40a87fa] | 157 | for p in model_info.parameters.call_parameters |
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| 158 | if p.type == 'volume'] |
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[4cc161e] | 159 | #import pylab; pylab.plot(vol_pars[0][0],vol_pars[0][1]); pylab.show() |
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[9e771a3] | 160 | dispersity, weight = dispersion_mesh(model_info, vol_pars) |
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| 161 | return dispersity, weight |
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[745b7bb] | 162 | |
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| 163 | |
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[fa79f5c] | 164 | def _make_sesans_transform(data): |
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| 165 | from sas.sascalc.data_util.nxsunit import Converter |
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| 166 | |
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| 167 | # Pre-compute the Hankel matrix (H) |
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| 168 | SElength = Converter(data._xunit)(data.x, "A") |
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| 169 | |
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| 170 | theta_max = Converter("radians")(data.sample.zacceptance)[0] |
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| 171 | q_max = 2 * np.pi / np.max(data.source.wavelength) * np.sin(theta_max) |
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| 172 | zaccept = Converter("1/A")(q_max, "1/" + data.source.wavelength_unit), |
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| 173 | |
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| 174 | Rmax = 10000000 |
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| 175 | hankel = sesans.SesansTransform(data.x, SElength, |
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| 176 | data.source.wavelength, |
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| 177 | zaccept, Rmax) |
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| 178 | return hankel |
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| 179 | |
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| 180 | |
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[7cf2cfd] | 181 | class DataMixin(object): |
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| 182 | """ |
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| 183 | DataMixin captures the common aspects of evaluating a SAS model for a |
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| 184 | particular data set, including calculating Iq and evaluating the |
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| 185 | resolution function. It is used in particular by :class:`DirectModel`, |
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| 186 | which evaluates a SAS model parameters as key word arguments to the |
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| 187 | calculator method, and by :class:`bumps_model.Experiment`, which wraps the |
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| 188 | model and data for use with the Bumps fitting engine. It is not |
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| 189 | currently used by :class:`sasview_model.SasviewModel` since this will |
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| 190 | require a number of changes to SasView before we can do it. |
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[803f835] | 191 | |
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| 192 | :meth:`_interpret_data` initializes the data structures necessary |
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| 193 | to manage the calculations. This sets attributes in the child class |
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| 194 | such as *data_type* and *resolution*. |
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| 195 | |
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| 196 | :meth:`_calc_theory` evaluates the model at the given control values. |
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| 197 | |
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| 198 | :meth:`_set_data` sets the intensity data in the data object, |
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| 199 | possibly with random noise added. This is useful for simulating a |
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| 200 | dataset with the results from :meth:`_calc_theory`. |
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[7cf2cfd] | 201 | """ |
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| 202 | def _interpret_data(self, data, model): |
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[a5b8477] | 203 | # type: (Data, KernelModel) -> None |
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[803f835] | 204 | # pylint: disable=attribute-defined-outside-init |
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| 205 | |
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[7cf2cfd] | 206 | self._data = data |
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| 207 | self._model = model |
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| 208 | |
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| 209 | # interpret data |
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[a769b54] | 210 | if hasattr(data, 'isSesans') and data.isSesans: |
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[7cf2cfd] | 211 | self.data_type = 'sesans' |
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| 212 | elif hasattr(data, 'qx_data'): |
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| 213 | self.data_type = 'Iqxy' |
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[ea75043] | 214 | elif getattr(data, 'oriented', False): |
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| 215 | self.data_type = 'Iq-oriented' |
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[7cf2cfd] | 216 | else: |
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| 217 | self.data_type = 'Iq' |
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| 218 | |
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| 219 | if self.data_type == 'sesans': |
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[fa79f5c] | 220 | res = _make_sesans_transform(data) |
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[803f835] | 221 | index = slice(None, None) |
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[7cf2cfd] | 222 | if data.y is not None: |
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[803f835] | 223 | Iq, dIq = data.y, data.dy |
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| 224 | else: |
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| 225 | Iq, dIq = None, None |
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[7cf2cfd] | 226 | elif self.data_type == 'Iqxy': |
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[6d6508e] | 227 | #if not model.info.parameters.has_2d: |
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[60eab2a] | 228 | # raise ValueError("not 2D without orientation or magnetic parameters") |
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[7cf2cfd] | 229 | q = np.sqrt(data.qx_data**2 + data.qy_data**2) |
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| 230 | qmin = getattr(data, 'qmin', 1e-16) |
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| 231 | qmax = getattr(data, 'qmax', np.inf) |
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| 232 | accuracy = getattr(data, 'accuracy', 'Low') |
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[1a8c11c] | 233 | index = (data.mask == 0) & (q >= qmin) & (q <= qmax) |
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[7cf2cfd] | 234 | if data.data is not None: |
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[803f835] | 235 | index &= ~np.isnan(data.data) |
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| 236 | Iq = data.data[index] |
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| 237 | dIq = data.err_data[index] |
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| 238 | else: |
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| 239 | Iq, dIq = None, None |
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| 240 | res = resolution2d.Pinhole2D(data=data, index=index, |
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| 241 | nsigma=3.0, accuracy=accuracy) |
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[7cf2cfd] | 242 | elif self.data_type == 'Iq': |
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[803f835] | 243 | index = (data.x >= data.qmin) & (data.x <= data.qmax) |
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[b9c19aa2] | 244 | mask = getattr(data, 'mask', None) |
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| 245 | if mask is not None: |
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[1a8c11c] | 246 | index &= (mask == 0) |
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[7cf2cfd] | 247 | if data.y is not None: |
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[803f835] | 248 | index &= ~np.isnan(data.y) |
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| 249 | Iq = data.y[index] |
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| 250 | dIq = data.dy[index] |
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| 251 | else: |
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| 252 | Iq, dIq = None, None |
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[7cf2cfd] | 253 | if getattr(data, 'dx', None) is not None: |
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[803f835] | 254 | q, dq = data.x[index], data.dx[index] |
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| 255 | if (dq > 0).any(): |
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| 256 | res = resolution.Pinhole1D(q, dq) |
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[7cf2cfd] | 257 | else: |
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[803f835] | 258 | res = resolution.Perfect1D(q) |
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| 259 | elif (getattr(data, 'dxl', None) is not None |
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| 260 | and getattr(data, 'dxw', None) is not None): |
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| 261 | res = resolution.Slit1D(data.x[index], |
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[4d8e0bb] | 262 | qx_width=data.dxl[index], |
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| 263 | qy_width=data.dxw[index]) |
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[7cf2cfd] | 264 | else: |
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[803f835] | 265 | res = resolution.Perfect1D(data.x[index]) |
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[ea75043] | 266 | elif self.data_type == 'Iq-oriented': |
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| 267 | index = (data.x >= data.qmin) & (data.x <= data.qmax) |
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| 268 | if data.y is not None: |
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| 269 | index &= ~np.isnan(data.y) |
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| 270 | Iq = data.y[index] |
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| 271 | dIq = data.dy[index] |
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| 272 | else: |
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| 273 | Iq, dIq = None, None |
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| 274 | if (getattr(data, 'dxl', None) is None |
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[40a87fa] | 275 | or getattr(data, 'dxw', None) is None): |
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[ea75043] | 276 | raise ValueError("oriented sample with 1D data needs slit resolution") |
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| 277 | |
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| 278 | res = resolution2d.Slit2D(data.x[index], |
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| 279 | qx_width=data.dxw[index], |
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| 280 | qy_width=data.dxl[index]) |
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[7cf2cfd] | 281 | else: |
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| 282 | raise ValueError("Unknown data type") # never gets here |
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| 283 | |
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| 284 | # Remember function inputs so we can delay loading the function and |
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| 285 | # so we can save/restore state |
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| 286 | self._kernel = None |
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[803f835] | 287 | self.Iq, self.dIq, self.index = Iq, dIq, index |
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| 288 | self.resolution = res |
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[7cf2cfd] | 289 | |
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| 290 | def _set_data(self, Iq, noise=None): |
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[a5b8477] | 291 | # type: (np.ndarray, Optional[float]) -> None |
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[803f835] | 292 | # pylint: disable=attribute-defined-outside-init |
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[7cf2cfd] | 293 | if noise is not None: |
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| 294 | self.dIq = Iq*noise*0.01 |
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| 295 | dy = self.dIq |
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| 296 | y = Iq + np.random.randn(*dy.shape) * dy |
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| 297 | self.Iq = y |
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[ea75043] | 298 | if self.data_type in ('Iq', 'Iq-oriented'): |
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[d1ff3a5] | 299 | if self._data.y is None: |
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| 300 | self._data.y = np.empty(len(self._data.x), 'd') |
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| 301 | if self._data.dy is None: |
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| 302 | self._data.dy = np.empty(len(self._data.x), 'd') |
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[7cf2cfd] | 303 | self._data.dy[self.index] = dy |
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| 304 | self._data.y[self.index] = y |
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| 305 | elif self.data_type == 'Iqxy': |
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[d1ff3a5] | 306 | if self._data.data is None: |
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| 307 | self._data.data = np.empty_like(self._data.qx_data, 'd') |
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| 308 | if self._data.err_data is None: |
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| 309 | self._data.err_data = np.empty_like(self._data.qx_data, 'd') |
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[7cf2cfd] | 310 | self._data.data[self.index] = y |
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[d1ff3a5] | 311 | self._data.err_data[self.index] = dy |
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[7cf2cfd] | 312 | elif self.data_type == 'sesans': |
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[d1ff3a5] | 313 | if self._data.y is None: |
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| 314 | self._data.y = np.empty(len(self._data.x), 'd') |
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[7cf2cfd] | 315 | self._data.y[self.index] = y |
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| 316 | else: |
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| 317 | raise ValueError("Unknown model") |
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| 318 | |
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| 319 | def _calc_theory(self, pars, cutoff=0.0): |
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[a5b8477] | 320 | # type: (ParameterSet, float) -> np.ndarray |
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[7cf2cfd] | 321 | if self._kernel is None: |
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[2c4a190] | 322 | # TODO: change interfaces so that resolution returns kernel inputs |
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| 323 | # Maybe have resolution always return a tuple, or maybe have |
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| 324 | # make_kernel accept either an ndarray or a pair of ndarrays. |
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| 325 | kernel_inputs = self.resolution.q_calc |
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| 326 | if isinstance(kernel_inputs, np.ndarray): |
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| 327 | kernel_inputs = (kernel_inputs,) |
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| 328 | self._kernel = self._model.make_kernel(kernel_inputs) |
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[7cf2cfd] | 329 | |
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[d18d6dd] | 330 | # Need to pull background out of resolution for multiple scattering |
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[b6d1d52] | 331 | default_background = self._model.info.parameters.common_parameters[1].default |
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| 332 | background = pars.get('background', default_background) |
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[d18d6dd] | 333 | pars = pars.copy() |
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| 334 | pars['background'] = 0. |
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| 335 | |
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[7cf2cfd] | 336 | Iq_calc = call_kernel(self._kernel, pars, cutoff=cutoff) |
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[40a87fa] | 337 | # Storing the calculated Iq values so that they can be plotted. |
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| 338 | # Only applies to oriented USANS data for now. |
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| 339 | # TODO: extend plotting of calculate Iq to other measurement types |
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| 340 | # TODO: refactor so we don't store the result in the model |
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[d1ff3a5] | 341 | self.Iq_calc = Iq_calc |
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[fa79f5c] | 342 | result = self.resolution.apply(Iq_calc) |
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| 343 | if hasattr(self.resolution, 'nx'): |
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| 344 | self.Iq_calc = ( |
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| 345 | self.resolution.qx_calc, self.resolution.qy_calc, |
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| 346 | np.reshape(Iq_calc, (self.resolution.ny, self.resolution.nx)) |
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| 347 | ) |
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[d18d6dd] | 348 | return result + background |
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[7cf2cfd] | 349 | |
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| 350 | |
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| 351 | class DirectModel(DataMixin): |
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[803f835] | 352 | """ |
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| 353 | Create a calculator object for a model. |
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| 354 | |
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| 355 | *data* is 1D SAS, 2D SAS or SESANS data |
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| 356 | |
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| 357 | *model* is a model calculator return from :func:`generate.load_model` |
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| 358 | |
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| 359 | *cutoff* is the polydispersity weight cutoff. |
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| 360 | """ |
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[7cf2cfd] | 361 | def __init__(self, data, model, cutoff=1e-5): |
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[a5b8477] | 362 | # type: (Data, KernelModel, float) -> None |
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[7cf2cfd] | 363 | self.model = model |
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| 364 | self.cutoff = cutoff |
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[803f835] | 365 | # Note: _interpret_data defines the model attributes |
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[7cf2cfd] | 366 | self._interpret_data(data, model) |
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[803f835] | 367 | |
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[16bc3fc] | 368 | def __call__(self, **pars): |
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[a5b8477] | 369 | # type: (**float) -> np.ndarray |
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[7cf2cfd] | 370 | return self._calc_theory(pars, cutoff=self.cutoff) |
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[803f835] | 371 | |
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[7cf2cfd] | 372 | def simulate_data(self, noise=None, **pars): |
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[a5b8477] | 373 | # type: (Optional[float], **float) -> None |
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[803f835] | 374 | """ |
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| 375 | Generate simulated data for the model. |
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| 376 | """ |
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[7cf2cfd] | 377 | Iq = self.__call__(**pars) |
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| 378 | self._set_data(Iq, noise=noise) |
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[ae7b97b] | 379 | |
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[745b7bb] | 380 | def profile(self, **pars): |
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| 381 | # type: (**float) -> None |
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| 382 | """ |
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| 383 | Generate a plottable profile. |
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| 384 | """ |
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[23df833] | 385 | return call_profile(self.model.info, pars) |
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[745b7bb] | 386 | |
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[803f835] | 387 | def main(): |
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[a5b8477] | 388 | # type: () -> None |
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[803f835] | 389 | """ |
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| 390 | Program to evaluate a particular model at a set of q values. |
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| 391 | """ |
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[ae7b97b] | 392 | import sys |
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[7cf2cfd] | 393 | from .data import empty_data1D, empty_data2D |
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[17bbadd] | 394 | from .core import load_model_info, build_model |
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[7cf2cfd] | 395 | |
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[ae7b97b] | 396 | if len(sys.argv) < 3: |
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[9404dd3] | 397 | print("usage: python -m sasmodels.direct_model modelname (q|qx,qy) par=val ...") |
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[ae7b97b] | 398 | sys.exit(1) |
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| 399 | model_name = sys.argv[1] |
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[aa4946b] | 400 | call = sys.argv[2].upper() |
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[304c775] | 401 | try: |
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| 402 | values = [float(v) for v in call.split(',')] |
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| 403 | except ValueError: |
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| 404 | values = [] |
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| 405 | if len(values) == 1: |
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| 406 | q, = values |
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| 407 | data = empty_data1D([q]) |
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| 408 | elif len(values) == 2: |
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| 409 | qx, qy = values |
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| 410 | data = empty_data2D([qx], [qy]) |
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[7cf2cfd] | 411 | else: |
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[304c775] | 412 | print("use q or qx,qy") |
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| 413 | sys.exit(1) |
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[7cf2cfd] | 414 | |
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[17bbadd] | 415 | model_info = load_model_info(model_name) |
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| 416 | model = build_model(model_info) |
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[7cf2cfd] | 417 | calculator = DirectModel(data, model) |
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[4cc161e] | 418 | pars = dict((k, (float(v) if not k.endswith("_pd_type") else v)) |
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[ae7b97b] | 419 | for pair in sys.argv[3:] |
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[803f835] | 420 | for k, v in [pair.split('=')]) |
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[304c775] | 421 | Iq = calculator(**pars) |
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| 422 | print(Iq[0]) |
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[ae7b97b] | 423 | |
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| 424 | if __name__ == "__main__": |
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[803f835] | 425 | main() |
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