| 1 | import copy |
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| 2 | |
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| 3 | import numpy as np |
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| 4 | |
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| 5 | from sas.sascalc.calculator.BaseComponent import BaseComponent |
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| 6 | |
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| 7 | class MultiplicationModel(BaseComponent): |
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| 8 | r""" |
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| 9 | Use for P(Q)\*S(Q); function call must be in the order of P(Q) and then S(Q): |
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| 10 | The model parameters are combined from both models, P(Q) and S(Q), except 1) 'radius_effective' of S(Q) |
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| 11 | which will be calculated from P(Q) via calculate_ER(), |
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| 12 | and 2) 'scale' in P model which is synchronized w/ volfraction in S |
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| 13 | then P*S is multiplied by a new parameter, 'scale_factor'. |
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| 14 | The polydispersion is applicable only to P(Q), not to S(Q). |
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| 15 | |
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| 16 | .. note:: P(Q) refers to 'form factor' model while S(Q) does to 'structure factor'. |
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| 17 | """ |
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| 18 | def __init__(self, p_model, s_model ): |
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| 19 | BaseComponent.__init__(self) |
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| 20 | """ |
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| 21 | :param p_model: form factor, P(Q) |
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| 22 | :param s_model: structure factor, S(Q) |
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| 23 | """ |
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| 24 | |
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| 25 | ## Setting model name model description |
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| 26 | self.description = "" |
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| 27 | self.name = p_model.name +" * "+ s_model.name |
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| 28 | self.description= self.name + "\n" |
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| 29 | self.fill_description(p_model, s_model) |
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| 30 | |
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| 31 | ## Define parameters |
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| 32 | self.params = {} |
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| 33 | |
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| 34 | ## Parameter details [units, min, max] |
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| 35 | self.details = {} |
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| 36 | |
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| 37 | ## Define parameters to exclude from multiplication model |
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| 38 | self.excluded_params={'radius_effective','scale','background'} |
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| 39 | |
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| 40 | ##models |
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| 41 | self.p_model = p_model |
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| 42 | self.s_model = s_model |
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| 43 | self.magnetic_params = [] |
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| 44 | ## dispersion |
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| 45 | self._set_dispersion() |
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| 46 | ## Define parameters |
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| 47 | self._set_params() |
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| 48 | ## New parameter:Scaling factor |
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| 49 | self.params['scale_factor'] = 1 |
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| 50 | self.params['background'] = 0 |
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| 51 | |
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| 52 | ## Parameter details [units, min, max] |
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| 53 | self._set_details() |
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| 54 | self.details['scale_factor'] = ['', 0.0, np.inf] |
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| 55 | self.details['background'] = ['',-np.inf,np.inf] |
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| 56 | |
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| 57 | #list of parameter that can be fitted |
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| 58 | self._set_fixed_params() |
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| 59 | ## parameters with orientation |
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| 60 | for item in self.p_model.orientation_params: |
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| 61 | self.orientation_params.append(item) |
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| 62 | for item in self.p_model.magnetic_params: |
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| 63 | self.magnetic_params.append(item) |
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| 64 | for item in self.s_model.orientation_params: |
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| 65 | if not item in self.orientation_params: |
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| 66 | self.orientation_params.append(item) |
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| 67 | # get multiplicity if model provide it, else 1. |
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| 68 | try: |
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| 69 | multiplicity = p_model.multiplicity |
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| 70 | except AttributeError: |
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| 71 | multiplicity = 1 |
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| 72 | ## functional multiplicity of the model |
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| 73 | self.multiplicity = multiplicity |
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| 74 | |
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| 75 | # non-fittable parameters |
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| 76 | self.non_fittable = p_model.non_fittable |
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| 77 | self.multiplicity_info = [] |
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| 78 | self.fun_list = [] |
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| 79 | if self.non_fittable > 1: |
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| 80 | try: |
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| 81 | self.multiplicity_info = p_model.multiplicity_info |
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| 82 | self.fun_list = p_model.fun_list |
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| 83 | self.is_multiplicity_model = True |
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| 84 | except AttributeError: |
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| 85 | pass |
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| 86 | else: |
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| 87 | self.is_multiplicity_model = False |
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| 88 | self.multiplicity_info = [0] |
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| 89 | |
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| 90 | def _clone(self, obj): |
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| 91 | """ |
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| 92 | Internal utility function to copy the internal data members to a |
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| 93 | fresh copy. |
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| 94 | """ |
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| 95 | obj.params = copy.deepcopy(self.params) |
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| 96 | obj.description = copy.deepcopy(self.description) |
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| 97 | obj.details = copy.deepcopy(self.details) |
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| 98 | obj.dispersion = copy.deepcopy(self.dispersion) |
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| 99 | obj.p_model = self.p_model.clone() |
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| 100 | obj.s_model = self.s_model.clone() |
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| 101 | #obj = copy.deepcopy(self) |
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| 102 | return obj |
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| 103 | |
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| 104 | |
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| 105 | def _set_dispersion(self): |
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| 106 | """ |
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| 107 | combine the two models' dispersions. Polydispersity should not be |
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| 108 | applied to s_model |
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| 109 | """ |
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| 110 | ##set dispersion only from p_model |
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| 111 | for name , value in self.p_model.dispersion.items(): |
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| 112 | self.dispersion[name] = value |
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| 113 | |
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| 114 | def getProfile(self): |
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| 115 | """ |
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| 116 | Get SLD profile of p_model if exists |
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| 117 | |
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| 118 | :return: (r, beta) where r is a list of radius of the transition points\ |
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| 119 | beta is a list of the corresponding SLD values |
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| 120 | |
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| 121 | .. note:: This works only for func_shell num = 2 (exp function). |
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| 122 | """ |
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| 123 | try: |
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| 124 | x, y = self.p_model.getProfile() |
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| 125 | except: |
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| 126 | x = None |
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| 127 | y = None |
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| 128 | |
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| 129 | return x, y |
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| 130 | |
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| 131 | def _set_params(self): |
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| 132 | """ |
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| 133 | Concatenate the parameters of the two models to create |
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| 134 | these model parameters |
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| 135 | """ |
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| 136 | |
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| 137 | for name , value in self.p_model.params.items(): |
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| 138 | if not name in self.params.keys() and name not in self.excluded_params: |
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| 139 | self.params[name] = value |
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| 140 | |
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| 141 | for name , value in self.s_model.params.items(): |
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| 142 | #Remove the radius_effective from the (P*S) model parameters. |
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| 143 | if not name in self.params.keys() and name not in self.excluded_params: |
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| 144 | self.params[name] = value |
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| 145 | |
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| 146 | # Set "scale and effec_radius to P and S model as initializing |
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| 147 | # since run P*S comes from P and S separately. |
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| 148 | self._set_backgrounds() |
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| 149 | self._set_scale_factor() |
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| 150 | self._set_radius_effective() |
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| 151 | |
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| 152 | def _set_details(self): |
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| 153 | """ |
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| 154 | Concatenate details of the two models to create |
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| 155 | this model's details |
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| 156 | """ |
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| 157 | for name, detail in self.p_model.details.items(): |
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| 158 | if name not in self.excluded_params: |
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| 159 | self.details[name] = detail |
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| 160 | |
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| 161 | for name , detail in self.s_model.details.items(): |
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| 162 | if not name in self.details.keys() or name not in self.exluded_params: |
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| 163 | self.details[name] = detail |
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| 164 | |
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| 165 | def _set_backgrounds(self): |
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| 166 | """ |
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| 167 | Set component backgrounds to zero |
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| 168 | """ |
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| 169 | if 'background' in self.p_model.params: |
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| 170 | self.p_model.setParam('background',0) |
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| 171 | if 'background' in self.s_model.params: |
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| 172 | self.s_model.setParam('background',0) |
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| 173 | |
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| 174 | |
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| 175 | def _set_scale_factor(self): |
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| 176 | """ |
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| 177 | Set scale=volfraction for P model |
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| 178 | """ |
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| 179 | value = self.params['volfraction'] |
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| 180 | if value is not None: |
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| 181 | factor = self.p_model.calculate_VR() |
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| 182 | if factor is None or factor == NotImplemented or factor == 0.0: |
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| 183 | val = value |
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| 184 | else: |
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| 185 | val = value / factor |
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| 186 | self.p_model.setParam('scale', value) |
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| 187 | self.s_model.setParam('volfraction', val) |
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| 188 | |
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| 189 | def _set_radius_effective(self): |
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| 190 | """ |
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| 191 | Set effective radius to S(Q) model |
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| 192 | """ |
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| 193 | if not 'radius_effective' in self.s_model.params.keys(): |
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| 194 | return |
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| 195 | effective_radius = self.p_model.calculate_ER() |
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| 196 | #Reset the effective_radius of s_model just before the run |
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| 197 | if effective_radius is not None and effective_radius != NotImplemented: |
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| 198 | self.s_model.setParam('radius_effective', effective_radius) |
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| 199 | |
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| 200 | def setParam(self, name, value): |
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| 201 | """ |
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| 202 | Set the value of a model parameter |
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| 203 | |
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| 204 | :param name: name of the parameter |
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| 205 | :param value: value of the parameter |
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| 206 | """ |
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| 207 | # set param to P*S model |
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| 208 | self._setParamHelper( name, value) |
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| 209 | |
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| 210 | ## setParam to p model |
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| 211 | # set 'scale' in P(Q) equal to volfraction |
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| 212 | if name == 'volfraction': |
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| 213 | self._set_scale_factor() |
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| 214 | elif name in self.p_model.getParamList() and name not in self.excluded_params: |
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| 215 | self.p_model.setParam( name, value) |
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| 216 | |
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| 217 | ## setParam to s model |
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| 218 | # This is a little bit abundant: Todo: find better way |
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| 219 | self._set_radius_effective() |
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| 220 | if name in self.s_model.getParamList() and name not in self.excluded_params: |
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| 221 | if name != 'volfraction': |
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| 222 | self.s_model.setParam( name, value) |
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| 223 | |
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| 224 | |
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| 225 | #self._setParamHelper( name, value) |
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| 226 | |
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| 227 | def _setParamHelper(self, name, value): |
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| 228 | """ |
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| 229 | Helper function to setparam |
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| 230 | """ |
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| 231 | # Look for dispersion parameters |
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| 232 | toks = name.split('.') |
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| 233 | if len(toks)==2: |
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| 234 | for item in self.dispersion.keys(): |
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| 235 | if item.lower()==toks[0].lower(): |
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| 236 | for par in self.dispersion[item]: |
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| 237 | if par.lower() == toks[1].lower(): |
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| 238 | self.dispersion[item][par] = value |
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| 239 | return |
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| 240 | else: |
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| 241 | # Look for standard parameter |
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| 242 | for item in self.params.keys(): |
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| 243 | if item.lower() == name.lower(): |
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| 244 | self.params[item] = value |
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| 245 | return |
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| 246 | |
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| 247 | raise ValueError("Model does not contain parameter %s" % name) |
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| 248 | |
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| 249 | |
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| 250 | def _set_fixed_params(self): |
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| 251 | """ |
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| 252 | Fill the self.fixed list with the p_model fixed list |
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| 253 | """ |
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| 254 | for item in self.p_model.fixed: |
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| 255 | self.fixed.append(item) |
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| 256 | |
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| 257 | self.fixed.sort() |
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| 258 | |
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| 259 | |
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| 260 | def run(self, x = 0.0): |
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| 261 | """ |
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| 262 | Evaluate the model |
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| 263 | |
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| 264 | :param x: input q-value (float or [float, float] as [r, theta]) |
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| 265 | :return: (scattering function value) |
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| 266 | """ |
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| 267 | # set effective radius and scaling factor before run |
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| 268 | self._set_radius_effective() |
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| 269 | self._set_scale_factor() |
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| 270 | return self.params['scale_factor'] * self.p_model.run(x) * \ |
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| 271 | self.s_model.run(x) + self.params['background'] |
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| 272 | |
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| 273 | def runXY(self, x = 0.0): |
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| 274 | """ |
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| 275 | Evaluate the model |
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| 276 | |
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| 277 | :param x: input q-value (float or [float, float] as [qx, qy]) |
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| 278 | :return: scattering function value |
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| 279 | """ |
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| 280 | # set effective radius and scaling factor before run |
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| 281 | self._set_radius_effective() |
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| 282 | self._set_scale_factor() |
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| 283 | out = self.params['scale_factor'] * self.p_model.runXY(x) * \ |
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| 284 | self.s_model.runXY(x) + self.params['background'] |
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| 285 | return out |
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| 286 | |
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| 287 | ## Now (May27,10) directly uses the model eval function |
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| 288 | ## instead of the for-loop in Base Component. |
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| 289 | def evalDistribution(self, x = []): |
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| 290 | """ |
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| 291 | Evaluate the model in cartesian coordinates |
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| 292 | |
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| 293 | :param x: input q[], or [qx[], qy[]] |
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| 294 | :return: scattering function P(q[]) |
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| 295 | """ |
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| 296 | # set effective radius and scaling factor before run |
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| 297 | self._set_radius_effective() |
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| 298 | self._set_scale_factor() |
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| 299 | out = self.params['scale_factor'] * self.p_model.evalDistribution(x) * \ |
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| 300 | self.s_model.evalDistribution(x) + self.params['background'] |
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| 301 | return out |
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| 302 | |
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| 303 | def set_dispersion(self, parameter, dispersion): |
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| 304 | """ |
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| 305 | Set the dispersion object for a model parameter |
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| 306 | |
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| 307 | :param parameter: name of the parameter [string] |
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| 308 | :dispersion: dispersion object of type DispersionModel |
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| 309 | """ |
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| 310 | value = None |
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| 311 | try: |
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| 312 | if parameter in self.p_model.dispersion.keys(): |
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| 313 | value = self.p_model.set_dispersion(parameter, dispersion) |
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| 314 | self._set_dispersion() |
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| 315 | return value |
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| 316 | except: |
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| 317 | raise |
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| 318 | |
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| 319 | def fill_description(self, p_model, s_model): |
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| 320 | """ |
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| 321 | Fill the description for P(Q)*S(Q) |
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| 322 | """ |
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| 323 | description = "" |
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| 324 | description += "Note:1) The radius_effective (effective radius) of %s \n"%\ |
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| 325 | (s_model.name) |
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| 326 | description += " is automatically calculated " |
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| 327 | description += "from size parameters (radius...).\n" |
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| 328 | description += " 2) For non-spherical shape, " |
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| 329 | description += "this approximation is valid \n" |
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| 330 | description += " only for limited systems. " |
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| 331 | description += "Thus, use it at your own risk.\n" |
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| 332 | description += "See %s description and %s description \n"% \ |
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| 333 | ( p_model.name, s_model.name ) |
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| 334 | description += " for details of individual models." |
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| 335 | self.description += description |
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