| 1 | """ |
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| 2 | Core-Multi-Shell model |
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| 3 | """ |
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| 4 | from sas.models.BaseComponent import BaseComponent |
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| 5 | from sas.models.CoreFourShellModel import CoreFourShellModel |
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| 6 | import copy |
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| 7 | max_nshells = 5 |
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| 8 | class CoreMultiShellModel(BaseComponent): |
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| 9 | """ |
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| 10 | This multi-model is based on CoreFourShellModel and provides the capability |
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| 11 | of changing the number of shells between 1 and 4. |
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| 12 | """ |
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| 13 | def __init__(self, multfactor=1): |
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| 14 | BaseComponent.__init__(self) |
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| 15 | """ |
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| 16 | :param n_shells: number of shells in the model, assumes 1<= n_shells <=4. |
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| 17 | """ |
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| 18 | |
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| 19 | ## Setting model name model description |
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| 20 | self.description="" |
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| 21 | model = CoreFourShellModel() |
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| 22 | self.model = model |
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| 23 | self.name = "CoreMultiShellModel" |
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| 24 | self.description="" |
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| 25 | self.n_shells = multfactor |
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| 26 | ## Define parameters |
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| 27 | self.params = {} |
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| 28 | |
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| 29 | ## Parameter details [units, min, max] |
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| 30 | self.details = {} |
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| 31 | |
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| 32 | # non-fittable parameters |
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| 33 | self.non_fittable = model.non_fittable |
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| 34 | |
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| 35 | ## dispersion |
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| 36 | self._set_dispersion() |
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| 37 | ## Define parameters |
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| 38 | self._set_params() |
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| 39 | |
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| 40 | ## Parameter details [units, min, max] |
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| 41 | self._set_details() |
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| 42 | |
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| 43 | #list of parameter that can be fitted |
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| 44 | self._set_fixed_params() |
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| 45 | self.orientation_params = [] |
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| 46 | self.magnetic_params = [] |
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| 47 | |
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| 48 | ## functional multiplicity info of the model |
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| 49 | # [int(maximum no. of functionality),"str(Titl), |
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| 50 | # [str(name of function0),...], [str(x-asix name of sld),...]] |
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| 51 | self.multiplicity_info = [max_nshells, "No. of Shells:", [], ['Radius']] |
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| 52 | |
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| 53 | ## parameters with orientation: can be removed since there is no orientational params |
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| 54 | self._set_orientation_params() |
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| 55 | |
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| 56 | def _clone(self, obj): |
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| 57 | """ |
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| 58 | Internal utility function to copy the internal |
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| 59 | data members to a fresh copy. |
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| 60 | """ |
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| 61 | obj.params = copy.deepcopy(self.params) |
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| 62 | obj.description = copy.deepcopy(self.description) |
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| 63 | obj.details = copy.deepcopy(self.details) |
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| 64 | obj.dispersion = copy.deepcopy(self.dispersion) |
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| 65 | obj.model = self.model.clone() |
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| 66 | |
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| 67 | return obj |
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| 68 | |
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| 69 | def _set_dispersion(self): |
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| 70 | """ |
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| 71 | model dispersions |
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| 72 | Polydispersion should not be applied to s_model |
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| 73 | """ |
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| 74 | ##set dispersion from model |
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| 75 | for name , value in self.model.dispersion.iteritems(): |
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| 76 | nshell = 0 |
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| 77 | if name.split('_').count('thick') > 0: |
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| 78 | while nshell < self.n_shells: |
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| 79 | nshell += 1 |
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| 80 | if name.split('_')[-1] == 'shell%s' % str(nshell): |
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| 81 | self.dispersion[name] = value |
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| 82 | else: |
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| 83 | continue |
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| 84 | else: |
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| 85 | self.dispersion[name] = value |
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| 86 | |
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| 87 | def _set_orientation_params(self): |
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| 88 | """ |
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| 89 | model orientation and magnetic parameters, same params for this model |
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| 90 | """ |
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| 91 | ##set dispersion from model |
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| 92 | for param in self.model.orientation_params: |
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| 93 | nshell = 0 |
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| 94 | if param.split('_')[-1].count('shell') < 1: |
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| 95 | #print "param", param, param.split('_')[-1].count('shell') |
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| 96 | self.orientation_params.append(param) |
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| 97 | self.magnetic_params.append(param) |
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| 98 | continue |
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| 99 | while nshell < self.n_shells: |
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| 100 | nshell += 1 |
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| 101 | if param.split('_')[-1] == 'shell%s' % str(nshell): |
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| 102 | self.orientation_params.append(param) |
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| 103 | self.magnetic_params.append(param) |
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| 104 | continue |
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| 105 | |
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| 106 | def _set_params(self): |
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| 107 | """ |
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| 108 | Concatenate the parameters of the model to create |
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| 109 | this model parameters |
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| 110 | """ |
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| 111 | # rearrange the parameters for the given # of shells |
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| 112 | for name , value in self.model.params.iteritems(): |
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| 113 | nshell = 0 |
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| 114 | if name.split('_').count('thick') > 0 or \ |
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| 115 | name.split('_').count('sld') > 0 or \ |
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| 116 | name[0] == 'M': |
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| 117 | if name.split('_')[-1] == 'solv' or \ |
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| 118 | name.split('_')[-1] == 'core0': |
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| 119 | self.params[name]= value |
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| 120 | continue |
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| 121 | while nshell < self.n_shells: |
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| 122 | nshell += 1 |
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| 123 | if name.split('_')[-1] == 'shell%s' % str(nshell): |
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| 124 | self.params[name]= value |
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| 125 | continue |
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| 126 | else: |
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| 127 | self.params[name]= value |
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| 128 | |
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| 129 | # set constrained values for the original model params |
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| 130 | self._set_xtra_model_param() |
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| 131 | |
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| 132 | def _set_details(self): |
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| 133 | """ |
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| 134 | Concatenate details of the original model to create |
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| 135 | this model details |
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| 136 | """ |
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| 137 | for name ,detail in self.model.details.iteritems(): |
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| 138 | if name in self.params.iterkeys(): |
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| 139 | self.details[name]= detail |
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| 140 | |
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| 141 | |
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| 142 | def _set_xtra_model_param(self): |
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| 143 | """ |
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| 144 | Set params of original model that are hidden from this model |
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| 145 | """ |
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| 146 | # look for the model parameters that are not in param list |
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| 147 | for key in self.model.params.iterkeys(): |
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| 148 | if key not in self.params.keys(): |
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| 149 | if key.split('_').count('thick') > 0: |
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| 150 | self.model.setParam(key, 0) |
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| 151 | continue |
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| 152 | |
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| 153 | for nshell in range(self.n_shells,max_nshells): |
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| 154 | if key.split('_').count('sld') > 0 and \ |
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| 155 | key.split('_')[-1] == 'shell%s' % str(nshell+1): |
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| 156 | try: |
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| 157 | if key[0] != 'M': |
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| 158 | value = self.model.params['sld_solv'] |
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| 159 | self.model.setParam(key, value) |
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| 160 | else: |
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| 161 | self.model.setParam(key, 0.0) |
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| 162 | except: pass |
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| 163 | |
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| 164 | |
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| 165 | def getProfile(self): |
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| 166 | """ |
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| 167 | Get SLD profile |
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| 168 | **Note:** This works only for func_shell num = 2. |
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| 169 | |
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| 170 | :return: (r, beta) where r is a list of radius of the transition points\ |
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| 171 | and beta is a list of the corresponding SLD values. |
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| 172 | """ |
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| 173 | r = [] |
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| 174 | beta = [] |
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| 175 | # for core at r=0 |
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| 176 | r.append(0) |
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| 177 | beta.append(self.params['sld_core0']) |
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| 178 | # for core at r=rad_core |
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| 179 | r.append(self.params['rad_core0']) |
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| 180 | beta.append(self.params['sld_core0']) |
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| 181 | |
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| 182 | # for shells |
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| 183 | for n in range(1, self.n_shells+1): |
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| 184 | # Left side of each shells |
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| 185 | r0 = r[len(r)-1] |
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| 186 | r.append(r0) |
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| 187 | exec "beta.append(self.params['sld_shell%s'% str(n)])" |
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| 188 | |
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| 189 | # Right side of each shells |
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| 190 | exec "r0 += self.params['thick_shell%s'% str(n)]" |
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| 191 | r.append(r0) |
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| 192 | exec "beta.append(self.params['sld_shell%s'% str(n)])" |
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| 193 | |
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| 194 | # for solvent |
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| 195 | r0 = r[len(r)-1] |
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| 196 | r.append(r0) |
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| 197 | beta.append(self.params['sld_solv']) |
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| 198 | r_solv = 5*r0/4 |
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| 199 | r.append(r_solv) |
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| 200 | beta.append(self.params['sld_solv']) |
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| 201 | |
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| 202 | return r, beta |
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| 203 | |
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| 204 | def setParam(self, name, value): |
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| 205 | """ |
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| 206 | Set the value of a model parameter |
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| 207 | |
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| 208 | :param name: name of the parameter |
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| 209 | :param value: value of the parameter |
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| 210 | """ |
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| 211 | # set param to new model |
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| 212 | self._setParamHelper( name, value) |
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| 213 | ## setParam to model |
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| 214 | if name == 'sld_solv': |
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| 215 | # the sld_*** model.params not in params must set to value of sld_solv |
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| 216 | for key in self.model.params.iterkeys(): |
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| 217 | if key not in self.params.keys(): |
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| 218 | if key.split('_')[0] == 'sld': |
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| 219 | self.model.setParam(key, value) |
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| 220 | elif key.split('_')[1] == 'sld': |
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| 221 | # mag params |
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| 222 | self.model.setParam(key, 0.0) |
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| 223 | self.model.setParam( name, value) |
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| 224 | |
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| 225 | def _setParamHelper(self, name, value): |
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| 226 | """ |
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| 227 | Helper function to setParam |
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| 228 | """ |
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| 229 | #look for dispersion parameters |
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| 230 | toks = name.split('.') |
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| 231 | if len(toks) == 2: |
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| 232 | for item in self.dispersion.keys(): |
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| 233 | if item.lower()==toks[0].lower(): |
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| 234 | for par in self.dispersion[item]: |
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| 235 | if par.lower() == toks[1].lower(): |
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| 236 | self.dispersion[item][par] = value |
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| 237 | return |
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| 238 | # Look for standard parameter |
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| 239 | for item in self.params.keys(): |
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| 240 | if item.lower()==name.lower(): |
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| 241 | self.params[item] = value |
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| 242 | return |
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| 243 | #raise ValueError, "Model does not contain parameter %s" % name |
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| 244 | |
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| 245 | |
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| 246 | def _set_fixed_params(self): |
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| 247 | """ |
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| 248 | Fill the self.fixed list with the model fixed list |
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| 249 | """ |
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| 250 | for item in self.model.fixed: |
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| 251 | if item.split('.')[0] in self.params.keys(): |
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| 252 | self.fixed.append(item) |
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| 253 | |
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| 254 | self.fixed.sort() |
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| 255 | |
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| 256 | def run(self, x = 0.0): |
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| 257 | """ |
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| 258 | Evaluate the model |
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| 259 | |
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| 260 | :param x: input q-value (float or [float, float] as [r, theta]) |
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| 261 | :return: (DAB value) |
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| 262 | """ |
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| 263 | # set effective radius and scaling factor before run |
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| 264 | |
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| 265 | return self.model.run(x) |
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| 266 | |
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| 267 | def runXY(self, x = 0.0): |
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| 268 | """ |
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| 269 | Evaluate the model |
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| 270 | |
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| 271 | :param x: input q-value (float or [float, float] as [qx, qy]) |
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| 272 | :return: DAB value |
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| 273 | """ |
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| 274 | # set effective radius and scaling factor before run |
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| 275 | |
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| 276 | return self.model.runXY(x) |
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| 277 | |
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| 278 | ## Now (May27,10) directly uses the model eval function |
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| 279 | ## instead of the for-loop in Base Component. |
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| 280 | def evalDistribution(self, x = []): |
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| 281 | """ |
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| 282 | Evaluate the model in cartesian coordinates |
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| 283 | |
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| 284 | :param x: input q[], or [qx[], qy[]] |
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| 285 | :return: scattering function P(q[]) |
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| 286 | """ |
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| 287 | # set effective radius and scaling factor before run |
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| 288 | return self.model.evalDistribution(x) |
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| 289 | |
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| 290 | def calculate_ER(self): |
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| 291 | """ |
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| 292 | Calculate the effective radius for P(q)*S(q) |
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| 293 | |
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| 294 | :return: the value of the effective radius |
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| 295 | """ |
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| 296 | return self.model.calculate_ER() |
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| 297 | |
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| 298 | def calculate_VR(self): |
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| 299 | """ |
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| 300 | Calculate the volf ratio for P(q)*S(q) |
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| 301 | |
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| 302 | :return: the value of the volf ratio |
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| 303 | """ |
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| 304 | return self.model.calculate_VR() |
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| 305 | |
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| 306 | def set_dispersion(self, parameter, dispersion): |
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| 307 | """ |
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| 308 | Set the dispersion object for a model parameter |
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| 309 | |
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| 310 | :param parameter: name of the parameter [string] |
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| 311 | :param dispersion: dispersion object of type DispersionModel |
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| 312 | """ |
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| 313 | value = None |
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| 314 | try: |
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| 315 | if parameter in self.model.dispersion.keys(): |
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| 316 | value = self.model.set_dispersion(parameter, dispersion) |
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| 317 | self._set_dispersion() |
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| 318 | return value |
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| 319 | except: |
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| 320 | raise |
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