| [8f20419d] | 1 | |
|---|
| 2 | from sans.models.BaseComponent import BaseComponent |
|---|
| 3 | from sans.models.ReflModel import ReflModel |
|---|
| 4 | from copy import deepcopy |
|---|
| 5 | from math import floor |
|---|
| 6 | from scipy.special import erf |
|---|
| [4b3d25b] | 7 | func_list = {'Erf':0, 'Linear':1} |
|---|
| [8f20419d] | 8 | max_nshells = 10 |
|---|
| 9 | class ReflectivityModel(BaseComponent): |
|---|
| 10 | """ |
|---|
| 11 | This multi-model is based on Parratt formalism and provides the capability |
|---|
| 12 | of changing the number of layers between 0 and 10. |
|---|
| 13 | """ |
|---|
| 14 | def __init__(self, multfactor=1): |
|---|
| 15 | BaseComponent.__init__(self) |
|---|
| 16 | """ |
|---|
| [4b3d25b] | 17 | :param multfactor: number of layers in the model, |
|---|
| 18 | assumes 0<= n_shells <=10. |
|---|
| [8f20419d] | 19 | """ |
|---|
| 20 | |
|---|
| 21 | ## Setting model name model description |
|---|
| 22 | self.description="" |
|---|
| 23 | model = ReflModel() |
|---|
| 24 | self.model = model |
|---|
| 25 | self.name = "ReflectivityModel" |
|---|
| 26 | self.description=model.description |
|---|
| 27 | self.n_layers = multfactor |
|---|
| 28 | ## Define parameters |
|---|
| 29 | self.params = {} |
|---|
| 30 | |
|---|
| 31 | ## Parameter details [units, min, max] |
|---|
| 32 | self.details = {} |
|---|
| 33 | |
|---|
| 34 | # non-fittable parameters |
|---|
| 35 | self.non_fittable = model.non_fittable |
|---|
| 36 | |
|---|
| 37 | # list of function in order of the function number |
|---|
| 38 | self.fun_list = self._get_func_list() |
|---|
| 39 | ## dispersion |
|---|
| 40 | self._set_dispersion() |
|---|
| 41 | ## Define parameters |
|---|
| 42 | self._set_params() |
|---|
| 43 | |
|---|
| 44 | ## Parameter details [units, min, max] |
|---|
| 45 | self._set_details() |
|---|
| 46 | |
|---|
| 47 | #list of parameter that can be fitted |
|---|
| 48 | self._set_fixed_params() |
|---|
| 49 | self.model.params['n_layers'] = self.n_layers |
|---|
| 50 | |
|---|
| 51 | ## functional multiplicity info of the model |
|---|
| 52 | # [int(maximum no. of functionality),"str(Titl), |
|---|
| 53 | # [str(name of function0),...], [str(x-asix name of sld),...]] |
|---|
| 54 | self.multiplicity_info = [max_nshells,"No. of Layers:",[],['Depth']] |
|---|
| 55 | |
|---|
| 56 | |
|---|
| 57 | def _clone(self, obj): |
|---|
| 58 | """ |
|---|
| 59 | Internal utility function to copy the internal |
|---|
| 60 | data members to a fresh copy. |
|---|
| 61 | """ |
|---|
| 62 | obj.params = deepcopy(self.params) |
|---|
| 63 | obj.non_fittable = deepcopy(self.non_fittable) |
|---|
| 64 | obj.description = deepcopy(self.description) |
|---|
| 65 | obj.details = deepcopy(self.details) |
|---|
| 66 | obj.dispersion = deepcopy(self.dispersion) |
|---|
| 67 | obj.model = self.model.clone() |
|---|
| 68 | |
|---|
| 69 | return obj |
|---|
| 70 | |
|---|
| 71 | |
|---|
| 72 | def _set_dispersion(self): |
|---|
| 73 | """ |
|---|
| 74 | model dispersions |
|---|
| 75 | """ |
|---|
| 76 | ##set dispersion from model |
|---|
| 77 | self.dispersion = {} |
|---|
| 78 | |
|---|
| 79 | |
|---|
| 80 | def _set_params(self): |
|---|
| 81 | """ |
|---|
| 82 | Concatenate the parameters of the model to create |
|---|
| 83 | this model parameters |
|---|
| 84 | """ |
|---|
| 85 | # rearrange the parameters for the given # of shells |
|---|
| 86 | for name , value in self.model.params.iteritems(): |
|---|
| 87 | n = 0 |
|---|
| 88 | pos = len(name.split('_'))-1 |
|---|
| 89 | if name.split('_')[0] == 'sldIM': |
|---|
| 90 | continue |
|---|
| 91 | elif name.split('_')[0] == 'func': |
|---|
| 92 | n= -1 |
|---|
| 93 | while n<self.n_layers: |
|---|
| 94 | n += 1 |
|---|
| 95 | if name.split('_')[pos] == 'inter%s' % str(n): |
|---|
| 96 | self.params[name]=value |
|---|
| 97 | continue |
|---|
| 98 | #continue |
|---|
| 99 | elif name.split('_')[pos][0:5] == 'inter': |
|---|
| 100 | n= -1 |
|---|
| 101 | while n<self.n_layers: |
|---|
| 102 | n += 1 |
|---|
| 103 | if name.split('_')[pos] == 'inter%s' % str(n): |
|---|
| 104 | self.params[name]= value |
|---|
| 105 | continue |
|---|
| 106 | elif name.split('_')[pos][0:4] == 'flat': |
|---|
| 107 | while n<self.n_layers: |
|---|
| 108 | n += 1 |
|---|
| 109 | if name.split('_')[pos] == 'flat%s' % str(n): |
|---|
| 110 | self.params[name]= value |
|---|
| 111 | continue |
|---|
| 112 | elif name == 'n_layers': |
|---|
| 113 | continue |
|---|
| 114 | else: |
|---|
| 115 | self.params[name]= value |
|---|
| 116 | |
|---|
| 117 | self.model.params['n_layers'] = self.n_layers |
|---|
| 118 | |
|---|
| 119 | # set constrained values for the original model params |
|---|
| 120 | self._set_xtra_model_param() |
|---|
| 121 | |
|---|
| 122 | def _set_details(self): |
|---|
| 123 | """ |
|---|
| 124 | Concatenate details of the original model to create |
|---|
| 125 | this model details |
|---|
| 126 | """ |
|---|
| 127 | for name ,detail in self.model.details.iteritems(): |
|---|
| 128 | if name in self.params.iterkeys(): |
|---|
| 129 | self.details[name]= detail |
|---|
| 130 | |
|---|
| 131 | |
|---|
| 132 | def _set_xtra_model_param(self): |
|---|
| 133 | """ |
|---|
| 134 | Set params of original model that are hidden from this model |
|---|
| 135 | """ |
|---|
| 136 | # look for the model parameters that are not in param list |
|---|
| 137 | for key in self.model.params.iterkeys(): |
|---|
| 138 | if key not in self.params.keys(): |
|---|
| 139 | if key.split('_')[0] == 'thick': |
|---|
| 140 | self.model.setParam(key, 0) |
|---|
| 141 | continue |
|---|
| 142 | if key.split('_')[0] == 'func': |
|---|
| 143 | self.model.setParam(key, 0) |
|---|
| 144 | continue |
|---|
| 145 | for nshell in range(self.n_layers,max_nshells): |
|---|
| 146 | if key.split('_')[1] == 'flat%s' % str(nshell+1): |
|---|
| 147 | try: |
|---|
| 148 | if key.split('_')[0] == 'sld': |
|---|
| 149 | value = self.model.params['sld_medium'] |
|---|
| 150 | elif key.split('_')[0] == 'sldIM': |
|---|
| 151 | value = self.model.params['sldIM_medium'] |
|---|
| 152 | self.model.setParam(key, value) |
|---|
| 153 | except: pass |
|---|
| 154 | |
|---|
| 155 | def _get_func_list(self): |
|---|
| 156 | """ |
|---|
| 157 | Get the list of functions in each layer (shell) |
|---|
| 158 | """ |
|---|
| 159 | #func_list = {} |
|---|
| 160 | return func_list |
|---|
| 161 | |
|---|
| 162 | def getProfile(self): |
|---|
| 163 | """ |
|---|
| 164 | Get SLD profile |
|---|
| 165 | |
|---|
| 166 | : return: (z, beta) where z is a list of depth of the transition points |
|---|
| 167 | beta is a list of the corresponding SLD values |
|---|
| 168 | """ |
|---|
| 169 | # max_pts for each layers |
|---|
| 170 | n_sub = 21 |
|---|
| 171 | z = [] |
|---|
| 172 | beta = [] |
|---|
| 173 | sub_range = floor(n_sub/2.0) |
|---|
| 174 | z.append(0) |
|---|
| [4b3d25b] | 175 | beta.append(self.params['sld_bottom0']) |
|---|
| [8f20419d] | 176 | |
|---|
| 177 | z0 = 0 |
|---|
| 178 | # for layers from the top |
|---|
| 179 | for n in range(1,self.n_layers+2): |
|---|
| 180 | i = n |
|---|
| 181 | |
|---|
| 182 | for j in range(0,2): |
|---|
| 183 | for n_s in range(-sub_range,sub_range+1): |
|---|
| 184 | if j==1: |
|---|
| 185 | if i==self.n_layers+1: |
|---|
| 186 | break |
|---|
| 187 | # shift half sub thickness for the first point |
|---|
| 188 | z0 += dz/2.0 |
|---|
| 189 | z.append(z0) |
|---|
| 190 | #z0 -= dz/2.0 |
|---|
| 191 | z0 += self.params['thick_flat%s'% str(i)] |
|---|
| 192 | |
|---|
| 193 | sld_i = self.params['sld_flat%s'% str(i)] |
|---|
| 194 | beta.append(self.params['sld_flat%s'% str(i)]) |
|---|
| 195 | else: |
|---|
| 196 | |
|---|
| 197 | dz = self.params['thick_inter%s'% str(i-1)]/n_sub |
|---|
| 198 | |
|---|
| 199 | if n_s == -sub_range: |
|---|
| 200 | # shift half sub thickness for the first point |
|---|
| 201 | z0 -= dz/2.0 |
|---|
| 202 | #exec "dz = self.params['thick_inter[%s-1]'% str(i)]/9" |
|---|
| 203 | #print "%d = %g \n"% (i,self.params['thick_inter3']) |
|---|
| 204 | z0 += dz |
|---|
| 205 | |
|---|
| 206 | if i == 1: |
|---|
| [4b3d25b] | 207 | sld_l = self.params['sld_bottom0'] |
|---|
| [8f20419d] | 208 | else: |
|---|
| 209 | sld_l = self.params['sld_flat%s'% str(i-1)] |
|---|
| 210 | if i == self.n_layers+1: |
|---|
| 211 | sld_r = self.params['sld_medium'] |
|---|
| 212 | else: |
|---|
| 213 | sld_r = self.params['sld_flat%s'% str(i)] |
|---|
| 214 | func_idx = self.params['func_inter%s'% str(i-1)] |
|---|
| 215 | func = self._get_func(n_s, n_sub, func_idx) |
|---|
| 216 | if sld_r>sld_l: |
|---|
| 217 | sld_i = (sld_r-sld_l)*func+sld_l |
|---|
| 218 | elif sld_r<sld_l: |
|---|
| 219 | sld_i = (sld_l-sld_r)*(1-func)+sld_r |
|---|
| 220 | else: |
|---|
| 221 | sld_i = sld_r |
|---|
| 222 | z.append(z0) |
|---|
| 223 | beta.append(sld_i) |
|---|
| 224 | if j==1: break |
|---|
| 225 | # put substrate and superstrate profile |
|---|
| 226 | # shift half sub thickness for the first point |
|---|
| 227 | z0 += dz/2.0 |
|---|
| 228 | z.append(z0) |
|---|
| 229 | beta.append(self.params['sld_medium']) |
|---|
| 230 | z_ext = z0/6.0 |
|---|
| 231 | |
|---|
| 232 | # put the extra points for the substrate |
|---|
| 233 | # and superstrate |
|---|
| 234 | z.append(z0+z_ext) |
|---|
| 235 | beta.append(self.params['sld_medium']) |
|---|
| 236 | z.insert(0,-z_ext) |
|---|
| [4b3d25b] | 237 | beta.insert(0,self.params['sld_bottom0']) |
|---|
| [8f20419d] | 238 | z = [z0 - x for x in z] |
|---|
| 239 | z.reverse() |
|---|
| 240 | beta.reverse() |
|---|
| 241 | return z, beta |
|---|
| 242 | |
|---|
| 243 | def _get_func(self, index, n_sub, func_idx): |
|---|
| 244 | """ |
|---|
| 245 | Get the function asked to buil sld profile |
|---|
| 246 | : param index: index of sub_layer |
|---|
| 247 | : param n_sub: total number of sub_layer |
|---|
| 248 | : param func_idx: an integer to identify a function |
|---|
| 249 | |
|---|
| 250 | : return out: the output from the function, float |
|---|
| 251 | """ |
|---|
| 252 | # cal bin_size |
|---|
| 253 | bin_size = 1.0/n_sub |
|---|
| 254 | # erf |
|---|
| 255 | if func_idx == 0: |
|---|
| 256 | out = erf(index/(n_sub/5.0))/2.0 + 0.5 |
|---|
| 257 | return out |
|---|
| 258 | else: |
|---|
| 259 | index += 0.5 |
|---|
| 260 | # linear |
|---|
| 261 | if func_idx == 1: |
|---|
| 262 | out = ((index + floor(n_sub/2.0))*bin_size) |
|---|
| 263 | # r_parabolic |
|---|
| 264 | elif func_idx == 2: |
|---|
| 265 | out = ((index + floor(n_sub/2.0))*bin_size)* \ |
|---|
| 266 | ((index + floor(n_sub/2.0))*bin_size) |
|---|
| 267 | # l_parabolic |
|---|
| 268 | elif func_idx == 3: |
|---|
| 269 | out = 1.0-(((index + floor(n_sub/2.0))*bin_size) - 1.0) *\ |
|---|
| 270 | (((index + floor(n_sub/2.0))*bin_size) - 1.0) |
|---|
| 271 | # r_cubic |
|---|
| 272 | elif func_idx == 4: |
|---|
| 273 | out = ((index + floor(n_sub/2.0))*bin_size)* \ |
|---|
| 274 | ((index + floor(n_sub/2.0))*bin_size)* \ |
|---|
| 275 | ((index + floor(n_sub/2.0))*bin_size) |
|---|
| 276 | # l_cubic |
|---|
| 277 | elif func_idx == 5: |
|---|
| 278 | out = 1.0+(((index + floor(n_sub/2.0)))*bin_size - 1.0) *\ |
|---|
| 279 | (((index + floor(n_sub/2.0)))*bin_size - 1.0) *\ |
|---|
| 280 | (((index + floor(n_sub/2.0)))*bin_size - 1.0) |
|---|
| 281 | # return output |
|---|
| 282 | return out |
|---|
| 283 | |
|---|
| 284 | def setParam(self, name, value): |
|---|
| 285 | """ |
|---|
| 286 | Set the value of a model parameter |
|---|
| 287 | |
|---|
| 288 | : param name: name of the parameter |
|---|
| 289 | : param value: value of the parameter |
|---|
| 290 | """ |
|---|
| 291 | # set param to new model |
|---|
| 292 | self._setParamHelper( name, value) |
|---|
| 293 | |
|---|
| 294 | ## setParam to model |
|---|
| 295 | if name=='sld_medium': |
|---|
| [4b3d25b] | 296 | # the sld_*** model.params not in params must set |
|---|
| 297 | # to value of sld_solv |
|---|
| [8f20419d] | 298 | for key in self.model.params.iterkeys(): |
|---|
| 299 | if key not in self.params.keys()and key.split('_')[0] == 'sld': |
|---|
| 300 | self.model.setParam(key, value) |
|---|
| 301 | |
|---|
| 302 | self.model.setParam( name, value) |
|---|
| 303 | |
|---|
| 304 | def _setParamHelper(self, name, value): |
|---|
| 305 | """ |
|---|
| 306 | Helper function to setParam |
|---|
| 307 | """ |
|---|
| 308 | |
|---|
| 309 | # Look for standard parameter |
|---|
| 310 | for item in self.params.keys(): |
|---|
| 311 | if item.lower()==name.lower(): |
|---|
| 312 | self.params[item] = value |
|---|
| 313 | return |
|---|
| 314 | |
|---|
| 315 | raise ValueError, "Model does not contain parameter %s" % name |
|---|
| 316 | |
|---|
| 317 | |
|---|
| 318 | def _set_fixed_params(self): |
|---|
| 319 | """ |
|---|
| 320 | Fill the self.fixed list with the model fixed list |
|---|
| 321 | """ |
|---|
| 322 | pass |
|---|
| 323 | |
|---|
| 324 | def run(self, x = 0.0): |
|---|
| 325 | """ |
|---|
| 326 | Evaluate the model |
|---|
| 327 | |
|---|
| 328 | :param x: input q, or [q,phi] |
|---|
| 329 | |
|---|
| 330 | :return: scattering function P(q) |
|---|
| 331 | |
|---|
| 332 | """ |
|---|
| 333 | |
|---|
| 334 | return self.model.run(x) |
|---|
| 335 | |
|---|
| 336 | def runXY(self, x = 0.0): |
|---|
| 337 | """ |
|---|
| 338 | Evaluate the model |
|---|
| 339 | |
|---|
| 340 | : param x: input q-value (float or [float, float] as [qx, qy]) |
|---|
| 341 | : return: scattering function value |
|---|
| 342 | """ |
|---|
| 343 | |
|---|
| 344 | return self.model.runXY(x) |
|---|
| 345 | |
|---|
| 346 | ## Now (May27,10) directly uses the model eval function |
|---|
| 347 | ## instead of the for-loop in Base Component. |
|---|
| 348 | def evalDistribution(self, x = []): |
|---|
| 349 | """ |
|---|
| 350 | Evaluate the model in cartesian coordinates |
|---|
| 351 | |
|---|
| 352 | : param x: input q[], or [qx[], qy[]] |
|---|
| 353 | : return: scattering function P(q[]) |
|---|
| 354 | """ |
|---|
| 355 | # set effective radius and scaling factor before run |
|---|
| 356 | return self.model.evalDistribution(x) |
|---|
| 357 | def calculate_ER(self): |
|---|
| 358 | """ |
|---|
| 359 | """ |
|---|
| 360 | return self.model.calculate_ER() |
|---|
| 361 | def set_dispersion(self, parameter, dispersion): |
|---|
| 362 | """ |
|---|
| 363 | Set the dispersion object for a model parameter |
|---|
| 364 | |
|---|
| 365 | : param parameter: name of the parameter [string] |
|---|
| 366 | :dispersion: dispersion object of type DispersionModel |
|---|
| 367 | """ |
|---|
| 368 | pass |
|---|
