| 1 | # A sample of an experimental model function for Sum(Pmodel1,Pmodel2) |
|---|
| 2 | import copy |
|---|
| 3 | from sas.models.pluginmodel import Model1DPlugin |
|---|
| 4 | import os |
|---|
| 5 | import sys |
|---|
| 6 | """ |
|---|
| 7 | ## ***************************************************************************** |
|---|
| 8 | Please select the 'Compile' from the menubar after the modification and saving. |
|---|
| 9 | Note that we recommend to save the file as a different file name. |
|---|
| 10 | Otherwise, it could be removed in the future on re-installation of the SasView. |
|---|
| 11 | ## ***************************************************************************** |
|---|
| 12 | """ |
|---|
| 13 | |
|---|
| 14 | # Available model names for this sum model |
|---|
| 15 | """ |
|---|
| 16 | BCCrystalModel, BEPolyelectrolyte, BarBellModel, BinaryHSModel, BroadPeakModel, |
|---|
| 17 | CSParallelepipedModel, CappedCylinderModel, CoreShellCylinderModel, |
|---|
| 18 | CoreShellEllipsoidModel, CoreShellModel, CorrLengthModel, CylinderModel, |
|---|
| 19 | DABModel, DebyeModel, EllipsoidModel, EllipticalCylinderModel, FCCrystalModel, |
|---|
| 20 | FlexCylEllipXModel, FlexibleCylinderModel, FractalCoreShellModel, FractalModel, |
|---|
| 21 | FuzzySphereModel, GaussLorentzGelModel, GuinierModel, GuinierPorodModel, |
|---|
| 22 | HardsphereStructure, HayterMSAStructure, HollowCylinderModel, LamellarFFHGModel, |
|---|
| 23 | LamellarModel, LamellarPCrystalModel, LamellarPSHGModel, LamellarPSModel, |
|---|
| 24 | LineModel, LorentzModel, MultiShellModel, ParallelepipedModel, PeakGaussModel, |
|---|
| 25 | PeakLorentzModel, PearlNecklaceModel, Poly_GaussCoil, PolymerExclVolume, |
|---|
| 26 | PorodModel, PowerLawAbsModel, SCCrystalModel, SphereModel, SquareWellStructure, |
|---|
| 27 | StackedDisksModel, StickyHSStructure, TeubnerStreyModel, TriaxialEllipsoidModel, |
|---|
| 28 | TwoLorentzianModel, TwoPowerLawModel, VesicleModel |
|---|
| 29 | """ |
|---|
| 30 | ## This is same as the Easy Custom Sum(p1 + p2) |
|---|
| 31 | # |
|---|
| 32 | # Custom model = scale_factor * (P1 + P2) |
|---|
| 33 | # |
|---|
| 34 | ## User can REPLACE model names below two arrowed lines (two names per line) |
|---|
| 35 | from sas.models.CylinderModel import CylinderModel as P1 #<======== |
|---|
| 36 | from sas.models.PolymerExclVolume import PolymerExclVolume as P2 #<======== |
|---|
| 37 | |
|---|
| 38 | # If you want to add your custom model, change the filename to your custom model |
|---|
| 39 | # FILE NAME without the extension(.py). And un-comment the line(ie., remove '#') |
|---|
| 40 | |
|---|
| 41 | # from filename import Model as P2 #<======== |
|---|
| 42 | |
|---|
| 43 | |
|---|
| 44 | #####DO NOT CHANGE ANYTHING BELOW THIS LINE |
|---|
| 45 | #####--------------------------------------------------------------------------- |
|---|
| 46 | class Model(Model1DPlugin): |
|---|
| 47 | """ |
|---|
| 48 | Use for p1(Q)+p2(Q); |
|---|
| 49 | Note: P(Q) refers to 'form factor' model. |
|---|
| 50 | """ |
|---|
| 51 | name = "" |
|---|
| 52 | def __init__(self): |
|---|
| 53 | Model1DPlugin.__init__(self, name=self.name) |
|---|
| 54 | """ |
|---|
| 55 | :param p_model1: a form factor, P(Q) |
|---|
| 56 | :param p_model2: another form factor, P(Q) |
|---|
| 57 | """ |
|---|
| 58 | p_model1 = P1() |
|---|
| 59 | p_model2 = P2() |
|---|
| 60 | ## Setting model name model description |
|---|
| 61 | self.description="" |
|---|
| 62 | |
|---|
| 63 | self.description = p_model1.name+"\n" |
|---|
| 64 | self.description += p_model2.name+"\n" |
|---|
| 65 | self.fill_description(p_model1, p_model2) |
|---|
| 66 | # Set the name same as the file name |
|---|
| 67 | self.name = self.get_fname() ##DO NOT CHANGE THIS LINE!!! |
|---|
| 68 | ## Define parameters |
|---|
| 69 | self.params = {} |
|---|
| 70 | |
|---|
| 71 | ## Parameter details [units, min, max] |
|---|
| 72 | self.details = {} |
|---|
| 73 | |
|---|
| 74 | # non-fittable parameters |
|---|
| 75 | self.non_fittable = p_model1.non_fittable |
|---|
| 76 | self.non_fittable += p_model2.non_fittable |
|---|
| 77 | |
|---|
| 78 | ##models |
|---|
| 79 | self.p_model1= p_model1 |
|---|
| 80 | self.p_model2= p_model2 |
|---|
| 81 | |
|---|
| 82 | |
|---|
| 83 | ## dispersion |
|---|
| 84 | self._set_dispersion() |
|---|
| 85 | ## Define parameters |
|---|
| 86 | self._set_params() |
|---|
| 87 | ## New parameter:Scaling factor |
|---|
| 88 | self.params['scale_factor'] = 1 |
|---|
| 89 | |
|---|
| 90 | ## Parameter details [units, min, max] |
|---|
| 91 | self._set_details() |
|---|
| 92 | self.details['scale_factor'] = ['', None, None] |
|---|
| 93 | ## Magnetic Panrameters |
|---|
| 94 | self.magnetic_params = [] |
|---|
| 95 | |
|---|
| 96 | #list of parameter that can be fitted |
|---|
| 97 | self._set_fixed_params() |
|---|
| 98 | ## parameters with orientation |
|---|
| 99 | for item in self.p_model1.orientation_params: |
|---|
| 100 | new_item = "p1_" + item |
|---|
| 101 | if not new_item in self.orientation_params: |
|---|
| 102 | self.orientation_params.append(new_item) |
|---|
| 103 | |
|---|
| 104 | for item in self.p_model2.orientation_params: |
|---|
| 105 | new_item = "p2_" + item |
|---|
| 106 | if not new_item in self.orientation_params: |
|---|
| 107 | self.orientation_params.append(new_item) |
|---|
| 108 | ## magnetic params |
|---|
| 109 | for item in self.p_model1.magnetic_params: |
|---|
| 110 | new_item = "p1_" + item |
|---|
| 111 | if not new_item in self.magnetic_params: |
|---|
| 112 | self.magnetic_params.append(new_item) |
|---|
| 113 | |
|---|
| 114 | for item in self.p_model2.magnetic_params: |
|---|
| 115 | new_item = "p2_" + item |
|---|
| 116 | if not new_item in self.magnetic_params: |
|---|
| 117 | self.magnetic_params.append(new_item) |
|---|
| 118 | # set multiplicity 1: muti_func Not supported. |
|---|
| 119 | multiplicity1 = 1 |
|---|
| 120 | multiplicity2 = 1 |
|---|
| 121 | ## functional multiplicity of the model |
|---|
| 122 | self.multiplicity1 = multiplicity1 |
|---|
| 123 | self.multiplicity2 = multiplicity2 |
|---|
| 124 | self.multiplicity_info = [] |
|---|
| 125 | |
|---|
| 126 | def _clone(self, obj): |
|---|
| 127 | """ |
|---|
| 128 | Internal utility function to copy the internal |
|---|
| 129 | data members to a fresh copy. |
|---|
| 130 | """ |
|---|
| 131 | obj.params = copy.deepcopy(self.params) |
|---|
| 132 | obj.description = copy.deepcopy(self.description) |
|---|
| 133 | obj.details = copy.deepcopy(self.details) |
|---|
| 134 | obj.dispersion = copy.deepcopy(self.dispersion) |
|---|
| 135 | obj.p_model1 = self.p_model1.clone() |
|---|
| 136 | obj.p_model2 = self.p_model2.clone() |
|---|
| 137 | #obj = copy.deepcopy(self) |
|---|
| 138 | return obj |
|---|
| 139 | |
|---|
| 140 | def _get_name(self, name1, name2): |
|---|
| 141 | """ |
|---|
| 142 | Get combined name from two model names |
|---|
| 143 | """ |
|---|
| 144 | p1_name = self._get_upper_name(name1) |
|---|
| 145 | if not p1_name: |
|---|
| 146 | p1_name = name1 |
|---|
| 147 | name = p1_name |
|---|
| 148 | name += "+" |
|---|
| 149 | p2_name = self._get_upper_name(name2) |
|---|
| 150 | if not p2_name: |
|---|
| 151 | p2_name = name2 |
|---|
| 152 | name += p2_name |
|---|
| 153 | return name |
|---|
| 154 | |
|---|
| 155 | def _get_upper_name(self, name=None): |
|---|
| 156 | """ |
|---|
| 157 | Get uppercase string from model name |
|---|
| 158 | """ |
|---|
| 159 | if name == None: |
|---|
| 160 | return "" |
|---|
| 161 | upper_name = "" |
|---|
| 162 | str_name = str(name) |
|---|
| 163 | for index in range(len(str_name)): |
|---|
| 164 | if str_name[index].isupper(): |
|---|
| 165 | upper_name += str_name[index] |
|---|
| 166 | return upper_name |
|---|
| 167 | |
|---|
| 168 | def _set_dispersion(self): |
|---|
| 169 | """ |
|---|
| 170 | combined the two models dispersions |
|---|
| 171 | Polydispersion should not be applied to s_model |
|---|
| 172 | """ |
|---|
| 173 | ##set dispersion only from p_model |
|---|
| 174 | for name , value in self.p_model1.dispersion.iteritems(): |
|---|
| 175 | #if name.lower() not in self.p_model1.orientation_params: |
|---|
| 176 | new_name = "p1_" + name |
|---|
| 177 | self.dispersion[new_name]= value |
|---|
| 178 | for name , value in self.p_model2.dispersion.iteritems(): |
|---|
| 179 | #if name.lower() not in self.p_model2.orientation_params: |
|---|
| 180 | new_name = "p2_" + name |
|---|
| 181 | self.dispersion[new_name]= value |
|---|
| 182 | |
|---|
| 183 | def function(self, x=0.0): |
|---|
| 184 | """ |
|---|
| 185 | """ |
|---|
| 186 | return 0 |
|---|
| 187 | |
|---|
| 188 | def getProfile(self): |
|---|
| 189 | """ |
|---|
| 190 | Get SLD profile of p_model if exists |
|---|
| 191 | |
|---|
| 192 | : return: (r, beta) where r is a list of radius of the transition points |
|---|
| 193 | beta is a list of the corresponding SLD values |
|---|
| 194 | : Note: This works only for func_shell# = 2 (exp function) |
|---|
| 195 | and is not supporting for p2 |
|---|
| 196 | """ |
|---|
| 197 | try: |
|---|
| 198 | x,y = self.p_model1.getProfile() |
|---|
| 199 | except: |
|---|
| 200 | x = None |
|---|
| 201 | y = None |
|---|
| 202 | |
|---|
| 203 | return x, y |
|---|
| 204 | |
|---|
| 205 | def _set_params(self): |
|---|
| 206 | """ |
|---|
| 207 | Concatenate the parameters of the two models to create |
|---|
| 208 | this model parameters |
|---|
| 209 | """ |
|---|
| 210 | |
|---|
| 211 | for name , value in self.p_model1.params.iteritems(): |
|---|
| 212 | # No 2D-supported |
|---|
| 213 | #if name not in self.p_model1.orientation_params: |
|---|
| 214 | new_name = "p1_" + name |
|---|
| 215 | self.params[new_name]= value |
|---|
| 216 | |
|---|
| 217 | for name , value in self.p_model2.params.iteritems(): |
|---|
| 218 | # No 2D-supported |
|---|
| 219 | #if name not in self.p_model2.orientation_params: |
|---|
| 220 | new_name = "p2_" + name |
|---|
| 221 | self.params[new_name]= value |
|---|
| 222 | |
|---|
| 223 | # Set "scale" as initializing |
|---|
| 224 | self._set_scale_factor() |
|---|
| 225 | |
|---|
| 226 | |
|---|
| 227 | def _set_details(self): |
|---|
| 228 | """ |
|---|
| 229 | Concatenate details of the two models to create |
|---|
| 230 | this model details |
|---|
| 231 | """ |
|---|
| 232 | for name ,detail in self.p_model1.details.iteritems(): |
|---|
| 233 | new_name = "p1_" + name |
|---|
| 234 | #if new_name not in self.orientation_params: |
|---|
| 235 | self.details[new_name]= detail |
|---|
| 236 | |
|---|
| 237 | for name ,detail in self.p_model2.details.iteritems(): |
|---|
| 238 | new_name = "p2_" + name |
|---|
| 239 | #if new_name not in self.orientation_params: |
|---|
| 240 | self.details[new_name]= detail |
|---|
| 241 | |
|---|
| 242 | def _set_scale_factor(self): |
|---|
| 243 | """ |
|---|
| 244 | Not implemented |
|---|
| 245 | """ |
|---|
| 246 | pass |
|---|
| 247 | |
|---|
| 248 | |
|---|
| 249 | def setParam(self, name, value): |
|---|
| 250 | """ |
|---|
| 251 | Set the value of a model parameter |
|---|
| 252 | |
|---|
| 253 | :param name: name of the parameter |
|---|
| 254 | :param value: value of the parameter |
|---|
| 255 | """ |
|---|
| 256 | # set param to p1+p2 model |
|---|
| 257 | self._setParamHelper(name, value) |
|---|
| 258 | |
|---|
| 259 | ## setParam to p model |
|---|
| 260 | model_pre = name.split('_', 1)[0] |
|---|
| 261 | new_name = name.split('_', 1)[1] |
|---|
| 262 | if model_pre == "p1": |
|---|
| 263 | if new_name in self.p_model1.getParamList(): |
|---|
| 264 | self.p_model1.setParam(new_name, value) |
|---|
| 265 | elif model_pre == "p2": |
|---|
| 266 | if new_name in self.p_model2.getParamList(): |
|---|
| 267 | self.p_model2.setParam(new_name, value) |
|---|
| 268 | elif name.lower() == 'scale_factor': |
|---|
| 269 | self.params['scale_factor'] = value |
|---|
| 270 | else: |
|---|
| 271 | raise ValueError, "Model does not contain parameter %s" % name |
|---|
| 272 | |
|---|
| 273 | def getParam(self, name): |
|---|
| 274 | """ |
|---|
| 275 | Set the value of a model parameter |
|---|
| 276 | |
|---|
| 277 | :param name: name of the parameter |
|---|
| 278 | |
|---|
| 279 | """ |
|---|
| 280 | # Look for dispersion parameters |
|---|
| 281 | toks = name.split('.') |
|---|
| 282 | if len(toks)==2: |
|---|
| 283 | for item in self.dispersion.keys(): |
|---|
| 284 | # 2D not supported |
|---|
| 285 | if item.lower()==toks[0].lower():# and \ |
|---|
| 286 | #item.lower() not in self.orientation_params \ |
|---|
| 287 | #and toks[0].lower() not in self.orientation_params: |
|---|
| 288 | for par in self.dispersion[item]: |
|---|
| 289 | if par.lower() == toks[1].lower(): |
|---|
| 290 | return self.dispersion[item][par] |
|---|
| 291 | else: |
|---|
| 292 | # Look for standard parameter |
|---|
| 293 | for item in self.params.keys(): |
|---|
| 294 | if item.lower()==name.lower():#and \ |
|---|
| 295 | #item.lower() not in self.orientation_params \ |
|---|
| 296 | #and toks[0].lower() not in self.orientation_params: |
|---|
| 297 | return self.params[item] |
|---|
| 298 | return |
|---|
| 299 | #raise ValueError, "Model does not contain parameter %s" % name |
|---|
| 300 | |
|---|
| 301 | def _setParamHelper(self, name, value): |
|---|
| 302 | """ |
|---|
| 303 | Helper function to setparam |
|---|
| 304 | """ |
|---|
| 305 | # Look for dispersion parameters |
|---|
| 306 | toks = name.split('.') |
|---|
| 307 | if len(toks)== 2: |
|---|
| 308 | for item in self.dispersion.keys(): |
|---|
| 309 | if item.lower()== toks[0].lower():# and \ |
|---|
| 310 | #item.lower() not in self.orientation_params: |
|---|
| 311 | for par in self.dispersion[item]: |
|---|
| 312 | if par.lower() == toks[1].lower():#and \ |
|---|
| 313 | #item.lower() not in self.orientation_params: |
|---|
| 314 | self.dispersion[item][par] = value |
|---|
| 315 | return |
|---|
| 316 | else: |
|---|
| 317 | # Look for standard parameter |
|---|
| 318 | for item in self.params.keys(): |
|---|
| 319 | if item.lower()== name.lower():#and \ |
|---|
| 320 | #item.lower() not in self.orientation_params: |
|---|
| 321 | self.params[item] = value |
|---|
| 322 | return |
|---|
| 323 | |
|---|
| 324 | raise ValueError, "Model does not contain parameter %s" % name |
|---|
| 325 | |
|---|
| 326 | |
|---|
| 327 | def _set_fixed_params(self): |
|---|
| 328 | """ |
|---|
| 329 | fill the self.fixed list with the p_model fixed list |
|---|
| 330 | """ |
|---|
| 331 | for item in self.p_model1.fixed: |
|---|
| 332 | new_item = "p1" + item |
|---|
| 333 | self.fixed.append(new_item) |
|---|
| 334 | for item in self.p_model2.fixed: |
|---|
| 335 | new_item = "p2" + item |
|---|
| 336 | self.fixed.append(new_item) |
|---|
| 337 | |
|---|
| 338 | self.fixed.sort() |
|---|
| 339 | |
|---|
| 340 | |
|---|
| 341 | def run(self, x = 0.0): |
|---|
| 342 | """ |
|---|
| 343 | Evaluate the model |
|---|
| 344 | |
|---|
| 345 | :param x: input q-value (float or [float, float] as [r, theta]) |
|---|
| 346 | :return: (scattering function value) |
|---|
| 347 | """ |
|---|
| 348 | self._set_scale_factor() |
|---|
| 349 | return self.params['scale_factor'] * \ |
|---|
| 350 | (self.p_model1.run(x) + self.p_model2.run(x)) |
|---|
| 351 | |
|---|
| 352 | def runXY(self, x = 0.0): |
|---|
| 353 | """ |
|---|
| 354 | Evaluate the model |
|---|
| 355 | |
|---|
| 356 | :param x: input q-value (float or [float, float] as [qx, qy]) |
|---|
| 357 | :return: scattering function value |
|---|
| 358 | """ |
|---|
| 359 | self._set_scale_factor() |
|---|
| 360 | return self.params['scale_factor'] * \ |
|---|
| 361 | (self.p_model1.runXY(x) + self.p_model2.runXY(x)) |
|---|
| 362 | |
|---|
| 363 | ## Now (May27,10) directly uses the model eval function |
|---|
| 364 | ## instead of the for-loop in Base Component. |
|---|
| 365 | def evalDistribution(self, x = []): |
|---|
| 366 | """ |
|---|
| 367 | Evaluate the model in cartesian coordinates |
|---|
| 368 | |
|---|
| 369 | :param x: input q[], or [qx[], qy[]] |
|---|
| 370 | :return: scattering function P(q[]) |
|---|
| 371 | """ |
|---|
| 372 | self._set_scale_factor() |
|---|
| 373 | return self.params['scale_factor'] * \ |
|---|
| 374 | (self.p_model1.evalDistribution(x) + \ |
|---|
| 375 | self.p_model2.evalDistribution(x)) |
|---|
| 376 | |
|---|
| 377 | def set_dispersion(self, parameter, dispersion): |
|---|
| 378 | """ |
|---|
| 379 | Set the dispersion object for a model parameter |
|---|
| 380 | |
|---|
| 381 | :param parameter: name of the parameter [string] |
|---|
| 382 | :dispersion: dispersion object of type DispersionModel |
|---|
| 383 | """ |
|---|
| 384 | value= None |
|---|
| 385 | new_pre = parameter.split("_", 1)[0] |
|---|
| 386 | new_parameter = parameter.split("_", 1)[1] |
|---|
| 387 | try: |
|---|
| 388 | if new_pre == 'p1' and \ |
|---|
| 389 | new_parameter in self.p_model1.dispersion.keys(): |
|---|
| 390 | value= self.p_model1.set_dispersion(new_parameter, dispersion) |
|---|
| 391 | if new_pre == 'p2' and \ |
|---|
| 392 | new_parameter in self.p_model2.dispersion.keys(): |
|---|
| 393 | value= self.p_model2.set_dispersion(new_parameter, dispersion) |
|---|
| 394 | self._set_dispersion() |
|---|
| 395 | return value |
|---|
| 396 | except: |
|---|
| 397 | raise |
|---|
| 398 | |
|---|
| 399 | def fill_description(self, p_model1, p_model2): |
|---|
| 400 | """ |
|---|
| 401 | Fill the description for P(Q)+P(Q) |
|---|
| 402 | """ |
|---|
| 403 | description = "" |
|---|
| 404 | description +="This model gives the summation of %s and %s.\n"% \ |
|---|
| 405 | ( p_model1.name, p_model2.name ) |
|---|
| 406 | self.description += description |
|---|
| 407 | |
|---|
| 408 | ## DO NOT MODIFY THE FOLLOWING LINES!!!!!!!!!!!!!!!! |
|---|
| 409 | def get_fname(self): |
|---|
| 410 | """ |
|---|
| 411 | Get the model name same as the file name |
|---|
| 412 | """ |
|---|
| 413 | path = sys._getframe().f_code.co_filename |
|---|
| 414 | basename = os.path.basename(path) |
|---|
| 415 | name, _ = os.path.splitext(basename) |
|---|
| 416 | return name |
|---|
| 417 | |
|---|
| 418 | if __name__ == "__main__": |
|---|
| 419 | m1= Model() |
|---|
| 420 | #m1.setParam("p1_scale", 25) |
|---|
| 421 | #m1.setParam("p1_length", 1000) |
|---|
| 422 | #m1.setParam("p2_scale", 100) |
|---|
| 423 | #m1.setParam("p2_rg", 100) |
|---|
| 424 | out1 = m1.runXY(0.01) |
|---|
| 425 | |
|---|
| 426 | m2= Model() |
|---|
| 427 | #m2.p_model1.setParam("scale", 25) |
|---|
| 428 | #m2.p_model1.setParam("length", 1000) |
|---|
| 429 | #m2.p_model2.setParam("scale", 100) |
|---|
| 430 | #m2.p_model2.setParam("rg", 100) |
|---|
| 431 | out2 = m2.p_model1.runXY(0.01) + m2.p_model2.runXY(0.01) |
|---|
| 432 | print "Testing at Q = 0.01:" |
|---|
| 433 | print out1, " = ", out2 |
|---|
| 434 | if out1 == out2: |
|---|
| 435 | print "===> Simple Test: Passed!" |
|---|
| 436 | else: |
|---|
| 437 | print "===> Simple Test: Failed!" |
|---|
