Source code for sas.models.CoreMultiShellModel

"""
    Core-Multi-Shell model
"""
from sas.models.BaseComponent import BaseComponent
from sas.models.CoreFourShellModel import CoreFourShellModel
import copy
max_nshells = 5
[docs]class CoreMultiShellModel(BaseComponent): """ This multi-model is based on CoreFourShellModel and provides the capability of changing the number of shells between 1 and 4. """ def __init__(self, multfactor=1): BaseComponent.__init__(self) """ :param n_shells: number of shells in the model, assumes 1<= n_shells <=4. """ ## Setting model name model description self.description="" model = CoreFourShellModel() self.model = model self.name = "CoreMultiShellModel" self.description="" self.n_shells = multfactor ## Define parameters self.params = {} ## Parameter details [units, min, max] self.details = {} # non-fittable parameters self.non_fittable = model.non_fittable ## dispersion self._set_dispersion() ## Define parameters self._set_params() ## Parameter details [units, min, max] self._set_details() #list of parameter that can be fitted self._set_fixed_params() self.orientation_params = [] self.magnetic_params = [] ## functional multiplicity info of the model # [int(maximum no. of functionality),"str(Titl), # [str(name of function0),...], [str(x-asix name of sld),...]] self.multiplicity_info = [max_nshells, "No. of Shells:", [], ['Radius']] ## parameters with orientation: can be removed since there is no orientational params self._set_orientation_params() def _clone(self, obj): """ Internal utility function to copy the internal data members to a fresh copy. """ obj.params = copy.deepcopy(self.params) obj.description = copy.deepcopy(self.description) obj.details = copy.deepcopy(self.details) obj.dispersion = copy.deepcopy(self.dispersion) obj.model = self.model.clone() return obj def _set_dispersion(self): """ model dispersions Polydispersion should not be applied to s_model """ ##set dispersion from model for name , value in self.model.dispersion.iteritems(): nshell = 0 if name.split('_').count('thick') > 0: while nshell < self.n_shells: nshell += 1 if name.split('_')[-1] == 'shell%s' % str(nshell): self.dispersion[name] = value else: continue else: self.dispersion[name] = value def _set_orientation_params(self): """ model orientation and magnetic parameters, same params for this model """ ##set dispersion from model for param in self.model.orientation_params: nshell = 0 if param.split('_')[-1].count('shell') < 1: #print "param", param, param.split('_')[-1].count('shell') self.orientation_params.append(param) self.magnetic_params.append(param) continue while nshell < self.n_shells: nshell += 1 if param.split('_')[-1] == 'shell%s' % str(nshell): self.orientation_params.append(param) self.magnetic_params.append(param) continue def _set_params(self): """ Concatenate the parameters of the model to create this model parameters """ # rearrange the parameters for the given # of shells for name , value in self.model.params.iteritems(): nshell = 0 if name.split('_').count('thick') > 0 or \ name.split('_').count('sld') > 0 or \ name[0] == 'M': if name.split('_')[-1] == 'solv' or \ name.split('_')[-1] == 'core0': self.params[name]= value continue while nshell < self.n_shells: nshell += 1 if name.split('_')[-1] == 'shell%s' % str(nshell): self.params[name]= value continue else: self.params[name]= value # set constrained values for the original model params self._set_xtra_model_param() def _set_details(self): """ Concatenate details of the original model to create this model details """ for name ,detail in self.model.details.iteritems(): if name in self.params.iterkeys(): self.details[name]= detail def _set_xtra_model_param(self): """ Set params of original model that are hidden from this model """ # look for the model parameters that are not in param list for key in self.model.params.iterkeys(): if key not in self.params.keys(): if key.split('_').count('thick') > 0: self.model.setParam(key, 0) continue for nshell in range(self.n_shells,max_nshells): if key.split('_').count('sld') > 0 and \ key.split('_')[-1] == 'shell%s' % str(nshell+1): try: if key[0] != 'M': value = self.model.params['sld_solv'] self.model.setParam(key, value) else: self.model.setParam(key, 0.0) except: pass
[docs] def getProfile(self): """ Get SLD profile : return: (r, beta) where r is a list of radius of the transition points beta is a list of the corresponding SLD values : Note: This works only for func_shell# = 2. """ r = [] beta = [] # for core at r=0 r.append(0) beta.append(self.params['sld_core0']) # for core at r=rad_core r.append(self.params['rad_core0']) beta.append(self.params['sld_core0']) # for shells for n in range(1, self.n_shells+1): # Left side of each shells r0 = r[len(r)-1] r.append(r0) exec "beta.append(self.params['sld_shell%s'% str(n)])" # Right side of each shells exec "r0 += self.params['thick_shell%s'% str(n)]" r.append(r0) exec "beta.append(self.params['sld_shell%s'% str(n)])" # for solvent r0 = r[len(r)-1] r.append(r0) beta.append(self.params['sld_solv']) r_solv = 5*r0/4 r.append(r_solv) beta.append(self.params['sld_solv']) return r, beta
[docs] def setParam(self, name, value): """ Set the value of a model parameter : param name: name of the parameter : param value: value of the parameter """ # set param to new model self._setParamHelper( name, value) ## setParam to model if name == 'sld_solv': # the sld_*** model.params not in params must set to value of sld_solv for key in self.model.params.iterkeys(): if key not in self.params.keys(): if key.split('_')[0] == 'sld': self.model.setParam(key, value) elif key.split('_')[1] == 'sld': # mag params self.model.setParam(key, 0.0) self.model.setParam( name, value)
def _setParamHelper(self, name, value): """ Helper function to setParam """ #look for dispersion parameters toks = name.split('.') if len(toks) == 2: for item in self.dispersion.keys(): if item.lower()==toks[0].lower(): for par in self.dispersion[item]: if par.lower() == toks[1].lower(): self.dispersion[item][par] = value return # Look for standard parameter for item in self.params.keys(): if item.lower()==name.lower(): self.params[item] = value return #raise ValueError, "Model does not contain parameter %s" % name def _set_fixed_params(self): """ Fill the self.fixed list with the model fixed list """ for item in self.model.fixed: if item.split('.')[0] in self.params.keys(): self.fixed.append(item) self.fixed.sort()
[docs] def run(self, x = 0.0): """ Evaluate the model : param x: input q-value (float or [float, float] as [r, theta]) : return: (DAB value) """ # set effective radius and scaling factor before run return self.model.run(x)
[docs] def runXY(self, x = 0.0): """ Evaluate the model : param x: input q-value (float or [float, float] as [qx, qy]) : return: DAB value """ # set effective radius and scaling factor before run return self.model.runXY(x) ## Now (May27,10) directly uses the model eval function ## instead of the for-loop in Base Component.
[docs] def evalDistribution(self, x = []): """ Evaluate the model in cartesian coordinates : param x: input q[], or [qx[], qy[]] : return: scattering function P(q[]) """ # set effective radius and scaling factor before run return self.model.evalDistribution(x)
[docs] def calculate_ER(self): """ Calculate the effective radius for P(q)*S(q) :return: the value of the effective radius """ return self.model.calculate_ER()
[docs] def calculate_VR(self): """ Calculate the volf ratio for P(q)*S(q) :return: the value of the volf ratio """ return self.model.calculate_VR()
[docs] def set_dispersion(self, parameter, dispersion): """ Set the dispersion object for a model parameter : param parameter: name of the parameter [string] :dispersion: dispersion object of type DispersionModel """ value = None try: if parameter in self.model.dispersion.keys(): value = self.model.set_dispersion(parameter, dispersion) self._set_dispersion() return value except: raise