from sas.models.BaseComponent import BaseComponent
from sas.models.OnionModel import OnionModel
import copy
max_nshells = 10
[docs]class OnionExpShellModel(BaseComponent):
"""
This multi-model is based on CoreMultiShellModel with exponential
func shells and provides the capability
of changing the number of shells between 1 and 10.
"""
def __init__(self, n_shells=1):
BaseComponent.__init__(self)
"""
:param n_shells: number of shells in the model,
assumes 1<= n_shells <=10.
"""
## Setting model name model description
self.description=""
model = OnionModel()
self.model = model
self.name = "OnionExpShellModel"
self.description=model.description
self.n_shells = n_shells
## Define parameters
self.params = {}
## Parameter details [units, min, max]
self.details = {}
## 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.model.params['n_shells'] = self.n_shells
## 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
for item in self.model.orientation_params:
self.orientation_params.append(item)
self.getProfile()
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
"""
##set dispersion from model
for name , value in self.model.dispersion.iteritems():
nshell = 0
if name.split('_')[0] == 'thick':
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_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
pos = len(name.split('_'))-1
if name.split('_')[0] == 'func':
continue
elif name.split('_')[pos][0:5] == 'shell':
while nshell<self.n_shells:
nshell += 1
if name.split('_')[pos] == 'shell%s' % str(nshell):
self.params[name]= value
continue
else:
self.params[name]= value
self.model.params['n_shells'] = self.n_shells
# 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('_')[0] == 'thick':
self.model.setParam(key, 0)
continue
if key.split('_')[0] == 'A':
self.model.setParam(key, 0)
continue
if key.split('_')[0] == 'func':
self.model.setParam(key, 2)
continue
for nshell in range(self.n_shells,max_nshells):
if key.split('_')[1] == 'sld_in_shell%s' % str(nshell+1):
try:
value = self.model.params['sld_solv']
self.model.setParam(key, value)
except: pass
[docs] def getProfile(self):
"""
Get SLD profile
: return: (r, beta) where r is a list of radius of the transition
points and beta is a list of the corresponding SLD values
"""
# max_pts for each shells
max_pts = 10
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)
beta.append(self.params['sld_in_shell%s'% str(n)])
A = self.params['A_shell%s'% str(n)]
from math import fabs
if fabs(A) <1.0e-16:
# Right side of each shells
r0 += self.params['thick_shell%s'% str(n)]
r.append(r0)
beta.append(self.params['sld_in_shell%s'% str(n)])
else:
from math import exp
rn = r0
for n_sub in range(0,max_pts):
# Right side of each sub_shells
rn += self.params['thick_shell%s'% str(n)]/10.0
r.append(rn)
slope = (self.params['sld_out_shell%s'% str(n)] \
-self.params['sld_in_shell%s'% str(n)]) \
/(exp(self.params['A_shell%s'% str(n)])-1)
const = (self.params['sld_in_shell%s'% str(n)]-slope)
beta_n = slope*exp((self.params['A_shell%s'% str(n)]* \
(rn-r0)/self.params['thick_shell%s'% str(n)])) + const
beta.append(beta_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()and key.split('_')[0] == 'sld':
self.model.setParam(key, value)
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()
pass
[docs] def run(self, x = 0.0):
"""
Evaluate the model
: param x: input q-value (float or [float, float] as [r, theta])
: return: (I value)
"""
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: I value
"""
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 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