Commit 54742f3e authored by Heller, William T.'s avatar Heller, William T.
Browse files

Merge branch 'scrub_code_for_min' into 'master' 

Scrub code for min

See merge request !29
parents e3a167e5 c721d718

sas_temper/param.py

+6 −6
Original line number Diff line number Diff line
@@ -25,7 +25,7 @@ import math as m 
import sas_temper.polydispersity as pd



class Param(object):

    def __init__(self, name, kind, min, max, coupled=None, polydispersity=None, pd_min=None, pd_max=None):

    def __init__(self, name, kind, minv, maxv, coupled=None, polydispersity=None, pd_min=None, pd_max=None):

        self.name = str(name)        # string:  the name of the parameter

        

        if kind in ["linear","log","integer","coupled","fixed"]:
@@ -36,13 +36,13 @@ class Param(object): 
            raise Exception(err_message)

        

        if kind in ["integer"]:

            self.min = min

            self.max = max

            self.min = minv

            self.max = maxv

            self.val = int(0.5*self.min+self.max)

            self.unc = 0.0

        else:

            self.min = np.float64(min)            # the minimum value

            self.max = np.float64(max)            # the maximum value

            self.min = np.float64(minv)            # the minimum value

            self.max = np.float64(maxv)            # the maximum value

            self.val = 0.5*(self.min + self.max)

            self.unc = 0.0
@@ -52,7 +52,7 @@ class Param(object): 
            self.coupled = None

    

        if polydispersity is not None:

            self.polydispersity = pd.Polydispersity(name=self.name,kind=polydispersity,min=pd_min,max=pd_max)

            self.polydispersity = pd.Polydispersity(name=self.name,kind=polydispersity,minv=pd_min,maxv=pd_max)

        else:

            self.polydispersity = None

sas_temper/parse_conf.py

+8 −8
Original line number Diff line number Diff line
@@ -78,14 +78,14 @@ def parse_config(name): 
            #now, we create a parameter

            if coupled_name is None:

                if pd_name is None:

                    cur_param = param.Param(name=txt1, kind=var_kind, min=min_val, max=max_val, coupled=None, polydispersity=None, pd_min=0.0, pd_max=0.0)

                    cur_param = param.Param(name=txt1, kind=var_kind, minv=min_val, maxv=max_val, coupled=None, polydispersity=None, pd_min=0.0, pd_max=0.0)

                else:

                    cur_param = param.Param(name=txt1, kind=var_kind, min=min_val, max=max_val, coupled=None, polydispersity=txt3, pd_min=pd_minval, pd_max=pd_maxval)

                    cur_param = param.Param(name=txt1, kind=var_kind, minv=min_val, maxv=max_val, coupled=None, polydispersity=txt3, pd_min=pd_minval, pd_max=pd_maxval)

            else:

                if pd_name is None:

                    cur_param = param.Param(name=txt1, kind=var_kind, min=min_val, max=max_val, coupled=coupled_name, polydispersity=None, pd_min=0.0, pd_max=0.0)

                    cur_param = param.Param(name=txt1, kind=var_kind, minv=min_val, maxv=max_val, coupled=coupled_name, polydispersity=None, pd_min=0.0, pd_max=0.0)

                else:

                    cur_param = param.Param(name=txt1, kind=var_kind, min=min_val, max=max_val, coupled=coupled_name, polydispersity=txt3, pd_min=pd_minval, pd_max=pd_maxval)

                    cur_param = param.Param(name=txt1, kind=var_kind, minv=min_val, maxv=max_val, coupled=coupled_name, polydispersity=txt3, pd_min=pd_minval, pd_max=pd_maxval)

            

            #and add it to the array of parameters

            model_params.append(cur_param)
@@ -129,14 +129,14 @@ def parse_config(name): 
                    #now, we create a parameter

                    if sq_coupled_name is None:

                        if sq_pd_name is None:

                            sq_cur_param = param.Param(name=txt2, kind=sq_var_kind, min=sq_min_val, max=sq_max_val, coupled=None, polydispersity=None, pd_min=0.0, pd_max=0.0)

                            sq_cur_param = param.Param(name=txt2, kind=sq_var_kind, minv=sq_min_val, maxv=sq_max_val, coupled=None, polydispersity=None, pd_min=0.0, pd_max=0.0)

                        else:

                            sq_cur_param = param.Param(name=txt2, kind=sq_var_kind, min=sq_min_val, max=sq_max_val, coupled=None, polydispersity=txt3, pd_min=pd_minval, pd_max=pd_maxval)

                            sq_cur_param = param.Param(name=txt2, kind=sq_var_kind, minv=sq_min_val, maxv=sq_max_val, coupled=None, polydispersity=txt3, pd_min=pd_minval, pd_max=pd_maxval)

                    else:

                        if sq_pd_name is None:

                            sq_cur_param = param.Param(name=txt2, kind=sq_var_kind, min=sq_min_val, max=sq_max_val, coupled=sq_coupled_name, polydispersity=None, pd_min=0.0, pd_max=0.0)

                            sq_cur_param = param.Param(name=txt2, kind=sq_var_kind, minv=sq_min_val, maxv=sq_max_val, coupled=sq_coupled_name, polydispersity=None, pd_min=0.0, pd_max=0.0)

                        else:

                            sq_cur_param = param.Param(name=txt2, kind=sq_var_kind, min=sq_min_val, max=sq_max_val, coupled=sq_coupled_name, polydispersity=txt4, pd_min=sq_pd_minval, pd_max=sq_pd_maxval)

                            sq_cur_param = param.Param(name=txt2, kind=sq_var_kind, minv=sq_min_val, maxv=sq_max_val, coupled=sq_coupled_name, polydispersity=txt4, pd_min=sq_pd_minval, pd_max=sq_pd_maxval)

    

                    #and add it to the array of structure factor parameters

                    s_of_q_params.append(sq_cur_param)

sas_temper/polydispersity.py

+3 −3
Original line number Diff line number Diff line
@@ -24,7 +24,7 @@ import numpy as np 
import math as m



class Polydispersity(object):

    def __init__(self, name, kind, min, max):

    def __init__(self, name, kind, minv, maxv):

        self.name = str(name)        # string:  the name of the parameter

        

        if kind in ["SchulzDispersion","GaussianDispersion","LogNormalDispersion","RectangleDispersion"]:
@@ -34,8 +34,8 @@ class Polydispersity(object): 
            err_message = "The polydispersity distribution type " + str(kind) + " is not valid"

            raise Exception(err_message)

        

        self.min = np.float64(min)            # the minimum value

        self.max = np.float64(max)            # the maximum value

        self.min = np.float64(minv)            # the minimum value

        self.max = np.float64(maxv)            # the maximum value

        self.val = 0.5*(self.min + self.max)

        self.unc = 0.0

sas_temper/sas_calc.py

+6 −6
Original line number Diff line number Diff line
@@ -28,10 +28,10 @@ def calc_profile(d, mc, usm): 
    

    for i in range(0,len(d.x)):

        tot = 0.0

        min = d.x[i] - 4.5*d.dx[i]

        minq = d.x[i] - 4.5*d.dx[i]

        qstep = 4.5*d.dx[i]/30.0

        for j in range(0,61):

            qv = m.fabs(min + j*qstep)

            qv = m.fabs(minq + j*qstep)

            tmp = np.interp(qv,usm.x,usm.y)

            # the number on the next line is ~sqrt(2*Pi)

            tot += tmp*qstep*m.exp(-(qv-d.x[i])*(qv-d.x[i])/(2.0*d.dx[i]*d.dx[i]))/(2.506628273*d.dx[i])
@@ -105,12 +105,12 @@ def calc_profile_usm(d, mc): 
# mc is the model configuration, d is the input data, mi is the calculated model profile

def chisq(mc, d, mi):

    # this is quite straightforward

    sum = 0

    sumv = 0

    for i in range(0,len(d.x)):

        sum += (d.y[i]-mi.y[i])*(d.y[i]-mi.y[i])/(d.dy[i]*d.dy[i])

        sumv += (d.y[i]-mi.y[i])*(d.y[i]-mi.y[i])/(d.dy[i]*d.dy[i])

        

    sum = m.sqrt(sum/(mc.free_params-1))

    sumv = m.sqrt(sumv/(mc.free_params-1))

    

    return sum

    return sumv