Changeset 84db7a5 in sasmodels


Ignore:
Timestamp:
Mar 17, 2016 10:47:47 AM (9 years ago)
Author:
krzywon
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, release_v0.94, release_v0.95, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
6824af5
Parents:
4373d62
Message:

Updated sesans scripting to be more command line focused AND modified hardsphere to effect_radius.

Files:
1 added
2 deleted
5 edited

Legend:

Unmodified
Added
Removed

  • example/sesans_parameters_css-hs.py

    ra98958b r84db7a5  
    88# Enter the model name to use 
    99model_name = "core_shell_sphere*hardsphere" 
     10 
     11# DO NOT MODIFY THIS LINE 
     12model = sesansfit.get_bumps_model(model_name) 
    1013 
    1114# Enter any custom parameters 
    … …  
    1922# Initial parameter values (if other than defaults) 
    2023initial_vals = { 
    21     "scale" : 0.09, 
    2224    "core_sld" : 1.0592, 
    2325    "solvent_sld" : 2.88, 
    24     "shell_sld" : 2.88, 
    2526    "radius" : 890, 
    26     "thickness" : 130, 
    27     "volfraction" : 0.45 
     27    "thickness" : 130 
    2828} 
    2929 
    … …  
    3636} 
    3737 
     38# Constraints 
     39# model.param_name = f(other params) 
     40# EXAMPLE: model.scale = model.radius*model.radius*(1 - phi) - where radius and scale are model functions and phi is 
     41# a custom parameter 
     42model.scale = phi*(1-phi) 
     43model.volfraction = phi 
     44model.shell_sld = pen*2.88 
     45 
    3846# Send to the fitting engine 
    3947problem = sesansfit.sesans_fit(sesans_file, model_name, initial_vals, custom_params, param_range) 

  • example/sesans_parameters_sphere.py

    ra98958b r84db7a5  
    99model_name = "sphere" 
    1010 
     11# DO NOT MODIFY THIS LINE 
     12model = sesansfit.get_bumps_model(model_name) 
     13 
    1114# Enter any custom parameters 
     15# name = Parameter(initial_value, name='name') 
    1216phi = Parameter(0.10, name='phi') 
     17# Add the parameters to this list that should be displayed in the fitting window 
    1318custom_params = {"phi" : phi} 
    1419 
    15 # SESANS data file 
     20# SESANS data file name 
    1621sesans_file = "sphere.ses" 
    1722 
    1823# Initial parameter values (if other than defaults) 
     24# "model_parameter_name" : value 
    1925initial_vals = { 
    20     "scale" : phi*(1 - phi), 
    2126    "sld" : 7.0, 
     27    "radius" : 1000, 
    2228    "solvent_sld" : 1.0, 
    23     "radius" : 1000, 
    2429} 
    2530 
    2631# Ranges for parameters if other than default 
     32# "model_parameter_name" : [min, max] 
    2733param_range = { 
    2834    "phi" : [0.001, 0.5], 
    … …  
    3036} 
    3137 
     38# Constraints 
     39# model.param_name = f(other params) 
     40# EXAMPLE: model.scale = model.radius*model.radius*(1 - phi) - where radius and scale are model functions and phi is 
     41# a custom parameter 
     42model.scale = phi*(1-phi) 
     43 
    3244# Send to the fitting engine 
    33 problem = sesansfit.sesans_fit(sesans_file, model_name, initial_vals, custom_params, param_range) 
     45# DO NOT MODIFY THIS LINE 
     46problem = sesansfit.sesans_fit(sesans_file, model, initial_vals, custom_params, param_range) 
     47 

  • example/sesansfit.py

    ra98958b r84db7a5  
    1 #TODO: Convert units properly (nm -> A) 
    2 #TODO: Implement constraints 
    3  
    41from bumps.names import * 
    5 from sasmodels import core, bumps_model 
     2from sasmodels import core, bumps_model, sesans 
    63 
    74HAS_CONVERTER = True 
    … …  
    118    HAS_CONVERTER = False 
    129 
    13 def sesans_fit(file, model_name, initial_vals={}, custom_params={}, param_range=[]): 
     10def get_bumps_model(model_name): 
     11    kernel = core.load_model(model_name) 
     12    model = bumps_model.Model(kernel) 
     13    return model 
     14 
     15def sesans_fit(file, model, initial_vals={}, custom_params={}, param_range=[]): 
    1416    """ 
    15  
    1617    @param file: SESANS file location 
    17     @param model_name: model name string - can be model, model_1 * model_2, and/or model_1 + model_2 
     18    @param model: Bumps model object or model name - can be model, model_1 * model_2, and/or model_1 + model_2 
    1819    @param initial_vals: dictionary of {param_name : initial_value} 
    1920    @param custom_params: dictionary of {custom_parameter_name : Parameter() object} 
    2021    @param param_range: dictionary of {parameter_name : [minimum, maximum]} 
     22    @param constraints: dictionary of {parameter_name : constraint} 
    2123    @return: FitProblem for Bumps usage 
    2224    """ 
    … …  
    2931            default_unit = "A" 
    3032            data_conv_q = Converter(data._xunit) 
     33            for x in data.x: 
     34                print x 
    3135            data.x = data_conv_q(data.x, units=default_unit) 
     36            for x in data.x: 
     37                print x 
    3238            data._xunit = default_unit 
    3339 
    … …  
    5157        data = SESANSData1D() 
    5258 
    53     radius = 1000 
     59    if "radius" in initial_vals: 
     60        radius = initial_vals.get("radius") 
     61    else: 
     62        radius = 1000 
    5463    data.Rmax = 3*radius # [A] 
    5564 
    56     kernel = core.load_model(model_name) 
    57     model = bumps_model.Model(kernel) 
     65    if isinstance(model, basestring): 
     66        model = get_bumps_model(model) 
    5867 
    59     # Load custom parameters, initial values and parameter constraints 
     68    # Load custom parameters, initial values and parameter ranges 
    6069    for k, v in custom_params.items(): 
    6170        setattr(model, k, v) 
    … …  
    6978            setattr(param.bounds, "limits", v) 
    7079 
    71     if False: # have sans data 
     80    if False: # for future implementation 
    7281        M_sesans = bumps_model.Experiment(data=data, model=model) 
    7382        M_sans = bumps_model.Experiment(data=sans_data, model=model) 

  • sasmodels/data.py

    r7824276 r84db7a5  
    440440 
    441441    if use_data or use_theory: 
     442        is_tof = np.any(data.lam!=data.lam[0]) 
    442443        if num_plots > 1: 
    443444            plt.subplot(1, num_plots, 1) 
    444445        if use_data: 
    445             plt.errorbar(data.x, data.y, yerr=data.dy) 
     446            if is_tof: 
     447                plt.errorbar(data.x, np.log(data.y)/(data.lam*data.lam), yerr=data.dy/data.y/(data.lam*data.lam)) 
     448            else: 
     449                plt.errorbar(data.x, data.y, yerr=data.dy) 
    446450        if theory is not None: 
    447             plt.plot(data.x, theory, '-', hold=True) 
     451            if is_tof: 
     452                plt.plot(data.x, np.log(theory)/(data.lam*data.lam), '-', hold=True) 
     453            else: 
     454                plt.plot(data.x, theory, '-', hold=True) 
    448455        if limits is not None: 
    449456            plt.ylim(*limits) 
    450         plt.xlabel('spin echo length (nm)') 
    451         plt.ylabel('polarization (P/P0)') 
     457 
     458        plt.xlabel('spin echo length ({})'.format(data._xunit)) 
     459        if is_tof: 
     460            plt.ylabel('(Log (P/P$_0$))/$\lambda^2$') 
     461        else: 
     462            plt.ylabel('polarization (P/P0)') 
     463 
    452464 
    453465    if resid is not None: 
    … …  
    455467            plt.subplot(1, num_plots, (use_data or use_theory) + 1) 
    456468        plt.plot(data.x, resid, 'x') 
    457         plt.xlabel('spin echo length (nm)') 
     469        plt.xlabel('spin echo length ({})'.format(data._xunit)) 
    458470        plt.ylabel('residuals (P/P0)') 
    459471 

  • sasmodels/models/hardsphere.py

    raa2edb2 r84db7a5  
    77the maths needs to be modified (no \Beta(Q) correction yet in sasview). 
    88 
    9 radius_effective is the effective hard sphere radius. 
     9effect_radius is the effective hard sphere radius. 
    1010volfraction is the volume fraction occupied by the spheres. 
    1111 
    … …  
    5353        systems. Though strictly the maths needs to be modified - 
    5454    which sasview does not do yet. 
    55     radius_effective is the hard sphere radius 
     55    effect_radius is the hard sphere radius 
    5656    volfraction is the volume fraction occupied by the spheres. 
    5757""" 
    … …  
    6060 
    6161#             ["name", "units", default, [lower, upper], "type","description"], 
    62 parameters = [["radius_effective", "Ang", 50.0, [0, inf], "volume", 
     62parameters = [["effect_radius", "Ang", 50.0, [0, inf], "volume", 
    6363               "effective radius of hard sphere"], 
    6464              ["volfraction", "", 0.2, [0, 0.74], "", 
    … …  
    7575      double D,A,B,G,X,X2,X4,S,C,FF,HARDSPH; 
    7676 
    77       if(fabs(radius_effective) < 1.E-12) { 
     77      if(fabs(effect_radius) < 1.E-12) { 
    7878               HARDSPH=1.0; 
    7979               return(HARDSPH); 
    … …  
    8484      A= (1.+2.*volfraction)*D; 
    8585      A *=A; 
    86       X=fabs(q*radius_effective*2.0); 
     86      X=fabs(q*effect_radius*2.0); 
    8787 
    8888      if(X < 5.E-06) { 
    … …  
    147147# VR defaults to 1.0 
    148148 
    149 demo = dict(radius_effective=200, volfraction=0.2, radius_effective_pd=0.1, radius_effective_pd_n=40) 
     149demo = dict(effect_radius=200, volfraction=0.2, effect_radius_pd=0.1, effect_radius_pd_n=40) 
    150150oldname = 'HardsphereStructure' 
    151 oldpars = dict(radius_effective="effect_radius",radius_effective_pd="effect_radius_pd",radius_effective_pd_n="effect_radius_pd_n") 
     151oldpars = dict(effect_radius="effect_radius",effect_radius_pd="effect_radius_pd",effect_radius_pd_n="effect_radius_pd_n") 
    152152# Q=0.001 is in the Taylor series, low Q part, so add Q=0.1, assuming double precision sasview is correct 
    153153tests = [ 
    154         [ {'scale': 1.0, 'background' : 0.0, 'radius_effective' : 50.0, 'volfraction' : 0.2, 
    155            'radius_effective_pd' : 0}, [0.001,0.1], [0.209128,0.930587]] 
     154        [ {'scale': 1.0, 'background' : 0.0, 'effect_radius' : 50.0, 'volfraction' : 0.2, 
     155           'effect_radius_pd' : 0}, [0.001,0.1], [0.209128,0.930587]] 
    156156        ] 
    157157# ADDED by: RKH  ON: 16Mar2016  using equations from FISH as better than orig sasview, see notes above. Added Taylor expansions at small Q,  
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