Changes in / [54954e1:6824af5] in sasmodels

Files:

• example/fit_sesans.py (added)
• example/sesans_parameters_css-hs.py (modified) (3 diffs)
• example/sesans_parameters_sphere.py (modified) (2 diffs)
• example/sesans_script_css-hs.py (deleted)
• example/sesans_script_sphere.py (deleted)
• example/sesansfit.py (modified) (5 diffs)
• sasmodels/data.py (modified) (2 diffs)
• sasmodels/models/hardsphere.py (modified) (6 diffs)

example/sesans_parameters_css-hs.py

@@ -8 +8 @@
 # Enter the model name to use
 model_name = "core_shell_sphere*hardsphere"
+
+# DO NOT MODIFY THIS LINE
+model = sesansfit.get_bumps_model(model_name)
 
 # Enter any custom parameters
@@ -19 +22 @@
 # Initial parameter values (if other than defaults)
 initial_vals = {
-    "scale" : 0.09,
     "core_sld" : 1.0592,
     "solvent_sld" : 2.88,
-    "shell_sld" : 2.88,
     "radius" : 890,
-    "thickness" : 130,
-    "volfraction" : 0.45
+    "thickness" : 130
 }
 
@@ -36 +36 @@
 }
 
+# Constraints
+# model.param_name = f(other params)
+# EXAMPLE: model.scale = model.radius*model.radius*(1 - phi) - where radius and scale are model functions and phi is
+# a custom parameter
+model.scale = phi*(1-phi)
+model.volfraction = phi
+model.shell_sld = pen*2.88
+
 # Send to the fitting engine
 problem = sesansfit.sesans_fit(sesans_file, model_name, initial_vals, custom_params, param_range)

example/sesans_parameters_sphere.py

@@ -9 +9 @@
 model_name = "sphere"
 
+# DO NOT MODIFY THIS LINE
+model = sesansfit.get_bumps_model(model_name)
+
 # Enter any custom parameters
+# name = Parameter(initial_value, name='name')
 phi = Parameter(0.10, name='phi')
+# Add the parameters to this list that should be displayed in the fitting window
 custom_params = {"phi" : phi}
 
-# SESANS data file
+# SESANS data file name
 sesans_file = "sphere.ses"
 
 # Initial parameter values (if other than defaults)
+# "model_parameter_name" : value
 initial_vals = {
-    "scale" : phi*(1 - phi),
     "sld" : 7.0,
+    "radius" : 1000,
     "solvent_sld" : 1.0,
-    "radius" : 1000,
 }
 
 # Ranges for parameters if other than default
+# "model_parameter_name" : [min, max]
 param_range = {
     "phi" : [0.001, 0.5],
@@ -30 +36 @@
 }
 
+# Constraints
+# model.param_name = f(other params)
+# EXAMPLE: model.scale = model.radius*model.radius*(1 - phi) - where radius and scale are model functions and phi is
+# a custom parameter
+model.scale = phi*(1-phi)
+
 # Send to the fitting engine
-problem = sesansfit.sesans_fit(sesans_file, model_name, initial_vals, custom_params, param_range)
+# DO NOT MODIFY THIS LINE
+problem = sesansfit.sesans_fit(sesans_file, model, initial_vals, custom_params, param_range)
+

example/sesansfit.py

@@ -1 @@
-#TODO: Convert units properly (nm -> A)
-#TODO: Implement constraints
-
 from bumps.names import *
-from sasmodels import core, bumps_model
+from sasmodels import core, bumps_model, sesans
 
 HAS_CONVERTER = True
@@ -11 +8 @@
     HAS_CONVERTER = False
 
-def sesans_fit(file, model_name, initial_vals={}, custom_params={}, param_range=[]):
+def get_bumps_model(model_name):
+    kernel = core.load_model(model_name)
+    model = bumps_model.Model(kernel)
+    return model
+
+def sesans_fit(file, model, initial_vals={}, custom_params={}, param_range=[]):
     """
-
     @param file: SESANS file location
-    @param model_name: model name string - can be model, model_1 * model_2, and/or model_1 + model_2
+    @param model: Bumps model object or model name - can be model, model_1 * model_2, and/or model_1 + model_2
     @param initial_vals: dictionary of {param_name : initial_value}
     @param custom_params: dictionary of {custom_parameter_name : Parameter() object}
     @param param_range: dictionary of {parameter_name : [minimum, maximum]}
+    @param constraints: dictionary of {parameter_name : constraint}
     @return: FitProblem for Bumps usage
     """
@@ -29 +31 @@
             default_unit = "A"
             data_conv_q = Converter(data._xunit)
+            for x in data.x:
+                print x
             data.x = data_conv_q(data.x, units=default_unit)
+            for x in data.x:
+                print x
             data._xunit = default_unit
 
@@ -51 +57 @@
         data = SESANSData1D()
 
-    radius = 1000
+    if "radius" in initial_vals:
+        radius = initial_vals.get("radius")
+    else:
+        radius = 1000
     data.Rmax = 3*radius # [A]
 
-    kernel = core.load_model(model_name)
-    model = bumps_model.Model(kernel)
+    if isinstance(model, basestring):
+        model = get_bumps_model(model)
 
-    # Load custom parameters, initial values and parameter constraints
+    # Load custom parameters, initial values and parameter ranges
     for k, v in custom_params.items():
         setattr(model, k, v)
@@ -69 +78 @@
             setattr(param.bounds, "limits", v)
 
-    if False: # have sans data
+    if False: # for future implementation
         M_sesans = bumps_model.Experiment(data=data, model=model)
         M_sans = bumps_model.Experiment(data=sans_data, model=model)

sasmodels/data.py

@@ -440 +440 @@
 
     if use_data or use_theory:
+        is_tof = np.any(data.lam!=data.lam[0])
         if num_plots > 1:
             plt.subplot(1, num_plots, 1)
         if use_data:
-            plt.errorbar(data.x, data.y, yerr=data.dy)
+            if is_tof:
+                plt.errorbar(data.x, np.log(data.y)/(data.lam*data.lam), yerr=data.dy/data.y/(data.lam*data.lam))
+            else:
+                plt.errorbar(data.x, data.y, yerr=data.dy)
         if theory is not None:
-            plt.plot(data.x, theory, '-', hold=True)
+            if is_tof:
+                plt.plot(data.x, np.log(theory)/(data.lam*data.lam), '-', hold=True)
+            else:
+                plt.plot(data.x, theory, '-', hold=True)
         if limits is not None:
             plt.ylim(*limits)
-        plt.xlabel('spin echo length (nm)')
-        plt.ylabel('polarization (P/P0)')
+
+        plt.xlabel('spin echo length ({})'.format(data._xunit))
+        if is_tof:
+            plt.ylabel('(Log (P/P$_0$))/$\lambda^2$')
+        else:
+            plt.ylabel('polarization (P/P0)')
+
 
     if resid is not None:
@@ -455 +467 @@
             plt.subplot(1, num_plots, (use_data or use_theory) + 1)
         plt.plot(data.x, resid, 'x')
-        plt.xlabel('spin echo length (nm)')
+        plt.xlabel('spin echo length ({})'.format(data._xunit))
         plt.ylabel('residuals (P/P0)')
 

sasmodels/models/hardsphere.py

@@ -7 +7 @@
 the maths needs to be modified (no \Beta(Q) correction yet in sasview).
 
-radius_effective is the effective hard sphere radius.
+effect_radius is the effective hard sphere radius.
 volfraction is the volume fraction occupied by the spheres.
 
@@ -53 +53 @@
         systems. Though strictly the maths needs to be modified -
     which sasview does not do yet.
-    radius_effective is the hard sphere radius
+    effect_radius is the hard sphere radius
     volfraction is the volume fraction occupied by the spheres.
 """
@@ -60 +60 @@
 
 #             ["name", "units", default, [lower, upper], "type","description"],
-parameters = [["radius_effective", "Ang", 50.0, [0, inf], "volume",
+parameters = [["effect_radius", "Ang", 50.0, [0, inf], "volume",
                "effective radius of hard sphere"],
               ["volfraction", "", 0.2, [0, 0.74], "",
@@ -75 +75 @@
       double D,A,B,G,X,X2,X4,S,C,FF,HARDSPH;
 
-      if(fabs(radius_effective) < 1.E-12) {
+      if(fabs(effect_radius) < 1.E-12) {
                HARDSPH=1.0;
                return(HARDSPH);
@@ -84 +84 @@
       A= (1.+2.*volfraction)*D;
       A *=A;
-      X=fabs(q*radius_effective*2.0);
+      X=fabs(q*effect_radius*2.0);
 
       if(X < 5.E-06) {
@@ -147 +147 @@
 # VR defaults to 1.0
 
-demo = dict(radius_effective=200, volfraction=0.2, radius_effective_pd=0.1, radius_effective_pd_n=40)
+demo = dict(effect_radius=200, volfraction=0.2, effect_radius_pd=0.1, effect_radius_pd_n=40)
 oldname = 'HardsphereStructure'
-oldpars = dict(radius_effective="effect_radius",radius_effective_pd="effect_radius_pd",radius_effective_pd_n="effect_radius_pd_n")
+oldpars = dict(effect_radius="effect_radius",effect_radius_pd="effect_radius_pd",effect_radius_pd_n="effect_radius_pd_n")
 # Q=0.001 is in the Taylor series, low Q part, so add Q=0.1, assuming double precision sasview is correct
 tests = [
-        [ {'scale': 1.0, 'background' : 0.0, 'radius_effective' : 50.0, 'volfraction' : 0.2,
-           'radius_effective_pd' : 0}, [0.001,0.1], [0.209128,0.930587]]
+        [ {'scale': 1.0, 'background' : 0.0, 'effect_radius' : 50.0, 'volfraction' : 0.2,
+           'effect_radius_pd' : 0}, [0.001,0.1], [0.209128,0.930587]]
         ]
 # ADDED by: RKH  ON: 16Mar2016  using equations from FISH as better than orig sasview, see notes above. Added Taylor expansions at small Q,