Changeset 6824af5 in sasmodels for example

Timestamp:

Mar 17, 2016 10:48:04 AM (8 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:

8898d0f, bdb653c

Parents:

84db7a5 (diff), 54954e1 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge remote-tracking branch 'origin/master'

Location:

example

Files:

• sesansfit.sh (modified) (1 diff, 1 prop)
• fit_sesans.py (added)
• sesans_parameters_css-hs.py (modified) (3 diffs)
• sesans_parameters_sphere.py (modified) (2 diffs)
• sesans_script_css-hs.py (deleted)
• sesans_script_sphere.py (deleted)
• sesansfit.py (modified) (5 diffs)

example/sesansfit.sh

@@ -8 +8 @@
 set -x
 
-python -m bumps.cli $*
+pythonw -m bumps.cli $*

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)