Changeset 7874e80 in sasmodels

Timestamp:

Mar 21, 2016 8:53:06 AM (9 years ago)

Author:

richardh

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:

bf59527

Parents:

a2f9aa2 (diff), e56883e (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 branch 'master' of ​https://github.com/SasView/sasmodels

Files:

• example/sesans_parameters_sphere.py (modified) (1 diff)
• example/sesansfit.py (modified) (2 diffs)
• sasmodels/bumps_model.py (modified) (1 diff)
• sasmodels/compare.py (modified) (1 diff)
• sasmodels/convert.py (modified) (2 diffs)
• sasmodels/models/multi_shell.c (deleted)
• sasmodels/models/multi_shell.py (deleted)
• sasmodels/models/multilayer_vesicle.c (added)
• sasmodels/models/multilayer_vesicle.py (added)
• sasmodels/models/linear_pearls.py (modified) (5 diffs)
• sasmodels/models/pearl_necklace.py (modified) (5 diffs)

example/sesans_parameters_sphere.py

@@ -27 +27 @@
     "sld" : 7.0,
     "radius" : 1000,
-    "solvent_sld" : 1.0,
+    "sld_solvent" : 1.0,
 }
 

example/sesansfit.py

@@ -54 +54 @@
 
     # Load custom parameters, initial values and parameter ranges
+    pars = model.parameters().copy()
+    pars.update(custom_params)
     for k, v in custom_params.items():
+        if k not in pars:
+            par_error("Can't set parameter %r in model"%k, pars)
         setattr(model, k, v)
         model._parameter_names.append(k)
     for k, v in initial_vals.items():
-        param = model.parameters().get(k)
+        if k not in pars:
+            par_error("Can't get parameter %r from model"%k, pars)
+        param = pars[k]
         param.value = v
     for k, v in param_range.items():
-        param = model.parameters().get(k)
-        if param is not None:
-            param.range(*v)
+        if k not in pars:
+            par_error("Can't set range on parameter %r in model"%k, pars)
+        param = pars[k]
+        param.range(*v)
 
     if False: # for future implementation
@@ -73 +80 @@
         problem = FitProblem(M_sesans)
     return problem
+
+
+def par_error(msg, pars):
+    raise ValueError(msg+"\nAvailable parameters: %s"%", ".join(sorted(pars.keys())))

sasmodels/bumps_model.py

@@ -238 +238 @@
         Not Implemented.
         """
+        if self.data_type == "sesans":
+            np.savetxt(basename+".dat", np.array([self._data.x, self.theory()]).T)
         pass
 

sasmodels/compare.py

@@ -366 +366 @@
         composition_type, parts = model_info['composition']
         if composition_type == 'product':
-            from sas.models.MultiplicationModel import MultiplicationModel
+            from sas.sascalc.fit.MultiplicationModel import MultiplicationModel
             P, S = [get_model(p) for p in model_info['oldname']]
             model = MultiplicationModel(P, S)

sasmodels/convert.py

@@ -156 +156 @@
         elif name == 'vesicle':
             del oldpars['volfraction']
+        elif name == 'multilayer_vesicle':
+            del oldpars['volfraction']
 
     return oldpars
@@ -195 +197 @@
         elif name == 'vesicle':
             pars['volfraction'] = 1
+        elif name == 'multilayer_vesicle':
+            pars['volfraction'] = 1
             

sasmodels/models/linear_pearls.py

@@ -57 +57 @@
     ["edge_sep",    "Ang",      350.0, [0, inf],     "", "Length of the string segment - surface to surface"],
     ["num_pearls",  "",           3.0, [0, inf],     "", "Number of the pearls"],
-    ["pearl_sld",   "1e-6/Ang^2", 1.0, [-inf, inf],  "", "SLD of the pearl spheres"],
-    ["solvent_sld", "1e-6/Ang^2", 6.3, [-inf, inf],  "", "SLD of the solvent"],
+    ["sld",   "1e-6/Ang^2", 1.0, [-inf, inf],  "", "SLD of the pearl spheres"],
+    ["sld_solvent", "1e-6/Ang^2", 6.3, [-inf, inf],  "", "SLD of the solvent"],
     ]
 # pylint: enable=bad-whitespace, line-too-long
@@ -68 +68 @@
             edge_sep=350.0,
             num_pearls=3,
-            pearl_sld=1.0,
-            solvent_sld=6.3)
+            sld=1.0,
+            sld_solvent=6.3)
 
 oldname = "LinearPearlsModel"
 
 oldpars = dict(edge_sep='edge_separation',
-               pearl_sld='sld_pearl',
-               solvent_sld='sld_solv')
+               sld='sld_pearl',
+               sld_solvent='sld_solv')
 
 """
@@ -84 +84 @@
     [{'radius':      20.0,
       'num_pearls':   2.0,
-      'pearl_sld':    1.0,
-      'solvent_sld':  6.3,
+      'sld':    1.0,
+      'sld_solvent':  6.3,
       'edge_sep':   400.0,
      }, 0.001, 185.135],
@@ -92 +92 @@
     [{'radius':     120.0,
       'num_pearls':   5.0,
-      'pearl_sld':    2.0,
-      'solvent_sld':  2.3,
+      'sld':    2.0,
+      'sld_solvent':  2.3,
       'edge_sep':   100.0,
      }, 0.01, 45.4984],
@@ -99 +99 @@
     [{'radius':       7.0,
       'num_pearls':   2.0,
-      'pearl_sld':   10.0,
-      'solvent_sld': 99.3,
+      'sld':   10.0,
+      'sld_solvent': 99.3,
       'edge_sep':    20.0,
      }, 1.0, 0.632811],

sasmodels/models/pearl_necklace.py

@@ -13 +13 @@
 ----------
 
-The output of the scattering intensity function for the PearlNecklaceModel is
+The output of the scattering intensity function for the pearl_necklace is
 given by (Schweins, 2004)
 
@@ -58 +58 @@
 
 name = "pearl_necklace"
-title = "Colloidal spheres chained together with o preferential orientation"
+title = "Colloidal spheres chained together with no preferential orientation"
 description = """
 Calculate form factor for Pearl Necklace Model
@@ -76 +76 @@
 
 #             ["name", "units", default, [lower, upper], "type","description"],
-parameters = [["radius", "Angstrom", 80.0, [0, inf], "volume",
+parameters = [["radius", "Ang", 80.0, [0, inf], "volume",
                "Mean radius of the chained spheres"],
-              ["edge_separation", "Angstrom", 350.0, [0, inf], "volume",
+              ["edge_separation", "Ang", 350.0, [0, inf], "volume",
                "Mean separation of chained particles"],
-              ["string_thickness", "Angstrom", 2.5, [0, inf], "volume",
+              ["string_thickness", "Ang", 2.5, [0, inf], "volume",
                "Thickness of the chain linkage"],
               ["number_of_pearls", "none", 3, [0, inf], "volume",
-               "Mean number of pearls in each necklace"],
-              ["sld", "Angstrom^2", 1.0, [-inf, inf], "",
+               "Number of pearls in the necklace (must be integer)"],
+              ["sld", "1e-6/Ang^2", 1.0, [-inf, inf], "",
                "Scattering length density of the chained spheres"],
-              ["string_sld", "Angstrom^2", 1.0, [-inf, inf], "",
+              ["sld_string", "1e-6/Ang^2", 1.0, [-inf, inf], "",
                "Scattering length density of the chain linkage"],
-              ["solvent_sld", "Angstrom^2", 6.3, [-inf, inf], "",
+              ["sld_solvent", "1e-6/Ang^2", 6.3, [-inf, inf], "",
                "Scattering length density of the solvent"],
              ]
@@ -117 +117 @@
 # parameters for demo
 demo = dict(scale=1, background=0, radius=80.0, edge_separation=350.0,
-            number_of_pearls=3, sld=1, solvent_sld=6.3, string_sld=1,
+            number_of_pearls=3, sld=1, sld_solvent=6.3, sld_string=1,
             string_thickness=2.5,
             radius_pd=.2, radius_pd_n=5,
@@ -129 +129 @@
 oldname = 'PearlNecklaceModel'
 oldpars = dict(scale='scale', background='background', radius='radius',
-               number_of_pearls='num_pearls', solvent_sld='sld_solv',
+               number_of_pearls='num_pearls', sld_solvent='sld_solv',
                string_thickness='thick_string', sld='sld_pearl',
-               string_sld='sld_string', edge_separation='edge_separation')
+               sld_string='sld_string', edge_separation='edge_separation')
 
 tests = [[{}, 0.001, 17380.245], [{}, 'ER', 115.39502]]