Changeset a006b63 in sasmodels

Timestamp:

Feb 18, 2015 3:04:51 PM (9 years ago)

Author:

jhbakker

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:

ff58110, e166cb9, 9c117a2

Parents:

0ac3db5 (diff), ea7ffce (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:

• sasmodels/generate.py (modified) (1 diff)
• sasmodels/model_test.py (added)
• sasmodels/models/cylinder.py (modified) (4 diffs)
• sasmodels/models/fcc.c (added)
• sasmodels/models/fcc.py (added)
• sasmodels/models/parallelepiped.c (added)
• sasmodels/models/parallelepiped.py (added)
• sasmodels/sasview_model.py (modified) (3 diffs)
• example/sesansfit.py (modified) (2 diffs)
• sasmodels/bumps_model.py (modified) (5 diffs)

sasmodels/generate.py

@@ -722 +722 @@
         parameters = COMMON_PARAMETERS + kernel_module.parameters,
         source = getattr(kernel_module, 'source', []),
+        oldname = kernel_module.oldname,
+        oldpars = kernel_module.oldpars,
         )
     # Fill in attributes which default to None

sasmodels/models/cylinder.py

@@ -43 +43 @@
 .. figure:: img/orientation2.jpg
 
-    Examples of the angles for oriented pp against the detector plane.
+    Examples of the angles for oriented cylinders against the detector plane.
 
 NB: The 2nd virial coefficient of the cylinder is calculated based on the
@@ -113 +113 @@
 title = "Right circular cylinder with uniform scattering length density."
 description = """
-     P(q)= 2*(sld - solvent_sld)*V*sin(qLcos(alpha/2))
-            /[qLcos(alpha/2)]*J1(qRsin(alpha/2))/[qRsin(alpha)]
+     f(q,alpha) = 2*(sld - solvent_sld)*V*sin(qLcos(alpha/2))
+                /[qLcos(alpha/2)]*J1(qRsin(alpha/2))/[qRsin(alpha)]
 
-            P(q,alpha)= scale/V*f(q)^(2)+background
+            P(q,alpha)= scale/V*f(q,alpha)^(2)+background
             V: Volume of the cylinder
             R: Radius of the cylinder
@@ -125 +125 @@
             :the ouput is P(q)=scale/V*integral
             from pi/2 to zero of...
-            f(q)^(2)*sin(alpha)*dalpha + background
+            f(q,alpha)^(2)*sin(alpha)*dalpha + background
 """
 
@@ -169 +169 @@
 oldpars=dict(theta='cyl_theta', phi='cyl_phi', sld='sldCyl', solvent_sld='sldSolv')
 
+
+# test values:
+# [
+#   [ {parameters}, q, I(q)],
+#   [ {parameters}, [q], [I(q)] ],
+#   [ {parameters}, [q1, q2, ...], [I(q1), I(q2), ...]],
+
+#   [ {parameters}, (qx, qy), I(qx, Iqy)],
+#   [ {parameters}, [(qx1, qy1), (qx2, qy2), ...], [I(qx1,qy1), I(qx2,qy2), ...],
+#   ...
+# ]
+# Precision defaults to 7 digits (relative) for single, 14 for double
+# May want a limited precision version that checks for 8-n or 15-n digits respectively
+tests = [
+    [{},  0.2, 0.041761386790780453],
+    [{'theta':10.0, 'phi':10.0}, [0.2], [0.041761386790780453]],
+    [{'theta':10.0, 'phi':10.0}, (0.2, 2.5), 0.038176446608393366],
+    [{'theta':10.0, 'phi':10.0}, [(0.2, 2.5)], [0.038176446608393366]],
+    ]
+

sasmodels/sasview_model.py

@@ -32 +32 @@
 
 
-def make_class(kernel_module, dtype='single'):
+def make_class(kernel_module, dtype='single', namestyle='name'):
     """
     Load the sasview model defined in *kernel_module*.
 
     Returns a class that can be used directly as a sasview model.
+
+    Defaults to using the new name for a model. Setting namestyle='name'
+    will produce a class with a name compatible with SasView
     """
     model =  load_model(kernel_module, dtype=dtype)
@@ -42 +45 @@
         SasviewModel.__init__(self, model)
     attrs = dict(__init__=__init__)
-    ConstructedModel = type(model.info['name'],  (SasviewModel,), attrs)
+    ConstructedModel = type(model.info[namestyle],  (SasviewModel,), attrs)
     return ConstructedModel
 
@@ -54 +57 @@
 
         self.name = model.info['name']
+        self.oldname = model.info['oldname']
         self.description = model.info['description']
         self.category = None

example/sesansfit.py

@@ -6 +6 @@
 
 
-radius = 1000
-if False: # fix when data loader exists
-    from sasmodels.dataloader import load_sesans, load_sans
-    data = load_sesans('mydatfile.pz')
-    sans_data = load_sans('mysansfile.xml')
+if True: # fix when data loader exists
+#    from sas.dataloader.readers\
+    from sas.dataloader.loader import Loader
+    loader=Loader()
+    data=loader.load('testsasview1.ses')
+    
+#    data = load_sesans('mydatfile.pz')
+#    sans_data = load_sans('mysansfile.xml')
+
 else:
     SElength = np.linspace(0, 2400, 61) # [A]
@@ -16 +20 @@
     err_data = np.ones_like(SElength)*0.03
 
-    class SesansData:
+    class SESANSData1D:
         #q_zmax = 0.23 # [A^-1]
-        q_zmax = 0.1 # [A^-1]
-        SElength = np.linspace(0, 2400, 61) # [A]
-        Rmax = 3*radius # [A]
-        wavelength = 2e-10 # [m]
+        zacceptance = 0.1 # [A^-1]
+        lam = 2e-10 # [m]
         thickness = 0.2 # [cm]
-        SElength = SElength
-        data = data
-        err_data = err_data
+        x = SElength
+        y = data
+        dy = err_data
     data = SesansData()
+print dir(data)
+
+radius = 1000
+data.Rmax = 3*radius # [A]
 
 phi = Parameter(0.1, name="phi")

sasmodels/bumps_model.py

@@ -217 +217 @@
 def _plot_sesans(data, theory, view):
     import matplotlib.pyplot as plt
-    resid = (theory - data.data)/data.err_data
+    resid = (theory - data.y)/data.dy
     plt.subplot(121)
-    plt.errorbar(data.SElength, data.data, yerr=data.err_data)
-    plt.plot(data.SElength, theory, '-', hold=True)
+    plt.errorbar(data.x, data.y, yerr=data.dy)
+    plt.plot(data.x, theory, '-', hold=True)
     plt.xlabel('spin echo length (A)')
     plt.ylabel('polarization')
     plt.subplot(122)
-    plt.plot(data.SElength, resid, 'x')
+    plt.plot(data.x, resid, 'x')
     plt.xlabel('spin echo length (A)')
     plt.ylabel('residuals')
@@ -267 +267 @@
         self.model = model
         self.cutoff = cutoff
-        if hasattr(data, 'SElength'):
+# TODO       if  isinstance(data,SESANSData1D)        
+        if hasattr(data, 'lam'):
             self.data_type = 'sesans'
         elif hasattr(data, 'qx_data'):
@@ -278 +279 @@
         # interpret data
         if self.data_type == 'sesans':
-            q = sesans.make_q(data.q_zmax, data.Rmax)
+            q = sesans.make_q(data.sample.zacceptance, data.Rmax)
             self.index = slice(None,None)
-            self.iq = data.data
-            self.diq = data.err_data
+            self.iq = data.y
+            self.diq = data.dy
             self._theory = np.zeros_like(q)
             q_vectors = [q]
@@ -353 +354 @@
             #self._theory[:] = self._fn.eval(pars, pd_pars)
             if self.data_type == 'sesans':
-                P = sesans.hankel(self.data.SElength, self.data.wavelength,
-                                  self.data.thickness, self._fn_inputs[0],
+                P = sesans.hankel(self.data.x, self.data.lam,
+                                  self.data.sample.thickness/10, self._fn_inputs[0],
                                   self._theory)
                 self._cache['theory'] = P
@@ -401 +402 @@
             self.data.data[self.index] = y
         elif self.data_type == 'sesans':
-            self.data.data[self.index] = y
+            self.data.y[self.index] = y
         else:
             raise ValueError("Unknown model")