Switch arguments in SFAverage.fromComposition.

It feels more natural to order SFAverage.fromComposition arguments as
(`composition`, `sftb`, `q`) and likewise fromStructure arguments as
(`structure`, `sftb`, `q`).

Author: pavoljuhas

diffpy/srreal/sfaverage.py

@@ -26,15 +26,15 @@
     from diffpy.srreal.scatteringfactortable import SFTXray
     xtb = SFTXray()
     qa = np.linspace(0, 25)
-    sfavg1 = SFAverage.fromComposition(xtb, {'Na' : 1, 'Cl' : 1}, qa)
-    sfavg2 = SFAverage.fromComposition(xtb, [('Mn', 1), ('O', 2)], qa)
+    sfavg1 = SFAverage.fromComposition({'Na' : 1, 'Cl' : 1}, xtb, qa)
+    sfavg2 = SFAverage.fromComposition([('Mn', 1), ('O', 2)], xtb, qa)
 
     from diffpy.Structure import loadStructure
     from diffpy.srreal.pdfcalculator import DebyePDFCalculator
     dpdfc = DebyePDFCalculator()
     dpdfc(loadStructure('rutile.cif'))
-    sfavg3 = SFAverage.fromStructure(dpdfc.scatteringfactortable,
-                                     dpdfc.getStructure(), dpdfc.qgrid)
+    sfavg3 = SFAverage.fromStructure(dpdfc.getStructure(),
+                                     dpdfc.scatteringfactortable, dpdfc.qgrid)
 """
 
 
@@ -76,18 +76,18 @@ class SFAverage(object):
     composition = None
 
     @classmethod
-    def fromStructure(cls, sftb, stru, q=0):
+    def fromStructure(cls, stru, sftb, q=0):
         """\
         Calculate average scattering factors from a structure object.
 
         Parameters
         ----------
-        sftb : ScatteringFactorTable
-            The ScatteringFactorTable object for looking up the values.
         stru : diffpy Structure or pyobjcryst Crystal or StructureAdapter
             The structure object that stores the atom species and their
             occupancies.  Can be any type with a registered conversion
             to the StructureAdapter class.
+        sftb : ScatteringFactorTable
+            The ScatteringFactorTable object for looking up the values.
         q : float or NumPy array (optional)
             The Q value in inverse Angstroms for which to lookup
             the scattering factor values.
@@ -105,7 +105,7 @@ def fromStructure(cls, sftb, stru, q=0):
         if hasattr(type(stru), 'composition'):
             composition = stru.composition
             if isinstance(composition, dict):
-                return cls.fromComposition(sftb, composition, q)
+                return cls.fromComposition(composition, sftb, q)
         # otherwise let's convert to a known structure type
         from diffpy.srreal.structureadapter import createStructureAdapter
         adpt = createStructureAdapter(stru)
@@ -114,21 +114,21 @@ def fromStructure(cls, sftb, stru, q=0):
             smbl = adpt.siteAtomType(i)
             cnt = adpt.siteOccupancy(i) * adpt.siteMultiplicity(i)
             composition[smbl] = composition.get(smbl, 0) + cnt
-        return cls.fromComposition(sftb, composition, q)
+        return cls.fromComposition(composition, sftb, q)
 
 
     @classmethod
-    def fromComposition(cls, sftb, composition, q=0):
+    def fromComposition(cls, composition, sftb, q=0):
         """\
         Calculate average scattering factors from atom concentrations.
 
         Parameters
         ----------
-        sftb : ScatteringFactorTable
-            The ScatteringFactorTable object for looking up the values.
         composition : dictionary or a list of (symbol, amount) pairs.
             The chemical composition for evaluating the average.  Atom
             symbols may repeat when it is a list of (symbol, amount) pairs.
+        sftb : ScatteringFactorTable
+            The ScatteringFactorTable object for looking up the values.
         q : float or NumPy array (optional)
             The Q value in inverse Angstroms for which to lookup
             the scattering factor values.

diffpy/srreal/tests/testsfaverage.py

@@ -30,7 +30,7 @@ def test_fromStructure_CdSe(self):
         """check SFAverage.fromStructure() for CdSe
         """
         cdse = loadDiffPyStructure('CdSe_cadmoselite.cif')
-        sfavg = SFAverage.fromStructure(self.sftx, cdse)
+        sfavg = SFAverage.fromStructure(cdse, self.sftx)
         fcd = self.sftx.lookup('Cd')
         fse = self.sftx.lookup('Se')
         self.assertTrue(isinstance(sfavg.f1sum, float))
@@ -39,29 +39,29 @@ def test_fromStructure_CdSe(self):
         self.assertEqual(4, sfavg.count)
         self.assertEqual(cdse.composition, sfavg.composition)
         qa = numpy.arange(0, 25, 0.1)
-        sfavg2 = SFAverage.fromStructure(self.sftx, cdse, qa)
+        sfavg2 = SFAverage.fromStructure(cdse, self.sftx, qa)
         self.assertTrue(isinstance(sfavg2.f1sum, numpy.ndarray))
         self.assertNotEqual(sfavg2.f1sum[0], sfavg2.f1sum[-1])
         self.assertEqual(sfavg.f1sum, sfavg2.f1sum[0])
         self.assertEqual(sfavg.f2sum, sfavg2.f2sum[0])
-        sfavg3 = SFAverage.fromStructure(self.sftn, cdse, qa)
+        sfavg3 = SFAverage.fromStructure(cdse, self.sftn, qa)
         self.assertEqual(sfavg3.f1sum[0], sfavg3.f1sum[-1])
         self.assertRaises(TypeError, SFAverage.fromStructure,
-                self.sftx, 'notastructure')
+                          'notastructure', self.sftx)
         return
 
 
     def test_fromComposition(self):
         """check SFAverage.fromComposition()
         """
-        sfavg1 = SFAverage.fromComposition(self.sftx, {'Na' : 1, 'Cl' : 1})
+        sfavg1 = SFAverage.fromComposition({'Na' : 1, 'Cl' : 1}, self.sftx)
         fm = ['Na', 0.25, 'Cl', 0.75, 'Cl', 0.25, 'Na', 0.5, 'Na', 0.25]
         smblcnts = zip(fm[0::2], fm[1::2])
-        sfavg2 = SFAverage.fromComposition(self.sftx, smblcnts)
+        sfavg2 = SFAverage.fromComposition(smblcnts, self.sftx)
         self.assertEqual(sfavg1.f1sum, sfavg2.f1sum)
         self.assertEqual(sfavg1.f2sum, sfavg2.f2sum)
         self.assertEqual(sfavg1.count, sfavg2.count)
-        sfempty = SFAverage.fromComposition(self.sftx, [])
+        sfempty = SFAverage.fromComposition([], self.sftx)
         self.assertEqual(0, sfempty.f1avg)
         self.assertEqual(0, sfempty.f2avg)
         self.assertEqual(0, sfempty.count)
@@ -85,7 +85,7 @@ def test_from_rutile(self):
         """
         rutile = loadObjCrystCrystal('rutile.cif')
         qa = numpy.arange(0, 25, 0.1)
-        sfavg = SFAverage.fromStructure(self.sftx, rutile, qa)
+        sfavg = SFAverage.fromStructure(rutile, self.sftx, qa)
         fti = self.sftx.lookup('Ti', qa)
         fo = self.sftx.lookup('O', qa)
         self.assertTrue(numpy.allclose((fti + 2 * fo) / 3.0, sfavg.f1avg))