Merge branch 'fix-atom-crash-on-numpy-int'

* add conversion utility extractdouble
* use `extractdouble` to convert Atom attributes

Close #20.

Author: pavoljuhas

src/diffpy/srreal/structureconverters.py

@@ -142,7 +142,7 @@ def _fetchDiffPyStructureData(adpt, stru):
     aa = AdapterAtom()
     for a0 in stru:
         aa.atomtype = a0.element
-        aa.occupancy = float(a0.occupancy)
+        aa.occupancy = a0.occupancy
         aa.anisotropy = a0.anisotropy
         # copy fractional coordinates
         aa.xyz_cartn = a0.xyz

src/diffpy/srreal/tests/teststructureadapter.py

@@ -599,6 +599,42 @@ def test_uij_cartn(self):
         self.assertEqual(0.023, a.uc23)
         return
 
+    def test_xc_yc_zc(self):
+        'check Atom properties xc, yc, zc.'
+        a = self.a
+        a.xc, a.yc, a.zc = numpy.arange(1, 4)
+        self.assertEqual(1.0, a.xc)
+        self.assertEqual(2.0, a.yc)
+        self.assertEqual(3.0, a.zc)
+        return
+
+    def test_occupancy(self):
+        'check Atom.occupancy'
+        a = self.a
+        a.occupancy, = numpy.arange(1)
+        self.assertEqual(0.0, a.occupancy)
+        a.occupancy = numpy.float32(0.5)
+        self.assertEqual(0.5, a.occupancy)
+        return
+
+    def test_anisotropy(self):
+        'check Atom.anisotropy'
+        a = self.a
+        nptrue, npfalse = (numpy.arange(2) < 1)
+        a.anisotropy = nptrue
+        self.assertTrue(a.anisotropy)
+        a.anisotropy = npfalse
+        self.assertFalse(a.anisotropy)
+        return
+
+    def test_ucij(self):
+        'check Atom attributes u11, u22, etc.'
+        a = self.a
+        a.uc11, a.uc22, a.uc33, a.uc12, a.uc13, a.uc23 = numpy.arange(1, 7)
+        uijexp = [[1, 4, 5], [4, 2, 6], [5, 6, 3]]
+        self.assertTrue(numpy.array_equal(uijexp, a.uij_cartn))
+        return
+
 # End of class TestAtom
 
 # ----------------------------------------------------------------------------

src/extensions/srreal_converters.cpp

@@ -282,6 +282,25 @@ NumPyArray_DoublePtr extractNumPyDoubleArray(::boost::python::object& obj)
 }
 
 
+/// extract double with a support for numpy.int types
+double extractdouble(boost::python::object obj)
+{
+    using namespace boost;
+    python::extract<double> getx(obj);
+    if (getx.check())  return getx();
+    PyObject* pobj = obj.ptr();
+    if (PyArray_CheckScalar(pobj))
+    {
+        double x;
+        PyArray_CastScalarToCtype(pobj, &x,
+                PyArray_DescrFromType(NPY_DOUBLE));
+        return x;
+    }
+    // nothing worked, call getx which will raise an exception
+    return getx();
+}
+
+
 /// extract integer with a support for numpy.int types
 int extractint(boost::python::object obj)
 {

src/extensions/srreal_converters.hpp

@@ -395,6 +395,10 @@ extractQuantityType(::boost::python::object obj,
 NumPyArray_DoublePtr extractNumPyDoubleArray(::boost::python::object& obj);
 
 
+/// extract double with a support for numpy numeric types
+double extractdouble(::boost::python::object obj);
+
+
 /// extract integer with a support for numpy.int types
 int extractint(::boost::python::object obj);
 

src/extensions/wrap_AtomicStructureAdapter.cpp

@@ -67,8 +67,11 @@ view to the data in C++ class.  Do not resize or reshape.\n\
 const char* doc_Atom_init_copy = "\
 Make a deep copy of an existing Atom.\n\
 ";
-const char* doc_Atom_xic = "Vector element in xyz_cartn";
-const char* doc_Atom_uijc = "Matrix element in uij_cartn";
+const char* doc_Atom_xic = "Vector element in xyz_cartn.";
+const char* doc_Atom_occ = "Fractional occupancy of this atom.";
+const char* doc_Atom_anisotropy =
+    "Boolean flag for anisotropic displacements.";
+const char* doc_Atom_uijc = "Matrix element in uij_cartn.";
 
 // class AtomicStructureAdapter
 
@@ -270,28 +273,55 @@ void set_uij_cartn(Atom& a, object& value)
 }
 
 
-double get_xc(const Atom& a)  { return a.xyz_cartn[0]; }
-void set_xc(Atom& a, double value)  { a.xyz_cartn[0] = value; }
-double get_yc(const Atom& a)  { return a.xyz_cartn[1]; }
-void set_yc(Atom& a, double value)  { a.xyz_cartn[1] = value; }
-double get_zc(const Atom& a)  { return a.xyz_cartn[2]; }
-void set_zc(Atom& a, double value)  { a.xyz_cartn[2] = value; }
-
-double get_uc11(const Atom& a)  { return a.uij_cartn(0, 0); }
-void set_uc11(Atom& a, double value)  { a.uij_cartn(0, 0) = value; }
-double get_uc22(const Atom& a)  { return a.uij_cartn(1, 1); }
-void set_uc22(Atom& a, double value)  { a.uij_cartn(1, 1) = value; }
-double get_uc33(const Atom& a)  { return a.uij_cartn(2, 2); }
-void set_uc33(Atom& a, double value)  { a.uij_cartn(2, 2) = value; }
-double get_uc12(const Atom& a)  { return a.uij_cartn(0, 1); }
-void set_uc12(Atom& a, double value) {
-    a.uij_cartn(0, 1) = a.uij_cartn(1, 0) = value; }
-double get_uc13(const Atom& a)  { return a.uij_cartn(0, 2); }
-void set_uc13(Atom& a, double value) {
-    a.uij_cartn(0, 2) = a.uij_cartn(2, 0) = value; }
-double get_uc23(const Atom& a)  { return a.uij_cartn(1, 2); }
-void set_uc23(Atom& a, double value) {
-    a.uij_cartn(1, 2) = a.uij_cartn(2, 1) = value; }
+template <const int i>
+double get_xyz(const Atom& a)
+{
+    return a.xyz_cartn[i];
+}
+
+template <const int i>
+void set_xyz(Atom& a, object value)
+{
+    a.xyz_cartn[i] = extractdouble(value);
+}
+
+
+double get_occ(const Atom& a)
+{
+    return a.occupancy;
+}
+
+void set_occ(Atom& a, object value)
+{
+    a.occupancy = extractdouble(value);
+}
+
+
+bool get_anisotropy(const Atom& a)
+{
+    return a.anisotropy;
+}
+
+void set_anisotropy(Atom& a, object value)
+{
+    a.anisotropy = bool(value);
+}
+
+
+template <const int i, const int j>
+double get_uc(const Atom& a)
+{
+    assert(i <= j);
+    return a.uij_cartn(i, j);
+}
+
+template <const int i, const int j>
+void set_uc(Atom& a, object value)
+{
+    assert(i <= j);
+    a.uij_cartn(i, j) = extractdouble(value);
+    if (i != j)  a.uij_cartn(j, i) = a.uij_cartn(i, j);
+}
 
 // template wrapper class for overloading of clone and _customPQConfig
 
@@ -524,20 +554,21 @@ void wrap_AtomicStructureAdapter()
         .add_property("xyz_cartn",
                 atom_class.attr("_get_xyz_cartn"),
                 set_xyz_cartn)
-        .add_property("xc", get_xc, set_xc, doc_Atom_xic)
-        .add_property("yc", get_yc, set_yc, doc_Atom_xic)
-        .add_property("zc", get_zc, set_zc, doc_Atom_xic)
-        .def_readwrite("occupancy", &Atom::occupancy)
-        .def_readwrite("anisotropy", &Atom::anisotropy)
+        .add_property("xc", get_xyz<0>, set_xyz<0>, doc_Atom_xic)
+        .add_property("yc", get_xyz<1>, set_xyz<1>, doc_Atom_xic)
+        .add_property("zc", get_xyz<2>, set_xyz<2>, doc_Atom_xic)
+        .add_property("occupancy", get_occ, set_occ, doc_Atom_occ)
+        .add_property("anisotropy", get_anisotropy, set_anisotropy,
+                doc_Atom_anisotropy)
         .add_property("uij_cartn",
                 atom_class.attr("_get_uij_cartn"),
                 set_uij_cartn)
-        .add_property("uc11", get_uc11, set_uc11, doc_Atom_uijc)
-        .add_property("uc22", get_uc22, set_uc22, doc_Atom_uijc)
-        .add_property("uc33", get_uc33, set_uc33, doc_Atom_uijc)
-        .add_property("uc12", get_uc12, set_uc12, doc_Atom_uijc)
-        .add_property("uc13", get_uc13, set_uc13, doc_Atom_uijc)
-        .add_property("uc23", get_uc23, set_uc23, doc_Atom_uijc)
+        .add_property("uc11", get_uc<0, 0>, set_uc<0, 0>, doc_Atom_uijc)
+        .add_property("uc22", get_uc<1, 1>, set_uc<1, 1>, doc_Atom_uijc)
+        .add_property("uc33", get_uc<2, 2>, set_uc<2, 2>, doc_Atom_uijc)
+        .add_property("uc12", get_uc<0, 1>, set_uc<0, 1>, doc_Atom_uijc)
+        .add_property("uc13", get_uc<0, 2>, set_uc<0, 2>, doc_Atom_uijc)
+        .add_property("uc23", get_uc<1, 2>, set_uc<1, 2>, doc_Atom_uijc)
         .def_pickle(SerializationPickleSuite<Atom,DICT_IGNORE>())
         ;