Bug fix for python bindings for non-contiguous input vectors

When a non-contiguous numpy vector (e.g. a sliced view into a numpy array) is
used as an input argument to a bound function, the underlying C++ object does
not properly account for strides in the input array.  Use the pybind11 numpy
interface to handle this properly, while still allowing type conversion.

Author: arahlin

core/CMakeLists.txt

@@ -136,6 +136,7 @@ add_spt3g_test(timestrings)
 add_spt3g_test(testcomplexconv)
 add_spt3g_test(droporphanmetadata)
 add_spt3g_test(networktest SLOWTEST)
+add_spt3g_test(non_contiguous_vectors)
 add_spt3g_test(non_double_timestreams)
 add_spt3g_test(endprocessing)
 add_spt3g_test(lazyreader)

core/src/G3Vector.cxx

@@ -80,14 +80,6 @@ auto vector_from_python(const py::array_t<T> &buf) {
 	if (buf.ndim() != 1)
 		throw py::type_error("Only valid 1D buffers can be copied to a vector");
 
-	return std::make_shared<V>(buf.data(), buf.data() + buf.size());
-}
-
-template <typename V>
-auto time_vector_from_python(const py::array_t<G3TimeStamp> &buf) {
-	if (buf.ndim() != 1)
-		throw py::type_error("Only valid 1D buffers can be copied to a vector");
-
 	auto rbuf = buf.template unchecked<1>();
 	auto vec = std::make_shared<V>(rbuf.shape(0));
 
@@ -124,7 +116,7 @@ struct vector_buffer<G3Time, V, C, Args...> {
 	static void impl(C &cls) {
 		cls.def_buffer(&time_vector_buffer_info<V>);
 		cls.def(py::init([](const py::array &v) {
-			return time_vector_from_python<V>(v);
+			return vector_from_python<G3TimeStamp, V>(v);
 		}), "Constructor from numpy array");
 		py::implicitly_convertible<py::buffer, V>();
 	}

core/tests/non_contiguous_vectors.py

@@ -0,0 +1,13 @@
+from spt3g import core
+import numpy as np
+
+data = np.random.randn(10, 10)
+
+# check that vectors created from non-contiguous input arrays
+# store the correct elements
+
+vec = core.G3VectorDouble(data[:, 0])
+np.testing.assert_array_equal(np.asarray(vec), data[:, 0])
+
+vec = core.G3VectorDouble(data[0, :])
+np.testing.assert_array_equal(np.asarray(vec), data[0, :])