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pybind11/tests/test_numpy_array.cpp
Nick Cullen 503ff2a6fb
view for numpy arrays (#987) 
* reshape

* more tests

* Update numpy.h

* Update test_numpy_array.py

* array view

* test

* Update test_numpy_array.cpp

* Update numpy.h

* Update numpy.h

* Update test_numpy_array.cpp

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix merge bug

* Make clang-tidy happy

* Add xfail for PyPy

* Fix casting issue

* Fix formatting

* Apply clang-tidy

* Address reviews on additional tests

* Fix ordering

* Do a little more reordering

* Fix typo

* Try improving tests

* Fix error in reshape

* Add one more reshape test

* Fix bugs and add test

* Relax test

* streamlining new tests; removing a few stray msg

* Fix style revert

* Fix clang-tidy

* Misc tweaks:
* Comment: matching style in file (///), responsibility sentence, consistent punctuation.
* Replacing `unsigned char` with `uint8_t` for max consistency.
* Removing `1` from `array_view1` because there is only one.

* Partial clang-format-diff.

Co-authored-by: ncullen93 <ncullen.th@dartmouth.edu>
Co-authored-by: NC Cullen <nicholas.c.cullen.th@dartmouth.edu>
Co-authored-by: Aaron Gokaslan <skylion.aaron@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Ralf Grosse-Kunstleve <rwgk@google.com>
2021-08-26 14:11:01 -07:00

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/*
tests/test_numpy_array.cpp -- test core array functionality
Copyright (c) 2016 Ivan Smirnov <i.s.smirnov@gmail.com>
All rights reserved. Use of this source code is governed by a
BSD-style license that can be found in the LICENSE file.
*/
#include "pybind11_tests.h"
#include <pybind11/numpy.h>
#include <pybind11/stl.h>
#include <cstdint>
#include <utility>
// Size / dtype checks.
struct DtypeCheck {
py::dtype numpy{};
py::dtype pybind11{};
};
template <typename T>
DtypeCheck get_dtype_check(const char* name) {
py::module_ np = py::module_::import("numpy");
DtypeCheck check{};
check.numpy = np.attr("dtype")(np.attr(name));
check.pybind11 = py::dtype::of<T>();
return check;
}
std::vector<DtypeCheck> get_concrete_dtype_checks() {
return {
// Normalization
get_dtype_check<std::int8_t>("int8"),
get_dtype_check<std::uint8_t>("uint8"),
get_dtype_check<std::int16_t>("int16"),
get_dtype_check<std::uint16_t>("uint16"),
get_dtype_check<std::int32_t>("int32"),
get_dtype_check<std::uint32_t>("uint32"),
get_dtype_check<std::int64_t>("int64"),
get_dtype_check<std::uint64_t>("uint64")
};
}
struct DtypeSizeCheck {
std::string name{};
int size_cpp{};
int size_numpy{};
// For debugging.
py::dtype dtype{};
};
template <typename T>
DtypeSizeCheck get_dtype_size_check() {
DtypeSizeCheck check{};
check.name = py::type_id<T>();
check.size_cpp = sizeof(T);
check.dtype = py::dtype::of<T>();
check.size_numpy = check.dtype.attr("itemsize").template cast<int>();
return check;
}
std::vector<DtypeSizeCheck> get_platform_dtype_size_checks() {
return {
get_dtype_size_check<short>(),
get_dtype_size_check<unsigned short>(),
get_dtype_size_check<int>(),
get_dtype_size_check<unsigned int>(),
get_dtype_size_check<long>(),
get_dtype_size_check<unsigned long>(),
get_dtype_size_check<long long>(),
get_dtype_size_check<unsigned long long>(),
};
}
// Arrays.
using arr = py::array;
using arr_t = py::array_t<uint16_t, 0>;
static_assert(std::is_same<arr_t::value_type, uint16_t>::value, "");
template<typename... Ix> arr data(const arr& a, Ix... index) {
return arr(a.nbytes() - a.offset_at(index...), (const uint8_t *) a.data(index...));
}
template<typename... Ix> arr data_t(const arr_t& a, Ix... index) {
return arr(a.size() - a.index_at(index...), a.data(index...));
}
template<typename... Ix> arr& mutate_data(arr& a, Ix... index) {
auto ptr = (uint8_t *) a.mutable_data(index...);
for (py::ssize_t i = 0; i < a.nbytes() - a.offset_at(index...); i++)
ptr[i] = (uint8_t) (ptr[i] * 2);
return a;
}
template<typename... Ix> arr_t& mutate_data_t(arr_t& a, Ix... index) {
auto ptr = a.mutable_data(index...);
for (py::ssize_t i = 0; i < a.size() - a.index_at(index...); i++)
ptr[i]++;
return a;
}
template<typename... Ix> py::ssize_t index_at(const arr& a, Ix... idx) { return a.index_at(idx...); }
template<typename... Ix> py::ssize_t index_at_t(const arr_t& a, Ix... idx) { return a.index_at(idx...); }
template<typename... Ix> py::ssize_t offset_at(const arr& a, Ix... idx) { return a.offset_at(idx...); }
template<typename... Ix> py::ssize_t offset_at_t(const arr_t& a, Ix... idx) { return a.offset_at(idx...); }
template<typename... Ix> py::ssize_t at_t(const arr_t& a, Ix... idx) { return a.at(idx...); }
template<typename... Ix> arr_t& mutate_at_t(arr_t& a, Ix... idx) { a.mutable_at(idx...)++; return a; }
#define def_index_fn(name, type) \
sm.def(#name, [](type a) { return name(a); }); \
sm.def(#name, [](type a, int i) { return name(a, i); }); \
sm.def(#name, [](type a, int i, int j) { return name(a, i, j); }); \
sm.def(#name, [](type a, int i, int j, int k) { return name(a, i, j, k); });
template <typename T, typename T2> py::handle auxiliaries(T &&r, T2 &&r2) {
if (r.ndim() != 2) throw std::domain_error("error: ndim != 2");
py::list l;
l.append(*r.data(0, 0));
l.append(*r2.mutable_data(0, 0));
l.append(r.data(0, 1) == r2.mutable_data(0, 1));
l.append(r.ndim());
l.append(r.itemsize());
l.append(r.shape(0));
l.append(r.shape(1));
l.append(r.size());
l.append(r.nbytes());
return l.release();
}
// note: declaration at local scope would create a dangling reference!
static int data_i = 42;
TEST_SUBMODULE(numpy_array, sm) {
try { py::module_::import("numpy"); }
catch (...) { return; }
// test_dtypes
py::class_<DtypeCheck>(sm, "DtypeCheck")
.def_readonly("numpy", &DtypeCheck::numpy)
.def_readonly("pybind11", &DtypeCheck::pybind11)
.def("__repr__", [](const DtypeCheck& self) {
return py::str("<DtypeCheck numpy={} pybind11={}>").format(
self.numpy, self.pybind11);
});
sm.def("get_concrete_dtype_checks", &get_concrete_dtype_checks);
py::class_<DtypeSizeCheck>(sm, "DtypeSizeCheck")
.def_readonly("name", &DtypeSizeCheck::name)
.def_readonly("size_cpp", &DtypeSizeCheck::size_cpp)
.def_readonly("size_numpy", &DtypeSizeCheck::size_numpy)
.def("__repr__", [](const DtypeSizeCheck& self) {
return py::str("<DtypeSizeCheck name='{}' size_cpp={} size_numpy={} dtype={}>").format(
self.name, self.size_cpp, self.size_numpy, self.dtype);
});
sm.def("get_platform_dtype_size_checks", &get_platform_dtype_size_checks);
// test_array_attributes
sm.def("ndim", [](const arr& a) { return a.ndim(); });
sm.def("shape", [](const arr& a) { return arr(a.ndim(), a.shape()); });
sm.def("shape", [](const arr& a, py::ssize_t dim) { return a.shape(dim); });
sm.def("strides", [](const arr& a) { return arr(a.ndim(), a.strides()); });
sm.def("strides", [](const arr& a, py::ssize_t dim) { return a.strides(dim); });
sm.def("writeable", [](const arr& a) { return a.writeable(); });
sm.def("size", [](const arr& a) { return a.size(); });
sm.def("itemsize", [](const arr& a) { return a.itemsize(); });
sm.def("nbytes", [](const arr& a) { return a.nbytes(); });
sm.def("owndata", [](const arr& a) { return a.owndata(); });
// test_index_offset
def_index_fn(index_at, const arr&);
def_index_fn(index_at_t, const arr_t&);
def_index_fn(offset_at, const arr&);
def_index_fn(offset_at_t, const arr_t&);
// test_data
def_index_fn(data, const arr&);
def_index_fn(data_t, const arr_t&);
// test_mutate_data, test_mutate_readonly
def_index_fn(mutate_data, arr&);
def_index_fn(mutate_data_t, arr_t&);
def_index_fn(at_t, const arr_t&);
def_index_fn(mutate_at_t, arr_t&);
// test_make_c_f_array
sm.def("make_f_array", [] { return py::array_t<float>({ 2, 2 }, { 4, 8 }); });
sm.def("make_c_array", [] { return py::array_t<float>({ 2, 2 }, { 8, 4 }); });
// test_empty_shaped_array
sm.def("make_empty_shaped_array", [] { return py::array(py::dtype("f"), {}, {}); });
// test numpy scalars (empty shape, ndim==0)
sm.def("scalar_int", []() { return py::array(py::dtype("i"), {}, {}, &data_i); });
// test_wrap
sm.def("wrap", [](const py::array &a) {
return py::array(
a.dtype(),
{a.shape(), a.shape() + a.ndim()},
{a.strides(), a.strides() + a.ndim()},
a.data(),
a
);
});
// test_numpy_view
struct ArrayClass {
int data[2] = { 1, 2 };
ArrayClass() { py::print("ArrayClass()"); }
~ArrayClass() { py::print("~ArrayClass()"); }
};
py::class_<ArrayClass>(sm, "ArrayClass")
.def(py::init<>())
.def("numpy_view", [](py::object &obj) {
py::print("ArrayClass::numpy_view()");
auto &a = obj.cast<ArrayClass&>();
return py::array_t<int>({2}, {4}, a.data, obj);
}
);
// test_cast_numpy_int64_to_uint64
sm.def("function_taking_uint64", [](uint64_t) { });
// test_isinstance
sm.def("isinstance_untyped", [](py::object yes, py::object no) {
return py::isinstance<py::array>(std::move(yes))
&& !py::isinstance<py::array>(std::move(no));
});
sm.def("isinstance_typed", [](const py::object &o) {
return py::isinstance<py::array_t<double>>(o) && !py::isinstance<py::array_t<int>>(o);
});
// test_constructors
sm.def("default_constructors", []() {
return py::dict(
"array"_a=py::array(),
"array_t<int32>"_a=py::array_t<std::int32_t>(),
"array_t<double>"_a=py::array_t<double>()
);
});
sm.def("converting_constructors", [](const py::object &o) {
return py::dict(
"array"_a=py::array(o),
"array_t<int32>"_a=py::array_t<std::int32_t>(o),
"array_t<double>"_a=py::array_t<double>(o)
);
});
// test_overload_resolution
sm.def("overloaded", [](const py::array_t<double> &) { return "double"; });
sm.def("overloaded", [](const py::array_t<float> &) { return "float"; });
sm.def("overloaded", [](const py::array_t<int> &) { return "int"; });
sm.def("overloaded", [](const py::array_t<unsigned short> &) { return "unsigned short"; });
sm.def("overloaded", [](const py::array_t<long long> &) { return "long long"; });
sm.def("overloaded",
[](const py::array_t<std::complex<double>> &) { return "double complex"; });
sm.def("overloaded", [](const py::array_t<std::complex<float>> &) { return "float complex"; });
sm.def("overloaded2",
[](const py::array_t<std::complex<double>> &) { return "double complex"; });
sm.def("overloaded2", [](const py::array_t<double> &) { return "double"; });
sm.def("overloaded2",
[](const py::array_t<std::complex<float>> &) { return "float complex"; });
sm.def("overloaded2", [](const py::array_t<float> &) { return "float"; });
// [workaround(intel)] ICC 20/21 breaks with py::arg().stuff, using py::arg{}.stuff works.
// Only accept the exact types:
sm.def(
"overloaded3", [](const py::array_t<int> &) { return "int"; }, py::arg{}.noconvert());
sm.def(
"overloaded3",
[](const py::array_t<double> &) { return "double"; },
py::arg{}.noconvert());
// Make sure we don't do unsafe coercion (e.g. float to int) when not using forcecast, but
// rather that float gets converted via the safe (conversion to double) overload:
sm.def("overloaded4", [](const py::array_t<long long, 0> &) { return "long long"; });
sm.def("overloaded4", [](const py::array_t<double, 0> &) { return "double"; });
// But we do allow conversion to int if forcecast is enabled (but only if no overload matches
// without conversion)
sm.def("overloaded5", [](const py::array_t<unsigned int> &) { return "unsigned int"; });
sm.def("overloaded5", [](const py::array_t<double> &) { return "double"; });
// test_greedy_string_overload
// Issue 685: ndarray shouldn't go to std::string overload
sm.def("issue685", [](const std::string &) { return "string"; });
sm.def("issue685", [](const py::array &) { return "array"; });
sm.def("issue685", [](const py::object &) { return "other"; });
// test_array_unchecked_fixed_dims
sm.def("proxy_add2", [](py::array_t<double> a, double v) {
auto r = a.mutable_unchecked<2>();
for (py::ssize_t i = 0; i < r.shape(0); i++)
for (py::ssize_t j = 0; j < r.shape(1); j++)
r(i, j) += v;
}, py::arg{}.noconvert(), py::arg());
sm.def("proxy_init3", [](double start) {
py::array_t<double, py::array::c_style> a({ 3, 3, 3 });
auto r = a.mutable_unchecked<3>();
for (py::ssize_t i = 0; i < r.shape(0); i++)
for (py::ssize_t j = 0; j < r.shape(1); j++)
for (py::ssize_t k = 0; k < r.shape(2); k++)
r(i, j, k) = start++;
return a;
});
sm.def("proxy_init3F", [](double start) {
py::array_t<double, py::array::f_style> a({ 3, 3, 3 });
auto r = a.mutable_unchecked<3>();
for (py::ssize_t k = 0; k < r.shape(2); k++)
for (py::ssize_t j = 0; j < r.shape(1); j++)
for (py::ssize_t i = 0; i < r.shape(0); i++)
r(i, j, k) = start++;
return a;
});
sm.def("proxy_squared_L2_norm", [](const py::array_t<double> &a) {
auto r = a.unchecked<1>();
double sumsq = 0;
for (py::ssize_t i = 0; i < r.shape(0); i++)
sumsq += r[i] * r(i); // Either notation works for a 1D array
return sumsq;
});
sm.def("proxy_auxiliaries2", [](py::array_t<double> a) {
auto r = a.unchecked<2>();
auto r2 = a.mutable_unchecked<2>();
return auxiliaries(r, r2);
});
sm.def("proxy_auxiliaries1_const_ref", [](py::array_t<double> a) {
const auto &r = a.unchecked<1>();
const auto &r2 = a.mutable_unchecked<1>();
return r(0) == r2(0) && r[0] == r2[0];
});
sm.def("proxy_auxiliaries2_const_ref", [](py::array_t<double> a) {
const auto &r = a.unchecked<2>();
const auto &r2 = a.mutable_unchecked<2>();
return r(0, 0) == r2(0, 0);
});
// test_array_unchecked_dyn_dims
// Same as the above, but without a compile-time dimensions specification:
sm.def("proxy_add2_dyn", [](py::array_t<double> a, double v) {
auto r = a.mutable_unchecked();
if (r.ndim() != 2) throw std::domain_error("error: ndim != 2");
for (py::ssize_t i = 0; i < r.shape(0); i++)
for (py::ssize_t j = 0; j < r.shape(1); j++)
r(i, j) += v;
}, py::arg{}.noconvert(), py::arg());
sm.def("proxy_init3_dyn", [](double start) {
py::array_t<double, py::array::c_style> a({ 3, 3, 3 });
auto r = a.mutable_unchecked();
if (r.ndim() != 3) throw std::domain_error("error: ndim != 3");
for (py::ssize_t i = 0; i < r.shape(0); i++)
for (py::ssize_t j = 0; j < r.shape(1); j++)
for (py::ssize_t k = 0; k < r.shape(2); k++)
r(i, j, k) = start++;
return a;
});
sm.def("proxy_auxiliaries2_dyn", [](py::array_t<double> a) {
return auxiliaries(a.unchecked(), a.mutable_unchecked());
});
sm.def("array_auxiliaries2", [](py::array_t<double> a) {
return auxiliaries(a, a);
});
// test_array_failures
// Issue #785: Uninformative "Unknown internal error" exception when constructing array from empty object:
sm.def("array_fail_test", []() { return py::array(py::object()); });
sm.def("array_t_fail_test", []() { return py::array_t<double>(py::object()); });
// Make sure the error from numpy is being passed through:
sm.def("array_fail_test_negative_size", []() { int c = 0; return py::array(-1, &c); });
// test_initializer_list
// Issue (unnumbered; reported in #788): regression: initializer lists can be ambiguous
sm.def("array_initializer_list1", []() { return py::array_t<float>(1); }); // { 1 } also works, but clang warns about it
sm.def("array_initializer_list2", []() { return py::array_t<float>({ 1, 2 }); });
sm.def("array_initializer_list3", []() { return py::array_t<float>({ 1, 2, 3 }); });
sm.def("array_initializer_list4", []() { return py::array_t<float>({ 1, 2, 3, 4 }); });
// test_array_resize
// reshape array to 2D without changing size
sm.def("array_reshape2", [](py::array_t<double> a) {
const auto dim_sz = (py::ssize_t)std::sqrt(a.size());
if (dim_sz * dim_sz != a.size())
throw std::domain_error("array_reshape2: input array total size is not a squared integer");
a.resize({dim_sz, dim_sz});
});
// resize to 3D array with each dimension = N
sm.def("array_resize3", [](py::array_t<double> a, size_t N, bool refcheck) {
a.resize({N, N, N}, refcheck);
});
// test_array_create_and_resize
// return 2D array with Nrows = Ncols = N
sm.def("create_and_resize", [](size_t N) {
py::array_t<double> a;
a.resize({N, N});
std::fill(a.mutable_data(), a.mutable_data() + a.size(), 42.);
return a;
});
sm.def("array_view",
[](py::array_t<uint8_t> a, const std::string &dtype) { return a.view(dtype); });
sm.def("reshape_initializer_list", [](py::array_t<int> a, size_t N, size_t M, size_t O) {
return a.reshape({N, M, O});
});
sm.def("reshape_tuple", [](py::array_t<int> a, const std::vector<int> &new_shape) {
return a.reshape(new_shape);
});
sm.def("index_using_ellipsis",
[](const py::array &a) { return a[py::make_tuple(0, py::ellipsis(), 0)]; });
// test_argument_conversions
sm.def(
"accept_double", [](const py::array_t<double, 0> &) {}, py::arg("a"));
sm.def(
"accept_double_forcecast",
[](const py::array_t<double, py::array::forcecast> &) {},
py::arg("a"));
sm.def(
"accept_double_c_style",
[](const py::array_t<double, py::array::c_style> &) {},
py::arg("a"));
sm.def(
"accept_double_c_style_forcecast",
[](const py::array_t<double, py::array::forcecast | py::array::c_style> &) {},
py::arg("a"));
sm.def(
"accept_double_f_style",
[](const py::array_t<double, py::array::f_style> &) {},
py::arg("a"));
sm.def(
"accept_double_f_style_forcecast",
[](const py::array_t<double, py::array::forcecast | py::array::f_style> &) {},
py::arg("a"));
sm.def(
"accept_double_noconvert", [](const py::array_t<double, 0> &) {}, "a"_a.noconvert());
sm.def(
"accept_double_forcecast_noconvert",
[](const py::array_t<double, py::array::forcecast> &) {},
"a"_a.noconvert());
sm.def(
"accept_double_c_style_noconvert",
[](const py::array_t<double, py::array::c_style> &) {},
"a"_a.noconvert());
sm.def(
"accept_double_c_style_forcecast_noconvert",
[](const py::array_t<double, py::array::forcecast | py::array::c_style> &) {},
"a"_a.noconvert());
sm.def(
"accept_double_f_style_noconvert",
[](const py::array_t<double, py::array::f_style> &) {},
"a"_a.noconvert());
sm.def(
"accept_double_f_style_forcecast_noconvert",
[](const py::array_t<double, py::array::forcecast | py::array::f_style> &) {},
"a"_a.noconvert());
// Check that types returns correct npy format descriptor
sm.def("test_fmt_desc_float", [](const py::array_t<float> &) {});
sm.def("test_fmt_desc_double", [](const py::array_t<double> &) {});
sm.def("test_fmt_desc_const_float", [](const py::array_t<const float> &) {});
sm.def("test_fmt_desc_const_double", [](const py::array_t<const double> &) {});
}
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