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replaced CApi numpy with boost numpy

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This commit is contained in:
Hans Dembinski
2017-11-03 00:13:43 +01:00
parent b1afcd036e
commit e12856b03d
4 changed files with 86 additions and 128 deletions
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33
src/python/axis.cpp
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@@ -12,10 +12,7 @@
#include <boost/python/def_visitor.hpp>
#include <boost/python/raw_function.hpp>
#ifdef HAVE_NUMPY
#define NO_IMPORT_ARRAY
#define PY_ARRAY_UNIQUE_SYMBOL boost_histogram_ARRAY_API
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
#include <boost/python/numpy.hpp>
#endif
#include <sstream>
#include <string>
@@ -23,6 +20,8 @@
#include <vector>
#include <utility>
namespace np = boost::python::numpy;
namespace boost {
namespace histogram {
@@ -132,22 +131,17 @@ template <typename T> python::str axis_get_label(const T& t) {
#ifdef HAVE_NUMPY
template <typename Axis> python::object axis_array_interface(const Axis& axis) {
using T = typename decay<decltype(axis[0].lower())>::type;
python::dict d;
auto shape = python::make_tuple(axis.size()+1);
d["shape"] = shape;
// d["typestr"] = dtype_typestr<typename Axis::bin_type>();
d["typestr"] = "|f8";
d["typestr"] = python::dtype_typestr<T>();
// make new array, and pass it to Python
auto dim = 1;
npy_intp shapes2[1] = { axis.size()+1 };
auto *a = (PyArrayObject*)PyArray_SimpleNew(dim, shapes2, NPY_DOUBLE);
auto *buf = (double *)PyArray_DATA(a);
PyArray_CLEARFLAGS(a, NPY_ARRAY_WRITEABLE);
// auto a = python::numpy::empty(shape, python::numpy::dtype::get_builtin<typename Axis::bin_type>());
// auto buf = reinterpret_cast<typename Axis::bin_type*>(axis.get_data());
auto a = np::empty(shape, np::dtype::get_builtin<T>());
auto buf = reinterpret_cast<T*>(a.get_data());
for (auto i = 0; i < axis.size()+1; ++i)
buf[i] = axis[i].lower();
d["data"] = python::object(python::handle<>((PyObject*)a));
d["data"] = a;
d["version"] = 3;
return d;
}
@@ -158,16 +152,11 @@ template <> python::object axis_array_interface<axis::category<>>(const axis::ca
d["shape"] = shape;
d["typestr"] = python::dtype_typestr<int>();
// make new array, and pass it to Python
auto dim = 1;
npy_intp shapes2[1] = { axis.size() };
auto *a = (PyArrayObject*)PyArray_SimpleNew(dim, shapes2, NPY_INT);
auto *buf = (int *)PyArray_DATA(a);
PyArray_CLEARFLAGS(a, NPY_ARRAY_WRITEABLE);
// auto a = python::numpy::empty(shape, python::numpy::dtype::get_builtin<typename Axis::bin_type>());
// auto buf = reinterpret_cast<typename Axis::bin_type*>(axis.get_data());
auto a = np::empty(shape, np::dtype::get_builtin<int>());
auto buf = reinterpret_cast<int*>(a.get_data());
for (auto i = 0; i < axis.size(); ++i)
buf[i] = axis[i];
d["data"] = python::object(python::handle<>((PyObject*)a));
d["data"] = a;
d["version"] = 3;
return d;
}

139
src/python/histogram.cpp
View File

@@ -17,16 +17,16 @@
#include <boost/variant/apply_visitor.hpp>
#include <boost/variant/static_visitor.hpp>
#ifdef HAVE_NUMPY
#define NO_IMPORT_ARRAY
#define PY_ARRAY_UNIQUE_SYMBOL boost_histogram_ARRAY_API
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
#include <boost/python/numpy.hpp>
#endif
#include <memory>
#ifndef BOOST_HISTOGRAM_AXIS_LIMIT
#define BOOST_HISTOGRAM_AXIS_LIMIT 32
#endif
namespace np = boost::python::numpy;
namespace boost {
namespace histogram {
@@ -78,38 +78,18 @@ public:
object operator()(const array<void>& b) const {
// cannot pass non-existent memory to numpy; make new
// zero-initialized uint8 array, and pass it
auto dim = len(shapes);
npy_intp shapes2[BOOST_HISTOGRAM_AXIS_LIMIT];
for (auto i = 0; i < dim; ++i) {
shapes2[i] = extract<npy_intp>(shapes[i]);
}
auto *a = (PyArrayObject*)PyArray_SimpleNew(dim, shapes2, NPY_UINT8);
for (auto i = 0; i < dim; ++i) {
PyArray_STRIDES(a)[i] = extract<npy_intp>(strides[i]);
}
auto *buf = (uint8_t *)PyArray_DATA(a);
std::fill(buf, buf + b.size, uint8_t(0));
PyArray_CLEARFLAGS(a, NPY_ARRAY_WRITEABLE);
return object(handle<>((PyObject*)a));
return np::zeros(tuple(shapes), np::dtype::get_builtin<uint8_t>());
}
object operator()(const array<mp_int>& b) const {
// cannot pass cpp_int to numpy; make new
// double array, fill it and pass it
auto dim = len(shapes);
npy_intp shapes2[BOOST_HISTOGRAM_AXIS_LIMIT];
for (auto i = 0; i < dim; ++i) {
shapes2[i] = extract<npy_intp>(shapes[i]);
}
auto *a = (PyArrayObject*)PyArray_SimpleNew(dim, shapes2, NPY_DOUBLE);
for (auto i = 0; i < dim; ++i) {
PyArray_STRIDES(a)[i] = extract<npy_intp>(strides[i]);
}
auto *buf = (double *)PyArray_DATA(a);
for (auto i = 0ul; i < b.size; ++i) {
auto a = np::empty(tuple(shapes), np::dtype::get_builtin<double>());
for (auto i = 0l, n = len(shapes); i < n; ++i)
const_cast<Py_intptr_t*>(a.get_strides())[i] = python::extract<int>(strides[i]);
auto *buf = (double *)a.get_data();
for (auto i = 0ul; i < b.size; ++i)
buf[i] = static_cast<double>(b[i]);
}
PyArray_CLEARFLAGS(a, NPY_ARRAY_WRITEABLE);
return object(handle<>((PyObject*)a));
return a;
}
};
@@ -204,51 +184,42 @@ python::object histogram_init(python::tuple args, python::dict kwargs) {
}
struct fetcher {
char type = 0;
union {
#ifdef HAVE_NUMPY
PyArrayObject* a;
#endif
double value;
};
#ifdef HAVE_NUMPY
~fetcher() {
if (type == 2) Py_DECREF((PyObject*)a);
}
#endif
long connect(python::object o) {
python::extract<double> get_double(o);
if (get_double.check()) {
type = 1;
value = get_double();
return 0;
}
#ifdef HAVE_NUMPY
a = (PyArrayObject*)PyArray_FROMANY(o.ptr(), NPY_DOUBLE, 1, 1, NPY_ARRAY_CARRAY);
if (a) {
type = 2;
return PyArray_SHAPE(a)[0];
}
#endif
PyErr_SetString(PyExc_ValueError, "cannot convert argument");
python::throw_error_already_set();
return 0;
}
bool empty() const { return type == 0; }
double operator[](long i) const {
#ifdef HAVE_NUMPY
if (type == 2) {
return *static_cast<double*>(PyArray_GETPTR1(a, i));
}
#endif
return value;
};
virtual ~fetcher() {}
virtual double at(long) const = 0;
long n = 0;
};
#ifdef HAVE_NUMPY
struct fetcher_seq : public fetcher {
fetcher_seq(python::object o)
: array(np::from_object(o, np::dtype::get_builtin<double>(), 1)) {
fetcher::n = array.shape(0);
}
~fetcher_seq() {}
double at(long i) const {
return reinterpret_cast<const double*>(array.get_data())[i];
}
np::ndarray array;
};
#endif
struct fetcher_val : public fetcher {
fetcher_val(double val)
: value(val) {}
double at(long) const { return value; }
double value;
};
std::unique_ptr<fetcher> make_fetcher(python::object o) {
python::extract<double> get_double(o);
if (get_double.check())
return std::unique_ptr<fetcher>(new fetcher_val(get_double()));
#ifdef HAVE_NUMPY
return std::unique_ptr<fetcher>(new fetcher_seq(o));
#endif
throw std::invalid_argument("python object is neither sequence nor number");
}
python::object histogram_fill(python::tuple args, python::dict kwargs) {
const auto nargs = python::len(args);
dynamic_histogram &self = python::extract<dynamic_histogram &>(args[0]);
@@ -266,11 +237,11 @@ python::object histogram_fill(python::tuple args, python::dict kwargs) {
python::throw_error_already_set();
}
fetcher fetch[BOOST_HISTOGRAM_AXIS_LIMIT];
std::unique_ptr<fetcher> fetch[BOOST_HISTOGRAM_AXIS_LIMIT];
long n = 0;
for (auto d = 0u; d < dim; ++d) {
python::object o = python::extract<python::object>(args[1 + d]);
const auto on = fetch[d].connect(o);
fetch[d] = make_fetcher(args[1 + d]);
const auto on = fetch[d]->n;
if (on > 0) {
if (n && on != n) {
PyErr_SetString(PyExc_ValueError, "lengths of sequences do not match");
@@ -280,15 +251,15 @@ python::object histogram_fill(python::tuple args, python::dict kwargs) {
}
}
fetcher fetch_weight;
std::unique_ptr<fetcher> fetch_weight;
const auto nkwargs = python::len(kwargs);
if (nkwargs > 0) {
if (nkwargs > 1 || !kwargs.has_key("weight")) {
PyErr_SetString(PyExc_RuntimeError, "only keyword weight allowed");
python::throw_error_already_set();
}
python::object o = kwargs.get("weight");
const auto on = fetch_weight.connect(o);
fetch_weight = make_fetcher(kwargs.get("weight"));
const auto on = fetch_weight->n;
if (on > 0) {
if (n && on != n) {
PyErr_SetString(PyExc_ValueError, "length of weight sequence does not match");
@@ -302,11 +273,11 @@ python::object histogram_fill(python::tuple args, python::dict kwargs) {
if (!n) ++n;
for (auto i = 0l; i < n; ++i) {
for (auto d = 0u; d < dim; ++d)
v[d] = fetch[d][i];
if (fetch_weight.empty()) {
self.fill(v, v + dim);
v[d] = fetch[d]->at(i);
if (fetch_weight) {
self.fill(v, v + dim, weight(fetch_weight->at(i)));
} else {
self.fill(v, v + dim, weight(fetch_weight[i]));
self.fill(v, v + dim);
}
}

20
src/python/module.cpp
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@@ -8,19 +8,7 @@
#include <boost/python/scope.hpp>
#include <boost/python/object.hpp>
#ifdef HAVE_NUMPY
#define PY_ARRAY_UNIQUE_SYMBOL boost_histogram_ARRAY_API
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
extern "C" {
#include <numpy/arrayobject.h>
#if PY_MAJOR_VERSION >= 3
static void *init_numpy() {
import_array();
return NULL;
}
#else
static void init_numpy() { import_array(); }
#endif
}
#include <boost/python/numpy.hpp>
#endif
namespace boost {
@@ -31,10 +19,10 @@ void register_histogram();
}
BOOST_PYTHON_MODULE(histogram) {
#ifdef HAVE_NUMPY
init_numpy();
#endif
using namespace boost::python;
#ifdef HAVE_NUMPY
numpy::initialize();
#endif
scope current;
object axis_module = object(
borrowed(PyImport_AddModule("histogram.axis"))