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#include <tiledb/tiledb> // C++
#include <tiledb/tiledb_experimental.h> // for `tiledb_subarray_has_label_range`
#include <tiledb/tiledb_experimental> // C++
#include "common.h"
#include <pybind11/numpy.h>
#include <pybind11/pybind11.h>
#include <pybind11/pytypes.h>
#include <pybind11/stl.h>
namespace libtiledbcpp {
using namespace tiledb;
namespace py = pybind11;
template <typename T> struct SubarrayDimensionManipulator {
static void copy(Subarray &subarray, Subarray &original, uint32_t dim_idx) {
for (uint64_t range_idx{0}; range_idx < original.range_num(dim_idx);
++range_idx) {
std::array<T, 3> range = original.range<T>(dim_idx, range_idx);
subarray.add_range(dim_idx, range[0], range[1], range[2]);
}
}
static py::ssize_t length(Subarray &subarray, uint32_t dim_idx) {
uint64_t length = 0;
for (uint64_t range_idx{0}; range_idx < subarray.range_num(dim_idx);
++range_idx) {
std::array<T, 3> range = subarray.range<T>(dim_idx, range_idx);
if (range[2] != 0 && range[1] != 1) {
throw TileDBPyError("Support for getting the lenght of ranges with a "
"stride is not yet implemented.");
}
auto range_length = static_cast<uint64_t>(range[1] - range[0]);
if (length > std::numeric_limits<uint64_t>::max() - range_length - 1) {
throw TileDBPyError("Overflow error computing subarray shape");
}
length += range_length + 1;
}
if (length > PY_SSIZE_T_MAX) {
throw TileDBPyError("Overflow error computing subarray shape");
}
return Py_SAFE_DOWNCAST(length, Py_ssize_t, uint64_t);
}
};
template <> struct SubarrayDimensionManipulator<std::string> {
static void copy(Subarray &subarray, Subarray &original, uint32_t dim_idx) {
for (uint64_t range_idx{0}; range_idx < original.range_num(dim_idx);
++range_idx) {
std::array<std::string, 2> range = original.range(dim_idx, range_idx);
subarray.add_range(dim_idx, range[0], range[1]);
}
}
static uint64_t length(Subarray &, uint32_t) {
throw TileDBPyError(
"Getting length of ranges is not supported on string dimensions.");
}
};
void add_dim_range(Subarray &subarray, uint32_t dim_idx, py::tuple r) {
if (py::len(r) == 0)
return;
else if (py::len(r) != 2)
TPY_ERROR_LOC("Unexpected range len != 2");
auto r0 = r[0];
auto r1 = r[1];
auto tiledb_type =
subarray.array().schema().domain().dimension(dim_idx).type();
try {
switch (tiledb_type) {
case TILEDB_INT32: {
using T = int32_t;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_INT64: {
using T = int64_t;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_INT8: {
using T = int8_t;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_UINT8: {
using T = uint8_t;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_INT16: {
using T = int16_t;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_UINT16: {
using T = uint16_t;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_UINT32: {
using T = uint32_t;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_UINT64: {
using T = uint64_t;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_FLOAT32: {
using T = float;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_FLOAT64: {
using T = double;
subarray.add_range(dim_idx, r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_STRING_ASCII:
case TILEDB_STRING_UTF8:
case TILEDB_CHAR: {
if (!py::isinstance<py::none>(r0) != !py::isinstance<py::none>(r1)) {
TPY_ERROR_LOC(
"internal error: ranges must both be strings or (None, None)");
} else if (!py::isinstance<py::none>(r0) &&
!py::isinstance<py::none>(r1) &&
!py::isinstance<py::str>(r0) && !py::isinstance<py::str>(r1) &&
!py::isinstance<py::bytes>(r0) &&
!py::isinstance<py::bytes>(r1)) {
TPY_ERROR_LOC(
"internal error: expected string type for var-length dim!");
}
if (!py::isinstance<py::none>(r0) && !py::isinstance<py::none>(r0))
subarray.add_range(dim_idx, r0.cast<std::string>(),
r1.cast<std::string>());
break;
}
case TILEDB_DATETIME_YEAR:
case TILEDB_DATETIME_MONTH:
case TILEDB_DATETIME_WEEK:
case TILEDB_DATETIME_DAY:
case TILEDB_DATETIME_HR:
case TILEDB_DATETIME_MIN:
case TILEDB_DATETIME_SEC:
case TILEDB_DATETIME_MS:
case TILEDB_DATETIME_US:
case TILEDB_DATETIME_NS:
case TILEDB_DATETIME_PS:
case TILEDB_DATETIME_FS:
case TILEDB_DATETIME_AS: {
case TILEDB_TIME_HR:
case TILEDB_TIME_MIN:
case TILEDB_TIME_SEC:
case TILEDB_TIME_MS:
case TILEDB_TIME_US:
case TILEDB_TIME_NS:
case TILEDB_TIME_PS:
case TILEDB_TIME_FS:
case TILEDB_TIME_AS:
py::dtype dtype = tdb_to_np_dtype(tiledb_type, 1);
auto dt0 = py::isinstance<py::int_>(r0) ? r0 : r0.attr("astype")(dtype);
auto dt1 = py::isinstance<py::int_>(r1) ? r1 : r1.attr("astype")(dtype);
// TODO, this is suboptimal, should define pybind converter
if (py::isinstance<py::int_>(dt0) && py::isinstance<py::int_>(dt1)) {
subarray.add_range(dim_idx, py::cast<int64_t>(dt0),
py::cast<int64_t>(dt1));
} else {
auto darray = py::array(py::make_tuple(dt0, dt1));
subarray.add_range(dim_idx, *(int64_t *)darray.data(0),
*(int64_t *)darray.data(1));
}
break;
}
default:
TPY_ERROR_LOC("Unknown dim type conversion!");
}
} catch (py::cast_error &e) {
(void)e;
std::string msg = "Failed to cast dim range '" + (std::string)py::repr(r) +
"' to dim type " + tiledb::impl::type_to_str(tiledb_type);
TPY_ERROR_LOC(msg);
}
}
void copy_ranges_on_dim(Subarray &subarray, Subarray original,
uint32_t dim_idx) {
auto tiledb_type =
subarray.array().schema().domain().dimension(dim_idx).type();
switch (tiledb_type) {
case TILEDB_INT32: {
using T = int32_t;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_INT64: {
using T = int64_t;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_INT8: {
using T = int8_t;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_UINT8: {
using T = uint8_t;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_INT16: {
using T = int16_t;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_UINT16: {
using T = uint16_t;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_UINT32: {
using T = uint32_t;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_UINT64: {
using T = uint64_t;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_FLOAT32: {
using T = float;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_FLOAT64: {
using T = double;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_STRING_ASCII:
case TILEDB_STRING_UTF8:
case TILEDB_CHAR: {
using T = std::string;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
case TILEDB_DATETIME_YEAR:
case TILEDB_DATETIME_MONTH:
case TILEDB_DATETIME_WEEK:
case TILEDB_DATETIME_DAY:
case TILEDB_DATETIME_HR:
case TILEDB_DATETIME_MIN:
case TILEDB_DATETIME_SEC:
case TILEDB_DATETIME_MS:
case TILEDB_DATETIME_US:
case TILEDB_DATETIME_NS:
case TILEDB_DATETIME_PS:
case TILEDB_DATETIME_FS:
case TILEDB_DATETIME_AS: {
case TILEDB_TIME_HR:
case TILEDB_TIME_MIN:
case TILEDB_TIME_SEC:
case TILEDB_TIME_MS:
case TILEDB_TIME_US:
case TILEDB_TIME_NS:
case TILEDB_TIME_PS:
case TILEDB_TIME_FS:
case TILEDB_TIME_AS:
using T = int64_t;
SubarrayDimensionManipulator<T>::copy(subarray, original, dim_idx);
break;
}
default:
TPY_ERROR_LOC("Unknown dim type conversion!");
}
}
py::ssize_t length_ranges(Subarray &subarray, uint32_t dim_idx) {
auto tiledb_type =
subarray.array().schema().domain().dimension(dim_idx).type();
switch (tiledb_type) {
case TILEDB_INT32: {
using T = int32_t;
return SubarrayDimensionManipulator<T>::length(subarray, dim_idx);
}
case TILEDB_INT64: {
using T = int64_t;
return SubarrayDimensionManipulator<T>::length(subarray, dim_idx);
}
case TILEDB_INT8: {
using T = int8_t;
return SubarrayDimensionManipulator<T>::length(subarray, dim_idx);
}
case TILEDB_UINT8: {
using T = uint8_t;
return SubarrayDimensionManipulator<T>::length(subarray, dim_idx);
}
case TILEDB_INT16: {
using T = int16_t;
return SubarrayDimensionManipulator<T>::length(subarray, dim_idx);
}
case TILEDB_UINT16: {
using T = uint16_t;
return SubarrayDimensionManipulator<T>::length(subarray, dim_idx);
}
case TILEDB_UINT32: {
using T = uint32_t;
return SubarrayDimensionManipulator<T>::length(subarray, dim_idx);
}
case TILEDB_UINT64: {
using T = uint64_t;
return SubarrayDimensionManipulator<T>::length(subarray, dim_idx);
}
case TILEDB_DATETIME_YEAR:
case TILEDB_DATETIME_MONTH:
case TILEDB_DATETIME_WEEK:
case TILEDB_DATETIME_DAY:
case TILEDB_DATETIME_HR:
case TILEDB_DATETIME_MIN:
case TILEDB_DATETIME_SEC:
case TILEDB_DATETIME_MS:
case TILEDB_DATETIME_US:
case TILEDB_DATETIME_NS:
case TILEDB_DATETIME_PS:
case TILEDB_DATETIME_FS:
case TILEDB_DATETIME_AS: {
case TILEDB_TIME_HR:
case TILEDB_TIME_MIN:
case TILEDB_TIME_SEC:
case TILEDB_TIME_MS:
case TILEDB_TIME_US:
case TILEDB_TIME_NS:
case TILEDB_TIME_PS:
case TILEDB_TIME_FS:
case TILEDB_TIME_AS:
using T = int64_t;
return SubarrayDimensionManipulator<T>::length(subarray, dim_idx);
}
default:
TPY_ERROR_LOC("Dimension length not supported on a dimension with the "
"given datatype.");
}
}
void add_dim_point_ranges(const Context &ctx, Subarray &subarray,
uint32_t dim_idx, pybind11::handle dim_range) {
// Cast range object to appropriately typed py::array.
auto tiledb_type =
subarray.array().schema().domain().dimension(dim_idx).type();
py::dtype dtype = tdb_to_np_dtype(tiledb_type, 1);
py::array ranges = dim_range.attr("astype")(dtype);
// Set point ranges using C-API.
tiledb_ctx_t *c_ctx = ctx.ptr().get();
tiledb_subarray_t *c_subarray = subarray.ptr().get();
ctx.handle_error(tiledb_subarray_add_point_ranges(
c_ctx, c_subarray, dim_idx, (void *)ranges.data(), ranges.size()));
}
void add_label_range(const Context &ctx, Subarray &subarray,
const std::string &label_name, py::tuple r) {
if (py::len(r) == 0)
return;
else if (py::len(r) != 2)
TPY_ERROR_LOC("Unexpected range len != 2");
auto r0 = r[0];
auto r1 = r[1];
auto tiledb_type = ArraySchemaExperimental::dimension_label(
ctx, subarray.array().schema(), label_name)
.label_type();
try {
switch (tiledb_type) {
case TILEDB_INT32: {
using T = int32_t;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_INT64: {
using T = int64_t;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_INT8: {
using T = int8_t;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_UINT8: {
using T = uint8_t;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_INT16: {
using T = int16_t;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_UINT16: {
using T = uint16_t;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_UINT32: {
using T = uint32_t;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_UINT64: {
using T = uint64_t;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_FLOAT32: {
using T = float;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_FLOAT64: {
using T = double;
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0.cast<T>(), r1.cast<T>());
break;
}
case TILEDB_STRING_ASCII:
case TILEDB_STRING_UTF8:
case TILEDB_CHAR: {
if (!py::isinstance<py::none>(r0) != !py::isinstance<py::none>(r1)) {
TPY_ERROR_LOC(
"internal error: ranges must both be strings or (None, None)");
} else if (!py::isinstance<py::none>(r0) &&
!py::isinstance<py::none>(r1) &&
!py::isinstance<py::str>(r0) && !py::isinstance<py::str>(r1) &&
!py::isinstance<py::bytes>(r0) &&
!py::isinstance<py::bytes>(r1)) {
TPY_ERROR_LOC(
"internal error: expected string type for var-length label!");
}
if (!py::isinstance<py::none>(r0) && !py::isinstance<py::none>(r0)) {
std::string r0_string = r0.cast<std::string>();
std::string r1_string = r1.cast<std::string>();
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
r0_string, r1_string);
}
break;
}
case TILEDB_DATETIME_YEAR:
case TILEDB_DATETIME_MONTH:
case TILEDB_DATETIME_WEEK:
case TILEDB_DATETIME_DAY:
case TILEDB_DATETIME_HR:
case TILEDB_DATETIME_MIN:
case TILEDB_DATETIME_SEC:
case TILEDB_DATETIME_MS:
case TILEDB_DATETIME_US:
case TILEDB_DATETIME_NS:
case TILEDB_DATETIME_PS:
case TILEDB_DATETIME_FS:
case TILEDB_DATETIME_AS: {
case TILEDB_TIME_HR:
case TILEDB_TIME_MIN:
case TILEDB_TIME_SEC:
case TILEDB_TIME_MS:
case TILEDB_TIME_US:
case TILEDB_TIME_NS:
case TILEDB_TIME_PS:
case TILEDB_TIME_FS:
case TILEDB_TIME_AS:
py::dtype dtype = tdb_to_np_dtype(tiledb_type, 1);
auto dt0 = py::isinstance<py::int_>(r0) ? r0 : r0.attr("astype")(dtype);
auto dt1 = py::isinstance<py::int_>(r1) ? r1 : r1.attr("astype")(dtype);
if (py::isinstance<py::int_>(dt0) && py::isinstance<py::int_>(dt1)) {
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
py::cast<int64_t>(dt0),
py::cast<int64_t>(dt1));
} else {
auto darray = py::array(py::make_tuple(dt0, dt1));
SubarrayExperimental::add_label_range(ctx, subarray, label_name,
*(int64_t *)darray.data(0),
*(int64_t *)darray.data(1));
}
break;
}
default:
TPY_ERROR_LOC("Unknown dimension label type conversion!");
}
} catch (py::cast_error &e) {
(void)e;
std::string msg = "Failed to cast label range '" +
(std::string)py::repr(r) + "' to label type " +
tiledb::impl::type_to_str(tiledb_type);
TPY_ERROR_LOC(msg);
}
}
bool has_label_range(const Context &ctx, Subarray &subarray, uint32_t dim_idx) {
int32_t has_label;
auto rc = tiledb_subarray_has_label_ranges(
ctx.ptr().get(), subarray.ptr().get(), dim_idx, &has_label);
if (rc == TILEDB_ERR) {
throw TileDBError("Failed to check dimension for label ranges");
}
return has_label == 1;
}
void init_subarray(py::module &m) {
py::class_<tiledb::Subarray>(m, "Subarray")
.def(py::init<Subarray>())
.def(py::init<const Context &, const Array &>(),
py::keep_alive<1, 2>() /* Keep context alive. */,
py::keep_alive<1, 3>() /* Keep array alive. */)
.def("__capsule__",
[](Subarray &subarray) {
return py::capsule(subarray.ptr().get(), "subarray");
})
.def("_add_dim_range",
[](Subarray &subarray, uint32_t dim_idx, py::tuple range) {
add_dim_range(subarray, dim_idx, range);
})
.def("_add_label_range",
[](Subarray &subarray, const Context &ctx,
const std::string &label_name, py::tuple range) {
add_label_range(ctx, subarray, label_name, range);
})
.def("_add_ranges_bulk",
[](Subarray &subarray, const Context &ctx, py::iterable ranges) {
uint32_t dim_idx = 0;
for (auto dim_range : ranges) {
if (py::isinstance<py::array>(dim_range)) {
add_dim_point_ranges(ctx, subarray, dim_idx, dim_range);
} else {
py::tuple dim_range_iter = dim_range.cast<py::iterable>();
for (auto r : dim_range_iter) {
py::tuple range_tuple = r.cast<py::tuple>();
add_dim_range(subarray, dim_idx, range_tuple);
}
}
dim_idx++;
}
})
.def("_add_dim_point_ranges",
[](Subarray &subarray, const Context &ctx, uint32_t dim_idx,
pybind11::handle dim_range) {
add_dim_point_ranges(ctx, subarray, dim_idx, dim_range);
})
.def("_add_ranges",
[](Subarray &subarray, const Context &ctx, py::iterable ranges) {
uint32_t dim_idx = 0;
for (auto dim_range : ranges) {
py::tuple dim_range_iter = dim_range.cast<py::iterable>();
for (auto r : dim_range_iter) {
py::tuple r_tuple = r.cast<py::tuple>();
add_dim_range(subarray, dim_idx, r_tuple);
}
dim_idx++;
}
})
.def("_add_label_ranges",
[](Subarray &subarray, const Context &ctx, py::iterable ranges) {
py::dict label_ranges = ranges.cast<py::dict>();
for (std::pair<py::handle, py::handle> pair : label_ranges) {
py::str label_name = pair.first.cast<py::str>();
py::tuple label_range_iter = pair.second.cast<py::iterable>();
for (auto r : label_range_iter) {
py::tuple r_tuple = r.cast<py::tuple>();
add_label_range(ctx, subarray, label_name, r_tuple);
}
}
})
.def("_has_label_range",
[](Subarray &subarray, const Context &ctx, uint32_t dim_idx) {
return has_label_range(ctx, subarray, dim_idx);
})
.def("copy_ranges",
[](Subarray &subarray, Subarray &original, py::iterable dims) {
for (auto dim_idx : dims) {
copy_ranges_on_dim(subarray, original, dim_idx.cast<uint32_t>());
}
})
.def("_range_num", py::overload_cast<const std::string &>(
&Subarray::range_num, py::const_))
.def("_range_num",
py::overload_cast<unsigned>(&Subarray::range_num, py::const_))
.def("_label_range_num",
[](Subarray &subarray, const Context &ctx,
const std::string &label_name) {
return SubarrayExperimental::label_range_num(ctx, subarray,
label_name);
})
.def("_shape",
[](Subarray &subarray, const Context &ctx) {
auto ndim = subarray.array().schema().domain().ndim();
// Create numpy array and get pointer to data.
py::array_t<py::ssize_t> shape(ndim);
py::buffer_info shape_result = shape.request();
py::ssize_t *shape_ptr =
static_cast<py::ssize_t *>(shape_result.ptr);
// Set size for each dimension.
for (uint32_t dim_idx{0}; dim_idx < ndim; ++dim_idx) {
shape_ptr[dim_idx] = length_ranges(subarray, dim_idx);
}
return shape;
})
// End definitions.
;
}
} // namespace libtiledbcpp
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