#include // for enums #include // C++ #include // for `tiledb_subarray_has_label_range` #include // C++ #include "common.h" #include #include #include #include namespace libtiledbcpp { using namespace tiledb; namespace py = pybind11; template 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 range = original.range(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 range = subarray.range(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(range[1] - range[0]); if (length > std::numeric_limits::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 { 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 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(), r1.cast()); break; } case TILEDB_INT64: { using T = int64_t; subarray.add_range(dim_idx, r0.cast(), r1.cast()); break; } case TILEDB_INT8: { using T = int8_t; subarray.add_range(dim_idx, r0.cast(), r1.cast()); break; } case TILEDB_UINT8: { using T = uint8_t; subarray.add_range(dim_idx, r0.cast(), r1.cast()); break; } case TILEDB_INT16: { using T = int16_t; subarray.add_range(dim_idx, r0.cast(), r1.cast()); break; } case TILEDB_UINT16: { using T = uint16_t; subarray.add_range(dim_idx, r0.cast(), r1.cast()); break; } case TILEDB_UINT32: { using T = uint32_t; subarray.add_range(dim_idx, r0.cast(), r1.cast()); break; } case TILEDB_UINT64: { using T = uint64_t; subarray.add_range(dim_idx, r0.cast(), r1.cast()); break; } case TILEDB_FLOAT32: { using T = float; subarray.add_range(dim_idx, r0.cast(), r1.cast()); break; } case TILEDB_FLOAT64: { using T = double; subarray.add_range(dim_idx, r0.cast(), r1.cast()); break; } case TILEDB_STRING_ASCII: case TILEDB_STRING_UTF8: case TILEDB_CHAR: { if (!py::isinstance(r0) != !py::isinstance(r1)) { TPY_ERROR_LOC( "internal error: ranges must both be strings or (None, None)"); } else if (!py::isinstance(r0) && !py::isinstance(r1) && !py::isinstance(r0) && !py::isinstance(r1) && !py::isinstance(r0) && !py::isinstance(r1)) { TPY_ERROR_LOC( "internal error: expected string type for var-length dim!"); } if (!py::isinstance(r0) && !py::isinstance(r0)) subarray.add_range(dim_idx, r0.cast(), r1.cast()); 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(r0) ? r0 : r0.attr("astype")(dtype); auto dt1 = py::isinstance(r1) ? r1 : r1.attr("astype")(dtype); // TODO, this is suboptimal, should define pybind converter if (py::isinstance(dt0) && py::isinstance(dt1)) { subarray.add_range(dim_idx, py::cast(dt0), py::cast(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::copy(subarray, original, dim_idx); break; } case TILEDB_INT64: { using T = int64_t; SubarrayDimensionManipulator::copy(subarray, original, dim_idx); break; } case TILEDB_INT8: { using T = int8_t; SubarrayDimensionManipulator::copy(subarray, original, dim_idx); break; } case TILEDB_UINT8: { using T = uint8_t; SubarrayDimensionManipulator::copy(subarray, original, dim_idx); break; } case TILEDB_INT16: { using T = int16_t; SubarrayDimensionManipulator::copy(subarray, original, dim_idx); break; } case TILEDB_UINT16: { using T = uint16_t; SubarrayDimensionManipulator::copy(subarray, original, dim_idx); break; } case TILEDB_UINT32: { using T = uint32_t; SubarrayDimensionManipulator::copy(subarray, original, dim_idx); break; } case TILEDB_UINT64: { using T = uint64_t; SubarrayDimensionManipulator::copy(subarray, original, dim_idx); break; } case TILEDB_FLOAT32: { using T = float; SubarrayDimensionManipulator::copy(subarray, original, dim_idx); break; } case TILEDB_FLOAT64: { using T = double; SubarrayDimensionManipulator::copy(subarray, original, dim_idx); break; } case TILEDB_STRING_ASCII: case TILEDB_STRING_UTF8: case TILEDB_CHAR: { using T = std::string; SubarrayDimensionManipulator::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::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::length(subarray, dim_idx); } case TILEDB_INT64: { using T = int64_t; return SubarrayDimensionManipulator::length(subarray, dim_idx); } case TILEDB_INT8: { using T = int8_t; return SubarrayDimensionManipulator::length(subarray, dim_idx); } case TILEDB_UINT8: { using T = uint8_t; return SubarrayDimensionManipulator::length(subarray, dim_idx); } case TILEDB_INT16: { using T = int16_t; return SubarrayDimensionManipulator::length(subarray, dim_idx); } case TILEDB_UINT16: { using T = uint16_t; return SubarrayDimensionManipulator::length(subarray, dim_idx); } case TILEDB_UINT32: { using T = uint32_t; return SubarrayDimensionManipulator::length(subarray, dim_idx); } case TILEDB_UINT64: { using T = uint64_t; return SubarrayDimensionManipulator::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::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(), r1.cast()); break; } case TILEDB_INT64: { using T = int64_t; SubarrayExperimental::add_label_range(ctx, subarray, label_name, r0.cast(), r1.cast()); break; } case TILEDB_INT8: { using T = int8_t; SubarrayExperimental::add_label_range(ctx, subarray, label_name, r0.cast(), r1.cast()); break; } case TILEDB_UINT8: { using T = uint8_t; SubarrayExperimental::add_label_range(ctx, subarray, label_name, r0.cast(), r1.cast()); break; } case TILEDB_INT16: { using T = int16_t; SubarrayExperimental::add_label_range(ctx, subarray, label_name, r0.cast(), r1.cast()); break; } case TILEDB_UINT16: { using T = uint16_t; SubarrayExperimental::add_label_range(ctx, subarray, label_name, r0.cast(), r1.cast()); break; } case TILEDB_UINT32: { using T = uint32_t; SubarrayExperimental::add_label_range(ctx, subarray, label_name, r0.cast(), r1.cast()); break; } case TILEDB_UINT64: { using T = uint64_t; SubarrayExperimental::add_label_range(ctx, subarray, label_name, r0.cast(), r1.cast()); break; } case TILEDB_FLOAT32: { using T = float; SubarrayExperimental::add_label_range(ctx, subarray, label_name, r0.cast(), r1.cast()); break; } case TILEDB_FLOAT64: { using T = double; SubarrayExperimental::add_label_range(ctx, subarray, label_name, r0.cast(), r1.cast()); break; } case TILEDB_STRING_ASCII: case TILEDB_STRING_UTF8: case TILEDB_CHAR: { if (!py::isinstance(r0) != !py::isinstance(r1)) { TPY_ERROR_LOC( "internal error: ranges must both be strings or (None, None)"); } else if (!py::isinstance(r0) && !py::isinstance(r1) && !py::isinstance(r0) && !py::isinstance(r1) && !py::isinstance(r0) && !py::isinstance(r1)) { TPY_ERROR_LOC( "internal error: expected string type for var-length label!"); } if (!py::isinstance(r0) && !py::isinstance(r0)) { std::string r0_string = r0.cast(); std::string r1_string = r1.cast(); 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(r0) ? r0 : r0.attr("astype")(dtype); auto dt1 = py::isinstance(r1) ? r1 : r1.attr("astype")(dtype); if (py::isinstance(dt0) && py::isinstance(dt1)) { SubarrayExperimental::add_label_range(ctx, subarray, label_name, py::cast(dt0), py::cast(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_(m, "Subarray") .def(py::init()) .def(py::init(), 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(dim_range)) { add_dim_point_ranges(ctx, subarray, dim_idx, dim_range); } else { py::tuple dim_range_iter = dim_range.cast(); for (auto r : dim_range_iter) { py::tuple range_tuple = r.cast(); 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(); for (auto r : dim_range_iter) { py::tuple r_tuple = r.cast(); 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(); for (std::pair pair : label_ranges) { py::str label_name = pair.first.cast(); py::tuple label_range_iter = pair.second.cast(); for (auto r : label_range_iter) { py::tuple r_tuple = r.cast(); 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()); } }) .def("_range_num", py::overload_cast( &Subarray::range_num, py::const_)) .def("_range_num", py::overload_cast(&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 shape(ndim); py::buffer_info shape_result = shape.request(); py::ssize_t *shape_ptr = static_cast(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