#include "common.h" #include std::unordered_map _tdb_to_np_name_dtype = { {TILEDB_INT32, "int32"}, {TILEDB_INT64, "int64"}, {TILEDB_FLOAT32, "float32"}, {TILEDB_FLOAT64, "float64"}, {TILEDB_INT8, "int8"}, {TILEDB_UINT8, "uint8"}, {TILEDB_INT16, "int16"}, {TILEDB_UINT16, "uint16"}, {TILEDB_UINT32, "uint32"}, {TILEDB_UINT64, "uint64"}, {TILEDB_STRING_ASCII, "S"}, {TILEDB_STRING_UTF8, "U1"}, {TILEDB_CHAR, "S1"}, {TILEDB_DATETIME_YEAR, "M8[Y]"}, {TILEDB_DATETIME_MONTH, "M8[M]"}, {TILEDB_DATETIME_WEEK, "M8[W]"}, {TILEDB_DATETIME_DAY, "M8[D]"}, {TILEDB_DATETIME_HR, "M8[h]"}, {TILEDB_DATETIME_MIN, "M8[m]"}, {TILEDB_DATETIME_SEC, "M8[s]"}, {TILEDB_DATETIME_MS, "M8[ms]"}, {TILEDB_DATETIME_US, "M8[us]"}, {TILEDB_DATETIME_NS, "M8[ns]"}, {TILEDB_DATETIME_PS, "M8[ps]"}, {TILEDB_DATETIME_FS, "M8[fs]"}, {TILEDB_DATETIME_AS, "M8[as]"}, /* duration types map to timedelta */ {TILEDB_TIME_HR, "m8[h]"}, {TILEDB_TIME_MIN, "m8[m]"}, {TILEDB_TIME_SEC, "m8[s]"}, {TILEDB_TIME_MS, "m8[ms]"}, {TILEDB_TIME_US, "m8[us]"}, {TILEDB_TIME_NS, "m8[ns]"}, {TILEDB_TIME_PS, "m8[ps]"}, {TILEDB_TIME_FS, "m8[fs]"}, {TILEDB_TIME_AS, "m8[as]"}, {TILEDB_BLOB, "byte"}, {TILEDB_BOOL, "bool"}, #if TILEDB_VERSION_MAJOR >= 2 && TILEDB_VERSION_MINOR >= 21 {TILEDB_GEOM_WKB, "byte"}, {TILEDB_GEOM_WKT, "S"}, #endif }; std::unordered_map _np_name_to_tdb_dtype = { {"int32", TILEDB_INT32}, {"int64", TILEDB_INT64}, {"float32", TILEDB_FLOAT32}, {"float64", TILEDB_FLOAT64}, {"int8", TILEDB_INT8}, {"uint8", TILEDB_UINT8}, {"int16", TILEDB_INT16}, {"uint16", TILEDB_UINT16}, {"uint32", TILEDB_UINT32}, {"uint64", TILEDB_UINT64}, {"datetime64[Y]", TILEDB_DATETIME_YEAR}, {"datetime64[M]", TILEDB_DATETIME_MONTH}, {"datetime64[W]", TILEDB_DATETIME_WEEK}, {"datetime64[D]", TILEDB_DATETIME_DAY}, {"datetime64[h]", TILEDB_DATETIME_HR}, {"datetime64[m]", TILEDB_DATETIME_MIN}, {"datetime64[s]", TILEDB_DATETIME_SEC}, {"datetime64[ms]", TILEDB_DATETIME_MS}, {"datetime64[us]", TILEDB_DATETIME_US}, {"datetime64[ns]", TILEDB_DATETIME_NS}, {"datetime64[ps]", TILEDB_DATETIME_PS}, {"datetime64[fs]", TILEDB_DATETIME_FS}, {"datetime64[as]", TILEDB_DATETIME_AS}, /* duration types map to timedelta */ {"timedelta64[h]", TILEDB_TIME_HR}, {"timedelta64[m]", TILEDB_TIME_MIN}, {"timedelta64[s]", TILEDB_TIME_SEC}, {"timedelta64[ms]", TILEDB_TIME_MS}, {"timedelta64[us]", TILEDB_TIME_US}, {"timedelta64[ns]", TILEDB_TIME_NS}, {"timedelta64[ps]", TILEDB_TIME_PS}, {"timedelta64[fs]", TILEDB_TIME_FS}, {"timedelta64[as]", TILEDB_TIME_AS}, {"bool", TILEDB_BOOL}, }; namespace tiledbpy::common { size_t buffer_nbytes(py::buffer_info &info) { return info.itemsize * std::accumulate(info.shape.begin(), info.shape.end(), 1, std::multiplies<>()); } bool expect_buffer_nbytes(py::buffer_info &info, tiledb_datatype_t datatype, size_t nelem) { size_t nbytes = buffer_nbytes(info); size_t nbytes_expected = tiledb_datatype_size(datatype) * nelem; return nbytes == nbytes_expected; } } // namespace tiledbpy::common py::dtype tdb_to_np_dtype(tiledb_datatype_t type, uint32_t cell_val_num) { if (type == TILEDB_CHAR || type == TILEDB_STRING_UTF8 || type == TILEDB_STRING_ASCII) { std::string base_str = (type == TILEDB_STRING_UTF8) ? "|U" : "|S"; if (cell_val_num < TILEDB_VAR_NUM) base_str += std::to_string(cell_val_num); return py::dtype(base_str); } if (cell_val_num == 1) { if (type == TILEDB_STRING_UTF16 || type == TILEDB_STRING_UTF32) TPY_ERROR_LOC("Unimplemented UTF16 or UTF32 string conversion!"); if (type == TILEDB_STRING_UCS2 || type == TILEDB_STRING_UCS4) TPY_ERROR_LOC("Unimplemented UCS2 or UCS4 string conversion!"); if (_tdb_to_np_name_dtype.count(type) == 1) return py::dtype(_tdb_to_np_name_dtype[type]); } if (cell_val_num == 2) { if (type == TILEDB_FLOAT32) return py::dtype("complex64"); if (type == TILEDB_FLOAT64) return py::dtype("complex128"); } if (cell_val_num == TILEDB_VAR_NUM) return tdb_to_np_dtype(type, 1); if (cell_val_num > 1) { py::dtype base_dtype = tdb_to_np_dtype(type, 1); py::tuple rec_elem = py::make_tuple("", base_dtype); py::list rec_list; for (size_t i = 0; i < cell_val_num; i++) rec_list.append(rec_elem); // note: we call the 'dtype' constructor b/c py::dtype does not accept // list auto np = py::module::import("numpy"); auto np_dtype = np.attr("dtype"); return np_dtype(rec_list); } TPY_ERROR_LOC("tiledb datatype not understood ('" + tiledb::impl::type_to_str(type) + "', cell_val_num: " + std::to_string(cell_val_num) + ")"); } tiledb_datatype_t np_to_tdb_dtype(py::dtype type) { auto name = py::str(py::getattr(type, "name")); if (_np_name_to_tdb_dtype.count(name) == 1) return _np_name_to_tdb_dtype[name]; auto kind = py::str(py::getattr(type, "kind")); if (kind.is(py::str("S"))) return TILEDB_STRING_ASCII; if (kind.is(py::str("U"))) return TILEDB_STRING_UTF8; TPY_ERROR_LOC("could not handle numpy dtype: " + py::getattr(type, "name").cast()); } bool is_tdb_num(tiledb_datatype_t type) { switch (type) { case TILEDB_INT8: case TILEDB_INT16: case TILEDB_UINT8: case TILEDB_INT32: case TILEDB_INT64: case TILEDB_UINT16: case TILEDB_UINT32: case TILEDB_UINT64: case TILEDB_FLOAT32: case TILEDB_FLOAT64: return true; default: return false; } } bool is_tdb_str(tiledb_datatype_t type) { switch (type) { case TILEDB_STRING_ASCII: case TILEDB_STRING_UTF8: case TILEDB_CHAR: return true; default: return false; } } py::size_t get_ncells(py::dtype type) { auto np = py::module::import("numpy"); auto np_issubdtype = np.attr("issubdtype"); auto np_complexfloating = np.attr("complexfloating"); auto np_character = np.attr("character"); py::bool_ ischaracter = np_issubdtype(type, np_character); if (ischaracter) { py::dtype base_dtype = np.attr("dtype")(py::make_tuple(type.attr("kind"), 1)); if (type.itemsize() == 0) return TILEDB_VAR_NUM; return type.itemsize() / base_dtype.itemsize(); } py::bool_ iscomplexfloating = np_issubdtype(type, np_complexfloating); if (iscomplexfloating) return 2; return 1; } py::array_t uint8_bool_to_uint8_bitmap(py::array_t validity_array) { // TODO profile, probably replace; avoid inplace reassignment auto np = py::module::import("numpy"); auto packbits = np.attr("packbits"); auto tmp = packbits(validity_array, "bitorder"_a = "little"); return tmp; } uint64_t count_zeros(py::array_t a) { uint64_t count = 0; for (py::ssize_t idx = 0; idx < a.size(); idx++) count += (a.data()[idx] == 0) ? 1 : 0; return count; }