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Copy patharray_to_vector.cpp
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1416 lines (1167 loc) · 46.2 KB
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// Licensed to the Apache Software Foundation (ASF) under one
// distributed with this work for additional information
// regarding copyright ownership. The ASF licenses this file
// or more contributor license agreements. See the NOTICE file
// to you under the Apache License, Version 2.0 (the
// "License"); you may not use this file except in compliance
// with the License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing,
// software distributed under the License is distributed on an
// "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
// KIND, either express or implied. See the License for the
// specific language governing permissions and limitations
// under the License.
#include "./arrow_types.h"
#include <arrow/array.h>
#include <arrow/builder.h>
#include <arrow/datum.h>
#include <arrow/table.h>
#include <arrow/util/bitmap_reader.h>
#include <arrow/util/bitmap_writer.h>
#include <arrow/util/int_util.h>
#include <cpp11/altrep.hpp>
#include <type_traits>
#include "./extension.h"
#include "./r_task_group.h"
namespace arrow {
using internal::checked_cast;
using internal::IntegersCanFit;
namespace r {
class Converter {
public:
explicit Converter(const std::shared_ptr<ChunkedArray>& chunked_array)
: chunked_array_(std::move(chunked_array)) {}
virtual ~Converter() {}
// Allocate a vector of the right R type for this converter
virtual SEXP Allocate(R_xlen_t n) const = 0;
// data[ start:(start + n) ] = NA
virtual Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const = 0;
// ingest the values from the array into data[ start : (start + n)]
//
// chunk_index indicates which of the chunk is being ingested into data. This is
// ignored by most implementations and currently only used with Dictionary
// arrays.
virtual Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n,
size_t chunk_index) const = 0;
// can this run in parallel ?
virtual bool Parallel() const { return true; }
// converter is passed as self to outlive the scope of Converter::Convert()
SEXP ScheduleConvertTasks(RTasks& tasks, std::shared_ptr<Converter> self) {
// try altrep first
SEXP alt = altrep::MakeAltrepVector(chunked_array_);
if (!Rf_isNull(alt)) {
return alt;
}
// otherwise use the Converter api:
// allocating the R vector upfront
SEXP out = PROTECT(Allocate(chunked_array_->length()));
// for each array, fill the relevant slice of `out`, potentially in parallel
R_xlen_t k = 0, i = 0;
for (const auto& array : chunked_array_->chunks()) {
auto n_chunk = array->length();
tasks.Append(Parallel(), [=] {
if (array->null_count() == n_chunk) {
return self->Ingest_all_nulls(out, k, n_chunk);
} else {
return self->Ingest_some_nulls(out, array, k, n_chunk, i);
}
});
k += n_chunk;
i++;
}
UNPROTECT(1);
return out;
}
// Converter factory
static std::shared_ptr<Converter> Make(
const std::shared_ptr<ChunkedArray>& chunked_array);
static SEXP LazyConvert(const std::shared_ptr<ChunkedArray>& chunked_array,
RTasks& tasks) {
auto converter = Make(chunked_array);
return converter->ScheduleConvertTasks(tasks, converter);
}
static SEXP Convert(const std::shared_ptr<ChunkedArray>& chunked_array,
bool use_threads) {
RTasks tasks(use_threads);
SEXP out = PROTECT(Converter::LazyConvert(chunked_array, tasks));
StopIfNotOk(tasks.Finish());
UNPROTECT(1);
return out;
}
static SEXP Convert(const std::shared_ptr<Array>& array) {
return Convert(std::make_shared<ChunkedArray>(array), false);
}
SEXP MaybeAltrep() { return altrep::MakeAltrepVector(chunked_array_); }
protected:
std::shared_ptr<ChunkedArray> chunked_array_;
};
template <typename SetNonNull, typename SetNull>
Status IngestSome(const std::shared_ptr<arrow::Array>& array, R_xlen_t n,
SetNonNull&& set_non_null, SetNull&& set_null) {
if (array->null_count()) {
internal::BitmapReader bitmap_reader(array->null_bitmap()->data(), array->offset(),
n);
for (R_xlen_t i = 0; i < n; i++, bitmap_reader.Next()) {
if (bitmap_reader.IsSet()) {
RETURN_NOT_OK(set_non_null(i));
} else {
RETURN_NOT_OK(set_null(i));
}
}
} else {
for (R_xlen_t i = 0; i < n; i++) {
RETURN_NOT_OK(set_non_null(i));
}
}
return Status::OK();
}
template <typename SetNonNull>
Status IngestSome(const std::shared_ptr<arrow::Array>& array, R_xlen_t n,
SetNonNull&& set_non_null) {
auto nothing = [](R_xlen_t i) { return Status::OK(); };
return IngestSome(array, n, std::forward<SetNonNull>(set_non_null), nothing);
}
std::shared_ptr<Array> CreateEmptyArray(const std::shared_ptr<DataType>& array_type) {
std::unique_ptr<arrow::ArrayBuilder> builder;
StopIfNotOk(arrow::MakeBuilder(gc_memory_pool(), array_type, &builder));
std::shared_ptr<arrow::Array> array;
StopIfNotOk(builder->Finish(&array));
return array;
}
template <typename Type>
class Converter_Int : public Converter {
using value_type = typename TypeTraits<Type>::ArrayType::value_type;
public:
explicit Converter_Int(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const { return Rf_allocVector(INTSXP, n); }
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
std::fill_n(INTEGER(data) + start, n, NA_INTEGER);
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
auto p_values = array->data()->GetValues<value_type>(1);
if (!p_values) {
return Status::Invalid("Invalid data buffer");
}
auto p_data = INTEGER(data) + start;
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = static_cast<int>(p_values[i]);
return Status::OK();
};
auto null_one = [&](R_xlen_t i) {
p_data[i] = NA_INTEGER;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
}
};
template <typename Type>
class Converter_Double : public Converter {
using value_type = typename TypeTraits<Type>::ArrayType::value_type;
public:
explicit Converter_Double(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const { return Rf_allocVector(REALSXP, n); }
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
std::fill_n(REAL(data) + start, n, NA_REAL);
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
auto p_values = array->data()->GetValues<value_type>(1);
if (!p_values) {
return Status::Invalid("Invalid data buffer");
}
auto p_data = REAL(data) + start;
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = static_cast<value_type>(p_values[i]);
return Status::OK();
};
auto null_one = [&](R_xlen_t i) {
p_data[i] = NA_REAL;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
}
};
class Converter_Date32 : public Converter {
public:
explicit Converter_Date32(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const {
SEXP data = PROTECT(Rf_allocVector(REALSXP, n));
Rf_classgets(data, Rf_mkString("Date"));
UNPROTECT(1);
return data;
}
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
std::fill_n(REAL(data) + start, n, NA_REAL);
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
auto p_values = array->data()->GetValues<int>(1);
if (!p_values) {
return Status::Invalid("Invalid data buffer");
}
auto p_data = REAL(data) + start;
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = static_cast<double>(p_values[i]);
return Status::OK();
};
auto null_one = [&](R_xlen_t i) {
p_data[i] = NA_REAL;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
}
};
template <typename StringArrayType>
struct Converter_String : public Converter {
public:
explicit Converter_String(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const { return Rf_allocVector(STRSXP, n); }
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
for (R_xlen_t i = 0; i < n; i++) {
SET_STRING_ELT(data, i + start, NA_STRING);
}
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
auto p_offset = array->data()->GetValues<int32_t>(1);
if (!p_offset) {
return Status::Invalid("Invalid offset buffer");
}
auto p_strings = array->data()->GetValues<char>(2, *p_offset);
if (!p_strings) {
// There is an offset buffer, but the data buffer is null
// There is at least one value in the array and not all the values are null
// That means all values are either empty strings or nulls so there is nothing to do
if (array->null_count()) {
arrow::internal::BitmapReader null_reader(array->null_bitmap_data(),
array->offset(), n);
for (int i = 0; i < n; i++, null_reader.Next()) {
if (null_reader.IsNotSet()) {
SET_STRING_ELT(data, start + i, NA_STRING);
}
}
}
return Status::OK();
}
StringArrayType* string_array = static_cast<StringArrayType*>(array.get());
const bool all_valid = array->null_count() == 0;
const bool strip_out_nuls = GetBoolOption("arrow.skip_nul", false);
bool nul_was_stripped = false;
if (all_valid) {
// no need to watch for missing strings
cpp11::unwind_protect([&] {
if (strip_out_nuls) {
for (int i = 0; i < n; i++) {
SET_STRING_ELT(data, start + i,
r_string_from_view_strip_nul(string_array->GetView(i),
&nul_was_stripped));
}
return;
}
for (int i = 0; i < n; i++) {
SET_STRING_ELT(data, start + i, r_string_from_view(string_array->GetView(i)));
}
});
} else {
cpp11::unwind_protect([&] {
arrow::internal::BitmapReader validity_reader(array->null_bitmap_data(),
array->offset(), n);
if (strip_out_nuls) {
for (int i = 0; i < n; i++, validity_reader.Next()) {
if (validity_reader.IsSet()) {
SET_STRING_ELT(data, start + i,
r_string_from_view_strip_nul(string_array->GetView(i),
&nul_was_stripped));
} else {
SET_STRING_ELT(data, start + i, NA_STRING);
}
}
return;
}
for (int i = 0; i < n; i++, validity_reader.Next()) {
if (validity_reader.IsSet()) {
SET_STRING_ELT(data, start + i, r_string_from_view(string_array->GetView(i)));
} else {
SET_STRING_ELT(data, start + i, NA_STRING);
}
}
});
}
if (nul_was_stripped) {
cpp11::safe[Rf_warning]("Stripping '\\0' (nul) from character vector");
}
return Status::OK();
}
bool Parallel() const { return false; }
private:
static SEXP r_string_from_view(std::string_view view) {
return Rf_mkCharLenCE(view.data(), view.size(), CE_UTF8);
}
static SEXP r_string_from_view_strip_nul(std::string_view view,
bool* nul_was_stripped) {
const char* old_string = view.data();
std::string stripped_string;
size_t stripped_len = 0, nul_count = 0;
for (size_t i = 0; i < view.size(); i++) {
if (old_string[i] == '\0') {
++nul_count;
if (nul_count == 1) {
// first nul spotted: allocate stripped string storage
stripped_string = std::string(view);
stripped_len = i;
}
// don't copy old_string[i] (which is \0) into stripped_string
continue;
}
if (nul_count > 0) {
stripped_string[stripped_len++] = old_string[i];
}
}
if (nul_count > 0) {
*nul_was_stripped = true;
stripped_string.resize(stripped_len);
return r_string_from_view(stripped_string);
}
return r_string_from_view(view);
}
};
class Converter_Boolean : public Converter {
public:
explicit Converter_Boolean(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const { return Rf_allocVector(LGLSXP, n); }
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
std::fill_n(LOGICAL(data) + start, n, NA_LOGICAL);
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
auto p_data = LOGICAL(data) + start;
auto p_bools = array->data()->GetValues<uint8_t>(1, 0);
if (!p_bools) {
return Status::Invalid("Invalid data buffer");
}
arrow::internal::BitmapReader data_reader(p_bools, array->offset(), n);
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = data_reader.IsSet();
data_reader.Next();
return Status::OK();
};
auto null_one = [&](R_xlen_t i) {
data_reader.Next();
p_data[i] = NA_LOGICAL;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
}
};
template <typename ArrayType>
class Converter_Binary : public Converter {
public:
using offset_type = typename ArrayType::offset_type;
explicit Converter_Binary(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const {
SEXP res = PROTECT(Rf_allocVector(VECSXP, n));
if (std::is_same<ArrayType, BinaryArray>::value) {
Rf_classgets(res, data::classes_arrow_binary);
} else {
Rf_classgets(res, data::classes_arrow_large_binary);
}
UNPROTECT(1);
return res;
}
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
const ArrayType* binary_array = checked_cast<const ArrayType*>(array.get());
auto ingest_one = [&](R_xlen_t i) {
offset_type ni;
auto value = binary_array->GetValue(i, &ni);
if (ni > R_XLEN_T_MAX) {
return Status::RError("Array too big to be represented as a raw vector");
}
SEXP raw = PROTECT(Rf_allocVector(RAWSXP, ni));
std::copy(value, value + ni, RAW(raw));
SET_VECTOR_ELT(data, i + start, raw);
UNPROTECT(1);
return Status::OK();
};
return IngestSome(array, n, ingest_one);
}
virtual bool Parallel() const { return false; }
};
class Converter_FixedSizeBinary : public Converter {
public:
explicit Converter_FixedSizeBinary(const std::shared_ptr<ChunkedArray>& chunked_array,
int byte_width)
: Converter(chunked_array), byte_width_(byte_width) {}
SEXP Allocate(R_xlen_t n) const {
SEXP res = PROTECT(Rf_allocVector(VECSXP, n));
Rf_classgets(res, data::classes_arrow_fixed_size_binary);
Rf_setAttrib(res, symbols::byte_width, Rf_ScalarInteger(byte_width_));
UNPROTECT(1);
return res;
}
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
const FixedSizeBinaryArray* binary_array =
checked_cast<const FixedSizeBinaryArray*>(array.get());
int byte_width = binary_array->byte_width();
auto ingest_one = [&, byte_width](R_xlen_t i) {
auto value = binary_array->GetValue(i);
SEXP raw = PROTECT(Rf_allocVector(RAWSXP, byte_width));
std::copy(value, value + byte_width, RAW(raw));
SET_VECTOR_ELT(data, i + start, raw);
UNPROTECT(1);
return Status::OK();
};
return IngestSome(array, n, ingest_one);
}
virtual bool Parallel() const { return false; }
private:
int byte_width_;
};
bool DictionaryChunkArrayNeedUnification(
const std::shared_ptr<ChunkedArray>& chunked_array) {
int n = chunked_array->num_chunks();
if (n < 2) {
return false;
}
const auto& arr_first =
internal::checked_cast<const DictionaryArray&>(*chunked_array->chunk(0));
for (int i = 1; i < n; i++) {
const auto& arr =
internal::checked_cast<const DictionaryArray&>(*chunked_array->chunk(i));
if (!(arr_first.dictionary()->Equals(arr.dictionary()))) {
return true;
}
}
return false;
}
class Converter_Dictionary : public Converter {
private:
bool need_unification_;
std::unique_ptr<arrow::DictionaryUnifier> unifier_;
std::vector<std::shared_ptr<Buffer>> arrays_transpose_;
std::shared_ptr<DataType> out_type_;
std::shared_ptr<Array> dictionary_;
public:
explicit Converter_Dictionary(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array),
need_unification_(DictionaryChunkArrayNeedUnification(chunked_array)) {
if (need_unification_) {
const auto& arr_type = checked_cast<const DictionaryType&>(*chunked_array->type());
unifier_ = ValueOrStop(DictionaryUnifier::Make(arr_type.value_type()));
size_t n_arrays = chunked_array->num_chunks();
arrays_transpose_.resize(n_arrays);
for (size_t i = 0; i < n_arrays; i++) {
const auto& dict_i =
*checked_cast<const DictionaryArray&>(*chunked_array->chunk(i)).dictionary();
StopIfNotOk(unifier_->Unify(dict_i, &arrays_transpose_[i]));
}
StopIfNotOk(unifier_->GetResult(&out_type_, &dictionary_));
} else {
const auto& dict_type = checked_cast<const DictionaryType&>(*chunked_array->type());
const auto& indices_type = *dict_type.index_type();
switch (indices_type.id()) {
case Type::UINT8:
case Type::INT8:
case Type::UINT16:
case Type::INT16:
case Type::INT32:
// TODO: also add int64, uint32, uint64 downcasts, if possible
break;
default:
cpp11::stop("Cannot convert Dictionary Array of type `%s` to R",
dict_type.ToString().c_str());
}
if (chunked_array->num_chunks() > 0) {
// DictionaryChunkArrayNeedUnification() returned false so we can safely assume
// the dictionary of the first chunk applies everywhere
const auto& dict_array =
checked_cast<const DictionaryArray&>(*chunked_array->chunk(0));
dictionary_ = dict_array.dictionary();
} else {
dictionary_ = CreateEmptyArray(dict_type.value_type());
}
}
}
SEXP Allocate(R_xlen_t n) const {
cpp11::writable::integers data(n);
data.attr("levels") = GetLevels();
if (GetOrdered()) {
Rf_classgets(data, arrow::r::data::classes_ordered);
} else {
Rf_classgets(data, arrow::r::data::classes_factor);
}
return data;
}
virtual bool Parallel() const { return false; }
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
std::fill_n(INTEGER(data) + start, n, NA_INTEGER);
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
const DictionaryArray& dict_array =
checked_cast<const DictionaryArray&>(*array.get());
auto indices = dict_array.indices();
switch (indices->type_id()) {
case Type::UINT8:
return Ingest_some_nulls_Impl<arrow::UInt8Type>(data, array, start, n,
chunk_index);
case Type::INT8:
return Ingest_some_nulls_Impl<arrow::Int8Type>(data, array, start, n,
chunk_index);
case Type::UINT16:
return Ingest_some_nulls_Impl<arrow::UInt16Type>(data, array, start, n,
chunk_index);
case Type::INT16:
return Ingest_some_nulls_Impl<arrow::Int16Type>(data, array, start, n,
chunk_index);
case Type::INT32:
return Ingest_some_nulls_Impl<arrow::Int32Type>(data, array, start, n,
chunk_index);
default:
break;
}
return Status::OK();
}
private:
template <typename Type>
Status Ingest_some_nulls_Impl(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
using index_type = typename arrow::TypeTraits<Type>::ArrayType::value_type;
auto indices = checked_cast<const DictionaryArray&>(*array).indices();
auto raw_indices = indices->data()->GetValues<index_type>(1);
auto p_data = INTEGER(data) + start;
auto null_one = [&](R_xlen_t i) {
p_data[i] = NA_INTEGER;
return Status::OK();
};
// convert the 0-based indices from the arrow Array
// to 1-based indices used in R factors
if (need_unification_) {
// transpose the indices before converting
auto transposed =
reinterpret_cast<const int32_t*>(arrays_transpose_[chunk_index]->data());
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = transposed[raw_indices[i]] + 1;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
} else {
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = static_cast<int>(raw_indices[i]) + 1;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
}
}
bool GetOrdered() const {
return checked_cast<const DictionaryType&>(*chunked_array_->type()).ordered();
}
SEXP GetLevels() const {
// R factor levels must be type "character" so coerce `dict` to STRSXP
// TODO (npr): this coercion should be optional, "dictionariesAsFactors" ;)
// Alternative: preserve the logical type of the dictionary values
// (e.g. if dict is timestamp, return a POSIXt R vector, not factor)
if (dictionary_->type_id() != Type::STRING) {
cpp11::safe[Rf_warning]("Coercing dictionary values to R character factor levels");
}
SEXP vec = PROTECT(Converter::Convert(dictionary_));
SEXP strings_vec = PROTECT(Rf_coerceVector(vec, STRSXP));
UNPROTECT(2);
return strings_vec;
}
};
class Converter_Struct : public Converter {
public:
explicit Converter_Struct(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array), converters() {
const auto& struct_type =
checked_cast<const arrow::StructType&>(*chunked_array->type());
int nf = struct_type.num_fields();
std::shared_ptr<arrow::Table> array_as_table =
ValueOrStop(arrow::Table::FromChunkedStructArray(chunked_array));
for (int i = 0; i < nf; i++) {
converters.push_back(Converter::Make(array_as_table->column(i)));
}
}
SEXP Allocate(R_xlen_t n) const {
// allocate a data frame column to host each array
// If possible, a column is dealt with directly with altrep
auto type =
checked_cast<const arrow::StructType*>(this->chunked_array_->type().get());
auto out =
arrow::r::to_r_list(converters, [n](const std::shared_ptr<Converter>& converter) {
SEXP out = converter->MaybeAltrep();
if (Rf_isNull(out)) {
out = converter->Allocate(n);
}
return out;
});
auto colnames = arrow::r::to_r_strings(
type->fields(),
[](const std::shared_ptr<Field>& field) { return field->name(); });
out.attr(symbols::row_names) = arrow::r::short_row_names(n);
out.attr(R_NamesSymbol) = colnames;
out.attr(R_ClassSymbol) = arrow::r::data::classes_tbl_df;
return out;
}
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
int nf = converters.size();
for (int i = 0; i < nf; i++) {
SEXP data_i = VECTOR_ELT(data, i);
// only ingest if the column is not altrep
if (!altrep::is_arrow_altrep(data_i)) {
StopIfNotOk(converters[i]->Ingest_all_nulls(data_i, start, n));
}
}
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
auto struct_array = checked_cast<const arrow::StructArray*>(array.get());
int nf = converters.size();
// Flatten() deals with merging of nulls
auto arrays = ValueOrStop(struct_array->Flatten(gc_memory_pool()));
for (int i = 0; i < nf; i++) {
SEXP data_i = VECTOR_ELT(data, i);
// only ingest if the column is not altrep
if (!altrep::is_arrow_altrep(data_i)) {
StopIfNotOk(converters[i]->Ingest_some_nulls(VECTOR_ELT(data, i), arrays[i],
start, n, chunk_index));
}
}
return Status::OK();
}
virtual bool Parallel() const {
// this can only run in parallel if all the
// inner converters can
for (const auto& converter : converters) {
if (!converter->Parallel()) return false;
}
return true;
}
private:
std::vector<std::shared_ptr<Converter>> converters;
};
double ms_to_seconds(int64_t ms) { return static_cast<double>(ms) / 1000; }
class Converter_Date64 : public Converter {
public:
explicit Converter_Date64(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const {
cpp11::writable::doubles data(n);
Rf_classgets(data, arrow::r::data::classes_POSIXct);
return data;
}
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
std::fill_n(REAL(data) + start, n, NA_REAL);
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
auto p_data = REAL(data) + start;
auto p_values = array->data()->GetValues<int64_t>(1);
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = static_cast<double>(p_values[i] / 1000);
return Status::OK();
};
auto null_one = [&](R_xlen_t i) {
p_data[i] = NA_REAL;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
}
};
template <typename value_type, typename unit_type = TimeType>
class Converter_Time : public Converter {
public:
explicit Converter_Time(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const {
cpp11::writable::doubles data(n);
data.attr("class") = cpp11::writable::strings({"hms", "difftime"});
// hms difftime is always stored as "seconds"
data.attr("units") = cpp11::writable::strings({"secs"});
return data;
}
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
std::fill_n(REAL(data) + start, n, NA_REAL);
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
int multiplier = TimeUnit_multiplier(array);
auto p_data = REAL(data) + start;
auto p_values = array->data()->GetValues<value_type>(1);
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = static_cast<double>(p_values[i]) / multiplier;
return Status::OK();
};
auto null_one = [&](R_xlen_t i) {
p_data[i] = NA_REAL;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
}
private:
int TimeUnit_multiplier(const std::shared_ptr<Array>& array) const {
// hms difftime is always "seconds", so multiply based on the Array's TimeUnit
switch (static_cast<unit_type*>(array->type().get())->unit()) {
case TimeUnit::SECOND:
return 1;
case TimeUnit::MILLI:
return 1000;
case TimeUnit::MICRO:
return 1000000;
case TimeUnit::NANO:
return 1000000000;
default:
return 0;
}
}
};
template <typename value_type, typename unit_type = DurationType>
class Converter_Duration : public Converter {
public:
explicit Converter_Duration(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const {
cpp11::writable::doubles data(n);
data.attr("class") = "difftime";
// difftime is always stored as "seconds"
data.attr("units") = cpp11::writable::strings({"secs"});
return data;
}
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
std::fill_n(REAL(data) + start, n, NA_REAL);
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
int multiplier = TimeUnit_multiplier(array);
auto p_data = REAL(data) + start;
auto p_values = array->data()->GetValues<value_type>(1);
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = static_cast<double>(p_values[i]) / multiplier;
return Status::OK();
};
auto null_one = [&](R_xlen_t i) {
p_data[i] = NA_REAL;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
}
private:
int TimeUnit_multiplier(const std::shared_ptr<Array>& array) const {
// difftime is always "seconds", so multiply based on the Array's TimeUnit
switch (static_cast<unit_type*>(array->type().get())->unit()) {
case TimeUnit::SECOND:
return 1;
case TimeUnit::MILLI:
return 1000;
case TimeUnit::MICRO:
return 1000000;
case TimeUnit::NANO:
return 1000000000;
default:
return 0;
}
}
};
template <typename value_type>
class Converter_Timestamp : public Converter_Time<value_type, TimestampType> {
public:
explicit Converter_Timestamp(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter_Time<value_type, TimestampType>(chunked_array) {}
SEXP Allocate(R_xlen_t n) const {
cpp11::writable::doubles data(n);
Rf_classgets(data, arrow::r::data::classes_POSIXct);
auto array_type =
checked_cast<const TimestampType*>(this->chunked_array_->type().get());
std::string tzone = array_type->timezone();
if (tzone.size() > 0) {
data.attr("tzone") = tzone;
}
return data;
}
};
template <typename Type>
class Converter_Decimal : public Converter {
public:
explicit Converter_Decimal(const std::shared_ptr<ChunkedArray>& chunked_array)
: Converter(chunked_array) {}
SEXP Allocate(R_xlen_t n) const { return Rf_allocVector(REALSXP, n); }
Status Ingest_all_nulls(SEXP data, R_xlen_t start, R_xlen_t n) const {
std::fill_n(REAL(data) + start, n, NA_REAL);
return Status::OK();
}
Status Ingest_some_nulls(SEXP data, const std::shared_ptr<arrow::Array>& array,
R_xlen_t start, R_xlen_t n, size_t chunk_index) const {
using DecimalArray = typename TypeTraits<Type>::ArrayType;
auto p_data = REAL(data) + start;
const auto& decimals_arr = checked_cast<const DecimalArray&>(*array);
auto ingest_one = [&](R_xlen_t i) {
p_data[i] = std::stod(decimals_arr.FormatValue(i).c_str());
return Status::OK();
};
auto null_one = [&](R_xlen_t i) {
p_data[i] = NA_REAL;
return Status::OK();
};
return IngestSome(array, n, ingest_one, null_one);
}
};
template <typename ListArrayType>
class Converter_List : public Converter {
private: