[GitHub] [arrow] pitrou commented on a change in pull request #10445: ARROW-9140: [R] Zero-copy Arrow to R where possible

[GitBox <gi...@apache.org>]

pitrou commented on a change in pull request #10445:
URL: https://github.com/apache/arrow/pull/10445#discussion_r648947602



##########
File path: r/src/altrep.cpp
##########
@@ -0,0 +1,180 @@
+// Licensed to the Apache Software Foundation (ASF) under one
+// or more contributor license agreements.  See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership.  The ASF licenses this 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 <cpp11/altrep.hpp>
+
+#include "./arrow_types.h"
+
+#if defined(HAS_ALTREP)
+
+#include <R_ext/Altrep.h>
+#include <arrow/array.h>
+
+namespace arrow {
+namespace r {
+
+struct array_nonull {
+  // altrep object around an Array with no nulls
+  // data1: an external pointer to a shared pointer to the Array
+  // data2: not used
+
+  static SEXP Make(R_altrep_class_t class_t, const std::shared_ptr<Array>& array) {
+    // we don't need the whole r6 object, just an external pointer
+    // that retain the array
+    cpp11::external_pointer<std::shared_ptr<Array>> xp(new std::shared_ptr<Array>(array));
+
+    SEXP res = R_new_altrep(class_t, xp, R_NilValue);
+    MARK_NOT_MUTABLE(res);
+
+    return res;
+  }
+
+  static Rboolean Inspect(SEXP x, int pre, int deep, int pvec,
+                          void (*inspect_subtree)(SEXP, int, int, int)) {
+    auto& array = Get(x);
+    Rprintf("std::shared_ptr<arrow::Array, %s, NONULL> (len=%d, ptr=%p)\n",
+            array->type()->ToString().c_str(), array->length(), array.get());
+    return TRUE;
+  }
+
+  static std::shared_ptr<Array>& Get(SEXP vec) {
+    return *cpp11::external_pointer<std::shared_ptr<Array>>(R_altrep_data1(vec));
+  }
+
+  static R_xlen_t Length(SEXP vec) { return Get(vec)->length(); }
+
+  static const void* Dataptr_or_null(SEXP vec) {
+    auto& array = Get(vec);
+
+    int size = array->type_id() == Type::INT32 ? sizeof(int) : sizeof(double);
+    return reinterpret_cast<const void*>(array->data()->buffers[1]->data() +
+                                         size * array->offset());

Review comment:
       Or `array->data()->GetValues<c_type>(1)` where `using c_type = typename ArrowType::c_type`.
   (`ArrowType` being the class template parameter, e.g. `Int64Type` or `DoubleType`)

##########
File path: r/src/altrep.cpp
##########
@@ -0,0 +1,180 @@
+// Licensed to the Apache Software Foundation (ASF) under one
+// or more contributor license agreements.  See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership.  The ASF licenses this 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 <cpp11/altrep.hpp>
+
+#include "./arrow_types.h"
+
+#if defined(HAS_ALTREP)
+
+#include <R_ext/Altrep.h>
+#include <arrow/array.h>
+
+namespace arrow {
+namespace r {
+
+struct array_nonull {
+  // altrep object around an Array with no nulls
+  // data1: an external pointer to a shared pointer to the Array
+  // data2: not used
+
+  static SEXP Make(R_altrep_class_t class_t, const std::shared_ptr<Array>& array) {
+    // we don't need the whole r6 object, just an external pointer
+    // that retain the array
+    cpp11::external_pointer<std::shared_ptr<Array>> xp(new std::shared_ptr<Array>(array));
+
+    SEXP res = R_new_altrep(class_t, xp, R_NilValue);
+    MARK_NOT_MUTABLE(res);
+
+    return res;
+  }
+
+  static Rboolean Inspect(SEXP x, int pre, int deep, int pvec,
+                          void (*inspect_subtree)(SEXP, int, int, int)) {
+    auto& array = Get(x);
+    Rprintf("std::shared_ptr<arrow::Array, %s, NONULL> (len=%d, ptr=%p)\n",
+            array->type()->ToString().c_str(), array->length(), array.get());
+    return TRUE;
+  }
+
+  static std::shared_ptr<Array>& Get(SEXP vec) {
+    return *cpp11::external_pointer<std::shared_ptr<Array>>(R_altrep_data1(vec));
+  }
+
+  static R_xlen_t Length(SEXP vec) { return Get(vec)->length(); }
+
+  static const void* Dataptr_or_null(SEXP vec) {
+    auto& array = Get(vec);
+
+    int size = array->type_id() == Type::INT32 ? sizeof(int) : sizeof(double);

Review comment:
       Is it possible to make this a template class instead of manually switching on the type at runtime?

##########
File path: r/src/altrep.cpp
##########
@@ -0,0 +1,180 @@
+// Licensed to the Apache Software Foundation (ASF) under one
+// or more contributor license agreements.  See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership.  The ASF licenses this 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 <cpp11/altrep.hpp>
+
+#include "./arrow_types.h"
+
+#if defined(HAS_ALTREP)
+
+#include <R_ext/Altrep.h>
+#include <arrow/array.h>
+
+namespace arrow {
+namespace r {
+
+struct array_nonull {
+  // altrep object around an Array with no nulls
+  // data1: an external pointer to a shared pointer to the Array
+  // data2: not used
+
+  static SEXP Make(R_altrep_class_t class_t, const std::shared_ptr<Array>& array) {
+    // we don't need the whole r6 object, just an external pointer
+    // that retain the array
+    cpp11::external_pointer<std::shared_ptr<Array>> xp(new std::shared_ptr<Array>(array));
+
+    SEXP res = R_new_altrep(class_t, xp, R_NilValue);
+    MARK_NOT_MUTABLE(res);
+
+    return res;
+  }
+
+  static Rboolean Inspect(SEXP x, int pre, int deep, int pvec,
+                          void (*inspect_subtree)(SEXP, int, int, int)) {
+    auto& array = Get(x);
+    Rprintf("std::shared_ptr<arrow::Array, %s, NONULL> (len=%d, ptr=%p)\n",
+            array->type()->ToString().c_str(), array->length(), array.get());
+    return TRUE;
+  }
+
+  static std::shared_ptr<Array>& Get(SEXP vec) {

Review comment:
       Return a const reference?

##########
File path: r/src/array_to_vector.cpp
##########
@@ -1275,7 +1276,22 @@ cpp11::writable::list to_dataframe_parallel(
 
 // [[arrow::export]]
 SEXP Array__as_vector(const std::shared_ptr<arrow::Array>& array) {
-  return arrow::r::ArrayVector__as_vector(array->length(), array->type(), {array});
+  auto type = array->type();
+
+#if defined(HAS_ALTREP)
+  if (array->null_count() == 0 && arrow::r::GetBoolOption("arrow.use_altrep", true)) {
+    switch (type->id()) {
+      case arrow::Type::DOUBLE:
+        return arrow::r::Make_array_nonull_dbl_vector(array);
+      case arrow::Type::INT32:
+        return arrow::r::Make_array_nonull_int_vector(array);
+      default:

Review comment:
       Is there a plan to support other types here?

##########
File path: r/src/altrep.cpp
##########
@@ -0,0 +1,180 @@
+// Licensed to the Apache Software Foundation (ASF) under one
+// or more contributor license agreements.  See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership.  The ASF licenses this 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 <cpp11/altrep.hpp>
+
+#include "./arrow_types.h"
+
+#if defined(HAS_ALTREP)
+
+#include <R_ext/Altrep.h>
+#include <arrow/array.h>
+
+namespace arrow {
+namespace r {
+
+struct array_nonull {
+  // altrep object around an Array with no nulls
+  // data1: an external pointer to a shared pointer to the Array
+  // data2: not used
+
+  static SEXP Make(R_altrep_class_t class_t, const std::shared_ptr<Array>& array) {
+    // we don't need the whole r6 object, just an external pointer
+    // that retain the array
+    cpp11::external_pointer<std::shared_ptr<Array>> xp(new std::shared_ptr<Array>(array));
+
+    SEXP res = R_new_altrep(class_t, xp, R_NilValue);
+    MARK_NOT_MUTABLE(res);
+
+    return res;
+  }
+
+  static Rboolean Inspect(SEXP x, int pre, int deep, int pvec,
+                          void (*inspect_subtree)(SEXP, int, int, int)) {
+    auto& array = Get(x);
+    Rprintf("std::shared_ptr<arrow::Array, %s, NONULL> (len=%d, ptr=%p)\n",
+            array->type()->ToString().c_str(), array->length(), array.get());
+    return TRUE;
+  }
+
+  static std::shared_ptr<Array>& Get(SEXP vec) {
+    return *cpp11::external_pointer<std::shared_ptr<Array>>(R_altrep_data1(vec));
+  }
+
+  static R_xlen_t Length(SEXP vec) { return Get(vec)->length(); }
+
+  static const void* Dataptr_or_null(SEXP vec) {
+    auto& array = Get(vec);
+
+    int size = array->type_id() == Type::INT32 ? sizeof(int) : sizeof(double);
+    return reinterpret_cast<const void*>(array->data()->buffers[1]->data() +
+                                         size * array->offset());
+  }
+
+  static SEXP Duplicate(SEXP vec, Rboolean) {
+    auto& array = Get(vec);
+    auto size = array->length();
+
+    bool int_array = array->type_id() == Type::INT32;
+
+    SEXP copy = PROTECT(Rf_allocVector(int_array ? INTSXP : REALSXP, array->length()));
+
+    memcpy(DATAPTR(copy), Dataptr_or_null(vec),
+           int_array ? (size * sizeof(int)) : (size * sizeof(double)));
+
+    UNPROTECT(1);
+    return copy;
+  }
+
+  static void* Dataptr(SEXP vec, Rboolean writeable) {
+    return const_cast<void*>(Dataptr_or_null(vec));
+  }
+
+  // by definition, there are no NA
+  static int No_NA(SEXP vec) { return 1; }
+
+  static void Init(R_altrep_class_t class_t, DllInfo* dll) {
+    // altrep
+    R_set_altrep_Length_method(class_t, array_nonull::Length);
+    R_set_altrep_Inspect_method(class_t, array_nonull::Inspect);
+    R_set_altrep_Duplicate_method(class_t, array_nonull::Duplicate);
+
+    // altvec
+    R_set_altvec_Dataptr_method(class_t, array_nonull::Dataptr);
+    R_set_altvec_Dataptr_or_null_method(class_t, array_nonull::Dataptr_or_null);
+  }
+};
+
+struct array_nonull_dbl_vector {
+  static R_altrep_class_t class_t;
+
+  static void Init(DllInfo* dll) {
+    class_t = R_make_altreal_class("array_nonull_dbl_vector", "arrow", dll);
+    array_nonull::Init(class_t, dll);
+    R_set_altreal_No_NA_method(class_t, array_nonull::No_NA);
+  }
+};
+
+struct array_nonull_int_vector {
+  static R_altrep_class_t class_t;
+
+  static void Init(DllInfo* dll) {
+    class_t = R_make_altinteger_class("array_nonull_int_vector", "arrow", dll);
+    array_nonull::Init(class_t, dll);
+    R_set_altinteger_No_NA_method(class_t, array_nonull::No_NA);
+  }
+};
+
+R_altrep_class_t array_nonull_int_vector::class_t;
+R_altrep_class_t array_nonull_dbl_vector::class_t;
+
+void Init_Altrep_classes(DllInfo* dll) {
+  array_nonull_dbl_vector::Init(dll);
+  array_nonull_int_vector::Init(dll);
+}
+
+SEXP Make_array_nonull_dbl_vector(const std::shared_ptr<Array>& array) {
+  return array_nonull::Make(array_nonull_dbl_vector::class_t, array);
+}
+
+SEXP Make_array_nonull_int_vector(const std::shared_ptr<Array>& array) {
+  return array_nonull::Make(array_nonull_int_vector::class_t, array);
+}
+
+}  // namespace r
+}  // namespace arrow
+
+// TODO: when arrow depends on R 3.5 we can eliminate this

Review comment:
       What does this mean? Does Arrow still support R versions before 3.5? @nealrichardson 

##########
File path: r/tests/testthat/test-altrep.R
##########
@@ -0,0 +1,52 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this 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.
+
+context("altrep")
+
+skip_if(getRversion() <= "3.5.0")
+
+test_that("altrep vectors from int32 arrays with no nulls", {
+  withr::local_options(list(arrow.use_altrep = TRUE))
+  v <- Array$create(1:1000)
+  expect_true(is_altrep_int_nonull(as.vector(v)))
+  expect_true(is_altrep_int_nonull(as.vector(v$Slice(1))))
+
+  withr::local_options(list(arrow.use_altrep = NULL))
+  v <- Array$create(1:1000)

Review comment:
       Can you also test with an empty array?

##########
File path: r/src/altrep.cpp
##########
@@ -0,0 +1,180 @@
+// Licensed to the Apache Software Foundation (ASF) under one
+// or more contributor license agreements.  See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership.  The ASF licenses this 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 <cpp11/altrep.hpp>
+
+#include "./arrow_types.h"
+
+#if defined(HAS_ALTREP)
+
+#include <R_ext/Altrep.h>
+#include <arrow/array.h>
+
+namespace arrow {
+namespace r {
+
+struct array_nonull {
+  // altrep object around an Array with no nulls
+  // data1: an external pointer to a shared pointer to the Array
+  // data2: not used
+
+  static SEXP Make(R_altrep_class_t class_t, const std::shared_ptr<Array>& array) {
+    // we don't need the whole r6 object, just an external pointer
+    // that retain the array
+    cpp11::external_pointer<std::shared_ptr<Array>> xp(new std::shared_ptr<Array>(array));
+
+    SEXP res = R_new_altrep(class_t, xp, R_NilValue);
+    MARK_NOT_MUTABLE(res);
+
+    return res;
+  }
+
+  static Rboolean Inspect(SEXP x, int pre, int deep, int pvec,
+                          void (*inspect_subtree)(SEXP, int, int, int)) {
+    auto& array = Get(x);
+    Rprintf("std::shared_ptr<arrow::Array, %s, NONULL> (len=%d, ptr=%p)\n",
+            array->type()->ToString().c_str(), array->length(), array.get());
+    return TRUE;
+  }
+
+  static std::shared_ptr<Array>& Get(SEXP vec) {
+    return *cpp11::external_pointer<std::shared_ptr<Array>>(R_altrep_data1(vec));
+  }
+
+  static R_xlen_t Length(SEXP vec) { return Get(vec)->length(); }
+
+  static const void* Dataptr_or_null(SEXP vec) {
+    auto& array = Get(vec);

Review comment:
       Nit, but should use `const auto&` when mutation is not intended.

##########
File path: r/tests/testthat/test-altrep.R
##########
@@ -0,0 +1,52 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this 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.
+
+context("altrep")
+
+skip_if(getRversion() <= "3.5.0")
+
+test_that("altrep vectors from int32 arrays with no nulls", {
+  withr::local_options(list(arrow.use_altrep = TRUE))
+  v <- Array$create(1:1000)
+  expect_true(is_altrep_int_nonull(as.vector(v)))
+  expect_true(is_altrep_int_nonull(as.vector(v$Slice(1))))
+
+  withr::local_options(list(arrow.use_altrep = NULL))
+  v <- Array$create(1:1000)
+  expect_true(is_altrep_int_nonull(as.vector(v)))
+  expect_true(is_altrep_int_nonull(as.vector(v$Slice(1))))
+
+  withr::local_options(list(arrow.use_altrep = FALSE))
+  expect_false(is_altrep_int_nonull(as.vector(v)))
+  expect_false(is_altrep_int_nonull(as.vector(v$Slice(1))))
+})
+
+test_that("altrep vectors from double arrays with no nulls", {

Review comment:
       Can you add tests for when there are nulls?

##########
File path: r/src/altrep.cpp
##########
@@ -0,0 +1,180 @@
+// Licensed to the Apache Software Foundation (ASF) under one
+// or more contributor license agreements.  See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership.  The ASF licenses this 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 <cpp11/altrep.hpp>
+
+#include "./arrow_types.h"
+
+#if defined(HAS_ALTREP)
+
+#include <R_ext/Altrep.h>
+#include <arrow/array.h>
+
+namespace arrow {
+namespace r {
+
+struct array_nonull {

Review comment:
       Is there a reason for the `lower_case` naming style? Note our C++ style guide asks for `CamelCase` function and class names.




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