带有指向 C 结构体的指针的 S4 对象 [英] S4 object with a pointer to a C struct
问题描述
我有一个用于编写 R 扩展的第三方 C 库.我需要创建在库中定义的一些结构(并初始化它们)我需要将它们作为 S4 对象的一部分进行维护(将这些结构视为定义计算状态,销毁它们将销毁所有剩余的计算和所有已经计算的结果).我正在考虑创建一个 S4 对象来将这些结构的指针保存为 void*
指针,但根本不清楚如何这样做,插槽的类型是什么?
I have a third-party C library I am using to write an R extension. I am required to create a few structs defined in the library (and initialize them) I need to maintain them as part of an S4 object (think of these structs as defining to state of a computation, to destroy them would be to destroy all remaining computation and the results of all that has been already computed).
I am thinking of creating a S4 object to hold pointers these structs as void*
pointers but it is not at all clear how to do so, what would be the type of the slot?
推荐答案
正如@hrbrmstr 所指出的,您可以使用 externalptr
类型来保持此类对象活着",这在本节 的编写 R 扩展,尽管我看不出有任何理由需要将任何内容存储为 void*
.如果您使用一点 C++ 没有任何问题,Rcpp 类 XPtr
可以消除相当多的与管理 EXTPTRSXP
相关的样板文件.例如,假设以下简化示例代表您的第三方库的 API:
As pointed out by @hrbrmstr, you can use the externalptr
type to keep such objects "alive", which is touched on in this section of Writing R Extensions, although I don't see any reason why you will need to store anything as void*
. If you don't have any issue with using a little C++, the Rcpp class XPtr
can eliminate a fair amount of the boilerplate involved with managing EXTPTRSXP
s. As an example, assume the following simplified example represents your third party library's API:
#include <Rcpp.h>
#include <stdlib.h>
typedef struct {
unsigned int count;
double total;
} CStruct;
CStruct* init_CStruct() {
return (CStruct*)::malloc(sizeof(CStruct));
}
void free_CStruct(CStruct* ptr) {
::free(ptr);
::printf("free_CStruct called.\n");
}
typedef Rcpp::XPtr<CStruct, Rcpp::PreserveStorage, free_CStruct> xptr_t;
当使用通过 new
创建的指针时,通常使用 Rcpp::XPtr
就足够了,因为 默认终结器 只需调用 delete
在保留目的.但是,由于您正在处理 C API,我们必须提供(默认)模板参数 Rcpp::PreserveStorage
,更重要的是,提供适当的终结器(free_CStruct
in这个例子),以便当相应的 R 对象被垃圾回收时,XPtr
不会在通过 malloc
等分配的内存上调用 delete
.
When working with pointers created via new
it is generally sufficient to use Rcpp::XPtr<SomeClass>
, because the default finalizer simply calls delete
on the held object. However, since you are dealing with a C API, we have to supply the (default) template parameter Rcpp::PreserveStorage
, and more importantly, the appropriate finalizer (free_CStruct
in this example) so that the XPtr
does not call delete
on memory allocated via malloc
, etc., when the corresponding R object is garbage collected.
继续这个例子,假设你编写了以下函数来与你的 CStruct
交互:
Continuing with the example, assume you write the following functions to interact with your CStruct
:
// [[Rcpp::export]]
xptr_t MakeCStruct() {
CStruct* ptr = init_CStruct();
ptr->count = 0;
ptr->total = 0;
return xptr_t(ptr, true);
}
// [[Rcpp::export]]
void UpdateCStruct(xptr_t ptr, SEXP x) {
if (TYPEOF(x) == REALSXP) {
R_xlen_t i = 0, sz = XLENGTH(x);
for ( ; i < sz; i++) {
if (!ISNA(REAL(x)[i])) {
ptr->count++;
ptr->total += REAL(x)[i];
}
}
return;
}
if (TYPEOF(x) == INTSXP) {
R_xlen_t i = 0, sz = XLENGTH(x);
for ( ; i < sz; i++) {
if (!ISNA(INTEGER(x)[i])) {
ptr->count++;
ptr->total += INTEGER(x)[i];
}
}
return;
}
Rf_warning("Invalid SEXPTYPE.\n");
}
// [[Rcpp::export]]
void SummarizeCStruct(xptr_t ptr) {
::printf(
"count: %d\ntotal: %f\naverage: %f\n",
ptr->count, ptr->total,
ptr->count > 0 ? ptr->total / ptr->count : 0
);
}
// [[Rcpp::export]]
int GetCStructCount(xptr_t ptr) {
return ptr->count;
}
// [[Rcpp::export]]
double GetCStructTotal(xptr_t ptr) {
return ptr->total;
}
// [[Rcpp::export]]
void ResetCStruct(xptr_t ptr) {
ptr->count = 0;
ptr->total = 0.0;
}
<小时>
此时,您已经完成了足够的工作,可以开始处理 R 中的 CStructs
:
ptr <- MakeCStruct()
将初始化一个CStruct
并将其作为externalptr
存储在 RUpdateCStruct(ptr, x)
将修改存储在CStruct
中的数据,SummarizeCStruct(ptr)
将打印摘要等.rm(ptr);gc()
将移除ptr
对象并强制垃圾收集器运行,从而调用free_CStruct(ptr)
并销毁 C 端的对象还有
ptr <- MakeCStruct()
will initialize aCStruct
and store it as anexternalptr
in RUpdateCStruct(ptr, x)
will modify the data stored in theCStruct
,SummarizeCStruct(ptr)
will print a summary, etc.rm(ptr); gc()
will remove theptr
object and force the garbage collector to run, thus callingfree_CStruct(ptr)
and destroying the object on the C side of things as well
您提到了使用 S4 类,这是将所有这些功能包含在一个地方的一种选择.这是一种可能性:
You mentioned the use of S4 classes, which is one option for containing all of these functions in a single place. Here's one possibility:
setClass(
"CStruct",
slots = c(
ptr = "externalptr",
update = "function",
summarize = "function",
get_count = "function",
get_total = "function",
reset = "function"
)
)
setMethod(
"initialize",
"CStruct",
function(.Object) {
.Object@ptr <- MakeCStruct()
.Object@update <- function(x) {
UpdateCStruct(.Object@ptr, x)
}
.Object@summarize <- function() {
SummarizeCStruct(.Object@ptr)
}
.Object@get_count <- function() {
GetCStructCount(.Object@ptr)
}
.Object@get_total <- function() {
GetCStructTotal(.Object@ptr)
}
.Object@reset <- function() {
ResetCStruct(.Object@ptr)
}
.Object
}
)
<小时>
然后,我们可以像这样使用CStruct
:
ptr <- new("CStruct")
ptr@summarize()
# count: 0
# total: 0.000000
# average: 0.000000
set.seed(123)
ptr@update(rnorm(100))
ptr@summarize()
# count: 100
# total: 9.040591
# average: 0.090406
ptr@update(rnorm(100))
ptr@summarize()
# count: 200
# total: -1.714089
# average: -0.008570
ptr@reset()
ptr@summarize()
# count: 0
# total: 0.000000
# average: 0.000000
rm(ptr); gc()
# free_CStruct called.
# used (Mb) gc trigger (Mb) max used (Mb)
# Ncells 484713 25.9 940480 50.3 601634 32.2
# Vcells 934299 7.2 1650153 12.6 1308457 10.0
<小时>
当然,另一种选择是使用 Rcpp Modules,它或多或少地处理 R 端的类定义样板(但是,使用引用类而不是 S4 类).
Of course, another option is to use Rcpp Modules, which more or less take care of the class definition boilerplate on the R side (using reference classes rather than S4 classes, however).
这篇关于带有指向 C 结构体的指针的 S4 对象的文章就介绍到这了,希望我们推荐的答案对大家有所帮助,也希望大家多多支持IT屋!