c++ - R 崩溃/中止使用带有 NA 输入的 Rcpp

Question

我想处理两个光栅图像(Ra 和 Rb)，其中 Ra 是像素值本身，Rb 是其邻居的值。以 sum 为例，假设有一个 3*3 的邻居，对于 Ra 中的每个像素，我将其值添加到 Rb 中的邻居像素的值，最后我将得到另一幅图像。

R 光栅包提供了一个焦点函数，它只适用于一个图像输入，我尝试修改 C++ 代码(enter link description here)以使用 Rcpp 接受两个图像输入。如果 Rb 的输入图像中没有缺失值，修改后的代码会很好地工作。但是，如果 Rb 中有 NA，R 总是会中止。具体来说，在第二次或第三次测试时中止。它可能类似于 this post .但是，如果输入 Rb 中没有 NA，它不会崩溃。看来我没有正确处理 NA。我对 C++ 没有很深的了解，有人可以帮我检查一下吗？

这是我的cpp文件:

#include <Rcpp.h>
#include <R.h>
#include <Rinternals.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <Rmath.h>
#include "Rdefines.h"
#include "R_ext/Rdynload.h"

using namespace Rcpp;
// [[Rcpp::export]]
NumericVector focal_quantile(NumericVector xd, int ngbb, NumericVector sf) {
  //the imges are transfered to vector, ngbb is the size of the window  
  R_len_t i, j, k, q;
  int wrows = ngbb;
  int wcols = ngbb;
  int wn = wrows * wcols;

  int nrow = 6;//the input raste has 6 rows
  int ncol = 7;//the input raste has 7 cols

  int n = nrow * ncol;
  NumericVector xans(n);
  NumericVector xx(wn);

  int wr = floor(wrows / 2);
  int wc = floor(wcols / 2);

  int nwc = ncol - wc - 1;
  int col = 0;

  // first rows
  for (i = 0; i < ncol*wr; i++) {// the first row, the resutl is set as NA as the neighbor does not have nine values   
    xans[i] = R_NaReal; 
  }

  for (i = ncol*wr; i < (ncol * (nrow-wr)); i++) {//start from the second row
    col = i % ncol;
    if ((col < wc) | (col > nwc)) {//the first pixel of the second is also set as NA
      xans[i] = R_NaReal;
    } else {// to get the nine values in the 3*3 windows
      q = 0;
      for (j = -wr; j <= wr; j++) {
        for (k = -wc; k <= wc; k++) {
          xx[q] = xd[j * ncol + k + i]; 
          q++;
        }
      }
      xx = na_omit(xx);
      int n_qt = xx.size();
      if (n_qt > 0){//
        xans[i]=sum(xx)+100*sf[i];// here is the calculation, my goal is more complicated than this example
      } else {
        xans[i] = R_NaReal;//R_NaReal
      }

    }
  }
  // last rows
  for (i = ncol * (nrow-wr); i < n; i++) {  
    xans[i] = R_NaReal;
  }
  return(xans);
}

然后使用sourceCpp编译

生成示例数据进行测试

  rr=raster(nrow=6,ncol=7)## example for Ra
  projection(rr)="+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=WGS84"
  rr[]=(2:43)*10
  rrqt=rr/43 ## example for Rb
  ##it works fine, if there is no NA in Ra
  #rr[1:10]=NA #window of global enviornment is refleshing and then aborts with such NAs 
  focal_quantile(rr[],3,rrqt[])

示例结果

 [1]       NA       NA       NA       NA       NA       NA       NA       NA 118918.6 130810.5 142702.3 154594.2 166486.0       NA       NA
[16] 202161.6 214053.5 225945.3 237837.2 249729.1       NA       NA 285404.7 297296.5 309188.4 321080.2 332972.1       NA       NA 368647.7
[31] 380539.5 392431.4 404323.3 416215.1       NA       NA       NA       NA       NA       NA       NA       NA

结果 NA 是可以接受的，因为窗口中没有九个值。对于这样的例子，我改变了光栅 rr 的值(没有 NA)。它工作顺利。当我在 rr 中引入 NA 时，例如上面代码的第六行。全局环境窗口正在刷新，Rstudio 中止。

session 信息是

R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Rcpp_0.12.11 raster_2.5-8 sp_1.2-3    

loaded via a namespace (and not attached):
[1] rgdal_1.2-5     tools_3.3.0     grid_3.3.0      lattice_0.20-35

非常感谢!

Answer 1

首先，您应该只使用 #include <Rcpp.h>陈述。您添加的其他 header 不需要或已包含在 Rcpp.h 中.

---

其次，引用NA的正确方式NumericVector 的值Rcpp 中的 s 是使用 NA_REAL 不是 R 的 R_NaReal .

---

第三，你有一个越界错误。如果将括号从 [] 切换为至 ()你有边界检测。 Rcpp 0.12.11 的错误是:

"Index out of bounds: [index=3; extent=3]."

因此，这将创建一个 "Undefined Behavior" (UB)触发 RStudio 崩溃。

有问题的行是:

xx(q) = xd(j * ncol + k + i); 
^^^^^

现在，您可能会说这没有意义，因为 xx 的长度永远不应为 3。但是，此行有问题的原因是因为您正在更改 xx 中找到的值。当你放下 NA值:

xx = na_omit(xx);

你真的应该声明一个新的xy vector ，如果这是目标或更新常量以确保避免越界错误。

---

实现

#include <Rcpp.h>

// [[Rcpp::export]]
Rcpp::NumericVector focal_quantile(Rcpp::NumericVector xd,
                                   int ngbb,
                                   Rcpp::NumericVector sf) {
  //the imges are transfered to vector, ngbb is the size of the window  
  R_len_t i, j, k, q;
  int wrows = ngbb;
  int wcols = ngbb;
  int wn = wrows * wcols;

  int nrow = 6;//the input raste has 6 rows
  int ncol = 7;//the input raste has 7 cols

  int n = nrow * ncol;
  Rcpp::NumericVector xans(n);
  Rcpp::NumericVector xx(wn);

  int wr = floor(wrows / 2);
  int wc = floor(wcols / 2);

  int nwc = ncol - wc - 1;
  int col = 0;

  // first rows
  for (i = 0; i < ncol*wr; i++) {// the first row, the resutl is set as NA as the neighbor does not have nine values   
    xans[i] = NA_REAL; 
  }

  for (i = ncol*wr; i < (ncol * (nrow-wr)); i++) {//start from the second row
    col = i % ncol;
    if ((col < wc) | (col > nwc)) {//the first pixel of the second is also set as NA
      xans[i] = NA_REAL;
    } else {// to get the nine values in the 3*3 windows
      q = 0;
      for (j = -wr; j <= wr; j++) {
        for (k = -wc; k <= wc; k++) {
          xx[q] = xd[j * ncol + k + i]; 
          q++;
        }
      }
      Rcpp::NumericVector xx_subset = na_omit(xx);
      int n_qt = xx_subset.size();
      if (n_qt > 0){//
        xans[i]=sum(xx_subset)+100*sf[i];// here is the calculation, my goal is more complicated than this example
      } else {
        xans[i] = NA_REAL;//NA_REAL
      }

    }
  }

  // last rows
  for (i = ncol * (nrow-wr); i < n; i++) {  
    xans[i] = NA_REAL;
  }
  return(xans);
}

测试用例:

library("raster")
rr = raster(nrow=6,ncol=7)## example for Ra
projection(rr) = "+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=WGS84"
rr[] = (2:43)*10
rrqt = rr/43 ## example for Rb
rr[1:10] = NA 
focal_quantile(rr[],3,rrqt[])

输出:

 [1]        NA        NA        NA        NA        NA        NA        NA        NA  742.5581  915.8140 1099.0698 1292.3256
[13] 1375.5814        NA        NA 1625.3488 1828.6047 2041.8605 2265.1163 2378.3721        NA        NA 2718.1395 2831.3953
[25] 2944.6512 3057.9070 3171.1628        NA        NA 3510.9302 3624.1860 3737.4419 3850.6977 3963.9535        NA        NA
[37]        NA        NA        NA        NA        NA        NA

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旁注

如果您查看要翻译的代码，请注意有一个 naonly 部分后跟 na 组件。所以，翻译不一定是 1-1。