[R] Request for help about running a loop and reading .NC files

[David Pierce]

 Hey Bhaskar,

Dave Pierce here, the author and maintainer of the ncdf4 package. What
platform are you working on? If you work on Linux, I'd be happy to send you
a new source tar version of the ncdf4 package I've made that handles this
case. It now has a settable parameter in nc_open called "return_on_error",
and if you set that to TRUE, then nc_open always returns. If no error was
encountered, then the return list element $error is FALSE, and if an error
was encountered, $error is set to TRUE. So you could do this:

for( ifile in 1:nfiles ) {
    nc = nc_open( filename[ifile], return_on_error=TRUE )
    if( nc$error == FALSE ) {
        ... do your processing here ...
        }
  else
        print(paste("Error encountered, skipping file", filename[ifile]))

Regards,

--Dave

On Tue, Mar 24, 2020 at 5:13 AM Bhaskar Mitra <bhaskar.kolkata using gmail.com>
wrote:

> Hello Everyone,
>
> I have written a loop which reads hundreds of .nc files
> and extract information from each .nc file and
> exports that corresponding information as a csv file.
>
> The loop works fine until it encounters a .nc file which it cannot read
> and the loop stops.
>
>  I would appreciate if anyone can suggest how can I modify
> the loop, whereby the loop will continue to run by bypassing those
> particular
> files which it cannot read or if any particular file has an error.
>
> In the end, I was also hoping to modify the loop such that it
> will generate a report which will inform me which
> files were not read by the loop.  The codes are given below
>
> Thanks for your help,
>
> Regards,
> Bhaskar Mitra
>
>
> #_------------------------------------------------------------------
>
>
> library(ncdf4)
> library(reshape2)
> library(dplyr)
> library(stringr)
>
>
> setwd("directory path")
>
> Output <- "directory path"
>
> flist <- list.files(path ="NCFiles/", pattern = "^.*\\.(nc|NC|Nc|Nc)$")
>
> for (i in 1: length(flist))
> {
>
>   nc <- nc_open(paste0("NCFiles/",flist[i]))
>   mean1 <- ncvar_get(nc,attributes(nc$dim)$names[3])
>   nc_close(nc)
>
>   mean_chl_df <- melt(mean1)
>   trial.table.df <-as.data.frame(mean_chl_df)
>
>
> write.csv(trial.table.df,paste0(Output,"/",tools::file_path_sans_ext(flist[i]),".csv"))
>
> }
>
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>
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-- 

-------------------------------------------------------------------
David W. Pierce
Division of Climate, Atmospheric Science, and Physical Oceanography
Scripps Institution of Oceanography
(858) 534-8276 (voice)  /  (858) 534-8561 (fax)    dpierce using ucsd.edu
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