将 netcdf 时间变量转换为 R 日期对象 [英] convert a netcdf time variable to an R date object

问题描述

我有一个带有时间序列的 netcdf 文件，时间变量具有以下典型元数据:

I have a netcdf file with a timeseries and the time variable has the following typical metadata:

    double time(time) ;
            time:standard_name = "time" ;
            time:bounds = "time_bnds" ;
            time:units = "days since 1979-1-1 00:00:00" ;
            time:calendar = "standard" ;
            time:axis = "T" ;

在 R 中，我想将时间转换为 R 日期对象.我目前通过读取单位属性并拆分字符串并使用第三个条目作为我的原点(因此假设间距为天"，时间为 00:00 等)以硬连线方式实现了这一点:

Inside R I want to convert the time into an R date object. I achieve this at the moment in a hardwired way by reading the units attribute and splitting the string and using the third entry as my origin (thus assuming the spacing is "days" and the time is 00:00 etc):

require("ncdf4")
f1<-nc_open("file.nc")
time<-ncvar_get(f1,"time")
tunits<-ncatt_get(f1,"time",attname="units")
tustr<-strsplit(tunits$value, " ")
dates<-as.Date(time,origin=unlist(tustr)[3])

这个硬接线解决方案适用于我的特定示例，但我希望 R 中可能有一个包可以很好地处理时间单位的 UNIDATA netcdf 数据约定并将它们安全地转换为 R 日期对象?

This hardwired solution works for my specific example, but I was hoping that there might be a package in R that nicely handles the UNIDATA netcdf data conventions for time units and convert them safely to an R date object?

推荐答案

没有，据我所知.我使用 lubridate 有这个方便的功能，它与您的基本相同.

There is not, that I know of. I have this handy function using lubridate, which is basically identical to yours.

getNcTime <- function(nc) {
    require(lubridate)
    ncdims <- names(nc$dim) #get netcdf dimensions
    timevar <- ncdims[which(ncdims %in% c("time", "Time", "datetime", "Datetime", "date", "Date"))[1]] #find time variable
    times <- ncvar_get(nc, timevar)
    if (length(timevar)==0) stop("ERROR! Could not identify the correct time variable")
    timeatt <- ncatt_get(nc, timevar) #get attributes
    timedef <- strsplit(timeatt$units, " ")[[1]]
    timeunit <- timedef[1]
    tz <- timedef[5]
    timestart <- strsplit(timedef[4], ":")[[1]]
    if (length(timestart) != 3 || timestart[1] > 24 || timestart[2] > 60 || timestart[3] > 60 || any(timestart < 0)) {
        cat("Warning:", timestart, "not a valid start time. Assuming 00:00:00\n")
        warning(paste("Warning:", timestart, "not a valid start time. Assuming 00:00:00\n"))
        timedef[4] <- "00:00:00"
    }
    if (! tz %in% OlsonNames()) {
        cat("Warning:", tz, "not a valid timezone. Assuming UTC\n")
        warning(paste("Warning:", timestart, "not a valid start time. Assuming 00:00:00\n"))
        tz <- "UTC"
    }
    timestart <- ymd_hms(paste(timedef[3], timedef[4]), tz=tz)
    f <- switch(tolower(timeunit), #Find the correct lubridate time function based on the unit
        seconds=seconds, second=seconds, sec=seconds,
        minutes=minutes, minute=minutes, min=minutes,
        hours=hours,     hour=hours,     h=hours,
        days=days,       day=days,       d=days,
        months=months,   month=months,   m=months,
        years=years,     year=years,     yr=years,
        NA
    )
    suppressWarnings(if (is.na(f)) stop("Could not understand the time unit format"))
    timestart + f(times)
}

您可能还想看看 ncdf4.helpers::nc.get.time.series

请注意，新提议且目前正在开发中的 awesome stars 包将自动处理日期，请参阅 第一篇博文 示例.

note that the newly-proposed and currently in developement awesome stars package will handle dates automatically, see the first blog post for an example.

另一种方法是直接使用 units 包，这就是 stars 使用的.可以做这样的事情:(仍然没有正确处理日历，我不确定 units 可以)

another way is to use the units package directly, which is what stars uses. One could do something like this: (still not handling the calendar correctly, I'm not sure units can)

getNcTime <- function(nc) { ##NEW VERSION, with the units package
    require(units)
    require(ncdf4)
    options(warn=1) #show warnings by default
    if (is.character(nc)) nc <- nc_open(nc)
    ncdims <- names(nc$dim) #get netcdf dimensions
    timevar <- ncdims[which(ncdims %in% c("time", "Time", "datetime", "Datetime", "date", "Date"))] #find (first) time variable
    if (length(timevar) > 1) {
        warning(paste("Found more than one time var. Using the first:", timevar[1]))
        timevar <- timevar[1]
    }
    if (length(timevar)!=1) stop("ERROR! Could not identify the correct time variable")
    times <- ncvar_get(nc, timevar) #get time data
    timeatt <- ncatt_get(nc, timevar) #get attributes
    timeunit <- timeatt$units
    units(times) <- make_unit(timeunit)
    as.POSIXct(time)
}

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