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I'm trying to get the chlorophyll a values from a NetCDF file using R software, but all I'm getting are missing values, NA. I would like to know if I'm doing something wrong or if the file really just has missing chlorophyll a values. I can get the Longitude and Latitude values with this method.

The file I'm using is from here https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/Mapped/Monthly/4km/chlor_a/ and I get missing values from any file I tried not only the one showed on the script.

require(rgdal)
require(maptools)
require(raster)
require(sp)
require(rorwr)
require(RNetCDF)

clorofila<- "C:\\Users\\User\\Desktop\\files\\A20172132017243.L3m_MO_CHL_chlor_a_4km.nc"

cla <- open.nc(clorofila)

print.nc(cla)
file.inq.nc(cla)

clor <- var.get.nc(cla,"chlor_a",start=c(1,1),count=c(8640,4320))
Long <- var.get.nc(cla,"lon")
Lat <- var.get.nc(cla, "lat")

With ncdf4 and raster I got the same results

require(ncdf4)

clorofila10<- "C:\\Users\\User\\Desktop\\files\\A20172132017243.L3m_MO_CHL_chlor_a_4km.nc"

nc <- nc_open(clorofila10)

val <- ncvar_get(nc, "chlor_a")
nc_close(nc)

raster

require(raster)
clorofila10<- "C:\\Users\\User\\Desktop\\files\\A20172132017243.L3m_MO_CHL_chlor_a_4km.nc"
clacla<-raster(clorofila10)
CHL1 <- raster(clorofila10, varname="chlor_a")
names(CHL1) <- 'chlor_a'

z <- getValues(CHL1)
  • You aren't actually showing us your results. If I do the same RNetCDF process as you, and then do all(is.na(clor)), I get FALSE, showing that not all the values are NA. There are a lot of NAs - 21 million compared to 16 million non-NA - but its not all NAs. Why do you think it is? – Spacedman Oct 13 '18 at 8:19
  • Reading the raster works for me too. Plotting it shows the NAs to be on the land, and the non-NAs to be in the seas and oceans. Is that what you expect from the dataset? – Spacedman Oct 13 '18 at 8:20
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You don't show what the issue is here, but I don't see any problem.

NOTE: this code downloads a 50 Mb file

f <- "A20172132017243.L3m_MO_CHL_chlor_a_4km.nc"
u <- "https://oceandata.sci.gsfc.nasa.gov/cgi/getfile"
curl::curl_download(file.path(u, f), f)
library(raster)
r <- raster(f, varname = "chlor_a")

range(values(r), na.rm = TRUE)
##[1]  0.01220753 99.85372162

## some values will be NA
extract(r, cbind(c(140, 150), c(-42, -50)))
#[1] 0.2061136        NA

I definitely recommend not reading all the values, keep them in the raster and use extract, cellFromXY, and related functions.

To get it off disk as a raster use readAll(raster(f)).

  • Thank you so much for your answer! My problem is that the result matrix from ncvar_get(nc, "chlor_a") or the result from getValues(CHL1) gives me all NA values from the begining till the end. Every single value is NA, and when I used the same functions previously on a Temperature netcdf file it gave me many temperature values intercalated with NA values. That was what I would expect in this case too, with chlor_a values. – TheBlueMagpie Oct 13 '18 at 2:43
  • I don't see that, the data is perfectly fine range(ncdf4::ncvar_get(ncdf4::nc_open(f), "chlor_a"), na.rm = TRUE) #[1] 0.01220753 99.85372162 – mdsumner Oct 13 '18 at 23:07

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