[R-sig-Geo] Extract VIIRS data in R

[Frederico Faleiro]

Hi Miluji,

the R in general do not handle very well with netCDF. However I
recommend you use the netcdf4 package before try others.
This link is a good start:
http://geog.uoregon.edu/bartlein/courses/geog490/week04-netCDF.html#get-coordinate-including-time-variables
.
The coordinates of this file is not in longitude and latitude, it use
"number_of_lines" for X Axis and "number_of_pixels" for Y Axis. This way
the difference between the cells is always one and raster package
interprete the difference as one degree and return an warning about it.
I open the file in the software Panoply (design to work with netCDF)  and
everything is OK apparently.
Check bellow some exploration of the data in R.

library(raster)
library(ncdf4)
library(rgdal)

# netcdf4 package
netcdf_file <- "VNP02DNB_NRT.A2020069.1048.001.nc"
nc <- nc_open(netcdf_file)
print(nc)
# check your variable is structured as:
observation_data/DNB_observations[number_of_pixels,number_of_lines]
# variables available
names(nc[["var"]])
# properties from your variable
ncatt_get(nc, "observation_data/DNB_observations")
# get the variables values and check the structure
obs_matrix <- ncvar_get(nc, "observation_data/DNB_observations")
str(obs_matrix)

# raster package
nc_r <- brick(netcdf_file, lvar=0, values=TRUE,
varname="observation_data/DNB_observations")
# [1] "vobjtovarid4: **** WARNING **** I was asked to get a varid for
dimension named number_of_pixels BUT this dimension HAS NO DIMVAR! Code
will probably fail at this point"
# [1] "vobjtovarid4: **** WARNING **** I was asked to get a varid for
dimension named number_of_lines BUT this dimension HAS NO DIMVAR! Code will
probably fail at this point"

Best regards,

Frederico Faleiro
Postdoctoral Researcher in the INCT-EECBio (https://www.eecbio.ufg.br/)
Federal University of Goiás | Brazil
RG: https://www.researchgate.net/profile/Frederico_Faleiro

On Tue, Mar 17, 2020 at 11:39 AM Miluji Sb <milujisb using gmail.com> wrote:

> Dear all,
>
> Hope everyone is keeping safe.
>
> I am trying to extract/read VIIRS nighttime lights data but the output
> seems rather strange.
>
> I have uploaded the file here
> <https://drive.google.com/open?id=1zpqXJ8AlEcnk6ApRb75tfQc4-Y8AfK5h> so as
> not exceed the size limit of the email.
>
> ## Code ##
> library(ncdf4)
> library(rgdal)
>
> netcdf_file <- c("VNP02DNB_NRT.A2020069.1048.001.nc")
> nl <- brick(netcdf_file, lvar=0, values=TRUE,
> varname="observation_data/DNB_observations")
>
> ## Detail ##
> class      : RasterLayer
> dimensions : 3232, 4064, 13134848  (nrow, ncol, ncell)
> resolution : 1, 1  (x, y)
> extent     : 0.5, 4064.5, 0.5, 3232.5  (xmin, xmax, ymin, ymax)
> crs        : NA
> source     : C:/Users/shour/Desktop/VNP02DNB_NRT.A2020069.1048.001.nc
> names      : DNB.observations.at.pixel.locations
> zvar       : observation_data/DNB_observations
>
> The spatial resolution is supposed to be 750m but this shows 1°. What am I
> doing wrong? Any help will be greatly appreciated. Thank you.
>
> Sincerely,
>
> Millu
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

	[[alternative HTML version deleted]]