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

[Miluji Sb]

Dear all,

Thank you everyone. The issue (as pointed out) is the following;

# [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"

I have contacted the VIIRS people and will keep you posted here. Thank you
again!

Best,

Milu

On Wed, Mar 18, 2020 at 3:34 PM Zia Ahmed <zia207 using gmail.com> wrote:

> This is might help you:
>
> https://zia207.github.io/geospatial-r-github.io/netCDF-data-processing.html
>
>
> Zia
>
> On Wed, Mar 18, 2020, 9:34 AM Frederico Faleiro <fvfaleiro using gmail.com>
> wrote:
>
>> 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]]
>> >
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>> >
>>
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>>
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