Geographic Information Systems Asked by DI S on November 5, 2020
I am working with MODIS EVI 250m file in NetCDF format and trying to get the stack of EVI layers.
So, I do:
# check nc-file for variables names
nc = nc_open(flist[1], write=FALSE, readunlim=TRUE, verbose=FALSE, auto_GMT=TRUE, suppress_dimvals=FALSE ) # open connection
nc # check attributes and var names
nc_close(nc) # close connection
and after
tmpin.s <- stack(flist[1], varname="_250m_16_days_EVI")
and I see the error with CRS
> tmpin.s <- stack(flist[1], varname="_250m_16_days_EVI")
[1] ">>>> WARNING <<< attribute epsg_code is an 8-byte value, but R"
[1] "does not support this data type. I am returning a double precision"
[1] "floating point, but you must be aware that this could lose precision!"
[1] ">>>> WARNING <<< attribute semi_major_axis is an 8-byte value, but R"
[1] "does not support this data type. I am returning a double precision"
[1] "floating point, but you must be aware that this could lose precision!"
Error in CRS(as.character(projection(crs))) : no colon in init= string
What am I doing wrong?
PS
Here is the output of netCDF file
File D:/2019_R_ncr/MOD13Q1.006_250m_NCRfull.nc (NC_FORMAT_NETCDF4):
3 variables (excluding dimension variables):
byte crs[] (Contiguous storage)
[1] ">>>> WARNING <<< attribute epsg_code is an 8-byte value, but R"
[1] "does not support this data type. I am returning a double precision"
[1] "floating point, but you must be aware that this could lose precision!"
[1] ">>>> WARNING <<< attribute semi_major_axis is an 8-byte value, but R"
[1] "does not support this data type. I am returning a double precision"
[1] "floating point, but you must be aware that this could lose precision!"
grid_mapping_name: latitude_longitude
_CoordinateAxisTypes: GeoX GeoY
epsg_code: 4326
horizontal_datum_name: WGS84
semi_major_axis: 6378137
inverse_flattening: 298.257223563
longitude_of_prime_meridian: 0
short _250m_16_days_EVI[lon,lat,time] (Chunking: [492,144,26]) (Compression: shuffle,level 4)
_FillValue: -3000
coordinates: time lat lon
grid_mapping: crs
valid_min: -2000
valid_max: 10000
long_name: 250m 16 days EVI
units: EVI
scale_factor_err: 0
add_offset_err: 0
calibrated_nt: 5
scale_factor: 1e-04
add_offset: 0
int _250m_16_days_VI_Quality[lon,lat,time] (Chunking: [389,121,21]) (Compression: shuffle,level 4)
_FillValue: 65535
coordinates: time lat lon
grid_mapping: crs
valid_min: 0
valid_max: 65534
long_name: 250m 16 days VI Quality
units: bit field
Legend:
Bit Fields Description (Right to Left):
[0-1] : MODLAND_QA [2 bit range]
00: VI produced, good quality
01: VI produced, but check other QA
10: Pixel produced, but most probably cloudy
11: Pixel not produced due to other reasons than clouds
[2-5] : VI usefulness [4 bit range]
0000: Highest quality
0001: Lower quality
0010..1010: Decreasing quality
1100: Lowest quality
1101: Quality so low that it is not useful
1110: L1B data faulty
1111: Not useful for any other reason/not processed
[6-7] : Aerosol quantity [2 bit range]
00: Climatology
01: Low
10: Average
11: High (11)
[8] : Adjacent cloud detected; [1 bit range]
1: Yes
0: No
[9] : Atmosphere BRDF correction performed [1 bit range]
1: Yes
0: No
[10] : Mixed clouds [1 bit range]
1: Yes
0: No
[11-13] : Land/Water Flag [3 bit range]
000: Shallow ocean
001: Land (Nothing else but land)
010: Ocean coastlines and lake shorelines
011: Shallow inland water
100: Ephemeral water
101: Deep inland water
110: Moderate or continental ocean
111: Deep ocean
[14] : Possible snow/ice [1 bit range]
1: Yes
0: No
[15] : Possible shadow [1 bit range]
1: Yes
0: No
3 dimensions:
time Size:415
standard_name: time
axis: T
calendar: julian
units: days since 2000-01-01 00:00:00
lat Size:2298
standard_name: latitude
units: degrees_north
_CoordinateAxisType: GeoY
axis: Y
lon Size:7377
standard_name: longitude
units: degrees_east
_CoordinateAxisType: GeoX
axis: X
7 global attributes:
_NCProperties: version=1|netcdflibversion=4.4.1.1|hdf5libversion=1.8.18
title: MOD13Q1.006 for aid0001
Conventions: CF-1.6
institution: Land Processes Distributed Active Archive Center (LP DAAC)
source: AppEEARS v2.28
references: See README.txt
history: See README.txt
...looks like you need to define your crs within stack()
;
x<-stack('yourfile.nc',
# varname = '_250m_16_days_EVI', crs=CRS("+init=epsg:4326"))
if this doesnt work, try to process your data in modis-native crs
'+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs'
with AppEARS
https://lpdaacsvc.cr.usgs.gov/appeears/
and reproject it with projectRaster()
also check your Date-Format:
class(getZ(x))
Answered by consumere on November 5, 2020
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