I am trying to make a shapefile where the zero values are taken out in order to reduce the amount of space used. I attempted to do this through the following procedure but only got more zero values displayed:
cdo gtc,0.000008 precip_2022110815_0p50.nc mask1.nc
cdo setctomiss,0 mask1.nc mask2.nc
cdo mul precip_2022110815_0p50.nc mask2.nc precip_2022110815_0p50_adjust.nc
cdo setctomiss,0 precip_2022110815_0p50_adjust.nc precip_2022110815_0p50_final.nc
gdal_contour -a precip -i 0.00001 precip_2022110815_0p50_final.nc precip_2022110815_0p50.shp
I got the netcdf from a grib file that was obtained from ftp.ncep.noaa.gov.
Is there anyway I could tweak this code or other methods I could use to get a shape file where all zero values are filtered out or even values below a certain threshold are filtered out? Is there a way to filter the values below a certain amount out from a grib2 file?
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I am analyzing a time series of data that is split by time into two NetCDF files (infiles). These files have a different number of variables/fields, by design. Traditionally I have been using Climate Data Operators (CDO) to easily merge two datasets sorted by time using the following command in a terminal:
cdo mergetime <infiles> <outfile>
this command merges any number of files "infiles" sorted by time and writes a new "outfile" containing a time series of all the data in each ; however this doesn't appear to work by default with cdo, as it kicks back the following:
cdo select (Abort): Input streams have different number of variables per timestep!
the statement is true, each file does have a different number of variables per timestep. But it prevents me from looking at the dataset as a whole. I have also tried the following modifications to the cdo command I use to merge the time series, without success:
cdo mergetime -select,name=<variable> <infiles> <outfile>
cdo -select,name=<variable> <infiles> <outfile>
I have read through the CDO Userguide and have not found any alternative solutions yet. I would be very grateful if anyone could offer a workaround for joining the two files into a single time-series of data (preferably in cdo but not necessarily) as I am running out of ideas.
On phone but you could delete the extra annoying new variables from files with nco like this
ncks -x -v var1,var2 in.nc out.nc
And then merge as usual. I think you can use the cdo delete operator to do the same thing.
I'm working with a netCDF file with a spatially averaged wind variable, which is a function of time only.
I would like to split the file into years with east wind and years with west wind.
I thought I would do it with cdo but I don't know how to write the condition.
Anything with splityear, 'u <0'?
I do not think this is advisable, as you will split the files in to two different NetCDF files with incompatible grids. In my view this would defeat the purpose of storing the data in NetCDF files.
But, if you wish to do it, there is a way within CDO. As you haven't provided files I can outline a strategy.
First create a mask file identifying cells with u<0:
cdo -setrtomiss,-10000,0 -selname,u infile.nc mask.nc
Then apply reducegrid to the infile using this mask:
cdo -reducegrid,mask.nc infile.nc outfile.nc
That should do it for the u condition. Just test that and modify it for the other variables.
How can I remove seasonality data from a timeseries with the data stored in a netcdf file? I would like to find a solution using Linux, while I used Grads and Ferret for visualization.
Thanks a lot!
You can use CDO to calculate the average for each day/month of the year and subtract from the origin file:
If the file contains daily data:
cdo sub in.nc -ydaymean in.nc deseasonalized.nc
Likewise if the data is monthly:
cdo sub in.nc -ymonmean in.nc deseasonalized.nc
The ydaymean and ymonmean commands calculate the annual cycle over the dataset in.nc, i.e. ymonmean returns 12 time slices, the average of all the january, february and so on, which is then subtracted from the original file using sub. I've used piping, but it may be easier to understand on two separate lines:
cdo ymonmean in.nc annual_cycle.nc
cdo sub in.nc annual_cycle.nc deseasonalized.nc
This does exactly the same, deseasonalized.nc will be identical (well almost, there will be a few bytes differences due to the different "history" log in the netcdf global metadata header), but you will also have a new file with the annual_cycle.nc inside it (might also be useful?).
When doing the subtraction, CDO detects that the number of timeslices is smaller in the second file to be subtracted and thus loops/cycles through it. Note as the seasonal cycle is calculated from the same file as the original data it is fine to simply use "sub" as, if the data starts in e.g. April, the results of ymonmean will also start from April. However, if you want to remove a seasonal cycle calculated from a different source, the start day/month may be different and you end up subtracting e.g. April mean from January! To avoid this, you can use the ymonsub command instead:
cdo ymonsub full_timeseries.nc seasonal_file.nc deseasonalised.nc
In addition, there are now also packages in both R and python to allow you to access the full functionality of cdo from within those languages without having to resort to using shell access tools.
Edit 2021: i now have a video on this topic you can view here https://youtu.be/jKlA1ouoQIs
I have 20 netCDF files containing oceanographic CTD data. Each file contains the same dimension and variable names, however they differ in the size of the vertical coordinate (ie. CTD profiles inshore have a smaller depth range than profiles offshore). I need to concatenate these separate files into one netCDF file with a record variable "station".
I have tried:
ncecat -u station *.nc outfile.nc
This concatenates the files in the correct way, but it takes the dimension size of the first netCDF file (which is the smallest) and so I lose the data below the depth of the shallowest CTD profile for the rest of the netCDF files.
I'm assuming I need to add FillValues (or similar) in place of the data that is shallower than the maximum depth of the deepest CTD profile.
Is there a way to do this using ncecat?
The closest you can get with ncecat alone is to use group aggregation to store each station profile as its own group in a netCDF4 file. Then you do not need to search for and fill-in any missing data:
ncecat --gag *.nc outfile.nc
Is there a quick way to know how many missing values are in a netcdf file? Possibly using R.
Currently I have to
hum<-nc_open("rhum.sig995.2008.nc")
rhum<-ncvar_get(hum, "rhum")
then manually look up the missing value by typing 'hum' and copy it into this operation
sum(abs(rhum - 9.96920996838687e+36) < -9.96920996838687e+36)
Is there a more direct way, especially if I have to work with hundreds of files? I would like to avoid copying and pasting the missing value, and also I am not sure with what kind of precision the number should be handled.
My suggestion is to use the excellent raster package:
install.packages(raster)
library(raster)
r <- raster("rhum.sig995.2008.nc", var="rhum")
NAnum <- summary(r)[6]
The total number of missing data points for variable names "var" can be stored in a new additional variable using
ncap2 -s "nmiss=number_miss(var)" in.nc out.nc
or
ncap2 -s "nmiss=var.number_miss()" in.nc out.nc
If your data has a time dimension and you want to see the total number of missing points summed over the space dimensions, then you can see this with
cdo info in.nc