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How would I write this using CDO?
Added by Eleanor Percy-Rouhaud over 1 year ago
Hi!
Im relatively new to CDO, but am loving the robustness of it so far. There is something i am struggling to do though - is there a way of counting how many non zero elements i have in a particular dimension of my data set? Its a netCDF data set (written in the inline code as ds). ive done it in python, the particular part about counting how many non missing data points there are, is:
data = ds['variable']
num_non_missing = np.count_nonzero(~np.isnan(data))
I would then need to store all these values somehow - either in another netcdf file, or ideally, tag it on to a new dimension in the netcdf file it belongs to (ds in this case). But thats getting ahead of myself - my main question: is there a way to count this non missing thing in cdo?
Thanks!
hi Eleanor!
First thing popping in my head is
- transform the data into a 0-1-mask where 1 is the value you need (be it zero, non-zero, missing values or whatever)
- sum up the field with the
fldsum operator
this with work individual levels or in full 3d.
If (like in your case) the mask is a normal missing value, the fldsum will ignore them anyway. you can check the number of missing values with
cdo infov
Does this help?
cheers
ralf
Hi!
thanks for your quick reply! It does help yes, the fldsum idea also came to me, but whats tripping me up a bit is transforming it into a 0-1 mask. I forgot to mention that I would loop this over a directory with about 20 files, which have different masks. Is there a way of doing this 'if its not 0' thing in cdo? or would it be better to somehow loop over the ranges for each file (they are well defined).
cheers,
eleanor
so .. is it based on missing values? or normal data values? if missing values are represented in the file in a CF-conform-way, the procedure is not dependent on the exact numeric value of the missing value
Hi,
maybe this is what you are looking for 
num_non_missing = cdo.fldsum(input='-expr,"tos=((tos > 0. ? 1 : 0))" -seltimestep,1 '+infile,
options='--reduce_dim',
returnXArray='tos')
print(num_non_missing.values)
For completeness: the variable name here in the example is 'tos' and only the first time step is selected
from cdo import Cdo
cdo = Cdo()
num_non_missing = cdo.fldsum(input='-expr,"tos=((tos > 0. ? 1 : 0))" -seltimestep,1 '+infile,
options='--reduce_dim',
returnXArray='tos')
print(num_non_missing.values)
this looks like the gtc operator (greater-than-constant).
What about
cdo.fldsum(input=' -gtc,1 '+infile, options='--reduce_dim', returnXArray='tos')
Out of curiosity, which of our suggestions is what you were looking for?
hi!
thanks again for all your responses 
I think the first answer with the fldsum is the most like what i was looking for, since it was most like what i tried before. but so far nothing is quite fully working for me, and i think its creating the 0-1 mask that is tripping me up. would i do this using setrtoc, for example cdo setrtoc,10,19.99999,1 '+mask+' '+temp_file ? but wouldn't this set all data points in that range equal to 1, even if they are NaN or 0 ?
To summarise, the fldsum i think is exactly what i need, im just a bit confused about how i can create a 0-1 mask ..
to add to this: in pure python, i did this using the non missing thing i wrote above, in my original question. in cdo, i am unsure how to implement the same idea, and cant think of another way that achieves the same thing.
setrtoc,10,19.99999,1 will not touch NaNs. If the NaN is not declaired a the missing value you will get problem working with these cells. Usually you want to avoid these points anyway, so setting then to be _missing values _ is my recommendation. CDO does ignore declared missing values (how to do this is part of the CF-convention) unless you ask for it
Eleanor Percy-Rouhaud wrote in RE: How would I write this using CDO?:
to add to this: in pure python, i did this using the non missing thing i wrote above, in my original question. in cdo, i am unsure how to implement the same idea, and cant think of another way that achieves the same thing.
check
cdo -h setrtomiss
for operators to change or set missing values
Ralf Mueller wrote in RE: How would I write this using CDO?:
setrtoc,10,19.99999,1 will not touch NaNs. If the NaN is not declaired a the missing value you will get problem working with these cells. Usually you want to avoid these points anyway, so setting then to be _missing values _ is my recommendation. CDO does ignore declared missing values (how to do this is part of the CF-convention) unless you ask for it
Ah okay, good to know that missing values are automatically ignored. I set them to missing values, and then the setrtoc,10, 19.99999,1 '+mask+' '+temp_file and fldsum ' +temp_file+' '+output_file should work. i do get a single valued array in my netcdf files out of it, but they are incorrect - way too big. this happens when i try it for a single file, or in a loop over a directory containing all the files i need to do this operation on. Its really strange. Ill think more on it, maybe it isnt wrong, or maybe i think of something!
thanks for all the replies, i really appreciate it
Eleanor, you could upload some sample of the data (may gzip/zip if needed). We are too close to solution to stop now ;-)
hi,
So sorry it took so long to reply! I agree, and I still haven't found a solution. I could upload a sample, but I guess it could also be any spatial data where a particular range is set to 1 and summed up over the whole area, like a land cover product for example...this would be good to test the command. In fact, I might try this later!
You'll hear from me again with some zipped data soon