[Numpy-discussion] [Cdat-discussion] Arrays containing NaNs
Charles Doutriaux
doutriaux1@llnl....
Fri Jul 25 09:22:43 CDT 2008
Hi Stephane,
This is a good suggestion, I'm ccing the numpy list on this. Because I'm
wondering if it wouldn't be a better fit to do it directly at the
numpy.ma level.
I'm sure they already thought about this (and 'inf' values as well) and
if they don't do it , there's probably some good reason we didn't think
of yet.
So before i go ahead and do it in MV2 I'd like to know the reason why
it's not in numpy.ma, they are probably valid for MVs too.
C.
Stephane Raynaud wrote:
> Hi,
>
> how about automatically (or at least optionally) masking all NaN
> values when creating a MV array?
>
> On Thu, Jul 24, 2008 at 11:43 PM, Arthur M. Greene
> <amg@iri.columbia.edu <mailto:amg@iri.columbia.edu>> wrote:
>
> Yup, this works. Thanks!
>
> I guess it's time for me to dig deeper into numpy syntax and
> functions, now that CDAT is using the numpy core for array
> management...
>
> Best,
>
> Arthur
>
>
> Charles Doutriaux wrote:
>
> Seems right to me,
>
> Except that the syntax might scare a bit the new users :)
>
> C.
>
> Andrew.Dawson@uea.ac.uk <mailto:Andrew.Dawson@uea.ac.uk> wrote:
>
> Hi,
>
> I'm not sure if what I am about to suggest is a good idea
> or not, perhaps Charles will correct me if this is a bad
> idea for any reason.
>
> Lets say you have a cdms variable called U with NaNs as
> the missing
> value. First we can replace the NaNs with 1e20:
>
> U.data[numpy.where(numpy.isnan(U.data))] = 1e20
>
> And remember to set the missing value of the variable
> appropriately:
>
> U.setMissing(1e20)
>
> I hope that helps, Andrew
>
>
>
> Hi Arthur,
>
> If i remember correctly the way i used to do it was:
> a= MV2.greater(data,1.) b=MV2.less_equal(data,1)
> c=MV2.logical_and(a,b) # Nan are the only one left
> data=MV2.masked_where(c,data)
>
> BUT I believe numpy now has way to deal with nan I
> believe it is numpy.nan_to_num But it replaces with 0
> so it may not be what you
> want
>
> C.
>
>
> Arthur M. Greene wrote:
>
> A typical netcdf file is opened, and the single
> variable extracted:
>
>
> fpr=cdms.open('prTS2p1_SEA_allmos.cdf')
> pr0=fpr('prcp') type(pr0)
>
> <class 'cdms2.tvariable.TransientVariable'>
>
> Masked values (indicating ocean in this case) show
> up here as NaNs.
>
>
> pr0[0,-15:-5,0]
>
> prcp array([NaN NaN NaN NaN NaN NaN 0.37745094
> 0.3460784 0.21960783 0.19117641])
>
> So far this is all consistent. A map of the first
> time step shows the proper land-ocean boundaries,
> reasonable-looking values, and so on. But there
> doesn't seem to be any way to mask
> this array, so, e.g., an 'xy' average can be
> computed (it
> comes out all nans). NaN is not equal to anything
> -- even
> itself -- so there does not seem to be any
> condition, among the
> MV.masked_xxx options, that can be applied as a
> test. Also, it
> does not seem possible to compute seasonal averages,
> anomalies, etc. -- they also produce just NaNs.
>
> The workaround I've come up with -- for now -- is
> to first generate a new array of identical shape,
> filled with 1.0E+20. One test I've found that can
> detect NaNs is numpy.isnan:
>
>
> isnan(pr0[0,0,0])
>
> True
>
> So it is _possible_ to tediously loop through
> every value in the old array, testing with isnan,
> then copying to the new array if the test fails.
> Then the axes have to be reset...
>
> isnan does not accept array arguments, so one
> cannot do, e.g.,
>
> prmasked=MV.masked_where(isnan(pr0),pr0)
>
> The element-by-element conversion is quite slow.
> (I'm still waiting for it to complete, in fact).
> Any suggestions for dealing with NaN-infested data
> objects?
>
> Thanks!
>
> AMG
>
> P.S. This is 5.0.0.beta, RHEL4.
>
>
> *^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*
> Arthur M. Greene, Ph.D.
> The International Research Institute for Climate and Society
> The Earth Institute, Columbia University, Lamont Campus
> Monell Building, 61 Route 9W, Palisades, NY 10964-8000 USA
> amg*at*iri-dot-columbia\dot\edu | http://iri.columbia.edu
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> --
> Stephane Raynaud
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