Add _FillValue to all active and debug tracer fields #571
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Nice work @wenshanw! Exactly what we discussed on Friday. |
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Note: This PR is based off of #533 so it should be rebased onto ocean/develop after that PR is merged and develop is merged into ocean/develop. |
mark-petersen
added a commit
that referenced
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Jul 13, 2020
Change name of missing value attribute from missing_value to _FillValue This PR changes the name of the missing value attribute in netCDF output files from missing_value to _FillValue. The _FillValue attribute can be set by adding a missing_value to individual variables and var_arrays in the Registry file (See #571 for an example). This change is needed because some analysis software, notably NCO, does not support the missing_value attribute by default and expects _FillValue instead.
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@wenshanw, this branch needs to be rebased onto If my branch looks good to you, you can just do a hard reset to mine. Go to the local directory where you have your Then, do a force push to your remote. The exact syntax will depend on what you named your remote. I called it |
TestingIn my rebased branch, I ran There are Looking at The remaining 5 tracer variables are a good start but we would need @wenshanw, I think you mentioned on at least two different calls that you thought all the variables from In any case, after the rebase, I think there's a considerable amount of work to do before |
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@wenshanw, could you change the name of the PR to something like "Add _FillValue to all active and debug tracer fields"? In the description of the PR at the top, could you edit to change "active tracers" to "active and debug tracers" in both items? |
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@xylar I am sorry I somehow had the impression to use this version. I have another version that I added So we've done rebased here, right? (after I force-pushed your |
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@xylar I remove the |
wenshanw
changed the title
Yes, by resetting to my branch and force-pushing, these commits are now "based" off of the current
Yes, that's right.
That's something for us to look into. One possibility is that MPAS variables default to being filled with zeros unless a different default value is set. But setting the fill value is supposed to also set that as the new default. So there must be somewhere that tendency variables get set to zero explicitly. @mark-petersen, could you help us track down where that is? |
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@mark-petersen, I think this is ready to review. I think it might make sense to add fill values to just these 5 variables as a starting point and have a follow-up PR for the remaining variables. Does that seem okay to you? |
xylar
approved these changes
Aug 27, 2020
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This PR does, indeed, add _FillValues to the following five variables in timeSeriesStatsDaily output:
timeDaily_avg_activeTracers_temperature:_FillValue = 9.96920996838687e+36 ;
timeDaily_avg_activeTracers_salinity:_FillValue = 9.96920996838687e+36 ;
timeDaily_avg_debugTracers_tracer1:_FillValue = 9.96920996838687e+36 ;
timeDaily_avg_debugTracers_tracer2:_FillValue = 9.96920996838687e+36 ;
timeDaily_avg_debugTracers_tracer3:_FillValue = 9.96920996838687e+36 ;
I want to do some additional testing (including checking the EC60to30 mesh and timeSeriesStatsMonthly) once fill values are in all variables.
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1, Added the
_FillValueattribute to active and debug tracers in the output NetCDF files.2, Replaced
-1e34with_FillValuein active and debug tracers.