Xarray: Adding Example/Tutorial of importing data to Xarray (Merge/conact/etc)

[NicWayand]

I love xarray for analysis but getting my data into xarray often takes a lot more time than I think it should. I am a hydrologist and very often hydro data is poorly stored/formatted, which means I need to do multiple merge/conact/combine_first operations etc. to get to a nice xarray dataset format. I think having more examples for importing different types of data would be helpful (for me and possibly others), instead of my current approach, which often entails trial and error.

I can start off by providing an example of importing funky hydrology data that hopefully would be general enough for others to use. Maybe we can compile other examples as well. With the end goal of adding to the readthedocs.

@klapo @jhamman

[shoyer]

I'm certainly always happy to see more tutorials and examples for the docs, especially when they hit on common workflows.

[klapo]

I have an example that I just struggled through that might be relevant to this idea. I'm running a point model using some arbitrary number of experiments (for the below example there are 28 experiments). Each experiment is opened and then stored in a dictionary resultsDict. The below excerpt extracts all of my scalar variables, concatenates them along an experiment dimension, and finally combines all scalar variables into a DataSet. I often find myself struggling to combine data (for instance meteorological stations) into a DataSet and I can never remember how to use merge and/or concat.

resultsDataSet = xr.Dataset()
for k in scalar_data_vars:
    if not 'scalar' in k:
        continue

    # Assign scalar value to a dataArray
    darray = xr.concat([resultsDict[scen][scalar_data_vars[0]] for scen in resultsDict], dim='expID')
    # Remove hru dimension, as it is unused
    darray = darray.squeeze('hru')

    resultsDataSet[k] = darray
print(resultsDataSet)

which yields

<xarray.Dataset>
Dimensions:                (expID: 28, time: 8041)
Coordinates:
  * time                   (time) datetime64[ns] 2008-10-01 ...
    hru                    int32 1
Dimensions without coordinates: expID
Data variables:
    scalarRainPlusMelt     (expID, time) float64 -9.999e+03 -9.999e+03 ...
    scalarSWE              (expID, time) float64 -9.999e+03 -9.999e+03 ...
    scalarSnowSublimation  (expID, time) float64 -9.999e+03 -9.999e+03 ...
    scalarInfiltration     (expID, time) float64 -9.999e+03 -9.999e+03 ...
    scalarSurfaceRunoff    (expID, time) float64 -9.999e+03 -9.999e+03 ...
    scalarSurfaceTemp      (expID, time) float64 -9.999e+03 -9.999e+03 ...
    scalarSenHeatTotal     (expID, time) float64 -9.999e+03 -9.999e+03 ...
    scalarLatHeatTotal     (expID, time) float64 -9.999e+03 -9.999e+03 ...
    scalarSnowDepth        (expID, time) float64 -9.999e+03 -9.999e+03 ...

And here is a helper function that can do this more generally, which I wrote a while back.

def combinevars(ds_in, dat_vars, new_dim_name='new_dim', combinevarname='new_var'):
    ds_out = xr.Dataset()
    ds_out = xr.concat([ds_in[dv] for dv in dat_vars], dim='new_dim')
    ds_out = ds_out.rename({'new_dim': new_dim_name})
    ds_out.coords[new_dim_name] = dat_vars
    ds_out.name = combinevarname

    return ds_out

[klapo]

Also, just a small thing in the docs for concat

The example includes this snippet
xr.concat([arr[0], arr[1]], pd.Index([-90, -100], name='new_dim'))
but as far as I can tell, name is not an argument accepted by concat

[shoyer]

Also, just a small thing in the docs for concat

This is a certainly confusing, but actually correct. name is a parameter to pd.Index().

[darothen]

@klapo! Great to see you here!

Happy to iterate with you on documenting this functionality. For reference, I wrote a package for my dissertation work to help automate the task of constructing multi-dimensional Datasets which include dimensions corresponding to experimental/ensemble factors. One of my on-going projects is to actually fully abstract this (I have a not-uploaded branch of the project which tries to build the notion of an "EnsembleDataset", which has the same relationship to a Dataset that an pandas Panel used to have to a DataFrame).

[klapo]

@darothen That sounds great!

I think we should be clearer. The issue that @NicWayand and I are highlighting is the coercing observational data, which often comes with some fairly heinous formatting issues, into an xarray format. The stacking of these data along a new dimension is usually the last step in this process, and one that can be frustrating. An example of this in practice can be found in this notebook (please be forgiving, it is one of the first things I ever wrote in python).

https://github.com/klapo/CalRad/blob/master/CR.SurfObs.DataIngest.xray.ipynb

The data flow looks like this:

• read the csv summarizing each station
• read data from one set of stations using pandas
• clean the data
• assign the data in a pandas DataFrame to a dictionary of DataFrames
• rinse and repeat for the other set of data
• concat the dictionary of DataFrames into a single DataFrame
• convert to an xarray DataSet

This example is a little ludicrous because I didn't know what I was doing, but I think that's the point. There is a lot of ambiguity on which tools to use at what point. Concatenating a dictionary of DataFrames into a single DataFrame and then converting to a DataSet was the only solution I could get to work, after a lot of trial and error, for putting these data in an xarray DataSet.

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[shoyer]

This is still relevant

[rabernat]

I feel like I am a ninja on this issue and I think I could write a good tutorial for this.

[dcherian]

+20 @rabernat

[dcherian]

I think you are a good candidate for expanding the tutorial on multidimensional coordinates too. This is such a common use case for model output...