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Usage and Examples

Reading Output

The routines for reading bpch files from disk into xarray.Datasets is based mostly on the xarray.open_dataset method. However, to handle some of the idiosyncrasies of GEOS-Chem output, our implementation of :py:func:`~xbpch.open_bpchdataset` has a few additional arguments to know about.

Main :py:func:`~xbpch.open_bpchdataset` Arguments

The majority of the time, you'll want to load/read data via xarray, using the method :py:func:`~xbpch.open_bpchdataset`, as shown in the :ref:`quick start`. This routine fundamentally requires three arguments:

  • filename: the full path to the output file you want to load
  • tracerinfo_file: the full path to the file tracerinfo.dat, which contains the names and indices of each tracer output by GEOS-Chem
  • diaginfo_file: the full path to the file diaginfo.dat, which contains the listing of categories and their tracer number offsets in the tracer output index.

If you don't pass a value for either tracerinfo_file or diaginfo_file, xbpch will look for them in the current directory, assuming the Default naming scheme. However, if it still can't find a file, it'll raise an error (we do not assume to know what is in your output!)

In many simulations, GEOS-Chem will write multiple timesteps of a large number of fields to a single output file. This can result in outputs on the order of 10's of GB! If you know for certain that you only want a specific tracer or category of tracers, you can supply a list of their names to either fields or categories.

For instance, using the v11-01 diagnostics for reference, we can load in any tracer with the name "O3" by passing

.. ipython:: python
    :verbatim:

    import xbpch
    o3_data = xbpch.open_bpchdataset("my_data.bpch", fields=['O3', ])

Alternatively, we can load all the tracers associated with a given category by specifying the categories argument. To grab all the saved 2D meteorology fields, this would entail

.. ipython:: python
    :verbatim:

    met_data = xbpch.open_bpchdataset(
        "my_data.bpch", categories=["DAO-FLDS", ]
    )


What Works and Doesn't Work

xbpch should work with most standard GEOS-Chem outputs going back to at least v9-02. It has been tested against some of these standard outputs, but not exhaustively. If you have an idiosyncratic GEOS-Chem output (e.g. from a specialized version of the model with custom tracers or a new grid), please give xbpch a try and if it fails, post a an Issue on our GitHub page to let us know.

The following configurations have been tested and vetted:

  • Standard output on standard grids
  • ND49 output on standard grids
  • ND49 output on nested North America grid (should work for all nested grids)

Eager vs Lazy Loading

One of the main advantages to using xbpch is that it allows you to access data without immediately need to read it all from disk. On a modern analysis cluster, this isn't a problem, but if you want to process output on your laptop, you can quickly run into situations where all of your data won't fit in memory. In those situations, you have to tediously block your analysis algorithms/pipeline.

Note

Even though you may request lazily-loaded data, xpbch still needs to read your input file to parse its contents. This requires iterating line-by-line through the input file, so it may take some time (about ~10 seconds to read a 6GB file on my late-2016 MacBook Pro). Unfortunately, if we don't do this, we can't infer the tracers or their distribution over multiple timesteps containined in the input file.

The keyword arguments memmap and dask control how data is read from your bpch files.

memmap
if enabled, the data for each timestep and variable will be accessed through a memory-map into the input file
dask
if enabled, the function to read each timestep for each variable will be wrapped in a dask.delayed object, initiating a task graph for accessing the data

Warning

Opening a dataset using memmap=True and dask=False will not work. Each memory-mapped array counts as an open file, which will quickly add up and hit your operating system's limit on simultaneously open files.

If dask=True is used to open a dataset, then all of the data in the bpch file is represented by dask.arrays, and all operations are lazy. That is, they are not evaluated until the user explicitly instruct them to be, and instead a graph representing your computation is constructed.

Chunking

When data is loaded with the dask flag enabled, all the operations necessary to create contiguous chunks of data are deferred. Because of the way data is written to bpch files by GEOS-Chem, these deferred actions are all based on single timesteps of data for each variable by default. Thus, in the parlance of dask, all the data is implicitly chunked on the time dimension.

When dask encounters chunked calculations, it will automatically attempt to parallelize them across all the cores available on your machine, and will attempt to limit the amount of data held in-memory at any give time.

To illustrate this, consider a monthly history dataset ds loaded via :py:func:`~xbpch.open_bpchdataset`. The inital task graph representing this data may look something like:

Monthly history dask read/concat graph

Tasks for reading and processing monthly output for a single variable in a year-long bpch output file

This graph illustrates that dask is expected to process 12 chunks of data - one for each month (timestep) in the dataset. The graph shows the operations for reading the data, casting it to the correct data type, and re-scaling, which are applied automatically by xbpch and xarray.

At this point, the data has only been processed in such a way that it fits the numpy.ndarray memory model, and thus can be used to construct xarray objects. A trivial calculation on this data may be to normalize the timeseries of data in each grid cell to have zero mean and unit variance. For any xarray.DataArray we could write this operation as

.. ipython:: python
    :verbatim:

    da_normal = (da - da.mean('time'))/da.std('time')

which produces the computational graph

Normalization calculation on monthly data

Computational graph for normalizing monthly data

A second key function of dask is to analyze and parse these computational graphs into a simplified form. In practice, the resulting graph will be much simpler, which can dramatically speed up your analysis. For instance, if you sub-sample the variables and timesteps used in your analysis, xbpch (through dask) will avoid reading extra, unused data from the input files you passed it.

Note

Sometimes it's advantagous to re-chunk a dataset (see here for a discussion on when this may be the case). This is easily accomplished through xarray, or can be done directly on the dask.arrays containing your data if you have a more complex analysis to perform.

Finally, it's important to know that the computational graphs that dask produces are never evaluated until you explicitly call .load() on a dask array or xarray Data{Array,set}. Different computations or uses for your data might imply an automatic load(); for instance, if you use the plotting wrapper built into xarray, it will (necessarily) eagerly load your data. If you'd like to monitor the progress of a very long analysis built through xbpch/xarray/dask, you can use the built-in diagnostic tools from dask:

.. ipython:: python
    :verbatim:

    from dask.diagnostics import ProgressBar

    # Construct some analysis
    my_ds = ...

    # Eagerly compute the results
    with ProgressBar() as pb:
        my_ds.load()

[####################################] | 100% Completed | 10.2s

Geographic Visualization

One easy application of xbpch is for the visualization of your data. For cartographic or geographic plots, we recommend using the cartopy package maintained by the UK Met Office.

Plotting on a cartopy map is straightforward. Suppose we have a Dataset ds read from a bpch file. We can first compute an analysis of interest - say, the difference between mean fields for summer versus winter:

.. ipython:: python
    :verbatim:

    ds_seas = ds.groupby("time.season").mean('time')
    diff = ds_seas.sel(season='DJF') - ds_seas.sel(season='JJA')

<xarray.Dataset>
Dimensions:      (lat: 91, lev: 47, lon: 144, nv: 2)
Coordinates:
  * lev          (lev) float64 0.9925 0.9775 0.9624 0.9473 0.9322 0.9171 ...
  * lon          (lon) float64 -180.0 -177.5 -175.0 -172.5 -170.0 -167.5 ...
  * lat          (lat) float64 -89.5 -88.0 -86.0 -84.0 -82.0 -80.0 -78.0 ...
  * nv           (nv) int64 0 1
Data variables:
    ANTHSRCE_O3  (lon, lat) float32 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ...
    IJ_AVG_S_O3  (lon, lat, lev) float32 -23.1014 -23.2715 -23.4614 -23.5216 ...

Plotting a portion of this dataset on a cartopy map is straightforward. First, we create a figure and add an axes with the map projection information encoded:

.. ipython:: python
    :verbatim:

    import matplotlib.pyplot as plt
    import cartopy.crs as ccrs

    fig = plt.figure()
    ax = fig.add_subplot(111, projection=ccrs.PlateCarree(), aspect='auto')

Then, we can plot our data as normal. cartopy has a few helper functions which we can use to add basic geographic elements such as coastlines and borders to the plot.

.. ipython:: python
    :verbatim:

    import cartopy.feature as cfeature

    # Select some data to plot
    da = diff.isel(lev=0).IJ_AVG_S_O3

    im = ax.contourf(da.lon.values, da.lat.values, da.values.T)
    cb = fig.colorbar(im, ax=ax, orientation='horizontal')
    ax.add_feature(cfeature.COASTLINE)
    ax.add_feature(cfeature.BORDERS)

cartopy plot

Example of a simple plot with cartopy

Alternatively, we can use xarray's matplotlib wrappers to automate some of this plotting for us. For instance, we can quickly make a faceted plot of our seasonal data (including with a cartopy axis) with just a few lines of code:

.. ipython:: python
    :verbatim:

    # Select some data to plot
    da = ds_seas.isel(lev=0).IJ_AVG_S_O3
    da = da - ds.isel(lev=0).IJ_AVG_S_O3.mean('time')

    g = da.plot.imshow('lon', 'lat', col='season', col_wrap=2,
                       subplot_kws=dict(projection=ccrs.Robinson()), transform=ccrs.PlateCarree())
    for ax in g.axes.flatten():
        ax.add_feature(cfeature.COASTLINE)

cartopy plot

Faceting over a non-coordinate dimension using xarray's built-in plotting tools.

There's a lot going on in this code sample:

  1. First, we take the seasonal mean data we formerly computed.
  2. Subtract out the annual mean from each seasonal mean.
  3. Use imshow to plot each grid cell in our dataset.
    • We tell the plotting function to use "lon" and `"lat" as the keys to access the x/y data for the dataset
    • We further instruct xarray to facet over the `"season" coordinate, and include two columns per row in the resulting facet grid
    • We pass a dictionary of keyword arguments to subplot_kws, which is used when creating each subplot in our facet grid. In this case, we tell each subplot to use a Robinson map projection
    • We pass a final keyword argument, transform, which is passed to each invocation of imshow() on the facet grid; this tells cartopy how to map from the projection data to our actual data. Here, a ccrs.PlateCarree() is a standard, equally-spaced latitude-longitude grid
  4. Iterate over each axis in the facet grid, and add our coastlines to it.

Timeseries Analysis

Another application that xbpch/xarray makes easy is timeseries analysis. For example, consider the timesries of ND49 output from the :ref:`quick start`. A classic timeseries analysis atmospheric chemistry is computing the daily maximum 8-hour average for a given tracer. The core of this computation can be achieved in just a few lines of code via xarray:

.. ipython:: python
    :verbatim:

    o3 = ds.IJ_AVG_S_O3
    mda8_o3 = (
        o3.rolling(time=8, min_periods=6).mean()
          .resample("D", "time", how='max')
    )

This code is highly performant; the .rolling() operation is farmed out to a high-performance C library (bottleneck) and all operations are applied by broadcasting over the time dimension.

Note

bottleneck does not work with dask arrays, so you will need to eagerly .load() the data into memory if it hasn't already been done. Future versions of xarray will wrap functionality in dask to perform these operations in parallel, but this is a work in progress.

Save to NetCDF

Without any extra work, datsets read in via xbpch can easily be serialized back to disk in NetCDF format

.. ipython:: python
    :verbatim:

    ds.to_netcdf("my_bpch_data.nc")

They can then be read back in via xarray

.. ipython:: python
    :verbatim:

    import xarray as xr
    ds = xr.open_dataset("my_bpch_data.nc")

Note

As of v0.2.0, immediately writing to netcdf may not work due to the way variable units and scaling factors are encoded when they are read into xbpch. This will be fixed once some upstream issues with xarray are patched. If you run into the following ValueError:

ValueError: Failed hard to prevent overwriting key 'scale_factor'

then before you save it, process it with the :meth:`xbpch.common.fix_attr_encoding()` method

.. ipython:: python
  :verbatim:

  my_ds = xbpch.common.fix_attr_encoding(my_ds)

  my_ds.to_netcdf("my_data.nc")