https://docs.xarray.dev/en/stable/_static/dataset-diagram-logo.png

Grouped Computations#

In this lesson, we discuss how to do scientific computations with defined “groups” of data within our xarray objects. Our learning goals are as follows:

  • Perform “split / apply / combine” workflows in Xarray using groupby, including

    • reductions within groups

    • transformations on groups

  • Use resample to change the time frequency of the data

import numpy as np
import xarray as xr
import matplotlib.pyplot as plt

# don't expand data by default
xr.set_options(display_expand_data=False)

%config InlineBackend.figure_format='retina'

Example Dataset#

First we load a dataset. We will use the NOAA Extended Reconstructed Sea Surface Temperature (ERSST) v5 product, a widely used and trusted gridded compilation of of historical data going back to 1854.

ds = xr.tutorial.load_dataset("ersstv5")
ds
<xarray.Dataset>
Dimensions:    (lat: 89, lon: 180, time: 624, nbnds: 2)
Coordinates:
  * lat        (lat) float32 88.0 86.0 84.0 82.0 ... -82.0 -84.0 -86.0 -88.0
  * lon        (lon) float32 0.0 2.0 4.0 6.0 8.0 ... 352.0 354.0 356.0 358.0
  * time       (time) datetime64[ns] 1970-01-01 1970-02-01 ... 2021-12-01
Dimensions without coordinates: nbnds
Data variables:
    time_bnds  (time, nbnds) float64 9.969e+36 9.969e+36 ... 9.969e+36 9.969e+36
    sst        (time, lat, lon) float32 -1.8 -1.8 -1.8 -1.8 ... nan nan nan nan
Attributes: (12/37)
    climatology:               Climatology is based on 1971-2000 SST, Xue, Y....
    description:               In situ data: ICOADS2.5 before 2007 and NCEP i...
    keywords_vocabulary:       NASA Global Change Master Directory (GCMD) Sci...
    keywords:                  Earth Science > Oceans > Ocean Temperature > S...
    instrument:                Conventional thermometers
    source_comment:            SSTs were observed by conventional thermometer...
    ...                        ...
    creator_url_original:      https://www.ncei.noaa.gov
    license:                   No constraints on data access or use
    comment:                   SSTs were observed by conventional thermometer...
    summary:                   ERSST.v5 is developed based on v4 after revisi...
    dataset_title:             NOAA Extended Reconstructed SST V5
    data_modified:             2022-06-07

Groupby#

Xarray copies Pandas’ very useful groupby functionality, enabling the “split / apply / combine” workflow on xarray DataArrays and Datasets.

Let’s examine a timeseries of SST at a single point.

ds.sst.sel(lon=300, lat=50).plot();
../_images/03.2_groupby_with_xarray_5_0.png

As we can see from the plot, the timeseries at any one point is totally dominated by the seasonal cycle. We would like to remove this seasonal cycle (called the “climatology”) in order to better see the long-term variaitions in temperature. We can accomplish this using groupby.

Before moving forward, we note that xarray correctly parsed the time index, resulting in a Pandas datetime index on the time dimension.

ds.time
<xarray.DataArray 'time' (time: 624)>
1970-01-01 1970-02-01 1970-03-01 1970-04-01 ... 2021-10-01 2021-11-01 2021-12-01
Coordinates:
  * time     (time) datetime64[ns] 1970-01-01 1970-02-01 ... 2021-12-01
Attributes:
    long_name:        Time
    delta_t:          0000-01-00 00:00:00
    avg_period:       0000-01-00 00:00:00
    prev_avg_period:  0000-00-07 00:00:00
    standard_name:    time
    axis:             T
    actual_range:     [19723. 81204.]

The syntax of Xarray’s groupby is almost identical to Pandas.

?ds.groupby

Identifying groups#

The most important argument is group: this defines the unique values or labels we will us to “split” the data for grouped analysis. We can pass either a DataArray or a name of a variable in the dataset. Let’s first use a DataArray.

Just like with Pandas, we can use the time index to extract specific components of dates and times. Xarray uses a special syntax for this .dt, called the DatetimeAccessor. See the documentation for more

ds.time.dt
<xarray.core.accessor_dt.DatetimeAccessor at 0x7fb470e26b30>
ds.time.dt.month
<xarray.DataArray 'month' (time: 624)>
1 2 3 4 5 6 7 8 9 10 11 12 1 2 3 4 5 ... 8 9 10 11 12 1 2 3 4 5 6 7 8 9 10 11 12
Coordinates:
  * time     (time) datetime64[ns] 1970-01-01 1970-02-01 ... 2021-12-01
ds.time.dt.year
<xarray.DataArray 'year' (time: 624)>
1970 1970 1970 1970 1970 1970 1970 1970 ... 2021 2021 2021 2021 2021 2021 2021
Coordinates:
  * time     (time) datetime64[ns] 1970-01-01 1970-02-01 ... 2021-12-01

Split step#

We can use these arrays in a groupby operation:

gb = ds.groupby(ds.time.dt.month)
gb
DatasetGroupBy, grouped over 'month'
12 groups with labels 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12.

Xarray also offers a more concise syntax when the variable you’re grouping on is already present in the dataset. This is identical to the previous line:

gb = ds.groupby("time.month")
gb
DatasetGroupBy, grouped over 'month'
12 groups with labels 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12.

gb is a DatasetGroupBy object. It represents a GroupBy operation and helpfully tells us the unique “groups” or labels found during the split step.

Xarrays' computation methods (groupby, groupby_bins, rolling, coarsen, weighted) all return special objects that represent the basic underlying computation pattern. For e.g. `gb` above is a `DatasetGroupBy` object that represents monthly groupings of the data in `ds` . It is usually helpful to save and reuse these objects for multiple operations (e.g. a mean and standard deviation calculation).

Apply & Combine#

Now that we have groups defined, it’s time to “apply” a calculation to the group. Like in Pandas, these calculations can either be:

  • aggregation or reduction: reduces the size of the group

  • transformation: preserves the group’s full size

At then end of the apply step, xarray will automatically combine the aggregated / transformed groups back into a single object.

Aggregations or Reductions#

Most commonly, we want to perform a reduction operation like sum or mean on our groups. Xarray conveniently provides these reduction methods on Groupby objects for both DataArrays and Datasets.

Here we calculate the monthly mean.

ds_mm = gb.mean()
ds_mm
<xarray.Dataset>
Dimensions:    (lat: 89, lon: 180, month: 12, nbnds: 2)
Coordinates:
  * lat        (lat) float32 88.0 86.0 84.0 82.0 ... -82.0 -84.0 -86.0 -88.0
  * lon        (lon) float32 0.0 2.0 4.0 6.0 8.0 ... 352.0 354.0 356.0 358.0
  * month      (month) int64 1 2 3 4 5 6 7 8 9 10 11 12
Dimensions without coordinates: nbnds
Data variables:
    time_bnds  (month, nbnds) float64 9.969e+36 9.969e+36 ... 9.969e+36
    sst        (month, lat, lon) float32 -1.8 -1.8 -1.8 -1.8 ... nan nan nan nan

So we did what we wanted to do: calculate the climatology at every point in the dataset. Let’s look at the data a bit.

Climatology at a specific point in the North Atlantic

ds_mm.sst.sel(lon=300, lat=50).plot();
../_images/03.2_groupby_with_xarray_26_0.png

Zonal Mean Climatology

ds_mm.sst.mean(dim="lon").plot.contourf(x="month", levels=12, vmin=-2, vmax=30);
../_images/03.2_groupby_with_xarray_28_0.png

Difference between January and July Climatology

(ds_mm.sst.sel(month=1) - ds_mm.sst.sel(month=7)).plot(vmax=10);
../_images/03.2_groupby_with_xarray_30_0.png

Custom Aggregations#

The most fundamental way to apply a function and combine the results together to use the .map method.

?gb.map

.map accepts as its argument a function that expects and returns xarray objects. We define a custom function. This function takes a single argument–the group dataset–and returns a new dataset to be combined:

def time_mean(a):
    return a.mean(dim="time")


gb.map(time_mean)
<xarray.Dataset>
Dimensions:    (lat: 89, lon: 180, month: 12, nbnds: 2)
Coordinates:
  * lat        (lat) float32 88.0 86.0 84.0 82.0 ... -82.0 -84.0 -86.0 -88.0
  * lon        (lon) float32 0.0 2.0 4.0 6.0 8.0 ... 352.0 354.0 356.0 358.0
  * month      (month) int64 1 2 3 4 5 6 7 8 9 10 11 12
Dimensions without coordinates: nbnds
Data variables:
    time_bnds  (month, nbnds) float64 9.969e+36 9.969e+36 ... 9.969e+36
    sst        (month, lat, lon) float32 -1.8 -1.8 -1.8 -1.8 ... nan nan nan nan

This is identical to gb.mean()

Apply by iteration#

We can manually iterate over the group. The iterator returns the key (group name) and the value (the actual dataset corresponding to that group) for each group.

You could apply any function you want in the loop but you would have to manually combine the results together.

for group_name, group_ds in gb:
    # stop iterating after the first loop
    break
print(group_name)
group_ds
1
<xarray.Dataset>
Dimensions:    (lat: 89, lon: 180, time: 52, nbnds: 2)
Coordinates:
  * lat        (lat) float32 88.0 86.0 84.0 82.0 ... -82.0 -84.0 -86.0 -88.0
  * lon        (lon) float32 0.0 2.0 4.0 6.0 8.0 ... 352.0 354.0 356.0 358.0
  * time       (time) datetime64[ns] 1970-01-01 1971-01-01 ... 2021-01-01
Dimensions without coordinates: nbnds
Data variables:
    time_bnds  (time, nbnds) float64 9.969e+36 9.969e+36 ... 9.969e+36 9.969e+36
    sst        (time, lat, lon) float32 -1.8 -1.8 -1.8 -1.8 ... nan nan nan nan
Attributes: (12/37)
    climatology:               Climatology is based on 1971-2000 SST, Xue, Y....
    description:               In situ data: ICOADS2.5 before 2007 and NCEP i...
    keywords_vocabulary:       NASA Global Change Master Directory (GCMD) Sci...
    keywords:                  Earth Science > Oceans > Ocean Temperature > S...
    instrument:                Conventional thermometers
    source_comment:            SSTs were observed by conventional thermometer...
    ...                        ...
    creator_url_original:      https://www.ncei.noaa.gov
    license:                   No constraints on data access or use
    comment:                   SSTs were observed by conventional thermometer...
    summary:                   ERSST.v5 is developed based on v4 after revisi...
    dataset_title:             NOAA Extended Reconstructed SST V5
    data_modified:             2022-06-07

Transformations#

Now we want to remove this climatology from the dataset, to examine the residual, called the anomaly, which is the interesting part from a climate perspective. Removing the seasonal climatology is a perfect example of a transformation: it operates over a group, but doesn’t change the size of the dataset. Here is one way to code it

def remove_time_mean(x):
    return x - x.mean(dim="time")


ds_anom = ds.groupby("time.month").map(remove_time_mean)
ds_anom
<xarray.Dataset>
Dimensions:    (lat: 89, lon: 180, time: 624, nbnds: 2)
Coordinates:
  * lat        (lat) float32 88.0 86.0 84.0 82.0 ... -82.0 -84.0 -86.0 -88.0
  * lon        (lon) float32 0.0 2.0 4.0 6.0 8.0 ... 352.0 354.0 356.0 358.0
  * time       (time) datetime64[ns] 1970-01-01 1970-02-01 ... 2021-12-01
Dimensions without coordinates: nbnds
Data variables:
    time_bnds  (time, nbnds) float64 0.0 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0
    sst        (time, lat, lon) float32 5.96e-07 5.96e-07 5.96e-07 ... nan nan

Xarray makes these sorts of transformations easy by supporting groupby arithmetic. This concept is easiest explained with an example:

gb = ds.groupby("time.month")
ds_anom = gb - gb.mean()
ds_anom
<xarray.Dataset>
Dimensions:    (lat: 89, lon: 180, time: 624, nbnds: 2)
Coordinates:
  * lat        (lat) float32 88.0 86.0 84.0 82.0 ... -82.0 -84.0 -86.0 -88.0
  * lon        (lon) float32 0.0 2.0 4.0 6.0 8.0 ... 352.0 354.0 356.0 358.0
  * time       (time) datetime64[ns] 1970-01-01 1970-02-01 ... 2021-12-01
    month      (time) int64 1 2 3 4 5 6 7 8 9 10 11 ... 2 3 4 5 6 7 8 9 10 11 12
Dimensions without coordinates: nbnds
Data variables:
    time_bnds  (time, nbnds) float64 0.0 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0
    sst        (time, lat, lon) float32 5.96e-07 5.96e-07 5.96e-07 ... nan nan

Now we can view the climate signal without the overwhelming influence of the seasonal cycle.

Timeseries at a single point in the North Atlantic

ds_anom.sst.sel(lon=300, lat=50).plot();
../_images/03.2_groupby_with_xarray_43_0.png

Difference between Jan. 1 2018 and Jan. 1 1970

(ds_anom.sel(time="2018-01-01") - ds_anom.sel(time="1970-01-01")).sst.plot();
../_images/03.2_groupby_with_xarray_45_0.png

Exercise#

Using groupby, plot the annual mean time series of SST at 300°E, 50°N

ds.groupby("time.year").mean().sst.sel(lon=300, lat=50).plot();
../_images/03.2_groupby_with_xarray_47_0.png

Resample#

Resampling means changing the time frequency of data, usually reducing to a coarser frequency: e.g. converting daily frequency data to monthly frequency data using mean to reduce the values. This operation can be thought of as a groupby operation where each group is a single month of data. Resampling can be applied only to time-index dimensions.

First note that ds_anom has data at monthly frequency (i.e. one point every month).

ds_anom.time
<xarray.DataArray 'time' (time: 624)>
1970-01-01 1970-02-01 1970-03-01 1970-04-01 ... 2021-10-01 2021-11-01 2021-12-01
Coordinates:
  * time     (time) datetime64[ns] 1970-01-01 1970-02-01 ... 2021-12-01
    month    (time) int64 1 2 3 4 5 6 7 8 9 10 11 ... 2 3 4 5 6 7 8 9 10 11 12
Attributes:
    long_name:        Time
    delta_t:          0000-01-00 00:00:00
    avg_period:       0000-01-00 00:00:00
    prev_avg_period:  0000-00-07 00:00:00
    standard_name:    time
    axis:             T
    actual_range:     [19723. 81204.]

Here we compute the five-year mean along the time dimension by passing time='5Y'. '5Y' is a special frequency string. Xarray uses pandas to convert such a frequency string to a groupby operation. See the pandas documentation for how to specify a different frequency.

resample_obj = ds_anom.resample(time="5Y")
resample_obj
DatasetResample, grouped over '__resample_dim__'
12 groups with labels 1970-12-31, ..., 2025-12-31.
Note: resample only works with proper datetime64 coordinate labels. Note the `dtype` of `time` in the repr above.

Resampling objects are exactly like groupby objects and allow reductions, iteration, etc.

ds_anom_resample = resample_obj.mean()
ds_anom_resample
<xarray.Dataset>
Dimensions:    (time: 12, lat: 89, lon: 180, nbnds: 2)
Coordinates:
  * time       (time) datetime64[ns] 1970-12-31 1975-12-31 ... 2025-12-31
  * lat        (lat) float32 88.0 86.0 84.0 82.0 ... -82.0 -84.0 -86.0 -88.0
  * lon        (lon) float32 0.0 2.0 4.0 6.0 8.0 ... 352.0 354.0 356.0 358.0
Dimensions without coordinates: nbnds
Data variables:
    time_bnds  (time, nbnds) float64 0.0 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0
    sst        (time, lat, lon) float32 -0.0005956 -0.0005648 ... nan nan
for label, group in resample_obj:
    break
print(label, "\n\n", group)
1970-12-31T00:00:00.000000000 

 <xarray.Dataset>
Dimensions:    (lat: 89, lon: 180, time: 12, nbnds: 2)
Coordinates:
  * lat        (lat) float32 88.0 86.0 84.0 82.0 ... -82.0 -84.0 -86.0 -88.0
  * lon        (lon) float32 0.0 2.0 4.0 6.0 8.0 ... 352.0 354.0 356.0 358.0
  * time       (time) datetime64[ns] 1970-01-01 1970-02-01 ... 1970-12-01
    month      (time) int64 1 2 3 4 5 6 7 8 9 10 11 12
Dimensions without coordinates: nbnds
Data variables:
    time_bnds  (time, nbnds) float64 0.0 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0
    sst        (time, lat, lon) float32 5.96e-07 5.96e-07 5.96e-07 ... nan nan
ds_anom.sst.sel(lon=300, lat=50).plot()
ds_anom_resample.sst.sel(lon=300, lat=50).plot(marker="o");
../_images/03.2_groupby_with_xarray_56_0.png

Exercise#

Using resample, plot the annual mean time series of SST at 300°E, 50°N.

Compare this output to the groupby output. What differences do you see?

resampled = ds.resample(time='Y').mean().sst.sel(lon=300, lat=50)
resampled.plot();
../_images/03.2_groupby_with_xarray_58_0.png

Let’s compare the grouped and resampled outputs.

  1. Note the different dimension names: when grouped, time is renamed to year. When resampled, the time dimension name is preserved

  2. The values for year are integers, while those for resampled.time are timestamps, similar to the input dataset

  3. But all values are equal

from IPython.display import display_html

grouped = ds.groupby("time.year").mean().sst.sel(lon=300, lat=50)
display_html(grouped)
display_html(resampled)
<xarray.DataArray 'sst' (year: 52)>
4.513 4.354 3.557 4.069 3.565 3.755 4.262 ... 5.812 5.82 5.307 5.131 5.649 6.264
Coordinates:
    lat      float32 50.0
    lon      float32 300.0
  * year     (year) int64 1970 1971 1972 1973 1974 ... 2017 2018 2019 2020 2021
<xarray.DataArray 'sst' (time: 52)>
4.513 4.354 3.557 4.069 3.565 3.755 4.262 ... 5.812 5.82 5.307 5.131 5.649 6.264
Coordinates:
  * time     (time) datetime64[ns] 1970-12-31 1971-12-31 ... 2021-12-31
    lat      float32 50.0
    lon      float32 300.0
np.array_equal(grouped.data, resampled.data)
True

Going further#

  1. See the documentation on groupby and resample

  2. Follow the tutorial on high-level computation patterns