Computations and Masks with Xarray


Overview

In this notebook, we will:

  1. Do basic arithmetic with DataArrays and Datasets

  2. Perform aggregation (reduction) along one or multiple dimensions of a DataArray or Dataset

  3. Compute climatology and anomaly using xarray’s “split-apply-combine” approach via .groupby()

  4. Perform weighted reductions along one or multiple dimensions of a DataArray or Dataset

  5. Provide an overview of masking data in xarray

  6. Mask data using .where() method

Prerequisites

Concepts

Importance

Notes

Introduction to Xarray

Necessary

  • Time to learn: 60 minutes


Imports

import matplotlib.pyplot as plt
import numpy as np
import xarray as xr
from pythia_datasets import DATASETS

Let’s open the monthly sea surface temperature (SST) data from the Community Earth System Model v2 (CESM2), which is a Global Climate Model:

filepath = DATASETS.fetch('CESM2_sst_data.nc')
ds = xr.open_dataset(filepath)
ds
/usr/share/miniconda/envs/pythia-book-dev/lib/python3.8/site-packages/xarray/conventions.py:512: SerializationWarning: variable 'tos' has multiple fill values {1e+20, 1e+20}, decoding all values to NaN.
  new_vars[k] = decode_cf_variable(
<xarray.Dataset>
Dimensions:    (time: 180, d2: 2, lat: 180, lon: 360)
Coordinates:
  * time       (time) object 2000-01-15 12:00:00 ... 2014-12-15 12:00:00
  * lat        (lat) float64 -89.5 -88.5 -87.5 -86.5 ... 86.5 87.5 88.5 89.5
  * lon        (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 356.5 357.5 358.5 359.5
Dimensions without coordinates: d2
Data variables:
    time_bnds  (time, d2) object 2000-01-01 00:00:00 ... 2015-01-01 00:00:00
    lat_bnds   (lat, d2) float64 -90.0 -89.0 -89.0 -88.0 ... 88.0 89.0 89.0 90.0
    lon_bnds   (lon, d2) float64 0.0 1.0 1.0 2.0 2.0 ... 358.0 359.0 359.0 360.0
    tos        (time, lat, lon) float32 ...
Attributes: (12/45)
    Conventions:            CF-1.7 CMIP-6.2
    activity_id:            CMIP
    branch_method:          standard
    branch_time_in_child:   674885.0
    branch_time_in_parent:  219000.0
    case_id:                972
    ...                     ...
    sub_experiment_id:      none
    table_id:               Omon
    tracking_id:            hdl:21.14100/2975ffd3-1d7b-47e3-961a-33f212ea4eb2
    variable_id:            tos
    variant_info:           CMIP6 20th century experiments (1850-2014) with C...
    variant_label:          r11i1p1f1

Arithmetic Operations

Arithmetic operations with a single DataArray automatically apply over all array values (like NumPy). This process is called vectorization. Let’s convert the air temperature from degrees Celsius to kelvins:

ds.tos + 273.15
<xarray.DataArray 'tos' (time: 180, lat: 180, lon: 360)>
array([[[      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        ...,
        [271.3552 , 271.3553 , 271.3554 , ..., 271.35495, 271.355  ,
         271.3551 ],
        [271.36005, 271.36014, 271.36023, ..., 271.35986, 271.35992,
         271.36   ],
        [271.36447, 271.36453, 271.3646 , ..., 271.3643 , 271.36435,
         271.3644 ]],

       [[      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
...
        [271.40677, 271.40674, 271.4067 , ..., 271.40695, 271.4069 ,
         271.40683],
        [271.41296, 271.41293, 271.41293, ..., 271.41306, 271.413  ,
         271.41296],
        [271.41772, 271.41772, 271.41772, ..., 271.41766, 271.4177 ,
         271.4177 ]],

       [[      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        ...,
        [271.39386, 271.39383, 271.3938 , ..., 271.39407, 271.394  ,
         271.39392],
        [271.39935, 271.39932, 271.39932, ..., 271.39948, 271.39944,
         271.39938],
        [271.40372, 271.40372, 271.40375, ..., 271.4037 , 271.4037 ,
         271.40372]]], dtype=float32)
Coordinates:
  * time     (time) object 2000-01-15 12:00:00 ... 2014-12-15 12:00:00
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5

Lets’s square all values in tos:

ds.tos ** 2
<xarray.DataArray 'tos' (time: 180, lat: 180, lon: 360)>
array([[[      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        ...,
        [3.2213385, 3.2209656, 3.220537 , ..., 3.2221622, 3.221913 ,
         3.2216525],
        [3.203904 , 3.203617 , 3.2032912, ..., 3.2045207, 3.2043478,
         3.2041442],
        [3.1881146, 3.1879027, 3.1876712, ..., 3.188714 , 3.1885312,
         3.1883302]],

       [[      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
...
        [3.0388296, 3.0389647, 3.0390673, ..., 3.038165 , 3.0383828,
         3.0386322],
        [3.0173173, 3.0173445, 3.0173297, ..., 3.0169601, 3.0171173,
         3.0172386],
        [3.000791 , 3.0007784, 3.0007539, ..., 3.000933 , 3.000896 ,
         3.0008452]],

       [[      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        [      nan,       nan,       nan, ...,       nan,       nan,
               nan],
        ...,
        [3.0839543, 3.0841148, 3.0842566, ..., 3.0832636, 3.0834875,
         3.0837412],
        [3.064733 , 3.0648024, 3.0648358, ..., 3.0642793, 3.0644639,
         3.0646174],
        [3.0494578, 3.0494475, 3.0494263, ..., 3.049596 , 3.0495603,
         3.0495107]]], dtype=float32)
Coordinates:
  * time     (time) object 2000-01-15 12:00:00 ... 2014-12-15 12:00:00
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5

Aggregation Methods

A very common step during data analysis is to summarize the data in question by computing aggregations like sum(), mean(), median(), min(), max() in which reduced data provide insight into the nature of large dataset. Let’s explore some of these aggregation methods.

Compute the mean:

ds.tos.mean()
<xarray.DataArray 'tos' ()>
array(14.250171, dtype=float32)

Because we specified no dim argument the function was applied over all dimensions, computing the mean of every element of tos across time and space. It is possible to specify a dimension along which to compute an aggregation. For example, to calculate the mean in time for all locations, specify the time dimension as the dimension along which the mean should be calculated:

ds.tos.mean(dim='time').plot(size=7);
../../_images/computation-masking_17_0.png

Compute the temporal min:

ds.tos.min(dim=['time'])
<xarray.DataArray 'tos' (lat: 180, lon: 360)>
array([[       nan,        nan,        nan, ...,        nan,        nan,
               nan],
       [       nan,        nan,        nan, ...,        nan,        nan,
               nan],
       [       nan,        nan,        nan, ...,        nan,        nan,
               nan],
       ...,
       [-1.8083605, -1.8083031, -1.8082187, ..., -1.8083988, -1.8083944,
        -1.8083915],
       [-1.8025414, -1.8024837, -1.8024155, ..., -1.8026428, -1.8026177,
        -1.8025846],
       [-1.7984415, -1.7983989, -1.7983514, ..., -1.7985678, -1.7985296,
        -1.7984871]], dtype=float32)
Coordinates:
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5

Compute the spatial sum:

ds.tos.sum(dim=['lat', 'lon'])
<xarray.DataArray 'tos' (time: 180)>
array([603767.  , 607702.5 , 603976.5 , 599373.56, 595119.94, 595716.75,
       598177.3 , 600670.6 , 597825.56, 591869.  , 590507.7 , 597189.2 ,
       605954.06, 609151.  , 606868.9 , 602329.9 , 599465.75, 601205.5 ,
       605144.4 , 608588.5 , 604046.9 , 598927.75, 597519.75, 603876.9 ,
       612424.44, 615765.2 , 612615.44, 606310.6 , 602034.4 , 600784.9 ,
       602013.5 , 603142.2 , 598850.9 , 591917.44, 589234.56, 596162.5 ,
       602942.06, 607196.9 , 604928.2 , 601735.6 , 599011.8 , 599490.9 ,
       600801.44, 602786.94, 598867.2 , 594081.8 , 593736.25, 598995.6 ,
       607285.25, 611901.06, 609562.75, 603527.3 , 600215.4 , 601372.6 ,
       604144.5 , 605376.75, 601256.2 , 595245.2 , 594002.06, 600490.4 ,
       611878.6 , 616563.  , 613050.8 , 605734.  , 600808.75, 600898.06,
       603930.56, 605644.7 , 599917.5 , 592048.06, 590082.8 , 596950.7 ,
       607701.94, 610844.7 , 609509.6 , 603380.94, 599838.1 , 600334.25,
       604386.6 , 607848.1 , 602155.2 , 594949.06, 593815.06, 598365.3 ,
       608730.8 , 612056.5 , 609922.5 , 603077.1 , 600134.1 , 602821.2 ,
       606152.75, 610257.8 , 604685.8 , 596858.  , 592894.8 , 599944.9 ,
       609764.44, 614610.75, 611434.75, 605606.4 , 603790.94, 605750.2 ,
       609250.06, 612935.7 , 609645.06, 601706.4 , 598896.5 , 605349.75,
       614671.8 , 618686.7 , 615895.2 , 609438.2 , 605399.56, 606126.75,
       607942.3 , 609680.4 , 604814.25, 595841.94, 591908.44, 595638.7 ,
       604798.94, 611327.1 , 609765.7 , 603727.56, 600970.  , 602514.  ,
       606303.7 , 609225.25, 603724.3 , 595944.8 , 594477.4 , 597807.4 ,
       607379.06, 611808.56, 610112.94, 607196.3 , 604733.06, 605488.25,
       610048.3 , 612655.75, 608906.25, 602349.7 , 601754.2 , 609220.4 ,
       619367.1 , 623783.2 , 619949.7 , 613369.06, 610190.8 , 611091.2 ,
       614213.44, 615665.06, 611722.2 , 606259.56, 605970.2 , 611463.3 ,
       619794.6 , 626036.5 , 623085.44, 616295.9 , 611886.3 , 611881.9 ,
       614420.75, 616853.56, 610375.44, 603471.5 , 602108.25, 608094.3 ,
       617450.7 , 623508.7 , 619830.2 , 612033.3 , 608737.2 , 610105.25,
       613692.7 , 616360.44, 611735.4 , 606512.7 , 604249.44, 608777.44],
      dtype=float32)
Coordinates:
  * time     (time) object 2000-01-15 12:00:00 ... 2014-12-15 12:00:00

Compute the temporal median:

ds.tos.median(dim='time')
<xarray.DataArray 'tos' (lat: 180, lon: 360)>
array([[       nan,        nan,        nan, ...,        nan,        nan,
               nan],
       [       nan,        nan,        nan, ...,        nan,        nan,
               nan],
       [       nan,        nan,        nan, ...,        nan,        nan,
               nan],
       ...,
       [-1.7648907, -1.7648032, -1.7647004, ..., -1.7650614, -1.7650102,
        -1.7649589],
       [-1.7590305, -1.7589546, -1.7588665, ..., -1.7591925, -1.7591486,
        -1.759095 ],
       [-1.7536805, -1.753602 , -1.7535168, ..., -1.753901 , -1.753833 ,
        -1.7537591]], dtype=float32)
Coordinates:
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5

The following table summarizes some other built-in xarray aggregations:

Aggregation

Description

count()

Total number of items

mean(), median()

Mean and median

min(), max()

Minimum and maximum

std(), var()

Standard deviation and variance

prod()

Compute product of elements

sum()

Compute sum of elements

argmin(), argmax()

Find index of minimum and maximum value

GroupBy: Split, Apply, Combine

Simple aggregations can give useful summary of our dataset, but often we would prefer to aggregate conditionally on some coordinate labels or groups. Xarray provides the so-called groupby operation which enables the split-apply-combine workflow on xarray DataArrays and Datasets. The split-apply-combine operation is illustrated in this figure

../../_images/xarray-split-apply-combine.jpeg

This makes clear what the groupby accomplishes:

  • The split step involves breaking up and grouping an xarray Dataset or DataArray depending on the value of the specified group key.

  • The apply step involves computing some function, usually an aggregate, transformation, or filtering, within the individual groups.

  • The combine step merges the results of these operations into an output xarray Dataset or DataArray.

We are going to use groupby to remove the seasonal cycle (“climatology”) from our dataset. See the xarray groupby user guide for more examples of what groupby can take as an input.

First, let’s select a gridpoint closest to a specified lat-lon, and plot a time series of SST at that point. The annual cycle will be quite evident.

ds.tos.sel(lon=310, lat=50, method='nearest').plot();
../../_images/computation-masking_27_0.png

Split

Let’s group data by month, i.e. all Januaries in one group, all Februaries in one group, etc.

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

In the above code, we are using the .dt DatetimeAccessor to extract specific components of dates/times in our time coordinate dimension. For example, we can extract the year with ds.time.dt.year. See also the equivalent Pandas documentation.

Xarray also offers a more concise syntax when the variable you’re grouping on is already present in the dataset. This is identical to ds.tos.groupby(ds.time.dt.month):

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

Apply & Combine

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

  • aggregation: 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.

Compute climatology

Let’s calculate the climatology at every point in the dataset:

tos_clim = ds.tos.groupby('time.month').mean()
tos_clim
<xarray.DataArray 'tos' (month: 12, lat: 180, lon: 360)>
array([[[       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        ...,
        [-1.780786 , -1.780688 , -1.7805718, ..., -1.7809757,
         -1.7809197, -1.7808627],
        [-1.7745041, -1.7744204, -1.7743237, ..., -1.77467  ,
         -1.774626 , -1.7745715],
        [-1.7691481, -1.7690798, -1.7690051, ..., -1.7693441,
         -1.7692844, -1.7692182]],

       [[       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
...
        [-1.7605033, -1.760397 , -1.7602725, ..., -1.760718 ,
         -1.7606541, -1.7605885],
        [-1.7544289, -1.7543424, -1.7542422, ..., -1.754608 ,
         -1.754559 , -1.7545002],
        [-1.7492163, -1.749148 , -1.7490736, ..., -1.7494118,
         -1.7493519, -1.7492864]],

       [[       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        ...,
        [-1.7711828, -1.7710832, -1.7709653, ..., -1.7713748,
         -1.7713183, -1.7712607],
        [-1.7648666, -1.7647841, -1.7646879, ..., -1.7650299,
         -1.7649865, -1.7649331],
        [-1.759478 , -1.7594113, -1.7593384, ..., -1.7596704,
         -1.7596117, -1.759547 ]]], dtype=float32)
Coordinates:
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5
  * month    (month) int64 1 2 3 4 5 6 7 8 9 10 11 12

Plot climatology at a specific point:

tos_clim.sel(lon=310, lat=50, method='nearest').plot();
../../_images/computation-masking_36_0.png

Plot zonal mean climatology:

tos_clim.mean(dim='lon').transpose().plot.contourf(levels=12, cmap='turbo');
../../_images/computation-masking_38_0.png

Calculate and plot the difference between January and December climatologies:

(tos_clim.sel(month=1) - tos_clim.sel(month=12)).plot(size=6, robust=True);
../../_images/computation-masking_40_0.png

Compute anomaly

Now let’s combine the previous steps to compute climatology and use xarray’s groupby arithmetic to remove this climatology from our original data:

gb = ds.tos.groupby('time.month')
tos_anom = gb - gb.mean(dim='time')
tos_anom
<xarray.DataArray 'tos' (time: 180, lat: 180, lon: 360)>
array([[[        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        ...,
        [-0.01402271, -0.01401687, -0.01401365, ..., -0.01406252,
         -0.01404917, -0.01403356],
        [-0.01544118, -0.01544476, -0.01545036, ..., -0.0154475 ,
         -0.01544321, -0.01544082],
        [-0.01638114, -0.01639009, -0.01639998, ..., -0.01635301,
         -0.01636147, -0.01637137]],

       [[        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
...
        [ 0.01727939,  0.01713431,  0.01698041, ...,  0.0176847 ,
          0.01755834,  0.01742125],
        [ 0.0173862 ,  0.0172919 ,  0.01719594, ...,  0.01766813,
          0.01757395,  0.01748013],
        [ 0.01693714,  0.01687253,  0.01680517, ...,  0.01709175,
          0.0170424 ,  0.01699162]],

       [[        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        ...,
        [ 0.01506364,  0.01491845,  0.01476014, ...,  0.01545238,
          0.0153321 ,  0.01520228],
        [ 0.0142287 ,  0.01412642,  0.01402068, ...,  0.0145216 ,
          0.01442552,  0.01432824],
        [ 0.01320827,  0.01314461,  0.01307774, ...,  0.0133611 ,
          0.0133127 ,  0.01326215]]], dtype=float32)
Coordinates:
  * time     (time) object 2000-01-15 12:00:00 ... 2014-12-15 12:00:00
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5
    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
tos_anom.sel(lon=310, lat=50, method='nearest').plot();
../../_images/computation-masking_43_0.png

Let’s compute and visualize the mean global anomaly over time. We need to specify both lat and lon dimensions in the dim argument to mean():

unweighted_mean_global_anom = tos_anom.mean(dim=['lat', 'lon'])
unweighted_mean_global_anom.plot();
../../_images/computation-masking_45_0.png

An operation which combines grid cells of different size is not scientifically valid unless each cell is weighted by the size of the grid cell. Xarray has a convenient .weighted() method to accomplish this

Let’s first load the cell area data from another CESM2 dataset that contains the weights for the grid cells:

filepath2 = DATASETS.fetch('CESM2_grid_variables.nc')
areacello = xr.open_dataset(filepath2).areacello
areacello
<xarray.DataArray 'areacello' (lat: 180, lon: 360)>
array([[1.078982e+08, 1.078982e+08, 1.078982e+08, ..., 1.078982e+08,
        1.078982e+08, 1.078982e+08],
       [3.236618e+08, 3.236618e+08, 3.236618e+08, ..., 3.236618e+08,
        3.236618e+08, 3.236618e+08],
       [5.393268e+08, 5.393268e+08, 5.393268e+08, ..., 5.393268e+08,
        5.393268e+08, 5.393268e+08],
       ...,
       [5.393268e+08, 5.393268e+08, 5.393268e+08, ..., 5.393268e+08,
        5.393268e+08, 5.393268e+08],
       [3.236618e+08, 3.236618e+08, 3.236618e+08, ..., 3.236618e+08,
        3.236618e+08, 3.236618e+08],
       [1.078982e+08, 1.078982e+08, 1.078982e+08, ..., 1.078982e+08,
        1.078982e+08, 1.078982e+08]])
Coordinates:
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5
Attributes:
    cell_methods:   area: sum
    comment:        TAREA
    description:    Cell areas for any grid used to report ocean variables an...
    frequency:      fx
    id:             areacello
    long_name:      Grid-Cell Area for Ocean Variables
    mipTable:       Ofx
    out_name:       areacello
    prov:           Ofx ((isd.003))
    realm:          ocean
    standard_name:  cell_area
    time_label:     None
    time_title:     No temporal dimensions ... fixed field
    title:          Grid-Cell Area for Ocean Variables
    type:           real
    units:          m2
    variable_id:    areacello

As before, let’s calculate area-weighted mean global anomaly:

weighted_mean_global_anom = tos_anom.weighted(areacello).mean(dim=['lat', 'lon'])

Let’s plot both unweighted and weighted means:

unweighted_mean_global_anom.plot(size=7)
weighted_mean_global_anom.plot()
plt.legend(['unweighted', 'weighted']);
../../_images/computation-masking_52_0.png

Other high level computation functionality

For example, resample to annual frequency:

r = ds.tos.resample(time='AS')
r
DataArrayResample, grouped over '__resample_dim__'
15 groups with labels 2000-01-01, 00:00:00, ..., 201....
r.mean()
<xarray.DataArray 'tos' (time: 15, lat: 180, lon: 360)>
array([[[       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        ...,
        [-1.7474419, -1.7474264, -1.7474008, ..., -1.7474308,
         -1.7474365, -1.7474445],
        [-1.7424874, -1.7424612, -1.7424251, ..., -1.742536 ,
         -1.7425283, -1.7425116],
        [-1.7382039, -1.7381679, -1.7381277, ..., -1.7383199,
         -1.7382846, -1.7382454]],

       [[       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
...
        [-1.6902231, -1.6899008, -1.6895409, ..., -1.6910189,
         -1.6907759, -1.6905178],
        [-1.6879102, -1.6876906, -1.6874666, ..., -1.6885366,
         -1.6883289, -1.688121 ],
        [-1.6883243, -1.6881752, -1.6880217, ..., -1.6886654,
         -1.6885542, -1.6884427]],

       [[       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        ...,
        [-1.6893266, -1.6893964, -1.6894479, ..., -1.6889572,
         -1.6890831, -1.6892204],
        [-1.6776317, -1.6777302, -1.6778082, ..., -1.6771463,
         -1.6773272, -1.677492 ],
        [-1.672563 , -1.6726688, -1.6727766, ..., -1.6723493,
         -1.6724195, -1.6724887]]], dtype=float32)
Coordinates:
  * time     (time) object 2000-01-01 00:00:00 ... 2014-01-01 00:00:00
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5

Compute a 5-month moving average:

m_avg = ds.tos.rolling(time=5, center=True).mean()
m_avg
<xarray.DataArray 'tos' (time: 180, lat: 180, lon: 360)>
array([[[        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        ...,
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan]],

       [[        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
...
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan]],

       [[        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        ...,
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan],
        [        nan,         nan,         nan, ...,         nan,
                 nan,         nan]]])
Coordinates:
  * time     (time) object 2000-01-15 12:00:00 ... 2014-12-15 12:00:00
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5
Attributes:
    cell_measures:  area: areacello
    cell_methods:   area: mean where sea time: mean
    comment:        Model data on the 1x1 grid includes values in all cells f...
    description:    This may differ from "surface temperature" in regions of ...
    frequency:      mon
    id:             tos
    long_name:      Sea Surface Temperature
    mipTable:       Omon
    out_name:       tos
    prov:           Omon ((isd.003))
    realm:          ocean
    standard_name:  sea_surface_temperature
    time:           time
    time_label:     time-mean
    time_title:     Temporal mean
    title:          Sea Surface Temperature
    type:           real
    units:          degC
    variable_id:    tos
lat = 50
lon = 310

m_avg.isel(lat=lat, lon=lon).plot(size=6)
ds.tos.isel(lat=lat, lon=lon).plot()
plt.legend(['5-month moving average', 'monthly data']);
../../_images/computation-masking_59_0.png

Masking Data

Using the xr.where() or .where() method, elements of an xarray Dataset or xarray DataArray that satisfy a given condition or multiple conditions can be replaced/masked. To demonstrate this, we are going to use the .where() method on the tos DataArray.

We will use the same sea surface temperature dataset:

ds
<xarray.Dataset>
Dimensions:    (time: 180, d2: 2, lat: 180, lon: 360)
Coordinates:
  * time       (time) object 2000-01-15 12:00:00 ... 2014-12-15 12:00:00
  * lat        (lat) float64 -89.5 -88.5 -87.5 -86.5 ... 86.5 87.5 88.5 89.5
  * lon        (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 356.5 357.5 358.5 359.5
Dimensions without coordinates: d2
Data variables:
    time_bnds  (time, d2) object 2000-01-01 00:00:00 ... 2015-01-01 00:00:00
    lat_bnds   (lat, d2) float64 -90.0 -89.0 -89.0 -88.0 ... 88.0 89.0 89.0 90.0
    lon_bnds   (lon, d2) float64 0.0 1.0 1.0 2.0 2.0 ... 358.0 359.0 359.0 360.0
    tos        (time, lat, lon) float32 nan nan nan nan ... -1.746 -1.746 -1.746
Attributes: (12/45)
    Conventions:            CF-1.7 CMIP-6.2
    activity_id:            CMIP
    branch_method:          standard
    branch_time_in_child:   674885.0
    branch_time_in_parent:  219000.0
    case_id:                972
    ...                     ...
    sub_experiment_id:      none
    table_id:               Omon
    tracking_id:            hdl:21.14100/2975ffd3-1d7b-47e3-961a-33f212ea4eb2
    variable_id:            tos
    variant_info:           CMIP6 20th century experiments (1850-2014) with C...
    variant_label:          r11i1p1f1

Using where with one condition

Imagine we wish to analyze just the last time in the dataset. We could of course use .isel() for this:

sample = ds.tos.isel(time=-1)
sample
<xarray.DataArray 'tos' (lat: 180, lon: 360)>
array([[      nan,       nan,       nan, ...,       nan,       nan,       nan],
       [      nan,       nan,       nan, ...,       nan,       nan,       nan],
       [      nan,       nan,       nan, ...,       nan,       nan,       nan],
       ...,
       [-1.756119, -1.756165, -1.756205, ..., -1.755922, -1.755986, -1.756058],
       [-1.750638, -1.750658, -1.750667, ..., -1.750508, -1.750561, -1.750605],
       [-1.74627 , -1.746267, -1.746261, ..., -1.746309, -1.746299, -1.746285]],
      dtype=float32)
Coordinates:
    time     object 2014-12-15 12:00:00
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5
Attributes:
    cell_measures:  area: areacello
    cell_methods:   area: mean where sea time: mean
    comment:        Model data on the 1x1 grid includes values in all cells f...
    description:    This may differ from "surface temperature" in regions of ...
    frequency:      mon
    id:             tos
    long_name:      Sea Surface Temperature
    mipTable:       Omon
    out_name:       tos
    prov:           Omon ((isd.003))
    realm:          ocean
    standard_name:  sea_surface_temperature
    time:           time
    time_label:     time-mean
    time_title:     Temporal mean
    title:          Sea Surface Temperature
    type:           real
    units:          degC
    variable_id:    tos

Unlike .isel() and .sel() that change the shape of the returned results, .where() preserves the shape of the original data. It accomplishes this by returning values from the original DataArray or Dataset if the condition is True, and fills in values (by default nan) wherever the condition is False.

Before applying it, let’s look at the .where() documentation. As the documention points out, the conditional expression in .where() can be:

  • a DataArray

  • a Dataset

  • a function

For demonstration purposes, let’s use .where() to mask locations with temperature values greater than 0:

masked_sample = sample.where(sample < 0.0)
masked_sample
<xarray.DataArray 'tos' (lat: 180, lon: 360)>
array([[       nan,        nan,        nan, ...,        nan,        nan,
               nan],
       [       nan,        nan,        nan, ...,        nan,        nan,
               nan],
       [       nan,        nan,        nan, ...,        nan,        nan,
               nan],
       ...,
       [-1.7561191, -1.7561648, -1.7562052, ..., -1.7559224, -1.7559862,
        -1.7560585],
       [-1.7506379, -1.7506577, -1.7506672, ..., -1.7505083, -1.750561 ,
        -1.7506049],
       [-1.7462697, -1.7462667, -1.7462606, ..., -1.7463093, -1.746299 ,
        -1.7462848]], dtype=float32)
Coordinates:
    time     object 2014-12-15 12:00:00
  * lat      (lat) float64 -89.5 -88.5 -87.5 -86.5 -85.5 ... 86.5 87.5 88.5 89.5
  * lon      (lon) float64 0.5 1.5 2.5 3.5 4.5 ... 355.5 356.5 357.5 358.5 359.5
Attributes:
    cell_measures:  area: areacello
    cell_methods:   area: mean where sea time: mean
    comment:        Model data on the 1x1 grid includes values in all cells f...
    description:    This may differ from "surface temperature" in regions of ...
    frequency:      mon
    id:             tos
    long_name:      Sea Surface Temperature
    mipTable:       Omon
    out_name:       tos
    prov:           Omon ((isd.003))
    realm:          ocean
    standard_name:  sea_surface_temperature
    time:           time
    time_label:     time-mean
    time_title:     Temporal mean
    title:          Sea Surface Temperature
    type:           real
    units:          degC
    variable_id:    tos

Let’s plot both our original sample, and the masked sample:

fig, axes = plt.subplots(ncols=2, figsize=(19, 6))
sample.plot(ax=axes[0])
masked_sample.plot(ax=axes[1]);
../../_images/computation-masking_70_0.png

Using where with multiple conditions

.where() allows providing multiple conditions. To do this, we need to make sure each conditional expression is enclosed in (). To combine conditions, we use the bit-wise and (&) operator and/or the bit-wise or (|). Let’s use .where() to mask locations with temperature values less than 25 and greater than 30:

sample.where((sample > 25) & (sample < 30)).plot(size=6);
../../_images/computation-masking_73_0.png

We can use coordinates to apply a mask as well. Below, we use the latitude and longitude coordinates to mask everywhere outside of the Niño 3.4 region:

sample.where(
    (sample.lat < 5) & (sample.lat > -5) & (sample.lon > 190) & (sample.lon < 240)
).plot(size=6);
../../_images/computation-masking_75_0.png

Using where with a custom fill value

.where() can take a second argument, which, if supplied, defines a fill value for the masked region. Below we fill masked regions with a constant 0:

sample.where((sample > 25) & (sample < 30), 0).plot(size=6);
../../_images/computation-masking_78_0.png

Summary

  • Similar to NumPy, arithmetic operations are vectorized over a DataArray

  • Xarray provides aggregation methods like sum() and mean(), with the option to specify which dimension over which the operation will be done

  • groupby enables the convenient split-apply-combine workflow

  • The .where() method allows for filtering or replacing of data based on one or more provided conditions

What’s next?

In the next notebook, we will work through an example of plotting the Niño 3.4 Index.