Quick start

Bitrounding by itself is straight forward. However, the decision on the number of bits to round to, is much more difficult. Xbitinfo uses information theory to guide a (quantitative) decision.

In order to arrive at an optimal compression strategy that fits the use-case(s) of the compressed dataset, Xbitinfo splits the compression pipeline into four main steps to provide customization options for each step:

1. Analysis of the bitwise information content of a dataset

2. Decision on a threshold of real information to preserve (e.g. 99%)

3. Bitround dataset accordingly (bitrounding)

4. Apply lossless compression of choice (e.g. zlib, blosc, zstd) and store the dataset

Step 0: Open dataset

import xbitinfo as xb

import xarray as xr

ds = xr.tutorial.load_dataset("eraint_uvz").astype("float32")

ds

<xarray.Dataset> Size: 8MB
Dimensions:    (month: 2, level: 3, latitude: 241, longitude: 480)
Coordinates:
  * month      (month) int32 8B 1 7
  * level      (level) int32 12B 200 500 850
  * latitude   (latitude) float32 964B 90.0 89.25 88.5 ... -88.5 -89.25 -90.0
  * longitude  (longitude) float32 2kB -180.0 -179.2 -178.5 ... 178.5 179.2
Data variables:
    z          (month, level, latitude, longitude) float32 3MB 1.068e+05 ... ...
    u          (month, level, latitude, longitude) float32 3MB 1.282 ... 3.539
    v          (month, level, latitude, longitude) float32 3MB -0.04676 ... 3...
Attributes:
    Conventions:  CF-1.0
    Info:         Monthly ERA-Interim data. Downloaded and edited by fabien.m...

xarray.Dataset

• Dimensions:
  • month: 2
  • level: 3
  • latitude: 241
  • longitude: 480
• Coordinates: (4)
  • month
    (month)
    int32
    1 7

    array([1, 7], dtype=int32)

  • level
    (level)
    int32
    200 500 850

    units :

    millibars

    long_name :

    pressure_level

    array([200, 500, 850], dtype=int32)

  • latitude
    (latitude)
    float32
    90.0 89.25 88.5 ... -89.25 -90.0

    units :

    degrees_north

    long_name :

    latitude

    array([ 90.  ,  89.25,  88.5 , ..., -88.5 , -89.25, -90.  ],
          shape=(241,), dtype=float32)

  • longitude
    (longitude)
    float32
    -180.0 -179.2 ... 178.5 179.2

    units :

    degrees_east

    long_name :

    longitude

    array([-180.  , -179.25, -178.5 , ...,  177.75,  178.5 ,  179.25],
          shape=(480,), dtype=float32)

• Data variables: (3)
  • z
    (month, level, latitude, longitude)
    float32
    1.068e+05 1.068e+05 ... 1.178e+04

    number_of_significant_digits :

    5

    units :

    m**2 s**-2

    long_name :

    Geopotential

    standard_name :

    geopotential

    array([[[[106837.516, 106839.234, 106837.516, ..., 106839.234,
              106837.516, 106839.234],
             [106856.484, 106858.21 , 106856.484, ..., 106856.484,
              106856.484, 106856.484],
             [106884.086, 106884.086, 106884.086, ..., 106884.086,
              106884.086, 106884.086],
             ...,
             [109795.94 , 109795.94 , 109795.94 , ..., 109795.94 ,
              109795.94 , 109795.94 ],
             [109802.836, 109804.56 , 109804.56 , ..., 109804.56 ,
              109802.836, 109802.836],
             [109808.01 , 109808.01 , 109808.01 , ..., 109808.01 ,
              109808.01 , 109808.01 ]],
    
            [[ 49723.58 ,  49723.58 ,  49723.58 , ...,  49723.58 ,
               49723.58 ,  49723.58 ],
             [ 49744.277,  49744.277,  49744.277, ...,  49746.004,
               49746.004,  49746.004],
             [ 49771.88 ,  49771.88 ,  49771.88 , ...,  49771.88 ,
               49771.88 ,  49771.88 ],
    ...
               47891.598,  47891.598],
             [ 47941.625,  47941.625,  47941.625, ...,  47943.348,
               47941.625,  47941.625],
             [ 47974.4  ,  47974.4  ,  47974.4  , ...,  47974.4  ,
               47974.4  ,  47974.4  ]],
    
            [[ 13485.926,  13485.926,  13485.926, ...,  13485.926,
               13485.926,  13485.926],
             [ 13484.2  ,  13484.2  ,  13484.2  , ...,  13484.2  ,
               13484.2  ,  13484.2  ],
             [ 13484.2  ,  13484.2  ,  13484.2  , ...,  13482.476,
               13482.476,  13484.2  ],
             ...,
             [ 11360.691,  11358.967,  11357.242, ...,  11364.142,
               11362.417,  11362.417],
             [ 11612.546,  11612.546,  11612.546, ...,  11612.546,
               11612.546,  11612.546],
             [ 11776.424,  11776.424,  11776.424, ...,  11776.424,
               11776.424,  11776.424]]]],
          shape=(2, 3, 241, 480), dtype=float32)

  • u
    (month, level, latitude, longitude)
    float32
    1.282 1.282 1.282 ... 3.578 3.539

    number_of_significant_digits :

    2

    units :

    m s**-1

    long_name :

    U component of wind

    standard_name :

    eastward_wind

    array([[[[ 1.2817602e+00,  1.2817602e+00,  1.2817602e+00, ...,
               1.2817602e+00,  1.2817602e+00,  1.2817602e+00],
             [ 2.0162134e+00,  2.0319405e+00,  2.0240769e+00, ...,
               2.0083499e+00,  2.0083499e+00,  2.0240769e+00],
             [ 2.8198657e+00,  2.8355927e+00,  2.8355927e+00, ...,
               2.7962751e+00,  2.7962751e+00,  2.8198657e+00],
             ...,
             [-5.0797796e-01, -4.9225092e-01, -4.8438740e-01, ...,
              -5.4729557e-01, -5.3156853e-01, -5.2370501e-01],
             [-5.7088619e-01, -5.6302267e-01, -5.4729557e-01, ...,
              -5.9447676e-01, -5.8661324e-01, -5.7874972e-01],
             [-5.3943205e-01, -5.3943205e-01, -5.3156853e-01, ...,
              -5.5515909e-01, -5.4729557e-01, -5.4729557e-01]],
    
            [[ 1.9218512e+00,  1.9061241e+00,  1.8903971e+00, ...,
               1.9611688e+00,  1.9533052e+00,  1.9375782e+00],
             [ 2.3040185e+00,  2.3040185e+00,  2.2820005e+00, ...,
               2.3354726e+00,  2.3197455e+00,  2.3197455e+00],
             [ 2.7428031e+00,  2.7428031e+00,  2.7349396e+00, ...,
               2.7663937e+00,  2.7506666e+00,  2.7585301e+00],
    ...
              -4.4680490e+00, -4.4680490e+00, -4.4995031e+00],
             [-3.5543075e+00, -3.5857615e+00, -3.5936251e+00, ...,
              -3.4929719e+00, -3.5071263e+00, -3.5385804e+00],
             [-2.3905058e+00, -2.4219599e+00, -2.4376869e+00, ...,
              -2.3197341e+00, -2.3354611e+00, -2.3669152e+00]],
    
            [[-1.6355559e-01, -1.5569207e-01, -1.5569207e-01, ...,
              -1.8714617e-01, -1.7928264e-01, -1.7141911e-01],
             [ 7.8692473e-03,  1.5732773e-02,  2.3596296e-02, ...,
              -1.5721327e-02, -7.8578023e-03,  5.7223951e-06],
             [ 2.7365637e-01,  2.8151992e-01,  2.8938344e-01, ...,
               2.4220228e-01,  2.5006580e-01,  2.6579285e-01],
             ...,
             [-1.6875067e+00, -1.6875067e+00, -1.6953702e+00, ...,
              -1.6639161e+00, -1.6717796e+00, -1.6796432e+00],
             [ 1.4531851e+00,  1.4295945e+00,  1.3902769e+00, ...,
               1.5554109e+00,  1.5239568e+00,  1.4925027e+00],
             [ 3.4851198e+00,  3.4536657e+00,  3.3986211e+00, ...,
               3.6250906e+00,  3.5779095e+00,  3.5385919e+00]]]],
          shape=(2, 3, 241, 480), dtype=float32)

  • v
    (month, level, latitude, longitude)
    float32
    -0.04676 -0.06253 ... 3.328 3.383

    number_of_significant_digits :

    2

    units :

    m s**-1

    long_name :

    V component of wind

    standard_name :

    northward_wind

    array([[[[-0.04675769, -0.06252575, -0.07829381, ...,  0.00771379,
              -0.00757645, -0.02334451],
             [ 0.14054775,  0.10948945,  0.08607627, ...,  0.22655535,
               0.19549705,  0.17208387],
             [ 0.33597612,  0.2967949 ,  0.25761366, ...,  0.45304203,
               0.4138608 ,  0.37515736],
             ...,
             [-0.6875143 , -0.70328236, -0.7185726 , ..., -0.656456  ,
              -0.6641011 , -0.6798692 ],
             [-0.5154991 , -0.53126717, -0.5389123 , ..., -0.49208593,
              -0.50020885, -0.507854  ],
             [-0.37502003, -0.38266516, -0.39078808, ..., -0.35160685,
              -0.35925198, -0.3673749 ]],
    
            [[-1.0778933 , -1.1094294 , -1.1328425 , ..., -1.0076537 ,
              -1.0310669 , -1.062603  ],
             [-0.92976904, -0.96082735, -0.99236345, ..., -0.8279934 ,
              -0.8595295 , -0.89823294],
             [-0.765399  , -0.81270313, -0.8514066 , ..., -0.6483331 ,
              -0.6875143 , -0.72669554],
    ...
               1.7187872 ,  1.6485476 ],
             [ 1.8358531 ,  1.7890267 ,  1.7345552 , ...,  1.9844551 ,
               1.9376287 ,  1.8908024 ],
             [ 1.9218607 ,  1.8908024 ,  1.8592663 , ...,  2.0155134 ,
               1.9844551 ,  1.952919  ]],
    
            [[ 0.51563644,  0.51563644,  0.51563644, ...,  0.5079913 ,
               0.5079913 ,  0.5079913 ],
             [ 0.54669476,  0.54669476,  0.54669476, ...,  0.5390496 ,
               0.5390496 ,  0.54669476],
             [ 0.585876  ,  0.585876  ,  0.585876  , ...,  0.585876  ,
               0.57823086,  0.585876  ],
             ...,
             [ 4.734309  ,  4.7500772 ,  4.7500772 , ...,  4.734309  ,
               4.718541  ,  4.734309  ],
             [ 3.195251  ,  3.226787  ,  3.2420774 , ...,  3.1250114 ,
               3.1484246 ,  3.179483  ],
             [ 3.4217377 ,  3.468564  ,  3.5077453 , ...,  3.2889037 ,
               3.328085  ,  3.3830342 ]]]],
          shape=(2, 3, 241, 480), dtype=float32)

• Attributes: (2)

  Conventions :

  CF-1.0

  Info :

  Monthly ERA-Interim data. Downloaded and edited by fabien.maussion@uibk.ac.at

xb.plot_distribution(ds);

NOTE: If you plan to use the example datasets provided by xarray, you will need to install the pooch package separately using the following command:

pip install pooch

Without installing pooch, you will not be able to download and load the example datasets, which may result in errors or unexpected behavior.

Step 1: Get information content per bit

using xbitinfo.xbitinfo.get_bitinformation()

info_per_bit = xb.get_bitinformation(ds, dim="longitude", implementation="python")

info_per_bit

<xarray.Dataset> Size: 1kB
Dimensions:     (bitfloat32: 32)
Coordinates:
  * bitfloat32  (bitfloat32) <U3 384B '±' 'e1' 'e2' 'e3' ... 'm21' 'm22' 'm23'
    dim         <U9 36B 'longitude'
Data variables:
    z           (bitfloat32) float64 256B 0.0 0.0 0.0 ... 0.005199 0.007699
    u           (bitfloat32) float64 256B 0.7816 0.4274 0.0 ... 0.01148 0.1475
    v           (bitfloat32) float64 256B 0.8752 0.7756 0.0 ... 0.06165 0.05304
Attributes:
    xbitinfo_description:       bitinformation calculated by xbitinfo.get_bit...
    python_repository:          https://github.com/observingClouds/xbitinfo
    julia_repository:           https://github.com/milankl/BitInformation.jl
    reference_paper:            http://www.nature.com/articles/s43588-021-001...
    xbitinfo_version:           0.0.5
    BitInformation.jl_version:  0.6.3

xarray.Dataset

• Dimensions:
  • bitfloat32: 32
• Coordinates: (2)
  • bitfloat32
    (bitfloat32)
    <U3
    '±' 'e1' 'e2' ... 'm21' 'm22' 'm23'

    description :

    name of the bits: '±' refers to the sign bit, 'e' to the exponents bits and 'm' to the mantissa bits.

    array(['±', 'e1', 'e2', 'e3', 'e4', 'e5', 'e6', 'e7', 'e8', 'm1', 'm2', 'm3',
           'm4', 'm5', 'm6', 'm7', 'm8', 'm9', 'm10', 'm11', 'm12', 'm13', 'm14',
           'm15', 'm16', 'm17', 'm18', 'm19', 'm20', 'm21', 'm22', 'm23'],
          dtype='<U3')

  • dim
    ()
    <U9
    'longitude'

    description :

    dimension of the source dataset along which the bitwise information has been analysed.

    array('longitude', dtype='<U9')

• Data variables: (3)
  • z
    (bitfloat32)
    float64
    0.0 0.0 0.0 ... 0.005199 0.007699

    long_name :

    z bitwise information

    units :

    1

    source_number_of_significant_digits :

    5

    source_units :

    m**2 s**-2

    source_long_name :

    Geopotential

    source_standard_name :

    geopotential

    array([0.        , 0.        , 0.        , 0.        , 0.91829583,
           0.91829583, 0.91829583, 0.91829583, 0.91829583, 0.40596261,
           0.97813287, 0.92341985, 0.94109422, 0.90208436, 0.82484959,
           0.71155894, 0.54404085, 0.34755517, 0.18092331, 0.07436806,
           0.02217038, 0.01245641, 0.00377219, 0.00628822, 0.01224325,
           0.00389673, 0.01004858, 0.0131198 , 0.00564089, 0.00887582,
           0.0051986 , 0.00769888])

  • u
    (bitfloat32)
    float64
    0.7816 0.4274 ... 0.01148 0.1475

    long_name :

    u bitwise information

    units :

    1

    source_number_of_significant_digits :

    2

    source_units :

    m s**-1

    source_long_name :

    U component of wind

    source_standard_name :

    eastward_wind

    array([7.81646180e-01, 4.27436423e-01, 0.00000000e+00, 0.00000000e+00,
           1.71227095e-04, 0.00000000e+00, 6.35104053e-01, 8.05002303e-01,
           6.78224433e-01, 5.35060838e-01, 3.99149342e-01, 2.46776345e-01,
           1.16042153e-01, 3.33513654e-02, 5.73779013e-03, 3.48614977e-03,
           5.59982312e-03, 9.19817640e-03, 7.71894512e-03, 5.38088606e-03,
           2.65337337e-03, 6.27602119e-04, 3.53690832e-04, 4.95650149e-04,
           3.34290451e-03, 2.51371722e-03, 2.11808385e-03, 1.17905219e-03,
           1.13182091e-03, 3.28875231e-03, 1.14760822e-02, 1.47515177e-01])

  • v
    (bitfloat32)
    float64
    0.8752 0.7756 ... 0.06165 0.05304

    long_name :

    v bitwise information

    units :

    1

    source_number_of_significant_digits :

    2

    source_units :

    m s**-1

    source_long_name :

    V component of wind

    source_standard_name :

    northward_wind

    array([8.75249762e-01, 7.75560757e-01, 0.00000000e+00, 0.00000000e+00,
           0.00000000e+00, 2.74549688e-03, 1.17783327e-01, 5.01420134e-01,
           4.06812530e-01, 2.29018531e-01, 1.01658673e-01, 2.73218922e-02,
           3.76688041e-03, 4.52212736e-04, 1.53181859e-04, 1.30129511e-04,
           5.09324245e-05, 4.18079116e-05, 3.43536304e-05, 2.87844951e-05,
           3.84562184e-05, 1.71014710e-04, 7.26738394e-04, 4.54372431e-04,
           6.11464268e-04, 5.30345968e-04, 2.06533122e-04, 7.77135473e-04,
           6.67379672e-03, 1.99001671e-02, 6.16532925e-02, 5.30433184e-02])

• Attributes: (6)

  xbitinfo_description :

  bitinformation calculated by xbitinfo.get_bitinformation wrapping bitinformation.jl

  python_repository :

  https://github.com/observingClouds/xbitinfo

  julia_repository :

  https://github.com/milankl/BitInformation.jl

  reference_paper :

  http://www.nature.com/articles/s43588-021-00156-2

  xbitinfo_version :

  0.0.5

  BitInformation.jl_version :

  0.6.3

Visualize information content

using xbitinfo.graphics.plot_bitinformation()

fig = xb.plot_bitinformation(info_per_bit)

Step 2: Set keepbits

Based on the visualization of the bitinformation plotted above, the number of keepbits can be directly obtained or calculated by setting a threshold of real information content to preserve (e.g. 99%) by using xbitinfo.xbitinfo.get_keepbits():

keepbits = xb.get_keepbits(info_per_bit, 0.99)
keepbits

<xarray.Dataset> Size: 68B
Dimensions:   (inflevel: 1)
Coordinates:
  * inflevel  (inflevel) float64 8B 0.99
    dim       <U9 36B 'longitude'
Data variables:
    z         (inflevel) int64 8B 10
    u         (inflevel) int64 8B 3
    v         (inflevel) int64 8B 2

xarray.Dataset

• Dimensions:
  • inflevel: 1
• Coordinates: (2)
  • inflevel
    (inflevel)
    float64
    0.99

    array([0.99])

  • dim
    ()
    <U9
    'longitude'

    description :

    dimension of the source dataset along which the bitwise information has been analysed.

    array('longitude', dtype='<U9')

• Data variables: (3)
  • z
    (inflevel)
    int64
    10

    array([10])

  • u
    (inflevel)
    int64
    3

    array([3])

  • v
    (inflevel)
    int64
    2

    array([2])

Step 3: Apply bitrounding

using xbitinfo.bitround.xr_bitround() or xbitinfo.bitround.jl_bitround(). The later does not work with chunked datasets and requires a working installation of Julia.

ds_bitrounded = xb.xr_bitround(ds, keepbits)

xr.concat([ds, ds_bitrounded], "bitround").isel(level=0)["v"].plot(
    col="bitround", row="month"
);

Step 4: Apply compression and save dataset

To leverage the results of bitrounding, the dataset needs to be stored with a (lossless) compression algorithm. Xbitinfo provides two convienience functions that can be used to store the bitrounded dataset into commonly used file formats with default compression settings.

These functions are xbitinfo.save_compressed.ToCompressed_Netcdf and xbitinfo.save_compressed.ToCompressed_Zarr.

NetCDF

ds_bitrounded.to_compressed_netcdf("bitrounded_compressed.nc")

ds.to_compressed_netcdf("compressed.nc")

ds.to_netcdf("original.nc")

!du -hs *.nc

7.5M	0.air_original.nc
532K	bitrounded_compressed.nc
4.1M	compressed.nc
8.0M	original.nc

!rm *.nc

Zarr

ds_bitrounded.to_compressed_zarr("bitrounded_compressed.zarr", mode="w")
ds.to_compressed_zarr("compressed.zarr", mode="w")
ds.to_zarr(
    "original.zarr", mode="w", encoding={v: {"compressors": None} for v in ds.data_vars}
);

/home/docs/checkouts/readthedocs.org/user_builds/xbitinfo/envs/v0.0.5/lib/python3.12/site-packages/zarr/core/group.py:2703: ZarrUserWarning: The `compressor` argument is deprecated. Use `compressors` instead.
  compressors = _parse_deprecated_compressor(
/home/docs/checkouts/readthedocs.org/user_builds/xbitinfo/envs/v0.0.5/lib/python3.12/site-packages/zarr/api/asynchronous.py:244: ZarrUserWarning: Consolidated metadata is currently not part in the Zarr format 3 specification. It may not be supported by other zarr implementations and may change in the future.
  warnings.warn(

!du -hs *.zarr

836K	air_bitrounded.zarr
1.1M	air_bitrounded_by_chunks.zarr
7.9M	air_compressed.zarr
1.1M	bitrounded_compressed.zarr
5.0M	compressed.zarr
11M	original.zarr

!rm -r *.zarr