YAXArrays.jl

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Read n-d array like-data

DiskArrays.jl

Get your chunks!

Named Dimensions

DimensionalData.jl

Select & Index!

Out of memory data

Zarr.jl

Chunkerd, compressed !

Rasterized spatial data

Rasters.jl

Read and manipulate !

Array-oriented data

NetCDF.jl

Scientific binary data.

Raster and vector data

ArchGDAL.jl

GDAL in Julia.

An interface for

GeoInterface.jl

geospatial data in Julia.

A higher level interface

GRIBDatasets.jl

for reading GRIB files.

Array-oriented data

NCDatasets.jl

Scientific binary data.

Select YAXArrays and Datasets ​

The dimensions or axes of an YAXArray are named making it easier to subset or query certain ranges of an array. Let's open an example Dataset used to select certain elements:

julia
using YAXArrays
using NetCDF
using Downloads: download

path = download("https://www.unidata.ucar.edu/software/netcdf/examples/tos_O1_2001-2002.nc", "example.nc")
ds = open_dataset(path)
YAXArray Dataset
Shared Axes: 
↓ lon Sampled{Float64} 1.0:2.0:359.0 ForwardOrdered Regular Points,
→ lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points,
↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
Variables: 
tos

Properties: Dict{String, Any}("cmor_version" => 0.96f0, "references" => "Dufresne et al, Journal of Climate, 2015, vol XX, p 136", "realization" => 1, "Conventions" => "CF-1.0", "contact" => "Sebastien Denvil, sebastien.denvil@ipsl.jussieu.fr", "history" => "YYYY/MM/JJ: data generated; YYYY/MM/JJ+1 data transformed  At 16:37:23 on 01/11/2005, CMOR rewrote data to comply with CF standards and IPCC Fourth Assessment requirements", "table_id" => "Table O1 (13 November 2004)", "source" => "IPSL-CM4_v1 (2003) : atmosphere : LMDZ (IPSL-CM4_IPCC, 96x71x19) ; ocean ORCA2 (ipsl_cm4_v1_8, 2x2L31); sea ice LIM (ipsl_cm4_v", "title" => "IPSL  model output prepared for IPCC Fourth Assessment SRES A2 experiment", "experiment_id" => "SRES A2 experiment"…)

Select a YAXArray ​

Get the sea surface temperature of the Dataset:

julia
tos = ds.tos
╭────────────────────────────────────────────────╮
│ 180×170×24 YAXArray{Union{Missing, Float32},3} │
├────────────────────────────────────────────────┴─────────────────────── dims ┐
  ↓ lon Sampled{Float64} 1.0:2.0:359.0 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤ 
  file size: 2.8 MB
└──────────────────────────────────────────────────────────────────────────────┘

which is the same as:

julia
tos = ds.cubes[:tos]
╭────────────────────────────────────────────────╮
│ 180×170×24 YAXArray{Union{Missing, Float32},3} │
├────────────────────────────────────────────────┴─────────────────────── dims ┐
  ↓ lon Sampled{Float64} 1.0:2.0:359.0 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤ 
  file size: 2.8 MB
└──────────────────────────────────────────────────────────────────────────────┘

Select elements ​

Using positional integer indexing:

julia
tos[lon = 1, lat = 1]
╭────────────────────────────────────────────────╮
│ 24-element YAXArray{Union{Missing, Float32},1} │
├────────────────────────────────────────────────┴─────────────────────── dims ┐
  ↓ Ti Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤ 
  file size: 96.0 bytes
└──────────────────────────────────────────────────────────────────────────────┘

Same but using named indexing:

julia
tos[lon = At(1), lat = At(-79.5)]
╭────────────────────────────────────────────────╮
│ 24-element YAXArray{Union{Missing, Float32},1} │
├────────────────────────────────────────────────┴─────────────────────── dims ┐
  ↓ Ti Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤ 
  file size: 96.0 bytes
└──────────────────────────────────────────────────────────────────────────────┘

Using special types:

julia
using CFTime
time1 = DateTime360Day(2001,01,16)
tos[time = At(time1)]
╭─────────────────────────────────────────────╮
│ 180×170 YAXArray{Union{Missing, Float32},2} │
├─────────────────────────────────────────────┴───────────────── dims ┐
  ↓ lon Sampled{Float64} 1.0:2.0:359.0 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points
├─────────────────────────────────────────────────────────────────────┴ metadata ┐
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├───────────────────────────────────────────────────────────────────── file size ┤ 
  file size: 119.53 KB
└────────────────────────────────────────────────────────────────────────────────┘

Select ranges ​

Here we subset an interval of a dimension using positional integer indexing.

julia
tos[lon = 1:10, lat = 1:10]
╭──────────────────────────────────────────────╮
│ 10×10×24 YAXArray{Union{Missing, Float32},3} │
├──────────────────────────────────────────────┴───────────────────────── dims ┐
  ↓ lon Sampled{Float64} 1.0:2.0:19.0 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -79.5:1.0:-70.5 ForwardOrdered Regular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤ 
  file size: 9.38 KB
└──────────────────────────────────────────────────────────────────────────────┘

Same but using named indexing:

julia
tos[lon = At(1.0:2:19), lat = At(-79.5:1:-70.5)]
╭──────────────────────────────────────────────╮
│ 10×10×24 YAXArray{Union{Missing, Float32},3} │
├──────────────────────────────────────────────┴───────────────────────── dims ┐
  ↓ lon Sampled{Float64} [1.0, 3.0, …, 17.0, 19.0] ForwardOrdered Irregular Points,
  → lat Sampled{Float64} [-79.5, -78.5, …, -71.5, -70.5] ForwardOrdered Irregular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤ 
  file size: 9.38 KB
└──────────────────────────────────────────────────────────────────────────────┘

Read more about the At selector in the package DimensionalData. Get values within a tolerances:

julia
tos[lon = At(1:10; atol = 1)]
╭───────────────────────────────────────────────╮
│ 10×170×24 YAXArray{Union{Missing, Float32},3} │
├───────────────────────────────────────────────┴──────────────────────── dims ┐
  ↓ lon Sampled{Float64} [1.0, 1.0, …, 9.0, 9.0] ForwardOrdered Irregular Points,
  → lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤ 
  file size: 159.38 KB
└──────────────────────────────────────────────────────────────────────────────┘

Closed and open intervals ​

Although a Between(a,b) function is available in DimensionalData, is recommended to use instead the a .. b notation:

julia
tos[lon = 90 .. 180]
╭───────────────────────────────────────────────╮
│ 45×170×24 YAXArray{Union{Missing, Float32},3} │
├───────────────────────────────────────────────┴──────────────────────── dims ┐
  ↓ lon Sampled{Float64} 91.0:2.0:179.0 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤ 
  file size: 717.19 KB
└──────────────────────────────────────────────────────────────────────────────┘

This describes a closed interval in which all points were included. More selectors from DimensionalData are available, such as Touches, Near, Where and Contains.

julia
using IntervalSets
julia
julia> tos[lon = OpenInterval(90, 180)]
╭───────────────────────────────────────────────╮
│ 45×170×24 YAXArray{Union{Missing, Float32},3} │
├───────────────────────────────────────────────┴──────────────────────── dims ┐
  ↓ lon Sampled{Float64} 91.0:2.0:179.0 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤
  file size: 717.19 KB
└──────────────────────────────────────────────────────────────────────────────┘
julia
julia> tos[lon = ClosedInterval(90, 180)]
╭───────────────────────────────────────────────╮
│ 45×170×24 YAXArray{Union{Missing, Float32},3} │
├───────────────────────────────────────────────┴──────────────────────── dims ┐
  ↓ lon Sampled{Float64} 91.0:2.0:179.0 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤
  file size: 717.19 KB
└──────────────────────────────────────────────────────────────────────────────┘
julia
julia> tos[lon =Interval{:open,:closed}(90,180)]
╭───────────────────────────────────────────────╮
│ 45×170×24 YAXArray{Union{Missing, Float32},3} │
├───────────────────────────────────────────────┴──────────────────────── dims ┐
  ↓ lon Sampled{Float64} 91.0:2.0:179.0 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤
  file size: 717.19 KB
└──────────────────────────────────────────────────────────────────────────────┘
julia
julia> tos[lon =Interval{:closed,:open}(90,180)]
╭───────────────────────────────────────────────╮
│ 45×170×24 YAXArray{Union{Missing, Float32},3} │
├───────────────────────────────────────────────┴──────────────────────── dims ┐
  ↓ lon Sampled{Float64} 91.0:2.0:179.0 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -79.5:1.0:89.5 ForwardOrdered Regular Points,
  ↗ Ti  Sampled{CFTime.DateTime360Day} [CFTime.DateTime360Day(2001-01-16T00:00:00), …, CFTime.DateTime360Day(2002-12-16T00:00:00)] ForwardOrdered Irregular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
  Dict{String, Any} with 10 entries:
  "units"          => "K"
  "missing_value"  => 1.0f20
  "history"        => " At   16:37:23 on 01/11/2005: CMOR altered the data in t…
  "cell_methods"   => "time: mean (interval: 30 minutes)"
  "name"           => "tos"
  "long_name"      => "Sea Surface Temperature"
  "original_units" => "degC"
  "standard_name"  => "sea_surface_temperature"
  "_FillValue"     => 1.0f20
  "original_name"  => "sosstsst"
├─────────────────────────────────────────────────────────────────── file size ┤
  file size: 717.19 KB
└──────────────────────────────────────────────────────────────────────────────┘

See tutorials for use cases.

Get a dimension ​

Get values, .e.g., axis tick labels, of a dimension that can be used for subseting:

julia
collect(tos.lat)
170-element Vector{Float64}:
 -79.5
 -78.5
 -77.5
 -76.5
 -75.5
 -74.5
 -73.5
 -72.5
 -71.5
 -70.5
   ⋮
  81.5
  82.5
  83.5
  84.5
  85.5
  86.5
  87.5
  88.5
  89.5

These values are defined as lookups in the package DimensionalData:

julia
lookup(tos, :lon)
Sampled{Float64} ForwardOrdered Regular DimensionalData.Dimensions.Lookups.Points
wrapping: 1.0:2.0:359.0

which is equivalent to:

julia
tos.lon.val
Sampled{Float64} ForwardOrdered Regular DimensionalData.Dimensions.Lookups.Points
wrapping: 1.0:2.0:359.0