From 1b41b7dbe6e9dab4cdc36279b9706a0906be7ab1 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Mon, 28 Oct 2024 14:37:11 +0000 Subject: [PATCH] build based on 15f9b56 --- dev/404.html | 4 ++-- dev/UserGuide/cache.html | 6 ++--- dev/UserGuide/chunk.html | 6 ++--- dev/UserGuide/combine.html | 6 ++--- dev/UserGuide/compute.html | 10 ++++---- dev/UserGuide/convert.html | 6 ++--- dev/UserGuide/create.html | 6 ++--- dev/UserGuide/faq.html | 24 +++++++++---------- dev/UserGuide/group.html | 6 ++--- dev/UserGuide/read.html | 6 ++--- dev/UserGuide/select.html | 6 ++--- dev/UserGuide/types.html | 6 ++--- dev/UserGuide/write.html | 10 ++++---- dev/api.html | 18 +++++++------- ...ym.js => UserGuide_compute.md.DWxtLB-7.js} | 2 +- ... => UserGuide_compute.md.DWxtLB-7.lean.js} | 2 +- ...c51Dug.js => UserGuide_faq.md.BgQQKKl0.js} | 16 ++++++------- ...n.js => UserGuide_faq.md.BgQQKKl0.lean.js} | 16 ++++++------- ...NylS.js => UserGuide_write.md.Dkj1D2rr.js} | 2 +- ...js => UserGuide_write.md.Dkj1D2rr.lean.js} | 2 +- ...{api.md.DI_7iOJZ.js => api.md.BNQXJsIs.js} | 6 ++--- ..._7iOJZ.lean.js => api.md.BNQXJsIs.lean.js} | 6 ++--- .../{app.DppJzMHz.js => app.BIEVvIPk.js} | 2 +- .../chunks/@localSearchIndexroot.CiHbfWyN.js | 1 + .../chunks/@localSearchIndexroot.DKNu5-N1.js | 1 - ...o_30sd.js => VPLocalSearchBox.vBfplM2r.js} | 2 +- .../{theme.DSJoXFCG.js => theme.CrYK124x.js} | 4 ++-- ...> development_contributors.md.bnl_XTwF.js} | 2 +- ...elopment_contributors.md.bnl_XTwF.lean.js} | 2 +- ...ex.md.DTlVqubU.js => index.md.CIaPcDRI.js} | 4 ++-- ...qubU.lean.js => index.md.CIaPcDRI.lean.js} | 4 ++-- dev/development/contribute.html | 6 ++--- dev/development/contributors.html | 8 +++---- dev/get_started.html | 6 ++--- dev/hashmap.json | 2 +- dev/index.html | 10 ++++---- dev/tutorials/mean_seasonal_cycle.html | 6 ++--- dev/tutorials/other_tutorials.html | 6 ++--- dev/tutorials/plottingmaps.html | 6 ++--- 39 files changed, 122 insertions(+), 122 deletions(-) rename dev/assets/{UserGuide_compute.md.D3PBp0ym.js => UserGuide_compute.md.DWxtLB-7.js} (97%) rename dev/assets/{UserGuide_compute.md.D3PBp0ym.lean.js => UserGuide_compute.md.DWxtLB-7.lean.js} (97%) rename dev/assets/{UserGuide_faq.md.BTc51Dug.js => UserGuide_faq.md.BgQQKKl0.js} (99%) rename dev/assets/{UserGuide_faq.md.BTc51Dug.lean.js => UserGuide_faq.md.BgQQKKl0.lean.js} (99%) rename dev/assets/{UserGuide_write.md.CRLfNylS.js => UserGuide_write.md.Dkj1D2rr.js} (99%) rename dev/assets/{UserGuide_write.md.CRLfNylS.lean.js => UserGuide_write.md.Dkj1D2rr.lean.js} (99%) rename dev/assets/{api.md.DI_7iOJZ.js => api.md.BNQXJsIs.js} (52%) rename dev/assets/{api.md.DI_7iOJZ.lean.js => api.md.BNQXJsIs.lean.js} (52%) rename dev/assets/{app.DppJzMHz.js => app.BIEVvIPk.js} (95%) create mode 100644 dev/assets/chunks/@localSearchIndexroot.CiHbfWyN.js delete mode 100644 dev/assets/chunks/@localSearchIndexroot.DKNu5-N1.js rename dev/assets/chunks/{VPLocalSearchBox.BMo_30sd.js => VPLocalSearchBox.vBfplM2r.js} (99%) rename dev/assets/chunks/{theme.DSJoXFCG.js => theme.CrYK124x.js} (99%) rename dev/assets/{development_contributors.md.aO-w06-b.js => development_contributors.md.bnl_XTwF.js} (98%) rename dev/assets/{development_contributors.md.aO-w06-b.lean.js => development_contributors.md.bnl_XTwF.lean.js} (98%) rename dev/assets/{index.md.DTlVqubU.js => index.md.CIaPcDRI.js} (93%) rename dev/assets/{index.md.DTlVqubU.lean.js => index.md.CIaPcDRI.lean.js} (93%) diff --git a/dev/404.html b/dev/404.html index bb626c4e..cfd3d062 100644 --- a/dev/404.html +++ b/dev/404.html @@ -8,7 +8,7 @@ - + @@ -18,7 +18,7 @@
- + \ No newline at end of file diff --git a/dev/UserGuide/cache.html b/dev/UserGuide/cache.html index 34058dfd..c6b46b0d 100644 --- a/dev/UserGuide/cache.html +++ b/dev/UserGuide/cache.html @@ -8,9 +8,9 @@ - + - + @@ -25,7 +25,7 @@ cachesize = 500 #MB cache(ds,maxsize = cachesize)

The above will wrap every array in the dataset into its own cache, where the 500MB are distributed equally across datasets. Alternatively individual caches can be applied to single YAXArrays

julia
yax = ds.avariable
 cache(yax,maxsize = 1000)
- + \ No newline at end of file diff --git a/dev/UserGuide/chunk.html b/dev/UserGuide/chunk.html index 33a7bd5b..4f9b2a0d 100644 --- a/dev/UserGuide/chunk.html +++ b/dev/UserGuide/chunk.html @@ -8,9 +8,9 @@ - + - + @@ -118,7 +118,7 @@ Variables: x, y, z

Suggestions on how to improve or add to these examples is welcome.

- + \ No newline at end of file diff --git a/dev/UserGuide/combine.html b/dev/UserGuide/combine.html index 2e6f9ac7..019d0a16 100644 --- a/dev/UserGuide/combine.html +++ b/dev/UserGuide/combine.html @@ -8,9 +8,9 @@ - + - + @@ -48,7 +48,7 @@ ├───────────────────────────────────────────────── loaded lazily ┤ data size: 96.0 bytes └────────────────────────────────────────────────────────────────┘ - + \ No newline at end of file diff --git a/dev/UserGuide/compute.html b/dev/UserGuide/compute.html index 6e966cc0..70b8ab2a 100644 --- a/dev/UserGuide/compute.html +++ b/dev/UserGuide/compute.html @@ -8,11 +8,11 @@ - + - + - + @@ -41,7 +41,7 @@ :origin => "user guide" ├──────────────────────────────────────────────────────────── loaded in memory ┤ data size: 35.16 KB -└──────────────────────────────────────────────────────────────────────────────┘

Modify elements of a YAXArray ​

julia
a[1,2,3]
0.983449169710096
julia
a[1,2,3] = 42
42
julia
a[1,2,3]
42.0

WARNING

Some arrays, e.g. those saved in a cloud object storage are immutable making any modification of the data impossible.

Arithmetics ​

Add a value to all elements of an array and save it as a new array:

julia
a2 = a .+ 5
╭──────────────────────────────╮
+└──────────────────────────────────────────────────────────────────────────────┘

Modify elements of a YAXArray ​

julia
a[1,2,3]
0.9099638962470454
julia
a[1,2,3] = 42
42
julia
a[1,2,3]
42.0

WARNING

Some arrays, e.g. those saved in a cloud object storage are immutable making any modification of the data impossible.

Arithmetics ​

Add a value to all elements of an array and save it as a new array:

julia
a2 = a .+ 5
╭──────────────────────────────╮
 │ 30×10×15 YAXArray{Float64,3} │
 ├──────────────────────────────┴───────────────────────────────────────── dims ┐
   ↓ time Sampled{Date} Date("2022-01-01"):Dates.Day(1):Date("2022-01-30") ForwardOrdered Regular Points,
@@ -426,7 +426,7 @@
 mapCube(mymean, a, indims=InDims("time"), outdims=OutDims())

In the last example, mapCube was used to map the mymean function. mapslices is a convenient function that can replace mapCube, where you can omit defining an extra function with the output argument as an input (e.g. mymean). It is possible to simply use mapslice

julia
mapslices(mean ∘ skipmissing, a, dims="time")

It is also possible to distribute easily the workload on a cluster, with little modification to the code. To do so, we use the ClusterManagers package.

julia
using Distributed
 using ClusterManagers
 addprocs(SlurmManager(10))
- + \ No newline at end of file diff --git a/dev/UserGuide/convert.html b/dev/UserGuide/convert.html index 55691969..3e0b9023 100644 --- a/dev/UserGuide/convert.html +++ b/dev/UserGuide/convert.html @@ -8,9 +8,9 @@ - + - + @@ -98,7 +98,7 @@ 3 0.522262 0.237824 0.165853 0.662295 0.327439 0.793913 4 0.365971 0.215988 0.520744 0.096862 0.625389 0.725765 5 0.271209 0.521769 0.858065 0.162134 0.181798 0.425153

INFO

At the moment there is no support to save a DimArray directly into disk as a NetCDF or a Zarr file.

- + \ No newline at end of file diff --git a/dev/UserGuide/create.html b/dev/UserGuide/create.html index 2470416b..d6899a94 100644 --- a/dev/UserGuide/create.html +++ b/dev/UserGuide/create.html @@ -8,9 +8,9 @@ - + - + @@ -68,7 +68,7 @@ a2, a3 Properties: Dict(:origin => "user guide") - + \ No newline at end of file diff --git a/dev/UserGuide/faq.html b/dev/UserGuide/faq.html index 302ff08d..891ecc65 100644 --- a/dev/UserGuide/faq.html +++ b/dev/UserGuide/faq.html @@ -8,11 +8,11 @@ - + - + - + @@ -218,18 +218,18 @@ Additional Axes: (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points) Variables: - latitudes - - Additional Axes: - (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points) - Variables: longitudes Additional Axes: (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points, → Time Sampled{Date} Date("2020-01-01"):Dates.Month(1):Date("2022-12-01") ForwardOrdered Regular Points) Variables: - temperature

If your dataset has been read from a file with Cube it is not loaded into memory, and you have to load the latitudes and longitudes YAXArrays into memory:

julia
latitudes_yasxa  = readcubedata(ds["latitudes"])
+  temperature
+
+  Additional Axes: 
+  (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points)
+  Variables: 
+  latitudes

If your dataset has been read from a file with Cube it is not loaded into memory, and you have to load the latitudes and longitudes YAXArrays into memory:

julia
latitudes_yasxa  = readcubedata(ds["latitudes"])
 longitudes_yasxa = readcubedata(ds["longitudes"])
 ds_subset = ds[points = Where(p-> latitudes_yasxa[p]  >= 20 && latitudes_yasxa[p]  <= 80 &&
                              longitudes_yasxa[p] >= 0  && longitudes_yasxa[p] <= 180
@@ -360,13 +360,13 @@
   (↓ time     Sampled{DateTime} [2020-01-01T00:00:00, …, 2020-01-21T19:00:00] ForwardOrdered Irregular Points,
   → variable Categorical{Symbol} [:Open, :High, :Low, :Close, :Volume] Unordered)
   Variables: 
-  Stock2
+  Stock1
 
   Additional Axes: 
   (↓ time     Sampled{DateTime} [2020-01-01T00:00:00, …, 2020-01-21T19:00:00] ForwardOrdered Irregular Points,
   → variable Categorical{Symbol} [:Open, :High, :Low, :Close, :Volume] Unordered)
   Variables: 
-  Stock1
+  Stock2
 
   Additional Axes: 
   (↓ time     Sampled{DateTime} [2020-01-01T00:00:00, …, 2020-01-21T19:00:00] ForwardOrdered Irregular Points,
@@ -399,7 +399,7 @@
 ├─────────────────────────────────────────────────── loaded in memory ┤
   summarysize: 172.0 bytes
 └─────────────────────────────────────────────────────────────────────┘

WARNING

Note that although their creation is allowed, it is not possible to save these types into Zarr or NetCDF.

- + \ No newline at end of file diff --git a/dev/UserGuide/group.html b/dev/UserGuide/group.html index db94c950..986312e3 100644 --- a/dev/UserGuide/group.html +++ b/dev/UserGuide/group.html @@ -8,9 +8,9 @@ - + - + @@ -210,7 +210,7 @@ rowgap!(fig.layout, 5) fig end

which shows a good agreement with the results first published by Joe Hamman.

- + \ No newline at end of file diff --git a/dev/UserGuide/read.html b/dev/UserGuide/read.html index 4b9615df..755dd755 100644 --- a/dev/UserGuide/read.html +++ b/dev/UserGuide/read.html @@ -8,9 +8,9 @@ - + - + @@ -138,7 +138,7 @@ ├──────────────────────────────────────────────────────────── loaded in memory ┤ data size: 2.8 MB └──────────────────────────────────────────────────────────────────────────────┘

Note how the loading status changes from loaded lazily to loaded in memory.

- + \ No newline at end of file diff --git a/dev/UserGuide/select.html b/dev/UserGuide/select.html index f3688d16..2c67a71e 100644 --- a/dev/UserGuide/select.html +++ b/dev/UserGuide/select.html @@ -8,9 +8,9 @@ - + - + @@ -314,7 +314,7 @@ 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
- + \ No newline at end of file diff --git a/dev/UserGuide/types.html b/dev/UserGuide/types.html index 1d71db83..17752468 100644 --- a/dev/UserGuide/types.html +++ b/dev/UserGuide/types.html @@ -8,9 +8,9 @@ - + - + @@ -21,7 +21,7 @@
YAXArrays.jl

Appearance


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.

Types ​

This section describes the data structures used to work with n-dimensional arrays in YAXArrays.

YAXArray ​

An Array stores a sequence of ordered elements of the same type usually across multiple dimensions or axes. For example, one can measure temperature across all time points of the time dimension or brightness values of a picture across X and Y dimensions. A one dimensional array is called Vector and a two dimensional array is called a Matrix. In many Machine Learning libraries, arrays are also called tensors. Arrays are designed to store dense spatial-temporal data stored in a grid, whereas a collection of sparse points is usually stored in data frames or relational databases.

A DimArray as defined by DimensionalData.jl adds names to the dimensions and their axes ticks for a given Array. These names can be used to access the data, e.g., by date instead of just by integer position.

A YAXArray is a subtype of a AbstractDimArray and adds functions to load and process the named arrays. For example, it can also handle very large arrays stored on disk that are too big to fit in memory. In addition, it provides functions for parallel computation.

Dataset ​

A Dataset is an ordered dictionary of YAXArrays that usually share dimensions. For example, it can bundle arrays storing temperature and precipitation that are measured at the same time points and the same locations. One also can store a picture in a Dataset with three arrays containing brightness values for red green and blue, respectively. Internally, those arrays are still separated allowing to chose different element types for each array. Analog to the (NetCDF Data Model)[https://docs.unidata.ucar.edu/netcdf-c/current/netcdf_data_model.html], a Dataset usually represents variables belonging to the same group.

(Data) Cube ​

A (Data) Cube is just a YAXArray in which arrays from a dataset are combined together by introducing a new dimension containing labels of which array the corresponding element came from. Unlike a Dataset, all arrays must have the same element type to be converted into a cube. This data structure is useful when we want to use all variables at once. For example, the arrays temperature and precipitation which are measured at the same locations and dates can be combined into a single cube. A more formal definition of Data Cubes are given in Mahecha et al. 2020

Dimension ​

A Dimension or axis as defined by DimensionalData.jl adds tick labels, e.g., to each row or column of an array. It's name is used to access particular subsets of that array.

- + \ No newline at end of file diff --git a/dev/UserGuide/write.html b/dev/UserGuide/write.html index 8c233805..4ca92b92 100644 --- a/dev/UserGuide/write.html +++ b/dev/UserGuide/write.html @@ -8,11 +8,11 @@ - + - + - + @@ -42,7 +42,7 @@ savecube(ds.tos, "tos.nc", driver=:netcdf)

Save an entire Dataset to a directory:

julia
savedataset(ds, path="ds.nc", driver=:netcdf)

netcdf compression ​

Save a dataset to NetCDF format with compression:

julia
n = 7 # compression level, number between 0 (no compression) and 9 (max compression)
 savedataset(ds, path="ds_c.nc", driver=:netcdf, compress=n)

Comparing it to the default saved file

julia
ds_info = stat("ds.nc")
 ds_c_info = stat("ds_c.nc")
-println("File size: ", "default: ", ds_info.size, " bytes", ", compress: ", ds_c_info.size, " bytes")
File size: default: 2963858 bytes, compress: 1159914 bytes

Overwrite a Dataset ​

If a path already exists, an error will be thrown. Set overwrite=true to delete the existing dataset

julia
savedataset(ds, path="ds.zarr", driver=:zarr, overwrite=true)

DANGER

Again, setting overwrite will delete all your previous saved data.

Look at the doc string for more information

YAXArrays.Datasets.savedataset Function

savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)

Saves a Dataset into a file at path with the format given by driver, i.e., driver=:netcdf or driver=:zarr.

Warning

overwrite = true, deletes ALL your data and it will create a new file.

source

Append to a Dataset ​

New variables can be added to an existing dataset using the append=true keyword.

julia
ds2 = Dataset(z = YAXArray(rand(10,20,5)))
+println("File size: ", "default: ", ds_info.size, " bytes", ", compress: ", ds_c_info.size, " bytes")
File size: default: 2963858 bytes, compress: 1159914 bytes

Overwrite a Dataset ​

If a path already exists, an error will be thrown. Set overwrite=true to delete the existing dataset

julia
savedataset(ds, path="ds.zarr", driver=:zarr, overwrite=true)

DANGER

Again, setting overwrite will delete all your previous saved data.

Look at the doc string for more information

YAXArrays.Datasets.savedataset Function

savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)

Saves a Dataset into a file at path with the format given by driver, i.e., driver=:netcdf or driver=:zarr.

Warning

overwrite = true, deletes ALL your data and it will create a new file.

source

Append to a Dataset ​

New variables can be added to an existing dataset using the append=true keyword.

julia
ds2 = Dataset(z = YAXArray(rand(10,20,5)))
 savedataset(ds2, path="ds.zarr", backend=:zarr, append=true)
julia
julia> open_dataset("ds.zarr", driver=:zarr)
YAXArray Dataset
 Shared Axes:
 None
@@ -92,7 +92,7 @@
  0.459041  0.761553   0.367809  0.414041
  0.223574  0.898926   0.647957  0.820737
  0.457984  0.839919   0.858795  0.1921

indeed, those entries had been updated.

- + \ No newline at end of file diff --git a/dev/api.html b/dev/api.html index 79c3ce03..cbceada6 100644 --- a/dev/api.html +++ b/dev/api.html @@ -8,11 +8,11 @@ - + - + - + @@ -20,20 +20,20 @@ -
YAXArrays.jl

Appearance


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.

API Reference ​

This section describes all available functions of this package.

Public API ​

YAXArrays.getAxis Method
julia
getAxis(desc, c)

Given an Axis description and a cube, returns the corresponding axis of the cube. The Axis description can be:

  • the name as a string or symbol.

  • an Axis object

source

YAXArrays.Cubes Module

The functions provided by YAXArrays are supposed to work on different types of cubes. This module defines the interface for all Data types that

source

YAXArrays.Cubes.YAXArray Type
julia
YAXArray{T,N}

An array labelled with named axes that have values associated with them. It can wrap normal arrays or, more typically DiskArrays.

Fields

  • axes: Tuple of Dimensions containing the Axes of the Cube

  • data: length(axes)-dimensional array which holds the data, this can be a lazy DiskArray

  • properties: Metadata properties describing the content of the data

  • chunks: Representation of the chunking of the data

  • cleaner: Cleaner objects to track which objects to tidy up when the YAXArray goes out of scope

source

YAXArrays.Cubes.caxes Function

Returns the axes of a Cube

source

YAXArrays.Cubes.caxes Method
julia
caxes

Embeds Cube inside a new Cube

source

YAXArrays.Cubes.concatenatecubes Method
julia
function concatenateCubes(cubelist, cataxis::CategoricalAxis)

Concatenates a vector of datacubes that have identical axes to a new single cube along the new axis cataxis

source

YAXArrays.Cubes.readcubedata Method
julia
readcubedata(cube)

Given any array implementing the YAXArray interface it returns an in-memory YAXArray from it.

source

YAXArrays.Cubes.setchunks Method
julia
setchunks(c::YAXArray,chunks)

Resets the chunks of a YAXArray and returns a new YAXArray. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savecube on the resulting array. The chunks argument can take one of the following forms:

  • a DiskArrays.GridChunks object

  • a tuple specifying the chunk size along each dimension

  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes

source

YAXArrays.Cubes.subsetcube Function

This function calculates a subset of a cube's data

source

YAXArrays.DAT.InDims Type
julia
InDims(axisdesc...;...)

Creates a description of an Input Data Cube for cube operations. Takes a single or multiple axis descriptions as first arguments. Alternatively a MovingWindow(@ref) struct can be passed to include neighbour slices of one or more axes in the computation. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.

Keyword arguments

  • artype how shall the array be represented in the inner function. Defaults to Array, alternatives are DataFrame or AsAxisArray

  • filter define some filter to skip the computation, e.g. when all values are missing. Defaults to AllMissing(), possible values are AnyMissing(), AnyOcean(), StdZero(), NValid(n) (for at least n non-missing elements). It is also possible to provide a custom one-argument function that takes the array and returns true if the compuation shall be skipped and false otherwise.

  • window_oob_value if one of the input dimensions is a MowingWindow, this value will be used to fill out-of-bounds areas

source

YAXArrays.DAT.MovingWindow Type
julia
MovingWindow(desc, pre, after)

Constructs a MovingWindow object to be passed to an InDims constructor to define that the axis in desc shall participate in the inner function (i.e. shall be looped over), but inside the inner function pre values before and after values after the center value will be passed as well.

For example passing MovingWindow("Time", 2, 0) will loop over the time axis and always pass the current time step plus the 2 previous steps. So in the inner function the array will have an additional dimension of size 3.

source

YAXArrays.DAT.OutDims Method
julia
OutDims(axisdesc;...)

Creates a description of an Output Data Cube for cube operations. Takes a single or a Vector/Tuple of axes as first argument. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.

  • axisdesc: List of input axis names

  • backend : specifies the dataset backend to write data to, must be either :auto or a key in YAXArrayBase.backendlist

  • update : specifies wether the function operates inplace or if an output is returned

  • artype : specifies the Array type inside the inner function that is mapped over

  • chunksize: A Dict specifying the chunksizes for the output dimensions of the cube, or :input to copy chunksizes from input cube axes or :max to not chunk the inner dimensions

  • outtype: force the output type to a specific type, defaults to Any which means that the element type of the first input cube is used

source

YAXArrays.DAT.CubeTable Method
julia
CubeTable()

Function to turn a DataCube object into an iterable table. Takes a list of as arguments, specified as a name=cube expression. For example CubeTable(data=cube1,country=cube2) would generate a Table with the entries data and country, where data contains the values of cube1 and country the values of cube2. The cubes are matched and broadcasted along their axes like in mapCube.

source

YAXArrays.DAT.cubefittable Method
julia
cubefittable(tab,o,fitsym;post=getpostfunction(o),kwargs...)

Executes fittable on the CubeTable tab with the (Weighted-)OnlineStat o, looping through the values specified by fitsym. Finally, writes the results from the TableAggregator to an output data cube.

source

YAXArrays.DAT.fittable Method
julia
fittable(tab,o,fitsym;by=(),weight=nothing)

Loops through an iterable table tab and thereby fitting an OnlineStat o with the values specified through fitsym. Optionally one can specify a field (or tuple) to group by. Any groupby specifier can either be a symbol denoting the entry to group by or an anynymous function calculating the group from a table row.

For example the following would caluclate a weighted mean over a cube weighted by grid cell area and grouped by country and month:

julia
fittable(iter,WeightedMean,:tair,weight=(i->abs(cosd(i.lat))),by=(i->month(i.time),:country))

source

YAXArrays.DAT.mapCube Method
julia
mapCube(fun, cube, addargs...;kwargs...)
+    
YAXArrays.jl
Appearance

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.
API Reference ​
This section describes all available functions of this package.
Public API ​
YAXArrays.getAxis Method
julia
getAxis(desc, c)
Given an Axis description and a cube, returns the corresponding axis of the cube. The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
YAXArrays.Cubes Module
The functions provided by YAXArrays are supposed to work on different types of cubes. This module defines the interface for all Data types that
source
YAXArrays.Cubes.YAXArray Type
julia
YAXArray{T,N}
An array labelled with named axes that have values associated with them. It can wrap normal arrays or, more typically DiskArrays.
Fields
  • axes: Tuple of Dimensions containing the Axes of the Cube
  • data: length(axes)-dimensional array which holds the data, this can be a lazy DiskArray
  • properties: Metadata properties describing the content of the data
  • chunks: Representation of the chunking of the data
  • cleaner: Cleaner objects to track which objects to tidy up when the YAXArray goes out of scope
source
YAXArrays.Cubes.caxes Function
Returns the axes of a Cube
source
YAXArrays.Cubes.caxes Method
julia
caxes
Embeds Cube inside a new Cube
source
YAXArrays.Cubes.concatenatecubes Method
julia
function concatenateCubes(cubelist, cataxis::CategoricalAxis)
Concatenates a vector of datacubes that have identical axes to a new single cube along the new axis cataxis
source
YAXArrays.Cubes.readcubedata Method
julia
readcubedata(cube)
Given any array implementing the YAXArray interface it returns an in-memory YAXArray from it.
source
YAXArrays.Cubes.setchunks Method
julia
setchunks(c::YAXArray,chunks)
Resets the chunks of a YAXArray and returns a new YAXArray. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savecube on the resulting array. The chunks argument can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
YAXArrays.Cubes.subsetcube Function
This function calculates a subset of a cube's data
source
YAXArrays.DAT.InDims Type
julia
InDims(axisdesc...;...)
Creates a description of an Input Data Cube for cube operations. Takes a single or multiple axis descriptions as first arguments. Alternatively a MovingWindow(@ref) struct can be passed to include neighbour slices of one or more axes in the computation. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
Keyword arguments
  • artype how shall the array be represented in the inner function. Defaults to Array, alternatives are DataFrame or AsAxisArray
  • filter define some filter to skip the computation, e.g. when all values are missing. Defaults to AllMissing(), possible values are AnyMissing(), AnyOcean(), StdZero(), NValid(n) (for at least n non-missing elements). It is also possible to provide a custom one-argument function that takes the array and returns true if the compuation shall be skipped and false otherwise.
  • window_oob_value if one of the input dimensions is a MowingWindow, this value will be used to fill out-of-bounds areas
source
YAXArrays.DAT.MovingWindow Type
julia
MovingWindow(desc, pre, after)
Constructs a MovingWindow object to be passed to an InDims constructor to define that the axis in desc shall participate in the inner function (i.e. shall be looped over), but inside the inner function pre values before and after values after the center value will be passed as well.
For example passing MovingWindow("Time", 2, 0) will loop over the time axis and always pass the current time step plus the 2 previous steps. So in the inner function the array will have an additional dimension of size 3.
source
YAXArrays.DAT.OutDims Method
julia
OutDims(axisdesc;...)
Creates a description of an Output Data Cube for cube operations. Takes a single or a Vector/Tuple of axes as first argument. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
  • axisdesc: List of input axis names
  • backend : specifies the dataset backend to write data to, must be either :auto or a key in YAXArrayBase.backendlist
  • update : specifies wether the function operates inplace or if an output is returned
  • artype : specifies the Array type inside the inner function that is mapped over
  • chunksize: A Dict specifying the chunksizes for the output dimensions of the cube, or :input to copy chunksizes from input cube axes or :max to not chunk the inner dimensions
  • outtype: force the output type to a specific type, defaults to Any which means that the element type of the first input cube is used
source
YAXArrays.DAT.CubeTable Method
julia
CubeTable()
Function to turn a DataCube object into an iterable table. Takes a list of as arguments, specified as a name=cube expression. For example CubeTable(data=cube1,country=cube2) would generate a Table with the entries data and country, where data contains the values of cube1 and country the values of cube2. The cubes are matched and broadcasted along their axes like in mapCube.
source
YAXArrays.DAT.cubefittable Method
julia
cubefittable(tab,o,fitsym;post=getpostfunction(o),kwargs...)
Executes fittable on the CubeTable tab with the (Weighted-)OnlineStat o, looping through the values specified by fitsym. Finally, writes the results from the TableAggregator to an output data cube.
source
YAXArrays.DAT.fittable Method
julia
fittable(tab,o,fitsym;by=(),weight=nothing)
Loops through an iterable table tab and thereby fitting an OnlineStat o with the values specified through fitsym. Optionally one can specify a field (or tuple) to group by. Any groupby specifier can either be a symbol denoting the entry to group by or an anynymous function calculating the group from a table row.
For example the following would caluclate a weighted mean over a cube weighted by grid cell area and grouped by country and month:
julia
fittable(iter,WeightedMean,:tair,weight=(i->abs(cosd(i.lat))),by=(i->month(i.time),:country))
source
YAXArrays.DAT.mapCube Method
julia
mapCube(fun, cube, addargs...;kwargs...)
 
 Map a given function `fun` over slices of all cubes of the dataset `ds`. 
 Use InDims to discribe the input dimensions and OutDims to describe the output dimensions of the function.
 For Datasets, only one output cube can be specified.
 In contrast to the mapCube function for cubes, additional arguments for the inner function should be set as keyword arguments.
 
-For the specific keyword arguments see the docstring of the mapCube function for cubes.
source
YAXArrays.DAT.mapCube Method
julia
mapCube(fun, cube, addargs...;kwargs...)
Map a given function fun over slices of the data cube cube. The additional arguments addargs will be forwarded to the inner function fun. Use InDims to discribe the input dimensions and OutDims to describe the output dimensions of the function.
Keyword arguments
  • max_cache=YAXDefaults.max_cache Float64 maximum size of blocks that are read into memory in bits e.g. max_cache=5.0e8. Or String. e.g. max_cache="10MB" ormax_cache=1GB``` defaults to approx 10Mb.
  • indims::InDims List of input cube descriptors of type InDims for each input data cube.
  • outdims::OutDims List of output cube descriptors of type OutDims for each output cube.
  • inplace does the function write to an output array inplace or return a single value> defaults to true
  • ispar boolean to determine if parallelisation should be applied, defaults to true if workers are available.
  • showprog boolean indicating if a ProgressMeter shall be shown
  • include_loopvars boolean to indicate if the varoables looped over should be added as function arguments
  • nthreads number of threads for the computation, defaults to Threads.nthreads for every worker.
  • loopchunksize determines the chunk sizes of variables which are looped over, a dict
  • kwargs additional keyword arguments are passed to the inner function
The first argument is always the function to be applied, the second is the input cube or a tuple of input cubes if needed.
source
YAXArrays.Datasets.Dataset Type
julia
Dataset object which stores an `OrderedDict` of YAXArrays with Symbol keys.
+For the specific keyword arguments see the docstring of the mapCube function for cubes.
source
YAXArrays.DAT.mapCube Method
julia
mapCube(fun, cube, addargs...;kwargs...)
Map a given function fun over slices of the data cube cube. The additional arguments addargs will be forwarded to the inner function fun. Use InDims to discribe the input dimensions and OutDims to describe the output dimensions of the function.
Keyword arguments
  • max_cache=YAXDefaults.max_cache Float64 maximum size of blocks that are read into memory in bits e.g. max_cache=5.0e8. Or String. e.g. max_cache="10MB" ormax_cache=1GB``` defaults to approx 10Mb.
  • indims::InDims List of input cube descriptors of type InDims for each input data cube.
  • outdims::OutDims List of output cube descriptors of type OutDims for each output cube.
  • inplace does the function write to an output array inplace or return a single value> defaults to true
  • ispar boolean to determine if parallelisation should be applied, defaults to true if workers are available.
  • showprog boolean indicating if a ProgressMeter shall be shown
  • include_loopvars boolean to indicate if the varoables looped over should be added as function arguments
  • nthreads number of threads for the computation, defaults to Threads.nthreads for every worker.
  • loopchunksize determines the chunk sizes of variables which are looped over, a dict
  • kwargs additional keyword arguments are passed to the inner function
The first argument is always the function to be applied, the second is the input cube or a tuple of input cubes if needed.
source
YAXArrays.Datasets.Dataset Type
julia
Dataset object which stores an `OrderedDict` of YAXArrays with Symbol keys.
 a dictionary of CubeAxes and a Dictionary of general properties.
-A dictionary can hold cubes with differing axes. But it will share the common axes between the subcubes.
source
YAXArrays.Datasets.Dataset Method
Dataset(; properties = Dict{String,Any}, cubes...)
Construct a YAXArray Dataset with global attributes properties a and a list of named YAXArrays cubes...
source
YAXArrays.Datasets.Cube Method
julia
Cube(ds::Dataset; joinname="Variable")
Construct a single YAXArray from the dataset ds by concatenating the cubes in the datset on the joinname dimension.
source
YAXArrays.Datasets.open_dataset Method
open_dataset(g; driver=:all)
Open the dataset at g with the given driver. The default driver will search for available drivers and tries to detect the useable driver from the filename extension.
source
YAXArrays.Datasets.savecube Method
julia
savecube(cube,name::String)
Save a YAXArray to the path.
Extended Help
The keyword arguments are:
  • name:
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • max_cache: The number of bits that are used as cache for the data handling.
  • backend: The backend, that is used to save the data. Falls back to searching the backend according to the extension of the path.
  • driver: The same setting as backend.
  • overwrite::Bool=false overwrite cube if it already exists
source
YAXArrays.Datasets.savedataset Method
savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)
Saves a Dataset into a file at path with the format given by driver, i.e., driver=:netcdf or driver=:zarr.
Warning
overwrite = true, deletes ALL your data and it will create a new file.
source
YAXArrays.Datasets.to_dataset Method
to_dataset(c;datasetaxis = "Variable", layername = "layer")
Convert a Data Cube into a Dataset. It is possible to treat one of the Cube's axes as a "DatasetAxis" i.e. the cube will be split into different parts that become variables in the Dataset. If no such axis is specified or found, there will only be a single variable in the dataset with the name layername
source
Internal API ​
YAXArrays.YAXDefaults Constant
Default configuration for YAXArrays, has the following fields:
  • workdir[]::String = "./" The default location for temporary cubes.
  • recal[]::Bool = false set to true if you want @loadOrGenerate to always recalculate the results.
  • chunksize[]::Any = :input Set the default output chunksize.
  • max_cache[]::Float64 = 1e8 The maximum cache used by mapCube.
  • cubedir[]::"" the default location for Cube() without an argument.
  • subsetextensions::Array{Any} = [] List of registered functions, that convert subsetting input into dimension boundaries.
source
YAXArrays.findAxis Method
julia
findAxis(desc, c)
Internal function
Extended Help
Given an Axis description and a cube return the index of the Axis.
The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
YAXArrays.getOutAxis Method
julia
getOutAxis
source
YAXArrays.get_descriptor Method
julia
get_descriptor(a)
Get the descriptor of an Axis. This is used to dispatch on the descriptor.
source
YAXArrays.match_axis Method
julia
match_axis
Internal function
Extended Help
Match the Axis based on the AxisDescriptor.
+A dictionary can hold cubes with differing axes. But it will share the common axes between the subcubes.
source
YAXArrays.Datasets.Dataset Method
Dataset(; properties = Dict{String,Any}, cubes...)
Construct a YAXArray Dataset with global attributes properties a and a list of named YAXArrays cubes...
source
YAXArrays.Datasets.Cube Method
julia
Cube(ds::Dataset; joinname="Variable")
Construct a single YAXArray from the dataset ds by concatenating the cubes in the datset on the joinname dimension.
source
YAXArrays.Datasets.open_dataset Method
open_dataset(g; driver=:all)
Open the dataset at g with the given driver. The default driver will search for available drivers and tries to detect the useable driver from the filename extension.
source
YAXArrays.Datasets.savecube Method
julia
savecube(cube,name::String)
Save a YAXArray to the path.
Extended Help
The keyword arguments are:
  • name:
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • max_cache: The number of bits that are used as cache for the data handling.
  • backend: The backend, that is used to save the data. Falls back to searching the backend according to the extension of the path.
  • driver: The same setting as backend.
  • overwrite::Bool=false overwrite cube if it already exists
source
YAXArrays.Datasets.savedataset Method
savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)
Saves a Dataset into a file at path with the format given by driver, i.e., driver=:netcdf or driver=:zarr.
Warning
overwrite = true, deletes ALL your data and it will create a new file.
source
YAXArrays.Datasets.to_dataset Method
to_dataset(c;datasetaxis = "Variable", layername = "layer")
Convert a Data Cube into a Dataset. It is possible to treat one of the Cube's axes as a "DatasetAxis" i.e. the cube will be split into different parts that become variables in the Dataset. If no such axis is specified or found, there will only be a single variable in the dataset with the name layername
source
Internal API ​
YAXArrays.YAXDefaults Constant
Default configuration for YAXArrays, has the following fields:
  • workdir[]::String = "./" The default location for temporary cubes.
  • recal[]::Bool = false set to true if you want @loadOrGenerate to always recalculate the results.
  • chunksize[]::Any = :input Set the default output chunksize.
  • max_cache[]::Float64 = 1e8 The maximum cache used by mapCube.
  • cubedir[]::"" the default location for Cube() without an argument.
  • subsetextensions::Array{Any} = [] List of registered functions, that convert subsetting input into dimension boundaries.
source
YAXArrays.findAxis Method
julia
findAxis(desc, c)
Internal function
Extended Help
Given an Axis description and a cube return the index of the Axis.
The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
YAXArrays.getOutAxis Method
julia
getOutAxis
source
YAXArrays.get_descriptor Method
julia
get_descriptor(a)
Get the descriptor of an Axis. This is used to dispatch on the descriptor.
source
YAXArrays.match_axis Method
julia
match_axis
Internal function
Extended Help
Match the Axis based on the AxisDescriptor.
 This is used to find different axes and to make certain axis description the same.
-For example to disregard differences of captialisation.
source
YAXArrays.Cubes.CleanMe Type
julia
mutable struct CleanMe
Struct which describes data paths and their persistency. Non-persistend paths/files are removed at finalize step
source
YAXArrays.Cubes.clean Method
julia
clean(c::CleanMe)
finalizer function for CleanMe struct. The main process removes all directories/files which are not persistent.
source
YAXArrays.Cubes.copydata Method
julia
copydata(outar, inar, copybuf)
Internal function which copies the data from the input inar into the output outar at the copybuf positions.
source
YAXArrays.Cubes.optifunc Method
julia
optifunc(s, maxbuf, incs, outcs, insize, outsize, writefac)
Internal
This function is going to be minimized to detect the best possible chunk setting for the rechunking of the data.
source
YAXArrays.DAT.DATConfig Type
Configuration object of a DAT process. This holds all necessary information to perform the calculations. It contains the following fields:
  • incubes::NTuple{NIN, YAXArrays.DAT.InputCube} where NIN: The input data cubes
  • outcubes::NTuple{NOUT, YAXArrays.DAT.OutputCube} where NOUT: The output data cubes
  • allInAxes::Vector: List of all axes of the input cubes
  • LoopAxes::Vector: List of axes that are looped through
  • ispar::Bool: Flag whether the computation is parallelized
  • loopcachesize::Vector{Int64}:
  • allow_irregular_chunks::Bool:
  • max_cache::Any: Maximal size of the in memory cache
  • fu::Any: Inner function which is computed
  • inplace::Bool: Flag whether the computation happens in place
  • include_loopvars::Bool:
  • ntr::Any:
  • do_gc::Bool: Flag if GC should be called explicitly. Probably necessary for many runs in Julia 1.9
  • addargs::Any: Additional arguments for the inner function
  • kwargs::Any: Additional keyword arguments for the inner function
source
YAXArrays.DAT.InputCube Type
Internal representation of an input cube for DAT operations
  • cube: The input data
  • desc: The input description given by the user/registration
  • axesSmall: List of axes that were actually selected through the description
  • icolon
  • colonperm
  • loopinds: Indices of loop axes that this cube does not contain, i.e. broadcasts
  • cachesize: Number of elements to keep in cache along each axis
  • window
  • iwindow
  • windowloopinds
  • iall
source
YAXArrays.DAT.OutputCube Type
Internal representation of an output cube for DAT operations
Fields
  • cube: The actual outcube cube, once it is generated
  • cube_unpermuted: The unpermuted output cube
  • desc: The description of the output axes as given by users or registration
  • axesSmall: The list of output axes determined through the description
  • allAxes: List of all the axes of the cube
  • loopinds: Index of the loop axes that are broadcasted for this output cube
  • innerchunks
  • outtype: Elementtype of the outputcube
source
YAXArrays.DAT.YAXColumn Type
julia
YAXColumn
A struct representing a single column of a YAXArray partitioned Table # Fields
  • inarBC
  • inds
source
YAXArrays.DAT.cmpcachmisses Method
Function that compares two cache miss specifiers by their importance
source
YAXArrays.DAT.getFrontPerm Method
Calculate an axis permutation that brings the wanted dimensions to the front
source
YAXArrays.DAT.getLoopCacheSize Method
Calculate optimal Cache size to DAT operation
source
YAXArrays.DAT.getOuttype Method
julia
getOuttype(outtype, cdata)
Internal function
Get the element type for the output cube
source
YAXArrays.DAT.getloopchunks Method
julia
getloopchunks(dc::DATConfig)
Internal function
Returns the chunks that can be looped over toghether for all dimensions.
-This computation of the size of the chunks is handled by [`DiskArrays.approx_chunksize`](@ref)
source
YAXArrays.DAT.permuteloopaxes Method
julia
permuteloopaxes(dc)
Internal function
Permute the dimensions of the cube, so that the axes that are looped through are in the first positions. This is necessary for a faster looping through the data.
source
YAXArrays.Cubes.setchunks Method
julia
setchunks(c::Dataset,chunks)
Resets the chunks of all or a subset YAXArrays in the dataset and returns a new Dataset. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savedataset on the resulting array. The chunks argument can take one of the following forms:
  • a NamedTuple or AbstractDict mapping from variable name to a description of the desired variable chunks
  • a NamedTuple or AbstractDict mapping from dimension name to a description of the desired variable chunks
  • a description of the desired variable chunks applied to all members of the Dataset
where a description of the desired variable chunks can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
YAXArrays.Datasets.collectfromhandle Method
Extracts a YAXArray from a dataset handle that was just created from a arrayinfo
source
YAXArrays.Datasets.createdataset Method
function createdataset(DS::Type,axlist; kwargs...)
Creates a new dataset with axes specified in axlist. Each axis must be a subtype of CubeAxis. A new empty Zarr array will be created and can serve as a sink for mapCube operations.
Keyword arguments
  • path="" location where the new cube is stored
  • T=Union{Float32,Missing} data type of the target cube
  • chunksize = ntuple(i->length(axlist[i]),length(axlist)) chunk sizes of the array
  • chunkoffset = ntuple(i->0,length(axlist)) offsets of the chunks
  • persist::Bool=true shall the disk data be garbage-collected when the cube goes out of scope?
  • overwrite::Bool=false overwrite cube if it already exists
  • properties=Dict{String,Any}() additional cube properties
  • globalproperties=Dict{String,Any} global attributes to be added to the dataset
  • fillvalue= T>:Missing ? defaultfillval(Base.nonmissingtype(T)) : nothing fill value
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • layername="layer" Fallback name of the variable stored in the dataset if no datasetaxis is found
source
YAXArrays.Datasets.getarrayinfo Method
Extract necessary information to create a YAXArrayBase dataset from a name and YAXArray pair
source
YAXArrays.Datasets.testrange Method
Test if data in x can be approximated by a step range
source

-    
+For example to disregard differences of captialisation.

source

YAXArrays.Cubes.CleanMe Type
julia
mutable struct CleanMe

Struct which describes data paths and their persistency. Non-persistend paths/files are removed at finalize step

source

YAXArrays.Cubes.clean Method
julia
clean(c::CleanMe)

finalizer function for CleanMe struct. The main process removes all directories/files which are not persistent.

source

YAXArrays.Cubes.copydata Method
julia
copydata(outar, inar, copybuf)

Internal function which copies the data from the input inar into the output outar at the copybuf positions.

source

YAXArrays.Cubes.optifunc Method
julia
optifunc(s, maxbuf, incs, outcs, insize, outsize, writefac)

Internal

This function is going to be minimized to detect the best possible chunk setting for the rechunking of the data.

source

YAXArrays.DAT.DATConfig Type

Configuration object of a DAT process. This holds all necessary information to perform the calculations. It contains the following fields:

  • incubes::NTuple{NIN, YAXArrays.DAT.InputCube} where NIN: The input data cubes

  • outcubes::NTuple{NOUT, YAXArrays.DAT.OutputCube} where NOUT: The output data cubes

  • allInAxes::Vector: List of all axes of the input cubes

  • LoopAxes::Vector: List of axes that are looped through

  • ispar::Bool: Flag whether the computation is parallelized

  • loopcachesize::Vector{Int64}:

  • allow_irregular_chunks::Bool:

  • max_cache::Any: Maximal size of the in memory cache

  • fu::Any: Inner function which is computed

  • inplace::Bool: Flag whether the computation happens in place

  • include_loopvars::Bool:

  • ntr::Any:

  • do_gc::Bool: Flag if GC should be called explicitly. Probably necessary for many runs in Julia 1.9

  • addargs::Any: Additional arguments for the inner function

  • kwargs::Any: Additional keyword arguments for the inner function

source

YAXArrays.DAT.InputCube Type

Internal representation of an input cube for DAT operations

  • cube: The input data

  • desc: The input description given by the user/registration

  • axesSmall: List of axes that were actually selected through the description

  • icolon

  • colonperm

  • loopinds: Indices of loop axes that this cube does not contain, i.e. broadcasts

  • cachesize: Number of elements to keep in cache along each axis

  • window

  • iwindow

  • windowloopinds

  • iall

source

YAXArrays.DAT.OutputCube Type

Internal representation of an output cube for DAT operations

Fields

  • cube: The actual outcube cube, once it is generated

  • cube_unpermuted: The unpermuted output cube

  • desc: The description of the output axes as given by users or registration

  • axesSmall: The list of output axes determined through the description

  • allAxes: List of all the axes of the cube

  • loopinds: Index of the loop axes that are broadcasted for this output cube

  • innerchunks

  • outtype: Elementtype of the outputcube

source

YAXArrays.DAT.YAXColumn Type
julia
YAXColumn

A struct representing a single column of a YAXArray partitioned Table # Fields

  • inarBC

  • inds

source

YAXArrays.DAT.cmpcachmisses Method

Function that compares two cache miss specifiers by their importance

source

YAXArrays.DAT.getFrontPerm Method

Calculate an axis permutation that brings the wanted dimensions to the front

source

YAXArrays.DAT.getLoopCacheSize Method

Calculate optimal Cache size to DAT operation

source

YAXArrays.DAT.getOuttype Method
julia
getOuttype(outtype, cdata)

Internal function

Get the element type for the output cube

source

YAXArrays.DAT.getloopchunks Method
julia
getloopchunks(dc::DATConfig)

Internal function

Returns the chunks that can be looped over toghether for all dimensions.
+This computation of the size of the chunks is handled by [`DiskArrays.approx_chunksize`](@ref)

source

YAXArrays.DAT.permuteloopaxes Method
julia
permuteloopaxes(dc)

Internal function

Permute the dimensions of the cube, so that the axes that are looped through are in the first positions. This is necessary for a faster looping through the data.

source

YAXArrays.Cubes.setchunks Method
julia
setchunks(c::Dataset,chunks)

Resets the chunks of all or a subset YAXArrays in the dataset and returns a new Dataset. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savedataset on the resulting array. The chunks argument can take one of the following forms:

  • a NamedTuple or AbstractDict mapping from variable name to a description of the desired variable chunks

  • a NamedTuple or AbstractDict mapping from dimension name to a description of the desired variable chunks

  • a description of the desired variable chunks applied to all members of the Dataset

where a description of the desired variable chunks can take one of the following forms:

  • a DiskArrays.GridChunks object

  • a tuple specifying the chunk size along each dimension

  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes

source

YAXArrays.Datasets.collectfromhandle Method

Extracts a YAXArray from a dataset handle that was just created from a arrayinfo

source

YAXArrays.Datasets.createdataset Method

function createdataset(DS::Type,axlist; kwargs...)

Creates a new dataset with axes specified in axlist. Each axis must be a subtype of CubeAxis. A new empty Zarr array will be created and can serve as a sink for mapCube operations.

Keyword arguments

  • path="" location where the new cube is stored

  • T=Union{Float32,Missing} data type of the target cube

  • chunksize = ntuple(i->length(axlist[i]),length(axlist)) chunk sizes of the array

  • chunkoffset = ntuple(i->0,length(axlist)) offsets of the chunks

  • persist::Bool=true shall the disk data be garbage-collected when the cube goes out of scope?

  • overwrite::Bool=false overwrite cube if it already exists

  • properties=Dict{String,Any}() additional cube properties

  • globalproperties=Dict{String,Any} global attributes to be added to the dataset

  • fillvalue= T>:Missing ? defaultfillval(Base.nonmissingtype(T)) : nothing fill value

  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays

  • layername="layer" Fallback name of the variable stored in the dataset if no datasetaxis is found

source

YAXArrays.Datasets.getarrayinfo Method

Extract necessary information to create a YAXArrayBase dataset from a name and YAXArray pair

source

YAXArrays.Datasets.testrange Method

Test if data in x can be approximated by a step range

source

+ \ No newline at end of file diff --git a/dev/assets/UserGuide_compute.md.D3PBp0ym.js b/dev/assets/UserGuide_compute.md.DWxtLB-7.js similarity index 97% rename from dev/assets/UserGuide_compute.md.D3PBp0ym.js rename to dev/assets/UserGuide_compute.md.DWxtLB-7.js index 62b72fa7..bb453e04 100644 --- a/dev/assets/UserGuide_compute.md.D3PBp0ym.js +++ b/dev/assets/UserGuide_compute.md.DWxtLB-7.js @@ -19,7 +19,7 @@ import{_ as i,c as a,a2 as n,o as t}from"./chunks/framework.DgSLhxNl.js";const g :origin => "user guide" ├──────────────────────────────────────────────────────────── loaded in memory ┤ data size: 35.16 KB -└──────────────────────────────────────────────────────────────────────────────┘

Modify elements of a YAXArray ​

julia
a[1,2,3]
0.983449169710096
julia
a[1,2,3] = 42
42
julia
a[1,2,3]
42.0

WARNING

Some arrays, e.g. those saved in a cloud object storage are immutable making any modification of the data impossible.

Arithmetics ​

Add a value to all elements of an array and save it as a new array:

julia
a2 = a .+ 5
╭──────────────────────────────╮
+└──────────────────────────────────────────────────────────────────────────────┘

Modify elements of a YAXArray ​

julia
a[1,2,3]
0.9099638962470454
julia
a[1,2,3] = 42
42
julia
a[1,2,3]
42.0

WARNING

Some arrays, e.g. those saved in a cloud object storage are immutable making any modification of the data impossible.

Arithmetics ​

Add a value to all elements of an array and save it as a new array:

julia
a2 = a .+ 5
╭──────────────────────────────╮
 │ 30×10×15 YAXArray{Float64,3} │
 ├──────────────────────────────┴───────────────────────────────────────── dims ┐
   ↓ time Sampled{Date} Date("2022-01-01"):Dates.Day(1):Date("2022-01-30") ForwardOrdered Regular Points,
diff --git a/dev/assets/UserGuide_compute.md.D3PBp0ym.lean.js b/dev/assets/UserGuide_compute.md.DWxtLB-7.lean.js
similarity index 97%
rename from dev/assets/UserGuide_compute.md.D3PBp0ym.lean.js
rename to dev/assets/UserGuide_compute.md.DWxtLB-7.lean.js
index 62b72fa7..bb453e04 100644
--- a/dev/assets/UserGuide_compute.md.D3PBp0ym.lean.js
+++ b/dev/assets/UserGuide_compute.md.DWxtLB-7.lean.js
@@ -19,7 +19,7 @@ import{_ as i,c as a,a2 as n,o as t}from"./chunks/framework.DgSLhxNl.js";const g
   :origin => "user guide"
 ├──────────────────────────────────────────────────────────── loaded in memory ┤
   data size: 35.16 KB
-└──────────────────────────────────────────────────────────────────────────────┘

Modify elements of a YAXArray ​

julia
a[1,2,3]
0.983449169710096
julia
a[1,2,3] = 42
42
julia
a[1,2,3]
42.0

WARNING

Some arrays, e.g. those saved in a cloud object storage are immutable making any modification of the data impossible.

Arithmetics ​

Add a value to all elements of an array and save it as a new array:

julia
a2 = a .+ 5
╭──────────────────────────────╮
+└──────────────────────────────────────────────────────────────────────────────┘

Modify elements of a YAXArray ​

julia
a[1,2,3]
0.9099638962470454
julia
a[1,2,3] = 42
42
julia
a[1,2,3]
42.0

WARNING

Some arrays, e.g. those saved in a cloud object storage are immutable making any modification of the data impossible.

Arithmetics ​

Add a value to all elements of an array and save it as a new array:

julia
a2 = a .+ 5
╭──────────────────────────────╮
 │ 30×10×15 YAXArray{Float64,3} │
 ├──────────────────────────────┴───────────────────────────────────────── dims ┐
   ↓ time Sampled{Date} Date("2022-01-01"):Dates.Day(1):Date("2022-01-30") ForwardOrdered Regular Points,
diff --git a/dev/assets/UserGuide_faq.md.BTc51Dug.js b/dev/assets/UserGuide_faq.md.BgQQKKl0.js
similarity index 99%
rename from dev/assets/UserGuide_faq.md.BTc51Dug.js
rename to dev/assets/UserGuide_faq.md.BgQQKKl0.js
index 628a1166..19e25637 100644
--- a/dev/assets/UserGuide_faq.md.BTc51Dug.js
+++ b/dev/assets/UserGuide_faq.md.BgQQKKl0.js
@@ -196,18 +196,18 @@ import{_ as i,c as a,a2 as n,o as e}from"./chunks/framework.DgSLhxNl.js";const t
   Additional Axes: 
   (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points)
   Variables: 
-  latitudes
-
-  Additional Axes: 
-  (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points)
-  Variables: 
   longitudes
 
   Additional Axes: 
   (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points,
   → Time   Sampled{Date} Date("2020-01-01"):Dates.Month(1):Date("2022-12-01") ForwardOrdered Regular Points)
   Variables: 
-  temperature

If your dataset has been read from a file with Cube it is not loaded into memory, and you have to load the latitudes and longitudes YAXArrays into memory:

julia
latitudes_yasxa  = readcubedata(ds["latitudes"])
+  temperature
+
+  Additional Axes: 
+  (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points)
+  Variables: 
+  latitudes

If your dataset has been read from a file with Cube it is not loaded into memory, and you have to load the latitudes and longitudes YAXArrays into memory:

julia
latitudes_yasxa  = readcubedata(ds["latitudes"])
 longitudes_yasxa = readcubedata(ds["longitudes"])
 ds_subset = ds[points = Where(p-> latitudes_yasxa[p]  >= 20 && latitudes_yasxa[p]  <= 80 &&
                              longitudes_yasxa[p] >= 0  && longitudes_yasxa[p] <= 180
@@ -338,13 +338,13 @@ import{_ as i,c as a,a2 as n,o as e}from"./chunks/framework.DgSLhxNl.js";const t
   (↓ time     Sampled{DateTime} [2020-01-01T00:00:00, …, 2020-01-21T19:00:00] ForwardOrdered Irregular Points,
   → variable Categorical{Symbol} [:Open, :High, :Low, :Close, :Volume] Unordered)
   Variables: 
-  Stock2
+  Stock1
 
   Additional Axes: 
   (↓ time     Sampled{DateTime} [2020-01-01T00:00:00, …, 2020-01-21T19:00:00] ForwardOrdered Irregular Points,
   → variable Categorical{Symbol} [:Open, :High, :Low, :Close, :Volume] Unordered)
   Variables: 
-  Stock1
+  Stock2
 
   Additional Axes: 
   (↓ time     Sampled{DateTime} [2020-01-01T00:00:00, …, 2020-01-21T19:00:00] ForwardOrdered Irregular Points,
diff --git a/dev/assets/UserGuide_faq.md.BTc51Dug.lean.js b/dev/assets/UserGuide_faq.md.BgQQKKl0.lean.js
similarity index 99%
rename from dev/assets/UserGuide_faq.md.BTc51Dug.lean.js
rename to dev/assets/UserGuide_faq.md.BgQQKKl0.lean.js
index 628a1166..19e25637 100644
--- a/dev/assets/UserGuide_faq.md.BTc51Dug.lean.js
+++ b/dev/assets/UserGuide_faq.md.BgQQKKl0.lean.js
@@ -196,18 +196,18 @@ import{_ as i,c as a,a2 as n,o as e}from"./chunks/framework.DgSLhxNl.js";const t
   Additional Axes: 
   (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points)
   Variables: 
-  latitudes
-
-  Additional Axes: 
-  (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points)
-  Variables: 
   longitudes
 
   Additional Axes: 
   (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points,
   → Time   Sampled{Date} Date("2020-01-01"):Dates.Month(1):Date("2022-12-01") ForwardOrdered Regular Points)
   Variables: 
-  temperature

If your dataset has been read from a file with Cube it is not loaded into memory, and you have to load the latitudes and longitudes YAXArrays into memory:

julia
latitudes_yasxa  = readcubedata(ds["latitudes"])
+  temperature
+
+  Additional Axes: 
+  (↓ points Sampled{Int64} [9, 13, …, 95, 100] ForwardOrdered Irregular Points)
+  Variables: 
+  latitudes

If your dataset has been read from a file with Cube it is not loaded into memory, and you have to load the latitudes and longitudes YAXArrays into memory:

julia
latitudes_yasxa  = readcubedata(ds["latitudes"])
 longitudes_yasxa = readcubedata(ds["longitudes"])
 ds_subset = ds[points = Where(p-> latitudes_yasxa[p]  >= 20 && latitudes_yasxa[p]  <= 80 &&
                              longitudes_yasxa[p] >= 0  && longitudes_yasxa[p] <= 180
@@ -338,13 +338,13 @@ import{_ as i,c as a,a2 as n,o as e}from"./chunks/framework.DgSLhxNl.js";const t
   (↓ time     Sampled{DateTime} [2020-01-01T00:00:00, …, 2020-01-21T19:00:00] ForwardOrdered Irregular Points,
   → variable Categorical{Symbol} [:Open, :High, :Low, :Close, :Volume] Unordered)
   Variables: 
-  Stock2
+  Stock1
 
   Additional Axes: 
   (↓ time     Sampled{DateTime} [2020-01-01T00:00:00, …, 2020-01-21T19:00:00] ForwardOrdered Irregular Points,
   → variable Categorical{Symbol} [:Open, :High, :Low, :Close, :Volume] Unordered)
   Variables: 
-  Stock1
+  Stock2
 
   Additional Axes: 
   (↓ time     Sampled{DateTime} [2020-01-01T00:00:00, …, 2020-01-21T19:00:00] ForwardOrdered Irregular Points,
diff --git a/dev/assets/UserGuide_write.md.CRLfNylS.js b/dev/assets/UserGuide_write.md.Dkj1D2rr.js
similarity index 99%
rename from dev/assets/UserGuide_write.md.CRLfNylS.js
rename to dev/assets/UserGuide_write.md.Dkj1D2rr.js
index aff1cbad..047d8a9d 100644
--- a/dev/assets/UserGuide_write.md.CRLfNylS.js
+++ b/dev/assets/UserGuide_write.md.Dkj1D2rr.js
@@ -20,7 +20,7 @@ import{_ as n,c as l,a2 as t,j as i,a,G as p,B as h,o as k}from"./chunks/framewo
 savecube(ds.tos, "tos.nc", driver=:netcdf)

Save an entire Dataset to a directory:

julia
savedataset(ds, path="ds.nc", driver=:netcdf)

netcdf compression ​

Save a dataset to NetCDF format with compression:

julia
n = 7 # compression level, number between 0 (no compression) and 9 (max compression)
 savedataset(ds, path="ds_c.nc", driver=:netcdf, compress=n)

Comparing it to the default saved file

julia
ds_info = stat("ds.nc")
 ds_c_info = stat("ds_c.nc")
-println("File size: ", "default: ", ds_info.size, " bytes", ", compress: ", ds_c_info.size, " bytes")
File size: default: 2963858 bytes, compress: 1159914 bytes

Overwrite a Dataset ​

If a path already exists, an error will be thrown. Set overwrite=true to delete the existing dataset

julia
savedataset(ds, path="ds.zarr", driver=:zarr, overwrite=true)

DANGER

Again, setting overwrite will delete all your previous saved data.

Look at the doc string for more information

`,29)),i("details",r,[i("summary",null,[s[0]||(s[0]=i("a",{id:"YAXArrays.Datasets.savedataset",href:"#YAXArrays.Datasets.savedataset"},[i("span",{class:"jlbinding"},"YAXArrays.Datasets.savedataset")],-1)),s[1]||(s[1]=a()),p(e,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),s[2]||(s[2]=i("p",null,'savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)',-1)),s[3]||(s[3]=i("p",null,[a("Saves a Dataset into a file at "),i("code",null,"path"),a(" with the format given by "),i("code",null,"driver"),a(", i.e., driver=:netcdf or driver=:zarr.")],-1)),s[4]||(s[4]=i("div",{class:"warning custom-block"},[i("p",{class:"custom-block-title"},"Warning"),i("p",null,"overwrite = true, deletes ALL your data and it will create a new file.")],-1)),s[5]||(s[5]=i("p",null,[i("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L567-L576",target:"_blank",rel:"noreferrer"},"source")],-1))]),s[7]||(s[7]=t(`

Append to a Dataset ​

New variables can be added to an existing dataset using the append=true keyword.

julia
ds2 = Dataset(z = YAXArray(rand(10,20,5)))
+println("File size: ", "default: ", ds_info.size, " bytes", ", compress: ", ds_c_info.size, " bytes")
File size: default: 2963858 bytes, compress: 1159914 bytes

Overwrite a Dataset ​

If a path already exists, an error will be thrown. Set overwrite=true to delete the existing dataset

julia
savedataset(ds, path="ds.zarr", driver=:zarr, overwrite=true)

DANGER

Again, setting overwrite will delete all your previous saved data.

Look at the doc string for more information

`,29)),i("details",r,[i("summary",null,[s[0]||(s[0]=i("a",{id:"YAXArrays.Datasets.savedataset",href:"#YAXArrays.Datasets.savedataset"},[i("span",{class:"jlbinding"},"YAXArrays.Datasets.savedataset")],-1)),s[1]||(s[1]=a()),p(e,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),s[2]||(s[2]=i("p",null,'savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)',-1)),s[3]||(s[3]=i("p",null,[a("Saves a Dataset into a file at "),i("code",null,"path"),a(" with the format given by "),i("code",null,"driver"),a(", i.e., driver=:netcdf or driver=:zarr.")],-1)),s[4]||(s[4]=i("div",{class:"warning custom-block"},[i("p",{class:"custom-block-title"},"Warning"),i("p",null,"overwrite = true, deletes ALL your data and it will create a new file.")],-1)),s[5]||(s[5]=i("p",null,[i("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L568-L577",target:"_blank",rel:"noreferrer"},"source")],-1))]),s[7]||(s[7]=t(`

Append to a Dataset ​

New variables can be added to an existing dataset using the append=true keyword.

julia
ds2 = Dataset(z = YAXArray(rand(10,20,5)))
 savedataset(ds2, path="ds.zarr", backend=:zarr, append=true)
julia
julia> open_dataset("ds.zarr", driver=:zarr)
YAXArray Dataset
 Shared Axes:
 None
diff --git a/dev/assets/UserGuide_write.md.CRLfNylS.lean.js b/dev/assets/UserGuide_write.md.Dkj1D2rr.lean.js
similarity index 99%
rename from dev/assets/UserGuide_write.md.CRLfNylS.lean.js
rename to dev/assets/UserGuide_write.md.Dkj1D2rr.lean.js
index aff1cbad..047d8a9d 100644
--- a/dev/assets/UserGuide_write.md.CRLfNylS.lean.js
+++ b/dev/assets/UserGuide_write.md.Dkj1D2rr.lean.js
@@ -20,7 +20,7 @@ import{_ as n,c as l,a2 as t,j as i,a,G as p,B as h,o as k}from"./chunks/framewo
 savecube(ds.tos, "tos.nc", driver=:netcdf)

Save an entire Dataset to a directory:

julia
savedataset(ds, path="ds.nc", driver=:netcdf)

netcdf compression ​

Save a dataset to NetCDF format with compression:

julia
n = 7 # compression level, number between 0 (no compression) and 9 (max compression)
 savedataset(ds, path="ds_c.nc", driver=:netcdf, compress=n)

Comparing it to the default saved file

julia
ds_info = stat("ds.nc")
 ds_c_info = stat("ds_c.nc")
-println("File size: ", "default: ", ds_info.size, " bytes", ", compress: ", ds_c_info.size, " bytes")
File size: default: 2963858 bytes, compress: 1159914 bytes

Overwrite a Dataset ​

If a path already exists, an error will be thrown. Set overwrite=true to delete the existing dataset

julia
savedataset(ds, path="ds.zarr", driver=:zarr, overwrite=true)

DANGER

Again, setting overwrite will delete all your previous saved data.

Look at the doc string for more information

`,29)),i("details",r,[i("summary",null,[s[0]||(s[0]=i("a",{id:"YAXArrays.Datasets.savedataset",href:"#YAXArrays.Datasets.savedataset"},[i("span",{class:"jlbinding"},"YAXArrays.Datasets.savedataset")],-1)),s[1]||(s[1]=a()),p(e,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),s[2]||(s[2]=i("p",null,'savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)',-1)),s[3]||(s[3]=i("p",null,[a("Saves a Dataset into a file at "),i("code",null,"path"),a(" with the format given by "),i("code",null,"driver"),a(", i.e., driver=:netcdf or driver=:zarr.")],-1)),s[4]||(s[4]=i("div",{class:"warning custom-block"},[i("p",{class:"custom-block-title"},"Warning"),i("p",null,"overwrite = true, deletes ALL your data and it will create a new file.")],-1)),s[5]||(s[5]=i("p",null,[i("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L567-L576",target:"_blank",rel:"noreferrer"},"source")],-1))]),s[7]||(s[7]=t(`

Append to a Dataset ​

New variables can be added to an existing dataset using the append=true keyword.

julia
ds2 = Dataset(z = YAXArray(rand(10,20,5)))
+println("File size: ", "default: ", ds_info.size, " bytes", ", compress: ", ds_c_info.size, " bytes")
File size: default: 2963858 bytes, compress: 1159914 bytes

Overwrite a Dataset ​

If a path already exists, an error will be thrown. Set overwrite=true to delete the existing dataset

julia
savedataset(ds, path="ds.zarr", driver=:zarr, overwrite=true)

DANGER

Again, setting overwrite will delete all your previous saved data.

Look at the doc string for more information

`,29)),i("details",r,[i("summary",null,[s[0]||(s[0]=i("a",{id:"YAXArrays.Datasets.savedataset",href:"#YAXArrays.Datasets.savedataset"},[i("span",{class:"jlbinding"},"YAXArrays.Datasets.savedataset")],-1)),s[1]||(s[1]=a()),p(e,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),s[2]||(s[2]=i("p",null,'savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)',-1)),s[3]||(s[3]=i("p",null,[a("Saves a Dataset into a file at "),i("code",null,"path"),a(" with the format given by "),i("code",null,"driver"),a(", i.e., driver=:netcdf or driver=:zarr.")],-1)),s[4]||(s[4]=i("div",{class:"warning custom-block"},[i("p",{class:"custom-block-title"},"Warning"),i("p",null,"overwrite = true, deletes ALL your data and it will create a new file.")],-1)),s[5]||(s[5]=i("p",null,[i("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L568-L577",target:"_blank",rel:"noreferrer"},"source")],-1))]),s[7]||(s[7]=t(`

Append to a Dataset ​

New variables can be added to an existing dataset using the append=true keyword.

julia
ds2 = Dataset(z = YAXArray(rand(10,20,5)))
 savedataset(ds2, path="ds.zarr", backend=:zarr, append=true)
julia
julia> open_dataset("ds.zarr", driver=:zarr)
YAXArray Dataset
 Shared Axes:
 None
diff --git a/dev/assets/api.md.DI_7iOJZ.js b/dev/assets/api.md.BNQXJsIs.js
similarity index 52%
rename from dev/assets/api.md.DI_7iOJZ.js
rename to dev/assets/api.md.BNQXJsIs.js
index dc3ff000..1aa40477 100644
--- a/dev/assets/api.md.DI_7iOJZ.js
+++ b/dev/assets/api.md.BNQXJsIs.js
@@ -1,10 +1,10 @@
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julia
getAxis(desc, c)
Given an Axis description and a cube, returns the corresponding axis of the cube. The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
',4))]),s("details",c,[s("summary",null,[e[3]||(e[3]=s("a",{id:"YAXArrays.Cubes",href:"#YAXArrays.Cubes"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes")],-1)),e[4]||(e[4]=a()),i(t,{type:"info",class:"jlObjectType jlModule",text:"Module"})]),e[5]||(e[5]=s("p",null,"The functions provided by YAXArrays are supposed to work on different types of cubes. This module defines the interface for all Data types that",-1)),e[6]||(e[6]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/Cubes/Cubes.jl#L1-L4",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",h,[s("summary",null,[e[7]||(e[7]=s("a",{id:"YAXArrays.Cubes.YAXArray",href:"#YAXArrays.Cubes.YAXArray"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.YAXArray")],-1)),e[8]||(e[8]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[9]||(e[9]=l('
julia
YAXArray{T,N}
An array labelled with named axes that have values associated with them. It can wrap normal arrays or, more typically DiskArrays.
Fields
  • axes: Tuple of Dimensions containing the Axes of the Cube
  • data: length(axes)-dimensional array which holds the data, this can be a lazy DiskArray
  • properties: Metadata properties describing the content of the data
  • chunks: Representation of the chunking of the data
  • cleaner: Cleaner objects to track which objects to tidy up when the YAXArray goes out of scope
source
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julia
caxes
Embeds Cube inside a new Cube
source
',3))]),s("details",g,[s("summary",null,[e[17]||(e[17]=s("a",{id:"YAXArrays.Cubes.concatenatecubes-Tuple{Any, DimensionalData.Dimensions.Dimension}",href:"#YAXArrays.Cubes.concatenatecubes-Tuple{Any, DimensionalData.Dimensions.Dimension}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.concatenatecubes")],-1)),e[18]||(e[18]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[19]||(e[19]=l('
julia
function concatenateCubes(cubelist, cataxis::CategoricalAxis)
Concatenates a vector of datacubes that have identical axes to a new single cube along the new axis cataxis
source
',3))]),s("details",A,[s("summary",null,[e[20]||(e[20]=s("a",{id:"YAXArrays.Cubes.readcubedata-Tuple{Any}",href:"#YAXArrays.Cubes.readcubedata-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.readcubedata")],-1)),e[21]||(e[21]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[22]||(e[22]=l('
julia
readcubedata(cube)
Given any array implementing the YAXArray interface it returns an in-memory YAXArray from it.
source
',3))]),s("details",f,[s("summary",null,[e[23]||(e[23]=s("a",{id:"YAXArrays.Cubes.setchunks-Tuple{YAXArray, Any}",href:"#YAXArrays.Cubes.setchunks-Tuple{YAXArray, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.setchunks")],-1)),e[24]||(e[24]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[25]||(e[25]=l('
julia
setchunks(c::YAXArray,chunks)
Resets the chunks of a YAXArray and returns a new YAXArray. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savecube on the resulting array. The chunks argument can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
',4))]),s("details",k,[s("summary",null,[e[26]||(e[26]=s("a",{id:"YAXArrays.Cubes.subsetcube",href:"#YAXArrays.Cubes.subsetcube"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.subsetcube")],-1)),e[27]||(e[27]=a()),i(t,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),e[28]||(e[28]=s("p",null,"This function calculates a subset of a cube's data",-1)),e[29]||(e[29]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/Cubes/Cubes.jl#L22-L24",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",m,[s("summary",null,[e[30]||(e[30]=s("a",{id:"YAXArrays.DAT.InDims",href:"#YAXArrays.DAT.InDims"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.InDims")],-1)),e[31]||(e[31]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[32]||(e[32]=l('
julia
InDims(axisdesc...;...)
Creates a description of an Input Data Cube for cube operations. Takes a single or multiple axis descriptions as first arguments. Alternatively a MovingWindow(@ref) struct can be passed to include neighbour slices of one or more axes in the computation. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
Keyword arguments
  • artype how shall the array be represented in the inner function. Defaults to Array, alternatives are DataFrame or AsAxisArray
  • filter define some filter to skip the computation, e.g. when all values are missing. Defaults to AllMissing(), possible values are AnyMissing(), AnyOcean(), StdZero(), NValid(n) (for at least n non-missing elements). It is also possible to provide a custom one-argument function that takes the array and returns true if the compuation shall be skipped and false otherwise.
  • window_oob_value if one of the input dimensions is a MowingWindow, this value will be used to fill out-of-bounds areas
source
',5))]),s("details",j,[s("summary",null,[e[33]||(e[33]=s("a",{id:"YAXArrays.DAT.MovingWindow",href:"#YAXArrays.DAT.MovingWindow"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.MovingWindow")],-1)),e[34]||(e[34]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[35]||(e[35]=l('
julia
MovingWindow(desc, pre, after)
Constructs a MovingWindow object to be passed to an InDims constructor to define that the axis in desc shall participate in the inner function (i.e. shall be looped over), but inside the inner function pre values before and after values after the center value will be passed as well.
For example passing MovingWindow("Time", 2, 0) will loop over the time axis and always pass the current time step plus the 2 previous steps. So in the inner function the array will have an additional dimension of size 3.
source
',4))]),s("details",C,[s("summary",null,[e[36]||(e[36]=s("a",{id:"YAXArrays.DAT.OutDims-Tuple",href:"#YAXArrays.DAT.OutDims-Tuple"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.OutDims")],-1)),e[37]||(e[37]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[38]||(e[38]=l('
julia
OutDims(axisdesc;...)
Creates a description of an Output Data Cube for cube operations. Takes a single or a Vector/Tuple of axes as first argument. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
  • axisdesc: List of input axis names
  • backend : specifies the dataset backend to write data to, must be either :auto or a key in YAXArrayBase.backendlist
  • update : specifies wether the function operates inplace or if an output is returned
  • artype : specifies the Array type inside the inner function that is mapped over
  • chunksize: A Dict specifying the chunksizes for the output dimensions of the cube, or :input to copy chunksizes from input cube axes or :max to not chunk the inner dimensions
  • outtype: force the output type to a specific type, defaults to Any which means that the element type of the first input cube is used
source
',4))]),s("details",D,[s("summary",null,[e[39]||(e[39]=s("a",{id:"YAXArrays.DAT.CubeTable-Tuple{}",href:"#YAXArrays.DAT.CubeTable-Tuple{}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.CubeTable")],-1)),e[40]||(e[40]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[41]||(e[41]=l('
julia
CubeTable()
Function to turn a DataCube object into an iterable table. Takes a list of as arguments, specified as a name=cube expression. For example CubeTable(data=cube1,country=cube2) would generate a Table with the entries data and country, where data contains the values of cube1 and country the values of cube2. The cubes are matched and broadcasted along their axes like in mapCube.
source
',3))]),s("details",E,[s("summary",null,[e[42]||(e[42]=s("a",{id:"YAXArrays.DAT.cubefittable-Tuple{Any, Any, Any}",href:"#YAXArrays.DAT.cubefittable-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.cubefittable")],-1)),e[43]||(e[43]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[44]||(e[44]=l('
julia
cubefittable(tab,o,fitsym;post=getpostfunction(o),kwargs...)
Executes fittable on the CubeTable tab with the (Weighted-)OnlineStat o, looping through the values specified by fitsym. Finally, writes the results from the TableAggregator to an output data cube.
source
',3))]),s("details",T,[s("summary",null,[e[45]||(e[45]=s("a",{id:"YAXArrays.DAT.fittable-Tuple{YAXArrays.DAT.CubeIterator, Any, Any}",href:"#YAXArrays.DAT.fittable-Tuple{YAXArrays.DAT.CubeIterator, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.fittable")],-1)),e[46]||(e[46]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[47]||(e[47]=l('
julia
fittable(tab,o,fitsym;by=(),weight=nothing)
Loops through an iterable table tab and thereby fitting an OnlineStat o with the values specified through fitsym. Optionally one can specify a field (or tuple) to group by. Any groupby specifier can either be a symbol denoting the entry to group by or an anynymous function calculating the group from a table row.
For example the following would caluclate a weighted mean over a cube weighted by grid cell area and grouped by country and month:
julia
fittable(iter,WeightedMean,:tair,weight=(i->abs(cosd(i.lat))),by=(i->month(i.time),:country))
source
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julia
mapCube(fun, cube, addargs...;kwargs...)
+import{_ as n,c as o,j as s,a as t,G as i,a2 as l,B as r,o as p}from"./chunks/framework.DgSLhxNl.js";const ce=JSON.parse('{"title":"API Reference","description":"","frontmatter":{},"headers":[],"relativePath":"api.md","filePath":"api.md","lastUpdated":null}'),d={name:"api.md"},u={class:"jldocstring custom-block",open:""},c={class:"jldocstring custom-block",open:""},h={class:"jldocstring custom-block",open:""},b={class:"jldocstring custom-block",open:""},y={class:"jldocstring custom-block",open:""},g={class:"jldocstring custom-block",open:""},A={class:"jldocstring custom-block",open:""},k={class:"jldocstring custom-block",open:""},f={class:"jldocstring custom-block",open:""},m={class:"jldocstring custom-block",open:""},j={class:"jldocstring custom-block",open:""},C={class:"jldocstring custom-block",open:""},D={class:"jldocstring custom-block",open:""},E={class:"jldocstring custom-block",open:""},T={class:"jldocstring custom-block",open:""},v={class:"jldocstring custom-block",open:""},X={class:"jldocstring custom-block",open:""},Y={class:"jldocstring custom-block",open:""},x={class:"jldocstring custom-block",open:""},F={class:"jldocstring custom-block",open:""},w={class:"jldocstring custom-block",open:""},L={class:"jldocstring custom-block",open:""},M={class:"jldocstring custom-block",open:""},O={class:"jldocstring custom-block",open:""},I={class:"jldocstring custom-block",open:""},B={class:"jldocstring custom-block",open:""},J={class:"jldocstring custom-block",open:""},P={class:"jldocstring custom-block",open:""},z={class:"jldocstring custom-block",open:""},N={class:"jldocstring custom-block",open:""},S={class:"jldocstring custom-block",open:""},q={class:"jldocstring custom-block",open:""},V={class:"jldocstring custom-block",open:""},G={class:"jldocstring custom-block",open:""},R={class:"jldocstring custom-block",open:""},W={class:"jldocstring custom-block",open:""},U={class:"jldocstring custom-block",open:""},$={class:"jldocstring custom-block",open:""},H={class:"jldocstring custom-block",open:""},K={class:"jldocstring custom-block",open:""},Z={class:"jldocstring custom-block",open:""},Q={class:"jldocstring custom-block",open:""},_={class:"jldocstring custom-block",open:""},ee={class:"jldocstring custom-block",open:""},se={class:"jldocstring custom-block",open:""},te={class:"jldocstring custom-block",open:""},ae={class:"jldocstring custom-block",open:""},ie={class:"jldocstring custom-block",open:""};function le(ne,e,oe,re,pe,de){const a=r("Badge");return p(),o("div",null,[e[162]||(e[162]=s("h1",{id:"API-Reference",tabindex:"-1"},[t("API Reference "),s("a",{class:"header-anchor",href:"#API-Reference","aria-label":'Permalink to "API Reference {#API-Reference}"'},"​")],-1)),e[163]||(e[163]=s("p",null,"This section describes all available functions of this package.",-1)),e[164]||(e[164]=s("h2",{id:"Public-API",tabindex:"-1"},[t("Public API "),s("a",{class:"header-anchor",href:"#Public-API","aria-label":'Permalink to "Public API {#Public-API}"'},"​")],-1)),s("details",u,[s("summary",null,[e[0]||(e[0]=s("a",{id:"YAXArrays.getAxis-Tuple{Any, Any}",href:"#YAXArrays.getAxis-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.getAxis")],-1)),e[1]||(e[1]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[2]||(e[2]=l('
julia
getAxis(desc, c)
Given an Axis description and a cube, returns the corresponding axis of the cube. The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
',4))]),s("details",c,[s("summary",null,[e[3]||(e[3]=s("a",{id:"YAXArrays.Cubes",href:"#YAXArrays.Cubes"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes")],-1)),e[4]||(e[4]=t()),i(a,{type:"info",class:"jlObjectType jlModule",text:"Module"})]),e[5]||(e[5]=s("p",null,"The functions provided by YAXArrays are supposed to work on different types of cubes. This module defines the interface for all Data types that",-1)),e[6]||(e[6]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/Cubes/Cubes.jl#L1-L4",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",h,[s("summary",null,[e[7]||(e[7]=s("a",{id:"YAXArrays.Cubes.YAXArray",href:"#YAXArrays.Cubes.YAXArray"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.YAXArray")],-1)),e[8]||(e[8]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[9]||(e[9]=l('
julia
YAXArray{T,N}
An array labelled with named axes that have values associated with them. It can wrap normal arrays or, more typically DiskArrays.
Fields
  • axes: Tuple of Dimensions containing the Axes of the Cube
  • data: length(axes)-dimensional array which holds the data, this can be a lazy DiskArray
  • properties: Metadata properties describing the content of the data
  • chunks: Representation of the chunking of the data
  • cleaner: Cleaner objects to track which objects to tidy up when the YAXArray goes out of scope
source
',5))]),s("details",b,[s("summary",null,[e[10]||(e[10]=s("a",{id:"YAXArrays.Cubes.caxes",href:"#YAXArrays.Cubes.caxes"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.caxes")],-1)),e[11]||(e[11]=t()),i(a,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),e[12]||(e[12]=s("p",null,"Returns the axes of a Cube",-1)),e[13]||(e[13]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/Cubes/Cubes.jl#L27",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",y,[s("summary",null,[e[14]||(e[14]=s("a",{id:"YAXArrays.Cubes.caxes-Tuple{DimensionalData.Dimensions.Dimension}",href:"#YAXArrays.Cubes.caxes-Tuple{DimensionalData.Dimensions.Dimension}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.caxes")],-1)),e[15]||(e[15]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[16]||(e[16]=l('
julia
caxes
Embeds Cube inside a new Cube
source
',3))]),s("details",g,[s("summary",null,[e[17]||(e[17]=s("a",{id:"YAXArrays.Cubes.concatenatecubes-Tuple{Any, DimensionalData.Dimensions.Dimension}",href:"#YAXArrays.Cubes.concatenatecubes-Tuple{Any, DimensionalData.Dimensions.Dimension}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.concatenatecubes")],-1)),e[18]||(e[18]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[19]||(e[19]=l('
julia
function concatenateCubes(cubelist, cataxis::CategoricalAxis)
Concatenates a vector of datacubes that have identical axes to a new single cube along the new axis cataxis
source
',3))]),s("details",A,[s("summary",null,[e[20]||(e[20]=s("a",{id:"YAXArrays.Cubes.readcubedata-Tuple{Any}",href:"#YAXArrays.Cubes.readcubedata-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.readcubedata")],-1)),e[21]||(e[21]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[22]||(e[22]=l('
julia
readcubedata(cube)
Given any array implementing the YAXArray interface it returns an in-memory YAXArray from it.
source
',3))]),s("details",k,[s("summary",null,[e[23]||(e[23]=s("a",{id:"YAXArrays.Cubes.setchunks-Tuple{YAXArray, Any}",href:"#YAXArrays.Cubes.setchunks-Tuple{YAXArray, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.setchunks")],-1)),e[24]||(e[24]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[25]||(e[25]=l('
julia
setchunks(c::YAXArray,chunks)
Resets the chunks of a YAXArray and returns a new YAXArray. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savecube on the resulting array. The chunks argument can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
',4))]),s("details",f,[s("summary",null,[e[26]||(e[26]=s("a",{id:"YAXArrays.Cubes.subsetcube",href:"#YAXArrays.Cubes.subsetcube"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.subsetcube")],-1)),e[27]||(e[27]=t()),i(a,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),e[28]||(e[28]=s("p",null,"This function calculates a subset of a cube's data",-1)),e[29]||(e[29]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/Cubes/Cubes.jl#L22-L24",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",m,[s("summary",null,[e[30]||(e[30]=s("a",{id:"YAXArrays.DAT.InDims",href:"#YAXArrays.DAT.InDims"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.InDims")],-1)),e[31]||(e[31]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[32]||(e[32]=l('
julia
InDims(axisdesc...;...)
Creates a description of an Input Data Cube for cube operations. Takes a single or multiple axis descriptions as first arguments. Alternatively a MovingWindow(@ref) struct can be passed to include neighbour slices of one or more axes in the computation. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
Keyword arguments
  • artype how shall the array be represented in the inner function. Defaults to Array, alternatives are DataFrame or AsAxisArray
  • filter define some filter to skip the computation, e.g. when all values are missing. Defaults to AllMissing(), possible values are AnyMissing(), AnyOcean(), StdZero(), NValid(n) (for at least n non-missing elements). It is also possible to provide a custom one-argument function that takes the array and returns true if the compuation shall be skipped and false otherwise.
  • window_oob_value if one of the input dimensions is a MowingWindow, this value will be used to fill out-of-bounds areas
source
',5))]),s("details",j,[s("summary",null,[e[33]||(e[33]=s("a",{id:"YAXArrays.DAT.MovingWindow",href:"#YAXArrays.DAT.MovingWindow"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.MovingWindow")],-1)),e[34]||(e[34]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[35]||(e[35]=l('
julia
MovingWindow(desc, pre, after)
Constructs a MovingWindow object to be passed to an InDims constructor to define that the axis in desc shall participate in the inner function (i.e. shall be looped over), but inside the inner function pre values before and after values after the center value will be passed as well.
For example passing MovingWindow("Time", 2, 0) will loop over the time axis and always pass the current time step plus the 2 previous steps. So in the inner function the array will have an additional dimension of size 3.
source
',4))]),s("details",C,[s("summary",null,[e[36]||(e[36]=s("a",{id:"YAXArrays.DAT.OutDims-Tuple",href:"#YAXArrays.DAT.OutDims-Tuple"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.OutDims")],-1)),e[37]||(e[37]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[38]||(e[38]=l('
julia
OutDims(axisdesc;...)
Creates a description of an Output Data Cube for cube operations. Takes a single or a Vector/Tuple of axes as first argument. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
  • axisdesc: List of input axis names
  • backend : specifies the dataset backend to write data to, must be either :auto or a key in YAXArrayBase.backendlist
  • update : specifies wether the function operates inplace or if an output is returned
  • artype : specifies the Array type inside the inner function that is mapped over
  • chunksize: A Dict specifying the chunksizes for the output dimensions of the cube, or :input to copy chunksizes from input cube axes or :max to not chunk the inner dimensions
  • outtype: force the output type to a specific type, defaults to Any which means that the element type of the first input cube is used
source
',4))]),s("details",D,[s("summary",null,[e[39]||(e[39]=s("a",{id:"YAXArrays.DAT.CubeTable-Tuple{}",href:"#YAXArrays.DAT.CubeTable-Tuple{}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.CubeTable")],-1)),e[40]||(e[40]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[41]||(e[41]=l('
julia
CubeTable()
Function to turn a DataCube object into an iterable table. Takes a list of as arguments, specified as a name=cube expression. For example CubeTable(data=cube1,country=cube2) would generate a Table with the entries data and country, where data contains the values of cube1 and country the values of cube2. The cubes are matched and broadcasted along their axes like in mapCube.
source
',3))]),s("details",E,[s("summary",null,[e[42]||(e[42]=s("a",{id:"YAXArrays.DAT.cubefittable-Tuple{Any, Any, Any}",href:"#YAXArrays.DAT.cubefittable-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.cubefittable")],-1)),e[43]||(e[43]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[44]||(e[44]=l('
julia
cubefittable(tab,o,fitsym;post=getpostfunction(o),kwargs...)
Executes fittable on the CubeTable tab with the (Weighted-)OnlineStat o, looping through the values specified by fitsym. Finally, writes the results from the TableAggregator to an output data cube.
source
',3))]),s("details",T,[s("summary",null,[e[45]||(e[45]=s("a",{id:"YAXArrays.DAT.fittable-Tuple{YAXArrays.DAT.CubeIterator, Any, Any}",href:"#YAXArrays.DAT.fittable-Tuple{YAXArrays.DAT.CubeIterator, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.fittable")],-1)),e[46]||(e[46]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[47]||(e[47]=l('
julia
fittable(tab,o,fitsym;by=(),weight=nothing)
Loops through an iterable table tab and thereby fitting an OnlineStat o with the values specified through fitsym. Optionally one can specify a field (or tuple) to group by. Any groupby specifier can either be a symbol denoting the entry to group by or an anynymous function calculating the group from a table row.
For example the following would caluclate a weighted mean over a cube weighted by grid cell area and grouped by country and month:
julia
fittable(iter,WeightedMean,:tair,weight=(i->abs(cosd(i.lat))),by=(i->month(i.time),:country))
source
',5))]),s("details",v,[s("summary",null,[e[48]||(e[48]=s("a",{id:"YAXArrays.DAT.mapCube-Tuple{Function, Dataset, Vararg{Any}}",href:"#YAXArrays.DAT.mapCube-Tuple{Function, Dataset, Vararg{Any}}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.mapCube")],-1)),e[49]||(e[49]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[50]||(e[50]=l(`
julia
mapCube(fun, cube, addargs...;kwargs...)
 
 Map a given function \`fun\` over slices of all cubes of the dataset \`ds\`. 
 Use InDims to discribe the input dimensions and OutDims to describe the output dimensions of the function.
 For Datasets, only one output cube can be specified.
 In contrast to the mapCube function for cubes, additional arguments for the inner function should be set as keyword arguments.
 
-For the specific keyword arguments see the docstring of the mapCube function for cubes.
source
`,2))]),s("details",X,[s("summary",null,[e[51]||(e[51]=s("a",{id:"YAXArrays.DAT.mapCube-Tuple{Function, Tuple, Vararg{Any}}",href:"#YAXArrays.DAT.mapCube-Tuple{Function, Tuple, Vararg{Any}}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.mapCube")],-1)),e[52]||(e[52]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[53]||(e[53]=l('
julia
mapCube(fun, cube, addargs...;kwargs...)
Map a given function fun over slices of the data cube cube. The additional arguments addargs will be forwarded to the inner function fun. Use InDims to discribe the input dimensions and OutDims to describe the output dimensions of the function.
Keyword arguments
  • max_cache=YAXDefaults.max_cache Float64 maximum size of blocks that are read into memory in bits e.g. max_cache=5.0e8. Or String. e.g. max_cache="10MB" ormax_cache=1GB``` defaults to approx 10Mb.
  • indims::InDims List of input cube descriptors of type InDims for each input data cube.
  • outdims::OutDims List of output cube descriptors of type OutDims for each output cube.
  • inplace does the function write to an output array inplace or return a single value> defaults to true
  • ispar boolean to determine if parallelisation should be applied, defaults to true if workers are available.
  • showprog boolean indicating if a ProgressMeter shall be shown
  • include_loopvars boolean to indicate if the varoables looped over should be added as function arguments
  • nthreads number of threads for the computation, defaults to Threads.nthreads for every worker.
  • loopchunksize determines the chunk sizes of variables which are looped over, a dict
  • kwargs additional keyword arguments are passed to the inner function
The first argument is always the function to be applied, the second is the input cube or a tuple of input cubes if needed.
source
',6))]),s("details",Y,[s("summary",null,[e[54]||(e[54]=s("a",{id:"YAXArrays.Datasets.Dataset",href:"#YAXArrays.Datasets.Dataset"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Dataset")],-1)),e[55]||(e[55]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[56]||(e[56]=l('
julia
Dataset object which stores an `OrderedDict` of YAXArrays with Symbol keys.\na dictionary of CubeAxes and a Dictionary of general properties.\nA dictionary can hold cubes with differing axes. But it will share the common axes between the subcubes.
source
',2))]),s("details",x,[s("summary",null,[e[57]||(e[57]=s("a",{id:"YAXArrays.Datasets.Dataset-Tuple{}",href:"#YAXArrays.Datasets.Dataset-Tuple{}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Dataset")],-1)),e[58]||(e[58]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[59]||(e[59]=s("p",null,"Dataset(; properties = Dict{String,Any}, cubes...)",-1)),e[60]||(e[60]=s("p",null,[a("Construct a YAXArray Dataset with global attributes "),s("code",null,"properties"),a(" a and a list of named YAXArrays cubes...")],-1)),e[61]||(e[61]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L28-L32",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",F,[s("summary",null,[e[62]||(e[62]=s("a",{id:"YAXArrays.Datasets.Cube-Tuple{Dataset}",href:"#YAXArrays.Datasets.Cube-Tuple{Dataset}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Cube")],-1)),e[63]||(e[63]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[64]||(e[64]=l('
julia
Cube(ds::Dataset; joinname="Variable")
Construct a single YAXArray from the dataset ds by concatenating the cubes in the datset on the joinname dimension.
source
',3))]),s("details",w,[s("summary",null,[e[65]||(e[65]=s("a",{id:"YAXArrays.Datasets.open_dataset-Tuple{Any}",href:"#YAXArrays.Datasets.open_dataset-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.open_dataset")],-1)),e[66]||(e[66]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[67]||(e[67]=s("p",null,"open_dataset(g; driver=:all)",-1)),e[68]||(e[68]=s("p",null,[a("Open the dataset at "),s("code",null,"g"),a(" with the given "),s("code",null,"driver"),a(". The default driver will search for available drivers and tries to detect the useable driver from the filename extension.")],-1)),e[69]||(e[69]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L340-L345",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",L,[s("summary",null,[e[70]||(e[70]=s("a",{id:"YAXArrays.Datasets.savecube-Tuple{Any, AbstractString}",href:"#YAXArrays.Datasets.savecube-Tuple{Any, AbstractString}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.savecube")],-1)),e[71]||(e[71]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[72]||(e[72]=l('
julia
savecube(cube,name::String)
Save a YAXArray to the path.
Extended Help
The keyword arguments are:
  • name:
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • max_cache: The number of bits that are used as cache for the data handling.
  • backend: The backend, that is used to save the data. Falls back to searching the backend according to the extension of the path.
  • driver: The same setting as backend.
  • overwrite::Bool=false overwrite cube if it already exists
source
',6))]),s("details",M,[s("summary",null,[e[73]||(e[73]=s("a",{id:"YAXArrays.Datasets.savedataset-Tuple{Dataset}",href:"#YAXArrays.Datasets.savedataset-Tuple{Dataset}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.savedataset")],-1)),e[74]||(e[74]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[75]||(e[75]=s("p",null,'savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)',-1)),e[76]||(e[76]=s("p",null,[a("Saves a Dataset into a file at "),s("code",null,"path"),a(" with the format given by "),s("code",null,"driver"),a(", i.e., driver=:netcdf or driver=:zarr.")],-1)),e[77]||(e[77]=s("div",{class:"warning custom-block"},[s("p",{class:"custom-block-title"},"Warning"),s("p",null,"overwrite = true, deletes ALL your data and it will create a new file.")],-1)),e[78]||(e[78]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L567-L576",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",O,[s("summary",null,[e[79]||(e[79]=s("a",{id:"YAXArrays.Datasets.to_dataset-Tuple{Any}",href:"#YAXArrays.Datasets.to_dataset-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.to_dataset")],-1)),e[80]||(e[80]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[81]||(e[81]=s("p",null,'to_dataset(c;datasetaxis = "Variable", layername = "layer")',-1)),e[82]||(e[82]=s("p",null,[a(`Convert a Data Cube into a Dataset. It is possible to treat one of the Cube's axes as a "DatasetAxis" i.e. the cube will be split into different parts that become variables in the Dataset. If no such axis is specified or found, there will only be a single variable in the dataset with the name `),s("code",null,"layername")],-1)),e[83]||(e[83]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L45-L53",target:"_blank",rel:"noreferrer"},"source")],-1))]),e[165]||(e[165]=s("h2",{id:"Internal-API",tabindex:"-1"},[a("Internal API "),s("a",{class:"header-anchor",href:"#Internal-API","aria-label":'Permalink to "Internal API {#Internal-API}"'},"​")],-1)),s("details",I,[s("summary",null,[e[84]||(e[84]=s("a",{id:"YAXArrays.YAXDefaults",href:"#YAXArrays.YAXDefaults"},[s("span",{class:"jlbinding"},"YAXArrays.YAXDefaults")],-1)),e[85]||(e[85]=a()),i(t,{type:"info",class:"jlObjectType jlConstant",text:"Constant"})]),e[86]||(e[86]=l('
Default configuration for YAXArrays, has the following fields:
  • workdir[]::String = "./" The default location for temporary cubes.
  • recal[]::Bool = false set to true if you want @loadOrGenerate to always recalculate the results.
  • chunksize[]::Any = :input Set the default output chunksize.
  • max_cache[]::Float64 = 1e8 The maximum cache used by mapCube.
  • cubedir[]::"" the default location for Cube() without an argument.
  • subsetextensions::Array{Any} = [] List of registered functions, that convert subsetting input into dimension boundaries.
source
',3))]),s("details",B,[s("summary",null,[e[87]||(e[87]=s("a",{id:"YAXArrays.findAxis-Tuple{Any, Any}",href:"#YAXArrays.findAxis-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.findAxis")],-1)),e[88]||(e[88]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[89]||(e[89]=l('
julia
findAxis(desc, c)
Internal function
Extended Help
Given an Axis description and a cube return the index of the Axis.
The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
',7))]),s("details",J,[s("summary",null,[e[90]||(e[90]=s("a",{id:"YAXArrays.getOutAxis-NTuple{5, Any}",href:"#YAXArrays.getOutAxis-NTuple{5, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.getOutAxis")],-1)),e[91]||(e[91]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[92]||(e[92]=l('
julia
getOutAxis
source
',2))]),s("details",P,[s("summary",null,[e[93]||(e[93]=s("a",{id:"YAXArrays.get_descriptor-Tuple{String}",href:"#YAXArrays.get_descriptor-Tuple{String}"},[s("span",{class:"jlbinding"},"YAXArrays.get_descriptor")],-1)),e[94]||(e[94]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[95]||(e[95]=l('
julia
get_descriptor(a)
Get the descriptor of an Axis. This is used to dispatch on the descriptor.
source
',3))]),s("details",z,[s("summary",null,[e[96]||(e[96]=s("a",{id:"YAXArrays.match_axis-Tuple{YAXArrays.ByName, Any}",href:"#YAXArrays.match_axis-Tuple{YAXArrays.ByName, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.match_axis")],-1)),e[97]||(e[97]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[98]||(e[98]=l(`
julia
match_axis
Internal function
Extended Help
Match the Axis based on the AxisDescriptor.
+For the specific keyword arguments see the docstring of the mapCube function for cubes.
source
`,2))]),s("details",X,[s("summary",null,[e[51]||(e[51]=s("a",{id:"YAXArrays.DAT.mapCube-Tuple{Function, Tuple, Vararg{Any}}",href:"#YAXArrays.DAT.mapCube-Tuple{Function, Tuple, Vararg{Any}}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.mapCube")],-1)),e[52]||(e[52]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[53]||(e[53]=l('
julia
mapCube(fun, cube, addargs...;kwargs...)
Map a given function fun over slices of the data cube cube. The additional arguments addargs will be forwarded to the inner function fun. Use InDims to discribe the input dimensions and OutDims to describe the output dimensions of the function.
Keyword arguments
  • max_cache=YAXDefaults.max_cache Float64 maximum size of blocks that are read into memory in bits e.g. max_cache=5.0e8. Or String. e.g. max_cache="10MB" ormax_cache=1GB``` defaults to approx 10Mb.
  • indims::InDims List of input cube descriptors of type InDims for each input data cube.
  • outdims::OutDims List of output cube descriptors of type OutDims for each output cube.
  • inplace does the function write to an output array inplace or return a single value> defaults to true
  • ispar boolean to determine if parallelisation should be applied, defaults to true if workers are available.
  • showprog boolean indicating if a ProgressMeter shall be shown
  • include_loopvars boolean to indicate if the varoables looped over should be added as function arguments
  • nthreads number of threads for the computation, defaults to Threads.nthreads for every worker.
  • loopchunksize determines the chunk sizes of variables which are looped over, a dict
  • kwargs additional keyword arguments are passed to the inner function
The first argument is always the function to be applied, the second is the input cube or a tuple of input cubes if needed.
source
',6))]),s("details",Y,[s("summary",null,[e[54]||(e[54]=s("a",{id:"YAXArrays.Datasets.Dataset",href:"#YAXArrays.Datasets.Dataset"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Dataset")],-1)),e[55]||(e[55]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[56]||(e[56]=l('
julia
Dataset object which stores an `OrderedDict` of YAXArrays with Symbol keys.\na dictionary of CubeAxes and a Dictionary of general properties.\nA dictionary can hold cubes with differing axes. But it will share the common axes between the subcubes.
source
',2))]),s("details",x,[s("summary",null,[e[57]||(e[57]=s("a",{id:"YAXArrays.Datasets.Dataset-Tuple{}",href:"#YAXArrays.Datasets.Dataset-Tuple{}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Dataset")],-1)),e[58]||(e[58]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[59]||(e[59]=s("p",null,"Dataset(; properties = Dict{String,Any}, cubes...)",-1)),e[60]||(e[60]=s("p",null,[t("Construct a YAXArray Dataset with global attributes "),s("code",null,"properties"),t(" a and a list of named YAXArrays cubes...")],-1)),e[61]||(e[61]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L28-L32",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",F,[s("summary",null,[e[62]||(e[62]=s("a",{id:"YAXArrays.Datasets.Cube-Tuple{Dataset}",href:"#YAXArrays.Datasets.Cube-Tuple{Dataset}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Cube")],-1)),e[63]||(e[63]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[64]||(e[64]=l('
julia
Cube(ds::Dataset; joinname="Variable")
Construct a single YAXArray from the dataset ds by concatenating the cubes in the datset on the joinname dimension.
source
',3))]),s("details",w,[s("summary",null,[e[65]||(e[65]=s("a",{id:"YAXArrays.Datasets.open_dataset-Tuple{Any}",href:"#YAXArrays.Datasets.open_dataset-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.open_dataset")],-1)),e[66]||(e[66]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[67]||(e[67]=s("p",null,"open_dataset(g; driver=:all)",-1)),e[68]||(e[68]=s("p",null,[t("Open the dataset at "),s("code",null,"g"),t(" with the given "),s("code",null,"driver"),t(". The default driver will search for available drivers and tries to detect the useable driver from the filename extension.")],-1)),e[69]||(e[69]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L341-L346",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",L,[s("summary",null,[e[70]||(e[70]=s("a",{id:"YAXArrays.Datasets.savecube-Tuple{Any, AbstractString}",href:"#YAXArrays.Datasets.savecube-Tuple{Any, AbstractString}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.savecube")],-1)),e[71]||(e[71]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[72]||(e[72]=l('
julia
savecube(cube,name::String)
Save a YAXArray to the path.
Extended Help
The keyword arguments are:
  • name:
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • max_cache: The number of bits that are used as cache for the data handling.
  • backend: The backend, that is used to save the data. Falls back to searching the backend according to the extension of the path.
  • driver: The same setting as backend.
  • overwrite::Bool=false overwrite cube if it already exists
source
',6))]),s("details",M,[s("summary",null,[e[73]||(e[73]=s("a",{id:"YAXArrays.Datasets.savedataset-Tuple{Dataset}",href:"#YAXArrays.Datasets.savedataset-Tuple{Dataset}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.savedataset")],-1)),e[74]||(e[74]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[75]||(e[75]=s("p",null,'savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)',-1)),e[76]||(e[76]=s("p",null,[t("Saves a Dataset into a file at "),s("code",null,"path"),t(" with the format given by "),s("code",null,"driver"),t(", i.e., driver=:netcdf or driver=:zarr.")],-1)),e[77]||(e[77]=s("div",{class:"warning custom-block"},[s("p",{class:"custom-block-title"},"Warning"),s("p",null,"overwrite = true, deletes ALL your data and it will create a new file.")],-1)),e[78]||(e[78]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L568-L577",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",O,[s("summary",null,[e[79]||(e[79]=s("a",{id:"YAXArrays.Datasets.to_dataset-Tuple{Any}",href:"#YAXArrays.Datasets.to_dataset-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.to_dataset")],-1)),e[80]||(e[80]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[81]||(e[81]=s("p",null,'to_dataset(c;datasetaxis = "Variable", layername = "layer")',-1)),e[82]||(e[82]=s("p",null,[t(`Convert a Data Cube into a Dataset. It is possible to treat one of the Cube's axes as a "DatasetAxis" i.e. the cube will be split into different parts that become variables in the Dataset. If no such axis is specified or found, there will only be a single variable in the dataset with the name `),s("code",null,"layername")],-1)),e[83]||(e[83]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L45-L53",target:"_blank",rel:"noreferrer"},"source")],-1))]),e[165]||(e[165]=s("h2",{id:"Internal-API",tabindex:"-1"},[t("Internal API "),s("a",{class:"header-anchor",href:"#Internal-API","aria-label":'Permalink to "Internal API {#Internal-API}"'},"​")],-1)),s("details",I,[s("summary",null,[e[84]||(e[84]=s("a",{id:"YAXArrays.YAXDefaults",href:"#YAXArrays.YAXDefaults"},[s("span",{class:"jlbinding"},"YAXArrays.YAXDefaults")],-1)),e[85]||(e[85]=t()),i(a,{type:"info",class:"jlObjectType jlConstant",text:"Constant"})]),e[86]||(e[86]=l('
Default configuration for YAXArrays, has the following fields:
  • workdir[]::String = "./" The default location for temporary cubes.
  • recal[]::Bool = false set to true if you want @loadOrGenerate to always recalculate the results.
  • chunksize[]::Any = :input Set the default output chunksize.
  • max_cache[]::Float64 = 1e8 The maximum cache used by mapCube.
  • cubedir[]::"" the default location for Cube() without an argument.
  • subsetextensions::Array{Any} = [] List of registered functions, that convert subsetting input into dimension boundaries.
source
',3))]),s("details",B,[s("summary",null,[e[87]||(e[87]=s("a",{id:"YAXArrays.findAxis-Tuple{Any, Any}",href:"#YAXArrays.findAxis-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.findAxis")],-1)),e[88]||(e[88]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[89]||(e[89]=l('
julia
findAxis(desc, c)
Internal function
Extended Help
Given an Axis description and a cube return the index of the Axis.
The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
',7))]),s("details",J,[s("summary",null,[e[90]||(e[90]=s("a",{id:"YAXArrays.getOutAxis-NTuple{5, Any}",href:"#YAXArrays.getOutAxis-NTuple{5, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.getOutAxis")],-1)),e[91]||(e[91]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[92]||(e[92]=l('
julia
getOutAxis
source
',2))]),s("details",P,[s("summary",null,[e[93]||(e[93]=s("a",{id:"YAXArrays.get_descriptor-Tuple{String}",href:"#YAXArrays.get_descriptor-Tuple{String}"},[s("span",{class:"jlbinding"},"YAXArrays.get_descriptor")],-1)),e[94]||(e[94]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[95]||(e[95]=l('
julia
get_descriptor(a)
Get the descriptor of an Axis. This is used to dispatch on the descriptor.
source
',3))]),s("details",z,[s("summary",null,[e[96]||(e[96]=s("a",{id:"YAXArrays.match_axis-Tuple{YAXArrays.ByName, Any}",href:"#YAXArrays.match_axis-Tuple{YAXArrays.ByName, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.match_axis")],-1)),e[97]||(e[97]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[98]||(e[98]=l(`
julia
match_axis
Internal function
Extended Help
Match the Axis based on the AxisDescriptor.
 This is used to find different axes and to make certain axis description the same.
-For example to disregard differences of captialisation.
source
`,5))]),s("details",N,[s("summary",null,[e[99]||(e[99]=s("a",{id:"YAXArrays.Cubes.CleanMe",href:"#YAXArrays.Cubes.CleanMe"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.CleanMe")],-1)),e[100]||(e[100]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[101]||(e[101]=l('
julia
mutable struct CleanMe
Struct which describes data paths and their persistency. Non-persistend paths/files are removed at finalize step
source
',3))]),s("details",S,[s("summary",null,[e[102]||(e[102]=s("a",{id:"YAXArrays.Cubes.clean-Tuple{YAXArrays.Cubes.CleanMe}",href:"#YAXArrays.Cubes.clean-Tuple{YAXArrays.Cubes.CleanMe}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.clean")],-1)),e[103]||(e[103]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[104]||(e[104]=l('
julia
clean(c::CleanMe)
finalizer function for CleanMe struct. The main process removes all directories/files which are not persistent.
source
',3))]),s("details",q,[s("summary",null,[e[105]||(e[105]=s("a",{id:"YAXArrays.Cubes.copydata-Tuple{Any, Any, Any}",href:"#YAXArrays.Cubes.copydata-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.copydata")],-1)),e[106]||(e[106]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[107]||(e[107]=l('
julia
copydata(outar, inar, copybuf)
Internal function which copies the data from the input inar into the output outar at the copybuf positions.
source
',3))]),s("details",V,[s("summary",null,[e[108]||(e[108]=s("a",{id:"YAXArrays.Cubes.optifunc-NTuple{7, Any}",href:"#YAXArrays.Cubes.optifunc-NTuple{7, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.optifunc")],-1)),e[109]||(e[109]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[110]||(e[110]=l('
julia
optifunc(s, maxbuf, incs, outcs, insize, outsize, writefac)
Internal
This function is going to be minimized to detect the best possible chunk setting for the rechunking of the data.
source
',4))]),s("details",G,[s("summary",null,[e[111]||(e[111]=s("a",{id:"YAXArrays.DAT.DATConfig",href:"#YAXArrays.DAT.DATConfig"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.DATConfig")],-1)),e[112]||(e[112]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[113]||(e[113]=l('
Configuration object of a DAT process. This holds all necessary information to perform the calculations. It contains the following fields:
  • incubes::NTuple{NIN, YAXArrays.DAT.InputCube} where NIN: The input data cubes
  • outcubes::NTuple{NOUT, YAXArrays.DAT.OutputCube} where NOUT: The output data cubes
  • allInAxes::Vector: List of all axes of the input cubes
  • LoopAxes::Vector: List of axes that are looped through
  • ispar::Bool: Flag whether the computation is parallelized
  • loopcachesize::Vector{Int64}:
  • allow_irregular_chunks::Bool:
  • max_cache::Any: Maximal size of the in memory cache
  • fu::Any: Inner function which is computed
  • inplace::Bool: Flag whether the computation happens in place
  • include_loopvars::Bool:
  • ntr::Any:
  • do_gc::Bool: Flag if GC should be called explicitly. Probably necessary for many runs in Julia 1.9
  • addargs::Any: Additional arguments for the inner function
  • kwargs::Any: Additional keyword arguments for the inner function
source
',3))]),s("details",R,[s("summary",null,[e[114]||(e[114]=s("a",{id:"YAXArrays.DAT.InputCube",href:"#YAXArrays.DAT.InputCube"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.InputCube")],-1)),e[115]||(e[115]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[116]||(e[116]=l('
Internal representation of an input cube for DAT operations
  • cube: The input data
  • desc: The input description given by the user/registration
  • axesSmall: List of axes that were actually selected through the description
  • icolon
  • colonperm
  • loopinds: Indices of loop axes that this cube does not contain, i.e. broadcasts
  • cachesize: Number of elements to keep in cache along each axis
  • window
  • iwindow
  • windowloopinds
  • iall
source
',3))]),s("details",W,[s("summary",null,[e[117]||(e[117]=s("a",{id:"YAXArrays.DAT.OutputCube",href:"#YAXArrays.DAT.OutputCube"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.OutputCube")],-1)),e[118]||(e[118]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[119]||(e[119]=l('
Internal representation of an output cube for DAT operations
Fields
  • cube: The actual outcube cube, once it is generated
  • cube_unpermuted: The unpermuted output cube
  • desc: The description of the output axes as given by users or registration
  • axesSmall: The list of output axes determined through the description
  • allAxes: List of all the axes of the cube
  • loopinds: Index of the loop axes that are broadcasted for this output cube
  • innerchunks
  • outtype: Elementtype of the outputcube
source
',4))]),s("details",U,[s("summary",null,[e[120]||(e[120]=s("a",{id:"YAXArrays.DAT.YAXColumn",href:"#YAXArrays.DAT.YAXColumn"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.YAXColumn")],-1)),e[121]||(e[121]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[122]||(e[122]=l('
julia
YAXColumn
A struct representing a single column of a YAXArray partitioned Table # Fields
  • inarBC
  • inds
source
',4))]),s("details",$,[s("summary",null,[e[123]||(e[123]=s("a",{id:"YAXArrays.DAT.cmpcachmisses-Tuple{Any, Any}",href:"#YAXArrays.DAT.cmpcachmisses-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.cmpcachmisses")],-1)),e[124]||(e[124]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[125]||(e[125]=s("p",null,"Function that compares two cache miss specifiers by their importance",-1)),e[126]||(e[126]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DAT/DAT.jl#L957-L959",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",H,[s("summary",null,[e[127]||(e[127]=s("a",{id:"YAXArrays.DAT.getFrontPerm-Tuple{Any, Any}",href:"#YAXArrays.DAT.getFrontPerm-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getFrontPerm")],-1)),e[128]||(e[128]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[129]||(e[129]=s("p",null,"Calculate an axis permutation that brings the wanted dimensions to the front",-1)),e[130]||(e[130]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DAT/DAT.jl#L1202",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",K,[s("summary",null,[e[131]||(e[131]=s("a",{id:"YAXArrays.DAT.getLoopCacheSize-NTuple{5, Any}",href:"#YAXArrays.DAT.getLoopCacheSize-NTuple{5, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getLoopCacheSize")],-1)),e[132]||(e[132]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[133]||(e[133]=s("p",null,"Calculate optimal Cache size to DAT operation",-1)),e[134]||(e[134]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DAT/DAT.jl#L1056",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",Z,[s("summary",null,[e[135]||(e[135]=s("a",{id:"YAXArrays.DAT.getOuttype-Tuple{Int64, Any}",href:"#YAXArrays.DAT.getOuttype-Tuple{Int64, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getOuttype")],-1)),e[136]||(e[136]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[137]||(e[137]=l('
julia
getOuttype(outtype, cdata)
Internal function
Get the element type for the output cube
source
',4))]),s("details",Q,[s("summary",null,[e[138]||(e[138]=s("a",{id:"YAXArrays.DAT.getloopchunks-Tuple{YAXArrays.DAT.DATConfig}",href:"#YAXArrays.DAT.getloopchunks-Tuple{YAXArrays.DAT.DATConfig}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getloopchunks")],-1)),e[139]||(e[139]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[140]||(e[140]=l('
julia
getloopchunks(dc::DATConfig)
Internal function
Returns the chunks that can be looped over toghether for all dimensions.\nThis computation of the size of the chunks is handled by [`DiskArrays.approx_chunksize`](@ref)
source
',4))]),s("details",_,[s("summary",null,[e[141]||(e[141]=s("a",{id:"YAXArrays.DAT.permuteloopaxes-Tuple{Any}",href:"#YAXArrays.DAT.permuteloopaxes-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.permuteloopaxes")],-1)),e[142]||(e[142]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[143]||(e[143]=l('
julia
permuteloopaxes(dc)
Internal function
Permute the dimensions of the cube, so that the axes that are looped through are in the first positions. This is necessary for a faster looping through the data.
source
',4))]),s("details",ee,[s("summary",null,[e[144]||(e[144]=s("a",{id:"YAXArrays.Cubes.setchunks-Tuple{Dataset, Any}",href:"#YAXArrays.Cubes.setchunks-Tuple{Dataset, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.setchunks")],-1)),e[145]||(e[145]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[146]||(e[146]=l('
julia
setchunks(c::Dataset,chunks)
Resets the chunks of all or a subset YAXArrays in the dataset and returns a new Dataset. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savedataset on the resulting array. The chunks argument can take one of the following forms:
  • a NamedTuple or AbstractDict mapping from variable name to a description of the desired variable chunks
  • a NamedTuple or AbstractDict mapping from dimension name to a description of the desired variable chunks
  • a description of the desired variable chunks applied to all members of the Dataset
where a description of the desired variable chunks can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
',6))]),s("details",se,[s("summary",null,[e[147]||(e[147]=s("a",{id:"YAXArrays.Datasets.collectfromhandle-Tuple{Any, Any, Any}",href:"#YAXArrays.Datasets.collectfromhandle-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.collectfromhandle")],-1)),e[148]||(e[148]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[149]||(e[149]=s("p",null,"Extracts a YAXArray from a dataset handle that was just created from a arrayinfo",-1)),e[150]||(e[150]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L473-L475",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",ae,[s("summary",null,[e[151]||(e[151]=s("a",{id:"YAXArrays.Datasets.createdataset-Tuple{Any, Any}",href:"#YAXArrays.Datasets.createdataset-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.createdataset")],-1)),e[152]||(e[152]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[153]||(e[153]=l('
function createdataset(DS::Type,axlist; kwargs...)
Creates a new dataset with axes specified in axlist. Each axis must be a subtype of CubeAxis. A new empty Zarr array will be created and can serve as a sink for mapCube operations.
Keyword arguments
  • path="" location where the new cube is stored
  • T=Union{Float32,Missing} data type of the target cube
  • chunksize = ntuple(i->length(axlist[i]),length(axlist)) chunk sizes of the array
  • chunkoffset = ntuple(i->0,length(axlist)) offsets of the chunks
  • persist::Bool=true shall the disk data be garbage-collected when the cube goes out of scope?
  • overwrite::Bool=false overwrite cube if it already exists
  • properties=Dict{String,Any}() additional cube properties
  • globalproperties=Dict{String,Any} global attributes to be added to the dataset
  • fillvalue= T>:Missing ? defaultfillval(Base.nonmissingtype(T)) : nothing fill value
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • layername="layer" Fallback name of the variable stored in the dataset if no datasetaxis is found
source
',6))]),s("details",te,[s("summary",null,[e[154]||(e[154]=s("a",{id:"YAXArrays.Datasets.getarrayinfo-Tuple{Any, Any}",href:"#YAXArrays.Datasets.getarrayinfo-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.getarrayinfo")],-1)),e[155]||(e[155]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[156]||(e[156]=s("p",null,"Extract necessary information to create a YAXArrayBase dataset from a name and YAXArray pair",-1)),e[157]||(e[157]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L442-L444",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",ie,[s("summary",null,[e[158]||(e[158]=s("a",{id:"YAXArrays.Datasets.testrange-Tuple{Any}",href:"#YAXArrays.Datasets.testrange-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.testrange")],-1)),e[159]||(e[159]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[160]||(e[160]=s("p",null,"Test if data in x can be approximated by a step range",-1)),e[161]||(e[161]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L312",target:"_blank",rel:"noreferrer"},"source")],-1))])])}const he=n(d,[["render",le]]);export{ce as __pageData,he as default};
+For example to disregard differences of captialisation.
source
`,5))]),s("details",N,[s("summary",null,[e[99]||(e[99]=s("a",{id:"YAXArrays.Cubes.CleanMe",href:"#YAXArrays.Cubes.CleanMe"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.CleanMe")],-1)),e[100]||(e[100]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[101]||(e[101]=l('
julia
mutable struct CleanMe
Struct which describes data paths and their persistency. Non-persistend paths/files are removed at finalize step
source
',3))]),s("details",S,[s("summary",null,[e[102]||(e[102]=s("a",{id:"YAXArrays.Cubes.clean-Tuple{YAXArrays.Cubes.CleanMe}",href:"#YAXArrays.Cubes.clean-Tuple{YAXArrays.Cubes.CleanMe}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.clean")],-1)),e[103]||(e[103]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[104]||(e[104]=l('
julia
clean(c::CleanMe)
finalizer function for CleanMe struct. The main process removes all directories/files which are not persistent.
source
',3))]),s("details",q,[s("summary",null,[e[105]||(e[105]=s("a",{id:"YAXArrays.Cubes.copydata-Tuple{Any, Any, Any}",href:"#YAXArrays.Cubes.copydata-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.copydata")],-1)),e[106]||(e[106]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[107]||(e[107]=l('
julia
copydata(outar, inar, copybuf)
Internal function which copies the data from the input inar into the output outar at the copybuf positions.
source
',3))]),s("details",V,[s("summary",null,[e[108]||(e[108]=s("a",{id:"YAXArrays.Cubes.optifunc-NTuple{7, Any}",href:"#YAXArrays.Cubes.optifunc-NTuple{7, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.optifunc")],-1)),e[109]||(e[109]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[110]||(e[110]=l('
julia
optifunc(s, maxbuf, incs, outcs, insize, outsize, writefac)
Internal
This function is going to be minimized to detect the best possible chunk setting for the rechunking of the data.
source
',4))]),s("details",G,[s("summary",null,[e[111]||(e[111]=s("a",{id:"YAXArrays.DAT.DATConfig",href:"#YAXArrays.DAT.DATConfig"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.DATConfig")],-1)),e[112]||(e[112]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[113]||(e[113]=l('
Configuration object of a DAT process. This holds all necessary information to perform the calculations. It contains the following fields:
  • incubes::NTuple{NIN, YAXArrays.DAT.InputCube} where NIN: The input data cubes
  • outcubes::NTuple{NOUT, YAXArrays.DAT.OutputCube} where NOUT: The output data cubes
  • allInAxes::Vector: List of all axes of the input cubes
  • LoopAxes::Vector: List of axes that are looped through
  • ispar::Bool: Flag whether the computation is parallelized
  • loopcachesize::Vector{Int64}:
  • allow_irregular_chunks::Bool:
  • max_cache::Any: Maximal size of the in memory cache
  • fu::Any: Inner function which is computed
  • inplace::Bool: Flag whether the computation happens in place
  • include_loopvars::Bool:
  • ntr::Any:
  • do_gc::Bool: Flag if GC should be called explicitly. Probably necessary for many runs in Julia 1.9
  • addargs::Any: Additional arguments for the inner function
  • kwargs::Any: Additional keyword arguments for the inner function
source
',3))]),s("details",R,[s("summary",null,[e[114]||(e[114]=s("a",{id:"YAXArrays.DAT.InputCube",href:"#YAXArrays.DAT.InputCube"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.InputCube")],-1)),e[115]||(e[115]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[116]||(e[116]=l('
Internal representation of an input cube for DAT operations
  • cube: The input data
  • desc: The input description given by the user/registration
  • axesSmall: List of axes that were actually selected through the description
  • icolon
  • colonperm
  • loopinds: Indices of loop axes that this cube does not contain, i.e. broadcasts
  • cachesize: Number of elements to keep in cache along each axis
  • window
  • iwindow
  • windowloopinds
  • iall
source
',3))]),s("details",W,[s("summary",null,[e[117]||(e[117]=s("a",{id:"YAXArrays.DAT.OutputCube",href:"#YAXArrays.DAT.OutputCube"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.OutputCube")],-1)),e[118]||(e[118]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[119]||(e[119]=l('
Internal representation of an output cube for DAT operations
Fields
  • cube: The actual outcube cube, once it is generated
  • cube_unpermuted: The unpermuted output cube
  • desc: The description of the output axes as given by users or registration
  • axesSmall: The list of output axes determined through the description
  • allAxes: List of all the axes of the cube
  • loopinds: Index of the loop axes that are broadcasted for this output cube
  • innerchunks
  • outtype: Elementtype of the outputcube
source
',4))]),s("details",U,[s("summary",null,[e[120]||(e[120]=s("a",{id:"YAXArrays.DAT.YAXColumn",href:"#YAXArrays.DAT.YAXColumn"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.YAXColumn")],-1)),e[121]||(e[121]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[122]||(e[122]=l('
julia
YAXColumn
A struct representing a single column of a YAXArray partitioned Table # Fields
  • inarBC
  • inds
source
',4))]),s("details",$,[s("summary",null,[e[123]||(e[123]=s("a",{id:"YAXArrays.DAT.cmpcachmisses-Tuple{Any, Any}",href:"#YAXArrays.DAT.cmpcachmisses-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.cmpcachmisses")],-1)),e[124]||(e[124]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[125]||(e[125]=s("p",null,"Function that compares two cache miss specifiers by their importance",-1)),e[126]||(e[126]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DAT/DAT.jl#L957-L959",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",H,[s("summary",null,[e[127]||(e[127]=s("a",{id:"YAXArrays.DAT.getFrontPerm-Tuple{Any, Any}",href:"#YAXArrays.DAT.getFrontPerm-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getFrontPerm")],-1)),e[128]||(e[128]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[129]||(e[129]=s("p",null,"Calculate an axis permutation that brings the wanted dimensions to the front",-1)),e[130]||(e[130]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DAT/DAT.jl#L1202",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",K,[s("summary",null,[e[131]||(e[131]=s("a",{id:"YAXArrays.DAT.getLoopCacheSize-NTuple{5, Any}",href:"#YAXArrays.DAT.getLoopCacheSize-NTuple{5, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getLoopCacheSize")],-1)),e[132]||(e[132]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[133]||(e[133]=s("p",null,"Calculate optimal Cache size to DAT operation",-1)),e[134]||(e[134]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DAT/DAT.jl#L1056",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",Z,[s("summary",null,[e[135]||(e[135]=s("a",{id:"YAXArrays.DAT.getOuttype-Tuple{Int64, Any}",href:"#YAXArrays.DAT.getOuttype-Tuple{Int64, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getOuttype")],-1)),e[136]||(e[136]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[137]||(e[137]=l('
julia
getOuttype(outtype, cdata)
Internal function
Get the element type for the output cube
source
',4))]),s("details",Q,[s("summary",null,[e[138]||(e[138]=s("a",{id:"YAXArrays.DAT.getloopchunks-Tuple{YAXArrays.DAT.DATConfig}",href:"#YAXArrays.DAT.getloopchunks-Tuple{YAXArrays.DAT.DATConfig}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getloopchunks")],-1)),e[139]||(e[139]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[140]||(e[140]=l('
julia
getloopchunks(dc::DATConfig)
Internal function
Returns the chunks that can be looped over toghether for all dimensions.\nThis computation of the size of the chunks is handled by [`DiskArrays.approx_chunksize`](@ref)
source
',4))]),s("details",_,[s("summary",null,[e[141]||(e[141]=s("a",{id:"YAXArrays.DAT.permuteloopaxes-Tuple{Any}",href:"#YAXArrays.DAT.permuteloopaxes-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.permuteloopaxes")],-1)),e[142]||(e[142]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[143]||(e[143]=l('
julia
permuteloopaxes(dc)
Internal function
Permute the dimensions of the cube, so that the axes that are looped through are in the first positions. This is necessary for a faster looping through the data.
source
',4))]),s("details",ee,[s("summary",null,[e[144]||(e[144]=s("a",{id:"YAXArrays.Cubes.setchunks-Tuple{Dataset, Any}",href:"#YAXArrays.Cubes.setchunks-Tuple{Dataset, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.setchunks")],-1)),e[145]||(e[145]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[146]||(e[146]=l('
julia
setchunks(c::Dataset,chunks)
Resets the chunks of all or a subset YAXArrays in the dataset and returns a new Dataset. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savedataset on the resulting array. The chunks argument can take one of the following forms:
  • a NamedTuple or AbstractDict mapping from variable name to a description of the desired variable chunks
  • a NamedTuple or AbstractDict mapping from dimension name to a description of the desired variable chunks
  • a description of the desired variable chunks applied to all members of the Dataset
where a description of the desired variable chunks can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
',6))]),s("details",se,[s("summary",null,[e[147]||(e[147]=s("a",{id:"YAXArrays.Datasets.collectfromhandle-Tuple{Any, Any, Any}",href:"#YAXArrays.Datasets.collectfromhandle-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.collectfromhandle")],-1)),e[148]||(e[148]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[149]||(e[149]=s("p",null,"Extracts a YAXArray from a dataset handle that was just created from a arrayinfo",-1)),e[150]||(e[150]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L474-L476",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",te,[s("summary",null,[e[151]||(e[151]=s("a",{id:"YAXArrays.Datasets.createdataset-Tuple{Any, Any}",href:"#YAXArrays.Datasets.createdataset-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.createdataset")],-1)),e[152]||(e[152]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[153]||(e[153]=l('
function createdataset(DS::Type,axlist; kwargs...)
Creates a new dataset with axes specified in axlist. Each axis must be a subtype of CubeAxis. A new empty Zarr array will be created and can serve as a sink for mapCube operations.
Keyword arguments
  • path="" location where the new cube is stored
  • T=Union{Float32,Missing} data type of the target cube
  • chunksize = ntuple(i->length(axlist[i]),length(axlist)) chunk sizes of the array
  • chunkoffset = ntuple(i->0,length(axlist)) offsets of the chunks
  • persist::Bool=true shall the disk data be garbage-collected when the cube goes out of scope?
  • overwrite::Bool=false overwrite cube if it already exists
  • properties=Dict{String,Any}() additional cube properties
  • globalproperties=Dict{String,Any} global attributes to be added to the dataset
  • fillvalue= T>:Missing ? defaultfillval(Base.nonmissingtype(T)) : nothing fill value
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • layername="layer" Fallback name of the variable stored in the dataset if no datasetaxis is found
source
',6))]),s("details",ae,[s("summary",null,[e[154]||(e[154]=s("a",{id:"YAXArrays.Datasets.getarrayinfo-Tuple{Any, Any}",href:"#YAXArrays.Datasets.getarrayinfo-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.getarrayinfo")],-1)),e[155]||(e[155]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[156]||(e[156]=s("p",null,"Extract necessary information to create a YAXArrayBase dataset from a name and YAXArray pair",-1)),e[157]||(e[157]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L443-L445",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",ie,[s("summary",null,[e[158]||(e[158]=s("a",{id:"YAXArrays.Datasets.testrange-Tuple{Any}",href:"#YAXArrays.Datasets.testrange-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.testrange")],-1)),e[159]||(e[159]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[160]||(e[160]=s("p",null,"Test if data in x can be approximated by a step range",-1)),e[161]||(e[161]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L312",target:"_blank",rel:"noreferrer"},"source")],-1))])])}const he=n(d,[["render",le]]);export{ce as __pageData,he as default};
diff --git a/dev/assets/api.md.DI_7iOJZ.lean.js b/dev/assets/api.md.BNQXJsIs.lean.js
similarity index 52%
rename from dev/assets/api.md.DI_7iOJZ.lean.js
rename to dev/assets/api.md.BNQXJsIs.lean.js
index dc3ff000..1aa40477 100644
--- a/dev/assets/api.md.DI_7iOJZ.lean.js
+++ b/dev/assets/api.md.BNQXJsIs.lean.js
@@ -1,10 +1,10 @@
-import{_ as n,c as o,j as s,a,G as i,a2 as l,B as r,o as p}from"./chunks/framework.DgSLhxNl.js";const ce=JSON.parse('{"title":"API Reference","description":"","frontmatter":{},"headers":[],"relativePath":"api.md","filePath":"api.md","lastUpdated":null}'),d={name:"api.md"},u={class:"jldocstring custom-block",open:""},c={class:"jldocstring custom-block",open:""},h={class:"jldocstring custom-block",open:""},b={class:"jldocstring custom-block",open:""},y={class:"jldocstring custom-block",open:""},g={class:"jldocstring custom-block",open:""},A={class:"jldocstring custom-block",open:""},f={class:"jldocstring custom-block",open:""},k={class:"jldocstring custom-block",open:""},m={class:"jldocstring custom-block",open:""},j={class:"jldocstring custom-block",open:""},C={class:"jldocstring custom-block",open:""},D={class:"jldocstring custom-block",open:""},E={class:"jldocstring custom-block",open:""},T={class:"jldocstring custom-block",open:""},v={class:"jldocstring custom-block",open:""},X={class:"jldocstring custom-block",open:""},Y={class:"jldocstring custom-block",open:""},x={class:"jldocstring custom-block",open:""},F={class:"jldocstring custom-block",open:""},w={class:"jldocstring custom-block",open:""},L={class:"jldocstring custom-block",open:""},M={class:"jldocstring custom-block",open:""},O={class:"jldocstring custom-block",open:""},I={class:"jldocstring custom-block",open:""},B={class:"jldocstring custom-block",open:""},J={class:"jldocstring custom-block",open:""},P={class:"jldocstring custom-block",open:""},z={class:"jldocstring custom-block",open:""},N={class:"jldocstring custom-block",open:""},S={class:"jldocstring custom-block",open:""},q={class:"jldocstring custom-block",open:""},V={class:"jldocstring custom-block",open:""},G={class:"jldocstring custom-block",open:""},R={class:"jldocstring custom-block",open:""},W={class:"jldocstring custom-block",open:""},U={class:"jldocstring custom-block",open:""},$={class:"jldocstring custom-block",open:""},H={class:"jldocstring custom-block",open:""},K={class:"jldocstring custom-block",open:""},Z={class:"jldocstring custom-block",open:""},Q={class:"jldocstring custom-block",open:""},_={class:"jldocstring custom-block",open:""},ee={class:"jldocstring custom-block",open:""},se={class:"jldocstring custom-block",open:""},ae={class:"jldocstring custom-block",open:""},te={class:"jldocstring custom-block",open:""},ie={class:"jldocstring custom-block",open:""};function le(ne,e,oe,re,pe,de){const t=r("Badge");return p(),o("div",null,[e[162]||(e[162]=s("h1",{id:"API-Reference",tabindex:"-1"},[a("API Reference "),s("a",{class:"header-anchor",href:"#API-Reference","aria-label":'Permalink to "API Reference {#API-Reference}"'},"​")],-1)),e[163]||(e[163]=s("p",null,"This section describes all available functions of this package.",-1)),e[164]||(e[164]=s("h2",{id:"Public-API",tabindex:"-1"},[a("Public API "),s("a",{class:"header-anchor",href:"#Public-API","aria-label":'Permalink to "Public API {#Public-API}"'},"​")],-1)),s("details",u,[s("summary",null,[e[0]||(e[0]=s("a",{id:"YAXArrays.getAxis-Tuple{Any, Any}",href:"#YAXArrays.getAxis-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.getAxis")],-1)),e[1]||(e[1]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[2]||(e[2]=l('
julia
getAxis(desc, c)
Given an Axis description and a cube, returns the corresponding axis of the cube. The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
',4))]),s("details",c,[s("summary",null,[e[3]||(e[3]=s("a",{id:"YAXArrays.Cubes",href:"#YAXArrays.Cubes"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes")],-1)),e[4]||(e[4]=a()),i(t,{type:"info",class:"jlObjectType jlModule",text:"Module"})]),e[5]||(e[5]=s("p",null,"The functions provided by YAXArrays are supposed to work on different types of cubes. This module defines the interface for all Data types that",-1)),e[6]||(e[6]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/Cubes/Cubes.jl#L1-L4",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",h,[s("summary",null,[e[7]||(e[7]=s("a",{id:"YAXArrays.Cubes.YAXArray",href:"#YAXArrays.Cubes.YAXArray"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.YAXArray")],-1)),e[8]||(e[8]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[9]||(e[9]=l('
julia
YAXArray{T,N}
An array labelled with named axes that have values associated with them. It can wrap normal arrays or, more typically DiskArrays.
Fields
  • axes: Tuple of Dimensions containing the Axes of the Cube
  • data: length(axes)-dimensional array which holds the data, this can be a lazy DiskArray
  • properties: Metadata properties describing the content of the data
  • chunks: Representation of the chunking of the data
  • cleaner: Cleaner objects to track which objects to tidy up when the YAXArray goes out of scope
source
',5))]),s("details",b,[s("summary",null,[e[10]||(e[10]=s("a",{id:"YAXArrays.Cubes.caxes",href:"#YAXArrays.Cubes.caxes"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.caxes")],-1)),e[11]||(e[11]=a()),i(t,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),e[12]||(e[12]=s("p",null,"Returns the axes of a Cube",-1)),e[13]||(e[13]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/Cubes/Cubes.jl#L27",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",y,[s("summary",null,[e[14]||(e[14]=s("a",{id:"YAXArrays.Cubes.caxes-Tuple{DimensionalData.Dimensions.Dimension}",href:"#YAXArrays.Cubes.caxes-Tuple{DimensionalData.Dimensions.Dimension}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.caxes")],-1)),e[15]||(e[15]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[16]||(e[16]=l('
julia
caxes
Embeds Cube inside a new Cube
source
',3))]),s("details",g,[s("summary",null,[e[17]||(e[17]=s("a",{id:"YAXArrays.Cubes.concatenatecubes-Tuple{Any, DimensionalData.Dimensions.Dimension}",href:"#YAXArrays.Cubes.concatenatecubes-Tuple{Any, DimensionalData.Dimensions.Dimension}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.concatenatecubes")],-1)),e[18]||(e[18]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[19]||(e[19]=l('
julia
function concatenateCubes(cubelist, cataxis::CategoricalAxis)
Concatenates a vector of datacubes that have identical axes to a new single cube along the new axis cataxis
source
',3))]),s("details",A,[s("summary",null,[e[20]||(e[20]=s("a",{id:"YAXArrays.Cubes.readcubedata-Tuple{Any}",href:"#YAXArrays.Cubes.readcubedata-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.readcubedata")],-1)),e[21]||(e[21]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[22]||(e[22]=l('
julia
readcubedata(cube)
Given any array implementing the YAXArray interface it returns an in-memory YAXArray from it.
source
',3))]),s("details",f,[s("summary",null,[e[23]||(e[23]=s("a",{id:"YAXArrays.Cubes.setchunks-Tuple{YAXArray, Any}",href:"#YAXArrays.Cubes.setchunks-Tuple{YAXArray, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.setchunks")],-1)),e[24]||(e[24]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[25]||(e[25]=l('
julia
setchunks(c::YAXArray,chunks)
Resets the chunks of a YAXArray and returns a new YAXArray. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savecube on the resulting array. The chunks argument can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
',4))]),s("details",k,[s("summary",null,[e[26]||(e[26]=s("a",{id:"YAXArrays.Cubes.subsetcube",href:"#YAXArrays.Cubes.subsetcube"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.subsetcube")],-1)),e[27]||(e[27]=a()),i(t,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),e[28]||(e[28]=s("p",null,"This function calculates a subset of a cube's data",-1)),e[29]||(e[29]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/Cubes/Cubes.jl#L22-L24",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",m,[s("summary",null,[e[30]||(e[30]=s("a",{id:"YAXArrays.DAT.InDims",href:"#YAXArrays.DAT.InDims"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.InDims")],-1)),e[31]||(e[31]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[32]||(e[32]=l('
julia
InDims(axisdesc...;...)
Creates a description of an Input Data Cube for cube operations. Takes a single or multiple axis descriptions as first arguments. Alternatively a MovingWindow(@ref) struct can be passed to include neighbour slices of one or more axes in the computation. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
Keyword arguments
  • artype how shall the array be represented in the inner function. Defaults to Array, alternatives are DataFrame or AsAxisArray
  • filter define some filter to skip the computation, e.g. when all values are missing. Defaults to AllMissing(), possible values are AnyMissing(), AnyOcean(), StdZero(), NValid(n) (for at least n non-missing elements). It is also possible to provide a custom one-argument function that takes the array and returns true if the compuation shall be skipped and false otherwise.
  • window_oob_value if one of the input dimensions is a MowingWindow, this value will be used to fill out-of-bounds areas
source
',5))]),s("details",j,[s("summary",null,[e[33]||(e[33]=s("a",{id:"YAXArrays.DAT.MovingWindow",href:"#YAXArrays.DAT.MovingWindow"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.MovingWindow")],-1)),e[34]||(e[34]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[35]||(e[35]=l('
julia
MovingWindow(desc, pre, after)
Constructs a MovingWindow object to be passed to an InDims constructor to define that the axis in desc shall participate in the inner function (i.e. shall be looped over), but inside the inner function pre values before and after values after the center value will be passed as well.
For example passing MovingWindow("Time", 2, 0) will loop over the time axis and always pass the current time step plus the 2 previous steps. So in the inner function the array will have an additional dimension of size 3.
source
',4))]),s("details",C,[s("summary",null,[e[36]||(e[36]=s("a",{id:"YAXArrays.DAT.OutDims-Tuple",href:"#YAXArrays.DAT.OutDims-Tuple"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.OutDims")],-1)),e[37]||(e[37]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[38]||(e[38]=l('
julia
OutDims(axisdesc;...)
Creates a description of an Output Data Cube for cube operations. Takes a single or a Vector/Tuple of axes as first argument. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
  • axisdesc: List of input axis names
  • backend : specifies the dataset backend to write data to, must be either :auto or a key in YAXArrayBase.backendlist
  • update : specifies wether the function operates inplace or if an output is returned
  • artype : specifies the Array type inside the inner function that is mapped over
  • chunksize: A Dict specifying the chunksizes for the output dimensions of the cube, or :input to copy chunksizes from input cube axes or :max to not chunk the inner dimensions
  • outtype: force the output type to a specific type, defaults to Any which means that the element type of the first input cube is used
source
',4))]),s("details",D,[s("summary",null,[e[39]||(e[39]=s("a",{id:"YAXArrays.DAT.CubeTable-Tuple{}",href:"#YAXArrays.DAT.CubeTable-Tuple{}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.CubeTable")],-1)),e[40]||(e[40]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[41]||(e[41]=l('
julia
CubeTable()
Function to turn a DataCube object into an iterable table. Takes a list of as arguments, specified as a name=cube expression. For example CubeTable(data=cube1,country=cube2) would generate a Table with the entries data and country, where data contains the values of cube1 and country the values of cube2. The cubes are matched and broadcasted along their axes like in mapCube.
source
',3))]),s("details",E,[s("summary",null,[e[42]||(e[42]=s("a",{id:"YAXArrays.DAT.cubefittable-Tuple{Any, Any, Any}",href:"#YAXArrays.DAT.cubefittable-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.cubefittable")],-1)),e[43]||(e[43]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[44]||(e[44]=l('
julia
cubefittable(tab,o,fitsym;post=getpostfunction(o),kwargs...)
Executes fittable on the CubeTable tab with the (Weighted-)OnlineStat o, looping through the values specified by fitsym. Finally, writes the results from the TableAggregator to an output data cube.
source
',3))]),s("details",T,[s("summary",null,[e[45]||(e[45]=s("a",{id:"YAXArrays.DAT.fittable-Tuple{YAXArrays.DAT.CubeIterator, Any, Any}",href:"#YAXArrays.DAT.fittable-Tuple{YAXArrays.DAT.CubeIterator, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.fittable")],-1)),e[46]||(e[46]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[47]||(e[47]=l('
julia
fittable(tab,o,fitsym;by=(),weight=nothing)
Loops through an iterable table tab and thereby fitting an OnlineStat o with the values specified through fitsym. Optionally one can specify a field (or tuple) to group by. Any groupby specifier can either be a symbol denoting the entry to group by or an anynymous function calculating the group from a table row.
For example the following would caluclate a weighted mean over a cube weighted by grid cell area and grouped by country and month:
julia
fittable(iter,WeightedMean,:tair,weight=(i->abs(cosd(i.lat))),by=(i->month(i.time),:country))
source
',5))]),s("details",v,[s("summary",null,[e[48]||(e[48]=s("a",{id:"YAXArrays.DAT.mapCube-Tuple{Function, Dataset, Vararg{Any}}",href:"#YAXArrays.DAT.mapCube-Tuple{Function, Dataset, Vararg{Any}}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.mapCube")],-1)),e[49]||(e[49]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[50]||(e[50]=l(`
julia
mapCube(fun, cube, addargs...;kwargs...)
+import{_ as n,c as o,j as s,a as t,G as i,a2 as l,B as r,o as p}from"./chunks/framework.DgSLhxNl.js";const ce=JSON.parse('{"title":"API Reference","description":"","frontmatter":{},"headers":[],"relativePath":"api.md","filePath":"api.md","lastUpdated":null}'),d={name:"api.md"},u={class:"jldocstring custom-block",open:""},c={class:"jldocstring custom-block",open:""},h={class:"jldocstring custom-block",open:""},b={class:"jldocstring custom-block",open:""},y={class:"jldocstring custom-block",open:""},g={class:"jldocstring custom-block",open:""},A={class:"jldocstring custom-block",open:""},k={class:"jldocstring custom-block",open:""},f={class:"jldocstring custom-block",open:""},m={class:"jldocstring custom-block",open:""},j={class:"jldocstring custom-block",open:""},C={class:"jldocstring custom-block",open:""},D={class:"jldocstring custom-block",open:""},E={class:"jldocstring custom-block",open:""},T={class:"jldocstring custom-block",open:""},v={class:"jldocstring custom-block",open:""},X={class:"jldocstring custom-block",open:""},Y={class:"jldocstring custom-block",open:""},x={class:"jldocstring custom-block",open:""},F={class:"jldocstring custom-block",open:""},w={class:"jldocstring custom-block",open:""},L={class:"jldocstring custom-block",open:""},M={class:"jldocstring custom-block",open:""},O={class:"jldocstring custom-block",open:""},I={class:"jldocstring custom-block",open:""},B={class:"jldocstring custom-block",open:""},J={class:"jldocstring custom-block",open:""},P={class:"jldocstring custom-block",open:""},z={class:"jldocstring custom-block",open:""},N={class:"jldocstring custom-block",open:""},S={class:"jldocstring custom-block",open:""},q={class:"jldocstring custom-block",open:""},V={class:"jldocstring custom-block",open:""},G={class:"jldocstring custom-block",open:""},R={class:"jldocstring custom-block",open:""},W={class:"jldocstring custom-block",open:""},U={class:"jldocstring custom-block",open:""},$={class:"jldocstring custom-block",open:""},H={class:"jldocstring custom-block",open:""},K={class:"jldocstring custom-block",open:""},Z={class:"jldocstring custom-block",open:""},Q={class:"jldocstring custom-block",open:""},_={class:"jldocstring custom-block",open:""},ee={class:"jldocstring custom-block",open:""},se={class:"jldocstring custom-block",open:""},te={class:"jldocstring custom-block",open:""},ae={class:"jldocstring custom-block",open:""},ie={class:"jldocstring custom-block",open:""};function le(ne,e,oe,re,pe,de){const a=r("Badge");return p(),o("div",null,[e[162]||(e[162]=s("h1",{id:"API-Reference",tabindex:"-1"},[t("API Reference "),s("a",{class:"header-anchor",href:"#API-Reference","aria-label":'Permalink to "API Reference {#API-Reference}"'},"​")],-1)),e[163]||(e[163]=s("p",null,"This section describes all available functions of this package.",-1)),e[164]||(e[164]=s("h2",{id:"Public-API",tabindex:"-1"},[t("Public API "),s("a",{class:"header-anchor",href:"#Public-API","aria-label":'Permalink to "Public API {#Public-API}"'},"​")],-1)),s("details",u,[s("summary",null,[e[0]||(e[0]=s("a",{id:"YAXArrays.getAxis-Tuple{Any, Any}",href:"#YAXArrays.getAxis-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.getAxis")],-1)),e[1]||(e[1]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[2]||(e[2]=l('
julia
getAxis(desc, c)
Given an Axis description and a cube, returns the corresponding axis of the cube. The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
',4))]),s("details",c,[s("summary",null,[e[3]||(e[3]=s("a",{id:"YAXArrays.Cubes",href:"#YAXArrays.Cubes"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes")],-1)),e[4]||(e[4]=t()),i(a,{type:"info",class:"jlObjectType jlModule",text:"Module"})]),e[5]||(e[5]=s("p",null,"The functions provided by YAXArrays are supposed to work on different types of cubes. This module defines the interface for all Data types that",-1)),e[6]||(e[6]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/Cubes/Cubes.jl#L1-L4",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",h,[s("summary",null,[e[7]||(e[7]=s("a",{id:"YAXArrays.Cubes.YAXArray",href:"#YAXArrays.Cubes.YAXArray"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.YAXArray")],-1)),e[8]||(e[8]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[9]||(e[9]=l('
julia
YAXArray{T,N}
An array labelled with named axes that have values associated with them. It can wrap normal arrays or, more typically DiskArrays.
Fields
  • axes: Tuple of Dimensions containing the Axes of the Cube
  • data: length(axes)-dimensional array which holds the data, this can be a lazy DiskArray
  • properties: Metadata properties describing the content of the data
  • chunks: Representation of the chunking of the data
  • cleaner: Cleaner objects to track which objects to tidy up when the YAXArray goes out of scope
source
',5))]),s("details",b,[s("summary",null,[e[10]||(e[10]=s("a",{id:"YAXArrays.Cubes.caxes",href:"#YAXArrays.Cubes.caxes"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.caxes")],-1)),e[11]||(e[11]=t()),i(a,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),e[12]||(e[12]=s("p",null,"Returns the axes of a Cube",-1)),e[13]||(e[13]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/Cubes/Cubes.jl#L27",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",y,[s("summary",null,[e[14]||(e[14]=s("a",{id:"YAXArrays.Cubes.caxes-Tuple{DimensionalData.Dimensions.Dimension}",href:"#YAXArrays.Cubes.caxes-Tuple{DimensionalData.Dimensions.Dimension}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.caxes")],-1)),e[15]||(e[15]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[16]||(e[16]=l('
julia
caxes
Embeds Cube inside a new Cube
source
',3))]),s("details",g,[s("summary",null,[e[17]||(e[17]=s("a",{id:"YAXArrays.Cubes.concatenatecubes-Tuple{Any, DimensionalData.Dimensions.Dimension}",href:"#YAXArrays.Cubes.concatenatecubes-Tuple{Any, DimensionalData.Dimensions.Dimension}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.concatenatecubes")],-1)),e[18]||(e[18]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[19]||(e[19]=l('
julia
function concatenateCubes(cubelist, cataxis::CategoricalAxis)
Concatenates a vector of datacubes that have identical axes to a new single cube along the new axis cataxis
source
',3))]),s("details",A,[s("summary",null,[e[20]||(e[20]=s("a",{id:"YAXArrays.Cubes.readcubedata-Tuple{Any}",href:"#YAXArrays.Cubes.readcubedata-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.readcubedata")],-1)),e[21]||(e[21]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[22]||(e[22]=l('
julia
readcubedata(cube)
Given any array implementing the YAXArray interface it returns an in-memory YAXArray from it.
source
',3))]),s("details",k,[s("summary",null,[e[23]||(e[23]=s("a",{id:"YAXArrays.Cubes.setchunks-Tuple{YAXArray, Any}",href:"#YAXArrays.Cubes.setchunks-Tuple{YAXArray, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.setchunks")],-1)),e[24]||(e[24]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[25]||(e[25]=l('
julia
setchunks(c::YAXArray,chunks)
Resets the chunks of a YAXArray and returns a new YAXArray. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savecube on the resulting array. The chunks argument can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
',4))]),s("details",f,[s("summary",null,[e[26]||(e[26]=s("a",{id:"YAXArrays.Cubes.subsetcube",href:"#YAXArrays.Cubes.subsetcube"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.subsetcube")],-1)),e[27]||(e[27]=t()),i(a,{type:"info",class:"jlObjectType jlFunction",text:"Function"})]),e[28]||(e[28]=s("p",null,"This function calculates a subset of a cube's data",-1)),e[29]||(e[29]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/Cubes/Cubes.jl#L22-L24",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",m,[s("summary",null,[e[30]||(e[30]=s("a",{id:"YAXArrays.DAT.InDims",href:"#YAXArrays.DAT.InDims"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.InDims")],-1)),e[31]||(e[31]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[32]||(e[32]=l('
julia
InDims(axisdesc...;...)
Creates a description of an Input Data Cube for cube operations. Takes a single or multiple axis descriptions as first arguments. Alternatively a MovingWindow(@ref) struct can be passed to include neighbour slices of one or more axes in the computation. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
Keyword arguments
  • artype how shall the array be represented in the inner function. Defaults to Array, alternatives are DataFrame or AsAxisArray
  • filter define some filter to skip the computation, e.g. when all values are missing. Defaults to AllMissing(), possible values are AnyMissing(), AnyOcean(), StdZero(), NValid(n) (for at least n non-missing elements). It is also possible to provide a custom one-argument function that takes the array and returns true if the compuation shall be skipped and false otherwise.
  • window_oob_value if one of the input dimensions is a MowingWindow, this value will be used to fill out-of-bounds areas
source
',5))]),s("details",j,[s("summary",null,[e[33]||(e[33]=s("a",{id:"YAXArrays.DAT.MovingWindow",href:"#YAXArrays.DAT.MovingWindow"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.MovingWindow")],-1)),e[34]||(e[34]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[35]||(e[35]=l('
julia
MovingWindow(desc, pre, after)
Constructs a MovingWindow object to be passed to an InDims constructor to define that the axis in desc shall participate in the inner function (i.e. shall be looped over), but inside the inner function pre values before and after values after the center value will be passed as well.
For example passing MovingWindow("Time", 2, 0) will loop over the time axis and always pass the current time step plus the 2 previous steps. So in the inner function the array will have an additional dimension of size 3.
source
',4))]),s("details",C,[s("summary",null,[e[36]||(e[36]=s("a",{id:"YAXArrays.DAT.OutDims-Tuple",href:"#YAXArrays.DAT.OutDims-Tuple"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.OutDims")],-1)),e[37]||(e[37]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[38]||(e[38]=l('
julia
OutDims(axisdesc;...)
Creates a description of an Output Data Cube for cube operations. Takes a single or a Vector/Tuple of axes as first argument. Axes can be specified by their name (String), through an Axis type, or by passing a concrete axis.
  • axisdesc: List of input axis names
  • backend : specifies the dataset backend to write data to, must be either :auto or a key in YAXArrayBase.backendlist
  • update : specifies wether the function operates inplace or if an output is returned
  • artype : specifies the Array type inside the inner function that is mapped over
  • chunksize: A Dict specifying the chunksizes for the output dimensions of the cube, or :input to copy chunksizes from input cube axes or :max to not chunk the inner dimensions
  • outtype: force the output type to a specific type, defaults to Any which means that the element type of the first input cube is used
source
',4))]),s("details",D,[s("summary",null,[e[39]||(e[39]=s("a",{id:"YAXArrays.DAT.CubeTable-Tuple{}",href:"#YAXArrays.DAT.CubeTable-Tuple{}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.CubeTable")],-1)),e[40]||(e[40]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[41]||(e[41]=l('
julia
CubeTable()
Function to turn a DataCube object into an iterable table. Takes a list of as arguments, specified as a name=cube expression. For example CubeTable(data=cube1,country=cube2) would generate a Table with the entries data and country, where data contains the values of cube1 and country the values of cube2. The cubes are matched and broadcasted along their axes like in mapCube.
source
',3))]),s("details",E,[s("summary",null,[e[42]||(e[42]=s("a",{id:"YAXArrays.DAT.cubefittable-Tuple{Any, Any, Any}",href:"#YAXArrays.DAT.cubefittable-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.cubefittable")],-1)),e[43]||(e[43]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[44]||(e[44]=l('
julia
cubefittable(tab,o,fitsym;post=getpostfunction(o),kwargs...)
Executes fittable on the CubeTable tab with the (Weighted-)OnlineStat o, looping through the values specified by fitsym. Finally, writes the results from the TableAggregator to an output data cube.
source
',3))]),s("details",T,[s("summary",null,[e[45]||(e[45]=s("a",{id:"YAXArrays.DAT.fittable-Tuple{YAXArrays.DAT.CubeIterator, Any, Any}",href:"#YAXArrays.DAT.fittable-Tuple{YAXArrays.DAT.CubeIterator, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.fittable")],-1)),e[46]||(e[46]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[47]||(e[47]=l('
julia
fittable(tab,o,fitsym;by=(),weight=nothing)
Loops through an iterable table tab and thereby fitting an OnlineStat o with the values specified through fitsym. Optionally one can specify a field (or tuple) to group by. Any groupby specifier can either be a symbol denoting the entry to group by or an anynymous function calculating the group from a table row.
For example the following would caluclate a weighted mean over a cube weighted by grid cell area and grouped by country and month:
julia
fittable(iter,WeightedMean,:tair,weight=(i->abs(cosd(i.lat))),by=(i->month(i.time),:country))
source
',5))]),s("details",v,[s("summary",null,[e[48]||(e[48]=s("a",{id:"YAXArrays.DAT.mapCube-Tuple{Function, Dataset, Vararg{Any}}",href:"#YAXArrays.DAT.mapCube-Tuple{Function, Dataset, Vararg{Any}}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.mapCube")],-1)),e[49]||(e[49]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[50]||(e[50]=l(`
julia
mapCube(fun, cube, addargs...;kwargs...)
 
 Map a given function \`fun\` over slices of all cubes of the dataset \`ds\`. 
 Use InDims to discribe the input dimensions and OutDims to describe the output dimensions of the function.
 For Datasets, only one output cube can be specified.
 In contrast to the mapCube function for cubes, additional arguments for the inner function should be set as keyword arguments.
 
-For the specific keyword arguments see the docstring of the mapCube function for cubes.
source
`,2))]),s("details",X,[s("summary",null,[e[51]||(e[51]=s("a",{id:"YAXArrays.DAT.mapCube-Tuple{Function, Tuple, Vararg{Any}}",href:"#YAXArrays.DAT.mapCube-Tuple{Function, Tuple, Vararg{Any}}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.mapCube")],-1)),e[52]||(e[52]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[53]||(e[53]=l('
julia
mapCube(fun, cube, addargs...;kwargs...)
Map a given function fun over slices of the data cube cube. The additional arguments addargs will be forwarded to the inner function fun. Use InDims to discribe the input dimensions and OutDims to describe the output dimensions of the function.
Keyword arguments
  • max_cache=YAXDefaults.max_cache Float64 maximum size of blocks that are read into memory in bits e.g. max_cache=5.0e8. Or String. e.g. max_cache="10MB" ormax_cache=1GB``` defaults to approx 10Mb.
  • indims::InDims List of input cube descriptors of type InDims for each input data cube.
  • outdims::OutDims List of output cube descriptors of type OutDims for each output cube.
  • inplace does the function write to an output array inplace or return a single value> defaults to true
  • ispar boolean to determine if parallelisation should be applied, defaults to true if workers are available.
  • showprog boolean indicating if a ProgressMeter shall be shown
  • include_loopvars boolean to indicate if the varoables looped over should be added as function arguments
  • nthreads number of threads for the computation, defaults to Threads.nthreads for every worker.
  • loopchunksize determines the chunk sizes of variables which are looped over, a dict
  • kwargs additional keyword arguments are passed to the inner function
The first argument is always the function to be applied, the second is the input cube or a tuple of input cubes if needed.
source
',6))]),s("details",Y,[s("summary",null,[e[54]||(e[54]=s("a",{id:"YAXArrays.Datasets.Dataset",href:"#YAXArrays.Datasets.Dataset"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Dataset")],-1)),e[55]||(e[55]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[56]||(e[56]=l('
julia
Dataset object which stores an `OrderedDict` of YAXArrays with Symbol keys.\na dictionary of CubeAxes and a Dictionary of general properties.\nA dictionary can hold cubes with differing axes. But it will share the common axes between the subcubes.
source
',2))]),s("details",x,[s("summary",null,[e[57]||(e[57]=s("a",{id:"YAXArrays.Datasets.Dataset-Tuple{}",href:"#YAXArrays.Datasets.Dataset-Tuple{}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Dataset")],-1)),e[58]||(e[58]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[59]||(e[59]=s("p",null,"Dataset(; properties = Dict{String,Any}, cubes...)",-1)),e[60]||(e[60]=s("p",null,[a("Construct a YAXArray Dataset with global attributes "),s("code",null,"properties"),a(" a and a list of named YAXArrays cubes...")],-1)),e[61]||(e[61]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L28-L32",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",F,[s("summary",null,[e[62]||(e[62]=s("a",{id:"YAXArrays.Datasets.Cube-Tuple{Dataset}",href:"#YAXArrays.Datasets.Cube-Tuple{Dataset}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Cube")],-1)),e[63]||(e[63]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[64]||(e[64]=l('
julia
Cube(ds::Dataset; joinname="Variable")
Construct a single YAXArray from the dataset ds by concatenating the cubes in the datset on the joinname dimension.
source
',3))]),s("details",w,[s("summary",null,[e[65]||(e[65]=s("a",{id:"YAXArrays.Datasets.open_dataset-Tuple{Any}",href:"#YAXArrays.Datasets.open_dataset-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.open_dataset")],-1)),e[66]||(e[66]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[67]||(e[67]=s("p",null,"open_dataset(g; driver=:all)",-1)),e[68]||(e[68]=s("p",null,[a("Open the dataset at "),s("code",null,"g"),a(" with the given "),s("code",null,"driver"),a(". The default driver will search for available drivers and tries to detect the useable driver from the filename extension.")],-1)),e[69]||(e[69]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L340-L345",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",L,[s("summary",null,[e[70]||(e[70]=s("a",{id:"YAXArrays.Datasets.savecube-Tuple{Any, AbstractString}",href:"#YAXArrays.Datasets.savecube-Tuple{Any, AbstractString}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.savecube")],-1)),e[71]||(e[71]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[72]||(e[72]=l('
julia
savecube(cube,name::String)
Save a YAXArray to the path.
Extended Help
The keyword arguments are:
  • name:
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • max_cache: The number of bits that are used as cache for the data handling.
  • backend: The backend, that is used to save the data. Falls back to searching the backend according to the extension of the path.
  • driver: The same setting as backend.
  • overwrite::Bool=false overwrite cube if it already exists
source
',6))]),s("details",M,[s("summary",null,[e[73]||(e[73]=s("a",{id:"YAXArrays.Datasets.savedataset-Tuple{Dataset}",href:"#YAXArrays.Datasets.savedataset-Tuple{Dataset}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.savedataset")],-1)),e[74]||(e[74]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[75]||(e[75]=s("p",null,'savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)',-1)),e[76]||(e[76]=s("p",null,[a("Saves a Dataset into a file at "),s("code",null,"path"),a(" with the format given by "),s("code",null,"driver"),a(", i.e., driver=:netcdf or driver=:zarr.")],-1)),e[77]||(e[77]=s("div",{class:"warning custom-block"},[s("p",{class:"custom-block-title"},"Warning"),s("p",null,"overwrite = true, deletes ALL your data and it will create a new file.")],-1)),e[78]||(e[78]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L567-L576",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",O,[s("summary",null,[e[79]||(e[79]=s("a",{id:"YAXArrays.Datasets.to_dataset-Tuple{Any}",href:"#YAXArrays.Datasets.to_dataset-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.to_dataset")],-1)),e[80]||(e[80]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[81]||(e[81]=s("p",null,'to_dataset(c;datasetaxis = "Variable", layername = "layer")',-1)),e[82]||(e[82]=s("p",null,[a(`Convert a Data Cube into a Dataset. It is possible to treat one of the Cube's axes as a "DatasetAxis" i.e. the cube will be split into different parts that become variables in the Dataset. If no such axis is specified or found, there will only be a single variable in the dataset with the name `),s("code",null,"layername")],-1)),e[83]||(e[83]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L45-L53",target:"_blank",rel:"noreferrer"},"source")],-1))]),e[165]||(e[165]=s("h2",{id:"Internal-API",tabindex:"-1"},[a("Internal API "),s("a",{class:"header-anchor",href:"#Internal-API","aria-label":'Permalink to "Internal API {#Internal-API}"'},"​")],-1)),s("details",I,[s("summary",null,[e[84]||(e[84]=s("a",{id:"YAXArrays.YAXDefaults",href:"#YAXArrays.YAXDefaults"},[s("span",{class:"jlbinding"},"YAXArrays.YAXDefaults")],-1)),e[85]||(e[85]=a()),i(t,{type:"info",class:"jlObjectType jlConstant",text:"Constant"})]),e[86]||(e[86]=l('
Default configuration for YAXArrays, has the following fields:
  • workdir[]::String = "./" The default location for temporary cubes.
  • recal[]::Bool = false set to true if you want @loadOrGenerate to always recalculate the results.
  • chunksize[]::Any = :input Set the default output chunksize.
  • max_cache[]::Float64 = 1e8 The maximum cache used by mapCube.
  • cubedir[]::"" the default location for Cube() without an argument.
  • subsetextensions::Array{Any} = [] List of registered functions, that convert subsetting input into dimension boundaries.
source
',3))]),s("details",B,[s("summary",null,[e[87]||(e[87]=s("a",{id:"YAXArrays.findAxis-Tuple{Any, Any}",href:"#YAXArrays.findAxis-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.findAxis")],-1)),e[88]||(e[88]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[89]||(e[89]=l('
julia
findAxis(desc, c)
Internal function
Extended Help
Given an Axis description and a cube return the index of the Axis.
The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
',7))]),s("details",J,[s("summary",null,[e[90]||(e[90]=s("a",{id:"YAXArrays.getOutAxis-NTuple{5, Any}",href:"#YAXArrays.getOutAxis-NTuple{5, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.getOutAxis")],-1)),e[91]||(e[91]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[92]||(e[92]=l('
julia
getOutAxis
source
',2))]),s("details",P,[s("summary",null,[e[93]||(e[93]=s("a",{id:"YAXArrays.get_descriptor-Tuple{String}",href:"#YAXArrays.get_descriptor-Tuple{String}"},[s("span",{class:"jlbinding"},"YAXArrays.get_descriptor")],-1)),e[94]||(e[94]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[95]||(e[95]=l('
julia
get_descriptor(a)
Get the descriptor of an Axis. This is used to dispatch on the descriptor.
source
',3))]),s("details",z,[s("summary",null,[e[96]||(e[96]=s("a",{id:"YAXArrays.match_axis-Tuple{YAXArrays.ByName, Any}",href:"#YAXArrays.match_axis-Tuple{YAXArrays.ByName, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.match_axis")],-1)),e[97]||(e[97]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[98]||(e[98]=l(`
julia
match_axis
Internal function
Extended Help
Match the Axis based on the AxisDescriptor.
+For the specific keyword arguments see the docstring of the mapCube function for cubes.
source
`,2))]),s("details",X,[s("summary",null,[e[51]||(e[51]=s("a",{id:"YAXArrays.DAT.mapCube-Tuple{Function, Tuple, Vararg{Any}}",href:"#YAXArrays.DAT.mapCube-Tuple{Function, Tuple, Vararg{Any}}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.mapCube")],-1)),e[52]||(e[52]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[53]||(e[53]=l('
julia
mapCube(fun, cube, addargs...;kwargs...)
Map a given function fun over slices of the data cube cube. The additional arguments addargs will be forwarded to the inner function fun. Use InDims to discribe the input dimensions and OutDims to describe the output dimensions of the function.
Keyword arguments
  • max_cache=YAXDefaults.max_cache Float64 maximum size of blocks that are read into memory in bits e.g. max_cache=5.0e8. Or String. e.g. max_cache="10MB" ormax_cache=1GB``` defaults to approx 10Mb.
  • indims::InDims List of input cube descriptors of type InDims for each input data cube.
  • outdims::OutDims List of output cube descriptors of type OutDims for each output cube.
  • inplace does the function write to an output array inplace or return a single value> defaults to true
  • ispar boolean to determine if parallelisation should be applied, defaults to true if workers are available.
  • showprog boolean indicating if a ProgressMeter shall be shown
  • include_loopvars boolean to indicate if the varoables looped over should be added as function arguments
  • nthreads number of threads for the computation, defaults to Threads.nthreads for every worker.
  • loopchunksize determines the chunk sizes of variables which are looped over, a dict
  • kwargs additional keyword arguments are passed to the inner function
The first argument is always the function to be applied, the second is the input cube or a tuple of input cubes if needed.
source
',6))]),s("details",Y,[s("summary",null,[e[54]||(e[54]=s("a",{id:"YAXArrays.Datasets.Dataset",href:"#YAXArrays.Datasets.Dataset"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Dataset")],-1)),e[55]||(e[55]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[56]||(e[56]=l('
julia
Dataset object which stores an `OrderedDict` of YAXArrays with Symbol keys.\na dictionary of CubeAxes and a Dictionary of general properties.\nA dictionary can hold cubes with differing axes. But it will share the common axes between the subcubes.
source
',2))]),s("details",x,[s("summary",null,[e[57]||(e[57]=s("a",{id:"YAXArrays.Datasets.Dataset-Tuple{}",href:"#YAXArrays.Datasets.Dataset-Tuple{}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Dataset")],-1)),e[58]||(e[58]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[59]||(e[59]=s("p",null,"Dataset(; properties = Dict{String,Any}, cubes...)",-1)),e[60]||(e[60]=s("p",null,[t("Construct a YAXArray Dataset with global attributes "),s("code",null,"properties"),t(" a and a list of named YAXArrays cubes...")],-1)),e[61]||(e[61]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L28-L32",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",F,[s("summary",null,[e[62]||(e[62]=s("a",{id:"YAXArrays.Datasets.Cube-Tuple{Dataset}",href:"#YAXArrays.Datasets.Cube-Tuple{Dataset}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.Cube")],-1)),e[63]||(e[63]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[64]||(e[64]=l('
julia
Cube(ds::Dataset; joinname="Variable")
Construct a single YAXArray from the dataset ds by concatenating the cubes in the datset on the joinname dimension.
source
',3))]),s("details",w,[s("summary",null,[e[65]||(e[65]=s("a",{id:"YAXArrays.Datasets.open_dataset-Tuple{Any}",href:"#YAXArrays.Datasets.open_dataset-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.open_dataset")],-1)),e[66]||(e[66]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[67]||(e[67]=s("p",null,"open_dataset(g; driver=:all)",-1)),e[68]||(e[68]=s("p",null,[t("Open the dataset at "),s("code",null,"g"),t(" with the given "),s("code",null,"driver"),t(". The default driver will search for available drivers and tries to detect the useable driver from the filename extension.")],-1)),e[69]||(e[69]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L341-L346",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",L,[s("summary",null,[e[70]||(e[70]=s("a",{id:"YAXArrays.Datasets.savecube-Tuple{Any, AbstractString}",href:"#YAXArrays.Datasets.savecube-Tuple{Any, AbstractString}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.savecube")],-1)),e[71]||(e[71]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[72]||(e[72]=l('
julia
savecube(cube,name::String)
Save a YAXArray to the path.
Extended Help
The keyword arguments are:
  • name:
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • max_cache: The number of bits that are used as cache for the data handling.
  • backend: The backend, that is used to save the data. Falls back to searching the backend according to the extension of the path.
  • driver: The same setting as backend.
  • overwrite::Bool=false overwrite cube if it already exists
source
',6))]),s("details",M,[s("summary",null,[e[73]||(e[73]=s("a",{id:"YAXArrays.Datasets.savedataset-Tuple{Dataset}",href:"#YAXArrays.Datasets.savedataset-Tuple{Dataset}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.savedataset")],-1)),e[74]||(e[74]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[75]||(e[75]=s("p",null,'savedataset(ds::Dataset; path = "", persist = nothing, overwrite = false, append = false, skeleton=false, backend = :all, driver = backend, max_cache = 5e8, writefac=4.0)',-1)),e[76]||(e[76]=s("p",null,[t("Saves a Dataset into a file at "),s("code",null,"path"),t(" with the format given by "),s("code",null,"driver"),t(", i.e., driver=:netcdf or driver=:zarr.")],-1)),e[77]||(e[77]=s("div",{class:"warning custom-block"},[s("p",{class:"custom-block-title"},"Warning"),s("p",null,"overwrite = true, deletes ALL your data and it will create a new file.")],-1)),e[78]||(e[78]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L568-L577",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",O,[s("summary",null,[e[79]||(e[79]=s("a",{id:"YAXArrays.Datasets.to_dataset-Tuple{Any}",href:"#YAXArrays.Datasets.to_dataset-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.to_dataset")],-1)),e[80]||(e[80]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[81]||(e[81]=s("p",null,'to_dataset(c;datasetaxis = "Variable", layername = "layer")',-1)),e[82]||(e[82]=s("p",null,[t(`Convert a Data Cube into a Dataset. It is possible to treat one of the Cube's axes as a "DatasetAxis" i.e. the cube will be split into different parts that become variables in the Dataset. If no such axis is specified or found, there will only be a single variable in the dataset with the name `),s("code",null,"layername")],-1)),e[83]||(e[83]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L45-L53",target:"_blank",rel:"noreferrer"},"source")],-1))]),e[165]||(e[165]=s("h2",{id:"Internal-API",tabindex:"-1"},[t("Internal API "),s("a",{class:"header-anchor",href:"#Internal-API","aria-label":'Permalink to "Internal API {#Internal-API}"'},"​")],-1)),s("details",I,[s("summary",null,[e[84]||(e[84]=s("a",{id:"YAXArrays.YAXDefaults",href:"#YAXArrays.YAXDefaults"},[s("span",{class:"jlbinding"},"YAXArrays.YAXDefaults")],-1)),e[85]||(e[85]=t()),i(a,{type:"info",class:"jlObjectType jlConstant",text:"Constant"})]),e[86]||(e[86]=l('
Default configuration for YAXArrays, has the following fields:
  • workdir[]::String = "./" The default location for temporary cubes.
  • recal[]::Bool = false set to true if you want @loadOrGenerate to always recalculate the results.
  • chunksize[]::Any = :input Set the default output chunksize.
  • max_cache[]::Float64 = 1e8 The maximum cache used by mapCube.
  • cubedir[]::"" the default location for Cube() without an argument.
  • subsetextensions::Array{Any} = [] List of registered functions, that convert subsetting input into dimension boundaries.
source
',3))]),s("details",B,[s("summary",null,[e[87]||(e[87]=s("a",{id:"YAXArrays.findAxis-Tuple{Any, Any}",href:"#YAXArrays.findAxis-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.findAxis")],-1)),e[88]||(e[88]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[89]||(e[89]=l('
julia
findAxis(desc, c)
Internal function
Extended Help
Given an Axis description and a cube return the index of the Axis.
The Axis description can be:
  • the name as a string or symbol.
  • an Axis object
source
',7))]),s("details",J,[s("summary",null,[e[90]||(e[90]=s("a",{id:"YAXArrays.getOutAxis-NTuple{5, Any}",href:"#YAXArrays.getOutAxis-NTuple{5, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.getOutAxis")],-1)),e[91]||(e[91]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[92]||(e[92]=l('
julia
getOutAxis
source
',2))]),s("details",P,[s("summary",null,[e[93]||(e[93]=s("a",{id:"YAXArrays.get_descriptor-Tuple{String}",href:"#YAXArrays.get_descriptor-Tuple{String}"},[s("span",{class:"jlbinding"},"YAXArrays.get_descriptor")],-1)),e[94]||(e[94]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[95]||(e[95]=l('
julia
get_descriptor(a)
Get the descriptor of an Axis. This is used to dispatch on the descriptor.
source
',3))]),s("details",z,[s("summary",null,[e[96]||(e[96]=s("a",{id:"YAXArrays.match_axis-Tuple{YAXArrays.ByName, Any}",href:"#YAXArrays.match_axis-Tuple{YAXArrays.ByName, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.match_axis")],-1)),e[97]||(e[97]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[98]||(e[98]=l(`
julia
match_axis
Internal function
Extended Help
Match the Axis based on the AxisDescriptor.
 This is used to find different axes and to make certain axis description the same.
-For example to disregard differences of captialisation.
source
`,5))]),s("details",N,[s("summary",null,[e[99]||(e[99]=s("a",{id:"YAXArrays.Cubes.CleanMe",href:"#YAXArrays.Cubes.CleanMe"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.CleanMe")],-1)),e[100]||(e[100]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[101]||(e[101]=l('
julia
mutable struct CleanMe
Struct which describes data paths and their persistency. Non-persistend paths/files are removed at finalize step
source
',3))]),s("details",S,[s("summary",null,[e[102]||(e[102]=s("a",{id:"YAXArrays.Cubes.clean-Tuple{YAXArrays.Cubes.CleanMe}",href:"#YAXArrays.Cubes.clean-Tuple{YAXArrays.Cubes.CleanMe}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.clean")],-1)),e[103]||(e[103]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[104]||(e[104]=l('
julia
clean(c::CleanMe)
finalizer function for CleanMe struct. The main process removes all directories/files which are not persistent.
source
',3))]),s("details",q,[s("summary",null,[e[105]||(e[105]=s("a",{id:"YAXArrays.Cubes.copydata-Tuple{Any, Any, Any}",href:"#YAXArrays.Cubes.copydata-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.copydata")],-1)),e[106]||(e[106]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[107]||(e[107]=l('
julia
copydata(outar, inar, copybuf)
Internal function which copies the data from the input inar into the output outar at the copybuf positions.
source
',3))]),s("details",V,[s("summary",null,[e[108]||(e[108]=s("a",{id:"YAXArrays.Cubes.optifunc-NTuple{7, Any}",href:"#YAXArrays.Cubes.optifunc-NTuple{7, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.optifunc")],-1)),e[109]||(e[109]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[110]||(e[110]=l('
julia
optifunc(s, maxbuf, incs, outcs, insize, outsize, writefac)
Internal
This function is going to be minimized to detect the best possible chunk setting for the rechunking of the data.
source
',4))]),s("details",G,[s("summary",null,[e[111]||(e[111]=s("a",{id:"YAXArrays.DAT.DATConfig",href:"#YAXArrays.DAT.DATConfig"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.DATConfig")],-1)),e[112]||(e[112]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[113]||(e[113]=l('
Configuration object of a DAT process. This holds all necessary information to perform the calculations. It contains the following fields:
  • incubes::NTuple{NIN, YAXArrays.DAT.InputCube} where NIN: The input data cubes
  • outcubes::NTuple{NOUT, YAXArrays.DAT.OutputCube} where NOUT: The output data cubes
  • allInAxes::Vector: List of all axes of the input cubes
  • LoopAxes::Vector: List of axes that are looped through
  • ispar::Bool: Flag whether the computation is parallelized
  • loopcachesize::Vector{Int64}:
  • allow_irregular_chunks::Bool:
  • max_cache::Any: Maximal size of the in memory cache
  • fu::Any: Inner function which is computed
  • inplace::Bool: Flag whether the computation happens in place
  • include_loopvars::Bool:
  • ntr::Any:
  • do_gc::Bool: Flag if GC should be called explicitly. Probably necessary for many runs in Julia 1.9
  • addargs::Any: Additional arguments for the inner function
  • kwargs::Any: Additional keyword arguments for the inner function
source
',3))]),s("details",R,[s("summary",null,[e[114]||(e[114]=s("a",{id:"YAXArrays.DAT.InputCube",href:"#YAXArrays.DAT.InputCube"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.InputCube")],-1)),e[115]||(e[115]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[116]||(e[116]=l('
Internal representation of an input cube for DAT operations
  • cube: The input data
  • desc: The input description given by the user/registration
  • axesSmall: List of axes that were actually selected through the description
  • icolon
  • colonperm
  • loopinds: Indices of loop axes that this cube does not contain, i.e. broadcasts
  • cachesize: Number of elements to keep in cache along each axis
  • window
  • iwindow
  • windowloopinds
  • iall
source
',3))]),s("details",W,[s("summary",null,[e[117]||(e[117]=s("a",{id:"YAXArrays.DAT.OutputCube",href:"#YAXArrays.DAT.OutputCube"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.OutputCube")],-1)),e[118]||(e[118]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[119]||(e[119]=l('
Internal representation of an output cube for DAT operations
Fields
  • cube: The actual outcube cube, once it is generated
  • cube_unpermuted: The unpermuted output cube
  • desc: The description of the output axes as given by users or registration
  • axesSmall: The list of output axes determined through the description
  • allAxes: List of all the axes of the cube
  • loopinds: Index of the loop axes that are broadcasted for this output cube
  • innerchunks
  • outtype: Elementtype of the outputcube
source
',4))]),s("details",U,[s("summary",null,[e[120]||(e[120]=s("a",{id:"YAXArrays.DAT.YAXColumn",href:"#YAXArrays.DAT.YAXColumn"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.YAXColumn")],-1)),e[121]||(e[121]=a()),i(t,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[122]||(e[122]=l('
julia
YAXColumn
A struct representing a single column of a YAXArray partitioned Table # Fields
  • inarBC
  • inds
source
',4))]),s("details",$,[s("summary",null,[e[123]||(e[123]=s("a",{id:"YAXArrays.DAT.cmpcachmisses-Tuple{Any, Any}",href:"#YAXArrays.DAT.cmpcachmisses-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.cmpcachmisses")],-1)),e[124]||(e[124]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[125]||(e[125]=s("p",null,"Function that compares two cache miss specifiers by their importance",-1)),e[126]||(e[126]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DAT/DAT.jl#L957-L959",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",H,[s("summary",null,[e[127]||(e[127]=s("a",{id:"YAXArrays.DAT.getFrontPerm-Tuple{Any, Any}",href:"#YAXArrays.DAT.getFrontPerm-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getFrontPerm")],-1)),e[128]||(e[128]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[129]||(e[129]=s("p",null,"Calculate an axis permutation that brings the wanted dimensions to the front",-1)),e[130]||(e[130]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DAT/DAT.jl#L1202",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",K,[s("summary",null,[e[131]||(e[131]=s("a",{id:"YAXArrays.DAT.getLoopCacheSize-NTuple{5, Any}",href:"#YAXArrays.DAT.getLoopCacheSize-NTuple{5, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getLoopCacheSize")],-1)),e[132]||(e[132]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[133]||(e[133]=s("p",null,"Calculate optimal Cache size to DAT operation",-1)),e[134]||(e[134]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DAT/DAT.jl#L1056",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",Z,[s("summary",null,[e[135]||(e[135]=s("a",{id:"YAXArrays.DAT.getOuttype-Tuple{Int64, Any}",href:"#YAXArrays.DAT.getOuttype-Tuple{Int64, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getOuttype")],-1)),e[136]||(e[136]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[137]||(e[137]=l('
julia
getOuttype(outtype, cdata)
Internal function
Get the element type for the output cube
source
',4))]),s("details",Q,[s("summary",null,[e[138]||(e[138]=s("a",{id:"YAXArrays.DAT.getloopchunks-Tuple{YAXArrays.DAT.DATConfig}",href:"#YAXArrays.DAT.getloopchunks-Tuple{YAXArrays.DAT.DATConfig}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getloopchunks")],-1)),e[139]||(e[139]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[140]||(e[140]=l('
julia
getloopchunks(dc::DATConfig)
Internal function
Returns the chunks that can be looped over toghether for all dimensions.\nThis computation of the size of the chunks is handled by [`DiskArrays.approx_chunksize`](@ref)
source
',4))]),s("details",_,[s("summary",null,[e[141]||(e[141]=s("a",{id:"YAXArrays.DAT.permuteloopaxes-Tuple{Any}",href:"#YAXArrays.DAT.permuteloopaxes-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.permuteloopaxes")],-1)),e[142]||(e[142]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[143]||(e[143]=l('
julia
permuteloopaxes(dc)
Internal function
Permute the dimensions of the cube, so that the axes that are looped through are in the first positions. This is necessary for a faster looping through the data.
source
',4))]),s("details",ee,[s("summary",null,[e[144]||(e[144]=s("a",{id:"YAXArrays.Cubes.setchunks-Tuple{Dataset, Any}",href:"#YAXArrays.Cubes.setchunks-Tuple{Dataset, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.setchunks")],-1)),e[145]||(e[145]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[146]||(e[146]=l('
julia
setchunks(c::Dataset,chunks)
Resets the chunks of all or a subset YAXArrays in the dataset and returns a new Dataset. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savedataset on the resulting array. The chunks argument can take one of the following forms:
  • a NamedTuple or AbstractDict mapping from variable name to a description of the desired variable chunks
  • a NamedTuple or AbstractDict mapping from dimension name to a description of the desired variable chunks
  • a description of the desired variable chunks applied to all members of the Dataset
where a description of the desired variable chunks can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
',6))]),s("details",se,[s("summary",null,[e[147]||(e[147]=s("a",{id:"YAXArrays.Datasets.collectfromhandle-Tuple{Any, Any, Any}",href:"#YAXArrays.Datasets.collectfromhandle-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.collectfromhandle")],-1)),e[148]||(e[148]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[149]||(e[149]=s("p",null,"Extracts a YAXArray from a dataset handle that was just created from a arrayinfo",-1)),e[150]||(e[150]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L473-L475",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",ae,[s("summary",null,[e[151]||(e[151]=s("a",{id:"YAXArrays.Datasets.createdataset-Tuple{Any, Any}",href:"#YAXArrays.Datasets.createdataset-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.createdataset")],-1)),e[152]||(e[152]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[153]||(e[153]=l('
function createdataset(DS::Type,axlist; kwargs...)
Creates a new dataset with axes specified in axlist. Each axis must be a subtype of CubeAxis. A new empty Zarr array will be created and can serve as a sink for mapCube operations.
Keyword arguments
  • path="" location where the new cube is stored
  • T=Union{Float32,Missing} data type of the target cube
  • chunksize = ntuple(i->length(axlist[i]),length(axlist)) chunk sizes of the array
  • chunkoffset = ntuple(i->0,length(axlist)) offsets of the chunks
  • persist::Bool=true shall the disk data be garbage-collected when the cube goes out of scope?
  • overwrite::Bool=false overwrite cube if it already exists
  • properties=Dict{String,Any}() additional cube properties
  • globalproperties=Dict{String,Any} global attributes to be added to the dataset
  • fillvalue= T>:Missing ? defaultfillval(Base.nonmissingtype(T)) : nothing fill value
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • layername="layer" Fallback name of the variable stored in the dataset if no datasetaxis is found
source
',6))]),s("details",te,[s("summary",null,[e[154]||(e[154]=s("a",{id:"YAXArrays.Datasets.getarrayinfo-Tuple{Any, Any}",href:"#YAXArrays.Datasets.getarrayinfo-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.getarrayinfo")],-1)),e[155]||(e[155]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[156]||(e[156]=s("p",null,"Extract necessary information to create a YAXArrayBase dataset from a name and YAXArray pair",-1)),e[157]||(e[157]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L442-L444",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",ie,[s("summary",null,[e[158]||(e[158]=s("a",{id:"YAXArrays.Datasets.testrange-Tuple{Any}",href:"#YAXArrays.Datasets.testrange-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.testrange")],-1)),e[159]||(e[159]=a()),i(t,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[160]||(e[160]=s("p",null,"Test if data in x can be approximated by a step range",-1)),e[161]||(e[161]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/36a49ff138ff62bb90fce6ca958bb78cee84a498/src/DatasetAPI/Datasets.jl#L312",target:"_blank",rel:"noreferrer"},"source")],-1))])])}const he=n(d,[["render",le]]);export{ce as __pageData,he as default};
+For example to disregard differences of captialisation.
source
`,5))]),s("details",N,[s("summary",null,[e[99]||(e[99]=s("a",{id:"YAXArrays.Cubes.CleanMe",href:"#YAXArrays.Cubes.CleanMe"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.CleanMe")],-1)),e[100]||(e[100]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[101]||(e[101]=l('
julia
mutable struct CleanMe
Struct which describes data paths and their persistency. Non-persistend paths/files are removed at finalize step
source
',3))]),s("details",S,[s("summary",null,[e[102]||(e[102]=s("a",{id:"YAXArrays.Cubes.clean-Tuple{YAXArrays.Cubes.CleanMe}",href:"#YAXArrays.Cubes.clean-Tuple{YAXArrays.Cubes.CleanMe}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.clean")],-1)),e[103]||(e[103]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[104]||(e[104]=l('
julia
clean(c::CleanMe)
finalizer function for CleanMe struct. The main process removes all directories/files which are not persistent.
source
',3))]),s("details",q,[s("summary",null,[e[105]||(e[105]=s("a",{id:"YAXArrays.Cubes.copydata-Tuple{Any, Any, Any}",href:"#YAXArrays.Cubes.copydata-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.copydata")],-1)),e[106]||(e[106]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[107]||(e[107]=l('
julia
copydata(outar, inar, copybuf)
Internal function which copies the data from the input inar into the output outar at the copybuf positions.
source
',3))]),s("details",V,[s("summary",null,[e[108]||(e[108]=s("a",{id:"YAXArrays.Cubes.optifunc-NTuple{7, Any}",href:"#YAXArrays.Cubes.optifunc-NTuple{7, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.optifunc")],-1)),e[109]||(e[109]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[110]||(e[110]=l('
julia
optifunc(s, maxbuf, incs, outcs, insize, outsize, writefac)
Internal
This function is going to be minimized to detect the best possible chunk setting for the rechunking of the data.
source
',4))]),s("details",G,[s("summary",null,[e[111]||(e[111]=s("a",{id:"YAXArrays.DAT.DATConfig",href:"#YAXArrays.DAT.DATConfig"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.DATConfig")],-1)),e[112]||(e[112]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[113]||(e[113]=l('
Configuration object of a DAT process. This holds all necessary information to perform the calculations. It contains the following fields:
  • incubes::NTuple{NIN, YAXArrays.DAT.InputCube} where NIN: The input data cubes
  • outcubes::NTuple{NOUT, YAXArrays.DAT.OutputCube} where NOUT: The output data cubes
  • allInAxes::Vector: List of all axes of the input cubes
  • LoopAxes::Vector: List of axes that are looped through
  • ispar::Bool: Flag whether the computation is parallelized
  • loopcachesize::Vector{Int64}:
  • allow_irregular_chunks::Bool:
  • max_cache::Any: Maximal size of the in memory cache
  • fu::Any: Inner function which is computed
  • inplace::Bool: Flag whether the computation happens in place
  • include_loopvars::Bool:
  • ntr::Any:
  • do_gc::Bool: Flag if GC should be called explicitly. Probably necessary for many runs in Julia 1.9
  • addargs::Any: Additional arguments for the inner function
  • kwargs::Any: Additional keyword arguments for the inner function
source
',3))]),s("details",R,[s("summary",null,[e[114]||(e[114]=s("a",{id:"YAXArrays.DAT.InputCube",href:"#YAXArrays.DAT.InputCube"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.InputCube")],-1)),e[115]||(e[115]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[116]||(e[116]=l('
Internal representation of an input cube for DAT operations
  • cube: The input data
  • desc: The input description given by the user/registration
  • axesSmall: List of axes that were actually selected through the description
  • icolon
  • colonperm
  • loopinds: Indices of loop axes that this cube does not contain, i.e. broadcasts
  • cachesize: Number of elements to keep in cache along each axis
  • window
  • iwindow
  • windowloopinds
  • iall
source
',3))]),s("details",W,[s("summary",null,[e[117]||(e[117]=s("a",{id:"YAXArrays.DAT.OutputCube",href:"#YAXArrays.DAT.OutputCube"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.OutputCube")],-1)),e[118]||(e[118]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[119]||(e[119]=l('
Internal representation of an output cube for DAT operations
Fields
  • cube: The actual outcube cube, once it is generated
  • cube_unpermuted: The unpermuted output cube
  • desc: The description of the output axes as given by users or registration
  • axesSmall: The list of output axes determined through the description
  • allAxes: List of all the axes of the cube
  • loopinds: Index of the loop axes that are broadcasted for this output cube
  • innerchunks
  • outtype: Elementtype of the outputcube
source
',4))]),s("details",U,[s("summary",null,[e[120]||(e[120]=s("a",{id:"YAXArrays.DAT.YAXColumn",href:"#YAXArrays.DAT.YAXColumn"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.YAXColumn")],-1)),e[121]||(e[121]=t()),i(a,{type:"info",class:"jlObjectType jlType",text:"Type"})]),e[122]||(e[122]=l('
julia
YAXColumn
A struct representing a single column of a YAXArray partitioned Table # Fields
  • inarBC
  • inds
source
',4))]),s("details",$,[s("summary",null,[e[123]||(e[123]=s("a",{id:"YAXArrays.DAT.cmpcachmisses-Tuple{Any, Any}",href:"#YAXArrays.DAT.cmpcachmisses-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.cmpcachmisses")],-1)),e[124]||(e[124]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[125]||(e[125]=s("p",null,"Function that compares two cache miss specifiers by their importance",-1)),e[126]||(e[126]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DAT/DAT.jl#L957-L959",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",H,[s("summary",null,[e[127]||(e[127]=s("a",{id:"YAXArrays.DAT.getFrontPerm-Tuple{Any, Any}",href:"#YAXArrays.DAT.getFrontPerm-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getFrontPerm")],-1)),e[128]||(e[128]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[129]||(e[129]=s("p",null,"Calculate an axis permutation that brings the wanted dimensions to the front",-1)),e[130]||(e[130]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DAT/DAT.jl#L1202",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",K,[s("summary",null,[e[131]||(e[131]=s("a",{id:"YAXArrays.DAT.getLoopCacheSize-NTuple{5, Any}",href:"#YAXArrays.DAT.getLoopCacheSize-NTuple{5, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getLoopCacheSize")],-1)),e[132]||(e[132]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[133]||(e[133]=s("p",null,"Calculate optimal Cache size to DAT operation",-1)),e[134]||(e[134]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DAT/DAT.jl#L1056",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",Z,[s("summary",null,[e[135]||(e[135]=s("a",{id:"YAXArrays.DAT.getOuttype-Tuple{Int64, Any}",href:"#YAXArrays.DAT.getOuttype-Tuple{Int64, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getOuttype")],-1)),e[136]||(e[136]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[137]||(e[137]=l('
julia
getOuttype(outtype, cdata)
Internal function
Get the element type for the output cube
source
',4))]),s("details",Q,[s("summary",null,[e[138]||(e[138]=s("a",{id:"YAXArrays.DAT.getloopchunks-Tuple{YAXArrays.DAT.DATConfig}",href:"#YAXArrays.DAT.getloopchunks-Tuple{YAXArrays.DAT.DATConfig}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.getloopchunks")],-1)),e[139]||(e[139]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[140]||(e[140]=l('
julia
getloopchunks(dc::DATConfig)
Internal function
Returns the chunks that can be looped over toghether for all dimensions.\nThis computation of the size of the chunks is handled by [`DiskArrays.approx_chunksize`](@ref)
source
',4))]),s("details",_,[s("summary",null,[e[141]||(e[141]=s("a",{id:"YAXArrays.DAT.permuteloopaxes-Tuple{Any}",href:"#YAXArrays.DAT.permuteloopaxes-Tuple{Any}"},[s("span",{class:"jlbinding"},"YAXArrays.DAT.permuteloopaxes")],-1)),e[142]||(e[142]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[143]||(e[143]=l('
julia
permuteloopaxes(dc)
Internal function
Permute the dimensions of the cube, so that the axes that are looped through are in the first positions. This is necessary for a faster looping through the data.
source
',4))]),s("details",ee,[s("summary",null,[e[144]||(e[144]=s("a",{id:"YAXArrays.Cubes.setchunks-Tuple{Dataset, Any}",href:"#YAXArrays.Cubes.setchunks-Tuple{Dataset, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Cubes.setchunks")],-1)),e[145]||(e[145]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[146]||(e[146]=l('
julia
setchunks(c::Dataset,chunks)
Resets the chunks of all or a subset YAXArrays in the dataset and returns a new Dataset. Note that this will not change the chunking of the underlying data itself, it will just make the data "look" like it had a different chunking. If you need a persistent on-disk representation of this chunking, use savedataset on the resulting array. The chunks argument can take one of the following forms:
  • a NamedTuple or AbstractDict mapping from variable name to a description of the desired variable chunks
  • a NamedTuple or AbstractDict mapping from dimension name to a description of the desired variable chunks
  • a description of the desired variable chunks applied to all members of the Dataset
where a description of the desired variable chunks can take one of the following forms:
  • a DiskArrays.GridChunks object
  • a tuple specifying the chunk size along each dimension
  • an AbstractDict or NamedTuple mapping one or more axis names to chunk sizes
source
',6))]),s("details",se,[s("summary",null,[e[147]||(e[147]=s("a",{id:"YAXArrays.Datasets.collectfromhandle-Tuple{Any, Any, Any}",href:"#YAXArrays.Datasets.collectfromhandle-Tuple{Any, Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.collectfromhandle")],-1)),e[148]||(e[148]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[149]||(e[149]=s("p",null,"Extracts a YAXArray from a dataset handle that was just created from a arrayinfo",-1)),e[150]||(e[150]=s("p",null,[s("a",{href:"https://github.com/JuliaDataCubes/YAXArrays.jl/blob/15f9b56137929e4816654e5e02cb5d6c74314608/src/DatasetAPI/Datasets.jl#L474-L476",target:"_blank",rel:"noreferrer"},"source")],-1))]),s("details",te,[s("summary",null,[e[151]||(e[151]=s("a",{id:"YAXArrays.Datasets.createdataset-Tuple{Any, Any}",href:"#YAXArrays.Datasets.createdataset-Tuple{Any, Any}"},[s("span",{class:"jlbinding"},"YAXArrays.Datasets.createdataset")],-1)),e[152]||(e[152]=t()),i(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),e[153]||(e[153]=l('
function createdataset(DS::Type,axlist; kwargs...)
Creates a new dataset with axes specified in axlist. Each axis must be a subtype of CubeAxis. A new empty Zarr array will be created and can serve as a sink for mapCube operations.
Keyword arguments
  • path="" location where the new cube is stored
  • T=Union{Float32,Missing} data type of the target cube
  • chunksize = ntuple(i->length(axlist[i]),length(axlist)) chunk sizes of the array
  • chunkoffset = ntuple(i->0,length(axlist)) offsets of the chunks
  • persist::Bool=true shall the disk data be garbage-collected when the cube goes out of scope?
  • overwrite::Bool=false overwrite cube if it already exists
  • properties=Dict{String,Any}() additional cube properties
  • globalproperties=Dict{String,Any} global attributes to be added to the dataset
  • fillvalue= T>:Missing ? defaultfillval(Base.nonmissingtype(T)) : nothing fill value
  • datasetaxis="Variable" special treatment of a categorical axis that gets written into separate zarr arrays
  • layername="layer" Fallback name of the variable stored in the dataset if no datasetaxis is found
source
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index bb9b073e..b04e5fe0 100644
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diff --git a/dev/assets/chunks/theme.DSJoXFCG.js b/dev/assets/chunks/theme.CrYK124x.js
similarity index 99%
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index 4c057429..bd036f5b 100644
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similarity index 98%
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diff --git a/dev/assets/development_contributors.md.aO-w06-b.lean.js b/dev/assets/development_contributors.md.bnl_XTwF.lean.js
similarity index 98%
rename from dev/assets/development_contributors.md.aO-w06-b.lean.js
rename to dev/assets/development_contributors.md.bnl_XTwF.lean.js
index 0e007e05..ffcbb0f1 100644
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diff --git a/dev/assets/index.md.DTlVqubU.js b/dev/assets/index.md.CIaPcDRI.js
similarity index 93%
rename from dev/assets/index.md.DTlVqubU.js
rename to dev/assets/index.md.CIaPcDRI.js
index af52df80..fee952bd 100644
--- a/dev/assets/index.md.DTlVqubU.js
+++ b/dev/assets/index.md.CIaPcDRI.js
@@ -1,8 +1,8 @@
-import{_ as s,c as a,a2 as t,o as e}from"./chunks/framework.DgSLhxNl.js";const g=JSON.parse(`{"title":"","description":"","frontmatter":{"layout":"home","hero":{"name":"YAXArrays.jl","text":"Yet another xarray-like Julia package","tagline":"A package for operating on out-of-core labeled arrays, based on stores like NetCDF, Zarr or GDAL.","image":{"src":"/logo.png","alt":"VitePress"},"actions":[{"theme":"brand","text":"Get Started","link":"/get_started"},{"theme":"alt","text":"View on Github","link":"https://github.com/JuliaDataCubes/YAXArrays.jl"},{"theme":"alt","text":"API reference","link":"/api"}]},"features":[{"title":"Flexible I/O capabilities","details":"Open and operate on NetCDF and Zarr datasets directly. Or bring in data from other sources with ArchGDAL.jl, GRIBDatasets.jl, GeoJSON.jl, HDF5.jl, Shapefile.jl, GeoParquet.jl, etc.","link":"/UserGuide/read"},{"title":"Interoperability","details":"Well integrated with Julia's ecosystem, i.e., distributed operations are native. And plotting with Makie.jl is well supported.","link":"/tutorials/plottingmaps"},{"title":"Named dimensions and GroupBy(in memory)","details":"Apply operations over named dimensions, select values by labels and integers as well as efficient split-apply-combine operations with groupby via DimensionalData.jl.","link":"/UserGuide/group"},{"title":"Efficiency","details":"Efficient mapslices(x)  and mapCube operations on huge multiple arrays, optimized for high-latency data access (object storage, compressed datasets).","link":"/UserGuide/compute"}]},"headers":[],"relativePath":"index.md","filePath":"index.md","lastUpdated":null}`),l={name:"index.md"};function n(p,i,h,r,k,o){return e(),a("div",null,i[0]||(i[0]=[t(`
How to Install YAXArrays.jl? ​
Since YAXArrays.jl is registered in the Julia General registry, you can simply run the following command in the Julia REPL:
julia
julia> using Pkg
+import{_ as s,c as a,a2 as t,o as e}from"./chunks/framework.DgSLhxNl.js";const g=JSON.parse(`{"title":"","description":"","frontmatter":{"layout":"home","hero":{"name":"YAXArrays.jl","text":"Yet another xarray-like Julia package","tagline":"A package for operating on out-of-core labeled arrays, based on stores like NetCDF, Zarr or GDAL.","image":{"src":"/logo.png","alt":"VitePress"},"actions":[{"theme":"brand","text":"Get Started","link":"/get_started"},{"theme":"alt","text":"View on Github","link":"https://github.com/JuliaDataCubes/YAXArrays.jl"},{"theme":"alt","text":"API reference","link":"/api"}]},"features":[{"title":"Flexible I/O capabilities","details":"Open and operate on NetCDF and Zarr datasets directly. Or bring in data from other sources with ArchGDAL.jl, GRIBDatasets.jl, GeoJSON.jl, HDF5.jl, Shapefile.jl, GeoParquet.jl, etc.","link":"/UserGuide/read"},{"title":"Interoperability","details":"Well integrated with Julia's ecosystem, i.e., distributed operations are native. And plotting with Makie.jl is well supported.","link":"/tutorials/plottingmaps"},{"title":"Named dimensions and GroupBy(in memory)","details":"Apply operations over named dimensions, select values by labels and integers as well as efficient split-apply-combine operations with groupby via DimensionalData.jl.","link":"/UserGuide/group"},{"title":"Efficiency","details":"Efficient mapslices(x)  and mapCube operations on huge multiple arrays, optimized for high-latency data access (object storage, compressed datasets).","link":"/UserGuide/compute"}]},"headers":[],"relativePath":"index.md","filePath":"index.md","lastUpdated":null}`),l={name:"index.md"};function n(p,i,h,k,r,o){return e(),a("div",null,i[0]||(i[0]=[t(`
How to Install YAXArrays.jl? ​
Since YAXArrays.jl is registered in the Julia General registry, you can simply run the following command in the Julia REPL:
julia
julia> using Pkg
 julia> Pkg.add("YAXArrays.jl")
 # or
 julia> ] # ']' should be pressed
-pkg> add YAXArrays
If you want to use the latest unreleased version, you can run the following command:
julia
pkg> add YAXArrays#master
Want interoperability? ​
Install the following package(s) for:
julia
using Pkg
+pkg> add YAXArrays
If you want to use the latest unreleased version, you can run the following command:
julia
pkg> add YAXArrays#master
Want interoperability? ​
Install the following package(s) for:
julia
using Pkg
 Pkg.add("ArchGDAL")
julia
using Pkg
 Pkg.add("NetCDF")
julia
using Pkg
 Pkg.add("Zarr")
julia
using Pkg
diff --git a/dev/assets/index.md.DTlVqubU.lean.js b/dev/assets/index.md.CIaPcDRI.lean.js
similarity index 93%
rename from dev/assets/index.md.DTlVqubU.lean.js
rename to dev/assets/index.md.CIaPcDRI.lean.js
index af52df80..fee952bd 100644
--- a/dev/assets/index.md.DTlVqubU.lean.js
+++ b/dev/assets/index.md.CIaPcDRI.lean.js
@@ -1,8 +1,8 @@
-import{_ as s,c as a,a2 as t,o as e}from"./chunks/framework.DgSLhxNl.js";const g=JSON.parse(`{"title":"","description":"","frontmatter":{"layout":"home","hero":{"name":"YAXArrays.jl","text":"Yet another xarray-like Julia package","tagline":"A package for operating on out-of-core labeled arrays, based on stores like NetCDF, Zarr or GDAL.","image":{"src":"/logo.png","alt":"VitePress"},"actions":[{"theme":"brand","text":"Get Started","link":"/get_started"},{"theme":"alt","text":"View on Github","link":"https://github.com/JuliaDataCubes/YAXArrays.jl"},{"theme":"alt","text":"API reference","link":"/api"}]},"features":[{"title":"Flexible I/O capabilities","details":"Open and operate on NetCDF and Zarr datasets directly. Or bring in data from other sources with ArchGDAL.jl, GRIBDatasets.jl, GeoJSON.jl, HDF5.jl, Shapefile.jl, GeoParquet.jl, etc.","link":"/UserGuide/read"},{"title":"Interoperability","details":"Well integrated with Julia's ecosystem, i.e., distributed operations are native. And plotting with Makie.jl is well supported.","link":"/tutorials/plottingmaps"},{"title":"Named dimensions and GroupBy(in memory)","details":"Apply operations over named dimensions, select values by labels and integers as well as efficient split-apply-combine operations with groupby via DimensionalData.jl.","link":"/UserGuide/group"},{"title":"Efficiency","details":"Efficient mapslices(x)  and mapCube operations on huge multiple arrays, optimized for high-latency data access (object storage, compressed datasets).","link":"/UserGuide/compute"}]},"headers":[],"relativePath":"index.md","filePath":"index.md","lastUpdated":null}`),l={name:"index.md"};function n(p,i,h,r,k,o){return e(),a("div",null,i[0]||(i[0]=[t(`
How to Install YAXArrays.jl? ​
Since YAXArrays.jl is registered in the Julia General registry, you can simply run the following command in the Julia REPL:
julia
julia> using Pkg
+import{_ as s,c as a,a2 as t,o as e}from"./chunks/framework.DgSLhxNl.js";const g=JSON.parse(`{"title":"","description":"","frontmatter":{"layout":"home","hero":{"name":"YAXArrays.jl","text":"Yet another xarray-like Julia package","tagline":"A package for operating on out-of-core labeled arrays, based on stores like NetCDF, Zarr or GDAL.","image":{"src":"/logo.png","alt":"VitePress"},"actions":[{"theme":"brand","text":"Get Started","link":"/get_started"},{"theme":"alt","text":"View on Github","link":"https://github.com/JuliaDataCubes/YAXArrays.jl"},{"theme":"alt","text":"API reference","link":"/api"}]},"features":[{"title":"Flexible I/O capabilities","details":"Open and operate on NetCDF and Zarr datasets directly. Or bring in data from other sources with ArchGDAL.jl, GRIBDatasets.jl, GeoJSON.jl, HDF5.jl, Shapefile.jl, GeoParquet.jl, etc.","link":"/UserGuide/read"},{"title":"Interoperability","details":"Well integrated with Julia's ecosystem, i.e., distributed operations are native. And plotting with Makie.jl is well supported.","link":"/tutorials/plottingmaps"},{"title":"Named dimensions and GroupBy(in memory)","details":"Apply operations over named dimensions, select values by labels and integers as well as efficient split-apply-combine operations with groupby via DimensionalData.jl.","link":"/UserGuide/group"},{"title":"Efficiency","details":"Efficient mapslices(x)  and mapCube operations on huge multiple arrays, optimized for high-latency data access (object storage, compressed datasets).","link":"/UserGuide/compute"}]},"headers":[],"relativePath":"index.md","filePath":"index.md","lastUpdated":null}`),l={name:"index.md"};function n(p,i,h,k,r,o){return e(),a("div",null,i[0]||(i[0]=[t(`
How to Install YAXArrays.jl? ​
Since YAXArrays.jl is registered in the Julia General registry, you can simply run the following command in the Julia REPL:
julia
julia> using Pkg
 julia> Pkg.add("YAXArrays.jl")
 # or
 julia> ] # ']' should be pressed
-pkg> add YAXArrays
If you want to use the latest unreleased version, you can run the following command:
julia
pkg> add YAXArrays#master
Want interoperability? ​
Install the following package(s) for:
julia
using Pkg
+pkg> add YAXArrays
If you want to use the latest unreleased version, you can run the following command:
julia
pkg> add YAXArrays#master
Want interoperability? ​
Install the following package(s) for:
julia
using Pkg
 Pkg.add("ArchGDAL")
julia
using Pkg
 Pkg.add("NetCDF")
julia
using Pkg
 Pkg.add("Zarr")
julia
using Pkg
diff --git a/dev/development/contribute.html b/dev/development/contribute.html
index 6366e4fc..1bd44eab 100644
--- a/dev/development/contribute.html
+++ b/dev/development/contribute.html
@@ -8,9 +8,9 @@
     
     
     
-    
+    
     
-    
+    
     
     
     
@@ -23,7 +23,7 @@
     
YAXArrays.jl
Appearance

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.
Contribute to YAXArrays.jl ​
Pull requests and bug reports are always welcome at the YAXArrays.jl GitHub repository.
Contribute to Documentation ​
Contributing with examples can be done by first creating a new file example here
new file
  • your_new_file.md at docs/src/UserGuide/
Once this is done you need to add a new entry here at the appropriate level.
add entry to docs
Your new entry should look like:
  • { text: 'Your title example', link: '/UserGuide/your_new_file.md' }
Build docs locally ​
If you want to take a look at the docs locally before doing a PR follow the next steps:
Install the dependencies in your system, locate yourself at the docs level folder, then do
sh
npm i
Then simply go to your docs env and activate it, i.e.
sh
docs> julia
 julia> ]
 pkg> activate .
Next, run the scripts. Generate files and build docs by running:
sh
include("make.jl")
Now go to your terminal in the same path docs> and run:
sh
npm run docs:dev
This should ouput http://localhost:5173/YAXArrays.jl/, copy/paste this into your browser and you are all set.

-    
+    
     
   
 
\ No newline at end of file
diff --git a/dev/development/contributors.html b/dev/development/contributors.html
index 7dcce884..7f0a773b 100644
--- a/dev/development/contributors.html
+++ b/dev/development/contributors.html
@@ -8,11 +8,11 @@
     
     
     
-    
+    
     
-    
+    
     
-    
+    
     
     
     
@@ -21,7 +21,7 @@
   
   
     
YAXArrays.jl
Appearance
Contributors
Current core contributors  
 They have taking the lead for the ongoing organizational maintenance and technical direction of ,  and . 
Fabian Gans
Fabian Gans
Geoscientific Programmer
Felix Cremer
Felix Cremer
PhD Candidate in Remote Sensing
Rafael Schouten
Rafael Schouten
Spatial/ecological modelling
Lazaro Alonso
Lazaro Alonso
Scientist. Data Visualization
Our valuable contributors
 We appreciate all contributions from the Julia community so that this ecosystem can thrive.

-    
+    
     
   
 
\ No newline at end of file
diff --git a/dev/get_started.html b/dev/get_started.html
index 067137d3..938bfe94 100644
--- a/dev/get_started.html
+++ b/dev/get_started.html
@@ -8,9 +8,9 @@
     
     
     
-    
+    
     
-    
+    
     
     
     
@@ -76,7 +76,7 @@
  0.853962   0.461652   0.438885  0.665833     0.0743642  0.81705   0.00997173
  0.515079   0.283788   0.258509  0.807171     0.234116   0.404819  0.3785
  0.864937   0.0916764  0.235899  0.047283     0.768363   0.937012  0.732556
Updates ​
TIP
The Julia Compiler is always improving. As such, we recommend using the latest stable version of Julia.
You may check the installed version with:
julia
pkg> st YAXArrays
INFO
With YAXArrays.jl 0.5 we switched the underlying data type to be a subtype of the DimensionalData.jl types. Therefore the indexing with named dimensions changed to the DimensionalData syntax. See the DimensionalData.jl docs.

-    
+    
     
   
 
\ No newline at end of file
diff --git a/dev/hashmap.json b/dev/hashmap.json
index 88430d59..6ad8e6ba 100644
--- a/dev/hashmap.json
+++ b/dev/hashmap.json
@@ -1 +1 @@
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diff --git a/dev/index.html b/dev/index.html
index d9917390..f8b37de5 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -8,11 +8,11 @@
     
     
     
-    
+    
     
-    
+    
     
-    
+    
     
     
     
@@ -24,12 +24,12 @@
 julia> Pkg.add("YAXArrays.jl")
 # or
 julia> ] # ']' should be pressed
-pkg> add YAXArrays
If you want to use the latest unreleased version, you can run the following command:
julia
pkg> add YAXArrays#master
Want interoperability? ​
Install the following package(s) for:
julia
using Pkg
+pkg> add YAXArrays
If you want to use the latest unreleased version, you can run the following command:
julia
pkg> add YAXArrays#master
Want interoperability? ​
Install the following package(s) for:
julia
using Pkg
 Pkg.add("ArchGDAL")
julia
using Pkg
 Pkg.add("NetCDF")
julia
using Pkg
 Pkg.add("Zarr")
julia
using Pkg
 Pkg.add(["GLMakie", "GeoMakie", "AlgebraOfGraphics", "DimensionalData"])
- + \ No newline at end of file diff --git a/dev/tutorials/mean_seasonal_cycle.html b/dev/tutorials/mean_seasonal_cycle.html index c1d1319b..977d4e9a 100644 --- a/dev/tutorials/mean_seasonal_cycle.html +++ b/dev/tutorials/mean_seasonal_cycle.html @@ -8,9 +8,9 @@ - + - + @@ -92,7 +92,7 @@ ax.xticklabelalign = (:right, :center) fig current_figure()

- + \ No newline at end of file diff --git a/dev/tutorials/other_tutorials.html b/dev/tutorials/other_tutorials.html index d3b5caa8..c058caf4 100644 --- a/dev/tutorials/other_tutorials.html +++ b/dev/tutorials/other_tutorials.html @@ -8,9 +8,9 @@ - + - + @@ -21,7 +21,7 @@
YAXArrays.jl

Appearance


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.

Other tutorials ​

If you are interested in learning how to work with YAXArrays for different use cases you can follow along one of the following tutorials.

  • Currently the overview tutorial is located at ESDLTutorials Repository

  • You can find further tutorial videos at the EO College. Beware that the syntax in the video tutorials might be slightly changed.

  • the other tutorials are still work in progress.

General overview of the functionality of YAXArrays ​

This tutorial provides a broad overview about the features of YAXArrays.

Table-style iteration over YAXArrays ​

Work in progress

Sometimes you want to combine the data that is represented in the data cube with other datasets, which are best described as a data frame. In this tutorial you will learn how to use the Tables.jl interface to iterate over the data in the YAXArray.

Combining multiple tiff files into a zarr based datacube ​

- + \ No newline at end of file diff --git a/dev/tutorials/plottingmaps.html b/dev/tutorials/plottingmaps.html index 571d5712..154e2396 100644 --- a/dev/tutorials/plottingmaps.html +++ b/dev/tutorials/plottingmaps.html @@ -8,9 +8,9 @@ - + - + @@ -74,7 +74,7 @@ zoom!(ax.scene, cameracontrols(ax.scene), 0.5) rotate!(ax.scene, 2.5) fig - + \ No newline at end of file