LH5Array{T, N} <: AbstractArray{T, N}

Array wrapper for HDF5.Datasets following the LEGEND data format as in ".lh5" files.

An LH5Array contains a HDF5.Dataset file and Unitful.Unitlike units as returned by getunits(file).getindexandappend!are supported.getindexessentially falls back togetindexforHDF5.Datasets, enabling the user to always read in the desired part of an ondisk array without having to load it in whole beforehand.append!` uses chunks to append the data provided to the ondisk array. It is important to note, that data is always appended along the last dimension of an array

Default constructors

LH5Array{T}(ds::HDF5.Dataset, u::Unitful.Unitlike)
LH5Array{T, N}(ds::HDF5.Dataset)
LH5Array(ds::Union{HDF5.Dataset, HDF5.H5DataStore})

Examples:

julia> using HDF5
julia> f = h5open("path/to/lh5/file", "r")
julia> l5 = LH5Array(f["path/to/HDF5/Dataset"])
[...]
julia> x = lh[1:10]     # load the first 10 elements of the ondisk array
[...]
julia> append!(lh, x)   # append those 10 elements to the ondisk array 
[...]

LH5Array(ds::HDF5.Dataset, ::Type{<:AbstractArray{<:Bool}}) = begin

return a LH5Array with dimensions equal to that of ds and element type Bool. Applying getindex! on LH5Array{Bool} will yield a BitArray.

LH5Array(ds::HDF5.Dataset, ::Type{<:AbstractArray{<:Tuple}})

return an Array of NTuples

LH5Array(ds::HDF5.Dataset, ::Type{<:AbstractArray})

return a LH5Array with dimensions equal to that of ds and element type equal to eltype(ds) * u

LH5Array(ds::HDF5.H5DataStore, ::Type{<:AbstractArrayOfSimilarArrays{<:RealQuantity}})

return an ArraysOfSimilarArrays where the field data is a LH5Array (see ArraysOfSimilarArrays)

LH5Array(ds::HDF5.H5DataStore, ::Type{<:Bool}) = begin

return a value with type Bool

LH5Array(ds::HDF5.Dataset, ::Type{<:String})

return a String.

LH5Array(ds::HDF5.Dataset, ::Type{<:Symbol})

return a Symbol.

LH5Array(ds::HDF5.Dataset, ::Type{<:Tuple})

return an Tuple

LH5Array(ds::HDF5.Dataset, ::Type{<:RealQuantity})

return a value with type RealQuantity

LH5Array(ds::HDF5.DataStore, ::Type{<:AbstractVector{<:AbstractVector{<:RealQuantity}}})

return a VectorOfVectors object where data is an LH5Array (see VectorOfArrays)

LH5Array(ds::HDF5.DataStore, ::Type{<:AbstractVector{<:RDWaveform}})

return an ArrayOfRDWaveforms where the field signal is either a VectorOfSimilarVectors with an LH5Array as data or VectorOfVectors with an LH5Array as data (see ArrayOfRDWaveforms and ArraysOfArrays)

LH5Array(ds::HDF5.H5DataStore, ::Type{<:AbstractEncodedArray{T, 1} where {T}})

return an EncodedArray

LH5Array(ds::HDF5.H5DataStore, ::Type{<:VectorOfEncodedArrays{T, 1} where {T}})

return a VectorOfEncodedArrays

LH5Array(ds::HDF5.H5DataStore, ::Type{<:VectorOfEncodedSimilarArrays{T, 1} where {T}})

return a VectorOfEncodedSimilarArrays

" LH5Array(ds::HDF5.H5DataStore, ::Type{<:Histogram{<:RealQuantity}})

return a Histogram.

LH5Array(ds::HDF5.Dataset, ::Type{<:NamedTuple{T}}) where T

return a NamedTuple where each field is the output of LH5Array applied to it.

LH5Array(ds::HDF5.DataStore, ::Type{<:TypedTables.Table{<:NamedTuple{(T)}}}) where T

return a Table where each column is the output of LH5Array applied to it.

LHDataStore <: AbstractDict{String,Any}

Dictionary wrapper for HDF5.H5DataStore objects, which were constructed according to the LEGEND data format in ".lh5" files.

Constructor:

LHDataStore(h5ds::HDF5.DataStore)

This return an LHDataStore object that wraps an h5ds which will typically be an HDF5.File be may also be an HDF5.H5DataStore (e.g. an HDF5.Group). in general.

To read or write ".lh5" file directly (without using HDF5.h5open first), we recommend using lh5open.

Supports getindex and setindex! where getindex(lh::LHDataStore, s) returns the output of LH5Array applied to data_store[s] and setindex! creates and writes HDF5.Groups and HDF5.Datasets using chunks of size 1000 to the ondisk array. Currently supported are objects with types: AbstractArray{<:RealQuantity}, ArraysOfSimilarArrays{<:RealQuantity}, VectorOfVectors{<:RealQuantity}, NamedTuple,TypedTables.Table, Vector{<:RDWaveform}. For AbstractArray{<:RealQuantity} It is assumed that the last axis of the provided array corresponds to the event number index.

Example

julia> using HDF5
julia> h5ds = h5open("path/to/lhf/file")
julia> lhf = LHDataStore(h5ds)
julia> lhf["raw"]
[...]
julia> using Unitful
julia> x = rand(100) * u"ns"
julia> lhf["new"] = x
[...]

add_entries!(lhd::LHDataStore, i::AbstractString, src::NamedTuple, 
    dest::NamedTuple=LH5Array(lhd.data_store[i]))

extend the NamedTuple dest at lhd[i] with elements from src.

add_entries!(lhd::LHDataStore, i::AbstractString, src::TypedTable.Table, 
    dest::TypedTable.Table=LH5Array(lhd.data_store[i]))

extend the Table dest at lhd[i] with columns from src.

delete_entry!(lhd::LHDataStore, i::AbstractString)

remove the dataset lhd[i] and adjust the datatype of the parent if necessary. Currently supported are elements of NamedTuple, TypedTable.Table or HDF5.Group.

lh5open(f, filename::AbstractString, access::AbstractString = "r")

Return f(lh5open(f, filename, access)).

Opens and closes the LEGEND HDF5 file filename automatically.

lh5open(filename::AbstractString, access::AbstractString = "r")

Open a LEGEND HDF5 file and return an LHDataStore object.

LEGEND HDF5 files typically use the file extention ".lh5".