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JLD2

HDF5-compatible file format in pure Julia

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JLD2

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JLD2 saves and loads Julia data structures in a format comprising a subset of HDF5, without any dependency on the HDF5 C library. It typically outperforms the previous JLD package (sometimes by multiple orders of magnitude) and often outperforms Julia's built-in serializer. While other HDF5 implementations supporting HDF5 File Format Specification Version 3.0 (i.e. libhdf5 1.10 or later) should be able to read the files that JLD2 produces, JLD2 is likely to be incapable of reading files created or modified by other HDF5 implementations. JLD2 does not aim to be backwards or forwards compatible with the previous JLD package.

The code here should work on Julia 0.6. It has extensive unit tests, but it has received little testing in the wild. Please use caution. If your tolerance for data loss is low, JLD may be a better choice at this time.

Reading and writing data

@save and @load macros

The @save and @load macros are the simplest way to interact with a JLD2 file. The @save macro writes one or more variables from the current scope to the JLD file. For example:

using JLD2, FileIO
hello = "world"
foo = :bar
@save "example.jld2" hello foo

This writes the variables hello and foo to datasets in a new JLD2 file named example.jld2. The @load macro loads variables out of a JLD2 file:

@load "example.jld2" hello foo

This assigns the contents of the hello and foo datasets to variables of the same name in the current scope.

It is best practice to explicitly name the variables to be loaded and saved from a file, so that it is clear from whence these variables arise. However, for convenience, JLD2 also provides variants of @load and @save that do not require variables to be named explicitly. When called with no variable arguments, @save <filename> writes all variables in the global scope of the current module to file <filename>, while @load <filename> loads all variables in file <filename>. When called with no variable arguments, @load requires that the file name is provided as a string literal, i.e., it is not possible to select the file at runtime.

save and load functions

The save and load functions, provided by FileIO, provide an alternative mechanism to read and write data from a JLD2 file. To use these functions, you must say using FileIO; it is not necessary to say using JLD2 since FileIO will determine the correct package automatically.

The save function accepts an Associative yielding the key/value pairs, where the key is a string representing the name of the dataset and the value represents its contents:

using FileIO
save("example.jld2", Dict("hello" => "world", "foo" => :bar))

The save function can also accept the dataset names and contents as arguments:

save("example.jld2", "hello", "world", "foo", :bar)

When using the save function, the file extension must be .jld2, since the extension .jld currently belongs to the previous JLD package.

If called with a filename argument only, the load function loads all datasets from the given file into a Dict:

load("example.jld2") # -> Dict{String,Any}("hello" => "world", "foo" => :bar)

If called with a single dataset name, load returns the contents of that dataset from the file:

load("example.jld2", "hello") # -> "world"

If called with multiple dataset names, load returns the contents of the given datasets as a tuple:

load("example.jld2", "hello", "foo") # -> ("hello", :bar)

File interface

It is also possible to interact with JLD2 files using a file-like interface. The jldopen function accepts a file name and an argument specifying how the file should be opened:

f = jldopen("example.jld2", "r")  # open read-only (default)
f = jldopen("example.jld2", "r+") # open read/write, failing if no file exists
f = jldopen("example.jld2", "w")  # open read/write, overwriting existing file
f = jldopen("example.jld2", "a+") # open read/write, preserving contents of existing file or creating a new file

Data can be written to the file using write(f, "name", data) or f["name"] = data, or read from the file using read(f, "name") or f["name"]. When you are done with the file, remember to call close(f).

Like open, jldopen also accepts a function as the first argument, permitting do-block syntax:

jldopen("example.jld2", "w") do file
    file["bigdata"] = randn(5)
end

Groups

It is possible to construct groups within a JLD2 file, which may or may not be useful for organizing your data. You can create groups explicitly:

jldopen("example.jld2", "w") do file
    mygroup = JLD2.Group(file, "mygroup")
    mygroup["mystuff"] = 42
end

or implicitly, by saving a variable with a name containing slashes as path delimiters:

jldopen("example.jld2", "w") do file
    file["mygroup/mystuff"] = 42
end
# or save("example.jld2", "mygroup/mystuff", 42)

Both of these examples yield the same group structure, which you can see at the REPL:

julia> file = jldopen("example.jld2", "r")
JLDFile /Users/simon/example.jld2 (read-only)
 └─📂 mygroup
    └─🔢 mystuff

Similarly, you can access groups directly:

jldopen("example.jld2", "r") do file
    @assert file["mygroup"]["mystuff"] == 42
end

or using slashes as path delimiters:

@assert load("example.jld2", "mygroup/mystuff") == 42

First Commit

07/02/2015

Last Touched

1 day ago

Commits

205 commits