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BartIO.jl

Coverage

BartIO.jl is a Julia package in order to interact with the Berkeley Advanced Reconstruction Toolbox (BART).

This package offers the possibility to

  • read and write cfl/hdr files used by BART
  • Call BART command (requires a BART installation

Input/Output files in the BART format (.cfl + .hdr)

To load BART data (stored in a .cfl and a .hdr header file), simply call read_cfl(filename), where filename can be either be without a filename extension, or it can include .cfl or .hdr.

To write BART compatible files, call write_cfl(filename, x), where filename can be either be without a filename extension, or it can include .cfl or .hdr and x is the data.

Calling BART functions

BartIO replicates the functionality of the Python wrapper

Requirements

BART has to be installed/compiled.

Setup

You will have to tell BartIO.jl where to find the BART executable:

    using BartIO
    set_bart_path("/path/to/bart")

How to use BartIO.jl

BART functions ca be called, e.g., by either of the to calls:

bart(0,"version")
k_phant = bart(1,"phantom -x64 -k")

In the first example, the leading argument 0 indicates that bart will not return anything. In the second example, the leading 1 indicates that bart will return 1 object. For certain functions, you will have provide BART with data, which can be done in the following way:

traj = bart(1,"traj -x 128 -y 256 -r")
k_phant = bart(1,"phantom -k -t", traj)
im_phant = bart(1,"nufft -i", traj, k_phant)

where traj and k_phant are arrays of ComplexF32 (BART works with single precision). Note, if you pass multiple arguments, they are concatenated at the end of the command line. The last 2 lines are equivalent to the command line call

bart phantom -k -t traj k_phant
bart nufft -i traj k_phant im_phant

Alternatively you can pass optional arrays with keywords

k_phant = bart(1,"phantom -k", t=traj)

To print all available BART functions, you can call bart() without arguments:

bart()

If you need help for the function you can use:

bart(0,"pics -h")

Alternatives

As an alternative, you can, from within Julia, manually perform a system call of BART:

pathto_bart_exec="/home/CODE/bart-master/bart"
run(`$pathto_bart_exec version`)