KJ

Julia package for LA-ICP-MS data reduction

📖 Documentation: https://pvermees.github.io/KJ.jl/

KJ ("Kasper Julia") is still in development and has not yet been added to the Julia package repository. However, if you want to play around with the current functionality, then you can install the package from GitHub. First, make sure that you have Julia installed on your system by downloading it from here. Then, at the Julia REPL:

import Pkg; Pkg.add(url="https://github.com/pvermees/KJ.jl.git")

To save yourself some time when you run KJ later on, it is useful (but not strictly necessary) to precompile the package now:

Pkg.precompile("KJ")

There are three ways to interact with KJ:

1. TUI: an interactive text-based user interface
2. REPL: the command-line interface
3. Hybrid: combining the TUI and REPL

TUI (text-based user interface)

The TUI() function starts a menu-driven KJ session:

julia> using KJ
julia> TUI()
----------
 KJ 0.8.2
----------

r: Read data files[*]
m: Specify the method[*]
t: Tabulate the samples
v: View and adjust each sample
i: Interferences
f: Fractionation[*]
b: Mass bias
p: Process the data[*]
e: Export the results
l: Logs and templates
o: Options
u: Update
c: Clear
a: Extra
x: Exit
?: Help

The workflow goes from the top to the bottom, with asterisks marking compulsory steps. To read ICP-MS data files, type r and proceed.

REPL (command-line interface)

Advanced users can interact with KJ via Julia's command line interface or REPL ("read-eval-print loop"). Here is an example of a carbonate U-Pb data reduction using WC-1 for time-dependent elemental fractionation correction between U and Pb and NIST-612 for mass-dependent fractionation correction of the Pb-isotopes. The script exports all the aliquots of the "Duff" sample to a JSON file that can be opened in IsoplotR:

myrun = load("data/carbonate", format="Agilent")
method = Gmethod(name="U-Pb", groups=Dict("WC1"=>"WC1"))
fit = process!(myrun, method)
export2IsoplotR(myrun, method, fit;
                prefix="Duff", fname="output/Duff.json")

Type ?load, ?process!, ?export2IsoplotR or ?KJ at the REPL to view the documentation.

TUI + REPL

You can seamlessly switch from the TUI to the REPL and back. The following example stores the TUI settings into a variable called ctrl (type ctrl at the REPL to view its contents). You can manipulate the contents of ctrl and sync it with the TUI using the setKJctrl!() function.

julia> using KJ
julia> TUI()
# ... use TUI ...
# press 'x' to exit

julia> ctrl = getKJctrl();
julia> KJ.plot(ctrl["run"][1])

Building the Documentation Locally

julia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
julia --project=docs docs/make.jl

The generated site will be placed in docs/build/.