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Plasmatrace

Julia package for LA-ICP-MS data reduction

Plasmatrace 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/Plasmatrace.git")

There are four ways to interact with Plasmatrace:

  1. TUI: an interactive text-based user interface
  2. TUI + GUI: a TUI augmented with graphical user interface elements
  3. REPL: the command-line interface
  4. Hybrid: combining the TUI, GUI and REPL

TUI (text-based user interface)

Here is a short example of a menu-driven Plasmatrace session:

julia> using Plasmatrace
julia> PT()
-------------------
 Plasmatrace 0.6.5
-------------------

r: Read data files[*]
m: Specify the method[*]
t: Tabulate the samples
s: Mark mineral standards[*]
g: Mark reference glasses[*]
v: View and adjust each sample
p: Process the data[*]
e: Export the results
l: Logs and templates
o: Options
u: Update
c: Clear
x: Exit
?: Help
r

a: Agilent
t: ThermoFisher
x: Exit
?: Help
a

d: Read a directory of individual data files
p: Parse the data from a single file using a laser log
(? for help, x to exit):
d

Enter the full path of the data directory (? for help, x to exit):
data/Lu-Hf

r: Read data files
m: Specify the method[*]
t: Tabulate the samples
s: Mark mineral standards[*]
g: Mark reference glasses[*]
v: View and adjust each sample
p: Process the data[*]
e: Export the results
l: Logs and templates
o: Options
u: Update
c: Clear
x: Exit
?: Help
v

TUI + GUI extension

You can augment the TUI with GUI elements (currently just file choosers) by installing the PTgui extension (installable from here):

julia> using Plasmatrace, PTgui
julia> PT(PTgui)
-------------------
 Plasmatrace 0.6.5
-------------------

r: Read data files[*]
m: Specify the method[*]
t: Tabulate the samples
s: Mark mineral standards[*]
g: Mark reference glasses[*]
v: View and adjust each sample
p: Process the data[*]
e: Export the results
l: Logs and templates
o: Options
u: Update
c: Clear
x: Exit
?: Help
r

a: Agilent
t: ThermoFisher
x: Exit
?: Help
a

d: Read a directory of individual data files
p: Parse the data from a single file using a laser log
(? for help, x to exit):
d

REPL (command-line interface)

Advanced users can interact with Plasmatrace 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:

method = "U-Pb"
run = load("data/carbonate",instrument="Agilent")
standards = Dict("WC1"=>"WC1")
glass = Dict("NIST612"=>"NIST612")
channels = Dict("d"=>"Pb207","D"=>"Pb206","P"=>"U238")
blk, fit = process!(run,method,channels,standards,glass)
export2IsoplotR(run,method,channels,blk,fit,prefix="Duff",fname="Duff.json")

Type ?load, ?process!, ?export2IsoplotR or ?PT 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 setPTctrl() function.

julia> using Plasmatrace
julia> PT()
-------------------
 Plasmatrace 0.6.5
-------------------

r: Read data files[*]
m: Specify the method[*]
t: Tabulate the samples
s: Mark mineral standards[*]
g: Mark reference glasses[*]
v: View and adjust each sample
p: Process the data[*]
e: Export the results
l: Logs and templates
o: Options
u: Update
c: Clear
x: Exit
?: Help
r

a: Agilent
t: ThermoFisher
x: Exit
?: Help
a

d: Read a directory of individual data files
p: Parse the data from a single file using a laser log
(? for help, x to exit):
d

Enter the full path of the data directory (? for help, x to exit):
data/Lu-Hf

r: Read data files
m: Specify the method[*]
t: Tabulate the samples
s: Mark mineral standards[*]
g: Mark reference glasses[*]
v: View and adjust each sample
p: Process the data[*]
e: Export the results
l: Logs and templates
o: Options
u: Update
c: Clear
x: Exit
?: Help
x

julia> ctrl = getPTctrl();
julia> plot(ctrl["run"][1])