Nucubes

This package provides tools for nuBall HDF5 data files gating and analysis. The main script is nucubes.jl which calculates gamma-gamma-gamma gates based on a configuration file (see example file gates_example.toml). This code is prepared for multi-threading and distributed computing.

Setup

1. Copy or clone the git repository to your local machine to some my_path (e.g. /home/user/codes/Julia/Nucubes)

2. Run julia, and in the REPL

julia> using Pkg
julia> Pkg.add(url="https://github.com/kmiernik/Nucubes.git")

3. For distributed computing:
   • Prepare passwordless login on all your machines (e.g. using keys, see this for instructions)
   • Perform step 2 on all your machines
   • Place the data files in the same location (e.g. /home/user/data/data.h5, or network drive) on all machines
   • For convenience create symbolic link to nucubes.jl script

   $ cd /home/user/data/
   $ sudo ln -s my_path/bin/nucubes.jl .
   

   • On your main computer create machines.txt file listing all your machines by IP or name, e.g.

   server.somewhere.edu.pl
   10.13.2.1
   

   • Prepare gates file based on gates_example.txt, with the above data file path

Running

• For local run

  $ julia [-t n] [-p m] nucubes.jl gates.txt
  

  where -t n setups n cores to be used and -p m to use m processes

• For distributed run

  $ julia [-t n] [-p m] --machine-file machines.txt nucubes.jl gates.txt
  

  where -t n setups number of cores to be used per machine, machine file defines where the calculations are to be run and gates.txt contain gates data. If you want to make calculations on your local computer as well add -p m.

Setup file (gates)

Gates are created in a TOML setup file. An example with explanations is given below

# Set default values for these parameters
[default]
    input = "data.h5"
    output = "gates.h5"
    target = "target_name"
    detectors = "ggg"
    ttype = "ppp"
    halfwidth = 1.0
    m = [3, 9]
    prompt = [20.0, 60.0]
    delayed = [80.0 400.0]

# Each gate always needs "z", "y" and "isotope"
# Each gate has some unique identifier (anything)
# comment is optional and is skipped during parsing
# valid = false can be used to skip the gate (valid = true is default,
and does not need to be placed)
[gate.1]
    z = 606.6
    y = 423.4
    isotope = "te136"
    comment = "4+->2+->0+"
    valid = false

# Default parameters can be overwritten for a given gate
[gate.2]
    input = "data2.h5"
    target = "some_other_target"
    z = 423.4
    y = 352.3
    isotope = "te136"
    m = [4, 9]

# If z(y) is number, the gate is +/- halfwidth, 
# if it is a vector, it will be used as lower and upper gate limit
# (so it can be non-symmetric if needed)
[gate.3]
    z = [422.4, 425.4]
    y = 352.3
    isotope = "te136"
    ttype = "ppd"
    comment = "4+->2+->0+"