Note: this toolbox is under active development and is subject to change.
First, download latest stable Julia version.
Please note that Julia uses the JULIA_NUM_THREADS
environmental variable to determine the number of threads available for
the program.
For optimal performance this number should be > 1 and, depending upon your CPU number of cores, usually is equal or more than the number of cores.
For Unix-based systems (Linux, FreeBSD, MacOS) this may be set in the
~/.profile
file or ~/.zshrc
or
~/.bashrc
(depending on your shell).
export JULIA_NUM_THREADS=12
The easiest way (which also works in Windows) it to set this variable
in the Julia startup.jl
file, located in
~/.julia/config
directory:
ENV["JULIA_NUM_THREADS"] = 12
ENV["JULIA_NUM_PRECOMPILE_TASKS"] = 12
(!) Setting the JULIA_NUM_PRECOMPILE_TASKS
variable
speeds up packages precompilation process.
(!) Note that the 32-bit x86 architecture does not support threading
due to lack of compiler runtime library support, so you may need to set
JULIA_NUM_THREADS=0
and
JULIA_NUM_PRECOMPILE_TASKS=0
if you’re on a 32-bit
system.
(!) If you encounter the following error:
dyld: Library not loaded: @rpath/libLLVM.dylib at pre-compilation
,
start Julia using:
julia --pkgimages=no
Since version 0.24.1, NeuroAnalyzer is registered in the Julia
general registry. Therefore, the easiest way of installing the package
is to press ]
to enter the package mode, and then add this
package:
@v1.10) pkg> add NeuroAnalyzer (
or
using Pkg
Pkg.add("NeuroAnalyzer.jl")
You may also manually add NeuroAnalyzer using Julia package manager:
using Pkg
Pkg.update()
Pkg.add(url="https://codeberg.org/AdamWysokinski/NeuroAnalyzer.jl")
Pkg.resolve() # if necessary
Pkg.update()
Another option is to initialize a new Julia environment for the package:
git clone https://codeberg.org/AdamWysokinski/NeuroAnalyzer.jl
cd NeuroAnalyzer.jl
julia --project
# or (in which case you may ignore the line `Pkg.activate(@__DIR__)` below)
julia
Activate the package in the Julia REPL:
using Pkg
Pkg.activate(@__DIR__)
Pkg.instantiate()
Pkg.resolve() # if necessary
Pkg.update()
Alternatively, you may download NeuroAnalyzer latest release:
unzip NeuroAnalyzer-*.zip
cd NeuroAnalyzer-*
julia --project
# or (in which case you may ignore the line `Pkg.activate(@__DIR__)` below)
julia
Activate the package in the Julia REPL:
using Pkg
Pkg.activate(@__DIR__)
Pkg.instantiate()
Pkg.resolve() # if necessary
Pkg.update()
The third option is to extend the Julia LOAD_PATH
variable in the ~/.julia/config/startup.jl
with the
NeuroAnalyzer folder (downloaded as cloned or zipped repository):
push!(LOAD_PATH, "path/to/NeuroAnalyzer/folder")
Start Julia and in the Julia REPL do the following:
using NeuroAnalyzer
Due to the nature of Julia compiler, initial startup of NeuroAnalyzer takes several seconds. To speedup the process, creating a custom sysimage for reduced latency using PackageCompiler.jl is recommended. See this tutorial how to do it.
Show version and info (for reproducibility):
na_version()
na_info()
Get help:
?NeuroAnalyzer.plot
For interactive GUI, use Pluto and PlutoUI:
using Pkg
Pkg.add("Pluto")
Pkg.add("PlutoUI")
Pkg.add("Gtk")
using Pluto
run() Pluto.
Example Pluto notebook is located here.
For non-interactive GUI, use Jupyter:
using Pkg
Pkg.add("IJulia")
using IJulia
notebook()
Example Jupyter notebook is located here.
NeuroAnalyzer is also available as the Docker image:
docker pull neuroanalyzer/neuroanalyzer:latest
xhost local:docker
docker run -e DISPLAY=:0 -v /tmp/.X11-unix:/tmp/.X11-unix -it neuroanalyzer