magneticresonanceimaging / bartio.jl Goto Github PK

malits/bartpy#4

maybe I should removed it from the package.

@JakobAsslaender We should do a release. We are using it in all our benchmark and a lot of my project and it works pretty well.

@tknopp Maybe we should move it to https://github.com/MagneticResonanceImaging ?

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• Documentation
• Test that path to bart folder exist and also that bart has been compiled (bart library is present in the folder)
• Edit codecov path to that repository

Do you have something else in mind ?

@aTrotier : I am really struggling with getting the PyCall functionality working, on all 3 computers that I am using. My latest error that I am getting is:

julia> bart = wrapper_bart(expanduser("/gpfs/home/asslaj01/Documents/toolboxes/bart/"))
Requirement already satisfied: numpy in /gpfs/scratch/asslaj01/.julia/conda/3/lib/python3.9/site-packages (1.22.3)
ERROR: PyError (PyImport_ImportModule

The Python package bart could not be imported by pyimport. Usually this means
that you did not install bart in the Python version being used by PyCall.

PyCall is currently configured to use the Julia-specific Python distribution
installed by the Conda.jl package.  To install the bart module, you can
use `pyimport_conda("bart", PKG)`, where PKG is the Anaconda
package that contains the module bart, or alternatively you can use the
Conda package directly (via `using Conda` followed by `Conda.add` etcetera).

Alternatively, if you want to use a different Python distribution on your
system, such as a system-wide Python (as opposed to the Julia-specific Python),
you can re-configure PyCall with that Python.   As explained in the PyCall
documentation, set ENV["PYTHON"] to the path/name of the python executable
you want to use, run Pkg.build("PyCall"), and re-launch Julia.

) <class 'ModuleNotFoundError'>
ModuleNotFoundError("No module named 'bart'")

Stacktrace:
 [1] pyimport(name::String)
   @ PyCall ~/.julia/packages/PyCall/ygXW2/src/PyCall.jl:558
 [2] wrapper_bart(pathtobart::String)
   @ BartIO ~/.julia/dev/BartIO/src/BartIO.jl:43
 [3] top-level scope
   @ REPL[6]:1

And, worst of all, these problems prevents me from using the read/write functionality and hence, makes the entire package un-usable. So my question is,

1. what are you using Pycall.jl for? Would it also be possible to just use system calls to BART?
2. would it be worth to re-structure the toolbox -- even though it is already small so that BartIO maybe just contains the read/write functionality and a separate package Bart.jl contains the wrapper functionality? Or are there other ways to ensure that the read/write functionality remains usable, even if PyCall does not precompile or is otherwise unusable?