I am trying to use SimpleITK via PythonCall inside a Pluto notebook. I want to load a DICOM image and then convert it to a numpy array. The code to do this is straightforward and works in pure python, but with PythonCall this produces an error. using CondaPkg, DICOM, PythonCall CondaPkg.add("Simple…

When you import PythonCall.jl at the start, an environment with Python 3.11 is created: Package Version Build Channel Size ───────────────────────────────────────────────────────────────────────────── Install: ──────────────────────────────────────────────…

It also errors in the other direction, trying to convert julia array to sitk Image function load_dcm_array(dcm_data::Vector{DICOM.DICOMData}) return array = cat( [dcm_data[i][tag"Pixel Data"] for i in 1:length(dcm_data)]...; dims=3 ) end dcms_jl = DICOM.dcmdir_parse(fixed_dicom_dir…

I figured out that I get the same error if I run this in a Jupyter notebook using Python kernel. And after restarting the kernel, the error goes away. Maybe something like that is occurring in Julia?

@tylerjthomas9 is exactly right. This is a known (but undocumented) gotcha - similar to how you shouldn’t install Julia packages after importing anything (it can lead to incompatible packages) - only in this case it’s the python interpreter itself which is incompatible, with more disastrous consequ…

[image] tylerjthomas9: Then, when SimpleITK is added to the conda environment, a different Python version is installed I.e. 3.9, but it’s unclear to me why. SimpleITK supports 3.11, and in Conda, i.e. conda-forge, 3.11 is support (as opposed to Anaconda, which supports at least 3.10 seemingly…

[image] Palli: I.e. 3.9, but it’s unclear to me why. SimpleITK supports 3.11, and in Conda supports at least 3.10 seemingly, should be fixable to 3.11. What version of Julia are you using? PythonCall.jl adds libstdcxx-ng bounds in conda to ensure that the Python packages are compatible with J…

Thank you so much, this is so simple and helpful. Saves me many more days of random debugging

Resurrecting this because I am still dealing with a similar issue. Just adding numpy and/or torch results in an error when doing this in Pluto I have tried with and without resolve begin using Pkg; Pkg.activate(temp = true) Pkg.add("CondaPkg") using CondaPkg # CondaPkg.add("numpy", resolve = f…

False alarm, it looks like it’s just called “pytorch” when using anaconda and “torch” when using pip This works correctly: begin using Pkg; Pkg.activate(temp = true) Pkg.add("CondaPkg") using CondaPkg CondaPkg.add("numpy") CondaPkg.add("pytorch") end

SimpleITK via PythonCall not loading NumPy

General Usage

Dale_James_Black October 17, 2023, 5:30pm 9

EDIT: Sorry this doesn’t belong in this thread. I opened up a separate topic for this here

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SimpleITK via PythonCall not loading NumPy

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