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jhennies / amst

Alignment to Median Smoothed Template for FIB-SEM data
GNU General Public License v3.0
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Installation issue on Windows #11

Open lorianstraker opened 2 months ago

lorianstraker commented 2 months ago

Hi @jhennies ,

I'm having some installation issues on my Windows machine. This is the machine specification: Dell Workstation - Windows 10 Enterprise 64 bits I have installed Anaconda3-2024.2-1 (64 bits).

I failed to install with the codes on the README, including the separate steps using pip. The fail installation starts in the fabio-2022.12.0.tar.gz (as in the text file that I copied from the prompt). amst_instalation_error.txt

I was just wondering how you made that wheel? Can you point me to the source code repository and build pipeline for it? I might then be able to install it myself.

Many thanks.

jhennies commented 2 months ago

Hi @lorianstraker,

It's been a while since I last installed this so I'm not surprised that the instructions are a bit outdated. What you could try using conda is this:

conda create -n amst-env -c conda-forge tifffile scikit-image=0.17.2 vigra silx[full] pyopencl
conda activate amst-env

and then, depending on whether you have GPU available:

conda install -c conda-forge ocl-icd-system

or not:

conda install -c conda-forge pocl

Then the pyelastix (which relies on the elastix installation, see the Readme):

pip install pyelastix
lorianstraker commented 2 months ago

Hi @jhennies ,

Thank you so much for these instructions and so quickly.

Sorry for bothering you further. I have ran these new code lines but I still didn't get it to go through all the steps without errors. This time, the GPU part failed, so I tried without GPU just in case. I also tried downloading the ocl-icd-system package from Anaconda.org and following their codes. I can't find my way around this. Either failed to solve the environment, not finding the packages, as follow:

(amst-env) (amst-env) PS C:\Users\cobrasl> conda install -c conda-forge ocl-icd-system Channels:

PackagesNotFoundError: The following packages are not available from current channels:

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

(amst-env) (amst-env) PS C:\Users\cobrasl> conda search ocl-icd-system --channel conda-forge Loading channels: done No match found for: ocl-icd-system. Search: ocl-icd-system

PackagesNotFoundError: The following packages are not available from current channels:

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

(amst-env) (amst-env) PS C:\Users\cobrasl>