Backend for the napari_nucleaizer plugin
Project description
nucleaizer-backend
Use in headless mode
Install MATLAB Runtime v99.
If ready, do not forget to set the LD_LIBRARY_PATH: the install prints out. OR set the MATLAB_RUNTIME_PATHS variable: e.g.:
MATLAB_RUNTIME=/MATLAB/MATLAB_Runtime export MATLAB_RUNTIME_PATHS=$MATLAB_RUNTIME/v99/runtime/glnxa64:$MATLAB_RUNTIME/v99/bin/glnxa64:$MATLAB_RUNTIME/v99/sys/os/glnxa64:$MATLAB_RUNTIME/v99/extern/bin/glnxa64
Install the stuff locally in a virtual environment:
python -m venv venv source venv/bin/activate (or .\Scripts\activate or something on Win) python -m pip install --upgrade pip python -m pip install -r requirements.txt python -m pip install -e .
If the install is readly, then one should create the nucleaizer_backend/cli_config.py file and setup the config values needed:
nucleaizer_dir: the directory where the models (.h5) files, configs, etc are staying. Prepare this dir first. Example: .nucleaizer_data_example in the shared distribution.
workflow_dir: a directory where the pipeline puts the intermediate results. May be empty or a result of a previous run.
inputs_dir: the input should go here with the subdirs train, val, test. Consult the training.py for the details. Example: nucleaizer_dataset in the shared distribution.
Then, call the entry point: python -m nucleaizer_backend.run_cli. See the corresponding script for the details.
Free software: MIT license
Documentation: https://nucleaizer-backend.readthedocs.io.
Features
TODO
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.1.0 (2021-02-03)
First release on PyPI.
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