AITW_microstructures

Port of the AITW microstructures code from Matlab to Python.

Install

cd <PATH to folder with pyproject.toml>
pip install .

Usage

Script

Example for birch microstructure generation.

from wood_microstructure import BirchMicrostructure, BirchParams

params = BirchParams.from_json('FILE_NAME.json')

for param in params:
    birch = BirchMicrostructure(param)
    birch.generate()

CLI

The installation will make available a wood_ms command line interface.

• Run wood_ms --help to see the available wood microstructures.
• Run wood_ms WOOD_TYPE --help flag to see all available options.

Example for birch microstructure generation:

wood_ms birch --json_file examples/example_birch.json

Tab autocompletion

Enabling tab autocompletion https://click.palletsprojects.com/en/stable/shell-completion/

E.G for bash run the command

eval "$(_WOOD_MS_COMPLETE=bash_source wood_ms)"

You can also add it to either ~/.bashrc or, if you are using a virtual environment, to bin/activate of the virtual environment to avoid running the command for every new shell.

NOTE

• W.R.T the matlab code, saveSlice in the json file can be a list[int] instead of just an int.
• Most functions have been optimized to have the loop over the Z slices as the outermost one. Since the Z slices are almost always treated independently, we can than run the loops over only the slices of interest.
• Need more testing with vessels