Python code for CIPHER pre-processing.

This code is a work in progress

Installation for standalone generation of CIPHER input files

• The best way to use this code is by setting up a virtual environment and installing all the packages listed in requirements.txt. You can set up a virtual environment like this:

python -m venv .venv
.venv/Scripts/activate
pip install -r requirements.txt

Alternatively, it is also possible to use a conda environment.

Notebook

After the environment is set up and activated, you can launch jupyter to run the demo_cipher_inputs.ipynb notebook.

Installation for MatFlow/DAMASK/MTEX segmentation workflow

• You will need to install the Matlab python package by following the instructions here.

• Note that you must run this code with a version of Python 3 that is compatible with your version of Matlab, as shown here.

• Note that for now, MatFlow can only be used on up to Python 3.8.

• The best way to use this code is by setting up a virtual environment and installing all the packages listed in requirements.txt, plus the Matlab Python package. You can set up a virtual environment like this (make sure python is a version of python that is compatible with your version of Matlab):

python -m venv .venv
.venv/Scripts/activate
pip install -r requirements.txt

Then follow the instructions linked above to install the Matlab Python package; make sure you do it within your new virtual environment.

Alternatively, it is also possible to use a conda environment.

Notebook

After the environment is set up and activated, you can launch jupyter to run the demo_segmentation.ipynb notebook.