Scripts were originally from the Plankline project controlled by OSU (citation's to be included). I have heavily modified and repurposed the code to suit our architecture and to improve logging and performance. These scripts are available as is and I make no claim to ownership or control of any potentially sensitive code. These are intended for in-house use at UAF.
The Plankline suite of processing scripts is split into three main modules: (1) segmentation, (2) classification, (3) analysis; and is unified with the scripts in this repository.
If you are new to linux and setting up a Plankline instance for the first time, please start with the Linues Setup and the Plankline Setup guides.
For documentation on how Plankline works, please see the Plankline reference.
Optionally we also have a preliminary Morphocluster setup guide for those that are interested.
To run plankline with a specific configuration file and input directory:
python3 segmentation.py -c <ini> -d <dir>
python3 classification.py -c <ini> -d <dir>
So for example:
python3 segmentation.py -c osu_test_config.ini -d /media/plankline/data/test_data