v1.2.0

Create new rules and scripts for extracting the names of the images that contain a plant in the orthomosaic, given the plant's segment ID. These are useful if you want to do some forensic work on the plants in an orthomosaic; you can go back to the original images that had that plant for more detail beyond what is in the orthomosaic.

The code in this release is mostly authored by @tommyfuu (with small suggestions by @aryarm)

There are also a number of minor changes to some of the scripts in the workflow. Namely: extract_features.py has a new try-except block to handle invalid markers and transform.py has a new try-except block to warn and error gracefully when the orthomosaic has too few pictures.

v1.1.0

This release adds a new rule to the pipeline for initializing Metashape and creating a metashape.lic file reproducibly.

It also makes some small, backwards-compatible changes to the original workflow. Namely, we now tell Snakemake about some of the metadata files stiched.files created by Metashape during the stitching step, so that if the stitching step fails, Snakemake can automatically cleanup those files.

v1.0.0

Our first release! The pipeline now has adequate documentation!