Seminal root angle extraction
Used for high-throughput phenotyping of rhizobox images.
Install
The latest version is available via PyPI (https://pypi.org/project/seminal-root-angle) for convenient installation with pip
pip install seminal-root-angle
Example usage
Assuming the following folder structure:
output
data
├── photos
│ ├── photo1.JPG
│ ├── photo2.JPG
│ └── ....
├── root_segmentations
│ ├── photo1.png
│ ├── photo2.png
│ └── ....
└── seed_segmentations
├── photo1.png
└── photo2.png
└── ....
Then the angles can be extracted to the output/angles.csv with the following python code:
from seminal_root_angle.extract import extract_all_angles
extract_all_angles(root_seg_dir='data/root_segmentations',
im_dataset_dir='data/photos',
seed_seg_dir='data/seed_segmentations',
max_seed_points_per_im=2,
debug_image_dir='output/debug_images',
output_csv_path='output/angles.csv',
error_csv_path='output/errors.csv')